Skip to main content

The Importance of Genetic and Epigenetic Research in the Brassica Vegetables in the Face of Climate Change

  • Chapter
  • First Online:
Genomic Designing of Climate-Smart Vegetable Crops

Abstract

The genus Brassica includes many economically important crops providing nutrition as well as health-promoting substances. Most cultivars of the Brassica vegetables are F1 hybrids, and breeding system was successfully established by effectively applying the phenomenon of heterosis or self-incompatibility. However, their production is constantly threatened by abiotic and biotic stresses such as the increasing numbers of races and isolates of pathogens, inappropriate cropping systems, and changing climate. Traditional methods of control are often costly and environmentally damaging, while the ideal way is to mine and use the abiotic or biotic resistance from the crop hosts. Fortunately, genomics and molecular genetics enables the rapid discover and application of plant breeding to improve adaptation to environmental conditions and abiotic or biotic resistance. Herein, we have summarized the important characteristics for breeding of the Brassica vegetables, including the trials for understanding the molecular mechanisms with genetic and epigenetic approaches. Some future perspectives are also given concerning how to efficiently use these genes and overcome global climate change.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  • Abe M, Kobayashi Y, Yamamoto S, Daimon Y, Yamaguchi A, Ikeda Y, Ichinoki H, Notaguchi M, Goto K, Araki T (2005) FD, a bZIP protein mediating signals from the floral pathway integrator FT at the shoot apex. Science 309:1052–1056

    Article  CAS  PubMed  Google Scholar 

  • Afrin KS, Rahim MA, Park JI, Natarajan S, Kim HT, Nou IS (2018) Identification of NBS-encoding genes linked to black rot resistance in cabbage (Brassica oleracea var. capitata). Mol Biol Rep 45:773–785

    Article  CAS  PubMed  Google Scholar 

  • Afzal Z, Howton T, Sun Y, Mukhtar M (2016) The roles of aquaporins in plant stress responses. J Dev Biol 4:9

    Article  PubMed Central  CAS  Google Scholar 

  • Aharon R, Shahak Y, Wininger S, Bendov R, Kapulnik Y, Galili G (2003) Overexpression of a plasma membrane aquaporin in transgenic tobacco improves plant vigor under favorable growth conditions but not under drought or salt stress. Plant Cell 15:439–447

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Altpeter F, Springer NM, Bartley LE, Blechl AE, Brutnell TP, Citovsky V, Conrad LJ, Gelvin SB, Jackson DP, Kausch AP, Lemaux PG, Medford JI, Orozco-Cárdenas ML, Tricoli DM, Van Eck J, Voytas DF, Walbot V, Wang K, Zhang ZJ, Stewart CN Jr (2016) Advancing crop transformation in the era of genome editing. Plant Cell 28:1510–1520

    CAS  PubMed  PubMed Central  Google Scholar 

  • Alvarez AM, Benedict AA, Mizumoto CY, Hunter JE, Gabriel DW (1994) Serological, pathological, and genetic diversity among strains of Xanthomonas campestris infecting crucifers. Mol Plant Pathol 84:1449–1457

    Google Scholar 

  • Amoah S, Kurup S, Lopez CM, Welham SJ, Powers SJ, Hopkins CJ, Wilkinson MJ, King GJ (2012) A hypomethylated population of Brassica rapa for forward and reverse epi-genetics. BMC Plant Biol 12:193

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Andrés F, Coupland G (2012) The genetic basis of flowering responses to seasonal cues. Nat Rev Genet 13:627–639

    Article  PubMed  CAS  Google Scholar 

  • Aneja B, Yadav NR, Kumar N, Yadav RC (2015) Hsp transcript induction is correlated with physiological changes under drought stress in Indian mustard. Physiol Mol Biol Plants 21:305–316

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Asano T, Hayashi N, Kikuchi S, Ohsugi R (2012) CDPK-mediated abiotic stress signaling. Plant Signal Behav 7:817–821

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ayers GW (1957) Races of Plasmodiophora brassicae. Can J Bot 35:923–932

    Article  Google Scholar 

  • Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3:e3376

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Baranwal VK, Mikkilineni V, Zehr UB, Tyagi AK, Kapoor S (2012) Heterosis: emerging ideas about hybrid vigour. J Exp Bot 63:6309–6314

    Article  CAS  PubMed  Google Scholar 

  • Barth S, Busimi AK, UtzH Friedrich, Melchinger AE (2003) Heterosis for biomass yield and related traits in five hybrids of Arabidopsis thaliana L. Heynh. Heredity 91:36–42

    Article  CAS  PubMed  Google Scholar 

  • Bateman AJ (1955) Self-incompatibility systems in angiosperms. III. Cruciferae. Heredity 9:52–68

    Google Scholar 

  • Bäurle I, Dean C (2006) The timing of developmental transitions in plants. Cell 125:655–664

    Article  PubMed  CAS  Google Scholar 

  • Bayer PE, Golicz AA, Tirnaz S, Chan CK, Edwards D, Batley J (2018) Variation in abundance of predicted resistance genes in the Brassica oleracea pangenome. Plant Biotechnol J 17:789–800

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Beauchemin C, Boutet N, Laliberté JF (2007) Visualization of the interaction between the precursors of VPg, the viral protein linked to the genome of turnip mosaic virus, and the translation eukaryotic initiation factor iso 4E in planta. J Virol 81:775–782

    Article  CAS  PubMed  Google Scholar 

  • Becker C, Hagmann J, Müller J, Koenig D, Stegle O, Borgwardt K, Weigel D (2011) Spontaneous epigenetic variation in the Arabidopsis thaliana methylome. Nature 480:245–249

    Article  CAS  PubMed  Google Scholar 

  • Bernatavichute YV, Zhang X, Cokus S, Pellegrini M, Jacobsen SE (2008) Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana. PLoS One 3:e3156

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Bhardwaj AR, Joshi G, Kukreja B, Malik V, Arora P, Pandey R, Shukla RN, Bankar KG, Katiyar-Agarwal S, Goel S, Jagannath A, Kumar A, Agarwal M (2015) Global insights into high temperature and drought stress regulated genes by RNA-Seq in economically important oilseed crop Brassica juncea. BMC Plant Biol 15:9

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Blank LM (1937) Fusarium resistance in Wisconsin all seasons cabbage. J Agri Res 55:497–510

    Google Scholar 

  • Blümel M, Dally N, Jung C (2015) Flowering time regulation in crops-what did we learn from Arabidopsis? Curr Opin Biotechnol 32:121–129

    Article  PubMed  CAS  Google Scholar 

  • Bosland PW, Williams PH, Morrison RH (1988) Influence of soil temperature on the expression of yellows and wilt of crucifers by Fusarium oxysporum. Plant Dis 72:777–780

    Article  Google Scholar 

  • Bradbury JF (1986) Guide to plant pathogenic bacteria. CAB International Mycological Institute

    Google Scholar 

  • Buczacki ST, Toxopeus H, Mattusch P, Johnston TD, Dixon GR, Hobolth LA (1975) Study of physiological specialization in Plasmodiophora brassicae: proposals for attempted rationalization through an international approach. Trans Br Mycol Soc 65:295–303

    Article  Google Scholar 

  • Burlakoti RR, Chen JR, Hsu CF, Burlakoti P, Kenyon L (2018) Molecular characterization, comparison of screening methods, and evaluation of cross-pathogenicity of black rot (Xanthomonas campestris pv. campestris) strains from cabbage, choy sum, leafy mustard, and pak choi from Taiwan. Plant Pathol 67:1589–1600

    Article  CAS  Google Scholar 

  • Byeon B, Bilichak A, Kovalchuk I (2018a) Tissue-specific heat-induced changes in the expression of ncRNA fragments in Brassica rapa plants. Biocatal Agri Biotechnol 14:338–356

    Article  Google Scholar 

  • Byeon B, Bilichak A, Kovalchuk I (2018b) Transgenerational response to heat stress in the form of differential expression of noncoding RNA fragments in Brassica rapa plants. Plant Genome 12:180022

    Google Scholar 

  • Camargo LEA, Williams PH, Osborn TC (1995) Mapping of quantitative trait loci controlling resistance of Brassica oleracea to Xanthomonas campestri pv. campestris in the field and green house. Genetics 85:1296–1300

    Google Scholar 

  • Cao TS, Srivastava S, Rahman MH, Kav NNV, Hotte N, Deyholos MK, Strelkov SE (2008) Proteome-level changes in the roots of Brassica napus as a result of Plasmodiophora brassicae infection. Plant Sci 174:97–115

    Article  CAS  Google Scholar 

  • Chalhoub B, Denoeud F, Liu S, Parkin IA, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B, Corréa M, Da Silva C, Just J, Falentin C, Koh CS, Le Clainche I, Bernard M, Bento P, Noel B, Labadie K, Alberti A, Charles M, Arnaud D, Guo H, Daviaud C, Alamery S, Jabbari K, Zhao M, Edger PP, Chelaifa H, Tack D, Lassalle G, Mestiri I, Schnel N, Le Paslier MC, Fan G, Renault V, Bayer PE, Golicz AA, Manoli S, Lee TH, Thi VH, Chalabi S, Hu Q, Fan C, Tollenaere R, Lu Y, Battail C, Shen J, Sidebottom CH, Wang X, Canaguier A, Chauveau A, Bérard A, Deniot G, Guan M, Liu Z, Sun F, Lim YP, Lyons E, Town CD, Bancroft I, Wang X, Meng J, Ma J, Pires JC, King GJ, Brunel D, Delourme R, Renard M, Aury JM, Adams KL, Batley J, Snowdon RJ, Tost J, Edwards D, Zhou Y, Hua W, Sharpe AG, Paterson AH, Guan C, Wincker P (2014) Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 345:950–953

    Article  CAS  PubMed  Google Scholar 

  • Charoenporn C, Kanokmedhakul S, Lin FC, Poeaim S, Soytong K (2010) Evaluation of bio-agent formulations to control Fusarium wilt of tomato. Afr J Biotechnol 9:5836–5844

    CAS  Google Scholar 

  • Chen J, Jing J, Zhan Z, Zhang T, Zhang C, Piao Z (2013) Identification of novel QTLs for isolate-specific partial resistance to Plasmodiophora brassicae in Brassica rapa. PLoS ONE 8:e85307

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chen J, Piao Y, Liu Y, Li X, Piao Z (2018) Genome-wide identification and expression analysis of chitinase gene family in Brassica rapa reveals its role in clubroot resistance. Plant Sci 270:257–267

    Article  CAS  PubMed  Google Scholar 

  • Chen SW, Liu T, Gao Y, Zhang C, Peng SD, Bai MB, Li SJ, Xu L, Zhou XY, Lin LB (2016) Discovery of clubroot-resistant genes in Brassica napus by transcriptome sequencing. Genet Mol Res 15:gmr.15038243

    Google Scholar 

  • Chen X, Ge X, Wang J, Tan C, King GJ, Liu K (2015) Genome-wide DNA methylation profiling by modified reduced representation bisulfite sequencing in Brassica rapa suggests that epigenetic modifications play a key role in polyploid genome evolution. Front Plant Sci 6:836

    PubMed  PubMed Central  Google Scholar 

  • Cheng F, Sun R, Hou X, Zheng H, Zhang F, Zhang Y, Liu B, Liang J, Zhuang M, Liu Y, Liu D, Wang X, Li P, Liu Y, Lin K, Bucher J, Zhang N, Wang Y, Wang H, Deng J, Liao Y, Wei K, Zhang X, Fu L, Hu Y, Liu J, Cai C, Zhang S, Zhang S, Li F, Zhang H, Zhang J, Guo N, Liu Z, Liu J, Sun C, Ma Y, Zhang H, Cui Y, Freeling MR, Borm T, Bonnema G, Wu J, Wang X (2016) Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea. Nat Genet 48:1218–1224

    Article  CAS  PubMed  Google Scholar 

  • Cheng F, Wu J, Fang L, Sun S, Liu B, Lin K, Bonnema G, Wang X (2012) Biased gene fractionation and dominant gene expression among the subgenomes of Brassica rapa. PLoS ONE 7:e36442

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cheng F, Wu J, Wang X (2014) Genome triplication drove the diversification of Brassica plants. Hor Res 1:14024

    Article  CAS  Google Scholar 

  • Cheng Y, Xie N, Jin P, Wang T (2015) DNA methylation and hydroxymethylation in stem cells. Cell Biochem Funct 33:161–173

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cheng Z, Targoll J, Huang X, Wu R (2002) Wheat LEA genes, PMA80 and PMA1959, enhance dehydration tolerance of transgenic rice (Oryza sativa L.). Mol Breed 10:71–82

    Article  CAS  Google Scholar 

  • Chiang MS, Crête R (1976) Diallel analysis of the inheritance of resistance to race 6 of Plasmodiophora brassicae in cabbage. Can J Plant Sci 56:865–868

    Article  Google Scholar 

  • Chisholm ST, Coaker G, Day B, Staskawicz BJ (2006) Host-microbe interactions: shaping the evolution of the plant immune response. Cell 124:803–814

    Article  CAS  PubMed  Google Scholar 

  • Chodavarapu RK, Feng S, Ding B, Simon SA, Lopez D, Jia Y, Wang GL, Meyers BC, Jacobsen SE, Pellegrini M (2012) Transcriptome and methylome interactions in rice hybrids. Proc Natl Acad Sci USA 109:12040–12045

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chookajorn T, Kachroo A, Ripoll DR, Clark AG, Nasrallah JB (2004) Specificity determinants and diversification of the Brassica self-incompatibility pollen ligand. Proc Natl Acad Sci USA 101:911–917

    Article  CAS  PubMed  Google Scholar 

  • Chu M, Song T, Falk KC, Zhang X, Liu X, Chang A, Lahlali R, McGregor L, Gossen BD, Yu F, Peng G (2014) Fine mapping of Rcr1 and analyses of its effect on transcriptome patterns during infection by Plasmodiophora brassicae. BMC Genom 15:1166

    Article  CAS  Google Scholar 

  • Chung H, Jeong YM, Mun JH, Lee SS, Chung WH, Yu HJ (2014) Construction of a genetic map based on high-throughput SNP genotyping and genetic mapping of a TuMV resistance locus in Brassica rapa. Mol Genet Genom 289:149–160

    Article  CAS  Google Scholar 

  • Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452:215–219

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cole SJ, Diener AC (2013) Diversity in receptor-like kinase genes is a major determinant of quantitative resistance to Fusarium oxysporum f. sp. matthioli. New Phytol 200:172–184

    Article  CAS  PubMed  Google Scholar 

  • Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339:819–823

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Corbesier L, Coupland G (2005) Photoperiodic flowering of Arabidopsis: integrating genetic and physiological approaches to characterization of the floral stimulus. Plant Cell Environ 28:54–66

    Article  CAS  Google Scholar 

  • Corbesier L, Vincent C, Jang S, Fornara F, Fan Q, Searle I, Giakountis A, Farrona S, Gissot L, Turnbull C, Coupland G (2007) FT protein movement contributes to long-distance signaling in floral induction of Arabidopsis. Science 316:1030–1033

    Article  CAS  PubMed  Google Scholar 

  • Crow JF (1998) 90 years ago: the beginning of hybrid maize. Genetics 148:923–928

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cruz R, Tenreiro R, Cruz L (2017) Assessment of Xanthomonas campestris pathovars affecting cruciferous plants in Portugal and disclosure of two novel X. campestris pv. campestris races. J Plant Pathol 99:403–414

    Google Scholar 

  • Cui XH, Hao FS, Chen H, Chen J, Wang XC (2008) Expression of the Vicia fabaVfPIP1 gene in Arabidopsis thaliana plants improves their drought resistance. J Plant Res 121:207–214

    Article  CAS  PubMed  Google Scholar 

  • Dalal M, Tayal D, Chinnusamy V, Bansal KC (2009) Abiotic stress and ABA-inducible Group 4 LEA from Brassica napus plays a key role in salt and drought tolerance. J Biotechnol 139:137–145

    Article  CAS  PubMed  Google Scholar 

  • Daly P, Tomkins B (1995) Production and postharvest handling of Chinese cabbage (Brassica rapa var. pekinensis). RIRDC 97:41

    Google Scholar 

  • Danquah A, de Zelicourt A, Colcombet J, Hirt H (2014) The role of ABA and MAPK signaling pathways in plant abiotic stress responses. Biotechnol Adv 32:40–52

    Article  CAS  PubMed  Google Scholar 

  • Dapp M, Reinders J, Bédiée A, Balsera C, Bucher E, Theiler G, Granier C, Paszkowski J (2015) Heterosis and inbreeding depression of epigenetic Arabidopsis hybrids. Nat Plants 1:15092

    Article  CAS  PubMed  Google Scholar 

  • Das T, Majumdar MH, Devi RT, Rajesh T (2016) Climate change impacts on plant diseases. SAARC J Agri 14:200–209

    Article  Google Scholar 

  • de Lima JC, Loss-Morais G, Margis R (2012) microRNAs play critical roles during plant development and in response to abiotic stresses. Genet Mol Biol 35(Suppl):1069–1077

    Article  PubMed  PubMed Central  Google Scholar 

  • De Lucia F, Crevillen P, Jones AM, Greb T, Dean C (2008) A PHD-polycomb repressive complex 2 triggers the epigenetic silencing of FLC during vernalization. Proc Natl Acad Sci USA 105:16831–16836

    Article  PubMed  PubMed Central  Google Scholar 

  • DeLucia EH, Nabity PD, Zavala JA, Berenbaum MR (2012) Climate change: resetting plant-insect interactions. Plant Physiol 160:1677–1685

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Deng W, Ying H, Helliwell CA, Taylor JM, Peacock WJ, Dennis ES (2011) FLOWERING LOCUS C (FLC) regulates development pathways throughout the life cycle of Arabidopsis. Proc Natl Acad Sci USA 108:6680–6685

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Diederichsen E, Frauen M, Linders EGA, Hatakeyama K, Hirai M (2009) Status and perspectives of clubroot resistance breeding in crucifer crops. J Plant Growth Regul 28:265–281

    Article  CAS  Google Scholar 

  • Diener AC (2013) Routine mapping of Fusarium wilt resistance in BC 1 populations of Arabidopsis thaliana. BMC Plant Biol 13:171

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Diener AC, Ausubel FM (2005) RESISTANCE TO FUSARIUM OXYSPORUM 1, a dominant Arabidopsis disease-resistance gene, is not race specific. Genetics 171:305–321

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dixon GR (1980) Variation in Plasmodiophora brassicae. Ann Appl Biol 94:278–280

    Article  Google Scholar 

  • Donald EC, Cross SJ, Lawrence JM, Porter IJ (2006) Pathotypes of Plasmodiophora brassicae, the cause of clubroot, in Australia. Ann Appl Biol 148:239–244

    Article  Google Scholar 

  • Dong MA, Farré EM, Thomashow MF (2011) Circadian clock-associated 1 and late elongated hypocotyl regulate expression of the C-repeat binding factor (CBF) pathway in Arabidopsis. Proc Natl Acad Sci USA 108:7241–7246

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dong X, Yi H, Lee J, Nou IS, Han CT, Hur Y (2015) Global gene-expression analysis to identify differentially expressed genes critical for the heat stress response in Brassica rapa. PLoS ONE 10:e0130451

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Doucet R, Shattuck VI, Stobbs LW (1990) Rutabaga germplasm TuMV-R possessing resistance to turnip mosaic virus. Hortic Sci 25:583–584

    Google Scholar 

  • Doullah MAU, Mohsin GM, Ishikawa K, Hori H, Okazaki K (2011) Construction of a linkage map and QTL analysis for black rot resistance in Brassica oleracea L. Intl J Nat Sci 1:1–6

    Article  Google Scholar 

  • Dowen RH, Pelizzola M, Schmitz RJ, Lister R, Dowen JM, Nery JR, Dixon JE, Ecker JR (2012) Widespread dynamic DNA methylation in response to biotic stress. Proc Natl Acad Sci USA 109:E2183–E2191

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Du J, Johnson LM, Jacobsen SE, Patel DJ (2015) DNA methylation pathways and their crosstalk with histone methylation. Nat Rev Mol Cell Biol 16:519–532

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Duvick DN (2001) Biotechnology in the 1930s: the development of hybrid maize. Nat Rev Genet 2:69–74

    Article  CAS  PubMed  Google Scholar 

  • Enya J, Togawa M, Takeuchi T, Yoshida S, Tsushima S, Arie T, Sakai T (2008) Biological and phylogenetic characterization of Fusarium oxysporum complex, which causes yellows on Brassica spp., and proposal of F. oxysporum f. sp. rapae, a novel forma specialis pathogenic on B. rapa in Japan. Phytopathology 98:475–483

    Article  CAS  PubMed  Google Scholar 

  • Fargier E, Manceau C (2007) Pathogenicity assays restrict the species Xanthomonas campestris into three pathovars and reveal nine races within X. campestris pv. campestris. Plant Pathol 56:805–818

    Article  Google Scholar 

  • Farnham MW, Keinath AP, Smith JP (2001) Characterization of Fusarium yellows resistance in collard. Plant Dis 85:890–894

    Article  PubMed  Google Scholar 

  • Feng S, Cokus SJ, Zhang X, Chen PY, Bostick M, Goll MG, Hetzel J, Jain J, Strauss SH, Halpern ME, Ukomadu C, Sadler KC, Pradhan S, Pellegrini M, Jacobsen SE (2010) Conservation and divergence of methylation patterning in plants and animals. Proc Natl Acad Sci USA 107:8689–8694

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Figdore SS, Ferreira ME, Slocum MK, Williams PH (1993) Association of RFLP markers with trait loci affecting clubroot resistance and morphological characters in Brassica oleracea L. Euphytica 69:33–44

    Article  CAS  Google Scholar 

  • Finnegan EJ, Dennis ES (2007) Vernalization-induced trimethylation of histone H3 lysine 27 at FLC is not maintained in mitotically quiescent cells. Curr Biol 17:1978–1983

    Article  CAS  PubMed  Google Scholar 

  • Fjellstrom RG, Williams PH (1997) Fusarium yellows and turnip mosaic virus resistance in Brassica rapa and B. juncea. HortSci 32:927–930

    Article  Google Scholar 

  • Flint-Garcia SA, Buckler ES, Tiffin P, Ersoz E, Springer NM (2009) Heterosis is prevalent for multiple traits in diverse maize germplasm. PLoS One 4:e7433

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Flor HH (1971) Current status of the gene-for-gene concept. Annu Rev Phytopathol 9:275–296

    Article  Google Scholar 

  • Fornara F, de Montaigu A, Coupland G (2010) SnapShot: control of flowering in Arabidopsis. Cell 141:550

    Article  PubMed  Google Scholar 

  • Franks SJ, Weis AE (2009) Climate change alters reproductive isolation and potential gene flow in an annual plant. Evol Appl 2:481–488

    Article  PubMed  PubMed Central  Google Scholar 

  • Fravel D, Olivain C, Alabouvette C (2003) Fusarium oxysporum and its biocontrol. New Phytol 157:493–502

    Article  PubMed  Google Scholar 

  • Friend DJC (1985) Brassica. In: Harlevy AH (ed) Handbook of Flowering. CRC Press, Boca Raton, FL, USA, pp 44–77

    Google Scholar 

  • Fuchs J, Demidov D, Houben A, Schubert I (2006) Chromosomal histone modification patterns–from conservation to diversity. Trends Plant Sci 11:199–208

    Article  CAS  PubMed  Google Scholar 

  • Fujimoto R, Kinoshita Y, Kawabe A, Kinoshita T, Takashima K, Nordborg M, Nasrallah ME, Shimizu KK, Kudoh H, Kakutani T (2008a) Evolution and control of imprinted FWA genes in the genus Arabidopsis. PLoS Genet 4:e1000048

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Fujimoto R, Nishio T (2003) Identification of S haplotypes in Brassica by dot blot analysis of SP11 alleles. Theor Appl Genet 106:1433–1437

    Article  CAS  PubMed  Google Scholar 

  • Fujimoto R, Nishio T (2007) Self-Incompatibility. Adv Bot Res 45:139–154

    Article  CAS  Google Scholar 

  • Fujimoto R, Okazaki K, Fukai E, Kusaba M, Nishio T (2006a) Comparison of the genome structure of the self-incompatibility (S) locus in interspecific pairs of S haplotypes. Genetics 173:1157–1167

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fujimoto R, Sasaki T, Inoue H, Nishio T (2008b) Hypomethylation and transcriptional reactivation of retrotransposon-like sequences in ddm1 transgenic plants of Brassica rapa. Plant Mol Biol 66:463–473

    Article  CAS  PubMed  Google Scholar 

  • Fujimoto R, Sasaki T, Ishikawa R, Osabe K, Kawanabe T, Dennis ES (2012a) Molecular mechanisms of epigenetic variation in plants. Intl J Mol Sci 13:9900–9922

    Article  CAS  Google Scholar 

  • Fujimoto R, Sasaki T, Kudoh H, Taylor JM, Kakutani T, Dennis ES (2011a) Epigenetic variation in the FWA gene within the genus Arabidopsis. Plant J 66:831–843

    Article  CAS  PubMed  Google Scholar 

  • Fujimoto R, Sugimura T, Fukai E, Nishio T (2006b) Suppression of gene expression of a recessive SP11/SCR allele by an untranscribedSP11/SCR allele in Brassica self-incompatibility. Plant Mol Biol 61:577–587

    Article  CAS  PubMed  Google Scholar 

  • Fujimoto R, Sugimura T, Nishio T (2006c) Gene conversion from SLG to SRK resulting in self-compatibility in Brassica rapa. FEBS Lett 580:425–430

    Article  CAS  PubMed  Google Scholar 

  • Fujimoto R, Takuno S, Sasaki T, Nishio T (2008c) The pattern of amplification and differentiation of Ty1-copia and Ty3-gypsy retrotransposons in Brassicaceae species. Genes Genet Syst 83:13–22

    Article  CAS  PubMed  Google Scholar 

  • Fujimoto R, Taylor JM, Sasaki T, Kawanabe T, Dennis ES (2011b) Genome wide gene expression in artificially synthesized amphidiploids of Arabidopsis. Plant Mol Biol 77:419–431

    Article  CAS  PubMed  Google Scholar 

  • Fujimoto R, Taylor JM, Shirasawa S, Peacock WJ, Dennis ES (2012b) Heterosis of Arabidopsis hybrids between C24 and Col is associated with increased photosynthesis capacity. Proc Natl Acad Sci USA 109:7109–7114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fujimoto R, Uezono K, Ishikura S, Osabe K, Peacock WJ, Dennis ES (2018) Recent research on the mechanism of heterosis is important for crop and vegetable breeding systems. Breed Sci 68:145–158

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fujita Y, Yoshida T, Yamaguchi-Shinozaki K (2013) Pivotal role of the AREB/ABF-SnRK2 pathway in ABRE-mediated transcription in response to osmotic stress in plants. Physiol Plant 147:15–27

    Article  CAS  PubMed  Google Scholar 

  • Fujiwara A, Inukai T, Kim BM, Masuta C (2011) Combinations of a host resistance gene and the CI gene of turnip mosaic virus differentially regulate symptom expression in Brassica rapa cultivars. Arch Virol 156:1575–1581

    Article  CAS  PubMed  Google Scholar 

  • Fujiwara S, Oda A, Yoshida R, Niinuma K, Miyata K, Tomozoe Y, Tajima T, Nakagawa M, Hayashi K, Coupland G, Mizoguchi T (2008) Circadian clock proteins LHY and CCA1 regulate SVP protein accumulation to control flowering in Arabidopsis. Plant Cell 20:2960–2971

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fukai E, Fujimoto R, Nishio T (2003) Genomic organization of the S core region and the S flanking regions of a class-II S haplotype in Brassica rapa. Mol Genet Genom 269:361–369

    Article  CAS  Google Scholar 

  • Fusco N, Micheletto L, Dal Corso G, Borgato L, Furini A (2005) Identification of cadmium-regulated genes by cDNA-AFLP in the heavy metal accumulator Brassica juncea L. J Exp Bot 56:3017–3027

    Article  CAS  PubMed  Google Scholar 

  • Gao G, Li J, Li H, Li F, Xu K, Yan G, Chen B, Qiao J, Wu X (2014) Comparison of the heat stress induced variations in DNA methylation between heat-tolerant and heat-sensitive rapeseed seedlings. Breed Sci 64:125–133

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Garg R, Chevala VN, Shankar R, Jain M (2015) Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response. Sci Rep 5:14922

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gendall AR, Levy YY, Wilson A, Dean C (2001) The VERNALIZATION 2 gene mediates the epigenetic regulation of vernalization in Arabidopsis. Cell 107:525–535

    Article  CAS  PubMed  Google Scholar 

  • Giraud H, Bauland C, Falque M, Madur D, Combes V, Jamin P, Monteil C, Laborde J, Palaffre C, Gaillard A, Blanchard P, Charcosset A, Moreau L (2017) Reciprocal genetics: Identifying QTL for general and specific combining abilities in hybrids between multiparental populations from two maize (Zea mays L.) heterotic groups. Genetics 207:1167–1180

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Girke A, Schierholt A, Becker HC (2012) Extending the rapeseed gene pool with resynthesized Brassica napus II: heterosis. Theor Appl Genet 124:1017–1026

    Article  PubMed  Google Scholar 

  • Glazebrook J (2005) Contrasting mechanisms of defense against biotrophic and necrotrophic pathogens. Annu Rev Phytopathol 43:205–227

    Article  CAS  PubMed  Google Scholar 

  • Golicz AA, Bayer PE, Barker GC, Edger PP, Kim H, Martinez PA, Chan CK, Severn-Ellis A, McCombie WR, Parkin IA, Paterson AH, Pires JC, Sharpe AG, Tang H, Teakle GR, Town CD, Batley J, Edwards D (2016) Thepangenome of an agronomically important crop plant Brassica oleracea. Nat Commun 7:13390

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Grandclément C, Thomas G (1996) Detection and analysis of QTLs based on RAPD markers for polygenic resistance to Plasmodiophora brassicae Woron in Brassica oleracea L. Theor Appl Genet 93:86–90

    Article  PubMed  Google Scholar 

  • Greaves IK, Groszmann M, Ying H, Taylor JM, Peacock WJ, Dennis ES (2012) Trans chromosomal methylation in Arabidopsis hybrids. Proc Natl Acad Sci USA 109:3570–3575

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Green RM, Tobin EM (2002) The role of CCA1 and LHY in the plant circadian clock. Dev Cell 2:516–518

    Article  CAS  PubMed  Google Scholar 

  • Green SK, Deng TC (1985) Turnip mosaic virus strains in cruciferous hosts in Taiwan. Plant Dis 69:28–31

    Article  Google Scholar 

  • Griffiths PD, Marek LF, Robertson LD (2009) Identification of crucifer accessions from the NC-7 and NE-9 plant introduction collections that are resistant to black rot (Xanthomonas campestris pv. campestris) races 1 and 4. Hortic Sci 44:284–288

    Google Scholar 

  • Groszmann M, Gonzalez-Bayon R, Greaves IK, Wang L, Huen AK, Peacock WJ, Dennis ES (2014) Intraspecific Arabidopsis hybrids show different patterns of heterosis despite the close relatedness of the parental genomes. Plant Physiol 166:265–280

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Groszmann M, Greaves IK, Albert N, Fujimoto R, Helliwell CA, Dennis ES, Peacock WJ (2011) Epigenetics in plants-vernalisation and hybrid vigour. Biochim Biophys Acta 1809:427–437

    Article  CAS  Google Scholar 

  • Groszmann M, Greaves IK, Fujimoto R, Peacock WJ, Dennis ES (2013) The role of epigenetics in hybrid vigour. Trends Genet 29:684–690

    Article  CAS  PubMed  Google Scholar 

  • Grover JW, Kendall T, Baten A, Burgess D, Freeling M, King GJ, Mosher RA (2018) Maternal components of RNA directed DNA methylation are required for seed development in Brassica rapa. Plant J 94:575–582

    Article  CAS  PubMed  Google Scholar 

  • Guo H, Dickson MH, Hunter JE (1991) Brassica napus sources of resistance to black rot in crucifers and inheritance of resistance. Hortic Sci 26:1545–1547

    Google Scholar 

  • Guo Y, Chen S, Li Z, Cowling WA (2014) Center of origin and centers of diversity in an ancient crop, Brassica rapa (Turnip Rape). J Hered 105:555–565

    Article  PubMed  Google Scholar 

  • Hamel LP, Sheen J, Séguin A (2014) Ancient signals: comparative genomics of green plant CDPKs. Trends Plant Sci 19:79–89

    Article  CAS  PubMed  Google Scholar 

  • Hamlyn BMG (1953) Quantitative studies on the transmission of cabbage black ring spot virus by Myzus persicae (Sulz.). Ann Appl Biol 40:393–402

    Article  Google Scholar 

  • Hansen M (1989) Genetic variation and inheritance of tolerance to clubroot (Plasmodiophora brassicae Wor.) and other quantitative character in cabbage(Brassica oleracea L). Hereditas 110:13–22

    Article  Google Scholar 

  • Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, Echipare L, O’Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol 28:1097–1105

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Haseyama Y, Kitashiba H, Okamoto S, Tonouchi E, Sakamoto K, Nishio T (2018) Nucleotide sequence analysis of S-locus genes to unify S haplotype nomenclature in radish. Mol Breed 38:116

    Article  CAS  Google Scholar 

  • Hatakeyama K, Horisaki A, Niikura S, Narusaka Y, Abe H, Yoshiaki H, Ishida M, Fukuoka H, Matsumoto S (2010) Mapping of quantitative trait loci for high level of self-incompatibility in Brassica rapa L. Genome 53:257–265

    Article  CAS  PubMed  Google Scholar 

  • Hatakeyama K, Niwa T, Kato T, Ohara T, Kakizaki T, Matsumoto S (2017) The tandem repeated organization of NB-LRR genes in the clubroot-resistant CRb locus in Brassica rapa L. Mol Geneti Genom 292:397–405

    Article  CAS  Google Scholar 

  • Hatakeyama K, Suwabe K, Tomita RN, Kato T, Nunome T, Fukuoka H, Matsumoto S (2013) Identification and characterization of CRR1a, a gene for resistance to clubroot disease (Plasmodiophora brassicae Woronin) in Brassica rapa L. PLoS ONE 8:e54745

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hatakeyama K, Takasaki T, Suzuki G, Nishio T, Watanabe M, Isogai A, Hinata K (2001) The S receptor kinase gene determines dominance relationships in stigma expression of self-incompatibility in Brassica. Plant J 26:69–76

    Article  CAS  PubMed  Google Scholar 

  • Hatakeyama K, Takasaki T, Watanabe M, Hinata K (1998) Molecular characterization of S locus genes, SLG and SRK, in a pollen-recessive self-incompatibility haplotype of Brassicarapa L. Genetics 149:1587–1597

    CAS  PubMed  PubMed Central  Google Scholar 

  • He G, Elling AA, Deng XW (2011) The epigenome and plant development. Annu Rev Plant Biol 62:411–435

    Article  CAS  PubMed  Google Scholar 

  • He G, Zhu X, Elling AA, Chen L, Wang X, Guo L, Liang M, He H, Zhang H, Chen F, Qi Y, Chen R, Deng XW (2010) Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell 22:17–33

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Helliwell CA, Wood CC, Robertson M, James Peacock W, Dennis ES (2006) The Arabidopsis FLC protein interacts directly in vivo with SOC1 and FT chromatin and is part of a high-molecular-weight protein complex. Plant J 46:183–192

    Article  CAS  PubMed  Google Scholar 

  • Heo JB, Sung S (2011) Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 331:76–79

    Article  CAS  PubMed  Google Scholar 

  • Hepworth SR, Valverde F, Ravenscroft D, Mouradov A, Coupland G (2002) Antagonistic regulation of flowering-time gene SOC1 by CONSTANS and FLC via separate promoter motifs. EMBO J 21:4327–4337

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hetherington AM, Brownlee C (2004) The generation of Ca2+ signals in plants. Annu Rev Plant Biol 55:401–427

    Article  CAS  PubMed  Google Scholar 

  • Hinata K, Okazaki K, Nishio T (1983) Gene analysis of self-compatibility in Brassicacampestris var. yellow sarson (a case of recessive epistatic modifier). In: Proceedings of the 6th International Rapeseed Conference, vol 1, pp 354–359

    Google Scholar 

  • Hirai M, Harada T, Kubo N, Tsukada M, Suwabe K, Matsumoto S (2004) A novel locus for clubroot resistance in Brassica rapa and its linkage markers. Theor Appl Genet 108:639–643

    Article  CAS  PubMed  Google Scholar 

  • Howden SM, Soussana JF, Tubiello FN, Chhetri N, Dunlop M, Meinke H (2007) Adapting agriculture to climate change. Proc Natl Acad Sci USA 104:19691–19696

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hrabak EM, Chan CW, Gribskov M, Harper JF, Choi JH, Halford N, Kudla J, Luan S, Nimmo HG, Sussman MR, Thomas M, Walker-Simmons K, Zhu JK, Harmon AC (2003) The Arabidopsis CDPK-SnRK superfamily of protein kinases. Plant Physiol 132:666–680

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huang XY, Tao P, Li BY, Wang WH, Yue ZC, Lei JL, Zhong XM (2015) Genome-wide identification, classification, and analysis of heat shock transcription factor family in Chinese cabbage (Brassica rapa pekinensis). Genet Mol Res 14:2189–2204

    Article  CAS  PubMed  Google Scholar 

  • Huang Z, Peng G, Liu X, Deora A, Falk KC, Gossen BD, McDonald MR, Yu F (2017) Fine mapping of a clubroot resistance gene in Chinese cabbage using SNP markers identified from bulked segregant RNA sequencing. Front Plant Sci 8:1448

    Article  PubMed  PubMed Central  Google Scholar 

  • Hughes SL, Hunter PJ, Sharpe AG, Kearsey MJ, Lydiate DJ, Walsh JA (2003) Genetic mapping of the novel turnip mosaic virus resistance gene TuRB03 in Brassica napus. Theor Appl Genet 107:1169–1173

    Article  CAS  PubMed  Google Scholar 

  • Huijser P, Schmid M (2011) The control of developmental phase transitions in plants. Development 138:4117–4129

    Article  CAS  PubMed  Google Scholar 

  • Hunter JE, Dickson MH, Ludwig JW (1987) Source of resistance to black rot of cabbage expressed in seedlings and adult plants. Plant Dis 71:263–266

    Article  Google Scholar 

  • Ignatov A, Kuginuki Y, Hida K (1998) Race-specific reaction of resistance to black rot in Brassica oleracea. Eur J Plant Pathol 104:821–827

    Article  Google Scholar 

  • Imaizumi T (2010) Arabidopsis circadian clock and photoperiodism: time to think about location. Curr Opi Plant Biol 13:83–89

    Article  CAS  Google Scholar 

  • Irwin JA, Soumpourou E, Lister C, Ligthart JD, Kennedy S, Dean C (2016) Nucleotide polymorphism affecting FLC expression underpins heading date variation in horticultural brassicas. Plant J 87:597–605

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Itabashi E, Osabe K, Fujimoto R, Kakizaki T (2018) Epigenetic regulation of agronomical traits in Brassicaceae. Plant Cell Rep 37:87–101

    Article  CAS  PubMed  Google Scholar 

  • Jacob P, Hirt H, Bendahmane A (2017) The heat-shock protein/chaperone network and multiple stress resistance. Plant Biotechnol J 15:405–414

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jamwal RS, Sharma PP (1986) Inheritance of resistance to black rot (Xanthomonas campestris pv. Campestris) in cauliflower (Brassica oleracea var. Botrytis). Euphytica 35:941–943

    Article  Google Scholar 

  • Jan FJ, Fagoaga C, Pang SZ, Gonsalves D (2000) A single chimeric transgene derived from two distinct viruses confers multi-virus resistance in transgenic plants through homology-dependent gene silencing. J Gen Virol 81:2103–2109

    Article  CAS  PubMed  Google Scholar 

  • Jeddeloh JA, Stokes TL, Richards EJ (1999) Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nat Genet 22:94–97

    Article  CAS  PubMed  Google Scholar 

  • Jenner CE, Sánchez F, Nettleship SB, Foster GD, Ponz F, Walsh JA (2000) The cylindrical inclusion gene of Turnip mosaic virus encodes a pathogenic determinant to the Brassica resistance gene TuRB01. Mol Plant Microbe Interact 13:1102–1108

    Article  CAS  PubMed  Google Scholar 

  • Jenner CE, Walsh JA (1996) Pathotypic variation in turnip mosaic virus with special reference to European isolates. Plant Pathol 45:848–856

    Article  Google Scholar 

  • Jenner CE, Wang X, Tomimura K, Ohshima K, Ponz F, Walsh JA (2003) The dual role of the potyvirus P3 protein of Turnip mosaic virus as a symptom and avirulence determinant in Brassicas. Mol Plant Microbe Interact 16:777–784

    Article  CAS  PubMed  Google Scholar 

  • Jenner CE, Wang XW, Ponz F, Walsh JA (2002) A fitness cost for Turnip mosaic virus to overcome host resistance. Virus Res 86:1–6

    Article  CAS  PubMed  Google Scholar 

  • Jensen BD, Vicente JG, Manandhar HK, Roberts SJ (2010) Occurrence and diversity of Xanthomonas campestris pv. campestris in vegetable Brassica fields in Nepal. Plant Dis 94:298–305

    Article  CAS  PubMed  Google Scholar 

  • Jia H, Wei X, Yang Y, Yuan Y, Wei F, Zhao Y, Yang S, Yao Q, Wang Z, Tian B, Zhang X (2017) Root RNA-seq analysis reveals a distinct transcriptome landscape between clubroot-susceptible and clubroot-resistant Chinese cabbage lines after Plasmodiophora brassicae infection. Plant Soil 421:93–105

    Article  CAS  Google Scholar 

  • Jiang H, Song W, Li A, Yang X, Sun D (2011) Identification of genes differentially expressed in cauliflower associated with resistance to Xanthomonas campestris pv. campestris. Mol Biol Rep 38:621–629

    Article  CAS  PubMed  Google Scholar 

  • Jin M, Lee SS, Ke L, Kim JS, Seo MS, Sohn SH, Park BS, Bonnema G (2014) Identification and mapping of a novel dominant resistance gene, TuRB07 to Turnip mosaic virus in Brassica rapa. Theor Appl Genet 127:509–519

    Article  CAS  PubMed  Google Scholar 

  • Johannes F, Porcher E, Teixeira FK, Saliba-Colombani V, Simon M, Agier N, Bulski A, Albuisson J, Heredia F, Audigier P, Bouchez D, Dillmann C, Guerche P, Hospital F, Colot V (2009) Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genet 5:e1000530

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Johnson R (1984) A critical analysis of durable resistance. Ann Rev Phytopathol 22:309–330

    Article  Google Scholar 

  • Jones DF (1917) Dominance of linked factors as a means of accounting for heterosis. Genetics 2:466–479

    CAS  PubMed  PubMed Central  Google Scholar 

  • Jones JDG, Dangl JL (2006) The plant immune system. Nature 444:323–329

    Article  CAS  PubMed  Google Scholar 

  • Jung C, Müller AE (2009) Flowering time control and applications in plant breeding. Trends Plant Sci 14:563–573

    Article  CAS  PubMed  Google Scholar 

  • Kachroo A, Schopfer CR, Nasrallah ME, Nasrallah JB (2001) Allele-specific receptor-ligand interaction in Brassica self-incompatibility. Science 293:1824–1826

    Article  CAS  PubMed  Google Scholar 

  • Kageyama K, Asano T (2009) Life cycle of Plasmodiophora brassicae. J Plant Growth Regul 28:203–211

    Article  CAS  Google Scholar 

  • Kakita M, Murase K, Iwano M, Matsumoto T, Watanabe M, Shiba H, Isogai A, Takayama S (2007a) Two distinct forms of M-locus protein kinase localize to the plasma membrane and interact directly with S-locus receptor kinase to transduce self-incompatibility signaling in Brassica rapa. Plant Cell 19:3961–3973

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kakita M, Shimosato H, Murase K, Isogai A, Takayama S (2007b) Direct interaction between S-locus receptor kinase and M-locus protein kinase involved in Brassica self-incompatibility signaling. Plant Biotechnol 24:185–190

    Article  CAS  Google Scholar 

  • Kakizaki T, Kato T, Fukino N, Ishida M, Hatakeyama K, Matsumoto S (2011) Identification of quantitative trait loci controlling late bolting in Chinese cabbage (Brassica rapa L.) parental line Nou 6 gou. Breed Sci 61:151–159

    Article  Google Scholar 

  • Kakizaki T, Takada Y, Ito A, Suzuki G, Shiba H, Takayama S, Isogai A, Watanabe M (2003) Linear dominance relationship among four class-II S haplotypes in pollen is determined by the expression of SP11 in Brassica self-incompatibility. Plant Cell Physiol 44:70–75

    Article  CAS  PubMed  Google Scholar 

  • Kalia P, Saha P, Ray S (2017) Development of RAPD and ISSR derived SCAR markers linked to Xca1Bo gene conferring resistance to black rot disease in cauliflower (Brassica oleracea var. botrytis L.). Euphytica 213:232

    Google Scholar 

  • Karan R, Deleon T, Biradar H, Subudhi PK (2012) Salt stress induced variation in DNA methylation pattern and its influence on gene expression in contrasting rice genotypes. PLoS ONE 7:e40203

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kardailsky I, Shukla VK, Ahn JH, Dagenais N, Christensen SK, Nguyen JT, Chory J, Harrison MJ, Weigel D (1999) Activation tagging of the floral inducer FT. Science 286:1962–1965

    Article  CAS  PubMed  Google Scholar 

  • Kato T, Hatakeyama K, Fukino N, Matsumoto S (2012) Identification of a clubroot resistance locus conferring resistance to a Plasmodiophora brassicae classified into pathotype group 3 in Chinese cabbage (Brassica rapa L.). Breed Sci 62:282–287

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kato T, Hatakeyama K, Fukino N, Matsumoto S (2013) Fine mapping of the clubroot resistance gene CRb and development of a useful selectable marker in Brassica rapa. Breed Sci 63:116–124

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kawamura K, Kawanabe T, Shimizu M, Nagano AJ, Saeki N, Okazaki K, Kaji M, Dennis ES, Osabe K, Fujimoto R (2016) Genetic distance of inbred lines of Chinese cabbage and its relationship to heterosis. Plant Gene 5:1–7

    Article  CAS  Google Scholar 

  • Kawamura K, Kawanabe T, Shimizu M, Okazaki K, Kaji M, Dennis ES, Osabe K, Fujimoto R (2015) Genetic characterization of inbred lines of Chinese cabbage by DNA markers; towards the application of DNA markers to breeding of F1 hybrid cultivars. Data Brief 6:229–237

    Article  PubMed  PubMed Central  Google Scholar 

  • Kawamura K, Shimizu M, Kawanabe T, Pu Z, Kodama T, Kaji M, Osabe K, Fujimoto R, Okazaki K (2017) Assessment of DNA markers for seed contamination testing and selection of disease resistance in cabbage. Euphytica 213:228

    Article  CAS  Google Scholar 

  • Kawanabe T, Ishikura S, Miyaji N, Sasaki T, Wu LM, Itabashi E, Takada S, Shimizu M, Takasaki-Yasuda T, Osabe K, Peacock WJ, Dennis ES, Fujimoto R (2016a) Role of DNA methylation in hybrid vigor in Arabidopsis thaliana. Proc Natl Acad Sci USA 113:E6704–E6711

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kawanabe T, Osabe K, Itabashi E, Okazaki K, Dennis ES, Fujimoto R (2016b) Development of primer sets that can verify the enrichment of histone modifications, and their application to examining vernalization-mediated chromatin changes in Brassica rapa L. Genes Genet Syst 91:1–10

    Article  CAS  PubMed  Google Scholar 

  • Kemp DB, Eichenseer K, Kiessling W (2015) Maximum rates of climate change are systematically underestimated in the geological record. Nat Commun 6:8890

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Khraiwesh B, Zhu JK, Zhu J (2012) Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants. Biochim Biophys Acta 1819:137–148

    Article  CAS  PubMed  Google Scholar 

  • Kifuji Y, Hanzawa H, Terasawa Y, Ashutosh Nishio T (2013) QTL analysis of black rot resistance in cabbage using newly developed EST-SNP markers. Euphytica 190:289–295

    Article  CAS  Google Scholar 

  • Kim DH, Doyle MR, Sung S, Amasino RM (2009) Vernalization: winter and the timing of flowering in plants. Annu Rev Cell Dev 25:277–299

    Article  CAS  Google Scholar 

  • Kim DH, Sung S (2017) Vernalization-triggered intragenic chromatin loop formation by long noncoding RNAs. Dev Cell 40:302–312

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim J, Kang WH, Hwang J, Yang HB, Dosun K, Oh CS, Kang BC (2014) Transgenic Brassica rapa plants over-expressing eIF(iso)4E variants show broad-spectrum Turnip mosaic virus (TuMV) resistance. Mol Plant Pathol 15:615–626

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim J, Kang WH, Yang HB, Park S, Jang CS, Yu HJ, Kang BC (2013) Identification of a broad-spectrum recessive gene in Brassica rapa and molecular analysis of the eIF4E gene family to develop molecular markers. Mol Breed 32:385–398

    Article  CAS  Google Scholar 

  • Kimura R, Sato K, Fujimoto R, Nishio T (2002) Recognition specificity of self-incompatibility maintained after the divergence of Brassicaoleracea and Brassicarapa. Plant J 29:215–223

    Article  CAS  PubMed  Google Scholar 

  • Kitamoto N, Nishikawa K, Tanimura Y, Urushibara S, Matsuura T, Yokoi S, Takahata Y, Yui S (2017) Development of late-bolting F1 hybrids of Chinese cabbage(Brassica rapa L.) allowing early spring cultivation without heating. Euphytica 213:292

    Google Scholar 

  • Kitamoto N, Yui S, Nishikawa K, Takahata Y, Yokoi S (2014) A naturally occurring long insertion in the first intron in the Brassica rapaFLC2 gene causes delayed bolting. Euphytica 196:213–223

    Article  CAS  Google Scholar 

  • Kobayashi Y, Kaya H, Goto K, Iwabuchi M, Araki T (1999) A pair of related genes with antagonistic roles in mediating flowering signals. Science 286:1960–1962

    Article  CAS  PubMed  Google Scholar 

  • Koh J, Chen G, Yoo MJ, Zhu N, Dufresne D, Erickson JE, Shao H, Chen S (2015) Comparative proteomic analysis of Brassica napus in response to drought stress. J Proteome Res 14:3068–3081

    Article  CAS  PubMed  Google Scholar 

  • Kole C, Quijada P, Michaels SD, Amasino RM, Osborn TC (2001) Evidence for homology of flowering-time genes VFR2 from Brassica rapa and FLC from Arabidopsis thaliana. Theor Appl Genet 102:425–430

    Article  CAS  Google Scholar 

  • Kolukisaoglu U, Weinl S, Blazevic D, Batistic O, Kudla J (2004) Calcium sensors and their interacting protein kinases: genomics of the Arabidopsis and rice CBL-CIPK signaling networks. Plant Physiol 134:43–58

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kotak S, Larkindale J, Lee U, von Koskull-Döring P, Vierling E, Scharf KD (2007) Complexity of the heat stress response in plants. Curr Opin Plant Biol 10:310–316

    Article  CAS  PubMed  Google Scholar 

  • Kuginuki Y, Ajisaka H, Yui M, Yoshikawa H, Hida K, Hirai M (1997) RAPD markers linked to a clubroot-resistance locus in Brassica rapa L. Euphytica 98:149–154

    Article  CAS  Google Scholar 

  • Kuginuki Y, Yoshikawa H, Hirai M (1999) Variation in virulence of Plasmodiophora brassicae in Japan tested with clubroot-resistant cultivars of Chinese cabbage (Brassica rapa L. ssp. pekinensis). Eur J Plant Pathol 105:327–332

    Article  Google Scholar 

  • Kusaba M, Nishio T (1999) Comparative analysis of S haplotypes with very similar SLG alleles in Brassicarapa and Brassicaoleracea. Plant J 17:83–91

    Article  CAS  PubMed  Google Scholar 

  • Kusaba M, Nishio T, Satta Y, Hinata K, Ockendon DJ (1997) Striking sequence similarity in inter- and intra-specific comparisons of class I SLG alleles from Brassica oleracea and Brassica campestris: Implication for the evolution and recognition mechanism. Proc Natl Acad Sci USA 94:7673–7678

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lai AG, Doherty CJ, Mueller-Roeber B, Kay SA, Schippers JH, Dijkwel PP (2012) CIRCADIAN CLOCK-ASSOCIATED 1 regulates ROS homeostasis and oxidative stress responses. Proc Natl Acad Sci USA 109:17129–17134

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Laird PW (2010) Principles and challenges of genome-wide DNA methylation analysis. Nat Rev Genet 11:191–203

    Article  CAS  PubMed  Google Scholar 

  • Lao X, Suwabe K, Niikura S, Kakita M, Iwano M, Takayama S (2014) Physiological and genetic analysis of CO2-induced breakdown of self-incompatibility in Brassica rapa. J Exp Bot 65:939–951

    Article  CAS  PubMed  Google Scholar 

  • Laurens F, Thomas G (1993) Inheritance of resistance to clubroot (Plasmodiophora brassicae Wor.) in kale (Brassica oleracea ssp. Acephala). Hereditas 119:253–262

    Article  Google Scholar 

  • Lauss K, Wardenaar R, Oka R, van Hulten MHA, Guryev V, Keurentjes JJB, Stam M, Johannes F (2018) Parental DNA methylation states are associated with heterosis in epigenetic hybrids. Plant Physiol 176:1627–1645

    Article  CAS  PubMed  Google Scholar 

  • Law JA, Jacobsen SE (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11:204–220

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lawrenson T, Shorinola O, Stacey N, Li C, Østergaard L, Patron N, Uauy C, Harwood W (2015) Induction of targeted, heritable mutations in barley and Brassica oleracea using RNA-guided Cas9 nuclease. Genome Biol 16:258

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lee H, Suh SS, Park E, Cho E, Ahn JH, Kim SG, Lee JS, Kwon YM, Lee I (2000) The AGAMOUS-LIKE 20 MADS domain protein integrates floral inductive pathways in Arabidopsis. Genes Dev 14:2366–2376

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lee J, Izzah NK, Choi BS, Joh HJ, Lee SC, Perumal S, Seo J, Ahn K, Jo EJ, Choi GJ, Nou IS, Yu Y, Yang TJ (2016) Genotyping-by-sequencing map permits identification of clubroot resistance QTLs and revision of the reference genome assembly in cabbage (Brassica oleracea L.). DNA Res 23:29–41

    CAS  PubMed  Google Scholar 

  • Lee J, Izzah NK, Jayakodi M, Perumal S, Joh HJ, Lee HJ, Lee SC, Park JY, Yang KW, Nou IS, Seo J, Yoo J, Suh Y, Ahn K, Lee JH, Choi GJ, Yu Y, Kim H, Yang TJ (2015) Genome-wide SNP identification and QTL mapping for black rot resistance in cabbage. BMC Plant Biol 15:32

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lee J, Song H, Han CT, Lim YP, Chung SM, Hur Y (2010) Expression characteristics of heat shock protein genes in two comparable inbred lines of Chinese cabbage, Chiifu and Kenshin. Genes Genom 32:247–257

    Article  CAS  Google Scholar 

  • Lehmann P, Jenner CE, Kozubek E, Greenland AJ, Walsh JA (2003) Coat protein-mediated resistance to Turnip mosaic virus in oilseed rape (Brassica napus). Mol Breed 11:83–94

    Article  CAS  Google Scholar 

  • Levy YY, Mesnage S, Mylne JS, Gendall AR, Dean C (2002) Multiple roles of Arabidopsis VRN1 in vernalization and flowering time control. Science 297:243–246

    Article  CAS  PubMed  Google Scholar 

  • Li E, Ling J, Wang G, Xiao J, Yang Y, Mao Z, Wang X, Xie B (2015a) Comparative proteomics analyses of two races of Fusarium oxysporum f. sp. conglutinans that differ in pathogenicity. Sci Rep 5:13663

    Google Scholar 

  • Li E, Wang G, Xiao J, Ling J, Yang Y, Xie B (2016a) A SIX1 homolog in Fusarium oxysporum f. sp. conglutinans is required for full virulence on cabbage. PLoS One 11:e0152273

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Li E, Wang G, Yang Y, Xiao J, Mao Z, Xie B (2015b) Microscopic analysis of the compatible and incompatible interactions between Fusarium oxysporum f. sp. conglutinans and cabbage. Eur J Plant Pathol 141:597–609

    Article  Google Scholar 

  • Li F, Kitashiba H, Inaba K, Nishio T (2009) A Brassica rapa linkage map of EST-based SNP markers for identification of candidate genes controlling flowering time and leaf morphological traits. DNA Res 6:311–323

    Article  CAS  Google Scholar 

  • Li G, Hu X, Hou L, Cao L, Wang Q, Wang D, Mu X, Zhang Y, Zhou X, Zhao Y, Xie CG (2018a) Molecular identification of BrHAB2a, one of the two AtHAB2-like proteins in Brassica rapa, is an important component of ABA signaling. Biochem Biophys Res Commun 503:495–500

    Article  CAS  PubMed  Google Scholar 

  • Li G, Qian W, Zhang SJ, Zhang SF, Li F, Zhang H, Wu J, Wang XW, Sun RF (2016b) Development of gene-based markers for the Turnip mosaic virus resistance gene retr02 in Brassica rapa. Plant Breed 135:466–470

    Article  CAS  Google Scholar 

  • Li G, Siddiqui H, Teng Y, Lin R, Wan XY, Li J, Lau OS, Ouyang X, Dai M, Wan J, Devlin PF, Deng XW, Wang H (2011) Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis. Nat Cell Biol 13:616–622

    Article  CAS  PubMed  Google Scholar 

  • Li H, Li X, Xuan Y, Jiang J, Wei Y, Piao Z (2018b) Genome wide identification and expression profiling of SWEET genes family reveals its role during Plasmodiophora brassicae-induced formation of clubroot in Brassica rapa. Front Plant Sci 9:207

    Google Scholar 

  • Li H, Yuan J, Wu M, Han Z, Li L, Jiang H, Jia Y, Han X, Liu M, Sun D, Chen C, Song W, Wang C (2018c) Transcriptome and DNA methylome reveal insights into yield heterosis in the curds of broccoli (Brassica oleracea L var. italic). BMC Plant Biol 18:168

    Google Scholar 

  • Li J, Huang Q, Sun M, Zhang T, Li H, Chen B, Xu K, Gao G, Li F, Yan G, Qiao J, Cai Y, Wu X (2016c) Global DNA methylation variations after short-term heat shock treatment in cultured microspores of Brassica napus cv. Topas. Sci Rep 6:38401

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li JF, Norville JE, Aach J, McCormack M, Zhang D, Bush J, Church GM, Sheen J (2013a) Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9. Nat Biotechnol 31:688–691

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li L, Luo Y, Chen B, Xu K, Zhang F, Li H, Huang Q, Xiao X, Zhang T, Hu J, Li F, Wu X (2016d) A genome-wide association study reveals new loci for resistance to clubroot disease in Brassica napus. Front Plant Sci 7:1483

    PubMed  PubMed Central  Google Scholar 

  • Li Q, Zhang X, Zeng Q, Zhang Z, Liu S, Pei Y, Wang S, Liu X, Xu W, Fu W, Zhao Z, Song X (2015c) Identification and mapping of a novel Turnip mosaic virus resistance gene TuRBCS01 in Chinese cabbage (Brassica rapa L.). Plant Breed 134:221–225

    Article  CAS  Google Scholar 

  • Li X, Ramchiary N, Dhandapani V, Choi SR, Hur Y, Nou IS, Yoon MK, Lim YP (2013b) Quantitative trait loci mapping in Brassica rapa revealed the structural and functional conservation of genetic loci governing morphological and yield component traits in the A, B, and C subgenomes of Brassica species. DNA Res 20:1–16

    Article  PubMed  CAS  Google Scholar 

  • Li X, Zhang S, Bai J, He Y (2016e) Tuning growth cycles of Brassica crops via natural antisense transcripts of BrFLC. Plant Biotechnol J 14:905–914

    Article  CAS  PubMed  Google Scholar 

  • Li Z, Zhang L, Wang A, Xu X, Li J (2013c) Ectopic overexpression of SlHsfA3, a heat stress transcription factor from tomato, confers increased thermotolerance and salt hypersensitivity in germination in transgenic Arabidopsis. PLoS ONE 8:e54880

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lin SI, Wang JG, Poon SY, Su CL, Wang SS, Chiou TJ (2005) Differential regulation of FLOWERING LOCUS C expression by vernalization in cabbage and Arabidopsis. Plant Physiol 137:1037–1048

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lindhout P (2002) The perspectives of polygenic resistance in breeding for durable disease resistance. Euphytica 124:217–226

    Article  CAS  Google Scholar 

  • Lippman ZB, Zamir D (2007) Heterosis: revisiting the magic. Trends Genet 23:60–66

    Article  CAS  PubMed  Google Scholar 

  • Lister R, O’Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523–536

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu G, Xia Y, Liu T, Dai S, Hou X (2018) The DNA methylome and association of differentially methylated regions with differential gene expression during heat stress in Brassica rapa. Intl J Mol Sci 19:1414

    Article  CAS  Google Scholar 

  • Liu J, Kim BM, Kaneko Y, Inukai T, Masuta C (2015) Identification of the TuNI gene causing systemic necrosis in Arabidopsis ecotype Ler infected with Turnip mosaic virus and characterization of its expression. J Gen Plant Pathol 81:180–191

    Article  CAS  Google Scholar 

  • Liu J, Liu X, Dai L, Wang G (2007) Recent progress in elucidating the structure, function and evolution of disease resistance genes in plants. J Genet Genom 34:765–776

    Article  Google Scholar 

  • Liu S, Liu Y, Yang X, Tong C, Edwards D, Parkin IAP, Zhao M, Ma J, Yu J, Huang S, Wang X, Wang J, Lu K, Fang Z, Bancroft I, Yang TJ, Hu Q, Wang X, Yue Z, Li H, Yang L, Wu J, Zhou Q, Wang W, King GJ, Pires JC, Lu C, Wu Z, Sampath P, Wang Z, Guo H, Pan S, Yang L, Min J, Zhang D, Jin D, Li W, Belcram H, Tu J, Guan M, Qi C, Du D, Li J, Jiang L, Batley J, Sharpe AG, Park BS, Ruperao P, Cheng F, Waminal NE, Huang Y, Dong C, Wang L, Li J, Hu Z, Zhuang M, Huang Y, Huang J, Shi J, Mei D, Liu J, Lee TH, Wang J, Jin H, Li Z, Li X, Zhang J, Xiao L, Zhou Y, Liu Z, Liu X, Qin R, Tang X, Liu W, Wang Y, Zhang Y, Lee J, Kim HH, Denoeud F, Xu X, Liang X, Hua W, Wang X, Wang J, Chalhoub B, Paterson AH (2014) The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nat Commun 5:3930

    Article  CAS  PubMed  Google Scholar 

  • Liu T, Li Y, Duan W, Huang F, Hou X (2017a) Cold acclimation alters DNA methylation patterns and confers tolerance to heat and increases growth rate in Brassica rapa. J Exp Bot 68:1213–1224

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu X, Han F, Kong C, Fang Z, Yang L, Zhang Y, Zhuang M, Liu Y, Li Z, Lv H (2017b) Rapid introgression of the Fusarium wilt resistance gene into an elite cabbage line through the combined application of a microspore culture, genome background analysis, and disease resistance-specific marker assisted foreground selection. Front Plant Sci 8:354

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lou P, Wu J, Cheng F, Cressman LG, Wang X, McClung CR (2012) Preferential retention of circadian clock genes during diploidization following whole genome triplication in Brassica rapa. Plant Cell 24:2415–2426

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lou P, Zhao J, Kim JS, Shen S, Del Carpio DP, Song X, Jin M, Vreugdenhil D, Wang X, Koornneef M, Bonnema G (2007) Quantitative trait loci for flowering time and morphological traits in multiple populations of Brassica rapa. J Exp Bot 58:4005–4016

    Article  CAS  PubMed  Google Scholar 

  • Lovelock DA, Donald CE, Conlan XA, Cahill DM (2013) Salicylic acid suppression of clubroot in broccoli (Brassicae oleracea var. italica) caused by the obligate biotroph Plasmodiophora brassicae. Austral Plant Pathol 42:141–153

    Article  CAS  Google Scholar 

  • Lowe AJ, Moule C, Trick M, Edwards KJ (2004) Efficient large-scale development of microsatellites for marker and mapping applications in Brassica crop species. Theor Appl Genet 108:1103–1112

    Article  CAS  PubMed  Google Scholar 

  • Lu SX, Webb CJ, Knowles SM, Kim SH, Wang Z, Tobin EM (2012) CCA1 and ELF3 Interact in the control of hypocotyl length and flowering time in Arabidopsis. Plant Physiol 158:1079–1088

    Article  CAS  PubMed  Google Scholar 

  • Ludwig AA, Romeis T, Jones JDG (2004) CDPK-mediated signalling pathways: specificity and cross-talk. J Exp Bot 55:181–188

    Article  CAS  PubMed  Google Scholar 

  • Ludwig-Müller J, Bennett RN, Kiddle G, Ihmig S, Ruppel M, Hilgenberg W (1999) The host range of Plasmodiophora brassicae and its relationship to endogenous glucosinolate content. New Phytol 141:443–458

    Article  Google Scholar 

  • Luo Y, Dong D, Su Y, Wang X, Peng Y, Peng J, Zhou C (2018) Transcriptome analysis of Brassica juncea var. tumida Tsen responses to Plasmodiophora brassicae primed by the biocontrol strain Zhihengliuella aestuarii. Funct Integr Genom 18:301–314

    Article  CAS  Google Scholar 

  • Lv H, Fang Z, Yang L, Zhang Y, Wang Q, Liu Y, Zhuang M, Yang Y, Xie B, Liu B, Liu J, Kang J, Wang X (2014a) Mapping and analysis of a novel candidate Fusarium wilt resistance gene FOC1 in Brassica oleracea. BMC Genom 15:1094

    Article  CAS  Google Scholar 

  • Lv HH, Wang QB, Yang LM, Fang ZY, Liu YM, Zhuang M, Zhang YY, Yang YH, Xie BY, Wang XW (2014b) Breeding of cabbage (Brassica oleracea L. var. capitata) with fusarium wilt resistance based on microspore culture and marker-assisted selection. Euphytica 200:465–473

    Article  Google Scholar 

  • Lv HH, Yang LM, Kang JG, Wang QB, Wang XW, Fang ZY, Liu YM, Zhuang M, Zhang YY, Lin Y, Yang YH, Xie BY, Liu B, Liu JS (2013) Development of InDel markers linked to Fusarium wilt resistance in cabbage. Mol Breed 32:961–967

    Article  CAS  Google Scholar 

  • Lydiate DJ, Pilcher RLR, Higgins EE, Walsh JA (2014) Genetic control of immunity to Turnip mosaic virus (TuMV) pathotype 1 in Brassica rapa (Chinese cabbage). Genome 57:419–425

    Article  CAS  PubMed  Google Scholar 

  • Lyons R, Stiller J, Powell J, Rusu A, Manners JM, Kazan K (2015) Fusarium oxysporum triggers tissue-specific transcriptional reprogramming in Arabidopsis thaliana. PLoS ONE 10:e0121902

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ma J, Hou X, Xiao D, Qi L, Wang F, Sun F, Wang Q (2010) Cloning and characterization of the BcTuR3 gene related to resistance to Turnip mosaic virus (TuMV) from non-heading Chinese cabbage. Plant Mol Biol Rep 28:588–596

    Article  CAS  Google Scholar 

  • Makarevitch I, Eichten SR, Briskine R, Waters AJ, Danilevskaya ON, Meeley RB, Myers CL, Vaughn MW, Springer NM (2013) Genomic distribution of maize facultative heterochromatin marked by trimethylation of H3K27. Plant Cell 25:780–793

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Manoharan RK, Shanmugam A, Hwang I, Park JI, Nou IS (2016) Expression of salicylic acid-related genes in Brassica oleracea var. capitata during Plasmodiophora brassicae infection. Genome 59:379–391

    Article  CAS  PubMed  Google Scholar 

  • Manzanares-Dauleux MJ, Delourme R, Baron F, Thomas G (2000) Mapping of one major gene and of QTLs involved in resistance to clubroot in Brassica napus. Theor Appl Genet 101:885–891

    Article  CAS  Google Scholar 

  • Martín ÁM, y Poch HLC, Herrera DM, Ponz F (1999) Resistances to Turnip mosaic potyvirus in Arabidopsis thaliana. Mol Plant Microbe Interact 12:1016–1021

    Article  Google Scholar 

  • Más P, Devlin PF, Panda S, Kay SA (2000) Functional interaction of phytochrome B and cryptochrome 2. Nature 408:207–211

    Article  PubMed  Google Scholar 

  • Massomo SMS, Mortensen NC, Mabagala RB, Newman MA, Hockenhull J (2004) Biological control of black rot (Xanthomonas campestris pv. campestris) of cabbage in Tanzania with Bacillus strains. J Plant Pathol 152:98–105

    Google Scholar 

  • Matsumoto E, Yasui C, Ohi M, Tsukada M (1998) Linkage analysis of RFLP markers for clubroot resistance and pigmentation in Chinese cabbage (Brassica rapa ssp. pekinensis). Euphytica 104:79–86

    Article  CAS  Google Scholar 

  • Matzke MA, Mosher RA (2014) RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nat Rev Genet 15:394–408

    Article  CAS  PubMed  Google Scholar 

  • McClung CR (2014) Wheels within wheels: new transcriptional feedback loops in the Arabidopsis circadian clock. F1000prime Rep 6:2

    Google Scholar 

  • McCormack E, Braam J (2003) Calmodulins and related potential calcium sensors of Arabidopsis. New Phytol 159:585–598

    Article  CAS  PubMed  Google Scholar 

  • Metzker ML (2010) Sequencing technologies-the next generation. Nat Rev Genet 11:31–46

    Article  CAS  PubMed  Google Scholar 

  • Meyer RC, Witucka-Wall H, Becher M, Blacha A, Boudichevskaia A, Dörmann P, Fiehn O, Friedel S, von Korff M, Lisec J, Melzer M, Repsilber D, Schmidt R, Scholz M, Selbig J, Willmitzer L, Altmann T (2012) Heterosis manifestation during early Arabidopsis seedling development is characterized by intermediate gene expression and enhanced metabolic activity in the hybrids. Plant J 71:669–683

    Article  CAS  PubMed  Google Scholar 

  • Michaels SD, Amasino RM (1999) FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell 11:949–956

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Miller M, Song Q, Shi X, Juenger TE, Chen ZJ (2015) Natural variation in timing of stress-responsive gene expression predicts heterosis in intraspecific hybrids of Arabidopsis. Nat Commun 6:7453

    Article  PubMed  Google Scholar 

  • Miura A, Yonebayashi S, Watanabe K, Toyama T, Shimada H, Kakutani T (2001) Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 411:212–214

    Article  CAS  PubMed  Google Scholar 

  • Miyaji N, Fujimoto R (2018) Hybrid vigor: importance of epigenetic processes and consequences for breeding. Adv Bot Res 88:247–275

    Article  Google Scholar 

  • Miyaji N, Shimizu M, Miyazaki J, Osabe K, Sato M, Ebe Y, Takada S, Kaji M, Dennis ES, Fujimoto R, Okazaki K (2017) Comparison of transcriptome profiles by Fusarium oxysporum inoculation between Fusarium yellows resistant and susceptible lines in Brassica rapa L. Plant Cell Rep 36:1841–1854

    Article  CAS  PubMed  Google Scholar 

  • Moll RH, Lonnquist JH, VélezFortuno J, Johnson EC (1965) The relationship of heterosis and genetic divergence in maize. Genetics 52:139–144

    CAS  PubMed  PubMed Central  Google Scholar 

  • Montoya JM, Raffaelli D (2010) Climate change, biotic interactions and ecosystem services. Phil Trans Roy Soc B 365:2013–2018

    Article  Google Scholar 

  • Moriguchi K, Kimizuka-Takagi C, Ishii K, Nomura K (1999) A genetic map based on RAPD, RFLP, isozyme, morphological markers and QTL analysis for clubroot resistance in Brassica oleracea. Breed Sci 49:257–265

    Article  CAS  Google Scholar 

  • Morrison RH, Mengistu A, Williams PH (1994) First report of race 2 of cabbage yellows caused by Fusarium oxysporum f. sp. conglutinans in Texas. Plant Dis 78:641

    Google Scholar 

  • Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628

    Article  CAS  PubMed  Google Scholar 

  • Murase K, Shiba H, Iwano M, Che FS, Watanabe M, Isogai A, Takayama S (2004) A membrane-anchored protein kinase involved in Brassica self-incompatibility signaling. Science 303:1516–1519

    Article  CAS  PubMed  Google Scholar 

  • Mylne JS, Barrett L, Tessadori F, Mesnage S, Johnson L, Bernatavichute YV, Jacobsen SE, Fransz P, Dean C (2006) LHP1, the Arabidopsis homologue of HETEROCHROMATIN PROTEIN1, is required for epigenetic silencing of FLC. Proc Natl Acad Sci USA 103:5012–5017

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nagaoka T, Doullah MAU, Matsumoto S, Kawasaki S, Ishikawa T, Hori H, Okazaki K (2010) Identification of QTLs that control clubroot resistance in Brassica oleracea and comparative analysis of clubroot resistance genes between B. rapa and B. oleracea. Theor Appl Genet 120:1335–1346

    Article  CAS  PubMed  Google Scholar 

  • Nakanishi T, Esashi Y, Hinata K (1969) Control of self-incompatibility by CO2 gas in Brassica. Plant Cell Physiol 10:925–927

    Article  CAS  Google Scholar 

  • Nakanishi T, Hinata K (1973) An effective time for CO2 gas treatment in overcoming self-incompatibility in Brassica. Plant Cell Physiol 14:873–879

    Google Scholar 

  • Nakashima K, Yamaguchi-Shinozaki K, Shinozaki K (2014) The transcriptional regulatory network in the drought response and its crosstalk in abiotic stress responses including drought, cold, and heat. Front Plant Sci 5:170

    Article  PubMed  PubMed Central  Google Scholar 

  • Namazkar S, Egsgaard H, Frenck G, Terkelsen T, Jørgensen RB (2015) Significant reductions in oil quality and lipid content of oilseed rape (Brassica napusL.) under climate change. Procedia Environ Sci 29:121–122

    Article  CAS  Google Scholar 

  • Nasrallah JB, Nishio T, Nasrallah ME (1991) The self-incompatibility genes of Brassica: expression and use in genetic ablation of floral tissues. Annu Rev Plant Physiol Plant Mol Biol 42:393–422

    Article  Google Scholar 

  • Nasrallah JB, Rundle SJ, Nasrallah ME (1994) Genetic evidence for the requirement of the BrassicaS-locus receptor kinase gene in the self-incompatibility response. Plant J 5:373–384

    Article  CAS  Google Scholar 

  • Neik TX, Barbetti MJ, Batley J (2017) Current status and challenges in identifying disease resistance genes in Brassica napus. Front Plant Sci 8:1788

    Article  PubMed  PubMed Central  Google Scholar 

  • Nekrasov V, Staskawicz B, Weigel D, Jones JDG, Kamoun S (2013) Targeted mutagenesis in the model plant Nicotiana benthamiana using Cas9 RNA-guided endonuclease. Nat Biotechnol 31:691–693

    Article  CAS  PubMed  Google Scholar 

  • Newbery F, Qi A, Fitt BDL (2016) Modelling impacts of climate change on arable crop diseases: progress, challenges and applications. Curr Opin Plant Biol 32:101–109

    Article  PubMed  Google Scholar 

  • Nguyen HD, Tran HTN, Ohshima K (2013) Genetic variation of the Turnip mosaicvirus population of Vietnam: a case study of founder, regional and local influences. Virus Res 171:138–149

    Article  CAS  PubMed  Google Scholar 

  • Nguyen ML, Monakhos GF, Komakhin RA, Monakhos SG (2018) The new clubroot resistance locus is located on chromosome A05 in Chinese cabbage (Brassica rapa L.). Russ J Genet 54:296–304

    Article  CAS  Google Scholar 

  • Ni Z, Kim ED, Ha M, Lackey E, Liu J, Zhang Y, Sun Q, Chen ZJ (2009) Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature 457:327–331

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Niederhuth CE, Bewick AJ, Ji L, Alabady MS, Do Kim K, Li Q, Rohr NA, Rambani A, Burke JM, Udall JA, Egesi C, Schmutz J, Grimwood J, Jackson SA, Springer NM, Schmitz RJ (2016) Widespread natural variation of DNA methylation within angiosperms. Genome Biol 17:194

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Niikura S, Matsuura S (2000) Genetic analysis of the reaction level of self-incompatibility to a 4% CO2 gas treatment in the radish (Raphanus sativus L.). Theor Appl Genet 101:1189–1193

    Article  CAS  Google Scholar 

  • Nishio T, Kusaba M, Sakamoto K, Ockendon DJ (1997) Polymorphism of the kinase domain of the S-locus receptor kinase gene (SRK) in Brassica oleracea L. Theor Appl Genet 95:335–342

    Article  CAS  Google Scholar 

  • Nishio T, Kusaba M, Watanabe M, Hinata K (1996) Registration of S alleles in Brassica campestris L by the restriction fragment sizes of SLGs.Theor ApplGenet 92:388–394

    Google Scholar 

  • Niwa Y, Ito S, Nakamichi N, Mizoguchi T, Niinuma K, Yamashino T, Mizuno T (2007) Genetic linkages of the circadian clock-associated genes, TOC1, CCA1 and LHY, in the photoperiodic control of flowering time in Arabidopsis thaliana. Plant Cell Physiol 48:925–937

    Article  CAS  PubMed  Google Scholar 

  • Nomura K, Minegishi Y, Kimizuka-Takagi C, Fujioka T, Moriguchi K, Shishido R, Ikehashi H (2005) Evaluation of F2 and F3 plants introgressed with QTLs for clubroot resistance in cabbage developed by using SCAR markers. Plant Breed 124:371–375

    Article  CAS  Google Scholar 

  • Nou IS, Watanabe M, Isogai A, Hinata K (1993) Comparison of S-alleles and S-glycoproteins between two wild populations of Brassica campestris in Turkey and Japan. Sex Plant Reprod 6:79–86

    Article  Google Scholar 

  • Nyalugwe EP, Barbetti MJ, Jones RAC (2014) Preliminary studies on resistance phenotypes to Turnip mosaic virus in Brassica napus and B. carinata from different continents and effects of temperature on their expression. Eur J Plant Pathol 139:687–706

    Article  Google Scholar 

  • Nyalugwe EP, Barbetti MJ, Jones RAC (2015a) Studies on resistance phenotypes to Turnip mosaic virus in five species of Brassicaceae, and identification of a virus resistance gene in Brassica juncea. Eur J Plant Pathol 141:647–666

    Article  CAS  Google Scholar 

  • Nyalugwe EP, Barbetti MJ, Jones RAC (2016) Strain specificity of Turnip mosaic virus resistance gene TuRBJU 01 in Brassica juncea. Eur J Plant Pathol 145:209–213

    Article  CAS  Google Scholar 

  • Nyalugwe EP, Jones RAC, Barbetti MJ, Kehoe MA (2015b) Biological and molecular variation amongst Australian Turnip mosaic virus isolates. Plant Pathol 64:1215–1223

    Article  CAS  Google Scholar 

  • Ockendon DJ (2000) The S-allele collection of Brassica oleracea. Acta Hortic 539:25–30

    Article  Google Scholar 

  • Oh S, Park S, van Nocker S (2008) Genic and global functions for Paf1C in chromatin modification and gene expression in Arabidopsis. PLoS Genet 4:e1000077

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ohshima K, Tomitaka Y, Wood JT, Minematsu Y, Kajiyama H, Tomimura K, Gibbs AJ (2007) Patterns of recombination in turnip mosaic virus genomic sequences indicate hotspots of recombination. J Gen Virol 88:298–315

    Article  CAS  PubMed  Google Scholar 

  • Ohshima K, Yamaguchi Y, Hirota R, Hamamoto T, Tomimura K, Tan Z, Sano T, Azuhata F, Walsh JA, Fletcher J, Chen J, Gera A, Gibbs A (2002) Molecular evolution of Turnip mosaic virus: evidence of host adaptation, genetic recombination and geographical spread. J Gen Virol 83:1511–1521

    Article  CAS  PubMed  Google Scholar 

  • Oikawa E, Takuno S, Izumita A, Sakamoto K, Hanzawa H, Kitashiba H, Nishio T (2011) Simple and efficient methods for S genotyping and S screening in genus Brassica by dot-blot analysis. Mol Breed 28:1–12

    Article  Google Scholar 

  • Okazaki K, Kusaba M, Ockendon DJ, Nishio T (1999) Characterization of S tester line in Brassica oleracea: polymorphism of restriction fragment length of SLG homologues and isoelectric points of S-locus glycoproteins. Theor Appl Genet 98:1329–1334

    Article  CAS  Google Scholar 

  • Okazaki K, Sakamoto K, Kikuchi R, Saito A, Togashi E, Kuginuki Y, Matsumoto S, Hirai M (2007) Mapping and characterization of FLC homologs and QTL analysis of flowering time in Brassica oleracea. Theor Appl Genet 114:595–608

    Article  CAS  PubMed  Google Scholar 

  • Okuzaki A, Ogawa T, Koizuka C, Kaneko K, Inaba M, Imamura J, Koizuka N (2018) CRISPER/Cas9-mediated genome editing of the fatty acid desaturase 2 gene in Brassica napus. Plant Physiol Biochem 131:63–69

    Article  CAS  PubMed  Google Scholar 

  • Olvera-Carrillo Y, Reyes JL, Covarrubias AA (2011) Late embryogenesis abundant proteins: versatile players in the plant adaptation to water limiting environments. Plant Signal Behav 6:586–589

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Osabe K, Sasaki T, Ishikawa R, Fujimoto R (2012) The role of DNA methylation in plants. In: Tatarinova TV, Sablok G (eds) DNA methylation: principles, mechanisms and challenges. NOVA Publishers, NY, USA, pp 35–66

    Google Scholar 

  • Osborn TC, Kole C, Parkin IA, Sharpe AG, Kuiper M, Lydiate DJ, Trick M (1997) Comparison of flowering time genes in Brassica rapa, B. napus and Arabidopsis thaliana. Genetics 146:1123–1129

    CAS  PubMed  PubMed Central  Google Scholar 

  • Oumouloud A, El-Otmani M, Chikh-Rouhou H, Garces Claver A, Gonzalez Torres R, Rerl-Treves R, Alvarez JM (2013) Breeding melon for resistance to Fusarium wilt: recent developments. Euphytica 192:155–169

    Article  CAS  Google Scholar 

  • Pang W, Fu P, Li X, Zhan Z, Yu S, Piao Z (2018) Identification and mapping of the clubroot resistance gene CRd in Chinese cabbage (Brassica rapa ssp. pekinensis). Front Plant Sci 9:653

    Google Scholar 

  • Pang Y, Li L, Ren F, Lu P, Wei P, Cai J, Xin L, Zhang J, Chen J, Wang X (2010) Overexpression of the tonoplast aquaporin AtTIP5;1 conferred tolerance to boron toxicity in Arabidopsis. J Genet Genom 37:389–397

    Article  CAS  Google Scholar 

  • Paritosh K, Yadava SK, Gupta V, Panjabi-Massand P, Sodhi YS, Pradhan AK, Pental D (2013) RNA-seq based SNPs in some agronomically important oleiferous lines of Brassica rapa and their use for genome-wide linkage mapping and specific-region fine mapping. BMC Genom 14:463

    Article  CAS  Google Scholar 

  • Park HJ, Jung WY, Lee SS, Song JH, Kwon SY, Kim H, Kim C, Ahn JC, Cho HS (2013) Use of heat stress responsive gene expression levels for early selection of heat tolerant cabbage (Brassica oleracea L.). Int J Mol Sci 14:11871–11894

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Park JI, Nou IS, Lee SS, Kang KK, Watanabe M (2001) Identification of S-genotypes by PCR-RFLP in breeding lines of Brassica. Mol Cells 12:227–232

    CAS  PubMed  Google Scholar 

  • Parkin IAP, Koh C, Tang H, Robinson SJ, Kagale S, Clarke WE, Town CD, Nixon J, Krishnakumar V, Bidwell SL, Denoeud F, Belcram H, Links MG, Just J, Clarke C, Bender T, Huebert T, Mason AS, Pires CJ, Barker G, Moore J, Walley PG, Manoli S, Batley J, Edwards D, Nelson MN, Wang X, Paterson AH, King G, Bancroft I, Chalhoub B, Sharpe AG (2014) Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biol 15:R77

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Peng L, Zhou L, Li Q, Wei D, Ren X, Song H, Mei J, Si J, Qian W (2018) Identification of quantitative trait loci for clubroot resistance in Brassica oleracea with the use of Brassica SNP microarray. Front Plant Sci 9:822

    Article  PubMed  PubMed Central  Google Scholar 

  • Peng Y, Lin W, Cai W, Arora R (2007) Overexpression of a Panax ginseng tonoplast aquaporin alters salt tolerance, drought tolerance and cold acclimation ability in transgenic Arabidopsis plants. Planta 226:729–740

    Article  CAS  PubMed  Google Scholar 

  • Piao Y, Jin K, He Y, Liu J, Liu S, Li X, Piao Z (2018) Genome-wide identification and role of MKK and MPK gene families in clubroot resistance of Brassica rapa. PLoS ONE 13:e0191015

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Piao Z, Ramchiary N, Lim YP (2009) Genetics of clubroot resistance in Brassica species. J Plant Growth Regul 28:252–264

    Article  CAS  Google Scholar 

  • Piao ZY, Deng YQ, Choi SR, Park YJ, Lim YP (2004) SCAR and CAPS mapping of CRb, a gene conferring resistance to Plasmodiophora brassicae in Chinese cabbage (Brassica rapa ssp. pekinensis). Theor Appl Genet 108:1458–1465

    Article  CAS  PubMed  Google Scholar 

  • Pink DAC, Sutherland RA, Walkey DGA (1986) Genetic analysis of resistance in Brussels sprout to cauliflower mosaic and turnip mosaic viruses. Ann Appl Biol 109:199–208

    Article  Google Scholar 

  • Pink DAC, Walkey DGA (1990) Resistance to turnip mosaic virus in white cabbage. Euphytica 51:101–107

    Google Scholar 

  • Pino Del Carpio D, Basnet RK, De Vos RC, Maliepaard C, Visser R, Bonnema G (2011) The patterns of population differentiation in a Brassica rapa core collection. Theor Appl Genet 122:1105–1118

    Article  PubMed  Google Scholar 

  • Ploetz RC (2006) Fusarium wilt of banana is caused by several pathogens referred to as Fusarium oxysporum f. sp. cubense. Phytopatholojy 96:653–656

    Article  Google Scholar 

  • Provvidenti R (1980) Evaluation of Chinese cabbage cultivars from Japan and the People’s Republic of China for resistance to turnip mosaic virus and cauliflower mosaic virus. J Amer Soc Hortic Sci 105:571–573

    Google Scholar 

  • Pu Z, Ino Y, Kimura Y, Tago A, Shimizu M, Natsume S, Sano Y, Fujimoto R, Kaneko K, Shea DJ, Fukai E, Fuji S-I, Hirano H, Okazaki K (2016) Changes in the proteome of xylem sap in Brassica oleracea in response to Fusarium oxysporum stress. Front Plant Sci 7:31

    Article  PubMed  PubMed Central  Google Scholar 

  • Pu ZJ, Shimizu M, Zhang YJ, Nagaoka T, Hayashi T, Hori H, Matsumoto S, Fujimoto R, Okazaki K (2012) Genetic mapping of a fusarium wilt resistance gene in Brassica oleracea. Mol Breed 30:809–818

    Article  CAS  Google Scholar 

  • Puhakainen T, Hess MW, Mäkelä P, Svensson J, Heino P, Palva ET (2004) Overexpression of multiple dehydrin genes enhances tolerance to freezing stress in Arabidopsis. Plant Mol Biol 54:743–753

    Article  CAS  PubMed  Google Scholar 

  • Putterill J, Laurie R, Macknight R (2004) It’s time to flower: the genetic control of flowering time. BioEssays 26:363–373

    Article  CAS  PubMed  Google Scholar 

  • Qian W, Zhang S, Zhang S, Li F, Zhang H, Wu J, Wang X, Walsh JA, Sun R (2013) Mapping and candidate-gene screening of the novel Turnip mosaic virus resistance gene retr02 in Chinese cabbage (Brassica rapa L.). Theor Appl Genet 126:179–188

    Article  CAS  PubMed  Google Scholar 

  • Quadrana L, Colot V (2016) Plant transgenerational epigenetics. Annu Rev Genet 50:467–491

    Article  CAS  PubMed  Google Scholar 

  • Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94–100

    Article  CAS  PubMed  Google Scholar 

  • Rahman M, McVetty PB, Li G (2007) Development of SRAP, SNP and multiplexed SCAR molecular markers for the major seed coat color gene in Brassica rapa L. Theor Appl Genet 115:1101–1107

    Article  CAS  PubMed  Google Scholar 

  • Raman H, Raman R, Coombes N, Song J, Prangnell R, Bandaranayake C, Tahira R, Sundaramoorthi V, Killian A, Meng J, Dennis ES (2016) Genome-wide association analyses reveal complex genetic architecture underlying natural variation for flowering time in canola. Plant Cell Environ 39:1228–1239

    Article  CAS  PubMed  Google Scholar 

  • Ramchiary N, Nguyen VD, Li X, Hong CP, Dhandapani V, Choi SR, Yu G, Piao ZY, Lim YP (2011) Genic microsatellite markers in Brassica rapa: development, characterization, mapping, and their utility in other cultivated and wild Brassica relatives. DNA Res 18:305–320

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Razi H, Howell EC, Newbury HJ, Kearsey MJ (2008) Does sequence polymorphism of FLC paralogues underlie flowering time QTL in Brassica oleracea? Theor Appl Genet 116:179–192

    Article  PubMed  Google Scholar 

  • Reinders J, Wulff BBH, Mirouze M, Marí-Ordóñez A, Dapp M, Rozhon W, Bucher E, Theiler G, Paszkowski J (2009) Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes. Genes Dev 23:939–950

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Robaglia C, Caranta C (2006) Translation initiation factors: a weak link in plant RNA virus infection. Trends Plant Sci 11:40–45

    Article  CAS  PubMed  Google Scholar 

  • Roberts DM, Harmon AC (1992) Calcium-modulated proteins: Targets of intracellular calcium signals in higher plants. Annu Rev Plant Physiol Plant Mol Biol 43:375–414

    Article  CAS  Google Scholar 

  • Rocherieux J, Glory P, Giboulot A, Boury S, Barbeyron G, Thomas G, Manzanares-Dauleux MJ (2004) Isolate-specific and broad-spectrum QTLs are involved in the control of clubroot in Brassica oleracea. Theor Appl Genet 108:1555–1563

    Article  CAS  PubMed  Google Scholar 

  • Rodríguez-Hernández AM, Gosalvez B, Sempere RN, Burgos L, Aranda MA, Truniger V (2012) Melon RNA interference (RNAi) lines silenced for Cm-eIF4E show broad virus resistance. Mol Plant Pathol 13:755–763

    Article  PubMed  PubMed Central  Google Scholar 

  • Rohde P, Hincha DK, Heyer AG (2004) Heterosis in the freezing tolerance of crosses between two Arabidopsis thaliana accessions (Columbia-0 and C24) that show differences in non-acclimated and acclimated freezing tolerance. Plant J 38:790–799

    Article  CAS  PubMed  Google Scholar 

  • Roudier F, Ahmed I, Bérard C, Sarazin A, Mary-Huard T, Cortijo S, Bouyer D, Caillieux E, Duvernois-Berthet E, Al-Shikhley L, Giraut L, Després B, Drevensek S, Barneche F, Dèrozier S, Brunaud V, Aubourg S, Schnittger A, Bowler C, Martin-Magniette ML, Robin S, Caboche M, Colot V (2011) Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO J 30:1928–1938

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rouhrazi K, Khodakaramian G (2014) Genetic fingerprinting of Iranian Xanthomonas campestris pv. campestris strains inducing black rot disease of crucifers. Eur J Plant Pathol 139:175–184

    Article  CAS  Google Scholar 

  • Ruffio-Châble V, Hervé Y, Dumas C, Gaude T (1997) Distribution of S-haplotypes and its relationship with self-incompatibility in Brassica oleracea. Part 1. In inbred lines of cauliflower (B. oleracea var ‘botrytis’). Theor Appl Genet 94:338–346

    Article  Google Scholar 

  • Rusholme RL, Higgins EE, Walsh JA, Lydiate DJ (2007) Genetic control of broad-spectrum resistance to turnip mosaic virus in Brassica rapa (Chinese cabbage). J Gen Virol 88:3177–3186

    Article  CAS  PubMed  Google Scholar 

  • Sade N, Vinocur BJ, Diber A, Shatil A, Ronen G, Nissan H, Wallach R, Karchi H, Moshelion M (2009) Improving plant stress tolerance and yield production: is the tonoplast aquaporin SlTIP2; 2 a key to isohydric to anisohydric conversion? New Phytol 181:651–661

    Article  CAS  PubMed  Google Scholar 

  • Saeki N, Kawanabe T, Ying H, Shimizu M, Kojima M, Abe H, Okazaki K, Kaji M, Taylor JM, Sakakibara H, Peacock WJ, Dennis ES, Fujimoto R (2016) Molecular and cellular characteristics of hybrid vigour in a commercial hybrid of Chinese cabbage. BMC Plant Biol 16:45

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Saha P, Kalia P, Sharma M, Singh D (2016) New source of black rot disease resistance in Brassica oleracea and genetic analysis of resistance. Euphytica 207:35–48

    Article  CAS  Google Scholar 

  • Saha P, Kalia P, Sonah H, Sharma TR (2014) Molecular mapping of black rot resistance locus Xca1bo on chromosome 3 in Indian cauliflower (Brassica oleracea var. botrytis L.). Plant Breed 133:268–274

    Article  CAS  Google Scholar 

  • Saito M, Kubo N, Matsumoto S, Suwabe K, Tsukada M, Hirai M (2006) Fine mapping of the clubroot resistance gene, Crr3, in Brassica rapa. Theor Appl Genet 114:81–91

    Article  CAS  PubMed  Google Scholar 

  • Sakamoto K, Kusaba M, Nishio T (2000) Single-seed PCR-RFLP analysis for the identification of S haplotypes in commercial F1 hybrid cultivars of broccoli and cabbage. Plant Cell Rep 19:400–406

    Article  CAS  PubMed  Google Scholar 

  • Sakamoto K, Nishio T (2001) Distribution of S haplotypes in commercial cultivars of Brassica rapa. Plant Breed 120:155–161

    Article  CAS  Google Scholar 

  • Sakamoto K, Saito A, Hayashida N, Taguchi G, Matsumoto E (2008) Mapping of isolate-specific QTLs for clubroot resistance in Chinese cabbage (Brassica rapa L. ssp. pekinensis). Theor Appl Genet 117:759–767

    Article  CAS  PubMed  Google Scholar 

  • Samach A, Onouchi H, Gold SE, Ditta GS, Schwarz-Sommer Z, Yanofsky MF, Coupland G (2000) Distinct roles of CONSTANS target genes in reproductive development of Arabidopsis. Science 288:1613–1616

    Article  CAS  PubMed  Google Scholar 

  • Sanders D, Brownlee C, Harper JF (1999) Communicating with calcium. Plant Cell 11:691–706

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sasaki T, Fujimoto R, Kishitani S, Nishio T (2011) Analysis of target sequences of DDM1s in Brassica rapa by MSAP. Plant Cell Rep 30:81–88

    Article  CAS  PubMed  Google Scholar 

  • Sato K, Nishio T, Kimura R, Kusaba M, Suzuki T, Hatakeyama K, Ockendon DJ, Satta Y (2002) Co-evolution of the S-locus genes, SRK, SLG and SP11/SCR, in Brassicaoleracea and B. rapa. Genetics 162:931–940

    CAS  PubMed  PubMed Central  Google Scholar 

  • Sato Y, Fujimoto R, Toriyama K, Nishio T (2003) Commonality of self-recognition specificity of S haplotypes between Brassica oleracea and Brassica rapa. Plant Mol Biol 52:617–626

    Article  CAS  PubMed  Google Scholar 

  • Sato Y, Okamoto S, Nishio T (2004) Diversification and alteration of recognition specificity of the pollen ligand SP11/SCR in self-incompatibility of Brassica and Raphanus. Plant Cell 16:3230–3241

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sato Y, Sato K, Nishio T (2006) Interspecific pairs of class II S haplotypes having different recognition specificities between Brassica oleracea and Brassica rapa. Plant Cell Physiol 47:340–345

    Article  CAS  PubMed  Google Scholar 

  • Schaad NW (1982) Detection of seedborne bacterial plant pathogens. Plant Dis 66:885–890

    Article  Google Scholar 

  • Scheben A, Wolter F, Batley J, Puchta H, Edwards D (2017) Towards CRISPER/Cas crops-bringing together genomics and genome editing. New Phytol 216:682–698

    Article  CAS  PubMed  Google Scholar 

  • Schield DR, Walsh MR, Card DC, Andrew AL, Adams RH, Castoe TA (2016) EpiRADseq: scalable analysis of genomewide patterns of methylation using next-generation sequencing. Methods Ecol Evol 7:60–69

    Article  Google Scholar 

  • Schmitz RJ, Schultz MD, Lewsey MG, O’Malley RC, Urich MA, Libiger O, Schork NJ, Ecker JR (2011) Transgenerational epigenetic instability is a source of novel methylation variants. Science 334:369–373

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schnable PS, Springer NM (2013) Progress toward understanding heterosis in crop plants. Annu Rev Plant Bio l64:71–88

    Article  CAS  PubMed  Google Scholar 

  • Schopfer CR, Nasrallah ME, Nasrallah JB (1999) The male determinant of self-incompatibility in Brassica. Science 286:1697–1700

    Article  CAS  PubMed  Google Scholar 

  • Schranz ME, Quijada P, Sung SB, Lukens L, Amasino R, Osborn TC (2002) Characterization and effects of the replicated flowering time gene FLC in Brassica rapa. Genetics 162:1457–1468

    CAS  PubMed  PubMed Central  Google Scholar 

  • Searle I, He Y, Turck F, Vincent C, Fornara F, Kröber S, Amasino RA, Coupland G (2006) The transcription factor FLC confers a flowering response to vernalization by repressing meristem competence and systemic signaling in Arabidopsis. Genes Dev 20:898–912

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Seo PJ, Park MJ, Lim MH, Kim SG, Lee M, Baldwin IT, Park CM (2012) A self-regulatory circuit of CIRCADIAN CLOCK-ASSOCIATED1 underlies the circadian clock regulation of temperature responses in Arabidopsis. Plant Cell 24:2427–2442

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shah ZH, Rehman HM, Akhtar T, Daur I, Nawaz MA, Ahmad MQ, Rana IA, Atif RM, Yang SH, Chung G (2017) Redox and ionic homeostasis regulations against oxidative, salinity and drought stress in wheat (A Systems Biology Approach). Front Genet 8:1–10

    Article  CAS  Google Scholar 

  • Shan Q, Wang Y, Li J, Zhang Y, Chen K, Liang Z, Zhang K, Liu J, Xi JJ, Qiu JL, Gao C (2013a) Targeted genome modification of crop plants using a CRISPR-Cas system. Nat Biotechnol 31:686–688

    Article  CAS  PubMed  Google Scholar 

  • Shan X, Wang X, Yang G, Wu Y, Su S, Li S, Liu H, Yuan Y (2013b) Analysis of the DNA methylation of maize (Zea mays L.) in response to cold stress based on methylation-sensitive amplified polymorphisms. J Plant Biol 56:32–38

    Article  CAS  Google Scholar 

  • Shanmugam A, Thamilarasan SG, Park JI, Jung MY, Nou IS (2016) Characterization and abiotic stress-responsive expression analysis of SGT1genesin Brassica oleracea. Genome 59:243–251

    Article  CAS  PubMed  Google Scholar 

  • Sharma BB, Kalia P, Yadava DK, Singh D, Sharma TR (2016) Genetics and molecular mapping of black rot resistance locus Xca1Bc on chromosome B-7 in Ethiopian mustard (Brassica carinata A. Braun). PLoS One 11:e0152290

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Shea DJ, Tomaru Y, Itabashi E, Nakamura Y, Miyazaki T, Kakizaki T, Naher TN, Shimizu M, Fujimoto R, Fukai E, Okazaki K (2018a) The production and characterization of a BoFLC2 introgressed Brassica rapa by repeated backcrossing to an F1. Breed Sci 68:316–325

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shea DJ, Itabashi E, Takada S, Fukai E, Kakizaki T, Fujimoto R, Okazaki K (2018b) The role of FLOWERING LOCUSC in vernalization of Brassica: the importance of vernalization research in the face of climate change. Crop Pasture Sci 69:30–39

    Article  CAS  Google Scholar 

  • Shea DJ, Shimizu M, Nishida N, Fukai E, Abe T, Fujimoto R, Okazaki K (2017) IntroMap: a signal analysis based method for the detection of genomic introgressions. BMC Genet 18:101

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Shea DJ, Shimizu M, Itabashi E, Miyaji N, Miyazaki J, Osabe K, Kaji M, Okazaki K, Fujimoto R (2018c) Genome re-sequencing, SNP analysis, and genetic mapping of the parental lines of a commercial F1 hybrid cultivar of Chinese cabbage. Breed Sci 68:375–380

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sheldon CC, Burn JE, Perez PP, Metzger J, Edwards JA, Peacock WJ, Dennis ES (1999) The FLF MADS box gene: a repressor of flowering in Arabidopsis regulated by vernalization and methylation. Plant Cell 11:445–458

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sheldon CC, Conn AB, Dennis ES, Peacock WJ (2002) Different regulatory regions are required for the vernalization-induced repression of FLOWERING LOCUS C and for the epigenetic maintenance of repression. Plant Cell 14:2527–2537

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shen H, He H, Li J, Chen W, Wang X, Guo L, Peng Z, He G, Zhong S, Qi Y, Terzaghi W, Deng XW (2012) Genome-wide analysis of DNA methylation and gene expression changes in two Arabidopsis ecotypes and their reciprocal hybrids. Plant Cell 24:875–892

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shen Y, Diener AC (2013) Arabidopsis thaliana RESISTANCE TO FUSARIUM OXYSPORUM 2 implicates tyrosine-sulfated peptide signaling in susceptibility and resistance to root infection. PLoS Genet 9:e1003525

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shen Y, Sun S, Hua S, Shen E, Ye CY, Cai D, Timko MP, Zhu QH, Fan L (2017) Analysis of transcriptional and epigenetic changes in hybrid vigor of allopolyploid Brassica napus uncovers key roles for small RNAs. Plant J 91:874–893

    Article  CAS  PubMed  Google Scholar 

  • Sherf AF, MacNab AA (1986) Vegetable diseases and their control. John Wiley & Sons

    Google Scholar 

  • Shi J, Li R, Zou J, Long Y, Meng J (2011) A dynamic and complex network regulates the heterosis of yield-correlated traits in rapeseed (Brassica napus L.). PLoS One 6:e21645

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shiba H, Iwano M, Entani T, Ishimoto K, Shimosato H, Che FS, Satta Y, Ito A, Takada Y, Watanebe M, Isogai A, Takayama S (2002) The dominance of alleles controlling self-incompatibility in Brassica pollen is regulated at the RNA level. Plant Cell 14:491–504

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shiba H, Kakizaki T, Iwano M, Tarutani Y, Watanabe M, Isogai A, Takayama S (2006) Dominance relationships between self-incompatibility alleles controlled by DNA methylation. Nat Genet 38:297–299

    Article  CAS  PubMed  Google Scholar 

  • Shimizu M, Fujimoto R, Ying H, Pu Z, Ebe Y, Kawanabe T, Saeki N, Taylor JM, Kaji M, Dennis ES, Okazaki K (2014) Identification of candidate genes for fusarium yellows resistance in Chinese cabbage by differential expression analysis. Plant Mol Biol 85:247–257

    Article  CAS  PubMed  Google Scholar 

  • Shimizu M, Pu Z, Kawanabe T, Kitashiba H, Matsumoto S, Ebe Y, Sano M, Funaki T, Fukai E, Fujimoto R, Okazaki K (2015) Map-based cloning of a candidate gene conferring Fusarium yellows resistance in Brassica oleracea. Theor Appl Genet 128:119–130

    Article  CAS  PubMed  Google Scholar 

  • Shinozaki K, Yamaguchi-Shinozaki K (2000) Molecular responses to dehydration and low temperature: Differences and cross-talk between two stress signaling pathways. Curr Opin Plant Biol 3:217–223

    Article  CAS  PubMed  Google Scholar 

  • Shinozaki K, Yamaguchi-Shinozaki K (2007) Gene networks involved in drought stress response and tolerance. J Exp Bot 58:221–227

    Article  CAS  PubMed  Google Scholar 

  • Shopan J, Mou H, Zhang L, Zhang C, Ma W, Walsh JA, Hu Z, Yang J, Zhang M (2017) Eukaryotic translation initiation factor 2B-beta (eIF2Bβ), a new class of plant virus resistance gene. Plant J 90:929–940

    Article  CAS  PubMed  Google Scholar 

  • Shull GH (1948) Whatis “heterosis”? Genetics 33:439–446

    CAS  PubMed  PubMed Central  Google Scholar 

  • Singer T, Yordan C, Martienssen RA (2001) Robertson’s Mutator transposons in A. thaliana are regulated by the chromatin-remodeling gene Decrease in DNA Methylation(DDM1). Genes Dev 15:591–602

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Singh D, Dhar S, Yadava DK (2011) Genetic and pathogenic variability of Indian strains of Xanthomonas campestris pv. campestris causing black rot disease in crucifers. Curr Microbiol 63:551–560

    Article  CAS  PubMed  Google Scholar 

  • Singh D, Rathaur PS, Vicente JG (2016) Characterization, genetic diversity and distribution of Xanthomonas campestris pv. campestris races causing black rot disease in cruciferous crops of India. Plant Pathol 65:1411–1418

    Article  CAS  Google Scholar 

  • Smith KM (1935) A virus disease of cultivated crucifers. Ann Appl Biol 22:239–242

    Article  Google Scholar 

  • Soengas P, Hand P, Vicente JG, Pole JM, Pink DAC (2007) Identification of quantitative trait loci for resistance to Xanthomonas campestris pv. campestris in Brassica rapa. Theor Appl Genet 114:637–645

    Article  CAS  PubMed  Google Scholar 

  • Song GS, Zhai HL, Peng YG, Zhang L, Wei G, Chen XY, Xiao YG, Wang L, Chen YJ, Wu B, Chen B, Zhang Y, Chen H, Feng XJ, Gong WK, Liu Y, Yin ZJ, Wang F, Liu GZ, Xu HL, Wei XL, Zhao XL, Ouwerkerk PB, Hankemeier T, Reijmers T, van der Heijden R, Lu CM, Wang M, van der Greef J, Zhu Z (2010) Comparative transcriptional profiling and preliminary study on heterosis mechanism of super-hybrid rice. Mol Plant 3:1012–1025

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Song J, Angel A, Howard M, Dean C (2012) Vernalization–a cold-induced epigenetic switch. J Cell Sci 125:3723–3731

    Article  CAS  PubMed  Google Scholar 

  • Song T, Chu M, Lahlali R, Yu F, Peng G (2016a) Shotgun label-free proteomic analysis of clubroot (Plasmodiophora brassicae) resistance conferred by the gene Rcr1 in Brassica rapa. Front Plant Sci 7:1013

    PubMed  PubMed Central  Google Scholar 

  • Song X, Liu G, Huang Z, Duan W, Tan H, Li Y, Hou X (2016b) Temperature expression patterns of genes and their coexpression with LncRNAs revealed by RNA-Seq in non-heading Chinese cabbage. BMC Genom 17:297

    Article  CAS  Google Scholar 

  • Song YH, Ito S, Imaizumi T (2013) Flowering time regulation: photoperiod- and temperature-sensing in leaves. Trends Plant Sci 18:575–583

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Song YH, Shim JS, Kinmonth-Schultz HA, Imaizumi T (2015) Photoperiodic flowering: time measurement mechanisms in leaves. Annu Rev Plant Biol 66:441–464

    Article  CAS  PubMed  Google Scholar 

  • Springer NM, Stupar RM (2007) Allelic variation and heterosis in maize: how do two halves make more than a whole? Genome Res 17:264–275

    Article  CAS  PubMed  Google Scholar 

  • Srikanth A, Schmid M (2011) Regulation of flowering time: all roads lead to Rome. Cell Mol Life Sci 68:2013–2037

    Article  CAS  PubMed  Google Scholar 

  • Staub T, Williams PH (1972) Factors influencing black rot lesion development in resistant and susceptible cabbage. Phytopathology 62:722–728

    Article  Google Scholar 

  • Stein JC, Howlett B, Boyes DC, Nasrallah ME, Nasrallah JB (1991) Molecular cloning of a putative receptor protein kinase gene encoded at the self-incompatibility locus of Brassicaoleracea. Proc Natl Acad Sci USA 88:8816–8820

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stief A, Altmann S, Hoffmann K, Pant BD, Scheible W, Bäurle I (2014) Arabidopsis miR156 regulates tolerance to recurring environmental stress through SPL transcription factors. Plant Cell 26:1792–1807

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stroud H, Do T, Du J, Zhong X, Feng S, Johnson L, Patel DJ, Jacobsen SE (2014) Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nat Struct Mol Biol 21:64–72

    Article  CAS  PubMed  Google Scholar 

  • Suh SK, Green SK, Park HG (1995) Genetics of resistance to five strains of turnip mosaic virus in Chinese cabbage. Euphytica 81:71–77

    Article  Google Scholar 

  • Sung S, Amasino RM (2004) Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3. Nature 427:159–164

    Article  CAS  PubMed  Google Scholar 

  • Sung S, He Y, Eshoo TW, Tamada Y, Johnson L, Nakahigashi K, Goto K, Jacobsen SE, Amasino RM (2006) Epigenetic maintenance of the vernalized state in Arabidopsis thaliana requires LIKE HETEROCHROMATIN PROTEIN 1. Nat Genet 38:706–710

    Article  CAS  PubMed  Google Scholar 

  • Suwabe K, Iketani H, Nunome T, Kage T, Hirai M (2002) Isolation and characterization of microsatellites in Brassica rapa L. Theor Appl Genet 104:1092–1098

    Article  CAS  PubMed  Google Scholar 

  • Suwabe K, Tsukazak H, Iketani H, Hatakeyama K, Kondo M, Fujimura M, Nunome T, Fukuoka H, Hirai M, Matsumoto S (2006) Simple sequence repeat-based comparative genomics between Brassica rapa and Arabidopsis thaliana: the genetic origin of clubroot resistance. Genetics 173:309–319

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Suwabe K, Tsukazaki H, Iketani H, Hatakeyama K, Fujimura M, Nunome T, Fukuoka H, Matsumoto S, Hirai M (2003) Identification of two loci for resistance to clubroot (Plasmodiophora brassicae Woronin) in Brassica rapa L. Theor Appl Genet 107:997–1002

    Article  CAS  PubMed  Google Scholar 

  • Suzuki G, Kai N, Hirose T, Fukui K, Nishio T, Takayama S, Isogai A, Watanabe M, Hinata K (1999) Genomic organization of the S locus: Identification and characterization of genes in SLG/SRK region of S9haplotype of Brassicacampestris (syn. rapa). Genetics 153:391–400

    CAS  PubMed  PubMed Central  Google Scholar 

  • Swiezewski S, Liu F, Magusin A, Dean C (2009) Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature 462:799–802

    Article  CAS  PubMed  Google Scholar 

  • Takahashi S, Fukushima N, Osabe K, Itabashi E, Shimizu M, Miyaji N, Takasaki-Yasuda T, Suzuki Y, Seki M, Fujimoto R (2018a) Identification of DNA methylated regions by using methylated DNA immunoprecipitation sequencing in Brassica rapa. Crop Pasture Sci 69:107–120

    Article  CAS  Google Scholar 

  • Takahashi S, Osabe K, Fukushima N, Takuno S, Miyaji N, Shimizu M, Takasaki-Yasuda T, Suzuki Y, Dennis ES, Seki M, Fujimoto R (2018b) Genome-wide characterization of DNA methylation, small RNA expression, and histone H3 lysine nine di-methylation in Brassica rapa L. DNA Res 25:511–520

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Takasaki T, Hatakeyama K, Suzuki G, Watanabe M, Isogai A, Hinata K (2000) The S receptor kinase determines self-incompatibility in Brassica stigma. Nature 403:913–916

    Article  CAS  PubMed  Google Scholar 

  • Takata K, Matsuzaki T, Tajika Y (2004) Aquaporins: Water channel proteins of the cell membrane. Prog Histochem Cytochem 39:1–83

    Article  CAS  PubMed  Google Scholar 

  • Takayama S, Shimosato H, Shiba H, Funato M, Che FS, Watanabe M, Iwano M, Isogai A (2001) Direct ligand-receptor complex interaction controls Brassica self-incompatibility. Nature 413:535–538

    Article  CAS  Google Scholar 

  • Takuno S, Fujimoto R, Sugimura T, Sato K, Okamoto S, Zhang SL, Nishio T (2007) Effects of recombination on hitchhiking diversity in the Brassica self-incompatibility locus complex. Genetics 177:949–958

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tarutani Y, Shiba H, Iwano M, Kakizaki T, Suzuki G, Watanabe M, Isogai A, Takayama S (2010) Trans-acting small RNA determines dominance relationships in Brassica self-incompatibility. Nature 466:983–986

    Article  CAS  PubMed  Google Scholar 

  • Taylor JD, Conway J, Roberts SJ, Astley D, Vicente JG (2002) Sources and origin of resistance to Xanthomonas campestris pv. campestris in Brassica genomes. Phytopathology 92:105–111

    Article  CAS  PubMed  Google Scholar 

  • Teixeira FK, Heredia F, Sarazin A, Roudier F, Boccara M, Ciaudo C, Cruaud C, Poulain J, Berdasco M, Fraga MF, Voinnet O, Wincker P, Esteller M, Colot V (2009) A role for RNAi in the selective correction of DNA methylation defects. Science 323:1600–1604

    Article  CAS  PubMed  Google Scholar 

  • Teutonico RA, Osborn TC (1994) Mapping of RFLP and qualitative trait loci in Brassica rapa and comparison to the linkage maps of B. napus, B. oleracea, and Arabidopsis thaliana. Theor Appl Genet 89:885–894

    Article  CAS  PubMed  Google Scholar 

  • Thompson KF, Taylor JP (1966) Non-linear dominance relationships between S-alleles. Heredity 21:345–362

    Article  Google Scholar 

  • Tisdale WB (1923) Influence of soil temperature and soil moisture upon the Fusarium disease in cabbage seedlings. J Agric Res 24:55–86

    Google Scholar 

  • Tomimura K, Špak J, Katis N, Jenner CE, Walsh JA, Gibbs AJ, Ohshima K (2004) Comparisons of the genetic structure of populations of Turnip mosaic virus in West and East Eurasia. Virology 330:408–423

    Article  CAS  PubMed  Google Scholar 

  • Tomita H, Shimizu M, Doullah MA, Fujimoto R, Okazaki K (2013) Accumulation of quantitative trait loci conferring broad-spectrum clubroot resistance in Brassica oleracea. Mol Breed 32:889–900

    Article  CAS  Google Scholar 

  • Tomitaka Y, Ohshima K (2006) A phylogeographical study of the Turnip mosaic virus population in East Asia reveals an ‘emergent’ lineage in Japan. Mol Ecol 15:4437–4457

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tomlinson JA (1987) Epidemiology and control of virus disease of vegetables. Ann Appl Biol 110:661–681

    Article  Google Scholar 

  • Tonosaki K, Osabe K, Kawanabe T, Fujimoto R (2016) The importance of reproductive barriers and the effect of allopolyploidization on crop breeding. Breed Sci 66:333–349

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tonu NN, Doullah MA, Shimizu M, Karim MM, Kawanabe T, Fujimoto R, Okazaki K (2013) Comparison of positions of QTLs conferring resistance to Xanthomonas campestris pv. campestris in Brassica oleracea. Amer J Plant Sci 4:11–20

    Article  Google Scholar 

  • Tortosa M, Cartea ME, Rodríguez VM, Velasco P (2018) Unraveling the metabolic response of Brassica oleracea exposed to Xanthomonas campestris pv. campestris. J Sci Food Agri 98:3675–3683

    Article  CAS  Google Scholar 

  • Toxopeus H, Janssen AMP (1975) Clubroot resistance in turnip II. The ‘slurry’ screening method and clubroot races in the Netherlands. Euphytica 24:751–755

    Article  Google Scholar 

  • Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY (2010) Long noncoding RNA as modular scaffold of histone modification complexes. Science 329:689–693

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tseng MJ, Liu CW, Yiu JC (2007) Enhanced tolerance to sulfur dioxide and salt stress of transgenic Chinese cabbage plants expressing both superoxide dismutase and catalase in chloroplasts. Plant Physiol Biochem 45:822–833

    Article  CAS  PubMed  Google Scholar 

  • Tsukahara S, Kobayashi A, Kawabe A, Mathieu O, Miura A, Kakutani T (2009) Bursts of retrotransposition reproduced in Arabidopsis. Nature 461:423–426

    Article  CAS  PubMed  Google Scholar 

  • Turck F, Fornara F, Coupland G (2008) Regulation and identity of florigen: FLOWERING LOCUS T moves center stage. Annu Rev Plant Biol 59:573–594

    Article  CAS  PubMed  Google Scholar 

  • Turck F, Roudier F, Farrona S, Martin-Magniette ML, Guillaume E, Buisine N, Gagnot S, Martienssen RA, Coupland G, Colot V (2007) Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27. PLoS Genet 3:e86

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Turnbull C (2011) Long-distance regulation of flowering time. J Exp Bot 62:4399–4413

    Article  CAS  PubMed  Google Scholar 

  • U N (1935) Genome analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization. Jap J Bot 7:389–452

    Google Scholar 

  • Ueno H, Matsumoto E, Aruga D, Kitagawa S, Matsumura H, Hayashida N (2012) Molecular characterization of the CRa gene conferring clubroot resistance in Brassica rapa. Plant Mol Biol 80:621–629

    Article  CAS  PubMed  Google Scholar 

  • Ulloa M, Hutmacher RB, Davis RM, Wright SD, Percy R, Marsh B (2006) Breeding for Fusarium wilt race 4 resistance in cotton under field and greenhouse conditions. J Cotton Sci 10:114–127

    Google Scholar 

  • Verma SS, Rahman MH, Deyholos MK, Basu U, Kav NNV (2014) Differential expression of miRNAs in Brassica napus root following infection with Plasmodiophora brassicae. PLoS ONE 9:e86648

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Vicente JG, Conway J, Roberts SJ, Taylor JD (2001) Identification and origin of Xanthomonas campestris pv. campestris races and related pathovars. Phytopathology 91:492–499

    Article  CAS  PubMed  Google Scholar 

  • Vicente JG, Holub EB (2013) Xanthomonas campestris pv. campestris (cause of black rot of crucifers) in the genomic era is still a worldwide threat to brassica crops. Mol Plant Pathol 14:2–18

    Article  CAS  PubMed  Google Scholar 

  • Vicente JG, Taylor JD, Sharpe AG, Parkin IAP, Lydiate DJ, King GJ (2002) Inheritance of race-specific resistance to Xanthomonas campestris pv. campestris in Brassica genomes. Phytopathology 92:1134–1141

    Article  CAS  PubMed  Google Scholar 

  • Vidalis A, Živković D, Wardenaar R, Roquis D, Tellier A, Johannes F (2016) Methylome evolution in plants. Genome Biol 17:264

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Vongs A, Kakutani T, Martienssen RA, Richards EJ (1993) Arabidopsis thaliana DNA methylation mutants. Science 260:1926–1928

    Article  CAS  PubMed  Google Scholar 

  • Voorrips RE (1995) Plasmodiophora brassicae: aspects of pathogenesis and resistance in Brassica oleracea. Euphytica 83:139–146

    Article  Google Scholar 

  • Voorrips RE, Jongerious MC, Kanne HJ (1997) Mapping of two genes for resistance to clubroot (Plasmodiophora brassicae) in a population of doubled haploid lines of Brassica oleracea by means of RFLP and AFLP markers. Theor Appl Genet 94:75–82

    Article  CAS  PubMed  Google Scholar 

  • Voorrips RE, Kanne HJ (1997) Genetic analysis of resistance to clubroot (Plasmodiophora brassicae) in Brassica oleracea. I. Analysis of symptom grades. Euphytica 93:31–39

    Article  Google Scholar 

  • Walker JC (1930) Inheritance of Fusarium resistance in cabbage. J Agri Res 40:721–745

    Google Scholar 

  • Walker JC (1933) Yellows-resistant lines of Early Jersey Wakefield cabbage. J Agri Res 46:639–648

    Google Scholar 

  • Walker JC, Blank LM (1934) Fusarium resistant Danish ballhead cabbage. J Agri Res 49:983–989

    Google Scholar 

  • Walker JC, Monteith JJ, Wellman FL (1927) Development of three midseason varieties of cabbage resistant to yellows (Fusarium conglutinans Woll.). J Agric Res 35:785–809

    Google Scholar 

  • Walsh JA (1989) Genetic control of immunity to turnip mosaic virus in winter oilseed rape (Brassica napus ssp. oleifera) and the effect of foreign isolates of the virus. Ann Appl Biol 115:89–99

    Article  Google Scholar 

  • Walsh JA, Jenner CE (2002) Turnip mosaic virus and the quest for durable resistance. Mol Plant Pathol 3:289–300

    Article  CAS  PubMed  Google Scholar 

  • Walsh JA, Rusholme RL, Hughes SL, Jenner CE, Bambridge JM, Lydiate DJ, Green SK (2002) Different classes of resistance to Turnip mosaic virus in Brassica rapa. Eur J Plant Pathol 108:15–20

    Article  Google Scholar 

  • Walsh JA, Sharpe AG, Jenner CE, Lydiate DJ (1999) Characterisation of resistance to turnip mosaic virus in oilseed rapa (Brassica napus) and genetic mapping of TuRB01. Theor Appl Genet 99:1149–1154

    Article  CAS  Google Scholar 

  • Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F, Huang S, Li X, Hua W, Wang J, Wang X, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu B, Li B, Liu B, Tong C, Song C, Duran C, Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang H, Wang H, Belcram H, Zhou H, Hirakawa H, Abe H, Guo H, Wang H, Jin H, Parkin IAP, Batley J, Kim JS, Just J, Li J, Xu J, Deng J, Kim JA, Li J, Yu J, Meng J, Wang J, Min J, Poulain J, Wang J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao M, Jin M, Ramchiary N, Drou N, Berkman PJ, Cai Q, Huang Q, Li R, Tabata S, Cheng S, Zhang S, Zhang S, Huang S, Sato S, Sun S, Kwon SJ, Choi SR, Lee TH, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li Y, Du Y, Liao Y, Lim Y, Narusaka Y, Wang Y, Wang Z, Li Z, Wang Z, Xiong Z, Zhang Z (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43:1035–1039

    Article  CAS  PubMed  Google Scholar 

  • Wang ZY, Kenigsbuch D, Sun L, Harel E, Ong MS, Tobin EM (1997) A Myb-related transcription factor is involved in the phytochrome regulation of an Arabidopsis Lhcb gene. Plant Cell 9:491–507

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wang ZY, Tobin EM (1998) Constitutive expression of the CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) gene disrupts circadian rhythms and suppresses its own expression. Cell 93:1207–1217

    Article  CAS  PubMed  Google Scholar 

  • Warwick SI, Francis A, Al-Shehbaz IA (2006) Brassicaceae: species checklist and database on CD-Rom. Plant Syst Evol 259:249–258

    Article  Google Scholar 

  • Wasilewska A, Vlad F, Sirichandra C, Redko Y, Jammes F, Valon C, Frei dit Fery N, Leung J (2008) An update on abscisic acid signaling in plants and more. Mol Plant 1:198–217

    Article  CAS  PubMed  Google Scholar 

  • Watanabe M, Ito A, Takada Y, Ninomiya C, Kakizaki T, Takahata T, Hatakeyama K, Hinata K, Suzuki G, Takasaki T, Satta Y, Shiba H, Takayama S, Isogai A (2000) Highly divergent sequences of the pollen self-incompatibility (S) gene in class-I S haplotypes of Brassicacampestris (syn. rapa) L. FEBS Lett 473:139–144

    Article  CAS  PubMed  Google Scholar 

  • Watanabe M, Ono T, Hatakeyama K, Takayama S, Isogai A, Hinata K (1997) Molecular characterization of SLG and S-related genes in a self-compatible Brassica campestris L. var. yellow sarson. Sex Plant Reprod 10:332–340

    Article  CAS  Google Scholar 

  • Weigel D, Ahn JH, Blázquez MA, Borevitz JO, Christensen SK, Fankhauser C, Ferrándiz C, Kardailsky I, Malancharuvil EJ, Neff MM, Nguyen JT, Sato S, Wang ZY, Xia Y, Dixon RA, Harrison MJ, Lamb CJ, Yanofsky MF, Chory J (2000) Activation tagging in Arabidopsis. Plant Physiol 122:1003–1013

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Werner S, Diederichsen E, Frauen M, Schondelmaier J, Jung C (2008) Genetic mapping of clubroot resistance genes in oilseed rape. Theor Appl Genet 116:363–372

    Article  CAS  PubMed  Google Scholar 

  • Wigge PA, Kim MC, Jaeger KE, Busch W, Schmid M, Lohmann JU, Weigel D (2005) Integration of spatial and temporal information during floral induction in Arabidopsis. Science 309:1056–1059

    Article  CAS  PubMed  Google Scholar 

  • Wit F, Van De Weg M (1964) Clubroot-resistance in turnips (Brassica campestris L.) I. Physiological races of the parasite and their identification in mixtures. Euphytica 13:9–18

    Article  Google Scholar 

  • Wittmann S, Chatel H, Fortin MG, Laliberté JF (1997) Interaction of the viral protein genome linked of Turnip mosaic potyvirus with the translational eukaryotic initiation factor (iso) 4E of Arabidopsis thaliana using the yeast two-hybrid system. Virol 234:84–92

    Article  CAS  Google Scholar 

  • Wood CC, Robertson M, Tanner G, Peacock WJ, Dennis ES, Helliwell CA (2006) The Arabidopsis thaliana vernalization response requires a polycomb-like protein complex that also includes VERNALIZATION INSENSITIVE 3. Proc Natl Acad Sci USA 103:14631–14636

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  • Wu P, Wang W, Duan W, Li Y, Hou X (2017) Comprehensive analysis of the CDPK-SnRK superfamily genes in Chinese cabbage and its evolutionary implications in plants. Front Plant Sci 8:162

    PubMed  PubMed Central  Google Scholar 

  • Xiao D, Zhao JJ, Hou XL, Basnet RK, Carpio DP, Zhang NW, Bucher J, Lin K, Cheng F, Wang XW, Bonnema G (2013) The Brassica rapaFLC homologue FLC2 is a key regulator of flowering time, identified through transcriptional co-expression networks. J Exp Bot 64:4503–4516

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xiao J, Lee US, Wagner D (2016) Tug of war: adding and removing histone lysine methylation in Arabidopsis. CurrOpin Plant Biol 34:41–53

    CAS  Google Scholar 

  • Xing M, Lv H, Ma J, Xu D, Li H, Yang L, Kang J, Wang X, Fang Z (2016) Transcriptome profiling of resistance to Fusarium oxysporum f. sp. conglutinans in cabbage (Brassica oleracea) roots. PLoS One 11:e0148048

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Xu L, Ren L, Chen K, Liu F, Fang X (2016) Putative role of IAA during the early response of Brassica napus L. to Plasmodiophora brassicae. Eur J Plant Pathol 145:601–613

    Article  CAS  Google Scholar 

  • Yamagishi H, Bhat SR (2014) Cytoplasmic male sterility in Brassicaceae crops. Breed Sci 64:38–47

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yan L, Loukoianov A, Tranquilli G, Helguera M, Fahima T, Dubcovsky J (2003) Positional cloning of the wheat vernalization gene VRN1. Proc Natl Acad Sci USA 100:6263–6268

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang J, Liu D, Wang X, Ji C, Cheng F, Liu B, Hu Z, Chen S, Pental D, Ju Y, Yao P, Li X, Xie K, Zhang J, Wang J, Liu F, Ma W, Shopan J, Zheng H, Mackenzie SA, Zhang M (2016) The genome sequence of allopolyploid Brassica juncea and analysis of differential homoeolog gene expression influencing selection. Nat Genet 50:1616

    Article  CAS  Google Scholar 

  • Yang L, Li B, Zheng XY, Li J, Yang M, Dong X, He G, An C, Deng XW (2015) Salicylic acid biosynthesis is enhanced and contributes to increased biotrophic pathogen resistance in Arabidopsis hybrids. Nat Commun 6:7309

    Article  CAS  PubMed  Google Scholar 

  • Yang M, Wang X, Ren D, Huang H, Xu M, He G, Deng XW (2017a) Genomic architecture of biomass heterosis in Arabidopsis. Proc Natl Acad Sci USA 114:8101–8106

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang Y, Zhu K, Li H, Han S, Meng Q, Khan SU, Fan C, Xie K, Zhou Y (2017b) Precise editing of CLAVATA genes in Brassica napus L. regulates multilocular silique development. Plant Biotechnol J 16:1322–1335

    Article  CAS  Google Scholar 

  • Yasuda S, Wada Y, Kakizaki T, Tarutani Y, Miura-Uno E, Murase K, Fujii S, Hioki T, Shimoda T, Takada Y, Shiba H, Takasaki-Yasuda T, Suzuki G, Watanabe M, Takayama S (2016) A complex dominance hierarchy is controlled by polymorphism of small RNAs and their targets. Nat Plants 3:16206

    Article  PubMed  CAS  Google Scholar 

  • Yeam I, Cavatorta JR, Ripoll DR, Kang BC, Jahn MM (2007) Functional dissection of naturally occurring amino acid substitutions in eIF4E that confers recessive potyvirus resistance in plants. Plant Cell 19:2913–2928

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yin Z, Rorat T, Szabala BM, Ziółkowska A, Malepszy S (2006) Expression of a Solanum sogarandinum SK3-type dehydrin enhances cold tolerance in transgenic cucumber seedlings. Plant Sci 170:1164–1172

    Article  CAS  Google Scholar 

  • Yoon JY, Green SK, Opeña RT (1993) Inheritance of resistance to turnip mosaic virus in Chinese cabbage. Euphytica 69:103–108

    Article  Google Scholar 

  • Yu F, Zhang X, Huang Z, Chu M, Song T, Falk KC, Deora A, Chen Q, Zhang Y, McGregor L, Gossen BD, McDonald MR, Peng G (2016) Identification of genome-wide variants and discovery of variants associated with Brassica rapa clubroot resistance gene Rcr1 through bulked segregant RNA sequencing. PLoS ONE 11:e0153218

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Yu F, Zhang X, Peng G, Falk KC, Strelkov SE, Gossen BD (2017) Genotyping-by-sequencing reveals three QTL for clubroot resistance to six pathotypes of Plasmodiophora brassicae in Brassica rapa. Sci Rep 7:4516

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Yu Q, Hu Y, Li J, Wu Q, Lin Z (2005) Sense and antisense expression of plasma membrane aquaporin BnPIP1 from Brassica napus in tobacco and its effects on plant drought resistance. Plant Sci 169:647–656

    Article  CAS  Google Scholar 

  • Yu X, Wang H, Lu Y, de Ruiter M, Cariaso M, Prins M, van Tunen A, He Y (2012) Identification of conserved and novel microRNAs that are responsive to heat stress in Brassica rapa. J Exp Bot 63:1025–1038

    Article  CAS  PubMed  Google Scholar 

  • Yu X, Yang J, Li X, Liu X, Sun C, Wu F, He Y (2013) Global analysis of cis-natural antisense transcripts and their heat-responsive nat-siRNAs in Brassica rapa. BMC Plant Biol 13:208

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zemach A, Kim MY, Hsieh PH, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer SL, Zilberman D (2013) The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell 153:193–205

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zemach A, McDaniel IE, Silva P, Zilberman D (2010) Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328:916–919

    Article  CAS  PubMed  Google Scholar 

  • Zhang J, Lu Y, Yuan Y, Zhang X, Geng J, Chen Y, Cloutier S, McVetty PB, Li G (2008) Map-based cloning and characterization of a gene controlling hairiness and seed coat color traits in Brassica rapa. Plant Mol Biol 5:553–563

    Google Scholar 

  • Zhang Q, Li Y, Xu T, Srivastava AK, Wang D, Zeng L, Yang L, He L, Zhang H, Zheng Z, Yang DL, Zhao C, Dong J, Gong Z, Liu R, Zhu JK (2016a) The chromatin remodeler DDM1 promotes hybrid vigor by regulating salicylic acid metabolism. Cell Discov 2:16027

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang T, Zhao Z, Zhang C, Pang W, Choi SR, Lim YP, Piao Z (2014) Fine genetic and physical mapping of the CRb gene conferring resistance to clubroot disease in Brassica rapa. Mol Breed 34:1173–1183

    Article  CAS  Google Scholar 

  • Zhang X, Bernatavichute YV, Cokus S, Pellegrini M, Jacobsen SE (2009) Genome-wide analysis of mono-, di-and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol 10:R62

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhang X, Clarenz O, Cokus S, Bernatavichute YV, Pellegrini M, Goodrich J, Jacobsen SE (2007) Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol 5:e129

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhang X, Liu Y, Fang Z, Li Z, Yang L, Zhuang M, Zhang Y, Lv H (2016b) Comparative transcriptome analysis between broccoli (Brassica oleracea var. italica) and wild cabbage (Brassica macrocarpa Guss.) in response to Plasmodiophora brassicae during different infection stages. Front Plant Sci 7:1929

    Google Scholar 

  • Zhang X, Meng L, Liu B, Hu Y, Cheng F, Liang J, Aarts MG, Wang X, Wu J (2015) A transposon insertion in FLOWERING LOCUS T is associated with delayed flowering in Brassica rapa. Plant Sci 241:211–220

    Article  CAS  PubMed  Google Scholar 

  • Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, Chen H, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE, Ecker JR (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126:1189–1201

    Article  CAS  PubMed  Google Scholar 

  • Zhao J, Kulkarni V, Liu N, Pino Del Carpio D, Bucher J, Bonnema G (2010) BrFLC2 (FLOWERING LOCUS C) as a candidate gene for a vernalization response QTL in Brassica rapa. J Exp Bot 61:1817–1825

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhen G, Qin P, Liu KY, Nie DY, Yang YZ, Deng XW, He H (2017) Genome-wide dissection of heterosis for yield traits in two-line hybrid rice populations. Sci Rep 7:7635

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zheng B, Chen X (2011) Dynamics of histone H3 lysine 27 trimethylation in plant development. Curr Opin Plant Biol 14:123–129

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou S, Hu W, Deng X, Ma Z, Chen L, Huang C, Wang C, Wang J, He Y, Yang G, He G (2012) Overexpression of the wheat aquaporin gene, TaAQP7, enhances drought tolerance in transgenic tobacco. PLoS ONE 7:e52439

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhu JK (2016) Abiotic stress signaling and responses in plants. Cell 167:313–324

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhu M, Assmann SM (2017) Metabolic signatures in response to abscisic acid (ABA) treatment in Brassica napus guard cells revealed by metabolomics. Sci Rep 7:12875

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhu QH, Stephen S, Kazan K, Jin G, Fan L, Taylor J, Dennis ES, Helliwell CA, Wang MB (2013) Characterization of the defense transcriptome responsive to Fusarium oxysporum-infection in Arabidopsis using RNA-seq. Gene 512:259–266

    Article  CAS  PubMed  Google Scholar 

  • Zielinski RE (1998) Calmodulin and calmodulin-binding proteins in plants. Annu Rev Plant Physiol Plant Mol Biol 49:697–725

    Article  CAS  PubMed  Google Scholar 

  • Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S (2007) Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 39:61–69

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Honghao Lv or Ryo Fujimoto .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2020 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Lv, H. et al. (2020). The Importance of Genetic and Epigenetic Research in the Brassica Vegetables in the Face of Climate Change. In: Kole, C. (eds) Genomic Designing of Climate-Smart Vegetable Crops. Springer, Cham. https://doi.org/10.1007/978-3-319-97415-6_3

Download citation

Publish with us

Policies and ethics