Abstract
During evolution, plant genomes have undergone duplications, deletions and rearrangements resulting in a wide variation in genome size and number of gene family members between different species. The variation in gene families is an important mechanism for adaptation to different environmental conditions. Allium species, such as bulb onion (Allium cepa), have a large unsequenced genome. However, high throughput transcriptome sequencing datasets are now available which provide an efficient way to identify the genes present in different Allium species. With this knowledge, strategies to accelerate physiological and genetic analysis for enhanced breeding can be developed. In this chapter, we will describe how RNA sequencing is providing a better understanding of Allium genetics and survey the diversity of gene families involved in bulbing, flowering, male fertility, flavonoid biosynthesis and sulphur assimilation in bulb onion. In general, we found that onion has a similar number of gene family members to other monocots, such as rice, which have much smaller genomes. This is consistent with the large genome size of Allium being due to a massive expansion of repetitive DNA.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Baldwin S, Revanna R, Thomson S, Pither-Joyce M, Wright K, Crowhurst R, Fiers M, Chen L, Macknight R, McCallum J (2012) A toolkit for bulk PCR-based marker design from next-generation sequence data: application for development of a framework linkage map in bulb onion (Allium cepa L.). BMC Genom 13:637
Baldwin S, Revanna R, Pither-Joyce M, Shaw M, Wright K, Thomson S, Moya L, Lee R, Macknight R, McCallum J (2013) Genetic analyses of bolting in bulb onion (Allium cepa L). Theor App Genet 127:535–547
Becker A, Theißen G (2003) The major clades of MADS-box genes and their role in the development and evolution of flowering plants. Mol Phylogenet Evol 29:464–489
Böhlenius H, Huang T, Charbonnel-Campaa L, Brunner AM, Jansson S, Strauss SH, Nilsson O (2006) CO/FT regulatory module controls timing of flowering and seasonal growth cessation in trees. Science 312:1040–1043
Bongue-Bartelsman M, O’Neill SD, Tong Y, Yoder JI (1994) Characterization of the gene encoding dihydroflavonol 4-reductase in tomato. Gene 138:153–157
Brewster JL (2008) Onions and other vegetable Alliums. CABI, Oxfordshire, UK
Cai J, Liu X, Vanneste K, Proost S, Tsai W-C, Liu K-W, Chen L-J, He Y, Xu Q, Bian C, Zheng Z, Sun F, Liu W, Hsiao Y-Y, Pan Z-J, Hsu C-C, Yang Y-P, Hsu Y-C, Chuang Y-C, Dievart A, Dufayard J-F, Xu X, Wang J-Y, Wang J, Xiao X-J, Zhao X-M, Du R, Zhang G-Q, Wang M, Su Y-Y, Xie G-C, Liu G-H, Li L-Q, Huang L-Q, Luo Y-B, Chen H-H, Peer YV, Liu Z-J (2015) The genome sequence of the orchid Phalaenopsis equestris. Nat Genet 47:65–72. https://doi.org/10.1038/ng.3149
Chanderbali AS, Berger BA, Howarth DG, Soltis PS, Soltis DE (2016) Evolving ideas on the origin and evolution of flowers: new perspectives in the genomic era. Genetics 202:1255–1265. https://doi.org/10.1534/genetics.115.182964
Chang YY, Chu YW, Chen CW, Leu WM, Hsu HF, Yang CH (2011) Characterization of oncidium ‘Gower Ramsey’ transcriptomes using 454 GS-FLX pyrosequencing and their application to the identification of genes associated with flowering time. Plant Cell Physiol 52:1532–1545. https://doi.org/10.1093/pcp/pcr101 Epub 2011 Jul 23
Chase CD (2007) Cytoplasmic male sterility: a window to the world of plant mitochondrial–nuclear interactions. Trends Genet 23:81–90
Chen L, Liu YG (2014) Male sterility and fertility restoration in crops. Annu Rev Plant Biol 65:579–606
De Jong WS, De Jong DM, De Jong H, Kalazich J, Bodis M (2003) An allele of dihydroflavonol 4-reductase associated with the ability to produce red anthocyanin pigments in potato (Solanum tuberosum L.). Theor Appl Genet 107:1375–1383
Dion E, Li L, Jean M, Belzile F (2007) An Arabidopsis MLH1 mutant exhibits reproductive defects and reveals a dual role for this gene in mitotic recombination. Plant J 51:431–440
Dodsworth S (2017) Petal, Sepal, or Tepal? B-genes and monocot flowers. Trends Plant Sci 22:8–10. https://doi.org/10.1016/j.tplants
Doebley JF, Gaut BS, Smith BD (2006) The molecular genetics of crop domestication. Cell 127:1309–1321
Dong Z, Danilevskaya O, Abadie T, Messina C, Coles N, Cooper M (2012) A gene regulatory network model for floral transition of the shoot apex in maize and its dynamic modeling. PLoS ONE 7(8):e43450. https://doi.org/10.1371/journal.pone.0043450
Duangjit J, Bohanec B, Chan AP, Town CD, Havey MJ (2013) Transcriptome sequencing to produce SNP-based genetic maps of onion. Theor Appl Genet 126:2093–2101
Fritsch RM, Friesen N (2002) Evolution, domestication and taxonomy. In: Rabinowitch HD, Currah L (eds) Allium crop science: recent advances. CABI, Wallingford, UK, pp 5–30
Fujii S, Bond CS, Small ID (2011) Selection patterns on restorer-like genes reveal a conflict between nuclear and mitochondrial genomes throughout angiosperm evolution. Proc Natl Acad Sci USA 108:1723–1728
Galsurker O, Doron-Faigenboim A, Teper-Bamnolker P, Daus A, Fridman Y, Lers A, Eshel D (2017) Cellular and molecular changes associated with onion skin formation involvement of programmed cell death. Front Plant Sci 7:2031. https://doi.org/10.3389/fpls.2016.02031
Guo YL (2013) Gene family evolution in green plants with emphasis on the origination and evolution of Arabidopsis thaliana genes. Plant J 73:941–951. https://doi.org/10.1111/tpj.12089
Han J, Thamilarasan SK, Natarajan S, Park J-I, Chung M-Y, Nou I-S (2016) De novo assembly and transcriptome analysis of bulb onion (Allium cepa L.) during cold acclimation using contrasting genotypes. PLoS ONE 11:e0161987. https://doi.org/10.1371/journal.pone.0161987
Hanelt P (1990) ‘Taxonomy, evolution and history’ in onions and allied crops. In: Rabinowitch HD, Brewster JL (eds) Botany, physiology, and genetics, vol 1. CRC Press, Boca Raton, pp 1–26
Heijmans K, Morel P, Vandenbussche M (2012) MADS-box genes and floral development: the dark side. J Exp Bot 63:5397–5404. https://doi.org/10.1093/jxb/ers233
Higgins JA, Bailey PC, Laurie DA (2010) Comparative genomics of flowering time pathways using Brachypodium distachyon as a model for the temperate grasses. PLoS ONE 5(4):e10065. https://doi.org/10.1371/journal.pone.0010065
Hsu CY, Adams JP, Kim H, No K, Ma C, Strauss SH, Drnevich J, Vandervelde L, Ellis JD, Rice BM, Wickett N, Gunter LE, Tuskan GA, Brunner AM, Page GP, Barakat A, Carlson JE, dePamphilis CW, Luthe DS, Yuceer C (2011) FLOWERING LOCUS T duplication coordinates reproductive and vegetative growth in perennial poplar. Proc Natl Acad Sci USA 108:10756–10761
Huang Y, Gou J, Jia Z, Yang L, Sun Y, Xiao X, Song F, Luo K (2012) Molecular cloning and characterization of two genes encoding dihydroflavonol-4-reductase from populus trichocarpa. PLoS ONE 7(2):e30364. https://doi.org/10.1371/journal.pone.0030364
Irish VF, Litt A (2005) Flower development and evolution: gene duplication, diversification and redeployment. Curr Opin Genet Dev 15:454–460
Islam MS, Studer S, Møller IM, Asp T (2014) Genetics and biology of cytoplasmic male sterility and its applications in forage and turf grass breeding. Plant Breeding 133:299–312
Jakse J, Meyer JDF, Suzuki G, McCallum J, Cheung F, Town CD, Havey MJ (2008) Pilot sequencing of onion genomic DNA reveals fragmented transposable elements, low gene densities, and significant gene enrichment after methy filtration. Mol Genet Genomics 280:287–292
Johansson M, Staiger D (2015) Time to flower: interplay between photoperiod and the circadian clock. J Exp Bot 66:719–730. https://doi.org/10.1093/jxb/eru441
Jones HA, Emsweller SL (1936) Development of the flower and macro-gametophyte of Allium cepa. J Agric Sci 10:415–428
Kamenetsky R, Faigenboim A, Mayer ES, Michael TB, Gershberg C, Kimhi S, Esquira I, Shalom SR, Eshel D, Rabinowitch HD, Sherman A (2015) Integrated transcriptome catalogue and organ-specific profiling of gene expression in fertile garlic (Allium sativum L.). BMC Genom 16:12
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
Karlgren A, Gyllenstrand N, Källman T, Sundström JF, Moore D, Lascoux M, Lagercrantz U (2011) Evolution of the PEBP gene family in plants: functional diversification in seed plant evolution. Plant Physiol 156:1967–1977
Khar A, Jakse J, Havey MJ (2008) Segregations for onion bulb colors reveal that red is controlled by at least three loci. J Am Soc Hortic Sci 133:42–47
Khosa JS, Lee R, Bräuning S, Lord J, Pither-Joyce M, McCallum J, Macknight RC (2016a) Doubled Haploid ‘CUDH2107’ as a reference for bulb onion (Allium cepa L.) research: development of a transcriptome catalogue and identification of transcripts associated with male fertility. PLoS ONE 11(11):e0166568. https://doi.org/10.1371/journal.pone.0166568
Khosa JS, McCallum J, Dhatt AS, Macknight R (2016b) Enhancing onion breeding using molecular tools. Plant Breed 135:9–20
Kim B, Kim K, Yang TJ, Kim S (2016) Completion of the mitochondrial genome sequence of onion (Allium cepa L.) containing the CMS-S male-sterile cytoplasm and identification of an independent event of the ccmF N gene split. Curr Genet 62:873–885
Kim MY, Kang YJ, Lee T, Lee S (2013) Divergence of flowering-related genes in three legume species. Plant Genome. https://doi.org/10.3835/plantgenome2013.03.0008
Kim S, Kim CW, Park M, Choi D (2015) Identification of candidate genes associated with fertility restoration of cytoplasmic male-sterility in onion (Allium cepa L.) using a combination of bulked segregant analysis and RNA-seq. Theor Appl Genet 128:2289–2299
Kim S, Binzel ML, Park SH, Yoo KS, Pike LM (2004a) Inactivation of DFR (dihydroflavonol 4-reductase) gene transcription results in blockage of anthocyanin production in yellow onions (Allium cepa). Mol Breed 14:253–263. https://doi.org/10.1023/B:MOLB.0000047770.92977.04
Kim S, Binzel ML, Yoo KS, Park S, Pike LM (2004b) Pink (P), a new locus responsible for a pink trait in onions (Allium cepa) resulting from natural mutations of anthocyanidin synthase. Mol Genet Genomics 272:18–27. https://doi.org/10.1007/s00438-004-1041-5
Kim S, Kim MS, Kim YM, Yeom SI, Cheong K, Kim KT, Jeon J, Kim S, Kim DS, Sohn SH, Lee YH, Choi D (2014) Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.). DNA Res 22:19–27
King JJ, Bradeen JM, Bark O, McCallum J, Havey MJ (1998) A low density genetic map of onion reveals a role for tandem duplication in the evolution of extremely large diploid genome. Theor Appl Genet 96:52–62
Kinoshita T, Ono N, Hayashi Y, Morimoto S, Nakamura S, Soda M, Kato Y, Ohnishi M, Nakano T, Inoue S, Shimazaki K (2011) FLOWERING LOCUST regulates stomatal opening. Curr Biol 21:1232–1238
Kloosterman B, Abelenda JA, Carretero-Gomez M, Oortwijn M, De Boer JM, Kowitwanich K, Horvath BM, Eck HJ, Smaczniak C, Prat S, Visser RGF, Bachem CWB (2013) Naturally occurring allele diversity allows potato cultivation in northern latitudes. Nature 495:246–250
Kopriva S (2006) Regulation of sulfate assimilation in Arabidopsis and beyond. Ann Bot 97:479–495
Krieger U, Lippman ZB, Zamir D (2010) The flowering gene SINGLE FLOWER TRUSS drives heterosis for yield in tomato. Nat Genet 42:459–463
Kuhl J, Cheung F, Yuan Q, Martin W, Zewdie Y, McCallum J, Catanach A, Rutherford P, Sink KC, Jenderek M, Prince JP, Town CD, Havey MJ (2004) A unique set of 11,008 expressed sequence tags (EST) reveals expressed sequence and genomic differences between monocot order asparagales and poales. Plant Cell 16:114–125
Lee R, Baldwin S, Kenel F, McCallum J, Macknight R (2013) FLOWERING LOCUS T genes control onion bulb formation and flowering. Nat Commun 4:2884
Li F, Zhang X, Hu R, Wu F, Ma J, Meng Y, Fu YF (2013) Identification and molecular characterization of FKF1 and GI homologous genes in soybean. PLoS ONE 8(11):e79036. https://doi.org/10.1371/journal.pone.0079036
Li L, Dion E, Richard G, Domingue O, Jean M, Belzile F (2009) The Arabidopsis DNA mismatch repair gene PMS1 restricts somatic recombination between homeologous sequences. Plant Mol Biol 69:675–684
Lin CS, Hsu CT, Liao DC, Chang WJ, Chou ML, Huang YT, Chen JJ, Ko SS, Chan MT, Shih MC (2016) Transcriptome-wide analysis of the MADS-box gene family in the orchid Erycina pusilla. Plant Biotechnol J 14:284–298. https://doi.org/10.1111/pbi.12383
Liu Q, Lan Y, Wen C, Zhao H, Wang J, Wang Y (2016) Transcriptome sequencing analyses between the cytoplasmic male sterile line and its maintainer line in welsh onion (Allium fistulosum L). IntJ Mol Sci 17:1058. https://doi.org/10.3390/ijms17071058
Liu Q, Wen C, Zhao H, Zhang L, Wang J, Wang Y (2014) RNA-Seq reveals leaf cuticular wax-related genes in Welsh onion. PLoS ONE 11:e113290. https://doi.org/10.1371/journal.pone.0113290
Liu T, Zeng L, Zhu S, Chen X, Tang Q, Mei S, Tang S (2015) Large-scale development of expressed sequence tag-derived simple sequence repeat markers by deep transcriptome sequencing in garlic (Allium sativum L.). Mol Breed 35:204
Martin LB, Fei Z, Giovannoni JJ, Rose JK (2013) Catalyzing plant science research with RNA-seq. Front Plant Sci 4:66. https://doi.org/10.3389/fpls.2013.00066/full
Masuzaki S, Shigyo M, Yamauchi N (2006) Complete assignment of structural genes involved in flavonoid biosynthesis influencing bulb color to individual chromosomes of the shallot (Allium cepa L.). Genes Genet Syst 81:255–263
McCallum J (2007) Onion. In: Kole C (ed) Genome mapping and molecular breeding in plants, vol 5. Springer, Heidelberg, Berlin, New York, pp 331–342
McManus MT, Joshi S, Searle B, Pither-Joyce M, Shaw M, Leung S, Albert N, Shigyo M, Jakse J, Havey MJ, McCallum J (2012) Genotypic variation in sulfur assimilation and metabolism of onion (Allium cepa L.) III. Characterization of sulfite reductase. Phytochem 83:34–42
Mondragón-Palomino M (2013) Perspectives on MADS-box expression during orchid flower evolution and development. Front Plant Sci 4:377. https://doi.org/10.3389/fpls.2013.00377
Moyroud E, Kusters E, Monniaux M, Koes R, Parcy F (2010) LEAFY blossoms. Trends Plant Sci 15:346–352
Murakami M, Tago Y, Yamashino T, Mizuno T (2007) Comparative overviews of clock-associated genes of Arabidopsis thaliana and Oryza sativa. Plant Cell Physiol 48:110–121
Mutz KO, Heilkenbrinker A, Lönne M, Walter JG, Stahl F (2013) Transcriptome analysis using next-generation sequencing. Curr Opin Biotechnol 24:22–30
Navarro C, Abelenda JA, Cruz-Oro E, Cuellar CA, Tamaki S, Silva J, Shimamoto K, Prat S (2011) Control of flowering and storage organ formation in potato by FLOWERING LOCUS T. Nature 478:119–122
Neta R, David-Schwartz R, Peretz Y, Sela I, Rabinowitch HD, Flaishman M, Kamenetsky R (2011) Flower development in garlic: the ups and downs of gaLFY expression. Planta 233:1063–1072. https://doi.org/10.1007/s00425-011-1361-8
Ng M, Yanofsky MF (2001) Function and evolution of the plant MADS-box gene family. Nat Rev Genet 2:186–195
Otani M, Sharifi A, Kubota S, Oizumi K, Uetake F, Hirai M, Hoshino Y, Kanno A, Nakano M (2016) Suppression of B function strongly supports the modified ABCE model in Tricyrtis sp. (Liliaceae). Sci Rep 6:24549. https://doi.org/10.1038/srep24549
Pang Y, Peel GJ, Wright E, Wang Z, Dixon RA (2007) Early steps in proanthocyanidin biosynthesis in the model legume Medicago truncatula. Plant Physiol 145:601–615
Pin P, Nilsson O (2012) The multifaceted roles of FLOWERING LOCUS T in plant development. Plant Cell Environ 35:1742–1755
Rajkumar H, Ramagoni RK, Anchoju VC, Vankudavath RN, Syed AUZ (2015) De novo transcriptome analysis of Allium cepa L. (onion) bulb to identify allergens and epitopes. PLoS ONE 10(8):e0135387. https://doi.org/10.1371/journal.pone.0135387
Ross-Ibarra J, Morrell PL, Gaut BS (2007) Plant domestication, a unique opportunity to identify the genetic basis of adaptation. Proc Natl Acad Sci 104(suppl 1):8641–8648
Rotem N, Shemesh E, Peretz Y, Akad F, Edelbaum O, Rabinowitch HD, Sela I, Kamenetsky R (2007) Reproductive development and phenotypic differences in garlic are associated with expression and splicing of LEAFY homologue gaLFY. J Exp Bot 58:1133–1141
Sanchez SE, Kay SA (2016) The plant circadian clock: from a simple timekeeper to a complex developmental manager. Cold Spring Harb Perspect Biol 8:12. https://doi.org/10.1101/cshperspect.a027748
Sandhu AP, Abdelnoor RV, Mackenzie SA (2007) Transgenic induction of mitochondrial rearrangements for cytoplasmic male sterility in crop plants. Proc Natl Acad Sci USA 104:1766–1770
Sawa M, Nusinow DA, Kay SA, Imaizumi T (2007) FKF1 and GIGANTEA complex formation is required for day-length measurement in Arabidopsis. Science 318:261–265
Schnable PS, Wise RP (1998) The molecular basis of cytoplasmic male sterility and fertility restoration. Trends Plant Sci 3:175–180
Scholten OE, van Kaauwen MPW, Shahin A, Hendrickx PM, Paul Keizer LC, Burger K, van Heusden AW, van der Linden CG, Vosman B (2016) SNP-markers in Allium species to facilitate introgression breeding in onion. BMC Plant Biol 16:187
Schwinn KE, Ngo H, Kenel F, Brummell DA, Albert NW, McCallum JA, Pither-Joyce M, Crowhurst NS, Eady C, Davies KM (2016) The Onion (Allium cepa L.) R2R3-MYB Gene MYB1 regulates anthocyanin biosynthesis. Front Plant Sci 7:1865. https://doi.org/10.3389/fpls.2016.01865
Shalom SR, Gillett D, Zemach H, Kimhi S, Forer I, Zutahy Y, Tam Y, Teper-Bamnolker P, Kamenetsky R, Eshel D (2015) Storage temperature controls the timing of garlic bulb formation via shoot apical meristem termination. Planta 242:951–962
Shemesh-Mayer E, Ben-Michael T, Rotem N, Rabinowitch HD, Doron-Faigenboim A, Kosmala A, Perlikowski D, Sherman A, Kamenetsky R (2015) Garlic (Allium sativum L.) fertility: transcriptome and proteome analyses provide insight into flower and pollen development. Front Plant Sci 6:271. https://doi.org/10.3389/fpls.2015.00271
Shih CH, Chu H, Tang LK, Sakamoto W, Maekawa M, Chu IK, Wang M, Lo C (2008) Functional characterization of key structural genes in rice flavonoid biosynthesis. Planta 228:1043–1054
Shimada N, Sasaki R, Sato S, Kaneko T, Tabata S, Aoki T, Ayabe SA (2005) Comprehensive analysis of six dihydroflavonol 4-reductases encoded by a gene cluster of the Lotus japonicus genome. J Exp Bot 56:2385–2573
Sohn SH, Ahn YK, Lee TH, Lee JE, Jeong MH, Seo CH, Chandra R, Kwon YS, Kim CW, Kim DS, Won SY, Kim JS, Choi D (2016) Construction of a draft reference transcripts of onion (Allium cepa) using long-read sequencing. Plant Biotechnol Rep 10:383–390
Sun X, Zhou S, Meng F, Liu S (2012) De novo assembly and characterization of the garlic (Allium sativum) bud transcriptome by Illumina sequencing. Plant Cell Rep 31:1823–1828
Sun XD, Ma GQ, Cheng B, Li H, Qi S (2013) Identification of differentially expressed genes in shoot apex of garlic (Allium sativum L.) using Illumina sequencing. J Plant Stud 2:136–148
Sun XD, Yu XH, Zhou SM, Liu SQ (2016) De novo assembly and characterization of the Welsh onion (Allium fitulosum L.) transcriptome using Illumina technology. Mol Genet Genomics 291:647–659
Sykes T, Yates S, Nagy I, Asp T, Small I, Studer B (2017) In silico identification of candidate genes for fertility restoration in cytoplasmic male sterile perennial ryegrass (Lolium perenne L.). Genome Biol Evol 9:351–362
Takahashi H, Kopriva S, Giordano M, Saito K, Hell R (2011) Sulfur assimilation in photosynthetic organisms: molecular functions and regulations of transporters and assimilatory enzymes. Ann Rev of Plant Biol 62:157–184
Taylor A, Massiah AJ, Thimas B (2010) Conservation of Arabidopsis thaliana photoperiodic flowering genes in onion (Allium Cepa L.). Plant Cell Physiol 51:1638–1647
Theißen G, Melzer R, Rümpler F (2016) MADS-domain transcription factors and the floral quartet model of flower development: linking plant development and evolution. Development 143:3259–3271. https://doi.org/10.1242/dev.134080
Thomson B, Zheng B, Wellmer F (2017) Floral organogenesis: when knowing your ABCs is not enough. Plant Physiol 173:56–64
Tsai WC, Pan ZJ, Hsiao YY, Chen LJ, Liu ZJ (2014) Evolution and function of MADS-box genes involved in orchid floral development. J Syst Evol 52:397–410
Tsukazaki H, Yaguchi S, Sato S, Hirakawa H, Katayose Y, Kanamori H, Kurita K, Itoh T, Kumagai M, Mizuno S, Hamada M, Fukuoka H, Yamashita K, McCallum JA, Shigyo M, Wako T (2015) Development of transcriptome shotgun assembly-derived markers in bunching onion (Allium fistulosum). Mol Breed 35:55
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
Varshney RK, Terauchi R, McCouch SR (2014) Harvesting the promising fruits of genomics: applying genome sequencing technologies to crop breeding. PLoS Biol 12:e1001883
Wellmer F, Graciet E, Riechmann JL (2014) Specification of floral organs in Arabidopsis. J Exp Bot 65:1–9
Wendel JF, Jackson SA, Meyers BC, Wing RA (2016) Evolution of plant genome architecture. Genome Biol 17:37. https://doi.org/10.1186/s13059-016-0908-1
Wickland DP, Hanzawa Y (2015) The FLOWERING LOCUS T/TERMINAL FLOWER 1 gene family: Functional evolution and molecular mechanisms. Mol Plant 8:983–997
Xie DY, Jackson LA, Cooper JD, Ferreira D, Paiva NL (2004) Molecular and biochemical analysis of two cDNA clones encoding dihydroflavonol-4-reductase from Medicago truncatula. Plant Physiol 134:979–994
Xu G, Kong H (2007) Duplication and divergence of floral MADS-box genes in grasses: evidence for the generation and modification of novel regulators. J Integr Plant Biol 49:927–939
Xu W, Dubos C, Lepiniec L (2015) Transcriptional control of flavonoid biosynthesis by MYB-bHLH-WDR complexes. Trends Plant Sci 20:176–185
Yang C, Ye Y, Song C, Chen D, Jiang B, Wang Y (2016) Cloning and functional identification of the AcLFY gene in Allium cepa. Biochem Biophys Res Commun 473:1100–1105
Zhang C, Zhang H, Zhan Z, Liu B, Chen Z, Liang Y (2016) Transcriptome analysis of sucrose metabolism during bulb swelling and development in onion (Allium cepa L.). Front Plant Sci 7:1425. https://doi.org/10.3389/fpls.2016.01425
Zhang J, Wu K, Zeng S, Teixeira da Silva JA, Zhao X, Tian C, Xia H, Duan J (2013) Transcriptome analysis of Cymbidium sinense and its application to the identification of genes associated with floral development. BMC Genom 14:279
Zheng X, Tang S, Zhu S, Dai Q, Liu T (2016a) Identification of an NAC transcription factor family by deep transcriptome sequencing in onion (Allium cepa L.). PLoS ONE 11(6):e0157871. https://doi.org/10.1371/journal.pone.0157871
Zheng XM, Wu FQ, Zhang X, Lin QB, Wang J, Guo XP, Lei CL, Cheng ZJ, Zou C, Wan JM (2016b) Evolution of the PEBP gene family and selective signature on FT-like clade. J Syst Evol 54:502–510
Zhou SM, Chen LM, Liu SQ, Wang XF, Sun XD (2015) De novo assembly and annotation of the Chinese chive (Allium tuberosum Rottler ex Spr.) transcriptome using the Illumina platform. PLoS ONE 10(7):e0133312. https://doi.org/10.1371/journal.pone.0133312
Zhu S, Tang S, Tan Z, Yu Y, Dai Q, Liu T (2017) Comparative transcriptomics provide insight into the morphogenesis and evolution of fistular leaves in Allium. BMC Genom 18:60. https://doi.org/10.1186/s12864-016-3474-8
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Khosa, J., Lee, R., McCallum, J., Macknight, R. (2018). Gene Family Evolution in Allium Species. In: Shigyo, M., Khar, A., Abdelrahman, M. (eds) The Allium Genomes. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-95825-5_10
Download citation
DOI: https://doi.org/10.1007/978-3-319-95825-5_10
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-95824-8
Online ISBN: 978-3-319-95825-5
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)