Skip to main content

Advertisement

SpringerLink
Log in

Translational genomics in Brassica crops: challenges, progress, and future prospects

  • Review Article
  • Published:
Plant Biotechnology Reports Aims and scope Submit manuscript

Abstract

The last two decades have been a period of rapid advancement in our understanding of plant biology and its related developmental processes. This advancement has been facilitated by the adoption of plant models for most of the economically important plant families, as well as the development of enriched genetic, genomic, transcriptomic and metabolomic resources. In recent years, sequencing projects on major crops have further enhanced our understanding of their genomic structure, evolution, gene functions, and, most importantly, this knowledge has been utilized for crop improvement. The Brassicaceae family contains several important research and agricultural species, including the model plant Arabidopsis thaliana and economically important Brassica crops that are of great importance to human health and agriculture. Exploiting heterosis for yield enhancement, increasing tolerance against biotic and abiotic factors, and improving nutritional value remain the priorities in Brassica crop improvement. This review summarizes the potential of recently adopted genetic and genomic resources, as well as the basic knowledge obtained from studying the closest model plant A. thaliana, to accelerate the crop improvement programs in Brassica crops.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Alonso JM, Stepanova AN, Leisse TJ, Kim CJ, Chen H et al (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301:653–657

    PubMed  Google Scholar 

  • Andersen JR, Lubberstedt T (2003) Functional markers in plants. Trends Plant Sci 8:554–560

    CAS  PubMed  Google Scholar 

  • Arumugam N, Mukhopadhyay A, Gupta V, Pental D, Pradhan AK (2000) Somatic cell hybridization of ‘oxy’ CMS Brassica juncea (AABB) with B. oleracea (CC) for correction of chlorosis and transfer of novel organelle combinations to allotetraploid Brassica. Theor Appl Genet 100:1043–1049

    Google Scholar 

  • Augustine R, Mukhopadhyay A, Bisht NC (2013) Targeted silencing of BjMYB28 transcription factor gene directs development of low glucosinolate lines in oilseed Brassica juncea. Plant Biot J (in press)

  • Bagheri H, El-Soda M, van Oorschot I, Hanhart C, Bonnema G, Jansen-van den Bosch T, Mank R, Keurentjes JJ, Meng L, Wu J, Koornneef M, Aarts MG (2012) Genetic analysis of morphological traits in a new, versatile, rapid-cycling Brassica rapa recombinant inbred line population. Front Plant Sci 3:183. doi:10.3389/fpls.2012.00183

    PubMed Central  PubMed  Google Scholar 

  • Bancroft I, Morgan C, Fraser F, Higgins J, Wells R, Clissold L, Baker D, Long Y, Meng J, Wang X, Liu S, Trick M (2011) Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing. Nat Biotechnol 29:762–766

    CAS  PubMed  Google Scholar 

  • Belimov AA, Safronova VI, Demchinskaya SV et al (2007) Intraspecific variability of cadmium tolerance in hydroponically grown Indian mustard (Brassica juncea (L.) Czern) seedlings. Acta Physiol Plant 29:473–478

    CAS  Google Scholar 

  • Bisht NC, Jagannath A, Gupta V, Burma PK, Pental D (2004) A two gene–two promoter system for enhanced expression of a restorer gene (barstar) and development of improved fertility restorer lines for hybrid seed production in crop plants. Mol Breed 14:129–144

    CAS  Google Scholar 

  • Bisht NC, Jagannath A, Burma PK, Pradhan AK, Pental D (2007) Retransformation of a male sterile barnase line with the barstar gene as an efficient alternative method to identify male sterile-restorer combinations for heterosis breeding. Plant Cell Rep 26:727–733

    CAS  PubMed  Google Scholar 

  • Bisht NC, Gupta V, Ramchiary N, Sodhi YS, Mukhopadhyay A, Arumugam N, Pental D, Pradhan AK (2009) Fine mapping of loci involved with GSL biosynthesis in oilseed mustard (Brassica juncea) using genomic information from allied species. Theor Appl Genet 118:413–421

    CAS  PubMed  Google Scholar 

  • Bodnaryk RP (1997) Will low-glucosinolate cultivars of the mustards Brassica juncea and Sinapis alba be vulnerable to insect pests? Can J Plant Sci 77:283–287

    Google Scholar 

  • Brown GG (1999) Unique aspects of cytoplasmic male sterility and fertility restoration in Brassica napus. J Hered 90:351–356

    CAS  Google Scholar 

  • Budar F, Delourme R, Pelletier G (2004) Male sterility. In: Pua EC, Douglas CJ (ed) Biotechnology in agriculture and forestry, vol 54. Springer, Berlin, pp 43–64

  • Bus A, Hecht J, Huettel B, Reinhardt R, Stich B (2012) High-throughput polymorphism detection and genotyping in Brassica napus using next-generation RAD sequencing. BMC Genom 13:281

    CAS  Google Scholar 

  • Cai CC, Tu J, Fu TD, Chen BY (2008) The genetic basis of flowering time and photoperiod sensitivity in rapeseed Brassica napus L. Russ J Genet 44:326–333

    CAS  Google Scholar 

  • Carcamo H, Olfert O, Dosdall L et al (2007) Resistance to cabbage seedpod weevil among selected Brassicaceae germplasm. Can Entomol 139:658–669

    Google Scholar 

  • Cartea ME, Velasco P (2008) Glucosinolates in Brassica foods: bioavailability in food and significance for human health. Phytochem Rev 7:213–229

    CAS  Google Scholar 

  • Chan EKF, Rowe HC, Kliebenstein DJ (2010) Understanding the evolution of defense metabolites in Arabidopsis thaliana using genome-wide association mapping. Genetics 185:991–1007

    CAS  PubMed Central  PubMed  Google Scholar 

  • Chan EKF, Rowe HC, Corwin JA, Joseph B, Kliebenstein DJ (2011) Combining genome-wide association mapping and transcriptional networks to identify novel genes controlling glucosinolates in Arabidopsis thaliana. PLoS Biol 9:e1001125

    CAS  PubMed Central  PubMed  Google Scholar 

  • Chander H, Bakhetia DRC (1998) Evaluation of some cruciferous genotypes at seedling stage for resistance to mustard aphid, Lipaphis erysimi (Kalt.) under screen house and field conditions. J Insect Sci 11:19–25

    Google Scholar 

  • Choi S, Teakle G, Plaha P et al (2007) The reference genetic linkage map for the multinational Brassica rapa genome sequencing project. Theor App Genet 115:777–792

    CAS  Google Scholar 

  • Clay NK, Adio AM, Carine C, Jander G, Ausubel FM (2009) GSL metabolites required for an Arabidopsis innate immune response. Science 323:95–101

    Google Scholar 

  • Dhandapani V, Ramchiary N, Paul P, Kim J, Choi SH, Lee J, Hur Y, Lim YP (2011) Identification of potential micro RNAs and their targets in Brassica rapa L. Mol Cells 32:21–37

    Google Scholar 

  • Diers BW, McVetty PBE, Osborn T (1996) Relationship between heterosis and genetic distance based on restriction fragment length polymorphism markers in oilseed rape (Brassica napus). Crop Sci 36:79–83

    Google Scholar 

  • Dupont J, White PJ, Johnston KM, Heggtveit HA, McDonald BE, Grundy SM, Bonanome A (1989) Food safety and health effects of canola oil. J Am Coll Nutr 8:360–375

    CAS  PubMed  Google Scholar 

  • Fahey JW, Zhang Y, Talalay P (1997) Broccoli sprouts: an exceptionally rich source of inducers of enzymes that protect against chemical carcinogens. Proc Natl Acad Sci USA 94:10367–10372

    CAS  PubMed Central  PubMed  Google Scholar 

  • Feng J, Long Y, Shi L, Shi J, Barker G, Meng J (2012) Characterization of metabolite quantitative trait loci and metabolic networks that control glucosinolate concentration in the seeds and leaves of Brassica napus. New Phytol 193:96–108

    CAS  PubMed  Google Scholar 

  • Ferreira ME, Satagopan J, Yandell BS, Williams PH, Osborn TC (1995) Mapping loci controlling vernalization requirement and flowering time in Brassica napus. Theor Appl Genet 90:727–732

    PubMed  Google Scholar 

  • Fourmann M, Barret P, Froger N, Baron C, Charlot F, Delourme R, Brunel D (2002) From Arabidopsis thaliana to Brassica napus: development of amplified consensus genetic markers (ACGM) for construction of a gene map. Theor Appl Genet 105:1196–1206

    CAS  PubMed  Google Scholar 

  • Franzke A, Lysak MA, Al-Shehbaz IA, Koch MA, Mummenhoff K (2011) Cabbage family affairs: the evolutionary history of Brassicaceae. Trends Plant Sci 16:108–116

    CAS  PubMed  Google Scholar 

  • Gholami M, Bekele WA, Schondelmaier J, Snowdon RJ (2012) A tailed PCR procedure for cost-effective, two-order multiplex sequencing of candidate genes in polyploid plants. Plant Biotechnol J 10:635–645

    CAS  PubMed  Google Scholar 

  • Gigolashvili T, Berger B, Flugge UI (2009) Specific and coordinated control of indole and aliphatic glucosinolate biosynthesis by R2R3-MYB transcription factors in Arabidopsis thaliana. Phytochem Rev 8:3–13

    CAS  Google Scholar 

  • Gland A, Röbbelen G, Thies W (1981) Variation of alkenyl glucosinolates in seeds of Brassica species. Z Pflanzenzuchtg 87:96–110

    CAS  Google Scholar 

  • Goffman FD, Thies W, Velasco L (1999) Chemotaxonomic value of tocopherols in Brassicaceae. Phytochemistry 50:793–798

    CAS  Google Scholar 

  • Gómez-Campo C, Tortosa ME, Tewari I et al (1999) Epicuticular wax columns in cultivated Brassica species and in their close wild relatives. Ann Bot 83:515–519

    Google Scholar 

  • Groszmann M, Greaves IK, Albertyn ZI, Scofield GN, Peacock WJ, Dennis ES (2011) Changes in 24-nt siRNA levels in Arabidopsis hybrids suggest an epigenetic contribution to hybrid vigor. Proc Natl Acad Sci USA 108:2617–2622

    Google Scholar 

  • Guo S, Zou J, Li R, Long Y, Chen S, Meng J (2012) A genetic linkage map of Brassica carinata constructed with a doubled haploid population. Theor Appl Genet 125:1113–1124

    CAS  PubMed  Google Scholar 

  • Gupta V, Mukhopadhyay A, Arumugam N, Sodhi YS, Pental D, Pradhan AK (2004) Molecular tagging of erucic acid trait in oilseed mustard (Brassica juncea) by QTL mapping and single nucleotide polymorphisms in FAE1 gene. Theor Appl Genet 108:743–749

    CAS  PubMed  Google Scholar 

  • Halkier BA, Gershenzon J (2006) Biology and biochemistry of glucosinolates. Annu Rev Plant Biol 57:303–333

    CAS  PubMed  Google Scholar 

  • Harper AL, Trick M, Higgins J, Fraser F, Clissold L, Wells R, Hattori C, Werner P, Bancroft I (2012) Associative transcriptomics of traits in the polyploid crop species Brassica napus. Nat Biotechnol 30:798–802

    CAS  PubMed  Google Scholar 

  • Hasan M, Friedt W, Pons-Kühnemann J, Freitag NM, Link K, Snowdon RJ (2008) Association of gene-linked SSR markers to seed glucosinolate content in oilseed rape (Brassica napus ssp. napus). Theor Appl Genet 116:1035–1049

    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

    CAS  PubMed Central  PubMed  Google Scholar 

  • He XF, Fang YY, Feng L, Guo HS (2008) Characterization of conserved and novel micro RNAs and their targets, including a TuMV-induced TIR–NBS–LRR class R gene-derived novel miRNA in Brassica. FEBS Lett 582:2445–2452

    CAS  PubMed  Google Scholar 

  • Heap IM (2009) International survey of herbicide-resistant weeds. http://www.weedscience.com

  • Higgins J, Magusin A, Trick M, Fraser F, Bancroft I (2012) Use of mRNA-Seq to discriminate contributions to the transcriptome from the constituent genomes of the polyploid crop species Brassica napus. BMC Genomics 13:247

    CAS  PubMed Central  PubMed  Google Scholar 

  • Himelblau E, Gilchrist EJ, Buono K, Bizzell C, Mentzer L, Vogelzang R, Osborn T, Amasino RM, Parkin IA, Haughn GW (2009) Forward and reverse genetics of rapid-cycling Brassica oleracea. Theor Appl Genet 118:953–961

    PubMed  Google Scholar 

  • Horiguchi G (2004) RNA silencing in plants: a shortcut to functional analysis. Differentiation 72:65–73

    CAS  PubMed  Google Scholar 

  • Hu X, Sullivan-Gilbert M, Gupta M, Thompson SA (2006) Mapping of the loci controlling oleic and linolenic acid contents and development of fad2 and fad3 allele-specific markers in canola (Brassica napus L.). Theor Appl Genet 113:497–507

    CAS  PubMed  Google Scholar 

  • Hu Z, Huang S, Sun M, Wang H, Hua W (2012) Development and application of single nucleotide polymorphism markers in the polyploid Brassica napus by 454 sequencing of expressed sequence tags. Plant Breed 131:293–299

    CAS  Google Scholar 

  • Irwin JA, Lister C, Soumpourou E, Zhang Y, Howell EC, Teakle G, Dean C (2012) Functional alleles of the flowering time regulator FRIGIDA in the Brassica oleracea genome. BMC Plant Biol 12:21

    CAS  PubMed Central  PubMed  Google Scholar 

  • Jagannath A, Bandyopadhyay P, Arumugam N, Gupta V, Burma PK, Pental D (2001) The use of a spacer DNA fragment insulates the tissue-specific expression of a cytotoxic gene (barnase) and allows high-frequency generation of transgenic male sterile lines in Brassica juncea L. Mol Breed 8:11–23

    CAS  Google Scholar 

  • Jagannath A, Arumugam N, Gupta V, Pradhan AK, Burma PK, Pental D (2002) Development of transgenic barstar lines and identification of a male sterile (barnase)/restorer (barstar) combination for heterosis breeding in Indian oilseed mustard (Brassica juncea). Curr Sci 82:46–52

    CAS  Google Scholar 

  • Jagannath A, Sodhi YS, Gupta V, Mukhopadhyay A, Arumugam N, Singh I, Rohatgi S, Burma PK, Pradhan AK, Pental D (2011) Eliminating expression of erucic acid-encoding loci allows the identification of “hidden” QTL contributing to oil quality fractions and oil content in Brassica juncea (Indian mustard). Theor Appl Genet 122:1091–1103

    CAS  PubMed  Google Scholar 

  • Jiang C, Ramchiary N, Ma Y et al (2011) Structural and functional comparative mapping between the Brassica A genomes in allotetraploid Brassica napus and diploid Brassica rapa. Theor Appl Genet 123:927–941

    CAS  PubMed  Google Scholar 

  • Johnston JS, Pepper AE, Hall AE, Chen ZJ, Hodnett G, Drabek J, Lopez R, Price HJ (2005) Evolution of genome size in Brassicaceae. Ann Bot 95:229–235

    CAS  PubMed  Google Scholar 

  • Kim JS, Chung TY, King GJ, Jin M, Yang TJ, Min YM, Kim H, Park BM (2006) A sequence tagged linkage map of Brassica rapa. Genetics 174:29–39

    CAS  PubMed Central  PubMed  Google Scholar 

  • Kim HR, Choi SR, Bae J, Hong CP, Lee SY, Hossain MD, Nguyen DV, Jin M, Park BS, Bang JW, Bancroft I, Lim YP (2009) Sequenced BAC anchored reference genetic map that reconciles the ten individual chromosomes of Brassica rapa. BMC Genomics 10:432

    PubMed Central  PubMed  Google Scholar 

  • Kim B, Yu H, Park S, Shin JY, Oh M, Kim N, Mun JH (2012) Identification and profiling of novel micro RNAs in the Brassica rapa genome based on small RNA deep sequencing. BMC Plant Biol 12:218

    CAS  PubMed Central  PubMed  Google Scholar 

  • Knaak C, Ecke W (1995) Genetic diversity and hybrid performance in European winter oilseed rape (Brassica napus L.). In: Proc 9th Int Rapeseed Congr, Cambridge, UK, 4–7 July 1995, pp 110–12

  • Kolte SJ, Bordoloi DK, Awasthi RP (1991) The search for resistance to major diseases of rapeseed and mustard in India. In: Proc GCIRC 8th Int Rapeseed Congr, Saskatoon, Saskatchewan, Canada, 9–11 July 1991, pp 219–225

  • Lagercrantz U (1998) Comparative mapping between Arabidopsis thaliana and Brassica nigra indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusions and frequent rearrangements. Genetics 150:1217–1228

    CAS  PubMed Central  PubMed  Google Scholar 

  • Lagercrantz U, Lydiate DJ (1996) Comparative genome mapping in Brassica. Genetics 144:1903–1910

    CAS  PubMed Central  PubMed  Google Scholar 

  • Lan TH, Paterson AH (2000) Comparative mapping of quantitative trait loci sculpting the curd of Brassica oleracea. Genetics 155:1927–1954

    CAS  PubMed Central  PubMed  Google Scholar 

  • Lee SC, Lim MH, Kim JA, Lee SI, Kim JS, Jin M, Kwon SJ, Mun JH, Kim YK, Kim HU, Hur Y, Park BS (2008) Transcriptome analysis in Brassica rapa under the abiotic stresses using Brassica 24 K oligo microarray. Mol Cells 26:595–605

    CAS  PubMed  Google Scholar 

  • Li Y, Ma C, Fu T, Yang G, Tu J, Chen Q, Wang T, Zhang X, Li C (2006) Construction of a molecular functional map of rapeseed (Brassica napus L.) using differentially expressed genes between hybrid and its parents. Euphytica 152:25–39

    CAS  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 16:311–323

    CAS  PubMed Central  PubMed  Google Scholar 

  • Li H, Yu SC, Zhang FL, Yu YJ, Zhao XY, Zhang DS, Zhao X (2011) Development of molecular markers linked to the resistant QTL for downy mildew in Brassica rapa L. ssp. pekinensis. Yi Chuan 33:1271–1278

    CAS  PubMed  Google Scholar 

  • Li X, Ramchiary N, Dhandapani V, Choi SR, Hur Y, Nou IS, Yoon MK, Lim YP (2013) 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

    PubMed Central  PubMed  Google Scholar 

  • Liu Q, Rimmer SR (1991) Inheritance of resistance in Brassica napus to an Ethiopian isolate of Albugo candida from Brassica carinata. Can J Plant Pathol 13:197–201

    Google Scholar 

  • Liu Z, Hammerlindl J, Keller W, McVetty PBE, Daayf F, Quiros CF, Li G (2011) MAM gene silencing leads to the induction of C3 and reduction of C4 and C5 side-chain aliphatic glucosinolates in Brassica napus. Mol Breed 27:467–478

    CAS  Google Scholar 

  • Liu Z, Hirani AH, McVetty PBE, Daayf F, Quiros CF, Li G (2012) Reducing progoitrin and enriching glucoraphanin in Brassica napus seeds through silencing of the GSL-ALK gene family. Plant Mol Biol 79:179–189

    CAS  PubMed  Google Scholar 

  • Long Y, Shi J, Qiu D, Li R, Zhang C, Wang J, Hou J, Zhao J, Shi L, Park B-S, Choi SR, Lim YP, Meng J (2007) Flowering time quantitative trait loci analysis of oilseed Brassica in multiple environments and genome wide alignment with Arabidopsis. Genetics 177:2433–2444

    Google Scholar 

  • Long Y, Wang Z, Sun Z, Fernando DW, McVetty PB, Li G (2011) Identification of two blackleg resistance genes and fine mapping of one of these two genes in a Brassica napus canola cultivar “Surpass 400”. Theor Appl Genet 122:1223–1231

    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

    CAS  PubMed  Google Scholar 

  • Lou P, Xie Q, Xu X, Edwards CE, Brock MT, Weinig C, McClung CR (2011) Genetic architecture of the circadian clock and flowering time in Brassica rapa. Theor Appl Genet 123:397–409

    CAS  PubMed  Google Scholar 

  • Love HR, Rakow G, Raney JP, Downey RK (1990a) Development of low glucosinolate mustard. Can J Plant Sci 70:419–424

    CAS  Google Scholar 

  • Love HR, Rakow G, Raney JP, Downey RK (1990b) Genetic control of 2-propenyl and 3-butenyl glucosinolates in mustard. Can J Plant Sci 70:425–429

    CAS  Google Scholar 

  • Love CG, Graham NS, O Lochlainn S, Bowen HC, May ST, White PJ, Broadley MR, Hammond JP, King GJ (2010) A Brassica exon array for whole-transcript gene expression profiling. PLoS One 5:e12812

    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

    CAS  PubMed  Google Scholar 

  • Lukens LN, Quijada PA, Udall J, Pires JC, Schranz ME, Osborn TC (2004) Genome redundancy and plasticity within ancient and recent Brassica crop species. Biol J Linn Soc 82:665–674

    Google Scholar 

  • Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290:1151–1155

    CAS  PubMed  Google Scholar 

  • Lysak MA, Koch MA, Pecinka A, Schubert I (2005) Chromosome triplication found across the tribe Brassiceae. Genome Res 15:516–525

    CAS  PubMed Central  PubMed  Google Scholar 

  • Lysak MA, Cheung K, Kitschke M, Bures P (2007) Ancestral chromosomal blocks are triplicated in Brassiceae species with varying chromosome number and genome size. Plant Physiol 145:402–410

    CAS  PubMed Central  PubMed  Google Scholar 

  • Mariani C, De Beuckeleer M, Truettner J, Leemans J, Goldberg RB (1990) Induction of male sterility in plants by a chimeric ribonuclease gene. Nature 347:737–741

    CAS  Google Scholar 

  • Mariani C, Gossele V, De Beuckeleer M, De Block M, Goldberg RB, De Greef W, Leemans J (1992) Achimaeric ribonuclease-inhibitor gene restores fertility to male sterile plants. Nature 357:384–387

    CAS  Google Scholar 

  • Mawson R, Heaney RK, Zdunczyk Z, Kozlowska H (1993) Rapeseed meal-glucosinolates and their antinutritional effects. Part II. Flavour and palatability. Mol Nutr Food Res 37:336–344

    CAS  Google Scholar 

  • Mayerhofer R, Wilde K, Mayerhofer M, Lydiate D, Bansal VK, Good AG, Parkin A (2005) Complexities of chromosome landing in a highly duplicated genome: toward map-based cloning of a gene controlling blackleg resistance in Brassica napus. Genetics 171:1977–1988

    CAS  PubMed Central  PubMed  Google Scholar 

  • McCallum CM, Comai L, Greene EA, Henikoff S (2000) Targeting Induced Local Lesions IN Genomes (TILLING) for plant functional genomics. Plant Physiol 123:439–442

    Google Scholar 

  • Mei DS, Wang HZ, Hu Q, Li YD, Xu YS, Li YC (2009) QTL analysis on plant height and flowering time in Brassica napus. Plant Breed 128:458–465

    Google Scholar 

  • Muangprom A, Osborn TC (2004) Characterization of a dwarf gene in Brassica rapa, including the identification of a candidate gene. Theor Appl Genet 108:1378–1384

    CAS  PubMed  Google Scholar 

  • Mun Jh, Sj Kwon, Tj Yang et al (2009) Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication. Genome Biol 10:R111

    PubMed Central  PubMed  Google Scholar 

  • Okazaki K, Sakamoto K, Kikuchi R, Saito A, Togashi E, Kuginuki Y, Matsumoto S, Hirai M (2006) Mapping and characterization of FLC homologs and QTL analysis of flowering time in Brassica oleracea. Theor Appl Genet 114:595–608

    PubMed  Google Scholar 

  • Osakabe K, Osakabe Y, Toki S (2010) Site-directed mutagenesis in Arabidopsis using custom-designed zincfinger nucleases. Proc Natl Acad Sci USA 107:12034–12039

    Google Scholar 

  • Osborn TC, Kole C, Parkin IAP, 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 Central  PubMed  Google Scholar 

  • Panjabi P, Jagannath A, Bisht N et al (2008) Comparative mapping of Brassica juncea and Arabidopsis thaliana using intron polymorphism (IP) markers: homeologous relationships, diversification and evolution of the A, B and C Brassica genomes. BMC Genom 9:113

  • Parkin IAP, Sharpe AG, Keith DJ, Lydiate DJ (1995) Identification of the A and C genomes of amphidiploid Brassica napus (oilseed rape). Genome 38:1122–1131

    CAS  PubMed  Google Scholar 

  • Parkin IAP, Gulden SM, Sharpe AG et al (2005) Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana. Genetics 171:765–781

    CAS  PubMed Central  PubMed  Google Scholar 

  • Pradhan AK, Sodhi YS, Mukhopadhyay A, Pental D (1993) Heterosis breeding in Indian mustard (Brassica juncea L. Czern & Coss): analysis of component characters contributing to heterosis for yield. Euphytica 69:219–229

    Google Scholar 

  • Pradhan AK, Gupta V, Mukhopadhyay A, Arumugam N, Sodhi YS, Pental D (2003) A high density linkage map in Brassica juncea (Indian mustard) using AFLP and RFLP markers. Theor Appl Genet 106:607–614

    CAS  PubMed  Google Scholar 

  • Prakash S, Bhat SR (2007) Contribution of wild crucifers in Brassica improvement: past accomplishment and future perspectives. In: Proc GCIRC 12th Int Rapeseed Congr, Wuhan, China, 26–30 March 2007, 1:213–15

  • Prakash S, Chopra VL (1988) Introgression of resistance to pod shatter in Brassica napus from Brassica juncea through non-homologous recombination. Plant Breed 101:167–168

    Google Scholar 

  • Qiu D, Morgan C, Shi J, Long Y, Liu J, Li R, Zhuang X, Wang Y, Tan X, Dietrich E, Weihmann T, Everett C, Vanstraelen S, Beckett P, Fraser F, Trick M, Barnes S, Wilmer J, Schmidt R, Li J, Li D, Meng J, Bancroft I (2006) A comparative linkage map of oilseed rape and its use for QTL analysis of seed oil and erucic acid content. Theor Appl Genet 114:67–80

    CAS  PubMed  Google Scholar 

  • Quijada PA, Udall JA, Lambert B, Osborn TC (2006) Quantitative trait analysis of seed yield and other complex traits in hybrid spring rapeseed (Brassica napus L.): 1. Identification of genomic regions from winter germplasm. Theor Appl Genet 113:549–561

    CAS  PubMed  Google Scholar 

  • Rahman M, Sun Z, McVetty PB, Li G (2008) High throughput genome-specific and gene-specific molecular markers for erucic acid genes in Brassica napus (L.) for marker-assisted selection in plant breeding. Theor Appl Genet 117:895–904

    CAS  PubMed  Google Scholar 

  • Ramachandran S, Buntin GD, All JN et al (1998) Diamondback moth (Lepidoptera: Plutellidae) resistance of Brassica napus and B. oleracea lines with differing leaf characteristics. J Econ Entomol 91:987–992

    Google Scholar 

  • Raman H, Raman R, Eckermann P, Coombes N, Manoli S, Zou X, Edwards D, Meng J, Prangnell R, Stiller J, Batley J, Luckett D, Wratten N, Dennis E (2012a) Genetic and physical mapping of flowering time loci in canola (Brassica napus L.). Theor Appl Genet 126:119–132

    PubMed  Google Scholar 

  • Raman H, Raman R, Nelson MN, Aslam MN, Rajasekaran R, Wratten N, Cowling WA, Kilian A, Sharpe AG, Schondelmaier J (2012b) Diversity array technology markers: genetic diversity analyses and linkage map construction in rapeseed (Brassica napus L.). DNA Res 19:51–65

    CAS  PubMed Central  PubMed  Google Scholar 

  • Ramchiary N, Bisht NC, Gupta V, Mukhopadhyay A, Arumugam N, Sodhi YS, Pental D, Pradhan AK (2007a) QTL analysis reveals context dependent loci for seed glucosinolate trait in the oilseed Brassica juncea: importance of recurrent selection backcross scheme for the identification of ‘true’ QTL. Theor Appl Genet 116:77–85

    CAS  PubMed  Google Scholar 

  • Ramchiary N, Padmaja KL, Sharma S, Gupta V, Sodhi YS, Mukhopadhyay A, Arumugam N, Pental D, Pradhan AK (2007b) Mapping of yield influencing QTL in Brassica juncea: implications for breeding of a major oilseed crop of dryland areas. Theor Appl Genet 115:807–817

    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

    CAS  PubMed Central  PubMed  Google Scholar 

  • Rana D, van den Boogaart T, O‘Neill CM et al (2004) Conservation of the microstructure of genome segments in Brassica napus and its diploid relatives. Plant J 40:725–733

    CAS  PubMed  Google Scholar 

  • Raymer PL (2002) Canola: an emerging oilseed crop. In: Janick J, Whipkey A (eds) Trends in new crops and new uses. ASHS, Alexandria, pp 122–126

  • Rosa EAS, Hesney RK, Fenwick GR, Portas C (1997) Glucosinolates in crop plants. Hortic Rev 19:99–215

    Google Scholar 

  • Roscoe TJ, Lessire R, Puyaubert J, Renard M, Delseny M (2001) Mutations in the fatty acid elongation 1 gene are associated with a loss of beta-ketoacyl-CoA synthase activity in low erucic acid rapeseed. FEBS Lett 492:107–111

    CAS  PubMed  Google Scholar 

  • Schmidt R, Bancroft I (2011) Genetics and genomics of the Brassicaceae. Plant genetics and genomics: crops and models, vol 9. Springer, New York

  • Schranz ME, Lysak MA, Mitchell-Olds T (2006) The ABC’s of comparative genomics in the Brassicaceae: building blocks of crucifer genomes. Trends Plant Sci 11:535–542

    Google Scholar 

  • Schwab R, Ossowski S, Riester M, Warthmann N, Weigel D (2006) Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 18:1121–1133

    Google Scholar 

  • Sebastian RL, Howell EC, King GJ, Marshall DF, Kearsey MJ (2002) An integrated AFLP and RFLP Brassica oleracea linkage map from two morphologically distinct doubled-haploid mapping populations. Theor Appl Genet 100:75–81

    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

    Google Scholar 

  • Sivaraman I, Arumugam N, Sodhi YS, Gupta V, Mukhopadhyay A, Pradhan AK, Burma PK, Pental D (2004) Development of high oleic and low linoleic acid transgenics in a zero erucic acid Brassica juncea L. (Indian mustard) line by antisense suppression of the fad2 gene. Mol Breed 13:365–375

    CAS  Google Scholar 

  • Smooker AM, Wells R, Morgan C, Beaudoin F, Cho K, Fraser F, Bancroft I (2011) The identification and mapping of candidate genes and QTL involved in the fatty acid desaturation pathway in Brassica napus. Theor Appl Genet 122:1075–1090

    CAS  PubMed  Google Scholar 

  • Sodhi YS, Mukhopadhyay A, Arumugam N, Verma JK, Gupta V, Pental D, Pradhan AK (2002) Genetic analysis of total glucosinolate in crosses involving a high glucosinolate Indian variety and a low glucosinolate line of Brassica juncea. Plant Breed 121:508–511

    CAS  Google Scholar 

  • Sodhi YS, Chandra A, Verma JK, Arumugam N, Mukhopadhyay A, Gupta V, Pental D, Pradhan AK (2006) A new cytoplasmic male sterility system for hybrid seed production in Indian oilseed mustard Brassica juncea. Theor Appl Genet 114:93–99

    CAS  PubMed  Google Scholar 

  • Sonderby IE, Geu-Flores F, Halkier BA (2010) Biosynthesis of glucosinolates—gene discovery and beyond. Trends Plant Sci 15:283–290

    Google Scholar 

  • Song KM, Suzuki JY, Slocum MK, Williams PH, Osborn TC (1991) A linkage map of Brassica rapa base on restriction fragment length polymorphism loci. Theor Appl Genet 82:296–304

    CAS  PubMed  Google Scholar 

  • Srivastava A, Gupta V, Pental D, Pradhan AK (2001) AFLP-based genetic diversity assessment amongst agronomically important natural and some newly synthesized lines of Brassica juncea. Theor Appl Genet 102:193–199

    CAS  Google Scholar 

  • Stephenson P, Baker D, Girin T, Perez A, Amoah S, King GJ, Østergaard L (2010) A rich TILLING resource for studying gene function in Brassica rapa. BMC Plant Biol 10:62

    PubMed Central  PubMed  Google Scholar 

  • Stringam GR, Thiagarajah MR (1995) Inheritance of alkenyl glucosinolates in traditional and microspore-derived doubled haploid populations of Brassica juncea L. Czern and Coss. In: Proc 9th Int Rapeseed Congr, Cambridge, UK, 4–7 July 1995, pp 804–806

  • Sun M, Hua W, Liu J, Huang S, Wang X, Liu G, Wang H (2012) Design of new genome- and gene-sourced primers and identification of QTL for seed oil content in a specially high-oil Brassica napus cultivar. PLoS ONE 7(10):e47037

    CAS  PubMed Central  PubMed  Google Scholar 

  • Tanhuanpaa PK, Vilkki JP, Vilkki HJ (1996) A linkage map of spring turnip rape based on RFLP and RAPD markers. Agric Food Sci Finl 5:209–217

    CAS  Google Scholar 

  • Teutonico RA, Osborn TC (1995) Mapping loci controlling vernalization requirement in Brassica rapa. Theor Appl Genet 91:1279–1283

    CAS  PubMed  Google Scholar 

  • Till BJ, Reynolds SH, Greene EA, Codomo CA, Enns LC, Johnson JE, Burtner C, Odden AR, Young K, Taylor NE et al (2003) Large-scale discovery of induced point mutations with high-throughput TILLING. Genome Res 13:524–530

    CAS  PubMed Central  PubMed  Google Scholar 

  • Town CD, Cheung F, Maiti R, Crabtree J, Haas BJ, Wortman JR, Hine EE, Althoff R, Arbogast TS, Tallon LJ, Vigouroux M, Trick M, Bancroft I (2006) Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. Plant Cell 18:1348–1359

    CAS  PubMed Central  PubMed  Google Scholar 

  • Trick M, Cheung F, Drou N, Fraser F, Lobenhofer EK, Hurban P, Magusin A, Town CD, Bancroft I (2009a) A newly-developed community microarray resource for transcriptome profiling in Brassica species enables the confirmation of Brassica-specific expressed sequences. BMC Plant Biol 9:50

    PubMed Central  PubMed  Google Scholar 

  • Trick M, Long Y, Meng J, Bancroft I (2009b) Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing. Plant Biotechnol J 7:334–346

    CAS  PubMed  Google Scholar 

  • Troncoso-Ponce MA, Kilaru A, Cao X, Durrett TP, Fan J, Jensen JK, Thrower NA, Pauly M, Wilkerson C, Ohlrogge JB (2011) Comparative deep transcriptional profiling of four developing oilseeds. Plant J 68:1014–1027

    CAS  PubMed Central  PubMed  Google Scholar 

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

    Google Scholar 

  • Uzunova M, Ecke W, Weissleder K, Robbelen G (1995) Mapping the genome of rapeseed (Brassica napus L). Construction of an RFLP linkage map and localization of QTLs for seed glucosinolate content. Theor Appl Genet 90:194–204

    CAS  PubMed  Google Scholar 

  • Varshney RK, Graner A, Sorrells ME (2005) Genomics-assisted breeding for crop improvement. Trends Plant Sci 10:621–630

    CAS  PubMed  Google Scholar 

  • Varshney RK, Nayak SN, May GD, Jackson SA (2009) Next-generation sequencing technologies and their implications for crop genetics and breeding. Trends Biotechnol 27:522–530

    CAS  PubMed  Google Scholar 

  • Wan Z, Jing B, Tu J, Ma C, Shen J, Yi B, Wen J, Huang T, Wang X, Fu T (2008) Genetic characterization of a new cytoplasmic male sterility system (hau) in Brassica juncea and its transfer to B. napus. Theor Appl Genet 116:355–362

    PubMed  Google Scholar 

  • Wang N, Wang Y, Tian F, King GJ, Zhang C, Long Y, Shi L, Meng J (2008) A functional genomics resource for Brassica napus: development of an EMS mutagenized population and discovery of FAE1 point mutations by TILLING. New Phytol 180:751–765

    CAS  PubMed  Google Scholar 

  • Wang H, Wu J, Sun S, Liu B, Cheng F, Sun R, Wang X (2011a) Glucosinolate biosynthetic genes in Brassica rapa. Gene 487:135–142

    CAS  PubMed  Google Scholar 

  • Wang N, Qian W, Suppanz I, Wei L, Mao B, Long Y, Meng J, Müller AE, Jung C (2011b) Flowering time variation in oilseed rape (Brassica napus L.) is associated with allelic variation in the FRIGIDA homologue BnaA.FRI.a. J Exp Bot 62:5641–5658

    CAS  PubMed Central  PubMed  Google Scholar 

  • Wang X, Wang H, Wang J et al (2011c) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43:1035–1039

    CAS  PubMed  Google Scholar 

  • Wang F, Li L, Li H, Liu L, Zhang Y, Gao J, Wang X (2012a) Transcriptome analysis of rosette and folding leaves in Chinese cabbage using high-throughput RNA sequencing. Genomics 99:299–307

    CAS  PubMed  Google Scholar 

  • Wang F, Li L, Liu L, Li H, Zhang Y, Yao Y, Ni Z, Gao J (2012b) High-throughput sequencing discovery of conserved and novel micro RNAs in chinese cabbage (Brassica rapa L. Ssp. Pekinensis). Mol Genet Genom 287:555–563

    CAS  Google Scholar 

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

  • Westman AL, Kresovich S, Dickson MH (1999) Regional variation in Brassica nigra and other weedy crucifers for disease reaction to Alternaria brassicicola and Xanthomonas campestris pv. campestris. Euphytica 106:253–259

    Google Scholar 

  • Xu MY, Dong Y, Zhang QX, Zhang L, Luo YZ, Sun J, Fan YL, Wang L (2012) Identification of miRNAs and their targets from Brassica napus by high-throughput sequencing and degradome analysis. BMC Genom 13:421

    CAS  Google Scholar 

  • Yang Q, Fan C, Guo Z, Qin J, Wu J, Li Q, Fu T, Zhou Y (2012) Identification of FAD2 and FAD3 genes in Brassica napus genome and development of allele-specific markers for high oleic and low linolenic acid contents. Theor Appl Genet 125:715–729

    CAS  PubMed  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. doi:10.1093/jxb/err337

    CAS  PubMed Central  PubMed  Google Scholar 

  • Zang YX, Kim HU, Kim JA, Lim MH, Jin M, Lee SC, Kwon SJ, Lee SI, Hong JK, Park TH, Mun JH, Seol YJ, Hong SB, Park BS (2009) Genome-wide identification of glucosinolate synthesis genes in Brassica rapa. FEBS J 276:3559–3574

    CAS  PubMed  Google Scholar 

  • Zhang F, Maeder ML, Wallace EU et al (2010) High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases. Proc Natl Acad Sci USA 107:12028–12033

    CAS  PubMed Central  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India

    Rehna Augustine, Gulab C. Arya, Deepti M. Nambiar, Roshan Kumar & Naveen C. Bisht

Authors
  1. Rehna Augustine
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Gulab C. Arya
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Deepti M. Nambiar
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Roshan Kumar
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Naveen C. Bisht
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Naveen C. Bisht.

Additional information

R. Augustine and G. C. Arya contributed equally to this review.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Augustine, R., Arya, G.C., Nambiar, D.M. et al. Translational genomics in Brassica crops: challenges, progress, and future prospects. Plant Biotechnol Rep 8, 65–81 (2014). https://doi.org/10.1007/s11816-013-0298-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11816-013-0298-8

Keywords

Search

Navigation