Skip to main content
Log in

Development and genetic mapping of microsatellite markers from whole genome shotgun sequences in Brassica oleracea

Molecular Breeding Aims and scope Submit manuscript

Abstract

The availability of whole genome shotgun sequences (WGSs) in Brassica oleracea provides an unprecedented opportunity for development of microsatellite or simple sequence repeat (SSR) markers for genome analysis and genetic improvement in Brassica species. In this study, a total of 56,465 non-redundant SSRs were identified from the WGSs in B. oleracea, with dinucleotide repeats being the most abundant, followed by tri-, tetra- and pentanucleotide repeats. From these, 1,398 new SSR markers (designated as BoGMS) with repeat length ≥25 bp were developed and used to survey polymorphisms with a panel of six rapeseed varieties, which is the largest number of SSR markers developed for the C genome in a single study. Of these SSR markers, 752 (69.5%) showed polymorphism among the six varieties. Of these, 266 markers that showed clear scorable polymorphisms between B. napus varieties No. 2127 and ZY821 were integrated into an existing B. napus genetic linkage map. These new markers are preferentially distributed on the linkage groups in the C genome, and significantly increased the number of SSR markers in the C genome. These SSR markers will be very useful for gene mapping and marker-assisted selection of important agronomic traits in Brassica species.

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

Access this article

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

  • Ayele M, Haas B, Kumar N, Wu H, Xiao Y, Van Aken S, Utterback T, Wortman J, White O, Town C (2005) Whole genome shotgun sequencing of Brassica oleracea and its application to gene discovery and annotation in Arabidopsis. Genome Res 15:487–495

    Article  PubMed  Google Scholar 

  • Batley J, Hopkins C, Cogan N, Hand M, Jewell E, Kaur J, Kaur S, Li X, Ling A, Love C (2007) Identification and characterization of simple sequence repeat markers from Brassica napus expressed sequences. Mol Ecol Notes 7:886–889

    Article  CAS  Google Scholar 

  • Breseghello F, Sorrells M (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172:1165–1177

    Article  PubMed  Google Scholar 

  • Chen C, Yu Q, Hou S, Li Y, Eustice M, Skelton RL, Veatch O, Herdes RE, Diebold L, Saw J, Feng Y, Qian W, Bynum L, Wang L, Moore PH, Paull RE, Alam M, Ming R (2007a) Construction of a sequence-tagged high-density genetic map of papaya for comparative structural and evolutionary genomics in Brassicales. Genetics 177:2481–2491

    Article  PubMed  CAS  Google Scholar 

  • Chen W, Zhang Y, Liu X, Chen B, Tu J, Tingdong F (2007b) Detection of QTL for six yield-related traits in oilseed rape (Brassica napus) using DH and immortalized F2 populations. Theor Appl Genet 115:849–858

    Article  PubMed  CAS  Google Scholar 

  • Chen S, Nelson M, Ghamkhar K, Fu T, Cowling W (2008) Divergent patterns of allelic diversity from similar origins: the case of oilseed rape (Brassica napus L.) in China and Australia. Genome 51:1–10

    Article  PubMed  Google Scholar 

  • Chen S, Zou J, Cowling W, Meng J (2010) Allelic diversity in a novel gene pool of canola-quality Brassica napus enriched with alleles from B. rapa and B. carinata. Crop Pasture Sci 61:483–492

    Article  CAS  Google Scholar 

  • Cheng X, Xu J, Xia S, Gu J, Yang Y, Fu J, Qian X, Zhang S, Wu J, Liu K (2009) Development and genetic mapping of microsatellite markers from genome survey sequences in Brassica napus. Theor Appl Genet 118:1121–1131

    Article  PubMed  CAS  Google Scholar 

  • Choi S, Teakle G, Plaha P, Kim J, Allender C, Beynon E, Piao Z, Soengas P, Han T, King G (2007) The reference genetic linkage map for the multinational Brassica rapa genome sequencing project. Theor Appl Genet 115:777–792

    Article  PubMed  CAS  Google Scholar 

  • Delourme R, Falentin C, Huteau V, Clouet V, Horvais R, Gandon B, Specel S, Hanneton L, Dheu JE, Deschamps M, Margale E, Vincourt P, Renard M (2006) Genetic control of oil content in oilseed rape (Brassica napus L.). Theor Appl Genet 113:1331–1345

    Article  PubMed  CAS  Google Scholar 

  • Doyle J, Doyle J (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15

    Google Scholar 

  • Fahey J, Florens HE (1995) The role of crucifers in cancer chemoprotection. In: Talalay P, Gustine DL (eds) Phytochemicals and health. American Society of Plant Physiologists, Rockville, MD, pp 87–93

    Google Scholar 

  • Gupta PK, Varshney RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113:163–185

    Article  CAS  Google Scholar 

  • Hasan M, Seyis F, Badani A, Pons-Kühnemann J, Friedt W, Lühs W, Snowdon R (2006) Analysis of genetic diversity in the Brassica napus L. gene pool using SSR markers. Genet Resour Crop Evol 53:793–802

    Article  CAS  Google Scholar 

  • Hong C, Plaha P, Koo D, Yang T, Choi S, Lee Y, Uhm T, Bang J, Edwards D, Bancroft I (2006) A survey of the Brassica rapa genome by BAC-end sequence analysis and comparison with Arabidopsis thaliana. Mol Cells 22:300–307

    PubMed  Google Scholar 

  • Hong C, Piao Z, Kang T, Batley J, Yang T, Hur Y, Bhak J, Park B, Edwards D, Lim Y (2007) Genomic distribution of simple sequence repeats in Brassica rapa. Mol Cells 23:349–356

    PubMed  CAS  Google Scholar 

  • Hopkins CJ, Cogan NOI, Hand M, Jewell E, Kaur J, Li X, Lim GAC, Ling AE, Love C, Mountford H, Todorovic M, Vardy M, Spangenberg GC, Edwards D, Batley J (2007) Sixteen new simple sequence repeat markers from Brassica juncea expressed sequences and their cross-species amplification. Mol Ecol Notes 7:697–700

    Article  CAS  Google Scholar 

  • Iniguez-Luy F, Voort A, Osborn T (2008) Development of a set of public SSR markers derived from genomic sequence of a rapid cycling Brassica oleracea L. genotype. Theor Appl Genet 117:977–985

    Article  PubMed  CAS  Google Scholar 

  • Iniguez-Luy F, Lukens L, Farnham M, Amasino R, Osborn T (2009) Development of public immortal mapping populations, molecular markers and linkage maps for rapid cycling Brassica rapa and B. oleracea. Theor Appl Genet 120:31–43

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Katari M, Balija V, Wilson R, Martienssen R, McCombie W (2005) Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana. Genome Res 15:496–504

    Article  PubMed  CAS  Google Scholar 

  • Katti M, Ranjekar P, Gupta V (2001) Differential distribution of simple sequence repeats in eukaryotic genome sequences. Mol Biol Evol 18:1161–1167

    PubMed  CAS  Google Scholar 

  • Kim H, Choi S, Bae J, Hong C, Lee S, Hossain M, Van Nguyen D, Jin M, Park B, Bang J (2009) Sequenced BAC anchored reference genetic map that reconciles the ten individual chromosomes of Brassica rapa. BMC Genomics 10:432

    Article  PubMed  Google Scholar 

  • Kosambi DD (1944) The estimation of map distance from recombination values. Ann Eugen 12:172–175

    Article  Google Scholar 

  • Kresovich S, Szewc-McFadden A, Bliek S, McFerson J (1995) Abundance and characterization of simple-sequence repeats (SSRs) isolated from a size-fractionated genomic library of Brassica napus L. (rapeseed). Theor Appl Genet 91:206–211

    Article  CAS  Google Scholar 

  • Lawson M, Zhang L (2006) Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes. Genome Biol 7:R14

    Article  PubMed  Google Scholar 

  • Lim Y, Plaha P, Choi S, Uhm T, Hong C, Bang J, Hur Y (2006) Toward unraveling the structure of Brassica rapa genome. Physiol Plant 126:585–591

    Article  CAS  Google Scholar 

  • Ling A, Kaur J, Burgess B, Hand M, Hopkins C, Li X, Love C, Vardy M, Walkiewicz M, Spangenberg G (2007) Characterization of simple sequence repeat markers derived in silico from Brassica rapa bacterial artificial chromosome sequences and their application in Brassica napus. Mol Ecol Notes 7:273–277

    Article  CAS  Google Scholar 

  • Liu HL (1983) Studies on the breeding of yellow-seeded Brassica napus. Proceedings of the 6th International Rapeseed Congress, Paris, France, pp 637–641

  • Lombard V, Delourme R (2001) A consensus linkage map for rapeseed (Brassica napus L.): construction and integration of three individual maps from DH populations. Theor Appl Genet 103:491–507

    Article  CAS  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 genomewide alignment with Arabidopsis. Genetics 177:2433–2444

    PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • McCouch SR, Teytelman L, Xu YB, Lobos KB, Clare K, Walton M, Fu BY, Maghirang R, Li ZK, Xing YZ, Zhang QF, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res 9:199–207

    Article  PubMed  CAS  Google Scholar 

  • Mitchell S, Kresovich S, Jester C, Hernandez C, Szewc-McFadden A (1997) Application of multiplex PCR and flourescence-based, semi-automated allele sizing technology for genotyping plant genetic resources. Crop Sci 37:617–624

    Article  CAS  Google Scholar 

  • Padmaja KL, Arumugam N, Gupta V, Mukhopadhyay A, Sodhi YS, Pental D, Pradhan AK (2005) Mapping and tagging of seed coat colour and the identification of microsatellite markers for marker-assisted manipulation of the trait in Brassica juncea. Theor Appl Genet 111:8–14

    Article  PubMed  CAS  Google Scholar 

  • Piquemal J, Cinquin E, Couton F, Rondeau C, Seignoret E, Doucet I, Perret D, Villeger M, Vincourt P, Blanchard P (2005) Construction of an oilseed rape (Brassica napus L.) genetic map with SSR markers. Theor Appl Genet 111:1514–1523

    Article  PubMed  CAS  Google Scholar 

  • Plieske J, Struss D (2001) Microsatellite markers for genome analysis in Brassica. I. Development in Brassica napus and abundance in Brassicaceae species. Theor Appl Genet 102:689–694

    Article  CAS  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

    Article  PubMed  CAS  Google Scholar 

  • Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:365–386

    PubMed  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  PubMed  CAS  Google Scholar 

  • Shoemaker RC, Grant D, Olson T, Warren WC, Wing R, Yu Y, Kim H, Cregan P, Joseph B, Futrell-Griggs M, Will N, Davito J, Walker J, Wallis J, Kremitski C, Scheer D, Clifton SW, Graves T, Nguyen H, Wu X, Luo M, Dvorak J, Nelson R, Cannon S, Tomkins J, Schmutz J, Stacey G, Jackson S (2008) Microsatellite discovery from BAC end sequences and genetic mapping to anchor the soybean physical and genetic maps. Genome 51:294–302

    Article  PubMed  CAS  Google Scholar 

  • Shultz J, Kazi S, Bashir R, Afzal J, Lightfoot D (2007) The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean. Theor Appl Genet 114:1081–1090

    Article  PubMed  CAS  Google Scholar 

  • Snowdon R, Lühs W, Friedt W (2006) Oilseed rape. In: Kole C (ed) Genome mapping and molecular breeding, vol 2: oilseeds. Springer Verlag, Heidelberg, pp 55–114

    Google Scholar 

  • Song Q, Shi J, Singh S, Fickus E, Costa J, Lewis J, Gill B, Ward R, Cregan P (2005) Development and mapping of microsatellite (SSR) markers in wheat. Theor Appl Genet 110:550–560

    Article  PubMed  CAS  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  PubMed  CAS  Google Scholar 

  • Suwabe K, Tsukazaki 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  PubMed  CAS  Google Scholar 

  • Suwabe K, Morgan C, Bancroft I (2008) Integration of Brassica A genome genetic linkage map between Brassica napus and B. rapa. Genome 51:169–176

    Article  PubMed  CAS  Google Scholar 

  • Szewc-McFadden A, Kresovich S, Bliek S, Mitchell S, McFerson J (1996) Identification of polymorphic, conserved simple sequence repeats (SSRs) in cultivated Brassica species. Theor Appl Genet 93:534–538

    Article  CAS  Google Scholar 

  • Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:1441–1452

    Article  PubMed  CAS  Google Scholar 

  • U N (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 (1999) Abundance, polymorphism and genetic mapping of microsatellites in oilseed rape (Brassica napus L.). Plant Breed 118:323–326

    Article  CAS  Google Scholar 

  • Van Ooijen JW, Voorrips RE (2001) JoinMap®3.0. Software for the calculation of genetic linkage maps. Plant Research International, Wageningen

    Google Scholar 

  • Varghese J, Rudolph B, Uzunova M, Ecke W (2000) Use of 5′-anchored primers for the enhanced recovery of specific microsatellite markers in Brassica napus L. Theor Appl Genet 101:115–119

    Article  CAS  Google Scholar 

  • Xiao S, Xu J, Li Y, Zhang L, Shi S, Wu J, Liu K (2007) Generation and mapping of SCAR and CAPS markers linked to the seed coat color gene in Brassica napus using a genome-walking technique. Genome 50:611–618

    Article  PubMed  CAS  Google Scholar 

  • Yang T, Kim J, Lim K, Kwon S, Kim J, Jin M, Park J, Lim M, Kim H, Kim S (2005) The Korea Brassica genome project: a glimpse of the Brassica genome based on comparative genome analysis with Arabidopsis. Comp Funct Genom 6:138–146

    Article  Google Scholar 

  • Yi G, Lee J, Lee S, Choi D, Kim B (2006) Exploitation of pepper EST–SSRs and an SSR-based linkage map. Theor Appl Genet 114:113–130

    Article  PubMed  CAS  Google Scholar 

  • Zhang X, Wessler S (2004) Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea. Proc Natl Acad Sci USA 101:5589–5594

    Article  PubMed  CAS  Google Scholar 

  • Zhang T, Yuan Y, Yu J, Guo W, Kohel R (2003) Molecular tagging of a major QTL for fiber strength in Upland cotton and its marker-assisted selection. Theor Appl Genet 106:262–268

    PubMed  CAS  Google Scholar 

  • Zhao JY, Becker HC, Zhang DQ, Zhang YF, Ecke W (2006) Conditional QTL mapping of oil content in rapeseed with respect to protein content and traits related to plant development and grain yield. Theor Appl Genet 113:33–38

    Article  PubMed  CAS  Google Scholar 

  • Zhou W, Kolb F, Bai G, Domier L, Boze L, Smith N (2003) Validation of a major QTL for scab resistance with SSR markers and use of marker-assisted selection in wheat. Plant Breed 122:40–46

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This research was supported by the National Key Basic Research and Development Plan of China (2006CB101600) and the National Science Foundation of China (30623012).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Kede Liu.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (XLS 412 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Li, H., Chen, X., Yang, Y. et al. Development and genetic mapping of microsatellite markers from whole genome shotgun sequences in Brassica oleracea . Mol Breeding 28, 585–596 (2011). https://doi.org/10.1007/s11032-010-9509-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11032-010-9509-y

Keywords

Navigation