Development and linkage mapping of unigene-derived microsatellite markers in Brassica rapa L

Breeding Science

Volumn 61, Issue 2, 2011, Pages 160-167

  Ge, Yu ^a   Ramchiary, Nirala ^b   Wang, Tao ^a   Liang, Cui ^a   Wang, Na ^a   Wang, Zhe ^a   Choi, Su Ryun ^b   Lim, Yong Pyo ^b   Piao, Zhong Yun ^a  

^a SHENYANG AGRICULTURAL UNIVERSITY   (China)

^b Chungnam National University   (South Korea)

Author keywords

Brassica rapa; Cross species transferability; Linkage map; UGMS markers

Indexed keywords

ANIMALIA; BRASSICA; BRASSICA JUNCEA; BRASSICA NAPUS; BRASSICA NIGRA; BRASSICA RAPA; BRASSICA RAPA SUBSP. RAPA;

EID: 79959646055     PISSN: 13447610     EISSN: 13473735     Source Type: Journal    
DOI: 10.1270/jsbbs.61.160     Document Type: Article

References (42)

1. Blanc, G., K. Hokamp and K.H. Wolfe (2003) A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res. 13: 137-144.
2. Castillo, A., H. Budak, R.K. Varshney, G. Dorado, A. Graner and P.Hernandez (2008) Transferability and polymorphism of barley EST-SSR markers used for phylogenetic analysis in Hordeum chilense. BMC Plant Biol. 8: 97.
3. Cheng, X.M., J. Xu, S. Xia, J. Gu, Y. Yang, J. Fu, X. Qian, S. Zhang, J.Wu and K. Liu (2009) Development and genetic mapping of microsatellite markers from genome survey sequences in Brassica napus. Theor. Appl. Genet. 118: 1121-1131.
4. Choi, S., G. Teakle, P. Plaha, J. Kim, C. Allender, E. Beynon, Z. Piao, P. Soengas, T. Han, G. King et al. (2007) The reference genetic linkage map for the multinational Brassica rapa genome sequencing project. Theor. Appl. Genet. 115: 777-792.
5. Chyi, Y.-S., M.E. Hoenecke and J.L. Sernyk (1992) A genetic linkage map of restriction fragment length polymorphism loci for Brassica rapa (syn. campestris). Genome 35: 746-757.
6. Guillemaut, P. and M.D. Laurence (1992) Isolation of plant DNA: a fast, inexpensive and reliable method. Plant Mol. Biol. Rep. 10: 60-65.
7. Hong, Y., X. Chen, X. Liang, H. Liu, G. Zhou, S. Li, S. Wen, C.C. Holbrook and B. Guo (2010) A SSR-based composite genetic linkage map for the cultivated peanut (Arachis hypogaea L.) genome. BMC Plant Biol. 10: 17.
8. Iniguez-Luy, F.L., A. Vande Voort and T.C. Osborn (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.
9. Iniguez-Luy, F.L., L. Lukens, M.W. Farnham, R.M. Amasino and T.C.Osborn (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.
10. Ishikawa, G., T. Nakamura, T. Ashida, M. Saito, S. Nasuda, T.R. Endo,
11. J.Z. Wu and T. Matsumoto (2008) Localization of anchor loci representing five hundred annotated rice genes to wheat chromosomes using PLUG markers. Theor. Appl. Genet. 118: 499-514.
12. Johnston, J.S., A.E. Pepper, A.E. Hall, Z.J. Chen, G. Hodnett, J. Drabek, R. Lopez and H.J. Price (2005) Evolution of genome size in Brassicaceae. Ann. Bot. London 95: 229-235.
13. Kaur, S., N.O.I. Cogan, G. Ye, R.C. Baillie, M.L. Hand, A.E. Ling, A.K.Mcgearey, J. Kaur, C.J. Hopkins, M. Todorovic et al. (2009) Genetic map construction and QTL mapping of resistance to blackleg (Leptosphaeria maculans) disease in Australian canola (Brassica napus L.) cultivars. Theor. Appl. Genet. 120: 71-83.
14. Kim, H.R., S.R. Choi, J.N. Bae, C.P. Hong, S.Y. Lee, M.J. Hossain, D.V. Nguyen, M.N. Jin, B.-S. Park, J.-W. Bang et al. (2009) Sequenced BAC anchored reference genetic map that reconciles the ten individual chromosomes of Brassica rapa. BMC Genomics 10: 432.
15. Kim, J.S., T.Y. Chung, G.J. King, M.N. Jin, T.-J. Yang, Y.-Mn. Jin, H.-I. Kimand and B.-S. Park (2006) A Sequence-Tagged Linkage Map of Brassica rapa. Genetics 174: 29-39.
16. Kosambi, D.D. (1944) The estimation of map distance from recombination values. Ann. Eugen. 12: 172-175.
17. Lagercrantz, U., H. Ellegren and L. Andersson (1993) The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucleic Acids Res. 21: 1111-1115.
18. Li, F., H. Kitashiba, K. Inaba and T. Nishio (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.
19. Lowe, A.J., A.E. Jones, A.F. Raybould, M. Trick, C.L. Moule and K.J.Edwards (2002) Transferability and genome specificity of a new set of microsatellite primers among Brassica species of the U triangle. Mol. Ecol. Notes 2: 7-11.
20. Lowe, A.J., C. Moule, M. Trick and K. Edwards (2004) Efficient largescale development of microsatellites for marker and mapping applications in Brassica crop species. Theor. Appl. Genet. 108: 1103-1112.
21. Morgante, M., M. Hanafey and W. Powell (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat. Genet. 30: 194-200.
22. Parida, S.K., K.A.R. Kumar, V. Dalal, N.K. Singh and T. Mohapatra (2006) Unigene derived microsatellite markers for the cereal genomes. Theor. Appl. Genet. 112: 808-817.
23. Parida, S.K., D.K. Yadava and T. Mohapatra (2010) Microsatellites in Brassica unigenes: relative abundance, marker design, and use in comparative physical mapping and genome analysis. Genome 53: 55-67.
24. Parkin, I.A.P., S.M. Gulden, A.G. Sharpe, L. Lukens, M. Trick, T.C. Osborn and D.J. Lydiate (2005) Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana. Genetics 171: 765-781.
25. Piquemal, J., E. Cinquin, F. Couton, C. Rondeau, E. Seignoret, I. Doucet, D. Perret, M.J. Villeger, P. Vincourt and P. Blanchard (2005) Construction of an oilseed rape (Brassica napus L.) genetic map with SSR markers. Theor. Appl. Genet. 111: 1514-1523.
26. Raji, A.A.J., J.V. Anderson, O.A. Koladel, C.D. Ugwul, A.G.O. Dixon and I.L. Ingelbrecht (2009) Gene-based microsatellites for cassava (Manihot esculenta Crantz): prevalence, polymorphisms, and cross-taxa utility. BMC Plant Biol. 9: 118.
27. Sanguinetti, C.J., E. Dias Neto and A.J. Simpson (1994) Rapid silver staining and recovery of PCR products separated on polyacrylamide gels. Biotechniques 17: 914-921.
28. Senthilvel, S., B. Jayashree, V. Mahalakshmi, P.S. Kumar, S. Nakka, T.Nepolean and C.T. Hash (2008) Development and mapping of simple sequence repeat markers for pearl millet from data mining of expressed sequence tags. BMC Plant Biol. 8: 119.
29. Sharma, R.K., P. Bhardwaj, R. Negi, T. Mohapatra and P.S. Ahuja (2009) Identification, characterization and utilization of unigene derived microsatellite markers in tea (Camellia sinensis L.). BMC Plant Biol. 9: 53.
30. Soengas, P., P. Hand, J.G. Vicente, J.M. Pole and D.A.C. Pink (2007) Identification of quantitative trait loci for resistance to Xanthomonas campestris pv. campestris in Brassica rapa.Theor. Appl. Genet. 114: 637-645.
31. Song, K.M., J.Y. Suzuki, M.K. Slocum, P.H. Williams and T.C. Osborn (1991) A linkage map of Brassica rapa (syn. campestris) based on restriction fragment length polymorphism loci. Theor. Appl. Genet. 82: 296-304.
32. Stam, P. (1993) Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. Plant J. 3: 739-744.
33. Suwabe, K., H. Iketani, T. Nunome, T. Kage and M. Hirai (2002) Isolation and characterization of microsatellites in Brassica rapa L. Theor. Appl. Genet. 104: 1092-1098.
34. Suwabe, K., H. Iketani, T. Nunome, A. Ohyama, M. Hirai and H. Fukuoka (2004) Characteristics of microsatellites in Brassica rapa genome and their potential utilization for comparative genomics in Cruciferae. Breed. Sci. 54: 85-90.
35. Suwabe, K., H. Tsukazaki, H. Iketani, K. Hatakeyama, M. Kondo, M.Fujimura, T. Nunome, H. Fukuoka, M. Hirai and S. Matsumoto (2006) Simple sequence repeat-based comparative genomics between Brassica rapa and Arabidopsis thaliana: the genetic origin of clubroot resistance. Genetics 173: 309-319.
36. Teutonico, R.A. and T.C. Osborn (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.
37. Uzunova, M.I. and W. Ecke (1999) Abundance, polymorphism and genetic mapping of microsatellites in oilseed rape (Brassica napus L.). Plant Breed. 118: 323-326.
38. Van Ooijen, J.W. and R.E. Voorrips (2001) JoinMap Version 3.0: software for the calculation of genetic linkage maps. CPRO-DLO, Wageningen.
39. Varshney, R.K., S. Nayak, B. Jayashree, K. Eshwar, H.D. Upadhyaya and D.A. Hoisington (2004) Development of cost-effective SNP assays for chickpea genome analysis and breeding. J. SAT Agric. Res. 3: 1.
40. Varshney, R.K., A. Graner and M.E. Sorrells (2005) Genetic microsatellite markers in plants: features and applications. Trends in Biotech. 23: 48-55.
41. Voorrips, R.E. (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J. Hered. 93: 77-78.
42. Yang, T.J., J.S. Kim, K.B. Lim, S.J. Kown, J.A. Kim, M. Jin, J.Y. Park, M.N. Lim, H.I. Kim, S.H. Kim et al. (2005) The Korea Brassica Genome Project: A glimpse of the Brassica gemone based on comparative genome analysis with Arabidopsis. Comp. Funct. Genom. 6: 138-146.