Abstract:Brassica napus (AACC, 2n=38) is the most widespread oil crop in China. As single nucleotide polymorphism (SNP) is the most important molecular marker technology, it is extremely important to study on SNP in understanding the forward genetics. In the past five years, the genome sequences of B. napus and its ancestry species, named Brassica rapa and Brassica oleracea, had been successfully assembled and released that could enable efficient study regarding SNP and its role in the genetic study of oilseed rape. This review summarized the biological characteristics and the techniques developed for studying SNP, highlighting the pivotal role of SNP in linkage map construction and association mapping in rapeseed. Moreover, it further signifies the importance of SNP in terms of germplasms' population structure as well as evolution analysis and marker associated breeding, which can provide researchers a better understanding regarding the value of SNP study in B. napus.
周龙华 蒋立希. SNP分子标记及其在甘蓝型油菜中应用的研究进展[J]. , 2016, 24(10): 1608-1616.
Zhou Longhua. SNP Molecular Marker and Research Progress of Its Application in Brassica napus. , 2016, 24(10): 1608-1616.
[1]杜海, 郎春秀, 王伏林, 陈锦清, 吴关庭.油菜种子油酸含量的遗传改良[J].核农学报, 2011, 25(6):1179-1183
[2]谭祖猛, 李云昌, 胡琼, 徐育松, 李英德.SSR和SRAP 标记研究油菜杂交种骨干亲本的遗传多样性[J].农业生物技术学报, 2009, 17(5):882-890
[3]周庆红, 曾勇军, 黄英金.油菜开花期QTL图谱整合及开花候选基因挖掘[J].核农学报, 2014, 28(4):0577-0585
[4]Batley J, Batley J, Hopkins C. J, Cogan N. O. I, Hand M, Jewell E, Kaur J.Identification and characterization of simple sequence repeat markers from Brassica napus expressed sequences[J].Molecular Ecology Notes, 2007, 7(5):886-889
[5]Batley J, Jewell E, Edwards D.Automated discovery of single nucleotide polymorphism and simple sequence repeat molecular genetic markers[J].Methods in Molecular Biology, 2007, 406(1):473-494
[6]Bus A, Korber N, Parkin I. A. P, Samans B, Snowdon R. J, Li J. Q, Stich B.Species- and genome-wide dissection of the shoot ionome in Brassica napus and its relationship to seedling development[J].Frontiers in Plant Science, 2014, 5(1):485-492
[7]Chalhoub B, Denoeud F, Liu S, Parkin I. A, Tang H, Wang X, Chiquet J, Belcram H, Tong, C, et al.Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome[J].Science, 2014, 345(6199):950-953
[8]Chen M. X, Xuan L. J, Wang Z, Zhou L. H, Li Z. L, Du X, Ali E, Zhang G. P, Jiang L. X..TRANSPARENT TESTA8 Inhibits Seed Fatty Acid Accumulation by Targeting Several Seed Development Regulators in Arabidopsis[J].Plant Physiology, 2014, 165(2):905-916
[9]Dalca, A.V. and M. Brudno. .Genome variation discovery with high-throughput sequencing data[J].Briefings in Bioinformatics, 2010, 11(1):3-14
[10]Duran C, Appleby N, Clark T, Wood D, Imelfort M, Batley J, Edwards D.AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants[J].Nucleic Acids Research, 2009, 37(1):951-953
[11]Durstewitz G, Polley A, Plieske J, Luerssen H, Graner E. M, Wieseke R, Ganal M. W..SNP discovery by amplicon sequencing and multiplex SNP genotyping in the allopolyploid species Brassica napus[J].Genome, 2010, 53(11):948-956
[12]Fourmann M, Barret P, Froger N, Baron C, Charlot F, Delourme R, Brunel D..From Arabidopsis thaliana to Brassica napus: development of amplified consensus genetic markers (ACGM) for construction of a gene map[J].Theoretical and Applied Genetics, 2002, 105(8):1196-1206
[13]Fritsche S, Wang X. X, Li J. Q, Stich B, Kopisch-Obuch F. J, Endrigkeit J, Leckband G, Dreyer F, Friedt W, Meng J. L, Jung C..A candidate gene-based association study of tocopherol content and composition in rapeseed (Brassica napus)[J].Frontiers in Plant Science, 2012, 3(129):1-24
[14]Ganal M. W, Polley A, Graner E. M, Plieske J, Wieseke R, Luerssen H, Durstewitz G.Large SNP arrays for genotyping in crop plants[J].Journal of Biosciences, 2012, 37(5):821-828
[15]Ganal M. W, Polley A, Graner E. M, Plieske J, Wieseke R, Luerssen H, Durstewitz G..Large SNP arrays for genotyping in crop plants[J].Journal of Biosciences, 2012, 37(5):821-828
[16]Hayward Alice, Mason Annaliese S, Dalton-Morgan Jessica, Zander Manuel, Edwards David, Batley Jacqueline. .SNP discovery and applications in Brassica napus[J].Journal of Plant Biotechnology, 2012, 39(1):49-61
[17]Imelfort M, Duran C, Batley J, Edwards D.Discovering genetic polymorphisms in next-generation sequencing data[J].Plant Biotechnology Journal, 2009, 7(4):312-317
[18]Korber N, Bus A, Li J, Higgins J, Bancroft I, Higgins E. E, Parkin I. A, Salazar-Colqui B, Snowdon R. J, Stich B..Seedling development traits in Brassica napus examined by gene expression analysis and association mapping[J].Bmc Plant Biology, 2015, 15(1):136-139
[19]Liu S, Liu Y, Yang X, Tong C, Edwards D, Parkin I. A, Zhao M, Ma J, Yu J.The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes[J].Nature Communications, 2014, 5(1):3930-3933
[20]Li F, Chen B. Y, Xu K, Wu J. F, Song W. L, Gao G. Z, Li J, Li H, Xiao X, Zhang T. Y, Wu X. M.Genome-Wide Association Study Dissects the Genetic Architecture of Seed Weight and Seed Quality in Rapeseed (Brassica napus L.)[J].DNA Research, 2014, 21(4):355-367
[21]Luo X, Ma C. Z, Yue Y, Hu K. N, Li Y. Y, Duan Z. Q, Wu M, Tu J. X, Shen J. X, Yi B, Fu T. D.Unravelling the complex trait of harvest index in rapeseed (Brassica napus L.) with association mapping[J].BMC Genomics, 2015, 16(1):379-381
[22]Li Feng, Chen Biyun, Xu Kun, Li Jun, Li Hao, Li Lixia, Xiao Xin, Zhang Tianyao, Nishio Takeshi, Wu Xiaoming..A genome-wide association study of plant height and primary branch number in rapeseed (Brassica napus)[J].Plant Science, 2016, 242(1):169-177
[23]Mohan M, Nair S, Bhagwat A, Krishna T. G, Yano M, Bhatia C. R, Sasaki T. .Genome mapping, molecular markers and marker-assisted selection in crop plants[J].Molecular Breeding, 197, 3(2):87-103
[24]Snowdon R.J. and Friedt W..Molecular markers in Brassica oilseed breeding: current status and future possibilities[J].Plant Breeding, 2004, 123(1):1-8
[25]Stokes D, Fraser F, Morgan C, O'Neill C. M, Dreos R, Magusin A, Szalma S, Bancroft I..An association transcriptomics approach to the prediction of hybrid performance[J].Molecular Breeding, 2010, 26(1):91-106
[26]Schiessl S, Iniguez-Luy F, Qian W, Snowdon R. J..Diverse regulatory factors associate with flowering time and yield responses in winter-type Brassica napus[J].BMC Genomics, 2015, 16(1):737-741
[27]Wang N. A, Shi L, Tian F, Ning H. C, Wu X. M, Long Y, Meng J. L..Assessment of FAE1 polymorphisms in three Brassica species using EcoTILLING and their association with differences in seed erucic acid contents[J].Bmc Plant Biology, 2010, 10(1):137-141
[28]Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun J. H.The genome of the mesopolyploid crop species Brassica rapa[J].Nature Genetics, 2011, 43(10):1035-1039
[29]Wang N. A, Qian W, Suppanz I, Wei L. J, Mao B. Z, Long Y, Meng J. L, Muller A. E, Jung, C..Flowering time variation in oilseed rape (Brassica napus L.) is associated with allelic variation in the FRIGIDA homologue BnaA.FRI.a[J].Journal of Experimental Botany, 2011, 62(15):5641-5658
[30]Wurschum T, Maurer H. P, Dreyer F, Reif J. C. .Effect of inter- and intragenic epistasis on the heritability of oil content in rapeseed (Brassica napus L.)[J].Theoretical Applied Genetics, 2013, 126(2):435-441
[31]Wang Z, Chen M, Chen T, Xuan L, Li Z, Du X, Zhou L, Zhang G, Jiang L..TRANSPARENT TESTA2 regulates embryonic fatty acid biosynthesis by targeting FUSCA3 during the early developmental stage of Arabidopsis seeds[J].Plant Journal, 2014, 77(5):757-769
[32]Wang J, Jian H, Wei L, Qu C, Xu X, Lu K, Qian W, Li J, Li M, Liu L..Genome-Wide Analysis of Seed Acid Detergent Lignin (ADL) and Hull Content in Rapeseed (Brassica napus L.)[J].PLoS One, 2015, 10(12):e0145045-e0145046
[33]Wei L, Jian H, Lu K, Filardo F, Yin N, Liu L, Qu C, Li W, Du H, Li J..Genome-wide association analysis and differential expression analysis of resistance to Sclerotinia stem rot in Brassica napus[J].Plant Biotechnology Journal, 2015, 1(1):1-13
[34]Xu L, Hu K, Zhang Z, Guan C, Chen S, Hua W, Li J.Genome-wide association study reveals the genetic architecture of flowering time in rapeseed (Brassica napus L.)[J].DNA Research, 2015, 1(1):1-10
[35]Zhu C. S, Gore M, Buckler E. S, Yu J. M..Status and Prospects of Association Mapping in Plants[J].Plant Genome, 2008, 1(1):5-20
[36]Zou J, Zhu J, Huang S, Tian E, Xiao Y, Fu D, Tu J, Fu T, Meng J. .Broadening the avenue of intersubgenomic heterosis in oilseed Brassica[J].Theoretical Applied Genetics, 2010, 120(2):283-290
[37]Zhang J, Mason A. S, Wu J, Liu S, Zhang X, Luo T, Redden R, Batley J, Hu L, Yan G. .Identification of Putative Candidate Genes for Water Stress Tolerance in Canola (Brassica napus)[J].Frontiers in Plant Science, 2015, 6(1):1058-1061
[38]Zhou L. H, Li Y. L, Hussain N, Li Z. L, Wu D. Z, Jiang, L. X. .Allelic Variation of BnaC.TT2.a and Its Association with Seed Coat Color and Fatty Acids in Rapeseed (Brassica napus L.)[J].PLoS One, 2016 , 11(1):1932-1936