|
|
|
| Development of Simple Sequence Repeat(SSR) and Insertion/Deletion(InDel) Markers in Chinese Cabbage(Brassica rapa ssp. pekinesis) and Analysis of Their Transferability |
|
|
|
|
Abstract In order to analyze the SSR distribution in genomic sequence of Brassica rapa and develop new SSR markers, the DNA sequences of Chinese cabbage A10(16899818~17299817) were screened using SSRHunter software and 394 Simple sequence repeats(SSRs) were mined with an average distance of 1.02 kb. Dinucleotide and trinucleotide repeat SSRs were the dominant types, accounting for 79.44% and 18.78%, respectively, of the SSR obtained. In order to improve the accuracy and to test the transferability of the developed SSRs, the mined SSRs were blasted and 15 SSR sequences were selected and primers were designed. Morever, some differences of Insertion/Deletion(InDels) rather than SSRs were found in some SSRs sequences and 19 InDels primers were designed. The 34 resultant primer pairs were used for polymorphism analysis in 6 genotypes of Chinese cabbage(Brassica rapa ssp. pekinesis). Twenty eight primer pairs had expected PCR products, accounting for 82.35% of designed primers, and 27 primer pairs showed polymorphisms, accounting for 79.41% of the designed primers. PCR products from 4 random SSR primer pairs were used for sequence analysis. The results showed that 100% of the fragments contained target SSRs. The percentage of available SSRs and InDels amplified in cabbage(B. oleracea), rapeseed(B. napus) and radish(Raphanus sativus) samples were 85.71%, 100% and 77.78%, respectively. It showed that these SSRs and InDels had good polymorphisms and transferability among Brassicaceae. A subset of 6 validated primers was also used to assess genetic diversity in a collection of 48 elite Brassicaceae germplasms. The dendrogram revealed that all germplasms were obviously classified into 3 groups, including Brassica rapa and Brassica oleracea, Raphanus sativus and Brassica napus, and the result accorded with the conventional taxonomy. The SSR and InDel markers can be used in genetic analysis of Brassica rapa.
|
|
Received: 14 May 2012
Published: 26 November 2018
|
|
|
|
| Cardle L.，Ramsay L.，Milbourne D.，Macaulay M.，Marshall D. and Waugh R.，2000. Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics，156：847~854Claire A.，Maurizio R.，Jody M. and Robert J. H.，2002. The application of SSRs characterized for grape (Vitis vinifera ) to conservation studied in vitaceae. American Journal of Botany，89：22~28Cui X. M.，Hou X. L. and Dong Y. X.，2005. Development of SSR primers of non-heading Chinese cabbage and transferability among closely Related species. Science & Technology Review，23：20~23（崔秀敏，侯喜林，董玉秀，2005.不结球白菜SSR引物的高效开发及其通用性研究.科技导报，23：20~23）Ge J，Xie H.，Cui C. S.，Hong J. M. and Ma R. C.，2005. Analysis of expressed sequence tags (ESTs) derived SSR markers in Chinese cabbage (Brassica campestris L.ssp. pekinensis). Journal of Agricultural Biotechnology，13 (4): 423~428（葛佳，谢华，崔崇士，2005.大白菜表达序列标签 SSR标记分析.农业生物技术学报， 13 (4)：423~428）Gupta P. K.，Balyan H. S.，Sharma P. C. and Ramesh B.，1996. Microsatellites in plants：A new class of molecular markers. Current Science，70 (1)：45~54Gupta P. K.，Rustgi S.，Sharma S.，Singh R.，Kumar N. and Balyan H. S.，2003. Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Molecular Genetics and Genomics，270：315~323Hormaza J. I.，2002. Molecular characterization and similarity relationships among apricot (Prunus armeniaca L.) genotypes using simple sequence repeats. Theoretical and Applied Genetics，104(2-3)：321~328Jia X. P.，Shi Y. S.，Song Y. C.，Wang G. Y.，Wang T. Y. and Li Y.，2007. Development of EST-SSR in foxtail millet （Setaria italica）. Genetic Resources and Crop Evolution，54：233~236Kantety R. V.，Rota M. L.，Matthews D. E. and Sorrells M. E.，2002. Data mining for simple sequence repeats in expressed sequence tags from barley maize，rice，sorghum and wheat. Plant Molecular Biology，48：501~510Katherine A. S. and Rob O.，2008. InDel markers distinguish Basmatis from other fragrant rice varieties. Field Crops Research，105：81~87Li X. B.，Zhang M. L. and Cui H. R.，2007. Analysis of SSR information in EST resource of oilseed rape．Chinese Journal of Oil Crop Sciences，29(1)：20~25（李小白，张明龙，崔海瑞，2007. 油菜EST资源的SSR信息分析.中国油料作物学报，29(1)：20~25）Pan C. H. and Li A.，2008. InDel and SNP Markers and Their Applications in Map-based Cloning of Rice Genes. Rice Science，15(4)：251~258Poncet V.，Rondeau M.，Tranchant C.，Cayrel A.，Hamon S. and Kochko A.，2006. SSR mining in coffee tree EST databases：Potential use of EST-SSRs as markers for the Coffea genus. Molecular Genetics and Genomics，276：436~449Powell W.，Machray G. C. and Provan J.，1996. Polymorphism revealed by simple sequence repeats. Trends in Plant Science，1 (7)：215~222Rassmann K.，Schl?tterer C. and Tautz D.，1991. Isolation of simple sequence loci for use in polymerase chain reaction-based DNA fingerprinting. Electrophoresis，12 (2-3)：113~118ShangGuan L. F.，Li X. Y.，Ning N.，Wang Y. Z.，Zhang Z. and Fang J. G.，2011. Development of EST-SSR Markers in Apricot. Acta Horticulturae Sinica，38(1)：43~54（上官凌飞，李晓颖，宁宁，王玉柱，章镇，房经贵，2011.杏 EST-SSR 标记的开发.园艺学报，38(1)：43~54）Song K. M. and Suzuki J. Y.，1991. A linkage map of Brassica rapa (syn.campestris) based on restriction fragment length polymorphism loci. Theoretical and Applied Genetics，82(3)：296~304Tautz D.，Schl?tterer C.，1994. Simple sequences. Current Opinion in Genetics & Development，4 (6)：832~837Tuskan G. A.，Gunter L. E.，Yang Z. M.，Yin T. M.，Sewell M. M. and DiFazio S. P.，2004. Characterization of microsatellites revealed by genomic sequencing of Populus trichocarpa. Canadian Journal of Forest Research，34：85~93Varshney R. K.，Graner A. and Sorrells M. E.，2005. Genic microsatellite markers in plants：Features and applications. Trends in Biotechnology，23(1)：48~55Wang Q.，Zhang L. G.，Zhang Z. F.，Hui M. X. and Zhang M. K.，2006. RAPD analysis of the crossing rate of the spring Chinese cabbage variety Guanchun. Acta Botanica Boreali-Occidentalia Sinica，26(4)：677~682（王绮，张鲁刚，张战凤，惠麦侠，张明科，2006.大白菜杂交种‘冠春’杂交率的 RAPD 分析. 西北植物学报，26(4)：677~682）Wang X. C.，Jiang S. L.，ShangGuan L. F.，Cao Y. F.，Qiao Y. S.，Zhang Z. and Fang J. G.，2010. Development of EST-derived SSR markers for pear and evaluation of their application in pear genetic diversity analysis. Scientia Agricultura Sinica，43(24)：5079~5087（王西成，姜淑苓，上官凌飞，曹玉芬，乔玉山，章镇，房经贵，2010.梨 EST-SSR 标记的开发及其在梨品种遗传多样性分析中的应用评价.中国农业科学，43(24)：5079~5087）Xu M. and Li H. G.，2008. Development and characterization of microsatellite markers from expressed sequence tags for liriodendron. Molecular Plant Breeding，6(3)：615~618（胥猛，李火根，2008.鹅掌楸EST-SSR引物开发及通用性分析.分子植物育种，6(3)：615~618）Yang X. and Yu Y. J.，2007. Linkage map construction and quantitative trait loci analysis for bolting based on a double haploid population of Brassica rapa. Journal of Integrative P1ant Biology，49(5)：664~671 |
|
|
|
