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Acta Agron Sin ›› 2014, Vol. 40 ›› Issue (07): 1213-1219.doi: 10.3724/SP.J.1006.2014.01213


Development and Universality Evaluation of EST-SSR Markers in Jute (Corchorus spp.) from GenBank Database

ZHANG Li-Wu**,YUAN Min-Hang**,HE Xiong-Wei,LIU Xing,FANG Ping-Ping,LIN Li-Hui,TAO Ai-Fen,XU Jian-Tang,QI Jian-Min*   

  1. Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops / College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
  • Received:2013-11-08 Revised:2014-03-04 Online:2014-07-12 Published:2014-04-08
  • Contact: 祁建民, E-mail: qijm863@163.com, Tel: 0591-87644898


Developing EST-SSR markers from GenBank Database is important in dissecting genetic base in jute. The aim of this study was to analyze SSR distribution in ESTs of jute, develop new EST-derived SSR markers, and validate polymorphisms of EST-SSR markers in jute. All 838 EST sequences of jute were downloaded from GenBank database. Sixty-six pairs of primers were screened by the software SSRPrimer and designed by the software Primer 3.0. The PCR products of these primers were detected by agarose gel electrophoresis. Polymorphism of six diverse accessions in jute was tested. Among these primers, 42 (63.6%) successfully amplified at least one clear and stable fragment from the jute genome and showed polymorphism between at least two diverse accessions. The polymorphic SSRs contained repeat motifs with (AT)n or (GC-)n, which could be regarded as the dominant motifs in jute. The EST-SSR markers in jute could be developed effectively, which can not only enrich the number of molecular markers, but also dissect genetic basis of important traits in jute.

Key words: Jute, EST, SSR, Marker development, Polymorphism

[1]熊和平. 麻类作物育种学. 北京: 中国农业科学技术出版社, 2008. pp 156–185

Xiong H P. Breeding Sciences of Bast and Leaf Fiber Crops. Beijing: China Agricultural Science and Technology Press, 2008. pp 156–185 (in Chinese)

[2]Rana M K, Arora K, Singh S, Singh A K. Multi-locus DNA fingerprinting and genetic diversity in jute (Corchorus spp.) based on sequence-related amplified polymorphism. J Plant Biochem Biotechnol, 2012, 22: 1–8

[3]Mir R R, Rustgi S, Sharma S, Singh R, Goyal A, Kumar J, Gaur A, Tyagi A, Khan H, Sinha M K, Balyan H S, Gupta P K. A preliminary genetic analysis of fibre traits and the use of new genomic SSRs for genetic diversity in jute. Euphytica, 2007, 161: 413–427

[4]Basu A, Ghosh M, Meyer R, Powell W, Basak S L, Sen S K. Analysis of genetic diversity in cultivated jute determined by means of SSR markers and AFLP profiling. Crop Sci, 2004, 44: 678–685

[5]Nishat S, Haseena K, Nadim A, Tofael K. Construction of an intraspecific linkage map of Jute. Asian J Plant Sci, 2006, 5: 758–762

[6]Das M, Banerjee S, Dhariwal R, Vyas S, Mir R, Topdar N, Kundu A, Khurana J, Tyagi A, Sarkar D, Sinha M, Balyan H, Gupta P. Development of SSR markers and construction of a linkage map in jute. J Genet, 2012, 91: 21–31

[7]Zhang L W, Li S P, Chen L, Yang G S. Identification and mapping of a major dominant quantitative trait locus controlling seeds per silique as a single Mendelian factor in Brassica napus L. Theor Appl Genet, 2012, 125: 695–705

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

[9]Russell J, Fuller J, Macaulay M, Hatz B, Jahoor A, Powell W, Waugh R. Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theor Appl Genet, 1997, 95: 714–722

[10]Pejic I, Ajmone-Marsan P, Morgante M, Kozumplick V, Castiglioni P, Taramino G, Motto M. Comparative analysis of genetic similarity among maize inbred lines detected by RFLPs, RAPDs, SSRs and AFLPs. Theor Appl Genet, 1998, 97: 1248–1255

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

[12]Li, H, Chen X, Yang Y, Xu J, Gu J, Fu J, Qian X, Zhang S, Wu J, Liu K. Development and genetic mapping of microsatellite markers from whole genome shotgun sequences in Brassica oleracea. Mol Breed, 2010, 28: 585–596

[13]Xu, J, Qian X, Wang X, Li R, Cheng X, Yang Y, Fu J, Zhang S, King G, Wu J, Liu K. Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa. BMC Genom, 2010, 11: 594–603

[14]周东新, 祁建民, 吴为人, 李维明. 黄麻DNA提取与RAPD反应体系的建立. 福建农业大学学报, 2001, 30: 334–339

Zhou D X, Qi J M, Wu W R, Li W M. Studies on DNA extraction and establishment of RAPD reaction system in jute. J Fujian Agric Univ, 2001, 30: 334–339 (in Chinese with English abstract)

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

[16]Goff S, Ricke D, Lan T, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange B, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun W, Chen L, Cooper B, Park S, Wood T, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller R M, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science, 2002, 296: 92–100

[17]张亚东, 彭婵, 李振芳, 杨彦伶, 胡兴宜. 基因组SSR与EST_SSR标记在杨树不同种间的遗传差异. 东北林业大学学报, 2011, 39(12): 8–11

Zhang Y D, Peng C, Li Z F, Yang Y L, Hu X Y. Genetic diversity of genomic- SSR and EST- SSR markers in interspecies of poplar. J Northeast For Univ, 2011, 39(12): 8–11 (in Chinese with English abstract)

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