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Acta Agron Sin ›› 2010, Vol. 36 ›› Issue (3): 410-421.doi: 10.3724/SP.J.1006.2010.00410

• CROP GENETICS & BREEDING · GERMPLASM RESOURCES · MOLECULAR GENETICS • Previous Articles     Next Articles

Development and Utiligaiton of Orthologous SSR Markers in Arachis through Soybean (Glycine max) EST

HONG Yan-Bin,CHEN Xiao-Ping,LIU Hai-Yan,ZHOU Gui-Yuan,LI Shao-Xiong,WEN Shi-Jie,LIANG Xuan-Qiang*
  

  1. Crops Research Institute, Guangdong Academy of Agricultural Sciences, Wushan 510640, China
  • Received:2009-10-12 Revised:2009-12-08 Online:2010-03-12 Published:2009-12-21
  • Contact: LIANG Xuan-Qiang, E-mail: liang804@yahoo.com; Tel: 020-87597315

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Abstract:

Lack of sufficient molecular markers hindered current genetic research in peanuts (Arachis hypogaea L.). It is necessary to enrich molecular markers for potential use in peanut breeding programs. Recently, EST-SSRs have received much attention with the higher level of transferability to closely related species and it can be rapidly developed from EST database by data mining at low cost. In this study, we mined SSRs from the soybean EST and analyzed their transferability in peanuts (Arachis hypogaea L.) and its wild species. A total of 394 370 soybean ESTs were clustered to generate 82 614 Uni-ESTs, 2 082 ESTs of which contained 2 191 SSRs with 1 SSR in 22.96 kb EST. Di-nucleotide motif (63.5%), followed by tri-nucleotide (30.9%), were the most abundant in soybean EST-SSR. The top two motif sequence types with high frequency were AG/CT (35.8%) and AT/AT (25.4%). Based on the 2082 SSR-ESTs, a total of 685 primer pairs were successfully designed and synthesized to test the amplification in four soybean cultivars. There were 582 primer pairs amplified effectively in soybean cultivars, 98 of which exhibited polymorphism. The cross-transferability of soybean EST-SSR was different among nine sections in Arachis, ranging from 12.4% to 15.7% with an average of 14.2%. Polymorphism analysis in Arachis section showed that 69 of the 79 orthologous SSR markers displayed polymorphsim in ten wild species, while only five markers had polymorphism in 22 cultivars. The PCR bands amplified in soybean and Arachis section by primer ES-105 were cloned and sequenced. The results revealed that the polymorphism among two soybean cultivarswas caused by little variation in SSR motif (AT)n, while the polymorphsim between soybean and Arachis section was contributed not only by the indel in SSR loci, but also by the frequence of the indel and substitution in franking region.The work indicated that the development of orthologous SSR markers for Arachis from soybean EST is feasible. There was a high level of polymorphism in Arachis sections for soybean-derived EST-SSR, therefore, the research of comparative genomics of Glycine and Arachis can be performed due to the high transferability of functional molecular markers.

Key words: Soybean, Arachis, EST, SSR

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