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Acta Agron Sin ›› 2009, Vol. 35 ›› Issue (2): 246-254.doi: 10.3724/SP.J.1006.2009.00246

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

Characterization and Application of EST-SSRs in Peanut(Arachis hypogaea L.)

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

  1. Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640,Guangdong,China
  • Received:2008-04-21 Revised:2008-09-11 Online:2009-02-12 Published:2008-12-10

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Abstract:

Peanut (Arachis hypogaea L.) is one of the most important oilseed crops in China. Although there is a great difference in growth habit, growth stage, and agronomic traits for peanuts, there is little polymorphism on the molecular level of RFLP, RAPD and AFLP. With development of peanut EST, a vast amount of available EST sequence has been documented. The objective of this study was to investigate distribution characteristics of EST-SSRs. Developed with a total of 20 160 EST from cDNA library of two peanut cultivars, There were 651 SSR-containing EST identified, on average, one SSR had 6.8 kb of EST sequence with tri-nucleotide motif (62.8%) as the most abundant motif types followed by di- (33.6%), tetra- (1.9%), hexa- (0.8%) and penta-nucleotide (0.8%). The top six motif types with high frequency included AG/TC (25.8%), AAG/TTC (19.1%), AAT/TTA (10.1%), ACC/TGG (7.4%), ACT/TGA (7.0%) and AT/TA (6.1%). Based on the 651 SSR-EST, a total of 233 primer pairs were successfully designed and a subset (100 pairs) were synthesized to test the amplification and polymorphism in 22 peanut cultivars, and to assess the transferability among 16 different wild species. The results showed that 86 primer pairs were amplified effectively in peanut cultivars, 10 primer pairs of which exhibited polymorphism with 2–3 alleles, with an average of 2.2 alleles, were detected. The cross-transferability of cultivated peanut EST-SSR markers to peanut wild species was very high, ranging from 12.5 to 100% with an average of 96%. Seventy-six markers exhibited polymorphism in wild species with 2–9 alleles, and an average of 4.06 alleles. The results indicated that peanut EST could be a resource for developing SSR. The high level of transferability to wild species also implied that EST-SSR is a potentially useful marker for genetic studies in wild species.

Key words: Peanut(Arachis hypogaea :.), EST, mining, SSR

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