ARS | Publication request: ESTs are a rich source of polymorphic SSRs for genomics and molecular breeding applications in peanut

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: December 1, 2007
Publication Date: January 11, 2008
Citation: Khanal, S., Tang, S., Beilinson, V., Miguel, P.S., Guo, B., Nielsen, N., Stalker, T., Cordonnier-Pratt, M., Pratt, L.H., Johnson, V.E. 2008. ESTs are a rich source of polymorphis SSRs for genomics and molecular breeding applications in peanut [abstract]. Proceedings of the Plant and Animal Genome XVI Conference, January 11-15, 2008, San Diego, California. p. 135.

Technical Abstract: Narrow genetic diversity and a deficiency of polymorphic DNA markers have hindered genetic mapping and the application of genomics and molecular breeding approaches in cultivated peanut (Arachis hypogaea L.). We developed and mined a peanut EST database for simple sequence repeats (SSRs), assessed the frequency of polymorphic SSRs in ESTs, and initiated the development of several hundred EST-SSR markers with the goal of breaking the DNA marker bottleneck in cultivated peanut. We assembled 84,229 ESTs into 26,809 unigenes, identified 4,470 perfect repeats, designed and tested primers for a broad spectrum of SSR motifs and repeat lengths, and screened 58 EST-SSR markers for polymorphisms among 28 tetraploid germplasm accessions (primarily Runner, Virginia, Spanish, and Valencia cultivars) and four diploid germplasm accessions (the parents of A. duranensis and A. batizocoi mapping populations). SSRs longer than 26 bp were two-fold more polymorphic than SSRs shorter than 26 bp. SSRs in exons and UTRs were equally polymorphic. Of the 58 EST-SSR markers, 55 (94.8%) were polymorphic, 32 (55.2%) were polymorphic in cultivated peanut (mean heterozygosity was 0.18), 27 (46.6%) were polymorphic in four cultivated peanut mapping populations, and 48 (82.8%) were polymorphic in two diploid mapping populations. ESTs are a rich source of polymorphic SSRs in peanut, and the frequency of polymorphic EST-SSRs seems to be more than sufficient for developing a critical mass of DNA markers for genomics and molecular breeding applications in cultivated peanut.