Development and validation of simple sequence repeat markers from Arachis hypogaea transcript sequences

Simple sequence repeats (SSRs) are important molecular markers for assessing genetic diversity in Arachis hypogaea L. and many other crops and constructing genetic linkage maps for important agricultural traits. In this study, 29,357 potential SSRs were identified in 22,806 unigenes assembled from A. hypogaea transcript sequences. Of these unigenes, 1883 and 4103 were annotated and assigned in Kyoto Encyclopedia of Genes and Genomes Orthology and Eukaryotic Orthologous Groups databases, respectively. Among the SSR motifs, mono- (19,065; 64.94%) and trinucleotide (5033; 17.14%) repeats were the most common, and the three most dominant motifs were A/T (18,358; 62.54%), AG/CT (2804; 9.55%), and AAG/CTT (1396; 4.76%). Polymerase chain reaction (PCR) primer pairs were designed for 4340 novel SSR markers and 210 new SSRs were validated using 24 A. hypogaea varieties. Of the 210, 191 (91%) yielded PCR products, with 37 (18%) identifying polymorphisms. The 37 polymorphic SSR markers detected 146 alleles (2-10 alleles per locus), and the average polymorphic information content was 0.403 (with a range of 0.077 to 0.819). The new SSRs enrich the current marker resources for A. hypogaea and may also be useful for genetic diversity analysis, functional genomics research, and molecular breeding.