Identification of SNP Variants Among Peanut (Arachis hypogaea L.) Cultivars, and Germplasm Accessions, and Wild Species By Illumina Sequencing

Understanding the complex genome of peanut is important for addressing crop productivity limited by biotic and abiotic stresses. Advances in sequencing technologies have provided opportunities to study complex transcriptomes with lower costs and enhanced power for identifying genetic variability. In this study, we used a diverse panel of 22 Arachis accessions representing seven Arachis hypogaea market classes, A-, B-, and K- genome diploids, a synthetic amphidiploid, and a tetraploid wild species to sequence the pod, leaf, and root transcriptomes for polymorphism detection. De novo assembly of quality-filtered sequences generated from 39,349 to 74,615 transcripts for tetraploids and from 31,800 to 44,635 for diploids, with an average N50 of 1376bp. The realignment of individual reads to contigs of the cultivar OLin enabled the detection of ca. 292,000 bi-allelic SNPs across all 22 genotypes. Diversity analysis based on these variants indicated grouping according to species and genome classifications.  The number of SNPs of A. hypogaea accessions compared to OLin ranged from 3,411 to 11,138; comparison of wild species to OLin identified 97,754 SNPs (for A. ipaensis), 111,370 (A. duranensis), and 171,777 (A. batizocoi).  Cluster analysis indicated that sequences of B genome diploid species were closest to the tetraploids, flowed by A genome species, then K genome species.  These data will serve as a valuable resource for gene identification and creating a catalog of allelic variants of peanut genes, and will also aid in marker-assisted breeding.