Genome-wide polymorphism detection in peanut using next-generation restriction-site-associated DNA (RAD) sequencing

Peanut (Arachis hypogaea) is an important oilseed crop. Low genetic variability and limited genetic resources are major hurdles in the improvement of peanut. In this study, we used next-generation sequencing of restriction-site-associated DNA (RAD) fragments for genome-wide discovery of SNPs and SSRs in 11 diverse peanut genotypes. Reduced representation RAD libraries of 11 peanut genotypes were sequenced on Illumina HiSeq 2000 platform. A total of 102 million reads, approximately 10 Gb of sequence data, were collected. High-quality RAD sequence reads of genotype Tiffrunner and accession A. ipaensis were clustered to make a non-redundant set of representative sequences and to serve as a reference sequence for tetraploid peanuts and diploid peanuts, respectively. By using deep multiple alignment, a total of 15,678 SNPs in diploid peanuts and 3248 SNPs in cultivated peanuts were identified. These SNPs were also successfully used to reveal the genetic relationship between the peanut genotypes. In addition, 21,615 putative SSRs were also identified in the RAD sequences with an average of one SSR per 3.4 Kb. The most frequent SSR motifs identified in peanut genome were dinucleotide (67.6 %) followed by trinucleotide (14.6 %) and tetranucleotide (12.5 %) repeats. The high-throughput RAD sequencing allowed rapid genome-wide discovery of molecular markers in peanut. The large number of SNPs and SSRs identified in this study will be useful for constructing high-density genetic linkage maps, QTL analysis, marker-assisted selection and comparative studies in peanut.