Target Amplicon Sequencing for Genotyping Genome-Wide Single Nucleotide Polymorphisms Identified by Whole-Genome Resequencing in Peanut

Abstract

Genome-wide genotyping data regarding breeding materials are essential resources for improving breeding efficiency, especially in plants with complex genomes with a high degree of polyploidy. Several current breeding efforts in cultivated peanut ( L.), which has a tetraploid genome, are devoted to developing high oleic acid cultivars. Genetic maps for such breeding programs have been developed using simple-sequence repeat (SSR) markers, the use of which requires time-consuming electrophoretic analyses. Next-generation sequencing (NGS) technology can overcome this technical hurdle. Initially, we attempted double-digest restriction site-associated DNA sequencing on peanut breeding materials used to develop high oleic acid cultivars. However, this method was not effective because few single nucleotide polymorphism (SNPs) were available because of low genetic diversity of the lines. The genome sequences of the probable diploid ancestors of cultivated peanut, Krapov. & W. C. Greg. and Krapov. & W. C. Greg., are available. Therefore, we next employed whole-genome resequencing analysis to obtain genome-wide SNP data. In this analysis, we observed large biases in the numbers and genomic positions of interspecific and intraspecific SNPs. For genome-wide genotyping, we selected a subset of SNPs covering the peanut genome as the targets of amplicon sequencing analysis. Using this technique, genome-wide genotypes of the breeding materials were easily and rapidly determined. The SNP information and analytic methods developed in this study should accelerate genetics, genomics, and breeding in peanut.