Chromosome regions linked to peanut black pod revealed by QTL-seq

Abstract The peanut black pod (BP) trait is controlled by a single dominant gene as revealed by a previous genetic study. However, the gene controlling BP is still unknown. In this study, a bulk segregant analysis aided by QTL-seq was utilized to identify genomic regions controlling the BP trait. A population of peanut segregating for the BP trait was developed by crossing a BP line and FloRun™ ‘331’ without BP trait. DNA samples of homozygous F2 lines of normal pod coloration and homozygous F2 lines of BP (homozygosity was validated by F3 plots) were equally pooled for deep sequencing together with the parental lines. A total of 220,714 single nucleotide polymorphisms (SNP) were found between the plants of BP and normally colored pods. Following the QTLseq pipeline, the ΔSNP-index and G′ statistics were calculated by comparing the alignments of the bulks to each parental reference genome, identifying a region of 5.36Mb on Chromosome B10 harboring the genes controlling the BP trait. SNPs within this region were further annotated, and three genes were identified as candidates for the BP trait. KASP markers were successfully developed for these SNPs and two of them were validated. The study of BP trait gives us more understanding of its genetic background, potential use in breeding programs, and potential benefits for growers in the southeast US.