Chromosome Regions Linked to Peanut Black ( <scp> <i>Arachis hypogaea</i> </scp> L.) Pod Revealed by QTLSeq

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. This study utilized a bulk segregant analysis aided by QTLseq to identify genomic regions linked with the BP trait. A population of peanuts segregating for the BP trait was developed by crossing a BP line and FloRun ‘331’ without the BP trait. DNA samples of F 2 individuals of normal pod colouration and F 2 individuals that were confirmed as homozygous for the BP validated based on their F 3 progeny were equally pooled for deep sequencing together with the parental lines. A total of 220,714 single nucleotide polymorphisms (SNPs) were found between the plants of BP and normally coloured 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 5.36 Mb on chromosome B10 harbouring genes linked to 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 were validated. The study of the BP trait gives us a better understanding of its genetic background, potential use in breeding programmes and potential benefits for growers in the Southeastern United States.