A SNP-based linkage mapping revealed a mutant-origin major quantitative trait locus for seed size in A05 chromosome of groundnut (Arachis hypogaea L.)

Seed size is directly involved in determining the yield of groundnut. Here, we report the identification of a main QTL for large seed size using a F-2 population of 'TG 89 x ICGV 15007'. A total of 122 F-2 individuals were genotyped with a total 345 markers which included 297 of ddRAD-seq SNP, 37 AhMITE, 9 SSR and 2 gene specific markers to construct a genetic linkage map spanning 3891.3 cM. QTL analysis revealed two major QTLs, one on linkage group A05 explaining 18.07% phenotypic variation and the other on A02 explaining 11.95% phenotypic variation. The major additive effect of qHKW_A05 was contributed by mutant allele. It was located between marker AhMITE470 and SNP_05_103140987 having a map interval 8.6 cM, corresponding to 4.53 Mbp (99.18-103.71 Mbp) in the genome. In close proximity to this QTL peak, an ortholog of BIG SEEDS 1 (Arahy.5M7JWE) located at 102.47 Mbp. Arahy.5M7JWE belongs to AhTIFY protein having key role in regulating organ size and growth. The study also reports generation of allele specific PCR based SNP markers and validation of its usage in marker assisted selection.