QTL Analysis for Cadmium and Zinc Accumulation in Tubers of Tetraploid Potato using SNP Dosage Data

The aim of this study was to construct single nucleotide polymorphism (SNP)-based genetic map of tetraploid potato and localize quantitative trait loci (QTL) influencing tuber accumulation of cadmium and zinc accumulation. We developed a segregating population comprising 188 F₁ progeny derived from crossing the cultivars Cara, (a low tuber cadmium accumulator) and Lady Rosetta (a high tuber cadmium accumulator). These progeny were genotyped using the SolCap 8303 SNP array and evaluated for cadmium, zinc and other agronomic traits. From 8303 SNPs, 6487 SNPs were polymorphic and 4533 SNPs were fitted into five genotype clusters. Linkage analysis and QTL mapping were performed using TetraploidSNPMap software that incorporates all allele dosage information. The final genetic map comprised 3755 SNP markers with average marker density of 2.94 per cM. QTL mapping identified 6 loci for cadmium on chromosomes 2, 3, 4, 5, 6 and 7, which explained genetic variance ranging from 3.43% to 7.23 %, and 2 loci for zinc explaining 4% and 22% of genetic variance on chromosome 5 and 6 respectively. QTL mapping reconfirmed major loci on chromosomes 5 and 10 for maturity/plant height and flower/tuber skin colour respectively. The major zinc QTL co-incided with the maturity locus, and when the residuals from regression of zinc on maturity were analyzed, 4 new loci for zinc were found on chromosomes 1, 3, 4, and 12. The results suggest that genetic control of cadmium and zinc accumulation in tubers is regulated by complex genetic factors.