Identification and validation of QTLs for tuber quality related traits in yam Dioscorea alata

Two diploid full-sib segregating populations composed of 193 progenies (population B, 74F × 14M) and 121 progenies (population A, 74F × Kabusa) were used to map several quality traits. All progenies and genitors were genotyped-by-sequencing (GBS). A consensus high-density genetic map was constructed containing 1579 SNP loci, with a total length of 2613.5 cM and an average distance of 1.68 cM between markers. Both populations were assessed over two consecutive years for seven important morpho-agronomic quality-related traits (tuber size, shape regularity, flesh colour, flesh oxidation, oxidation ratio, tubercular roots and skin texture). The heritabilities of most traits were high. Quantitative trait loci (QTLs) were identified for all the traits studied. Thirty-four QTLs were detected on 8 of the 20 yam chromosomes. The fraction of total phenotypic variance attributable to a single QTL ranged from 11.1 to 43.5%. We detected significant correlations between traits and QTL co-localizations that were consistent with these correlations. Nine QTLs were validated on a diversity panel, including three for tuber size, three for shape regularity, two for skin texture and one for tubercular roots. The validated QTLs should be useful for breeding programs using marker-assisted selection to improve yam tuber quality.