QTL mapping identifies haplotypes associated with apical sprout length in potato

Potato (Solanum tuberosum L.) tuber sprouting is a key determinant of postharvest quality, influencing storage life, marketability, and seed tuber performance. Premature sprouting during storage reduces potato quality and causes major economic losses, making the genetic dissection of sprouting traits essential for breeding cultivars with superior storage performance. Herein, we aimed to map quantitative trait loci (QTL) for three sprouting traits, namely apical sprout length (ASL), days to sprouting (DTS), and number of sprouts (NOS), in an interconnected multi-parental potato population (N = 294). Using tubers obtained from a completely randomized design trial under greenhouse conditions and stored in a cold chamber at 4 °C, we observed substantial genetic variation for all traits, with ASL varying from 2.0~47.7 mm (median = 4.05 mm), DTS from 71~244 days (median = 149 days), and NOS from 0~9 (median = 3). DTS showed significant negative correlations with ASL (r = −0.33) and NOS (r = −0.27). A consensus linkage map spanning 2,313.75 cM with 2,263 single-nucleotide polymorphisms was constructed using mappoly R package. Phenotypes were regressed on founder’s haplotype probabilities using the diaQTL R package. A major QTL explaining 22% of ASL variation was identified on chromosome 3. Additive-effect parental haplotype alleles, such as haplotype 1 from ‘MB9846-1’ and haplotypes 2 and 4 from ‘Monalisa’ increasing ASL, and haplotype 3 from Monalisa reducing ASL, highlighted valuable targets for marker-assisted breeding. These findings provide important genomic resources for haplotype-targeted parental selection to develop potato cultivars with enhanced storage quality.