Combining BSA-Seq, High-Density Genetic Map, and RNA-Seq to Identify Candidate Genes Controlling Embryo Spot Trait in Potato

Embryo spots on potato seed enhance the efficiency of doubled haploid screening by facilitating selection. While the spots are known to involve anthocyanin accumulation, their genetic regulation remains unclear. Here, loci and genes regulating spot formation were investigated. An F1 population was generated by crossing the haploid inducer IVP101 (embryo-spotted male parent) with the diploid inbred line Y8 (non-spotted female parent). Subsequent BSA-seq of the extreme F1 pools mapped a locus to chromosome 10 (49.96–54.31 Mb). QTL mapping via a high-density genetic map of the F2 segregating population (derived from F1 selfing) identified four QTLs (on chromosomes 2, 5, 10, 11). These included the QTLs qSP10-1 (explaining 23.85% of phenotypic variance) and qSP11-1 (18.23%). qSP11-1 overlapped with the reported P locus encoding flavonoid 3′,5′-hydroxylase (F3′5′H), whereas qSP10-1 confirmed the BSA-seq results. Integration of the BSA-seq and QTL mapping results narrowed the target gene locus to a 384.6 kb interval at the end of chromosome 10. Transcriptome sequencing of spotted vs. non-spotted F1 seed, together with gene expression profiling in the qSP10-1 interval, identified five differentially expressed candidate genes. These findings clarify the genetic basis of potato embryo spot formation and provide a reference for breeding and further research.