Development and Application of SSR Markers for the QTL qPHS8-1 Associated with Pre-Harvest Sprouting in Tartary Buckwheat

Pre-harvest sprouting (PHS) is a major agronomic problem that limits the yield and quality of Tartary buckwheat. Developing molecular markers closely linked to PHS resistance is important for breeding. In this study, a population of 218 XJ-RILs derived from a cross between the PHS-susceptible cultivar ‘Xiaomiqiao’ and the PHS-resistant cultivar ‘Jinqiaomai 2′ was used as the experimental material. Within the physical interval of the PHS-related QTL locus qPHS8-1 (8,530,000–9,650,000 bp) in Tartary buckwheat, SSR locus mining, primer design, and polymorphism screening were performed, followed by correlation analysis combining germination phenotypes with molecular markers. A total of 218 SSR loci were identified within this interval, mainly consisting of di-nucleotide (42.66%) and mono-nucleotide (31.19%) repeats. Short repeat motifs were predominantly composed of A/T and AT/AT. Among 114 primer pairs, five polymorphic SSR primers (PHS-8, PHS-23, PHS-29, PHS-65, and PHS-89) were selected. Association analysis showed that lines carrying the maternal allele exhibited significantly higher germination percentage, germination energy, and germination index than those carrying the paternal allele (p < 0.01). Cluster analysis further divided the population into four genetic groups, showing clear parental background differentiation consistent with the PHS phenotypes. The five SSR markers developed in this study can be used for marker-assisted selection for PHS resistance in Tartary buckwheat and provide a molecular basis for elucidating the genetic regulatory mechanisms underlying this trait.