Identification of phenological QTLs using a combination of high- and low-coverage whole genome sequencing in Japanese plum ( <i>Prunus salicina</i> Lindl.)

The genetic control of phenological traits in Japanese plum (<i>Prunus salicina</i> Lindl.) was investigated through quantitative trait loci (QTL) analysis in three segregating F₁ populations: 'Black Splendor' × 'Pioneer' (BS×PIO), 'Red Beaut' × 'Black Splendor' (RB×BS), and 'Red Beaut' × 'Santa Rosa Precoz' (RB×SRP), comprising 121, 103, and 103 seedlings, respectively. Whole-genome sequencing (~80×) was conducted for the four parents, and progenies were genotyped using a cost-efficient reduced-representation sequencing strategy. SNPs heterozygous in one parent and homozygous in the other were used to build six parental linkage maps. Phenological traits, including beginning, full, and end of flowering (BF, FF, EF), flowering intensity (FI), ripening date (RD), fruit development period (FDP), and productivity (P), were evaluated over three years. A total of 53 QTLs were identified for flowering stages, 16 for RD, 18 for FDP, 10 for FI, and 16 for P. Many QTLs were stable across years. Major QTLs for flowering traits were mapped to LG1, LG2, LG4, and LG6, with a strong QTL for FF on LG6 of 'Black Splendor'. In BS×PIO, BF was uncorrelated with FF and EF, indicating distinct genetic control likely inherited from 'PIO', a low-chill cultivar. RD and FDP were consistently associated with LG4, while productivity QTLs were detected on LG1, LG2, and LG4, often overlapping, suggesting pleiotropic or tightly linked loci. In addition, candidate genes within stable QTLs were detected, providing immediate targets for functional studies. This study provides one of the first genome-wide QTL analyses of phenology in Japanese plum using low-coverage whole genome sequencing and offers valuable tools for marker-assisted breeding in this species.