GBS-based marker–trait association and genetic mapping for enhanced QTL significance in apricot progenies (<i>Prunus armeniaca</i> L.)

Genotyping by sequencing (GBS) offers a powerful tool for high-resolution mapping by identifying single-nucleotide polymorphisms (SNPs) aligned to a reference genome. This study aimed to construct high-density genetic maps for two apricot populations, 'Bergeron' × 'Currot' ('B × C') and 'Goldrich' × 'Currot' ('G × C'), to identify marker-trait associations linked to fruit quality traits and resistance to powdery mildew. A total of 134 'B × C' and 159 'G × C' seedlings were genotyped, resulting in 2,442 mapped markers—642 for 'Bergeron', 667 for 'Currot' ('B × C'), 607 for 'Goldrich', and 526 for 'Currot' ('G × C')—covering genetic distances of 596.6, 713.6, 545.1, and 741.2 cM, respectively. This high-resolution mapping enabled the detection of the most significant QTLs for traits such as skin color (LG3, LOD 25), blush color (LG1, LOD 7.6), and soluble solids content (LG4, LOD 12.1), along with other minor QTLs. However, the acidity and the powdery mildew resistance QTLs showed lower and inconsistent significance across different years. Additionally, several candidate genes associated with these traits were identified within the most significant genomic regions using the 'Currot' reference genome available in NCBI. These findings provide valuable resources for the development of molecular markers that aim to improve breeding strategies in apricot breeding programs, particularly those focused on enhancing fruit quality. These results lay a promising foundation for mid-term implementation in marker-assisted and genomic selection, pending further validation across diverse genetic backgrounds and environmental conditions.