Association mapping revealed phenolic content-related SNPs and haplotypes in pecan (Carya illinoinensis)

Phenolics are essential quality components in pecan nuts, influencing the nutritional value of various varieties. Conventional breeding methods for pecan trees are time-consuming and laborious due to their considerable height and extended juvenile period. Molecular marker-assisted selection offers the potential to expedite the breeding process. In this study, we examined the allelic variations of five phenolics biosynthesis-related genes within a germplasm population. The linkage disequilibrium (LD) values (r²) between single nucleotide polymorphisms (SNPs) of each gene were analyzed, demonstrating a decrease in r² to less than 0.2 within a 1.0 kb distance. The contents of total phenolics, total flavonoids, and condensed tannins in the kernels of each individual were assessed over two consecutive years. Following this, association mapping was conducted. A total of 29 significant marker-trait pairs and eight significant haplotype-trait pairs were observed. Among these, three SNPs in CiPAL4 and two haplotypes in CiCHS3 were consistently identified over both years. The explanation rates of the SNPs for the observed traits ranged from 3.45 to 14.39% (p < 0.05). This study offers valuable insights into the molecular basis underlying phenolic biosynthesis in pecan trees, which will enhance the efficiency of quality improvement in this plant and other species within the Carya genus.