Genetic Variation in the Main Cultivar Collection of Castanea henryi Revealed by Genome Resequencing

<i>Castanea henryi</i> is an important economic tree species in China. Its nutrient-rich nuts play a key role in raising farmers' income in mountainous areas, promoting forestry industry development, and maintaining ecological balance, thereby providing significant economic and ecological value. To systematically elucidate the genetic characteristics of major <i>C. henryi</i> cultivars in China, this study conducted phenotypic trait measurements on 42 cultivars collected from Taining and Jian'ou in Fujian Province. Combined with whole-genome resequencing technology and using the <i>C. henryi</i> genome as a reference, systematic analyses were carried out. The results indicated that the Jian'ou group (HJO) generally exhibited superior performance in key fruit phenotypic traits compared to the Taining group (HTNC), with greater phenotypic diversity observed within the HJO group. Clustering analysis of phenotypic traits further revealed a cross-geographic convergent clustering pattern among the 42 <i>C. henryi</i> cultivars. Further analysis revealed that the overall genetic diversity of the 42 <i>C. henryi</i> cultivars was relatively low (observed heterozygosity: HJO = 0.0275, HTNC = 0.0194). Notably, parameters such as heterozygosity, minor allele frequency, nucleotide polymorphism, and polymorphic information content were slightly higher in the Jian'ou group compared to the Taining group. Divergent selection signal analysis (<i>Fst</i> top 5%) identified 3129 genomic regions under divergent selection. Genes within these regions showed homology to 1205 <i>Arabidopsis thaliana</i> genes, reflecting adaptive divergence driven by differential historical selection pressures between the two groups. Population genetic structure analysis indicated that the two regional groups exhibit high genetic similarity and low differentiation. This study reveals low genetic diversity and high genetic background homogeneity among <i>C. henryi</i> cultivars, findings that could inform the design of future breeding strategies.