Genetic Diversity and Landscape Genomics of Carya dabieshanensis (M.C. Liu and Z.J. Li) in a Heterogenous Habitat

Carya dabieshanensis is a species of significant economic value due to its unique flavor and nutritional properties as a snack food, as well as its durable wood, which is highly suitable for furniture production. Known for its remarkable adaptability to environmental stress, this species serves as a valuable genetic resource for enhancing hickory cultivars. However, its restricted distribution and limited availability of high-quality germplasm have impeded large-scale cultivation and hindered industry development. While the genetic diversity and genomic basis of its environmental adaptation hold great promise for future breeding programs, no studies to date have utilized SNP markers to explore its genetic diversity or the genomic mechanisms underlying environmental adaptability. In this study, we analyzed 60 samples from 12 natural populations of C. dabieshanensis, representing its global distribution. Using the Carya illinoinensis (Wangenh. and K. Koch) genome as a reference, we employed Specific Locus Amplified Fragment Sequencing (SLAF-seq) to generate high-quality SNP data. By integrating population and landscape genomics approaches, we investigated the genetic structure and diversity of wild populations and identified key environmental factors driving genetic differentiation. Our population genomics analysis revealed 9,120,926 SNP markers, indicating substantial genetic diversity (π = 1.335 × 10−3 to 1.750 × 10−3) and significant genetic differentiation among populations (FST = 0.117–0.354). Landscape genomics analysis identified BIO3 (Isothermality), BIO6 (Min Temperature of Coldest Month), and BIO14 (Precipitation of Driest Month) as critical environmental factors shaping genetic diversity. This study provides essential insights into the genetic resources of C. dabieshanensis, facilitating the development of climate-resilient cultivars and offering a scientific foundation for the conservation and sustainable management of its wild populations.