Population genomics of Mexican landraces of the squash <i>Cucurbita moschata</i> reveals structure and environmental adaptation

Abstract The study of genomic diversity in domesticated species provides insights into their evolution and mechanisms of local adaptation, which are essential for conservation under climate change. Cucurbita moschata is a crop that is grown worldwide, with high landrace diversity in Mexico. Although previous studies have primarily focused on commercial varieties, landraces represent a valuable genetic reservoir. In this study we aimed to characterize the genomic diversity and structure of C. moschata, identify loci associated with environmental variables, and evaluate the best speciation model within the Argyrosperma group species. We analysed landraces from 24 Mexican localities, using nuclear Single Nucleotide Polymorphism (SNP) data. We assessed genetic structure through clustering analyses, performed an environmental association analysis, identified candidate loci potentially under selection, and inferred the evolutionary history with Approximate Bayesian Computation (ABC). Our results revealed that C. moschata has notable genetic variation (HT = 0.213) with low inbreeding signals (FIS = 0.0265). We identified two major landrace groups: one in the Yucatan Peninsula and another in the rest of Mexico. Furthermore, we found ecological structure, with landraces clustering according to arid and semi-arid conditions, vs. tropical regions. Outlier-based analyses revealed candidate loci related to abiotic stress responses, offering hypotheses for future studies on the adaptive potential of C. moschata landraces.