Population Genomics of Chinese Melia azedarach Germplasm: Latitudinal Genetic Structure, Spatial–Climatic Associations, and Climate-Associated Candidate Genes

To understand how geography shapes the genetic variation of Melia azedarach, we sequenced the whole genomes of 91 accessions from 91 maternal half-sib families across 15 provenances maintained in the National Germplasm Bank of China, an ex situ collection representing conserved germplasm. Genetic diversity increased from south to north (He: 0.098 to 0.333), whereas the Hainan population showed relatively low within-population diversity and, as confirmed by pairwise Fst, was highly differentiated from the mainland, forming an independent group. A Mantel test confirmed a significant isolation-by-distance (IBD) pattern (r = 0.307, p = 0.001). Redundancy analysis (RDA) explained 17.23% of the individual-level genetic variance, but a partial redundancy analysis (partial RDA) showed that most of this association was attributable to population structure, with the environmental variables explaining negligible independent variance after conditioning on population structure. Genome-wide association analysis (GWAS) further identified candidate loci potentially associated with climate-related traits, including a temperature-associated gene encoding a leucine-rich receptor-like protein kinase and a precipitation-associated gene encoding the stress-related protein RAR1. Together, these results map the genome-wide genetic diversity and spatial–climatic associations of M. azedarach. This study provides a genetic basis for evaluating banked resources, molecular breeding, and protecting this important tree species.