Among-Population Differentiation and East-to-West Decline in Genetic Diversity of Lactarius vividus from Southern China Revealed by Seven Novel SSR Markers

Lactarius vividus is a wild edible ectomycorrhizal mushroom widely distributed in southern China, where it forms an obligate symbiotic relationship with Pinus species. However, its genetic diversity and population differentiation remain poorly understood. We collected 95 basidiomata from ten geographic populations spanning seven provinces across an east–west transect of southern China and developed seven SSR primer pairs at the genomic level to investigate its genetic diversity, population differentiation and spatial genetic structure. Genetic diversity showed a clear east-to-west declining trend, being highest in population AQ (Anhui Province) and lowest in KM (Yunnan Province). Observed heterozygosity (Ho) was lower than expected heterozygosity (He) in most population-locus combinations, and many tests showed significant departures from Hardy–Weinberg equilibrium (HWE), indicating a pronounced heterozygote deficit. Analysis of molecular variance (AMOVA) showed substantial population differentiation, with 63% of the total genetic variation occurring among populations. A Mantel test detected a significant positive association between genetic and geographic distances (r = 0.322, p = 0.032), consistent with isolation by distance (IBD). STRUCTURE identified three genetic clusters, while DAPC and UPGMA analyses further revealed geographic differentiation and admixture or genetic overlap among some samples. These findings provide a basis for prioritising geographically distinct populations in the conservation and sustainable management of this wild edible mushroom.