Population genetic diversity and structure, demographic history and deleterious mutations analysed by whole-genome resequencing in Salvia daiguii : a plant species with extremely small populations from China

BACKGROUND AND AIMS: Sage is globally recognized for its significant ornamental and medicinal values. Salvia daiguii, a perennial herb native to Zhangjiajie, Hunan Province, China, has a graceful plant shape, dense flowers, high stress tolerance, and high medicinal value. However, this species is at high risk of extinction owing to its narrow geographic distribution, habitat fragmentation, and multiple anthropogenic disturbances. METHODS: This study aimed to understand the genetic mechanisms underlying the endangered status of S. daiguii by investigating the population genetic diversity and structure, linkage disequilibrium decay, demographic history, inbreeding, and the genetic load of the species populations. Whole-genome resequencing was conducted on 28 samples collected from three distinct populations. KEY RESULTS: Analysis of these samples yielded 3,755,203 high-quality SNPs. The results showed evidence of gene flow, moderate genetic diversity, and low-to-moderate genetic differentiation among the three S. daiguii populations. Demographic history analyses indicated a continued decline in effective population size. Genetic load analysis indicated minimal inbreeding, but revealed the accumulation of putative deleterious mutations across the populations. These mutations were predominantly enriched in functional categories related to cellular and metabolism processes. CONCLUSIONS: This study integrated multiple population genetic inference methods to elucidate the genetic basis of S. daiguii endangered status at the genomic level. These methods provide an applicable framework for the conservation genomics of plant species with extremely small populations. Moreover, this genetic data further informs the prioritization of conservation units and genetic rescue strategies, contributing to an evidence-based frameworks for global plant conservation.