Genetic Diversity and Structure of Geodorum eulophioides, a Plant Species with Extremely Small Populations in China

Abstract

Geodorum eulophioides is a unique and endangered species belonging to the Orchidaceae family in China. It has great potential as an ornamental horticultural plant. However, little is known about its genetic diversity and reasons for being endangered due to its narrow distribution and few populations in the wild. To effectively evaluate and conserve available resources, the genetic diversity and population structure of G. eulophioides were analyzed in this study. A total of 94 individuals from 10 natural populations were studied using site-specific amplified fragment sequencing (SLAF-seq). Based on the 76,340 SNPs detected by SLAF-seq, genetic diversity analysis was performed and markers associated with environmental variables were determined. The results showed that the level of genetic diversity in the 10 natural populations studied was low, with PIC values ranging from 0.1874 to 0.2156. FIS values ranged from −0.2376 to 0.2658, with excess and deficiency in heterozygotes. FST values ranged from 0.0482 to 0.3144, with genetic variation among populations. AMOVA results showed that the genetic variation among populations accounted for 21.35% of the total variation, and the remaining genetic variation among individuals within populations was 78.65%. The results of the population structure analysis showed that 94 individuals were classified into three major groups and two subgroups. Environmental association analysis using Bayenv2 and LFMM yielded thirty and eighteen putative adaptive loci, respectively, and five specific functional genes were annotated. In summary, this study provides further insight into the genetic structure of G. eulophioides and provides a reference for protection and restoration.