Genetic variation and population structure analysis of Leymus chinensis (Trin.) Tzvelev from Eurasian steppes using SSR makers

Abstract

Leymus chinensis (Trin.) Tzvelev is an important perennial grass species extensively dispersed in the typical grassland communities of the Eurasian steppe region. It is relished by livestock due to its high quality and being a nutritionally valuable forage crop. L. chinensis has recently gained extensive consideration on its genetic diversity. However, genetic diversity studies on L. chinensis using SSR markers is currently limited. In the present study, we investigate the genetic variation and population structure analysis of L. chinensis from Eurasian steppes using SSR makers. For the genetic diversity, nineteen SSR markers were used and a total of 133 alleles were identified across the 166 L. chinensis plants. Our findings illustrated that the polymorphic rate for all SSR markers was greater than 80%, with the exception of SSR12i and SSR6c, which had polymorphism rates of 50% and 75%, respectively. The gene diversity (H) ranged from 0.0545 for SSR12i to 0.4720 for SSR25v, and the average was 0.3136. Furthermore, genetic diversity analysis indicated that the 166 samples could be grouped into five main population clusters based on their maximum membership coefficients which were assigned as Pop1 to Pop5. Among the five populations, the largest values of allele (total number of detected alleles), Ne (effective number of alleles) and Na (observed mean number of alleles) was found to be higher in Pop1, with values of 61, 1.461, and 1.977, respectively. Additionally, AMOVA showed that 13% of the total genetic variation occurred among the population and 87% genetic variation within the populations of the species. Whereas, the pairwise Fst specified the moderate genetic variation ranging from 0.0336 to 0.0731. Finally, the principal coordinate analysis revealed that the x-axis and y-axis explained 5.72% and 4.86% of the variation in molecular data, respectively. Taken together, these SSR markers provide new insights for a more precise understanding of the genetic diversity of L. chinensis germplasm and could potentially enhance the breeding program of L. chinensis.