Population genetic variability and structure of Elymus breviaristatus (Poaceae: Triticeae) endemic to Qinghai–Tibetan Plateau inferred from SSR markers

• SRAP marker was used for determining population structure in Elymus breviaristatus.
• There is no significant isolation by distance while using ΦST as genetic distance.
• An obvious population structure and genetic differentiation were detected.
• AMOVA showed that more genetic variance occurred within populations.
• Habitat destruction may contribute to present distribution of genetic diversity.

Elymus breviaristatus, a short-lived perennial grass species with ecological importance and forage value, is narrowly distributed in a few locations in the natural grassland of southeast of Qinghai–Tibet Plateau (QTP). Its populations are declining due to habitat loss and grassland degradation. This project is aim to investigate genetic diversity and genetic structure of this species for its conservation and management, using SSR data obtained from seven natural populations sampled from southeast of QTP. Seventeen selected primer pairs generated a total of 166 polymorphic bands. The Shannon diversity was comparably low within populations (0.115), but higher at the species level (0.251). An obvious population structure and high level of genetic differentiation (AMOVA-derived ΦST = 0.48, G′STG′ST = 0.54 from Shannon index) were detected by clustering, principle coordinate analysis and STRCTURE. All clustering approaches supported a demarcation of the seven populations into four major clades which failed to correspond to their geographical origin. The Mantel test revealed no significant isolation by distance (IBD) when used pairwise-ΦST (r = 0.149) as genetic distance, which indicating that geographical separation do not act as barriers for gene flow. Self-fertilization is considered to be the major factor contributing to high genetic divergence within this species. Furthermore, habitat destruction and limited seed dispersal due to increasing anthropogenic pressure on the species may play an important role in shaping present distribution of genetic diversity. Suggestions for conservation strategies are provided to preserve the genetic resources of this species.