Inflorescence Trait Diversity and Genotypic Differentiation as Influenced by the Environment in Elymus nutans Griseb. from Qinghai–Tibet Plateau

The alpine forage grass species Elymus nutans Griseb. is widely distributed in the Qinghai–Tibet Plateau and the Himalayas due to its high adaptability. However, it has become threatened by climate warming and excessive grazing. Thus, understanding its genetic and phenotypic information is crucial to aid resource management and conservation efforts. In this study, microsatellite markers were developed based on RNA-seq transcriptome data from E. nutans Griseb. varieties ‘Aba’ and ‘Kangbei’, resulting in the identification of 48,457 SSRs from 304,554 de novo assembled unigenes. Seventeen polymorphic markers, 13 inflorescence phenotypic traits, and seed shattering values were determined for 31 E. nutans accessions collected from eastern Tibet. The molecular markers generated 134 well-amplified bands with a mean Nei’s genetic diversity of 0.31 and a Shannon information index of 0.46. Pairwise genetic similarity ranged from 0.554 to 0.895, with an average of 0.729. Based on the molecular marker data, all accessions were divided into two classes via the unweighted pair-group method with arithmetic mean (UPGMA), the Markov chain Monte Carlo method, and the principal coordinate analysis (PCA) method. We used Tassel analysis to determine 11 loci with a significant relationship to phenotypic traits, and Pearson’s correlation analysis showed that some inflorescence traits were significantly influenced by the environment. Furthermore, we detected strong patterns of isolation by both environment (IBE) and distance (IBD) via Mantel analysis. This study provides valuable insights into the genetic and phenotypic differentiation of E. nutans, informing germplasm resource evaluation and future breeding.