Leymus chinensis is the main dominant species in the eastern Eurasian steppe， with significant ecological and production values. However， its low seed yield severely restricts its practical application. To identify the associated loci for the seed yield traits of L. chinensis and to discover key molecular markers， this study used 300 diverse accessions of L. chinensis as materials， measured five yield traits including spikelet number per spike， floret number per spikelet， total number of florets， seed number per spikelet and seed setting rate， and conducted a genome-wide association analysis （GWAS） using a mixed linear model. The results showed that seed number per spikelet exhibited the highest coefficient of variation （CV=0.52）， indicating substantial potential for genetic improvement. The seed setting rate was regulated by an independent genetic mechanism and was the key limiting factor for seed yield. GWAS analysis combined with gene functional annotation identified 120 key single nucleotide polymorphisms （SNPs） and identified EZ1 and multiple MADS-box and WRKY transcription factors as key candidate genes regulating seed yield. Based on 14 SNPs significantly associated with seed setting rate， 8 elite alleles were obtained. Notably， the CT genotype at the Lc5Ns_97563471 locus exhibited a high mean seed setting rate of 66.6%. This study revealed the genetic characteristics of L. chinensis seed yield being regulated by multiple genes， and the identified candidate genes and elite SNP loci can serve as direct targets for molecular marker-assisted breeding.

Leymus chinensis  /  Seed setting rate  /  Seed yield  /  Genome-wide association study  /  Superior allelic variation