A 50 K SNP target‑enrichment panel for allotetraploid Leymus chinensis: empowering genomics and breeding in a complex forage grass

Leymus chinensis (sheepgrass) is a perennial grass of ecological and agricultural importance in the Eurasian steppe, yet genomic research and breeding are hindered by its large, complex allotetraploid genome. Here, we present the first high-density 50 K SNP target‑enrichment panel for sheepgrass, developed from whole-genome resequencing of 100 diverse accessions. After rigorous filtering, 51,696 SNPs were selected with broad coverage across genome. Functional annotation revealed that 64.3% of SNPs are located in genic regions and 35.7% in intergenic regions. SNP density varied among chromosomes, ranging from 3.94 SNPs/Mb (chromosome 3Ns) to 8.92 SNPs/Mb (chromosome 2Xm). The panel exhibited high reproducibility (genotype concordance > 98%) and transferability to other Leymus species, with call and coverage rates exceeding 98%. Genotyping of 648 sheepgrass samples revealed clear genetic differentiation among natural populations, hybrids, and cultivars, with breeding varieties showing gene flow between wild and cultivated groups. Using the panel, GWAS on 276 accessions for five agronomic traits identified significant loci associated with total number of spikes, grain weight per spike, and germination rate, and led to the selection of candidate genes including XIAO, KCS17, and ACO1. Overall, this 50 K SNP panel provides a robust, cost-effective platform for high-resolution genotyping, association studies, population analysis, and molecular breeding in sheepgrass.