Abstract: To analyze the genetic characteristics ofMarmota himalayana, this study performed whole-genome resequencing on 100 Himalayan marmots from seven regions in Qinghai Province, identifying a total of 9868432 SNPs and 1205326 insertions/deletions （InDels）. Further analysis of genetic diversity, population structure, kinship, and runs of homozygosity （ROH） revealed that the marmot population exhibited high genetic diversity, with an average nucleotide diversity of 0.00007635, an average observed heterozygosity of 0.423830, an average expected heterozygosity of 0.407072, and an average polymorphism information content of 0.31468. Inter-population differentiation was moderate to low, with sufficient gene flow. The IBS matrix and G matrix indicated that individuals were generally distantly related. Genetic structure analysis revealed that the marmot population structure was primarily influenced by geographic isolation. ROHs detection showed low recent inbreeding levels, indicating good genetic health. This study provided a scientific basis for the conservation of marmot genetic resources and the precise prevention and control of plague.

Key words: Himalayan marmot （Marmota himalayana）, whole-genome resequencing, genetic diversity, population structure；population evolution