Genome-wide assessment of runs of homozygosity and inbreeding in Inner Mongolia cashmere goats reveals candidate genes for economic traits

Introduction To facilitate the conservation and sustainable utilization of the Inner Mongolia Cashmere Goat (IMCG)-an important genetic resource and economically valuable breed-this study performed a genome homozygosity assessment of its Erlangshan subtype population, analyzed the distribution characteristics of runs of homozygosity (ROH), and compared inbreeding coefficients estimated using different methods. Methods A total of 384 individuals were genotyped using the Illumina Goat SNP70K BeadChip. PLINK software was employed to conduct ROH analysis, estimate genomic inbreeding coefficients, and identify ROH islands based on the obtained SNP data. Results The results revealed 3,622 ROH segments in the population, with an average total ROH length of 71.48 Mb per individual. The inbreeding coefficients based on ROH (F ROH ) and observed homozygosity (F HOM ) were 0.0290 and −0.0126, respectively, showing a strong positive correlation ( r = 0.97). In addition, 14 ROH islands were identified on chromosomes 2, 5, 7, 8, 9, 13, 17, 19, 24, 25, and 26. Within these regions, 238 genes were annotated, including key genes such as HDAC1 , MIR21 , DNASE1L2 , and ACACA , which may be implicated in reproductive traits, hair follicle development, and milk fat metabolism. Conclusion This study systematically characterized ROH patterns in IMCG, indicating a generally low level of genomic inbreeding in the population, though certain individuals still require attention. The identification of genes related to economically important traits further reveals the genetic distinctiveness and breeding potential of IMCG, providing valuable insights for informing future conservation and breeding strategies.