Fine-scale assessment of ROH patterns and genomic inbreeding in diverse horse breeds using two SNP array densities.

BACKGROUND: Inbreeding is caused by mating between related individuals and is associated with reduced fitness and performance. Generally, in the horse population, inbreeding is caused by geographically restricted areas and intensive natural or artificial selection. For this reason, assessing accurate inbreeding is essential for developing and implementing effective breeding strategies aimed at preserving genetic diversity and reducing the harmful consequences of inbreeding. One of the most accurate approaches for assessing genomic inbreeding and autozygosity is through the analysis of runs of homozygosity (ROH), which are long stretches of homozygous genotypes inherited from common ancestors and provide valuable insights into population diversity, demographic history, and selection. METHODS: In this study, we analyzed the distribution of ROH, estimated genomic inbreeding coefficients, and mapped ROH islands across 14 diverse horse breeds. We used 670 K and MNEc2M SNP array datasets, comprising 279,040 SNPs from 424 horses and 1,083,942 SNPs from 438 horses, respectively. A total of 35,396 and 17,382 ROHs were detected in all breeds for the 670 K and MNEc2M SNP array datasets, respectively. RESULTS: The majority of the detected ROHs were < 16 Mb (only 2.23% and 1.38% were greater than 16 Mb in for the 670 K and MNEc2M SNP array datasets, respectively) and the average total number of ROHs per individual were 81.36 ± 33.38 and 38.71 ± 22.73 for the 670 K and MNEc2M SNP array datasets, respectively. The mean ROH length per individual was 248.57 Mb for the 670 K SNP array and 89.56 Mb for the MNEc2M SNP array. Genomic inbreeding based on ROH (FROH) was relatively higher than homozygosity-based inbreeding (FHOM) and ranged from 0.0364 ± 0.0049 to 0.2357 ± 0.0584 and from 0.004 ± 0.0044 to 0.1102 ± 0.0779 for 670 K and MNEc2M SNP array datasets, respectively. CONCLUSIONS: We identified genomic regions with high ROH coverage so called ROH islands that may reflect recent selection events. Several chromosomes, including ECA7 and ECA11, contained large ROH islands that include genes associated with important traits such as pigmentation, fertility, and performance. These ROH islands represent genomic footprints of past selection events and serve as candidate regions for future functional and association studies.