Genomic inbreeding and runs of homozygosity in Mexican Coreño Creole cattle

The genetic diversity of Mexican creole cattle can be affected by increased homozygosity and the negative consequences of inbreeding depression, compromising years of adaptation. Therefore, the purpose of the study was to identify runs of homozygosity (ROH) and estimate inbreeding coefficients in Coreño creole cattle. A total of 48 Coreño creole cattle were genotyped using Illumina BovineHD BeadChip (777 K), where 3,085 ROH were identified. The average number of ROH per individual was 65.64, while the average number of SNP per ROH was 883. The mean sum of ROH distances per animal was 217.26 ± 21 Mb. 87.42% of the ROH were short, 6.35% medium and 6.22% long. El Encinal was the location with the highest number of ROH (1,124). The mean inbreeding coefficients obtained from the ROH were 0.047 in C.E. El Verdineño, 0.069 in Jazmines de Coyultitla, and 0.122 for El Encinal. The number of ROH by size and the inbreeding coefficient from ROH (F_ROH) were different for each location, which may suggest differences in population structure, that might affect genetic diversity. This is one of the first genomic inbreeding analyses for Coreño Creole cattle.