Genome-wide assessment of runs of homozygosity in ongole grade cattle

Runs of homozygosity (ROH) is a method for identifying homozygous genomic regions that may indicate strong past selection in the population. This study aimed to look for ROH occurrence in Ongole Grade cattle using previously published Bovine 50K SNP data. In total, genotypes of 83 samples were included in the analysis. Quality control was performed in Plink v1.9 based on the following parameters: variance call rate ≥95%, individual call rate ≥90%, and only autosomes were allowed. The consecutive ROH was measured using the detectRuns package in R v4.1.0. We identified 2,458 ROH segments with a number per chromosome ranging from 11 to 208, and the average length was 0.97 Mb. On BTA 4, 6, 10, 13, 16, 20, and 23, eight ROH regions containing 15 candidate genes were discovered. Based on gene ontology enrichment, those identified genes were related to growth traits, milk traits, immune systems, and feed efficiency in cattle. In summary, we assessed autozygosity patterns across the genome in Ongole Grade cattle and found candidate genes that overlapped with ROH for several important traits. These findings could help us understand the adaptation mechanisms that occur in the Ongole Grade cattle population and aid in selection and breeding programs.