Genome-wide assessment of runs of homozygosity in Sahiwal cattle of Pakistan

Abstract

Runs of homozygosity (ROH) are extensive stretches of homozygous genotypes present in an individual genome inherited from each of its parents. Selection pressures have been one of the core causes of a reduction in genetic diversity in some genomic regions, leading to an accumulation of ROH in these regions. An individual’s ROH can provide information about the past of his population, including the extent of inbreeding, recent bottlenecks, and positive selection. The study aimed to evaluate the degree of autozygosity throughout the genome in Sahiwal cattle to discern and describe ROH patterns. In addition, we also estimated the rate of inbreeding based on ROH in Sahiwal cattle. A sample of 98 Sahiwal bulls from various public institutional herds and private livestock farms in the Punjab province of Pakistan was used for this study. All animals were genotyped using the 140k BovineHD SNP chip. The study identified ROH in all animals. The mean ROH per animal was 29.71, with values extending from 2.35 to 85.31. The mean length of the ROH was 5.84 Mb, and the longest segment was 51.43 Mb (1,727 SNPs) found on BTA3. Results revealed that genome-wide ROH for Sahiwal was typically composed of many short and medium segments (2–4 Mb and 4–8 Mb), accounting for approximately 54.18% of all detected ROH. The inbreeding coefficient based on ROH (FROH) ranged from 0.016 to 0.057. The study revealed several genes, including STAT1, ATP1A1, OLR1, and CD4, which are known genes related to milk production. Thus, understanding ROH patterns, an inbreeding coefficient derived from ROH, and candidate genes associated with significant economic traits can help explain the mechanisms governing these traits in Sahiwal cattle.