Exploring haplotype block structure, runs of homozygosity and effective population size among dairy cattle breeds of India

Abstract

Abstract The present study investigated the haplotype structure, runs of homozygosity (ROH), effective population size and persistence of gametic phase among three indigenous dairy cattle breeds viz. Sahiwal (n = 19), Tharparkar (n = 17) and Gir (n = 16) using Illumina BovineHD BeadChip assay. The filtered SNPs after quality control ranged from 44% in Sahiwal to 53% in Gir. The highest number of haplotype blocks was observed in Tharparkar (15640) and the lowest in Sahiwal (8027) spanning 17.3% and 7.8% of genome, respectively. The average block length was found close to 26 kb which suggests that multiple recombination events fragmented the ancestral haplotypes into smaller sizes. Gir cattle had the largest number of runs of homozygosity (ROH) regions (1762) followed by Tharparkar (1528) and Sahiwal (1138). Without pedigree information, inbreeding coefficients estimated from ROH (FROH) revealed that Gir had the highest FROH (0.099) proposing more inbreeding rate in this population. Effective population size (Ne) decreased slowly over the last 60 generations and at 13 generations ago; Ne was estimated as 70 for all the three dairy breeds. The highest gametic phase correlation (r = 0.78) was observed for Sahiwal and Tharparkar breed pair suggesting formulation of multi-breed reference population for successful implementation of genomic selection among dairy breeds.