Estimation of genome-wide patterns of homozygosity, heterozygosity and inbreeding in crossbred dairy cattle population in Pakistan

The present study aimed to explore runs of homozygosity (ROH), Heterozygosity Enriched Regions (HER) using the sliding window approach in both PLINK and detectRUNS, as well as the consecutive SNP approach in detectRUNS and their association with important economic traits. Genomic inbreeding coefficient based on ROH and heterosis coefficient based on HER were also estimated among crossbred (n = 81) by using GGP_HDv3_C genotyping assay. Total ROH varied from around 600 in the sliding window approach and almost double in the Consecutive SNP approach of detectRUNS. Similarly, the HER are 756 in the sliding window and 771 in the Consecutive SNP method. The mean inbreeding coefficient range varied in different approaches, i.e., 0.016–0.022 is observed based on ROH (Froh), and the heterosis coefficient based on HER (Frohet) is 0.0019. Top ROH and HER regions contain important genes related to dairy (EHHADH, CACNA1C, MICALL1, EIF3L, GTPBP1, SYNGR1, ATF4, GRAP2, FAM83F, ACO2), immunity (LIPH, TMEM41A, PEX26, CDC42EPI, CXXC5, PSD2, PURA, CYSTM1, RNF14), growth and carcass (MAGEF1, TGS1, LYN, CHCHD7, FAM110B, SDCBP, SH3BP1, GGA1, TRIOBP, PICK1, MAFF, TOMM22, MGAT3, TNRC6B, ADSL, EP300, SMDT1, MATR3) traits. These findings may provide valuable insights into the understanding of genome-wide homozygosity and heterozygosity patterns and genetic architecture of the Pakistani crossbred cattle.