Whole-genome SNP markers reveal runs of homozygosity in indigenous cattle breeds of Pakistan

Abstract

The runs of homozygosity (ROH) were identified in 14 Pakistani cattle breeds (n = 105) by genotyping with the Illumina 50 K SNP BeadChip. These breeds were categorized into Dairy, Dual, and Draft breeds based on their utility and production performance. We identified a total of 10,936 ROHs which mainly consisted of a high number of shorter segments (1–4 Mb). Dairy group exhibited the highest level of inbreeding (F_ROH: 0.078 ± 0.028) while the lowest (F_ROH: 0.002 ± 0.008) was observed in Dual group. In 48 genomic regions identified with a high frequency of ROH, 207 genes were detected in the three breed groups. A substantially higher number of ROH islands detected in dairy breeds indicated the impact of the positive selection pressure over the years. Important candidate genes and QTL were detected in the ROH islands associated with economic traits like milk production, reproduction, meat, carcass, and health traits in dairy cattle.

Keywords:

• Runs of homozygosity
• indigenous cattle
• candidate genes
• QTL

Disclosure statement

The authors declare that they have no competing interests.

Author contributions

M.S.R. and T.D. designed the study and analyzed the data. M.S.R., J.R., and F.H. interpreted the data. T.D., M.S.R., and F.H. wrote the drafted manuscript. All the authors reviewed the paper. All authors have read and agreed to the current version of the manuscript.

Data availability statement

All data generated or analyzed during this study are included in either this article or the supplementary files.

Additional information

Funding

This study was funded by the National Natural Science Foundation of China (3216200192) and the Natural Science Foundation of Guangxi (2020GXNSFDA297032).