Genome-wide scan for runs of homozygosity identifies candidate genes in Wannan Black pigs

  • Wu, Xudong (College of Animal Science and Technology, Anhui Agricultural University) ;
  • Zhou, Ren (College of Animal Science and Technology, Anhui Agricultural University) ;
  • Zhang, Wei (College of Animal Science and Technology, Anhui Agricultural University) ;
  • Cao, Bangji (College of Animal Science and Technology, Anhui Agricultural University) ;
  • Xia, Jing (College of Animal Science and Technology, Anhui Agricultural University) ;
  • Wang, Caiyun (College of Animal Science and Technology, Anhui Agricultural University) ;
  • Zhang, Xiaodong (College of Animal Science and Technology, Anhui Agricultural University) ;
  • Chu, Mingxing (Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences) ;
  • Yin, Zongjun (College of Animal Science and Technology, Anhui Agricultural University) ;
  • Ding, Yueyun (College of Animal Science and Technology, Anhui Agricultural University)
  • Received : 2020.09.28
  • Accepted : 2021.02.07
  • Published : 2021.12.01


Objective: Runs of homozygosity (ROH) are contiguous lengths of homozygous genotypes that can reveal inbreeding levels, selection pressure, and mating schemes. In this study, ROHs were evaluated in Wannan Black pigs to assess the inbreeding levels and the genome regions with high ROH frequency. Methods: In a previous study, we obtained 501.52 GB of raw data from resequencing (10×) of the genome and identified 21,316,754 single-nucleotide variants in 20 Wannan Black pig samples. We investigated the number, length, and frequency of ROH using resequencing data to characterize the homozygosity in Wannan Black pigs and identified genomic regions with high ROH frequencies. Results: In this work, 1,813 ROHs (837 ROHs in 100 to 500 kb, 449 ROHs in 500 to 1,000 kb, 527 ROHs in >1,000 kb) were identified in all samples, and the average genomic inbreeding coefficient (FROH) in Wannan Black pigs was 0.5234. Sixty-one regions on chromosomes 2, 3, 7, 8, 13, 15, and 16 harbored ROH islands. In total, 105 genes were identified in 42 ROH islands, among which some genes were related to production traits. Conclusion: This is the first study to identify ROH across the genome of Wannan Black pigs, the Chinese native breed of the Anhui province. Overall, Wannan Black pigs have high levels of inbreeding due to the influence of ancient and recent inbreeding due to the genome. These findings are a reliable resource for future studies and contribute to save and use the germplasm resources of Wannan Black pigs.



This work was supported by the National Natural Science Foundation of China (31972531), Special Projects of the Central Government Guiding Local Science and Technology Development of Anhui Provincial (202007d06020016), Anhui Provincial Science and Technology Major Project (17030 701008, 17030701061) and the Anhui Provincial Modern Industrial Technology System of Swine.


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