Genome-Wide Scan for Runs of Homozygosity Identifies Candidate Genes Related to Economically Important Traits in Chinese Merino
Sangang He,
Jiang Di,
Bing Han,
Lei Chen,
Mingjun Liu,
Wenrong Li
Affiliations
Sangang He
Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture; Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Xinjiang, Urumqi 830026, China
Jiang Di
Xinjiang Wool sheep and Cashmere Goat Key Breeding Lab, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Xinjiang, Urumqi 830026, China
Bing Han
Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture; Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Xinjiang, Urumqi 830026, China
Lei Chen
Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture; Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Xinjiang, Urumqi 830026, China
Mingjun Liu
Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture; Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Xinjiang, Urumqi 830026, China
Wenrong Li
Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture; Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Xinjiang, Urumqi 830026, China
In this study, we estimated the number, length, and frequency of runs of homozygosity (ROH) in 635 Chinese Merino and identified genomic regions with high ROH frequency using the OvineSNP50 whole-genome genotyping array. A total of 6039 ROH exceeding 1 Mb were detected in 634 animals. The average number of ROH in each animal was 9.23 and the average length was 5.87 Mb. Most of the ROH were less than 10 Mb, accounting for 88.77% of the total number of detected ROH. In addition, Ovies aries chromosome (OAR) 21 and OAR3 exhibited the highest and lowest coverage of chromosomes by ROH, respectively. OAR1 displayed the highest number of ROH, while the lowest number of ROH was found on OAR24. An inbreeding coefficient of 0.023 was calculated from ROH greater than 1 Mb. Thirteen regions on chromosomes 1, 2, 3, 5, 6, 10, 11, and 16 were found to contain ROH hotspots. Within the genome regions of OAR6 and OAR11, NCAPG/LCORL, FGF11 and TP53 were identified as the candidate genes related to body size, while the genome region of OAR10 harbored RXFP2 gene responsible for the horn trait. These findings indicate the adaptive to directional trait selection in Chinese Merino.
