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Zhou C, Zhang Y, Ma T, Wu D, Yang Y, Wang D, Li X, Guo S, Yang S, Song Y, Zhang Y, Zuo Y, Cao G. Whole-Genome Resequencing of Ujimqin Sheep Identifies Genes Associated with Vertebral Number. Animals (Basel) 2024; 14:677. [PMID: 38473062 DOI: 10.3390/ani14050677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/07/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
The number of vertebrae is a crucial economic trait that can significantly impact the carcass length and meat production in animals. However, our understanding of the quantitative trait loci (QTLs) and candidate genes associated with the vertebral number in sheep (Ovis aries) remains limited. To identify these candidate genes and QTLs, we collected 73 Ujimqin sheep with increased numbers of vertebrae (T13L7, T14L6, and T14L7) and 23 sheep with normal numbers of vertebrae (T13L6). Through high-throughput genome resequencing, we obtained a total of 24,130,801 effective single-nucleotide polymorphisms (SNPs). By conducting a selective-sweep analysis, we discovered that the most significantly selective region was located on chromosome 7. Within this region, we identified several genes, including VRTN, SYNDIG1L, LTBP2, and ABCD4, known to regulate the spinal development and morphology. Further, a genome-wide association study (GWAS) performed on sheep with increased and normal vertebral numbers confirmed that ABCD4 is a candidate gene for determining the number of vertebrae in sheep. Additionally, the most significant SNP on chromosome 7 was identified as a candidate QTL. Moreover, we detected two missense mutations in the ABCD4 gene; one of these mutations (Chr7: 89393414, C > T) at position 22 leads to the conversion of arginine (Arg) to glutamine (Gln), which is expected to negatively affect the protein's function. Notably, a transcriptome expression profile in mouse embryonic development revealed that ABCD4 is highly expressed during the critical period of vertebral formation (4.5-7.5 days). Our study highlights ABCD4 as a potential major gene influencing the number of vertebrae in Ujimqin sheep, with promising prospects for future genome-assisted breeding improvements in sheep.
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Affiliation(s)
- Chuanqing Zhou
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010010, China
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010020, China
| | - Yue Zhang
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010010, China
| | - Teng Ma
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010010, China
| | - Dabala Wu
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010070, China
| | - Yanyan Yang
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010070, China
| | - Daqing Wang
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010070, China
| | - Xiunan Li
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010070, China
| | - Shuchun Guo
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010070, China
| | - Siqi Yang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010020, China
| | - Yongli Song
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010020, China
| | - Yong Zhang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010020, China
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yongchun Zuo
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot 010020, China
| | - Guifang Cao
- College of Veterinary Medicine, Inner Mongolia Agricultural University, Hohhot 010010, China
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