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Ding W, Gong W, Bou T, Shi L, Lin Y, Shi X, Li Z, Wu H, Dugarjaviin M, Bai D, Zhao Y. Preliminary Study on the Genetic Structure and Functional Candidate Genes of Grassland-Thoroughbreds Based on Whole-Genome Resequencing. Animals (Basel) 2025; 15:1462. [PMID: 40427339 PMCID: PMC12108167 DOI: 10.3390/ani15101462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2025] [Revised: 05/09/2025] [Accepted: 05/13/2025] [Indexed: 05/29/2025] Open
Abstract
Speed and endurance are the primary goals in racehorse breeding. The Grassland-Thoroughbred is a newly developed breed in northern China that combines speed, endurance, and environmental adaptability. However, current research on the genetic background of this breed and the genes associated with athletic performance remains limited. We conducted whole-genome resequencing on Mongolian (MG), Thoroughbred (TB), Xilingol (XL), and Grassland-Thoroughbred (CY) horses, generating 3813.74 Gb of clean data after quality control. The number of transitions was significantly higher than that of transversions. The SNPs were mainly located in intergenic regions, followed by intronic regions. Principal component analysis, population structure analysis, and phylogenetic tree results indicated that the CYs had a distinct genetic background from MGs, TBs, and XLs, but based on PCA and phylogenetic clustering, they showed greater genetic similarity to Thoroughbreds. Using fixation index (Fst) and nucleotide diversity ratio (π ratio) analyses between CYs and the other three horse populations, 70, 76, and 80 candidate genes were identified from the intersection of the two methods, respectively. A total of 179 candidate genes were obtained from the union of the three groups. Candidate genes associated with athletic performance (ATF2, NDUFS7, PRKG1, IGFN1, MTOR, TTN) and growth and development (MTOR, IGFN1, COL21A1, NEDD4, PIEZO1) were screened. These genes are related to athletic ability and developmental processes in the CY population. Our study reveals genomic information associated with important traits in Grassland-Thoroughbreds and identifies valuable candidate genes, laying a foundation for future breeding and trait association studies.
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Affiliation(s)
- Wenqi Ding
- Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (W.D.); (W.G.); (T.B.); (L.S.); (Y.L.); (X.S.); (Z.L.); (H.W.); (M.D.); (D.B.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Wendian Gong
- Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (W.D.); (W.G.); (T.B.); (L.S.); (Y.L.); (X.S.); (Z.L.); (H.W.); (M.D.); (D.B.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Tugeqin Bou
- Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (W.D.); (W.G.); (T.B.); (L.S.); (Y.L.); (X.S.); (Z.L.); (H.W.); (M.D.); (D.B.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Lin Shi
- Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (W.D.); (W.G.); (T.B.); (L.S.); (Y.L.); (X.S.); (Z.L.); (H.W.); (M.D.); (D.B.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Yanan Lin
- Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (W.D.); (W.G.); (T.B.); (L.S.); (Y.L.); (X.S.); (Z.L.); (H.W.); (M.D.); (D.B.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Xiaoyuan Shi
- Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (W.D.); (W.G.); (T.B.); (L.S.); (Y.L.); (X.S.); (Z.L.); (H.W.); (M.D.); (D.B.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Zheng Li
- Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (W.D.); (W.G.); (T.B.); (L.S.); (Y.L.); (X.S.); (Z.L.); (H.W.); (M.D.); (D.B.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Huize Wu
- Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (W.D.); (W.G.); (T.B.); (L.S.); (Y.L.); (X.S.); (Z.L.); (H.W.); (M.D.); (D.B.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Manglai Dugarjaviin
- Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (W.D.); (W.G.); (T.B.); (L.S.); (Y.L.); (X.S.); (Z.L.); (H.W.); (M.D.); (D.B.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Dongyi Bai
- Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (W.D.); (W.G.); (T.B.); (L.S.); (Y.L.); (X.S.); (Z.L.); (H.W.); (M.D.); (D.B.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Yiping Zhao
- Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, China; (W.D.); (W.G.); (T.B.); (L.S.); (Y.L.); (X.S.); (Z.L.); (H.W.); (M.D.); (D.B.)
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China
- Equus Research Center, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
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