Preliminary Study on the Genetic Structure and Functional Candidate Genes of Grassland-Thoroughbreds Based on Whole-Genome Resequencing
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 ath...
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2025-05-01
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| author | Wenqi Ding Wendian Gong Tugeqin Bou Lin Shi Yanan Lin Xiaoyuan Shi Zheng Li Huize Wu Manglai Dugarjaviin Dongyi Bai Yiping Zhao |
| author_facet | Wenqi Ding Wendian Gong Tugeqin Bou Lin Shi Yanan Lin Xiaoyuan Shi Zheng Li Huize Wu Manglai Dugarjaviin Dongyi Bai Yiping Zhao |
| author_sort | Wenqi Ding |
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| description | 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 (<i>ATF2</i>, <i>NDUFS7</i>, <i>PRKG1</i>, <i>IGFN1</i>, <i>MTOR</i>, <i>TTN</i>) and growth and development (<i>MTOR</i>, <i>IGFN1</i>, <i>COL21A1</i>, <i>NEDD4</i>, <i>PIEZO1</i>) 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. |
| format | Article |
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| institution | DOAJ |
| issn | 2076-2615 |
| language | English |
| publishDate | 2025-05-01 |
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| series | Animals |
| spelling | doaj-art-e18933c0830b4e4aa403a8f899ae7d342025-08-20T03:14:35ZengMDPI AGAnimals2076-26152025-05-011510146210.3390/ani15101462Preliminary Study on the Genetic Structure and Functional Candidate Genes of Grassland-Thoroughbreds Based on Whole-Genome ResequencingWenqi Ding0Wendian Gong1Tugeqin Bou2Lin Shi3Yanan Lin4Xiaoyuan Shi5Zheng Li6Huize Wu7Manglai Dugarjaviin8Dongyi Bai9Yiping Zhao10Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, ChinaKey Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, ChinaKey Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, ChinaKey Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, ChinaKey Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, ChinaKey Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, ChinaKey Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, ChinaKey Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, ChinaKey Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, ChinaKey Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, ChinaKey Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, ChinaSpeed 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 (<i>ATF2</i>, <i>NDUFS7</i>, <i>PRKG1</i>, <i>IGFN1</i>, <i>MTOR</i>, <i>TTN</i>) and growth and development (<i>MTOR</i>, <i>IGFN1</i>, <i>COL21A1</i>, <i>NEDD4</i>, <i>PIEZO1</i>) 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.https://www.mdpi.com/2076-2615/15/10/1462grassland-thoroughbredsselection signalwhole-genome resequencing |
| spellingShingle | Wenqi Ding Wendian Gong Tugeqin Bou Lin Shi Yanan Lin Xiaoyuan Shi Zheng Li Huize Wu Manglai Dugarjaviin Dongyi Bai Yiping Zhao Preliminary Study on the Genetic Structure and Functional Candidate Genes of Grassland-Thoroughbreds Based on Whole-Genome Resequencing Animals grassland-thoroughbreds selection signal whole-genome resequencing |
| title | Preliminary Study on the Genetic Structure and Functional Candidate Genes of Grassland-Thoroughbreds Based on Whole-Genome Resequencing |
| title_full | Preliminary Study on the Genetic Structure and Functional Candidate Genes of Grassland-Thoroughbreds Based on Whole-Genome Resequencing |
| title_fullStr | Preliminary Study on the Genetic Structure and Functional Candidate Genes of Grassland-Thoroughbreds Based on Whole-Genome Resequencing |
| title_full_unstemmed | Preliminary Study on the Genetic Structure and Functional Candidate Genes of Grassland-Thoroughbreds Based on Whole-Genome Resequencing |
| title_short | Preliminary Study on the Genetic Structure and Functional Candidate Genes of Grassland-Thoroughbreds Based on Whole-Genome Resequencing |
| title_sort | preliminary study on the genetic structure and functional candidate genes of grassland thoroughbreds based on whole genome resequencing |
| topic | grassland-thoroughbreds selection signal whole-genome resequencing |
| url | https://www.mdpi.com/2076-2615/15/10/1462 |
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