Analysis of ROH Characteristics Across Generations in Grassland-Thoroughbred Horses and Identification of Loci Associated with Athletic Traits
The core objective of racehorse breeding is to enhance the speed and endurance of the horses. The Grassland-Thoroughbred is an emerging horse breed developed in northern China in recent years, characterized by excellent speed performance, enduring stamina, and strong environmental adaptability. Howe...
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2025-07-01
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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 |
| author_facet | Wenqi Ding Wendian Gong Tugeqin Bou Lin Shi Yanan Lin Xiaoyuan Shi Zheng Li Huize Wu Manglai Dugarjaviin Dongyi Bai |
| author_sort | Wenqi Ding |
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| description | The core objective of racehorse breeding is to enhance the speed and endurance of the horses. The Grassland-Thoroughbred is an emerging horse breed developed in northern China in recent years, characterized by excellent speed performance, enduring stamina, and strong environmental adaptability. However, research on the genetic characteristics within this breed and the genes associated with athletic performance remains relatively limited. We conducted whole-genome resequencing of Grassland-Thoroughbred F1, F2, F3, and the crossbred population (CY) and obtained a total of 4056.23 Gb of high-quality data after quality control. The single nucleotide polymorphisms (SNPs) were primarily distributed in intergenic regions, followed by intronic regions. Principal component analysis (PCA) and STRUCTURE revealed clear distinctions among the generations, with a notable overlap between CY and F3. Using the SNP dataset, we analyzed the number and length distribution patterns of runs of homozygosity (ROHs) in the genomes of different generational groups of Grassland-Thoroughbreds. Short ROHs ranging from 0.5 to 2 Mb were the most abundant, with the following distribution: F1 (85.15%) > F2 (82.92%) > CY (78.75%) > F3 (77.51%). Medium-length ROHs (2–8 Mb) and long ROHs (>8 Mb) together exhibited a similar but opposite trend. The average length of ROHs was 1.57 Mb. The inbreeding coefficients (F_ROH) among different generational groups of Grassland-Thoroughbreds were as follows: F1 (0.0942) < F2 (0.1197) < CY (0.1435) < F3 (0.1497). Through ROH island analysis, 10 high-frequency ROH regions were identified and annotated with 120 genes. Genomic regions and candidate genes associated with athletic traits—<i>ACAD8</i>, <i>OPCML</i>, <i>PRDX2</i>, <i>NTM</i>, <i>NDUFB7</i>, <i>SCL25A15</i>, <i>FOXO1</i>, and <i>SLC4A10</i>—were identified. These genes may play important roles in regulating muscle performance, mitochondrial energy supply, and learning and memory processes in horses and are closely associated with the athletic ability of the Grassland-Thoroughbred population. This study is the first to systematically characterize the genomic diversity and inbreeding dynamics of the Grassland-Thoroughbred during the breeding process. It identifies candidate genes that may influence athletic performance, thereby providing an important molecular foundation and theoretical basis for the genetic improvement and performance-based selection of this emerging breed. |
| format | Article |
| id | doaj-art-4ea46568cd584a6e9fdf32ddea457015 |
| institution | DOAJ |
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| spelling | doaj-art-4ea46568cd584a6e9fdf32ddea4570152025-08-20T02:45:42ZengMDPI AGAnimals2076-26152025-07-011514206810.3390/ani15142068Analysis of ROH Characteristics Across Generations in Grassland-Thoroughbred Horses and Identification of Loci Associated with Athletic TraitsWenqi Ding0Wendian Gong1Tugeqin Bou2Lin Shi3Yanan Lin4Xiaoyuan Shi5Zheng Li6Huize Wu7Manglai Dugarjaviin8Dongyi Bai9Key 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, ChinaThe core objective of racehorse breeding is to enhance the speed and endurance of the horses. The Grassland-Thoroughbred is an emerging horse breed developed in northern China in recent years, characterized by excellent speed performance, enduring stamina, and strong environmental adaptability. However, research on the genetic characteristics within this breed and the genes associated with athletic performance remains relatively limited. We conducted whole-genome resequencing of Grassland-Thoroughbred F1, F2, F3, and the crossbred population (CY) and obtained a total of 4056.23 Gb of high-quality data after quality control. The single nucleotide polymorphisms (SNPs) were primarily distributed in intergenic regions, followed by intronic regions. Principal component analysis (PCA) and STRUCTURE revealed clear distinctions among the generations, with a notable overlap between CY and F3. Using the SNP dataset, we analyzed the number and length distribution patterns of runs of homozygosity (ROHs) in the genomes of different generational groups of Grassland-Thoroughbreds. Short ROHs ranging from 0.5 to 2 Mb were the most abundant, with the following distribution: F1 (85.15%) > F2 (82.92%) > CY (78.75%) > F3 (77.51%). Medium-length ROHs (2–8 Mb) and long ROHs (>8 Mb) together exhibited a similar but opposite trend. The average length of ROHs was 1.57 Mb. The inbreeding coefficients (F_ROH) among different generational groups of Grassland-Thoroughbreds were as follows: F1 (0.0942) < F2 (0.1197) < CY (0.1435) < F3 (0.1497). Through ROH island analysis, 10 high-frequency ROH regions were identified and annotated with 120 genes. Genomic regions and candidate genes associated with athletic traits—<i>ACAD8</i>, <i>OPCML</i>, <i>PRDX2</i>, <i>NTM</i>, <i>NDUFB7</i>, <i>SCL25A15</i>, <i>FOXO1</i>, and <i>SLC4A10</i>—were identified. These genes may play important roles in regulating muscle performance, mitochondrial energy supply, and learning and memory processes in horses and are closely associated with the athletic ability of the Grassland-Thoroughbred population. This study is the first to systematically characterize the genomic diversity and inbreeding dynamics of the Grassland-Thoroughbred during the breeding process. It identifies candidate genes that may influence athletic performance, thereby providing an important molecular foundation and theoretical basis for the genetic improvement and performance-based selection of this emerging breed.https://www.mdpi.com/2076-2615/15/14/2068Grassland-Thoroughbredswhole-genome resequencingROH |
| spellingShingle | Wenqi Ding Wendian Gong Tugeqin Bou Lin Shi Yanan Lin Xiaoyuan Shi Zheng Li Huize Wu Manglai Dugarjaviin Dongyi Bai Analysis of ROH Characteristics Across Generations in Grassland-Thoroughbred Horses and Identification of Loci Associated with Athletic Traits Animals Grassland-Thoroughbreds whole-genome resequencing ROH |
| title | Analysis of ROH Characteristics Across Generations in Grassland-Thoroughbred Horses and Identification of Loci Associated with Athletic Traits |
| title_full | Analysis of ROH Characteristics Across Generations in Grassland-Thoroughbred Horses and Identification of Loci Associated with Athletic Traits |
| title_fullStr | Analysis of ROH Characteristics Across Generations in Grassland-Thoroughbred Horses and Identification of Loci Associated with Athletic Traits |
| title_full_unstemmed | Analysis of ROH Characteristics Across Generations in Grassland-Thoroughbred Horses and Identification of Loci Associated with Athletic Traits |
| title_short | Analysis of ROH Characteristics Across Generations in Grassland-Thoroughbred Horses and Identification of Loci Associated with Athletic Traits |
| title_sort | analysis of roh characteristics across generations in grassland thoroughbred horses and identification of loci associated with athletic traits |
| topic | Grassland-Thoroughbreds whole-genome resequencing ROH |
| url | https://www.mdpi.com/2076-2615/15/14/2068 |
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