Ding Wenqi, Gong Wendian, Bou Tugeqin, Shi Lin, Lin Yanan, Shi Xiaoyuan, Li Zheng, Wu Huize, Dugarjaviin Manglai, Bai Dongyi
Key Laboratory of Equus Germplasm Innovation (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Hohhot 010018, China.
Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot 010018, China.
Animals (Basel). 2025 May 18;15(10):1458. doi: 10.3390/ani15101458.
Copy number variation (CNV) is an important source of genetic variation. However, studies utilizing whole-genome sequencing to investigate CNVs in horse populations and their effects on traits remain relatively limited. This study aims to address the lack of research on the impact of copy number variation (CNV) on racing performance in horse populations, providing new insights for locally bred racing breeds. We analyzed 60 offspring derived from the crossbreeding of Thoroughbred horses and Xilingol horses. These horses were temporarily named "Grassland-Thoroughbred" and were divided into two groups: 30 racing horses and 30 non-racing horses. A total of 89,527 CNVs were identified. After merging overlapping CNVs, 982 copy number variation regions (CNVRs) were recognized, among which the racing horse group (RH) had 29 unique CNVRs, while the non-racing horse group (NR) had 4 unique CNVRs. In addition, a total of 195 genes overlapping with CNVRs were identified. Transcriptomic analysis revealed 120 differentially expressed genes, with expressed in both CNVR-overlapping genes and mRNA. Both CNVR-overlapping genes and differentially expressed genes were enriched in the MAPK signaling pathway; CNV may affect gene expression through gene dosage effects or regulatory mechanisms. Using Vst statistical analysis, we further screened candidate CNVRs in autosomes that exceeded the 95% differentiation threshold between the RH and NR populations. Several key genes associated with energy metabolism and muscle function were identified, including , , , , , and . These findings provide new insights into the genetic structural variation in racing performance and adaptability, fill the gap in CNV studies in the genomics of Grassland-Thoroughbred horses, and offer valuable genomic data for optimizing breeding strategies in native racing horse populations.
拷贝数变异（CNV）是遗传变异的一个重要来源。然而，利用全基因组测序来研究马群体中的CNV及其对性状的影响的研究仍然相对有限。本研究旨在解决关于拷贝数变异（CNV）对马群体赛跑性能影响的研究不足问题，为本地培育的赛马品种提供新的见解。我们分析了60匹由纯种马和锡林郭勒马杂交产生的后代。这些马被暂时命名为“草原 - 纯种马”，并分为两组：30匹赛马和30匹非赛马。共鉴定出89,527个CNV。在合并重叠的CNV后，识别出982个拷贝数变异区域（CNVR），其中赛马组（RH）有29个独特的CNVR，而非赛马组（NR）有4个独特的CNVR。此外，共鉴定出195个与CNVR重叠的基因。转录组分析揭示了120个差异表达基因，这些基因在CNVR重叠基因和mRNA中均有表达。CNVR重叠基因和差异表达基因均富集于MAPK信号通路；CNV可能通过基因剂量效应或调控机制影响基因表达。使用Vst统计分析，我们进一步在常染色体中筛选出超过RH和NR群体之间95%分化阈值的候选CNVR。鉴定出了几个与能量代谢和肌肉功能相关的关键基因，包括 、 、 、 、 和 。这些发现为赛跑性能和适应性的遗传结构变异提供了新的见解，填补了草原 - 纯种马基因组学中CNV研究的空白，并为优化本地赛马群体的育种策略提供了有价值的基因组数据。
