Ma Jun, Gao Xue, Li Junya, Gao Huijiang, Wang Zezhao, Zhang Lupei, Xu Lingyang, Gao Han, Li Hongwei, Wang Yahui, Zhu Bo, Cai Wentao, Wang Congyong, Chen Yan
Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
Beijing Lianyu Beef Cattle Breeding Technology Limited Company, Beijing 100193, China.
Animals (Basel). 2021 Dec 6;11(12):3469. doi: 10.3390/ani11123469.
Huaxi cattle, a specialized beef cattle breed in China, has the characteristics of fast growth, high slaughter rate, and net meat rate, good reproductive performance, strong stress resistance, and wide adaptability. In this study, we evaluated the genetic diversity, population structure, and genetic relationships of Huaxi cattle and its ancestor populations at the genome-wide level, as well as detecting the selection signatures of Huaxi cattle. Principal component analysis (PCA) and phylogenetic analysis revealed that Huaxi cattle were obviously separated from other cattle populations. The admixture analysis showed that Huaxi cattle has distinct genetic structures among all populations at K = 4. It can be concluded that Huaxi cattle has formed its own unique genetic features. Using integrated haplotype score (iHS) and composite likelihood ratio (CLR) methods, we identified 143 and 199 potentially selected genes in Huaxi cattle, respectively, among which nine selected genes (, , , , , , , , and ) related to ion binding, muscle growth and differentiation, and immunity were detected by both methods. Our study sheds light on the unique genetic feature and phylogenetic relationship of Huaxi cattle, provides a basis for the genetic mechanism analysis of important economic traits, and guides further intensive breeding improvement of Huaxi cattle.
华西牛是中国的一个专门化肉牛品种，具有生长速度快、屠宰率和净肉率高、繁殖性能良好、抗应激能力强以及适应性广等特点。在本研究中，我们在全基因组水平上评估了华西牛及其祖先群体的遗传多样性、群体结构和遗传关系，并检测了华西牛的选择印记。主成分分析（PCA）和系统发育分析表明，华西牛与其他牛群体明显分离。混合分析表明，在K = 4时，华西牛在所有群体中具有独特的遗传结构。可以得出结论，华西牛已经形成了自己独特的遗传特征。使用综合单倍型评分（iHS）和复合似然比（CLR）方法，我们分别在华西牛中鉴定出143个和199个潜在的选择基因，其中两种方法均检测到9个与离子结合、肌肉生长和分化以及免疫相关的选择基因（、、、、、、、、和）。我们的研究揭示了华西牛独特的遗传特征和系统发育关系，为重要经济性状的遗传机制分析提供了依据，并指导华西牛进一步的集约化育种改良。
