Wu Sheng, Chen Zhiwen, Zhou Xiaohong, Lu Juanhong, Tian Yingping, Jiang Yaozhou, Liu Qinsong, Wang Zhong, Li Hui, Qu Lujiang, Zhang Fuping
Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, College of Animal Sciences, Guizhou University, Guiyang, 550025, Guizhou Province, China.
Department of Animal Genetics and Breeding, State Key Laboratory of Animal Nutrition, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Poult Sci. 2024 Dec;103(12):104383. doi: 10.1016/j.psj.2024.104383. Epub 2024 Oct 5.
Guizhou province in China is rich in indigenous chicken breeds, playing an essential role in the genetic improvement of modern chickens. Genetic diversity has decreased in recent decades due to accelerated breeding processes and changing conservation priorities. To determine the genetic diversity and population structure of Guizhou indigenous chicken breeds, we used 55K genotyping arrays to conduct population genetic analysis on 233 individuals from 8 Guizhou indigenous breeds and 263 individuals from 9 Guizhou indigenous chicken populations. We evaluated the genetic diversity parameter (heterozygosity, proportion of polymorphic markers, and nucleotide diversity), linkage disequilibrium (LD), population structure, and genetic differentiation (F and genetics distance). Genetic diversity results indicated that the genetic diversity of chicken breeds in Guizhou province is relatively affluent. Among Guizhou breeds, Baiyi black-bone and Guizhou yellow chicken displayed the lowest genetic diversity, as the 2 breeds exhibit lower PN and heterozygosity, the extent of linkage disequilibrium is higher. According to the LD pattern, Guizhou indigenous breeds can be divided into 3 categories. Population structure analysis showed a certain degree of genetic differentiation among local chickens in Guizhou. We argue that Chishui black-bone and Puan black-bone chickens are 2 different geographical regional groups of the same breed. In principal component analysis, individuals from the 2 groups clustered together, and the phylogenetic tree results showed that the 2 groups clustered together to form a branch independent of other breeds, and they displayed an identical pattern of ancestral lineage composition. The research results will provide a reference for protecting local chicken genetic resources in Guizhou Province and promote the protection and utilization of genetic resources.
中国贵州省拥有丰富的本土鸡品种，在现代鸡的遗传改良中发挥着重要作用。近几十年来，由于育种进程加速和保护重点的变化，遗传多样性有所下降。为了确定贵州本土鸡品种的遗传多样性和种群结构，我们使用55K基因分型芯片对来自8个贵州本土品种的233只个体和来自9个贵州本土鸡群体的263只个体进行了群体遗传分析。我们评估了遗传多样性参数（杂合度、多态性标记比例和核苷酸多样性）、连锁不平衡（LD）、种群结构和遗传分化（F和遗传距离）。遗传多样性结果表明，贵州省鸡品种的遗传多样性较为丰富。在贵州的品种中，白羽乌骨鸡和贵州黄鸡的遗传多样性最低，因为这两个品种的多态性标记比例和杂合度较低，连锁不平衡程度较高。根据连锁不平衡模式，贵州本土品种可分为3类。种群结构分析表明贵州本地鸡之间存在一定程度的遗传分化。我们认为赤水乌骨鸡和普安乌骨鸡是同一品种的两个不同地理区域群体。在主成分分析中，这两个群体的个体聚集在一起，系统发育树结果表明这两个群体聚集在一起形成一个独立于其他品种的分支，并且它们显示出相同的祖先谱系组成模式。研究结果将为保护贵州省地方鸡遗传资源提供参考，并促进遗传资源的保护和利用。
