Genetic Diversity and Phyletic Evolution of Eleven Chinese Indigenous and Three Commercial Chicken Breeds by mtDNA Sequences

ABSTRACT Chinese indigenous chicken breeds are geographically widespread, and a total of 116 indigenous chicken breeds are listed as Chinese national genetic resources. However, these indigenous chicken breeds are facing serious challenges as declining population and germplasm degeneration because lots of commercial chicken breeds had been introduced. In this study, the genetic variations of eleven Chinese indigenous chicken breeds of Sichuan province and three commercial chicken breeds were investigated based on the partial mitochondrial DNA D-loop of 487bp in length. 147 individuals from 14 breeds were examined and 34 haplotypes were observed. Genetic diversity analysis showed that the highest haplotype diversity level was found in Dahen Chicken (DH) population, while the Arbor Acres Chicken (WF) and Roman layer (RM) showed lower genetic diversity levels. The long-term artificial selection may lead to reduced nucleotide diversity. Genetic population differentiation analysis indicated that most of the variation (80.80%) was attributed to variations among breeds. Phylogenetic analysis revealed that these individuals were divided into four distinct genetic clades, including cluster A, B, C and D. Eighteen haplotypes were classified as cluster A, eight haplotypes were classified as cluster B, five haplotypes were classified as cluster C and three haplotypes were classified as cluster D. There was no breed-specific clade. Our study firstly identified the population’s genetic structure of Chinese indigenous chickens and the most important commercial breeds in Sichuan province, though the genetic diversity of indigenous breeds did not suffer obvious decrease, but could be helpful for efficient artificial breeding selection and genetic resources conservation.

摘要：中国地方鸡品种地理分布广泛，目前共有116个地方鸡品种被列入中国国家级畜禽遗传资源名录。然而，由于大量商业鸡品种的引入，这些地方鸡品种正面临种群数量下降、种质退化等严峻挑战。本研究基于长度为487bp的线粒体DNA D-loop（mitochondrial DNA D-loop）片段，对四川省11个中国地方鸡品种及3个商业鸡品种的遗传变异进行了分析。本研究共检测了14个品种的147个个体，共观察到34个单倍型（haplotype）。遗传多样性分析结果显示，大骨鸡（Dahen Chicken, DH）种群的单倍型多样性水平最高，而爱拔益加肉鸡（Arbor Acres Chicken, WF）与罗曼蛋鸡（Roman layer, RM）的遗传多样性水平较低。长期人工选择可能会导致核苷酸多样性（nucleotide diversity）降低。群体遗传分化分析表明，绝大多数变异（80.80%）来自品种间的遗传差异。系统发育分析显示，供试个体被划分为4个独立的遗传进化枝，分别为簇A、B、C、D；其中18个单倍型归为簇A，8个归为簇B，5个归为簇C，3个归为簇D，未发现品种特异性进化枝。本研究首次明确了四川省地方鸡品种及主要商业鸡品种的群体遗传结构，尽管供试地方品种的遗传多样性未出现明显下降，但本研究结果可为高效人工选育及遗传资源保护提供重要参考。