关键词: 黄鸡, 线粒体DNA D-loop, 遗传变异, 遗传分化, 群体历史

Abstract:

【Objective】 Indigenous yellow-feathered chicken is an important poultry genetic resource in China. The genetic diversity of these chickens was evaluated to facilitate scientific protection policies and to improve their use.【Method】 A total of 1283 mitochondrial DNA fragments (mtDNA D-loop, 519 bp) were investigated including 694 de novo and 589 previously published units from 28 indigenous yellow-feathered chicken breeds from southern China. These data were subsequently used to calculate the genetic diversity, to construct median-joining networks of haplotypes, and to investigate geographical distribution patterns of haplotypes by using principal coordinate analysis, analysis of molecular variance, and neutral test. The origin of rare haplogroups was inferred from the geographical distribution pattern of mitochondrial DNA haplogroups of Asian and Pacific indigenous chickens.【Result】One hundred and one mutation sites were detected in 1 283 samples, of which 92 were polymorphic. One hundred and sixty-nine haplotypes, belonging to haplogroups A-E and G, were defined. The predominant haplogroups were A (15.43%), B (49.26%), C (18.55%), and E (16.37%), while D (0.31%) and G (0.08%) were the rare haplogroups within the total samples. Chickens from Henan Province covered all six haplogroups; Chickens from Guangdong Province had the largest number of haplotypes (64), whereas those from Zhejiang (19) and Hainan (12) Provinces had the lowest. Haplogroups A and B occurred in all 28 breeds. Haplogroup D existed only in Huainan yellow, Gushi, Ningdu yellow and Xiayan chickens, whereas haplogroup G only occurred in Gushi chickens. The distribution frequency of haplogroup D and the number of haplotypes indicated that haplogroup D of indigenous yellow-feathered chickens in southern China could originated from Southeast Asia. The evidence from geographical distribution and median-joining networks of haplogroup G indicated that haplogroup G of chickens from Henan Province and South Asia could originated from Southwest China. The indigenous yellow-feathered chickens in southern China had a total haplotype diversity of 0.903±0.005 and nucleotide diversity of 0.01269±n.d. Indigenous yellow-feathered chickens from Henan and Hunan Provinces had the highest level of haplotype diversity of 0.916±0.011 and 0.01358±0.00039, respectively, and the nucleotide diversity of 0.913±0.012 and 0.01345±0.00042, respectively. The lowest level of haplotype diversity was found in Hainan Province (0.736±0.076), and the lowest level of nucleotide diversity was found in Jiangxi Province (0.00981±0.00072). Huainan yellow, Gushi and Yunyang da chickens retained the highest level of haplotype diversity; Jianghan, Huainan yellow and Huanglang chickens had the highest level of nucleotide diversity, whereas the haplotype diversity and nucleotide diversity in Hongshan, Guangxi yellow and Xiaoshan chickens were the lowest. Wenchang chickens were genetically close to Hentian chickens, which was consistent with their breeding history. The population genetic structure of yellow-feathered chickens was less clear, and the molecular variance component of within-population was significantly higher than others. The neutral test indicated that the yellow-feathered chickens in southern China did not sustain obvious population expansion at the breed level, with the exception of haplogroups A, B and E.【Conclusion】 The results suggested that yellow-feathered chickens had a good conservation status with high level of genetic diversity, although Hongshan, Xiaoshan and Guangxi yellow chickens required further protection. Hybridization between chickens was common in yellow-feathered chickens, which had experienced population expansion. Indigenous chickens from Southeast Asia and Southwest China had substantial genetic contributions to indigenous yellow-feathered chickens in southern China.

Key words: yellow-feathered chicken, mitochondrial DNA D-loop, genetic variation, genetic divergence, demographic history