Abstract:Black bone chickens (Gallus gallus domesticus) are excellent indigenous chicken resources in China and commonly believed to have medicinal properties. The study on the genetic diversity and breed identification of the black bone chickens is of great significance for genetic conservation. For this study, the complete mitochondrial DNA D-loop sequences of 197 chickens from 5 breeds (Silkie, Dongxiang Blue-eggshell, Jinhu Black-bone, Yugan Black-bone and Zhu Si) were analyzed. The size of full-length chicken mtDNA D-loop of 5 black bone breeds were 1 231 to 1 232 bp, with a single-base deletion from the 859 bp site in the 1 231 bp sequences. A total of 27 variable sites that defined 18 haplotypes were identified. The average haplotype diversity, nucleotide diversity and mean number of nucleotide differences were 0.862±0.013, 0.005 80±0.001 07 and 7.137, respectively. The median network showed that genetic structure of the mtDNA haplotypes of black bone chickens were distributed across 4 clades (haplogroups): Clades A, B, C, and E. However, haplogroups were dispersed in different breeds, and the distribution of morphology and geographical pattern was not obvious. This study data suggested that genetic distance between Zhu Si and Silkie was longer than the other breeds, which verified that Zhu Si chickens were hybridized from fast-growing broiler as maternal line. Chinese black bone chicken had relatively lower genetic diversity and likely shared 4 common maternal lineages. The results could be used as a reference for preservation, improvement and identification of Chinese black bone chickens.
[1] 包文斌, 陈国宏, 吴信生, 等. 2007. 中国红原鸡和泰国红原鸡遗传多样性分析[J]. 遗传, 29(5): 587-592. (Bao W B, Chen G H, Wu X S, et al.2007. Genetic diversity of red junglefowl in China (Gallus gallus spadiceus) and red junglefowl (Gallus gallus gallus) in Thailand[J]. Hereditas (Beijing), 29(5): 587-592.) [2] 高玉时, 贾晓旭, 唐修君, 等. 2015. 基于线粒体基因组D-loop区全序列分析安义瓦灰鸡遗传多样性及其起源进化关系[J]. 农业生物技术学报, 23(7): 940-944. (Gao Y S, Jia X X, Tang X J, et al.2015. The genetic diversity and origin analysis of Anyi Tile-like chickens (Gallus gallus domestiaus) based on mitochondrial DNA D-loop sequence[J]. Journal of Agricultural Biotechnology, 23(7): 940-944.) [3] 国家畜禽遗传资源委员会. 2011. 中国畜禽遗传资源志: 家禽志[M]. 中国农业出版社, 北京. pp. 2-3. (China National Commission of Animal Genetic Resources. 2011. Animal Genetic Resources in China: Poultry[M]. China Agriculture Press, Beijing, China. pp. 2-3.) [4] 贾晓旭, 唐修君, 樊艳凤, 等. 2017.华东地区地方鸡品种mtDNA控制区遗传多样性[J]. 生物多样性, 25(5): 540-548. (Jia X X, Tang X J, Fan Y F, et al.2017. Genetic diversity of local chicken breeds in east China based on mitochondrial DNA D-loop region[J]. Biodiversity Science, 25(5): 540-548.) [5] 陆俊贤, 贾晓旭, 唐修君, 等. 2016. 2个云南原始鸡种遗传多样性及其与红色原鸡的亲缘关系[J]. 浙江大学学报(农业与生命科学版), 42(3): 385-390. (Lu J X, Jia X X, Tang X J, et al.2016. Genetic diversity of two local Yunnan chicken breeds and their relationships with red junglefowl[J]. Journal of Zhejiang University (Agriculture and Life Sciences), 42(3): 385-390.) [6] 王荣琼, 孙利民, 胡瑀, 等. 2020. 盐津乌骨鸡mtDNA D-loop区遗传多样性及其保种效果分析[J].家畜生态学报, 2020, 41(11): 18-23. (Wang R Q, Sun L M, Hu Yet al.2020. Genetic diversity and conservation effect of Yanjin black-bone chicken based on genetic marker of mtDNA D-loop region[J]. Acta Ecologiae Animalis Domastici, 41(11): 18-23) [7] 翁茁先, 黄佳琼, 张仕豪, 等. 2019. 利用线粒体COⅠ基因揭示中国乌骨鸡遗传多样性和群体遗传结构[J].生物多样性, 27(6): 667-676. (Wen Z X, Huang J Q, Zhang S Het al.2019. Genetic diversity and population structure of black-bone chickens in China revealed by mitochondrial COⅠ gene sequences[J]. Biodiversity Science, 27(6): 667-676.) [8] 徐文娟, 朱文奇, 束婧婷, 等. 2014. 我国主要乌骨鸡品种遗传多样性和系统进化研究[J].中国畜牧杂志, 50(23): 10-14. (Xu W J, Zhu W Q, Shu J Tet al.2014. Study on genetic diversity and phylogenetic evolution in Chinese main black-bone chicken breeds[J]. Chinese Journal of Animal Science, 50(23): 10-14) [9] 赵习彬, 王保健, 简克灵, 等. 2017. 基于线粒体细胞色素氧化酶b (cytb)全基因序列分析我国部分地区兔痒螨的遗传变异特征[J]. 畜牧兽医学报, 48(4): 714-721. (Zhao X B, Wang B J, Jian K L, et al.2017. Analysis of the characteristics of genetic variability within Psoroptes cuniculi isolates in some regions of China, inferred by mitochondrial cytochrome oxidase b gene[J]. ActaVeterinaria et Zootechnica Sinica, 48(4): 714-721.) [10] Bandelt H J, Forster P, Röhl A.1999. Median-joining networks for inferring intraspecific phylogenies[J]. Molecular Biology & Evolution, 16(1): 37-48. [11] Gao Y S, Jia X X, Tang X J, et al.2017. The genetic diversity of chicken breeds from Jiangxi, assessed with BCDO2 and the complete mitochondrial DNA D-loop region[J]. PLOS ONE, 12(3): e0173192. [12] Jia X X, Tang X J, Lu J X, et al.2016. The investigation of genetic diversity and evolution of Daweishan Mini chicken based on the complete mitochondrial (mt) DNA D-loop region sequence[J]. Mitochondrial DNA, 27(4): 3001-3004. [13] Liu Y P, Wu G S, Yao Y G, et al.2006. Multiple maternal origins of chickens: Out of the Asian jungles[J]. Molecular Phylogenetics & Evolution, 38(1): 12-19. [14] Miao Y W, Peng M S, Wu G S, et al.2013. Chicken domestication: an updated perspective based on mitochondrial genomes[J]. Heredity, 110(3): 277-282. [15] Rozas J, Sanchezelbarrio J C, Messeguer X, et al.2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods[J]. Bioinformatics, 19(18): 2496-2497. [16] Tamura K, Stecher G, Peterson D, et al.2013. MEGA6: Molecular evolutionary genetics analysis, version 6.0[J]. Molecular Biology and Evolution. 30(12): 2725-2729. [17] Thompson J D, Gibson T J, Plewniak F, et al.1997. The ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools[J]. Nucleic Acids Research, 25(24): 4876-4882. [18] Wang M S, Thakur M, Peng M S, et al.2020. 863 genomes reveal the origin and domestication of chicken[J]. Cell Research, 30(8): 693-701.