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

doi:10.17520/biods.2019013

生物多样性 ›› 2019, Vol. 27 ›› Issue (6): 667-676. DOI: 10.17520/biods.2019013

• 研究报告: 动物多样性 • 上一篇下一篇

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

翁茁先^1,^2,³,黄佳琼²,张仕豪²,余锴纯²,钟福生^1,^2,³,黄勋和^2,^3,^*(),张彬^1,^*()

1 湖南农业大学动物科学技术学院, 长沙 410128
2 嘉应学院生命科学学院, 广东梅州 514015
3 广东省五华三黄鸡科技创新中心, 广东梅州 514015

收稿日期:2019-01-17 接受日期:2019-05-20 出版日期:2019-06-20 发布日期:2019-06-14
通讯作者: 黄勋和,张彬
基金资助:
广东省公益研究与能力建设项目(2016A030303068);嘉应学院省市共建重点建设项目(嘉院[2017]27号)

Genetic diversity and population structure of black-bone chickens in China revealed by mitochondrial COI gene sequences

Weng Zhuoxian^1,^2,³,Huang Jiaqiong²,Zhang Shihao²,Yu Kaichun²,Zhong Fusheng^1,^2,³,Huang Xunhe^2,^3,^*(),Zhang Bin^1,^*()

1 College of Animal Science & Technology, Hunan Agricultural University, Changsha 410128
2 School of Life Science, Jiaying University, Meizhou, Guangdong 514015
3 Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, Meizhou, Guangdong 514015

Received:2019-01-17 Accepted:2019-05-20 Online:2019-06-20 Published:2019-06-14
Contact: Huang Xunhe,Zhang Bin

摘要/Abstract

摘要：

全面了解中国乌骨鸡的遗传背景有利于保护和开发利用其种质资源。本研究测定了中国12个乌骨鸡品种线粒体细胞色素c氧化酶亚基I (cytochrome c oxidase subunit I, COI)基因, 比较分析其遗传多样性和群体遗传结构。255份乌骨鸡样品共检测到22个变异位点, 占分析位点的3.17%; 核苷酸多样性为0.00142-0.00339, 单倍型多样性为0.380-0.757, 其中略阳乌鸡核苷酸多样性最高, 德化黑鸡最低。检测到7个氨基酸变异位点, 来自6个品种共11个个体。定义了24种单倍型, 其中单倍型H1和H3为12个乌骨鸡品种共享, 出现频率分别为115次和64次; 盐津乌骨鸡单倍型数最多, 广西乌鸡最少。中性检验与错配分析显示实验种群未经历显著的群体扩张事件。分子变异分析显示81.06%的变异来自群体内; 品种间遗传距离为0.002-0.004, 品种间遗传分化系数F_st值为-0.035至0.594, 雪峰乌骨鸡与其他种群间的遗传分化程度最高。邻接树显示, 乌骨鸡未能独立形成分支, 不能从家鸡和红原鸡中有效区分开来。中国乌骨鸡中介网络图将24个单倍型分为3条进化主支, 呈现出一定的品种特异性, 由无量山乌骨鸡、云南盐津乌骨鸡和雪峰乌骨鸡组成单倍型H8、H9、H11、H12游离于这3条进化主支之外。增加其他家鸡和红原鸡COI基因的中介网络图主体结构与中国乌骨鸡的相同。结果表明中国乌骨鸡品种遗传多样性较低, 但品种间遗传分化显著, 可能是从当地家鸡中选育而来, 需要加强种质资源的保护。

关键词: 乌骨鸡, 线粒体COI基因, 遗传变异, 遗传分化

Abstract

Comprehensively evaluating the genetic diversity of Chinese black-bone chickens will facilitate conservation and utilization initiatives for this invaluable genetic resource. Mitochondrial cytochrome c oxidase subunit I (COI) gene sequences were obtained from 12 black-bone chicken breeds in China. These sequences were then used to analyze the genetic variation and population structure. A total of 22 mutation sites were detected from 255 individuals representing 3.17% of all sites. The nucleotide diversity and haplotype diversity ranged from 0.00142 to 0.00339 and from 0.380 to 0.757, respectively. Lueyang black chicken has the highest level of genetic diversity and Dehua the lowest. Seven amino acid variations were detected from 11 individuals from six breeds. A total of 24 haplotypes were defined, where haplotype H1 and H3 are shared by 12 black-bone chicken breeds with a frequency of 115 and 64, respectively. Yanjin had the greatest number of haplotypes, while Guangxi has the fewest. Neutrality tests and mismatch distribution analysis revealed that these populations have not experienced significant population expansion. Most of the genetic variations observed were intra-population variation (81.06%) as indicated in AMOVA analysis. Pairwise fixation indexes F_st values among 12 populations range from -0.035 to 0.594, and genetic distance ranges from 0.002 to 0.004. The genetic differentiation indexes between Xuefeng and other populations was the greatest. Black-bone chickens cannot be separated from domestic chickens and red junglefowls within the neighbor-joining tree. The median-joining network of black-bone chickens is classified into three main clusters with the characteristic of specific breeds, while haplotype H8, H9, H11 and H12 existing in Wuliangshan, Yanjin, Xuefeng are not directly related to the three main clusters. The median-joining network of black-bone chickens and additional domestic chickens and red junglefowls does not change the main structure of the tree. The results presented here indicate that the genetic diversity of Chinese black-bone chickens is low but significant genetic differentiation is evident. The Chinese black-bone chickens may be selected in situ from domestic chickens. Overall, the results suggest that more attention should be paid to germplasm resource protection of these fascinating breeds.

Key words: black-bone chicken, mitochondrial COI, genetic variation, genetic divergence

翁茁先, 黄佳琼, 张仕豪, 余锴纯, 钟福生, 黄勋和, 张彬 (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. 生物多样性, 27, 667-676. DOI: 10.17520/biods.2019013.

Weng Zhuoxian, Huang Jiaqiong, Zhang Shihao, Yu Kaichun, Zhong Fusheng, Huang Xunhe, Zhang Bin (2019) Genetic diversity and population structure of black-bone chickens in China revealed by mitochondrial COI gene sequences. Biodiversity Science, 27, 667-676. DOI: 10.17520/biods.2019013.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2019013

https://www.biodiversity-science.net/CN/Y2019/V27/I6/667

图/表 10

参考文献 34

[1]	Bandelt HJ, Forster P, Röhl A ( 1999) Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16, 37-48. DOI URL
[2]	China National Commission of Animal Genetic Resources( 2011) Animal Genetic Resources in China: Poultry. China Agriculture Press, Beijing. (in Chinese)
	[ 国家畜禽遗传资源委员会( 2011) 中国畜禽遗传资源志: 家禽志. 中国农业出版社, 北京.]
[3]	Dharmayanthi AB, Terai Y, Sulandari S, Zein MSA, Akiyama T, Satta Y ( 2017) The origin and evolution of fibromelanosis in domesticated chickens: Genomic comparison of Indonesian Cemani and Chinese Silkie breeds. PLoS ONE, 4, e0173147.
[4]	Ekarius C ( 2007) Storey’s Illustrated Guide to Poultry Breeds. Storey Publishing, Massachusetts.
[5]	Excoffier L, Lischer HE ( 2010) Arlequin suite ver. 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10, 564-567. DOI URL
[6]	Feng CG, Gao Y, Dorshorst B, Song C, Gu XR, Li QY, Li JX, Liu TX, Rubin CJ, Zhao YQ, Wang YQ, Fei J, Li HF, Chen KW, Qu H, Shu DM, Ashwell C, Da Y, Andersson L, Hu X, Li N ( 2014) A cis-regulatory mutation of PDSS2 causes silky-feather in chickens. PLoS Genetics, 8, e1004576.
[7]	Grant W, Bowen B ( 1998) Shallow population histories in deep evolutionary lineages of marine fishes: Insights from sardines and anchovies and lessons for conservation. Journal of Heredity, 89, 415-426. DOI URL
[8]	Groeneveld LF, Lenstra JA, Eding H, Toro MA, Scherf B, Pilling D, Negrini R, Finlay EK, Han JL, Groeneveld E, Weigend S, GLOBALDIV Consortium ( 2010) Genetic diversity in farm animals—A review. Animal Genetics, 41, 6-31. DOI URL
[9]	Hall TA ( 1999) Bioedit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95-98.
[10]	Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM ( 2004) Identification of birds through DNA barcodes. PLoS Biology, 2, 1657-1663.
[11]	Huang XH, Chen JB, He DL, Zhang XQ, Zhong FS ( 2016) DNA barcoding of indigenous chickens in China: A reevaluation. Scientia Agricultura Sinica, 49, 2622-2633. (in Chinese with English abstract)
	[ 黄勋和, 陈洁波, 何丹林, 张细权, 钟福生 ( 2016) DNA条形码技术鉴定中国地方鸡品种的重新评估. 中国农业科学, 49, 2622-2633.]
[12]	Huang XH, Wu YJ, Miao YW, Peng MS, Chen X, He DL, Suwannapoom C, Du BW, Li XY, Weng ZX, Jin SH, Song JJ, Wang MS, Chen JB, Li WN, Otecko NO, Geng ZY, Qu XY, Wu YP, Yang XR, Jin JQ, Han JL, Zhong FS, Zhang XQ, Zhang YP ( 2018) Was chicken domesticated in northern China? New evidence from mitochondrial genomes. Science Bulletin, 63, 743-746. DOI URL
[13]	Jia XX, Tang XJ, Fan YF, Lu JX, Huang SH, Ge QL, Gao YS, Han W ( 2017) Genetic diversity of local chicken breeds in East China based on mitochondrial DNA D-loop region. Biodiversity Science, 25, 540-548. (in Chinese with English abstract)
	[ 贾晓旭, 唐修君, 樊艳凤, 陆俊贤, 黄胜海, 葛庆联, 高玉时, 韩威 ( 2017) 华东地区地方鸡品种mtDNA控制区遗传多样性. 生物多样性, 25, 540-548.]
[14]	Kameshpandian P, Thomas S, Nagarajan M ( 2016) Genetic diversity and relationship of Indian Muscovy duck populations. Mitochondrial DNA Part A, 29, 1-5.
[15]	Li SZ ( 2005) Bencao Gangmu, 2nd edn. People’s Medical Publishing House, Beijing. (in Chinese)
	[ 李时珍 ( 2005) 本草纲目(第2版). 人民卫生出版社, 北京.]
[16]	Lin MM, Wang GQ, He ZG, Ma P, Liu Y ( 2017) Genetic diversity of Tianshui black-bone chicken based on DNA D-loop sequences. China Poultry, 39(1), 57-59. (in Chinese)
	[ 林萌萌, 王国琪, 何振刚, 马平, 刘玉 ( 2017) 天水乌鸡线粒体DNA D-loop序列遗传多样性分析. 中国家禽, 39(1), 57-59.]
[17]	Liu HT ( 2006) The formation, utilization and development of Dehua black-bone chicken. Fujian Journal of Animal Husbandry and Veterinary Medicine, 2(S1), 50-52. (in Chinese)
	[ 刘鸿涛 ( 2006) 德化黑鸡的形成、利用现状与发展思路. 福建畜牧兽医, 2(S1), 50-52.]
[18]	Liu YP ( 2002) Genetic Diversity of Chinese Black-bone Chickens and Origin of Domestic Chickens. PhD dissertation, Sichuan Agricultural University, Ya’an, Sichuan. (in Chinese with English abstract)
	[ 刘益平 ( 2002) 中国乌骨鸡遗传多样性及家鸡起源研究. 博士学位论文, 四川农业大学, 四川雅安.]
[19]	Liu YP, Wu GS, Yao YG, Miao YW, Luikart GD, Baig M, Pereira AB, Ding ZL, Palanichamy MG, Zhang YP ( 2006) Multiple maternal origins of chickens: Out of the Asian jungles. Molecular Phylogenetics and Evolution, 38, 12-19. DOI URL
[20]	Miao YW, Sun LM, Tong JJ, Li DL, Yuan YY, Yang MC, Hao WF, Huo JL, Yang R, Yu SL ( 2013) Maternal genetic analysis of Puer Maojiao and Nanjian Lver black-bone chicken using mtDNA D-loop sequences. Acta Ecologiae Animalis Domastici, 34(7), 10-14. (in Chinese with English abstract)
	[ 苗永旺, 孙利民, 童晶晶, 李大林, 袁跃云, 杨满灿, 郝伟峰, 霍金龙, 杨润, 余仕亮 ( 2013) 普洱毛脚乌鸡与南涧绿耳乌鸡线粒体DNA母系遗传分析. 家畜生态学报, 34(7), 10-14.]
[21]	Peters J, Lebrasseur O, Deng H, Larson D ( 2016) Holocene cultural history of red jungle fowl (Gallus gallus) and its domestic descendant in East Asia. Quaternary Science Reviews, 142, 102-119. DOI URL
[22]	Ren G, Ma H, Ma C, Wang W, Chen W, Ma L ( 2016) Genetic diversity and population structure of Portunus sanguinolentus (Herbst, 1783) revealed by mtDNA COI sequences. Mitochondrial DNA Part A: DNA Mapping, Sequencing, and Analysis, 28, 740-746.
[23]	Rousset F ( 1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics , 145, 1219-1228.
[24]	Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sánchez-Gracia A ( 2017) DnaSP 6: DNA sequence polymorphism analysis of large datasets. Molecular Biology Evolution, 34, 3299-3302. DOI URL
[25]	Tamura K, Stecher G, Peterson D, Filipski A, Kumar S ( 2013) MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Molecular Biology & Evolution, 30, 2725-2729.
[26]	Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG ( 1997) The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 25, 4876-4882. DOI URL
[27]	Tu YJ, Gao YS, Su YJ, Wang KH, Tong HB ( 2011) Genetic diversity and phylogenetic analysis of COI gene in some indigenous chicken breeds. Journal of Anhui Agricultural University, 38, 39-42. (in Chinese with English abstract)
	[ 屠云洁, 高玉时, 苏一军, 王克华, 童海兵 ( 2011) 我国部分地方鸡种COI基因多态性及其分子系统进化研究. 安徽农业大学学报, 38, 39-42.]
[28]	Wang L, Li Q, Kong LF, Yu H ( 2018) Population genetic structure and demographic history of Barbatia virescens along Chinese coast based on mitochondrial COI sequences. Oceanologia et Limnologia Sinica, 49, 87-95. (in Chinese with English abstract)
	[ 王玲, 李琪, 孔令锋, 于红 ( 2018) 基于COI基因的中国沿海青蚶野生群体遗传结构及种群动态研究. 海洋与湖沼, 49, 87-95.]
[29]	Wei L, Liu SG, Shi XW ( 2008) Genetic diversity of the Xuefeng black bone chicken based on microsatellite markers. Biodiversity Science, 16, 503-508. (in Chinese with English abstract)
	[ 魏麟, 刘胜贵, 史宪伟 ( 2008) 雪峰乌骨鸡自然群体遗传多样性的微卫星分析. 生物多样性, 16, 503-508.]
[30]	Wu HH, Xie RQ ( 1999) The origin, history and usage of black-bone chickens. Guide to Chinese Poultry, 16(11), 56. (in Chinese)
	[ 吾豪华, 谢若泉 ( 1999) 乌鸡产地、历史及作用浅议. 中国家禽导刊, 16(11), 56.]
[31]	Xiang H, Gao J, Yu B, Xiang H, Gao JQ, Yu BQ, Zhou H, Cai DW, Zhang YW, Chen XY, Wang X, Hofreiter M, Zhao XB ( 2014) Early Holocene chicken domestication in northern China. Proceedings of the National Academy of Sciences, USA, 111, 17564-17569.
[32]	Xu WJ, Zhu WQ, Shu JT, Song C, Chen KW ( 2014) Study on genetic diversity and phylogenetic evolution in Chinese main black-bone chicken. Chinese Journal of Animal Science, 50(23), 10-14. (in Chinese with English abstract)
	[ 徐文娟, 朱文奇, 束婧婷, 宋迟, 陈宽维 ( 2014) 我国主要乌骨鸡品种遗传多样性和系统进化研究. 中国畜牧杂志, 50(23), 10-14.]
[33]	Yuan J ( 2010) Zooarchaeological study on the domestic animals in ancient China. Quaternary Science, 30, 298-306. (in Chinese with English abstract)
	[ 袁靖 ( 2010) 中国古代家养动物的动物考古学研究. 第四纪研究, 30, 298-306.]
[34]	Zhang T, Du W, Lu H, Wang L ( 2018) Genetic diversity of mitochondrial DNA of Chinese black-bone chicken. Brazilian Journal of Poultry Science, 20, 565-572. DOI URL

代号 Code	品种名 Breed	产地 Origin	样本量 Sample size
LY	略阳乌鸡 Lueyang chicken	陕西省略阳县 Lueyang, Shaanxi	10
WLS	无量山乌骨鸡 Wuliangshan black-bone chicken	云南省南涧县 Nanjian, Yunnan	25
YJ	盐津乌骨鸡 Yanjin black-bone chicken	云南省盐津县 Yanjin, Yunnan	24
ZX	竹乡鸡 Zhuxiang chicken	贵州省赤水市 Chishui, Guizhou	32
XF	雪峰乌骨鸡 Xuefeng black-bone chicken	湖南省洪江市 Hongjiang, Hunan	19
JS	江山乌骨鸡 Jiangshan black-bone chicken	浙江省江山市 Jiangshan, Zhejiang	21
SK	丝羽乌骨鸡 Silkies	江西省泰和县 Taihe, Jiangxi	25
YG	余干乌骨鸡 Yugan black-bone chicken	江西省余干县 Yugan, Jiangxi	18
HY	黄羽黑鸡 Huangyu black chicken	江西省宜春市 Yichun, Jiangxi	18
DH	德化黑鸡 Dehua black chicken	福建省德化县 Dehua, Fujian	22
JH	金湖乌凤鸡 Jinhu black-bone chicken	福建省泰宁县 Taining, Fujian	24
GX	广西乌鸡 Guangxi black-bone chicken	广西东兰县 Donglan, Guangxi	17

代号 Code	品种名 Breed	产地 Origin	样本量 Sample size
LY	略阳乌鸡 Lueyang chicken	陕西省略阳县 Lueyang, Shaanxi	10
WLS	无量山乌骨鸡 Wuliangshan black-bone chicken	云南省南涧县 Nanjian, Yunnan	25
YJ	盐津乌骨鸡 Yanjin black-bone chicken	云南省盐津县 Yanjin, Yunnan	24
ZX	竹乡鸡 Zhuxiang chicken	贵州省赤水市 Chishui, Guizhou	32
XF	雪峰乌骨鸡 Xuefeng black-bone chicken	湖南省洪江市 Hongjiang, Hunan	19
JS	江山乌骨鸡 Jiangshan black-bone chicken	浙江省江山市 Jiangshan, Zhejiang	21
SK	丝羽乌骨鸡 Silkies	江西省泰和县 Taihe, Jiangxi	25
YG	余干乌骨鸡 Yugan black-bone chicken	江西省余干县 Yugan, Jiangxi	18
HY	黄羽黑鸡 Huangyu black chicken	江西省宜春市 Yichun, Jiangxi	18
DH	德化黑鸡 Dehua black chicken	福建省德化县 Dehua, Fujian	22
JH	金湖乌凤鸡 Jinhu black-bone chicken	福建省泰宁县 Taining, Fujian	24
GX	广西乌鸡 Guangxi black-bone chicken	广西东兰县 Donglan, Guangxi	17

品种名 Breed	变异位点数 No. of variable sites	平均核苷酸差异 Average K (k)	核苷酸多样性 Nucleotide diversity (π)	单倍型多样性 Haplotype diversity (h)
略阳乌鸡 LY	6	2.356	0.00339 ± 0.00064	0.733 ± 0.120
无量山乌骨鸡 WLS	6	1.653	0.00238 ± 0.00026	0.743 ± 0.051
盐津乌骨鸡 YJ	10	2.036	0.00293 ± 0.00042	0.757 ± 0.075
竹乡鸡 ZX	7	2.018	0.00290 ± 0.00028	0.730 ± 0.056
雪峰乌骨鸡 XF	6	1.310	0.00188 ± 0.00069	0.380 ± 0.134
江山乌骨鸡 JS	7	1.952	0.00281 ± 0.00048	0.729 ± 0.078
丝羽乌骨鸡 SK	7	0.993	0.00143 ± 0.00044	0.537 ± 0.115
余干乌骨鸡 YG	5	1.804	0.00260 ± 0.00025	0.680 ± 0.074
黄羽黑鸡 HY	5	1.523	0.00219 ± 0.00051	0.634 ± 0.093
德化黑鸡 DH	4	0.987	0.00142 ± 0.00047	0.455 ± 0.114
金湖乌凤鸡 JH	5	1.486	0.00214 ± 0.00044	0.572 ± 0.095
广西乌鸡 GX	3	1.456	0.00209 ± 0.00034	0.485 ± 0.079

品种名 Breed	变异位点数 No. of variable sites	平均核苷酸差异 Average K (k)	核苷酸多样性 Nucleotide diversity (π)	单倍型多样性 Haplotype diversity (h)
略阳乌鸡 LY	6	2.356	0.00339 ± 0.00064	0.733 ± 0.120
无量山乌骨鸡 WLS	6	1.653	0.00238 ± 0.00026	0.743 ± 0.051
盐津乌骨鸡 YJ	10	2.036	0.00293 ± 0.00042	0.757 ± 0.075
竹乡鸡 ZX	7	2.018	0.00290 ± 0.00028	0.730 ± 0.056
雪峰乌骨鸡 XF	6	1.310	0.00188 ± 0.00069	0.380 ± 0.134
江山乌骨鸡 JS	7	1.952	0.00281 ± 0.00048	0.729 ± 0.078
丝羽乌骨鸡 SK	7	0.993	0.00143 ± 0.00044	0.537 ± 0.115
余干乌骨鸡 YG	5	1.804	0.00260 ± 0.00025	0.680 ± 0.074
黄羽黑鸡 HY	5	1.523	0.00219 ± 0.00051	0.634 ± 0.093
德化黑鸡 DH	4	0.987	0.00142 ± 0.00047	0.455 ± 0.114
金湖乌凤鸡 JH	5	1.486	0.00214 ± 0.00044	0.572 ± 0.095
广西乌鸡 GX	3	1.456	0.00209 ± 0.00034	0.485 ± 0.079

单倍型 Haplotype	变异位点 Variation sites	单倍型在品种的分布(频率) Haplotype distribution in breeds (frequency)	合计 Total
AP003321	6666666666677777777777 7777788889900012233333 1146704890012331537788 0255272216776245331467 ACATGTTTAATGAGACAGTCCA
H1	......................	LY5, WLS10, YJ4, ZX14, XF1, JS10, SK17, YG7, HY10, DH16, JH15, GX6	115
H2	T.....................	ZX1	1
H3	...C.C...G............	LY2, WLS2, YJ1, ZX9, XF15, JS4, SK2, YG8, HY2, DH3, JH5, GX11	64
H4	T..C.C...G............	ZX2	2
H5	C..............T......	ZX1	1
H6	..GC.C...G............	ZX1	1
H7	...............T......	WLS1, YJ1, ZX4, JS4, SK2, YG1, HY1, DH3, JH3	20
H8	.........G...A........	WLS7, YJ11, XF2	20
H9	.........G..........T.	WLS5, YJ1	6
H10	......C...............	YJ4	4
H11	..G....C.G...A........	YJ1	1
H12	.GG......G..........T.	YJ1	1
H13	..................C...	SK1	1
H14	................G.....	SK2	2
H15	................GC....	SK1	1
H16	....................TG	LY1	1
H17	...C.C...G..G.........	LY2	2
H18	...............T...T..	XF1	1
H19	...C.C...G....G.......	JS1, JH1	2
H20	...CAC...G............	JS1	1
H21	...........A...T......	JS1	1
H22	.....C...G............	YG1	1
H23	..........A...........	YG1	1
H24	........G......T......	HY5	5

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

Genetic diversity and population structure of black-bone chickens in China revealed by mitochondrial COI gene sequences

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品种名 Breed	变异位点 Variation sites	氨基酸变异 Amino acid variation	变异数 Variation number
AP003321	0000122 1235124 9010875 YLTEVDI
竹乡鸡 ZX	F......	酪氨酸→苯丙氨酸 Tyrosine → Phenylalanine	3
竹乡鸡 ZX	S......	酪氨酸→丝氨酸 Tyrosine → Serine	1
竹乡鸡 ZX	..A....	苏氨酸→丙氨酸 Threonine → Alanine	1
盐津乌骨鸡 YJ	..A....	苏氨酸→丙氨酸 Threonine → Alanine	1
盐津乌骨鸡 YJ	.VA....	亮氨酸→缬氨酸, 苏氨酸→丙氨酸 Leucine → Valine, Threonine → Alanine	1
丝羽乌骨鸡 SK	.....H.	天冬氨酸→组氨酸 Asparagine → Histidine	1
略阳乌鸡 LY	......V	异亮氨酸→缬氨酸 Isoleucine → Valine	1
江山乌骨鸡 JS	...K...	谷氨酸→赖氨酸 Glutamic acid → Lysine	1
余干乌骨鸡 YG	....E..	缬氨酸→谷氨酸 Valine → Glutamic acid	1

品种名 Breed	Tajima’s D		Fu’s Fs
品种名 Breed	D	P	Fs	P
略阳乌鸡 LY	0.45768	0.70000	0.96375	0.68900
无量山乌骨鸡 WLS	0.12109	0.56400	0.49464	0.62700
盐津乌骨鸡 YJ	-0.79944	0.25300	-1.69126	0.17200
竹乡鸡 ZX	0.99606	0.85100	-0.31381	0.45400
雪峰乌骨鸡 XF	-0.76698	0.25300	0.57269	0.65900
江山乌骨鸡 JS	0.01119	0.54100	-0.25147	0.44900
丝羽乌骨鸡 SK	-1.43529	0.07300	-1.92588	0.07000
余干乌骨鸡 YG	0.76262	0.79100	0.24173	0.59100
黄羽黑鸡 HY	0.15067	0.60000	0.87825	0.69200
德化黑鸡 DH	-0.28222	0.43600	1.28651	0.75700
金湖乌凤鸡 JH	0.31722	0.67500	1.19223	0.77300
广西乌鸡 GX	1.81444	0.97700	3.86919	0.94800
平均 Average	0.11225	0.55950	0.44305	0.57342
方差 Squared deviation	0.87539	0.26761	1.50012	0.25155

变异起源 Source of variation	自由度 df	平方和 Sum of squares	方差组分 Variance components	方差比例 Percentage of variance (%)
群体间 Among populations	11	52.622	0.18826	18.94
群体内 Within populations	243	195.743	0.805553	81.06
总变异 Total variation	254	248.365	0.99378	100

Breed	LY	WLS	YJ	ZX	XF	JS	SK	YG	HY	DH	JH	GX
LY		0.003	0.004	0.003	0.003	0.003	0.003	0.003	0.003	0.003	0.003	0.003
WLS	0.116^*		0.003	0.003	0.004	0.004	0.002	0.002	0.003	0.002	0.003	0.003
YJ	0.189^*	0.017		0.004	0.004	0.004	0.003	0.004	0.004	0.003	0.003	0.004
ZX	-0.018	0.134^*	0.207^*		0.003	0.003	0.003	0.003	0.003	0.002	0.003	0.003
XF	0.231^*	0.427^*	0.433^*	0.248^*		0.004	0.004	0.003	0.004	0.004	0.003	0.002
JS	0.004	0.121^*	0.196^*	-0.014	0.341^*		0.002	0.003	0.003	0.003	0.002	0.003
SK	0.178^*	0.192^*	0.269^*	0.134^*	0.594^*	0.074^*		0.003	0.002	0.001	0.002	0.003
YG	-0.035	0.170^*	0.234^*	-0.011	0.158^*	0.032	0.250^*		0.003	0.002	0.003	0.002
HY	0.165^*	0.204^*	0.261^*	0.120^*	0.535^*	0.051	0.079^*	0.223^*		0.002	0.002	0.004
DH	0.117	0.160^*	0.243^*	0.072	0.551^*	0.011	-0.012	0.182^*	0.044		0.002	0.003
JH	0.013	0.121^*	0.206^*	-0.001	0.403^*	-0.033	0.445	0.546	0.067	-0.011		0.003
GX	0.054	0.305^*	0.343^*	0.089^*	0.029	0.173^*	0.441^*	-0.002	0.393^*	0.383^*	0.220^*

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