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

doi:10.17520/biods.2019013

Abstract

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

Weng Zhuoxian, Huang Jiaqiong, Zhang Shihao, Yu Kaichun, Zhong Fusheng, Huang Xunhe, Zhang Bin. Genetic diversity and population structure of black-bone chickens in China revealed by mitochondrial COI gene sequences[J]. Biodiv Sci, 2019, 27(6): 667-676.

Add to citation manager EndNote|Ris|BibTeX

URL: https://www.biodiversity-science.net/EN/10.17520/biods.2019013

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

Figures/Tables 10

References 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