广东省地方鸡线粒体遗传多样性与母系起源

doi:10.17520/biods.2017259

生物多样性 ›› 2018, Vol. 26 ›› Issue (3): 238-247. DOI: 10.17520/biods.2017259

• 研究报告: 动物多样性 • 上一篇下一篇

广东省地方鸡线粒体遗传多样性与母系起源

黄勋和^1,², 余哲琪¹, 翁茁先^1,^2,³, 何丹林⁴, 易振华⁴, 李威娜^1,², 陈洁波^1,², 张细权⁴, 杜炳旺⁵, 钟福生^1,^2,^3,^*()

1 (嘉应学院生命科学学院, 广东梅州 514015)
2 (广东省五华三黄鸡科技创新中心, 广东梅州 514015)
3 (湖南农业大学动物科学技术学院, 长沙 410128)
4 (华南农业大学动物科学学院, 广州 510642)
5 (广东海洋大学农学院, 广东湛江 524088)

收稿日期:2017-10-08 接受日期:2017-12-27 出版日期:2018-03-20 发布日期:2018-05-05
通讯作者: 钟福生
作者简介:# 共同第一作者
基金资助:
广东省自然科学基金(2014A030307018)、广东省公益研究与能力建设项目(2015A020208020,2016A030303068)和嘉应学院省市共建重点建设项目(嘉院(2017)27号)

Mitochondrial genetic diversity and maternal origin of Guangdong indigenous chickens

Xunhe Huang^1,², Zheqi Yu¹, Zhuoxian Weng^1,^2,³, Danlin He⁴, Zhenhua Yi⁴, Weina Li^1,², Jiebo Chen^1,², Xiquan Zhang⁴, Bingwang Du⁵, Fusheng Zhong^1,^2,^3,^*()

1 School of Life Sciences, Jiaying University, Meizhou, Guangdong 514015
2 Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, Meizhou, Guangdong 514015
3 College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128
4 College of Animal Sciences, South China Agricultural University, Guangzhou, Guangdong 510642
5 College of Agriculture, Guangdong Ocean University, Zhanjiang, Guangdong 524088

Received:2017-10-08 Accepted:2017-12-27 Online:2018-03-20 Published:2018-05-05
Contact: Zhong Fusheng
About author:# Co-first authors

摘要/Abstract

摘要：

系统评估地方鸡的遗传变异水平并追溯其母系起源, 可为保护利用优质家禽种质资源库提供科学依据。本研究测定了广东省和邻省共12个地方鸡品种的线粒体DNA D-loop序列, 分析品种间的遗传距离与系统关系, 并构建单倍型系统发生树和中介网络图。360份样品共检测到60个突变位点, 均为转换。定义了85种单倍型, 归属于单倍型类群A、B、C和E, 在12个鸡品种中均有分布, 其中B是优势单倍型类群(187个, 51.94%), E次之(76个, 21.11%)。B02 和C01是优势单倍型(85个, 23.61%; 48个, 13.33%), 为12个鸡品种共有; E03位居第三(35个, 9.72%), 杏花鸡、黄郎鸡和宁都三黄鸡未见此单倍型。杏花鸡集中分布在单倍型类群B, 惠阳胡须鸡和中山沙栏鸡则主要分布在单倍型类群E; 怀乡鸡的单倍型数量最多, 中山沙栏鸡的最少。广东地方鸡品种间遗传距离为0.012-0.015, 单倍型多样性0.805 ± 0.047至0.949 ± 0.026, 核苷酸多样性0.0102 ± 0.0017至0.0138 ± 0.0009。邻接树和中介网络图将85种单倍型划分为进化枝A、B、C和E, 广东省与邻省地方鸡单倍型的地理分布模式相似。中性检验显示广东地方鸡未经历明显的群体历史扩张。结果表明广东地方鸡处于较好的保护状态, 遗传多样性水平较高, 品种的形成受到邻省和北方家鸡的影响, 东南亚红原鸡对广东地方鸡也有重要的遗传贡献。

关键词: 广东地方鸡, 线粒体DNA, D-loop, 遗传多样性, 起源

Abstract

The evaluation of the genetic diversity of indigenous chickens and the tracing of their matrilineal origin need to be facilitated to protect and utilize the germplasm bank of quality poultry. Twelve indigenous chicken breeds from Guangdong Province and its adjacent regions were used for mitochondrial DNA (mtDNA) D-loop sequencing, and analyses of genetic distance and genetic relationship between breeds were conducted. We constructed a phylogenetic tree and median-joining network based on haplotypes. Sixty mutation sites were detected in 360 samples, and all of these were found to be in transition. Eighty-five haplotypes, belonging to haplogroups A, B, C, and E, were defined. B was the predominant haplogroup (187, 51.94%), followed by E (76, 21.11%). Haplogroups A, B, C, and E were distributed in all the 12 breeds. B02 and C01 were the predominant haplotypes (85, 23.61%; 48, 13.33%), which were shared by all twelve breeds; and E03 ranked third (35, 9.72%), and was absent in the Xinghua, Huanglang and Ningdu yellow chicken. Xinghua chickens occurred mainly in haplogroup B, while Huiyang bearded and Zhongshan shalan chickens were distributed mainly in E. The number of haplotypes of Huaixiang chicken was the largest, while the Zhongshan shalan chicken had the fewest. The genetic distance between Guangdong chicken breeds ranged from 0.012 to 0.015, with haplotype diversity and nucleotide diversity ranging from 0.805 ± 0.047 to 0.949 ± 0.026, and from 0.0102 ± 0.0017 to 0.0138 ± 0.0009, respectively. Eighty-five haplotypes were divided into clades A, B, C, and E in the phylogenetic tree and median-joining network. Similar patterns of geographical distribution of mtDNA haplotypes was found in the chicken from Guangdong Province and its adjacent regions. A neutral test indicated that Guangdong indigenous chickens have not sustained obvious population expansion. Our results suggested that Guangdong chickens have a desirable conservation status, as they carry high levels of genetic diversity, and demographic histories were influenced to some extent, by the gene flow of domestic chickens from adjacent provinces and northern China. The red junglefowls from Southeast Asia have an important genetic contribution to the indigenous chickens of Guangdong Province.

Key words: Guangdong indigenous chicken, mitochondrial DNA, D-loop, genetic diversity, origin

黄勋和, 余哲琪, 翁茁先, 何丹林, 易振华, 李威娜, 陈洁波, 张细权, 杜炳旺, 钟福生 (2018) 广东省地方鸡线粒体遗传多样性与母系起源. 生物多样性, 26, 238-247. DOI: 10.17520/biods.2017259.

Xunhe Huang, Zheqi Yu, Zhuoxian Weng, Danlin He, Zhenhua Yi, Weina Li, Jiebo Chen, Xiquan Zhang, Bingwang Du, Fusheng Zhong (2018) Mitochondrial genetic diversity and maternal origin of Guangdong indigenous chickens. Biodiversity Science, 26, 238-247. DOI: 10.17520/biods.2017259.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2017259

https://www.biodiversity-science.net/CN/Y2018/V26/I3/238

图/表 7

参考文献 31

[1]	Bandelt HJ, Forster P, Rohl A (1999) Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16, 37-48. DOI URL PMID
[2]	Chen GH, Wang KH, Wang JY, Ding C, Yang N (2004) oultry Genetic Resources in China. Shanghai Scientific and Technical Publishers, Shanghai. (in Chinese)
	[陈国宏, 王克华, 王金玉, 丁铲, 杨宁 (2004) 中国禽类遗传资源. 上海科学技术出版社, 上海.]
[3]	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.]
[4]	Editorial Committee of Local Historiography of Guangdong(2004) Guangdong Provincial Local-Records Compilation: Executive Summary. Guangdong People Press, Guangzhou. (in Chinese)
	[广东省地方史志编纂委员会(2004) 广东省志?总述. 广东人民出版社, 广州.]
[5]	Fu Y, Niu D, Luo J, Ruan H, He GQ, Zhang YP (2001) Studies of the origin of Chinese domestic fowls. Acta Genetica Sinica, 28, 411-417. (in Chinese)
	[傅衍, 牛冬, 罗静, 阮晖, 何国庆, 张亚平 (2001) 中国家鸡的起源探讨. 遗传学报, 28, 411-417.]
[6]	Fumihito A, Miyake T, Sumi S, Takada M, Ohno S, Kondo N (1994) One subspecies of the red jungle fowl (Gallus gallus gallus) suffices as the matriarchic ancestor of all domestic breeds. Proceedings of the National Academy of Sciences, USA, 91, 12505-12509. DOI URL PMID
[7]	Gao YS, Jia XX, Tang XJ, Fan YF, Lu JX, Huang SH, Tang MJ (2017) The genetic diversity of chicken breeds from Jiangxi, assessed with BCDO2 and the complete mitochondrial DNA D-loop region. PLoS ONE, 12, e0173192. DOI URL PMID
[8]	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. DOI URL
[9]	Huang XH, Chen JB, He DL, Zhang XQ, Zhong FS (2016c) DNA barcoding of indigenous chickens in China: A reevaluation. Scientia Agricultura Sinica, 49, 2622-2633. (in Chinese with English abstract) DOI URL
	[黄勋和, 陈洁波, 何丹林, 张细权, 钟福生 (2016c) DNA条形码技术鉴定地方鸡品种的重新评估. 中国农业科学, 49, 2622-2633.] DOI URL
[10]	Huang XH, Li LZ, Zhang JF, He DL, Zhang XQ, Chen JB, Li WN, Du BW, Zhong FS (2016a) Evaluation of diversity and evolution of the microsatellite LEI0258 in chicken MHC-B region from South China. Acta Veterinaria et Zootechnica Sinica, 47, 2175-2183. (in Chinese with English abstract)
	[黄勋和, 李丽芝, 张金枫, 何丹林, 张细权, 陈洁波, 李威娜, 杜炳旺, 钟福生 (2016a) 华南家鸡MHC-B区域复合微卫星位点LEI0258的遗传多样性与进化研究. 畜牧兽医学报, 47, 2175-2183.]
[11]	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, DOI: 10.1016/j.scib.2017.12.004. DOI URL
[12]	Huang XH, Zhang JF, He DL, Zhang XQ, Zhong FS, Li WN, Zheng QM, Chen JB, Du BW (2016) Genetic diversity and population structure of indigenous chicken breeds in South China. Frontiers of Agricultural Science and Engineering, 3, 97-101. DOI URL
[13]	Huang XH, Zhang JF, Tan KF, Li LZ, Li WN, Zhong FS (2016b) Diversity and evolution of the highly tandem repeat LEI0258 with in MHC-B region in Wuhua three-yellow chicken. Guangdong Agricultural Sciences, 43, 163-168. (in Chinese with English abstract) DOI URL
	[黄勋和, 张金枫, 谭坤凤, 李丽芝, 李威娜, 钟福生 (2016b) 五华三黄鸡MHC-B区域复合微卫星位点LEI0258遗传多样性与进化研究. 广东农业科学, 43, 163-168.] DOI URL
[14]	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) DOI URL
	[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.] DOI URL
[15]	Lan D, Hu YD, Zhu Q, Liu Y (2017) Mitochondrial DNA study in domestic chicken. Mitochondrial DNA Part A: DNA Mapping, Sequencing, and Analysis, 28, 25-29. DOI URL PMID
[16]	Langford SM, Kraitsek S, Baskerville B, Ho SYW, Gongora J (2013) Australian and Pacific contributions to the genetic diversity of Norfolk Island feral chickens. BMC Genetics, 14, 91. DOI URL PMID
[17]	Lawler A (2015) Why Did the Chicken Cross the World? G Duckworth, New York.
[18]	Liao YY, Mo GD, Sun JL, Wei FY, Liao DJ (2016) Genetic diversity of Guangxi chicken breeds assessed with microsatellites and the mitochondrial DNA D-loop region. Molecular Biology Reports, 43, 415-425. DOI URL PMID
[19]	Liu YP, Wu GS, Yao YG, Miao YW, Luikart G, Baig M, Beja-Pereira A, 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 PMID
[20]	Miao YW, Peng MS, Wu GS, Ouyang YN, Yang ZY, Yu N, Liang JP, Pianchou G, Beja-Pereira A, Mitra B, Palanichamy MG, Baig M, Chaudhuri TK, Shen YY, Kong QP, Murphy RW, Yao YG, Zhang YP (2013) Chicken domestication: An updated perspective based on mitochondrial genomes. Heredity, 110, 277-282. DOI URL
[21]	Peng MS, Shi NN, Yao YG, Zhang YP (2015) Caveats about interpretation of ancient chicken mtDNAs from northern China. Proceedings of the National Academy of Sciences, USA, 112, E1970-E1971. DOI URL PMID
[22]	Peters J, Lebrasseur O, Best J, Miller H, Fothergill T, Dobney K, Thomas RM, Maltby M, Sykes N, Hanotte O, O’Connor T, Collins MJ, Larson G (2015) Questioning new answers regarding Holocene chicken domestication in China. Proceedings of the National Academy of Sciences, USA, 112, E2416. DOI URL PMID
[23]	Qu H, Shu DM, Yang CF (2004) The actuality and development proposal in Guangdong quality chicken germplasm resources. Guangdong Agricultural Sciences, 31(6), 4-7. (in Chinese) DOI URL
	[瞿浩, 舒鼎铭, 杨纯芬 (2004) 广东优质鸡种质资源的现状及发展建议. 广东农业科学, 31(6), 4-7.] DOI URL
[24]	Qu LJ, Li XY, Xu GF, Chen KW, Yang HJ, Zhang LC, Wu GQ, Hou ZC, Xu GY, Yang N (2006) Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers. Science in China Series C: Life Science, 49, 332-341. DOI URL PMID
[25]	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 PMID
[26]	Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Molecular Biology and Evolution, 30, 2725-2729. DOI URL PMID
[27]	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 PMID
[28]	Wu YP, Huo JH, Xie JF, Liu LX, Wei QP, Xie MG, Kang ZF, Ji HY, Ma YH (2014) Phylogeography and origin of Chinese domestic chicken. Mitochondrial DNA, 25, 126-130. DOI URL PMID
[29]	Xiang H, Gao JQ, Yu BQ, Zhou H, Cai DW, Zhang YW, Chen XY, Wang X, Michael H, Zhao XB (2014) Early Holocene chicken domestication in northern China. Proceedings of the National Academy of Sciences, USA, 111, 11564-11569.
[30]	Zhang L, Zhang P, Li QQ, Gaur U, Liu YP, Zhu Q, Zhao XL, Wang Y, Yin HD, Hu YD, Liu AP, Li DY (2017) Genetic evidence from mitochondrial DNA corroborates the origin of Tibetan chickens. PLoS ONE, 12, e0172945. DOI URL PMID
[31]	Zhang XQ, Liang SD, Zhang DX (2006) Review on new breed selection of quality chicken in Guangdong Province. China Poultry, 28(1), 9-11. (in Chinese) DOI URL
	[张细权, 梁少东, 张德祥 (2006) 广东优质鸡新品种选育回顾. 中国家禽, 28(1), 9-11.] DOI URL

品种 Breed	代号 Code	产地 Origin
怀乡鸡 Huaixiang chicken	HX	广东省信宜市 Xinyi, Guangdong
杏花鸡 Xinghua chicken	XH	广东省封开县 Fengkai, Guangdong
阳山鸡 Yangshan chicken	YS	广东省阳山县 Yangshan, Guangdong
清远麻鸡 Qingyuan spotted chicken	QY	广东省清远市 Qingyuan, Guangdong
惠阳胡须鸡 Huiyang bearded chicken	HY	广东省惠州市 Huizhou, Guangdong
五华三黄鸡 Wuhua yellow chicken	WH	广东省五华县 Wuhua, Guangdong
中山沙栏鸡 Zhongshan shalan chicken	SL	广东省中山市 Zhongshan, Guangdong
广西三黄鸡 Guangxi yellow chicken	GX	广西省桂平市 Guiping, Guangxi
文昌鸡 Wenchang chicken	WC	海南省文昌市 Wenchang, Hainan
河田鸡 Hetian chicken	HT	福建省长汀县 Changting, Fujian
黄郎鸡 Huanglang chicken	HL	湖南省衡南县 Hengnan, Hunan
宁都三黄鸡 Ningdu yellow chicken	ND	江西省宁都县 Ningdu, Jiangxi

品种 Breed	代号 Code	产地 Origin
怀乡鸡 Huaixiang chicken	HX	广东省信宜市 Xinyi, Guangdong
杏花鸡 Xinghua chicken	XH	广东省封开县 Fengkai, Guangdong
阳山鸡 Yangshan chicken	YS	广东省阳山县 Yangshan, Guangdong
清远麻鸡 Qingyuan spotted chicken	QY	广东省清远市 Qingyuan, Guangdong
惠阳胡须鸡 Huiyang bearded chicken	HY	广东省惠州市 Huizhou, Guangdong
五华三黄鸡 Wuhua yellow chicken	WH	广东省五华县 Wuhua, Guangdong
中山沙栏鸡 Zhongshan shalan chicken	SL	广东省中山市 Zhongshan, Guangdong
广西三黄鸡 Guangxi yellow chicken	GX	广西省桂平市 Guiping, Guangxi
文昌鸡 Wenchang chicken	WC	海南省文昌市 Wenchang, Hainan
河田鸡 Hetian chicken	HT	福建省长汀县 Changting, Fujian
黄郎鸡 Huanglang chicken	HL	湖南省衡南县 Hengnan, Hunan
宁都三黄鸡 Ningdu yellow chicken	ND	江西省宁都县 Ningdu, Jiangxi

单倍型 Haplotype	变异位点^*Variable sites	单倍型的品种分布(频率) Haplotype distribution in breeds (frequency)	合计 Total
NC_007235	111111222222222222222222222222223333333333333333333334444444 356899011112223334445556788989990011123333445566689991334467 387279102790250792362691413162694603590135274523741690456960 TGTTTTTCATCTACTAAGTTATATAAAAAACTTTCCTACTTAAATTCCTACTGTAGCTAT
A01	..C.....G....T.....C...C............C.......................	HX2, HY1, QY3, WH4, XH2, YS3, SL2, GX1, WC1, HL1	20
A02	..C.....G....T.....C...C............C.......C...............	XH1	1
A03	..C.....G....T.....C...C........G...C.......................	XH1	1
A04	..C.....G....T..G..C...C............C.......................	HY1, YS2	3
A05	..C....TG....T.....C...C............C.......................	HX1	1
A06	..C.....G....T.....C...C............C.........T.....A.......	HY1	1
A07	..C.....G....T.....C...C............C...............A.......	HX1, HT1, HL2	4
A08	..C.....G....T.....C...C............C...C...................	HY1	1
A09	..C.....G....T.....C...C..G.........C..............C......G.	HL1	1
A10	..C.....G....T.....C...C............C........C......A.......	HL1	1
A11	..C.....G....T..G..C...C............C...............A.......	HT1	1
A12	..C.....G..C.T.....C...C............C...............A.......	HT2	2
B01	............................................................	XH2, ND1	3
B02	.......................C....................................	HX6, HY6, QY7, WH5, XH8, YS9, SL5, HT1, GX20, WC13, HL2, ND3	85
B03	.......................C......T.............................	XH2, GX1, WC1, HL1	5
B04	.......................C.....................C..............	XH3	3
B05	......................GC.........C..........................	XH3	3
B06	.....................A.C....................................	XH2	2
B07	.......................C.............................C......	XH1	1
B08	.....................C.C....................................	WH2, YS2, GX1, WC1, HL1	7
B09	.......................C..........................T.........	HX1, WH1, YS1, HT1, ND1	5
B10	...................C...C....................................	HX1	1
B11	..............C........C....................................	HX1	1
B12	.......................C............................A.......	HX3, WH3, HT6, HL2, ND9	23
B13	..........T............C............................A.......	HX1, ND2	3
B14	.......................C......T.....................A.......	HX1	1
B15	.......................C..........................T.A.......	HX1	1
B16	............................................C...............	WH1	1
B17	............................................C.......A.......	WH1	1
B18	.......................C.......C............................	QY1	1
B19	.......................C.........C..........................	QY1, WC1	2
B20	.......................C.G..................................	QY1	1
B21	...C...................C....................................	QY1	1
B22	.......................C.............G......................	QY1	1
B23	..................C....C....................................	SL2	2
B24	.......................CG...................................	SL1	1
B25	.......................C...............C....................	HY1	1
单倍型 Haplotype	变异位点^*Variable sites	单倍型的品种分布(频率) Haplotype distribution in breeds (frequency)	合计 Total
B26	.......................C.........................G..........	GX1	1
B27	.......................C.................G..................	GX1	1
B28	......C................C.....G..............................	GX1	1
B29	......................GC.........C....T.....................	GX1	1
B30	.......................C...........T........................	WC1	1
B31	.......................C.................................C..	WC1	1
B32	.......................C..........................A.........	WC1	1
B33	.......................C....................C...............	HL2	2
B34	.......................C.....................C......A.......	HL1	1
B35	.....................C.C...............................C....	HL1	1
B36	.............T.........C............................A.......	HL1	1
B37	.......................C..............................G.T..C	HL1	1
B38	.......................C...G........................A.......	HL1	1
B39	..........T............C....................................	ND1	1
B40	................C......C....................................	ND1	1
B41	.......................C.........C..................A.......	ND2	2
B42	.................................C..................A.......	ND3	3
B43	.......................C.....G..............................	HT1	1
B44	.......................C.....G......................A.......	HT3	3
B45	.......................C...........................C........	HT1	1
B46	C.........T............C....................................	HT1	1
B47	.......................C...................G........A.......	HT1	1
B48	.....................C.C............................A.......	HX2, ND1	3
C01	........G........ACC.C.C.G........T.C.....G....TC...........	HX2, HY7, QY2, WH4, XH3, YS6, SL6, HT2, GX2, WC4, HL5, ND5	48
C02	........G........ACC.C.C.G........T.C.....G....TC.T.........	XH1, HL2	3
C03	........G........ACC.C.C.G.......CT.C..........TC...........	HX2	2
C04	.......TG........ACC.C.C.G........T.C.....G....TC...........	WH1	1
C05	........G........ACC.C.C.G........T.C.T...G....TC.T.........	HL1	1
C06	....C...G........ACC.C.C.G........T.C..........TC...........	HL1	1
C07	........G........ACC.C.C..........T.C.....G....TC...........	HT2	2
C08	........G........ACC.C...G........T.C.....G....TC...........	HT2	2
E01	.....C..GC........CC.C............T.C...................T...	HY1, QY1, WH1, XH1, YS1, SL3, WC1	9
E02	........GC........CC.C............T.C.....G.............T...	YS1	1
E03	........GC........CC.C............T.C...................T...	HX1, HY8, QY5, WH2, YS2, SL11, HT1, GX1, WC4	35
E04	........GC..G.....CC.C............T.C.T.................T...	QY3, YS2	5
E05	.A......GC........CC.C............T.C...................T...	YS1	1
E06	........GC........CC.C............T.C.......C...........T...	HX1, HY1	2
E07	........GC........CC.C............T.C.T.................T...	HX1, HY1, WC1	3
E08	........GC........CC.C............T.C...............A...T...	HX1, WH2, HT2, HL2	7
E09	.....C..GC........CC.C............T.C...............A...T...	WH3	3
E10	........GC........CC.C......G.....T.C......T............T...	QY1	1
E11	........GC........C..C............T.C...................T...	QY1	1
E12	........GC........CCTC............T.C...................T...	QY1	1
E13	........GC.....G..CC.C............T.C...................T...	QY1	1
E14	........GC........CCTC............T.C...............A...T...	HY1	1
E15	........GC........CC.C............T.C.............A.....T...	HY1	1
E16	........GC........CC.C............T.C.....G.........A...T...	HT2, HL1	3
E17	........G..C......CC.C...........CT.C.............A.........	ND1	1

单倍型 Haplotype	变异位点^*Variable sites	单倍型的品种分布(频率) Haplotype distribution in breeds (frequency)	合计 Total
NC_007235	111111222222222222222222222222223333333333333333333334444444 356899011112223334445556788989990011123333445566689991334467 387279102790250792362691413162694603590135274523741690456960 TGTTTTTCATCTACTAAGTTATATAAAAAACTTTCCTACTTAAATTCCTACTGTAGCTAT
A01	..C.....G....T.....C...C............C.......................	HX2, HY1, QY3, WH4, XH2, YS3, SL2, GX1, WC1, HL1	20
A02	..C.....G....T.....C...C............C.......C...............	XH1	1
A03	..C.....G....T.....C...C........G...C.......................	XH1	1
A04	..C.....G....T..G..C...C............C.......................	HY1, YS2	3
A05	..C....TG....T.....C...C............C.......................	HX1	1
A06	..C.....G....T.....C...C............C.........T.....A.......	HY1	1
A07	..C.....G....T.....C...C............C...............A.......	HX1, HT1, HL2	4
A08	..C.....G....T.....C...C............C...C...................	HY1	1
A09	..C.....G....T.....C...C..G.........C..............C......G.	HL1	1
A10	..C.....G....T.....C...C............C........C......A.......	HL1	1
A11	..C.....G....T..G..C...C............C...............A.......	HT1	1
A12	..C.....G..C.T.....C...C............C...............A.......	HT2	2
B01	............................................................	XH2, ND1	3
B02	.......................C....................................	HX6, HY6, QY7, WH5, XH8, YS9, SL5, HT1, GX20, WC13, HL2, ND3	85
B03	.......................C......T.............................	XH2, GX1, WC1, HL1	5
B04	.......................C.....................C..............	XH3	3
B05	......................GC.........C..........................	XH3	3
B06	.....................A.C....................................	XH2	2
B07	.......................C.............................C......	XH1	1
B08	.....................C.C....................................	WH2, YS2, GX1, WC1, HL1	7
B09	.......................C..........................T.........	HX1, WH1, YS1, HT1, ND1	5
B10	...................C...C....................................	HX1	1
B11	..............C........C....................................	HX1	1
B12	.......................C............................A.......	HX3, WH3, HT6, HL2, ND9	23
B13	..........T............C............................A.......	HX1, ND2	3
B14	.......................C......T.....................A.......	HX1	1
B15	.......................C..........................T.A.......	HX1	1
B16	............................................C...............	WH1	1
B17	............................................C.......A.......	WH1	1
B18	.......................C.......C............................	QY1	1
B19	.......................C.........C..........................	QY1, WC1	2
B20	.......................C.G..................................	QY1	1
B21	...C...................C....................................	QY1	1
B22	.......................C.............G......................	QY1	1
B23	..................C....C....................................	SL2	2
B24	.......................CG...................................	SL1	1
B25	.......................C...............C....................	HY1	1
单倍型 Haplotype	变异位点^*Variable sites	单倍型的品种分布(频率) Haplotype distribution in breeds (frequency)	合计 Total
B26	.......................C.........................G..........	GX1	1
B27	.......................C.................G..................	GX1	1
B28	......C................C.....G..............................	GX1	1
B29	......................GC.........C....T.....................	GX1	1
B30	.......................C...........T........................	WC1	1
B31	.......................C.................................C..	WC1	1
B32	.......................C..........................A.........	WC1	1
B33	.......................C....................C...............	HL2	2
B34	.......................C.....................C......A.......	HL1	1
B35	.....................C.C...............................C....	HL1	1
B36	.............T.........C............................A.......	HL1	1
B37	.......................C..............................G.T..C	HL1	1
B38	.......................C...G........................A.......	HL1	1
B39	..........T............C....................................	ND1	1
B40	................C......C....................................	ND1	1
B41	.......................C.........C..................A.......	ND2	2
B42	.................................C..................A.......	ND3	3
B43	.......................C.....G..............................	HT1	1
B44	.......................C.....G......................A.......	HT3	3
B45	.......................C...........................C........	HT1	1
B46	C.........T............C....................................	HT1	1
B47	.......................C...................G........A.......	HT1	1
B48	.....................C.C............................A.......	HX2, ND1	3
C01	........G........ACC.C.C.G........T.C.....G....TC...........	HX2, HY7, QY2, WH4, XH3, YS6, SL6, HT2, GX2, WC4, HL5, ND5	48
C02	........G........ACC.C.C.G........T.C.....G....TC.T.........	XH1, HL2	3
C03	........G........ACC.C.C.G.......CT.C..........TC...........	HX2	2
C04	.......TG........ACC.C.C.G........T.C.....G....TC...........	WH1	1
C05	........G........ACC.C.C.G........T.C.T...G....TC.T.........	HL1	1
C06	....C...G........ACC.C.C.G........T.C..........TC...........	HL1	1
C07	........G........ACC.C.C..........T.C.....G....TC...........	HT2	2
C08	........G........ACC.C...G........T.C.....G....TC...........	HT2	2
E01	.....C..GC........CC.C............T.C...................T...	HY1, QY1, WH1, XH1, YS1, SL3, WC1	9
E02	........GC........CC.C............T.C.....G.............T...	YS1	1
E03	........GC........CC.C............T.C...................T...	HX1, HY8, QY5, WH2, YS2, SL11, HT1, GX1, WC4	35
E04	........GC..G.....CC.C............T.C.T.................T...	QY3, YS2	5
E05	.A......GC........CC.C............T.C...................T...	YS1	1
E06	........GC........CC.C............T.C.......C...........T...	HX1, HY1	2
E07	........GC........CC.C............T.C.T.................T...	HX1, HY1, WC1	3
E08	........GC........CC.C............T.C...............A...T...	HX1, WH2, HT2, HL2	7
E09	.....C..GC........CC.C............T.C...............A...T...	WH3	3
E10	........GC........CC.C......G.....T.C......T............T...	QY1	1
E11	........GC........C..C............T.C...................T...	QY1	1
E12	........GC........CCTC............T.C...................T...	QY1	1
E13	........GC.....G..CC.C............T.C...................T...	QY1	1
E14	........GC........CCTC............T.C...............A...T...	HY1	1
E15	........GC........CC.C............T.C.............A.....T...	HY1	1
E16	........GC........CC.C............T.C.....G.........A...T...	HT2, HL1	3
E17	........G..C......CC.C...........CT.C.............A.........	ND1	1

品种 Breed	突变位点数 Variable sites	单倍型数量 No. of haplotypes	单倍型类群(个体数) Haplogroups (individuals)	单倍型多样性 Haplotype diversity (SD)	核苷酸多样性 Nucleotide diversity (SD)	平均核苷酸差异 Average number of nucleotide differences	Tajima’s D检验 Tajima’s D test
HX	26	19 (A=4, B=9, C=2, E=4)	A(5), B(17), C(4), E(4)	0.949 (0.026)	0.0123 (0.0014)	6.382	-0.0987
HY	25	12(A=3, B=2, C=1, E=6)	A(3), B(7), C(7), E(13)	0.853 (0.039)	0.0132 (0.0008)	6.837	0.2969
QY	27	15 (A=1, B=6, C=1, E=7)	A(3), B(12), C(2), E(13)	0.913 (0.032)	0.0127 (0.0008)	6.623	-0.1011
WH	21	13 (A=1, B=6, C=2, E=4)	A(4), B(13), C(5), E(8)	0.929 (0.022)	0.0138 (0.0009)	7.177	1.2395
XH	25	13 (A=3, B=7, C=2, E=1)	A(4), B(21), C(4), E(1)	0.906 (0.036)	0.0102 (0.0017)	5.285	-0.6955
YS	22	11 (A=2, B=3, C=1, E=5)	A(5), B(12), C(6), E(7)	0.867 (0.042)	0.0134 (0.0009)	6.989	0.9093
SL	18	7 (A=1, B=3, C=1, E=2)	A(2), B(8), C(6), E(14)	0.805 (0.047)	0.0120 (0.0009)	6.248	1.2923
GX	24	10 (A=1, B=7, C=1, E=1)	A(1), B (26), C(2), E(1)	0.561 (0.109)	0.0055 (0.0018)	2.839	-1.8847^*
HL	30	20 (A=4, B=10, C=4, E=2)	A(5), B(13), C(9), E(3)	0.963 (0.021)	0.0155 (0.0009)	8.025	0.2160
HT	25	17 (A=3, B=8, C=3, E=3)	A(4), B(15), C(6), E(5)	0.945 (0.025)	0.0141 (0.0011)	7.317	0.5680
ND	18	12 (B=10, C=1, E=1)	B(24), C(5), E(1)	0.876 (0.041)	0.0097 (0.0019)	5.039	0.1757
WC	23	12 (A=1, B=7, C=1, E=3)	A(1), B(19), C(4), E(6)	0.793 (0.067)	0.0108 (0.0015)	5.630	-0.1070
合计Total	60	85 (A=12, B=48, C=8, E=17)	A(37), B(187), C(60), E(76)	0.909 (0.010)	0.0130 (0.0003)	6.739	-0.9237

广东省地方鸡线粒体遗传多样性与母系起源

Mitochondrial genetic diversity and maternal origin of Guangdong indigenous chickens

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品种 breed	XH	YS	HX	WH	QY	SL	HY	GX	WC	HL	ND	HT
XH		0.001	0.000	0.001	0.002	0.003	0.003	0.000	0.000	0.001	0.001	0.001
YS	0.013		0.000	0.000	0.000	0.000	0.000	0.002	0.000	0.000	0.002	0.000
HX	0.012	0.013		0.000	0.001	0.002	0.002	0.001	0.000	0.000	0.000	0.000
WH	0.013	0.014	0.013		0.000	0.000	0.000	0.002	0.000	0.000	0.001	0.000
QY	0.013	0.013	0.014	0.014		0.000	0.000	0.003	0.000	0.001	0.003	0.001
SL	0.015	0.013	0.014	0.014	0.013		0.000	0.005	0.002	0.001	0.005	0.002
HY	0.015	0.014	0.015	0.014	0.013	0.012		0.005	0.002	0.001	0.004	0.002
GX	0.008	0.012	0.010	0.012	0.012	0.014	0.015		0.001	0.002	0.001	0.002
WC	0.011	0.013	0.012	0.013	0.012	0.013	0.014	0.009		0.001	0.001	0.001
HL	0.014	0.015	0.014	0.015	0.015	0.015	0.016	0.013	0.014		0.001	0.000
ND	0.011	0.014	0.012	0.013	0.014	0.016	0.016	0.008	0.011	0.014		0.001
HT	0.013	0.015	0.013	0.014	0.015	0.015	0.015	0.012	0.013	0.015	0.013

地区 Region	个体数Individuals	单倍型^a/个体数 Haplotypes^a/individuals
地区 Region	个体数Individuals	A	B	C	D	E	F	G	H	I	Z
广东省 Guangdong	210	8(4)/26	26(13)/90	5(2)/34		15(5)/60
中国北方 northern China	273	25(12)/111	11(6)/66	11(2)/59	2/2	8/35
中国南方^bsouthern China	863	28(17)/182	67(45)/394	22(12)/131	5 (3)/13	17(3)/137	1/1	2/4			1(1)/1
中国西南 southwest China	1,153	36(19)/366	22(12)/260	6(2)/29		9/98	22(16)/152	40(31)/237	3(3)/11
东南亚 Southeast Asia	621	38(29)/146	53(41)/289	5(2)/19	45(41)/67	15(9)/42	12(9)/38	4(1)/11	2 (2)/2	3(3)/7
南亚 South Asia	603	3(1)/14	4(1)/16	19(16)/31	17(10)/56	102(79)/450	3(1)/12	11(9)/21		1(1)/3
合计 Total	3,723

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