中国地方品种黄鸡线粒体DNA D-loop遗传多样性研究

doi:10.3864/j.issn.0578-1752.2022.22.016

Abstract

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

HUANG XunHe,WENG ZhuoXian,LI WeiNa,WANG Qing,HE DanLin,LUO Wei,ZHANG XiQuan,DU BingWang. Genetic Diversity of Indigenous Yellow-Feathered Chickens in Southern China Inferred from Mitochondrial DNA D-Loop Region[J].Scientia Agricultura Sinica, 2022, 55(22): 4526-4538.

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URL: https://www.chinaagrisci.com/EN/10.3864/j.issn.0578-1752.2022.22.016

https://www.chinaagrisci.com/EN/Y2022/V55/I22/4526

Figures/Tables 8

Table 1

Sample information"

样品/数据来源：1：本研究；2：Miao et al，2013；3：Gao et al，2017；4：黄勋和等，2016；5：黄勋和等，2018；6：Liu et al，2006

Sample or data references: 1: This study; 2: Miao et al, 2013; 3: Gao et al, 2017; 4: Huang et al, 2016; 5: Huang et al, 2018; 6: Liu et al, 2006

品种 Breed	数量 No. of samples	产地 Origin	来源 Reference
固始鸡 Guishi chicken	102	河南省固始县 Gushi, Henan	1 (68), 2 (34)
正阳三黄鸡 Zhengyang yellow chicken	51	河南省正阳县 Zhengyang, Henan	1 (51)
淮北麻鸡 Huaibei partridge chicken	30	安徽省宿州市 Suzhou, Anhui	1 (30)
淮南麻黄鸡 Huainan yellow chicken	38	安徽省淮南市 Huainan, Anhui	1 (31), 2 (7)
洪山鸡 Hongshan chicken	23	湖北省随州市 Suizhou, Hubei	1 (23)
江汉鸡 Jianhan chicken	22	湖北省荆州市 Jingzhou, Hubei	1 (22)
郧阳大鸡 Yunyang da chicken	38	湖北省竹山县 Zhushan, Hubei	1 (38)
桃源鸡 Taoyuan chicken	50	湖南省桃源县 Taoyuan, Hunan	1 (50)
黄郎鸡 Huanglang chicken	50	湖南省衡南县 Hengnan, Hunan	4 (50)
东安鸡 Dongan chicken	39	湖南省东安县 Dongan, Hunan	1 (39)
白耳黄鸡Baier yellow chicken	54	江西省广丰县 Guangfeng, Jiangxi	1 (24), 3 (30)
崇仁麻鸡 Chongren partridge chicken	50	江西省崇仁县 Chongren, Jiangxi	1 (20), 3 (30)
宁都黄鸡 Ningdu yellow chicken	49	江西省宁都县 Ningdu, Jiangxi	1 (19), 5 (30)
仙居鸡 Xianju chicken	59	浙江省仙居县 Xiandu, Zhejiang	1 (29), 3 (30)
萧山鸡 Xiaoshan chicken	30	浙江省萧山区 Xiaoshan, Zhejiang	1 (30)
河田鸡 Hetian chciken	59	福建省长汀县 Changting, Fujian	1 (15), 2 (14), 5 (30)
惠阳胡须鸡 Huiyang bearded chicken	41	广东省惠州市 Huizhou, Guangdong	1 (5), 5 (30), 6 (6)
清远麻鸡 Qingyuan spotted chicken	97	广东省清远市 Qingyuan, Guangdong	1 (9), 2 (44), 5 (30), 6 (6)
五华三黄鸡 Wuhua yellow chicken	89	广东省五华县 Wuhua, Guangdong	1 (59), 5 (30)
杏花鸡 Xinghua chicken	36	广东省封开县 Fengkai, Guangdong	1 (6), 5 (30)
阳山鸡 Yangshan chicken	36	广东省阳山县 Yangshan, Guangdong	1 (6), 5 (30)
中山沙栏鸡 Zhongshan shalan chicken	36	广东省中山市 Zhongshan, Guangdong	1 (6), 5 (30)
怀乡鸡 Huaixiang chicken	81	广东省信宜市 Xinyi, Guangdong	1 (51), 5 (30)
广西麻鸡 Guangxi partridge chicken	20	广西壮族自治区灵山县 Lingshan, Guangxi	1 (20)
霞烟鸡 Xiayan chicken	20	广西壮族自治区容县 Rongxian, Guangxi	1 (20)
瑶鸡 Yao chicken	19	广西壮族自治区南丹县 Nandan, Guangxi	1 (19)
广西三黄鸡 Guangxi yellow chicken	30	广西壮族自治区桂平市 Guiping, Guangxi	5 (30)
文昌鸡 Wenchang chicken	34	海南省文昌市 Wenchang, Hainan	1 (4), 3 (30)

Table 1

Table 2

Genetic diversity of mtDNA D-loop of 28 indigenous yellow-feathered chicken breeds from southern China"

^*：在P<0.05水平显著差异；^**：在P<0.01水平显著差异 ^*: Significant at P<0.05; ^**: Significant at P<0.01

^*: Significant at P<0.05; ^**: Significant at P<0.01

项目 Item	样本数 Number of samples	突变位点数 Variable sites	单倍型数量 No. of haplotypes	单倍型多样性 Haplotype diversity (SD)	核苷酸多样性 Nucleotide diversity (SD)	Tajima’s D检验 Tajima’s D test	Fu's Fs检验 Fu's Fs test
固始鸡 Guishi chicken	102	33	24	0.895 (0.015)	0.01303 (0.00047)	0.30028	-2.03043
正阳三黄鸡 Zhengyang yellow chicken	51	33	23	0.892 (0.033)	0.01306 (0.00097)	-0.25454	-5.05604
河南 Henan	153	45	41	0.916 (0.011)	0.01358 (0.00039)	-0.30834	-11.4107^*
淮北麻鸡 Huaibei partridge chicken	30	17	10	0.834 (0.053)	0.01160 (0.00101)	1.37901	1.15094
淮南麻黄鸡 Huainan yellow chicken	38	33	16	0.909 (0.028)	0.01429 (0.00065)	-0.19534	-1.00983
安徽 Anhui	68	35	22	0.896 (0.021)	0.01322 (0.00049)	-0.19686	-2.5084
洪山鸡 Hongshan chicken	23	18	7	0.562 (0.120)	0.00654 (0.00196)	-1.22171	0.37056
江汉鸡 Jianhan chicken	22	21	7	0.814 (0.062)	0.01453 (0.00116)	1.12581	3.74049
郧阳大鸡 Yunyang da chicken	38	25	19	0.892 (0.036)	0.01104 (0.00119)	-0.12650	-4.82923
湖北 Hubei	83	34	28	0.815 (0.040)	0.01137 (0.00086)	-0.33876	-7.2807^*
桃源鸡 Taoyuan chicken	50	25	14	0.851 (0.034)	0.01242 (0.00076)	0.50544	0.49295
黄郎鸡 Huanglang chicken	50	30	20	0.877 (0.034)	0.01328 (0.00102)	0.09547	-2.69839
东安鸡 Dongan chicken	39	20	10	0.831 (0.039)	0.01048 (0.00100)	0.49914	1.53744
湖南 Hunan	139	39	34	0.913 (0.012)	0.01345 (0.00042)	-0.04289	-6.36177
白耳黄鸡Baier yellow chicken	54	19	10	0.853 (0.025)	0.01098 (0.00091)	1.37634	2.77912
崇仁麻鸡 Chongren partridge chicken	50	21	9	0.767 (0.041)	0.00862 (0.00126)	-0.14757	2.06066
宁都黄鸡 Ningdu yellow chicken	49	19	12	0.724 (0.065)	0.00678 (0.00153)	-0.40462	-1.01641
江西 Jiangxi Province	153	33	27	0.912 (0.010)	0.00981 (0.00072)	-0.14096	-4.49767
仙居鸡 Xianju chicken	59	21	9	0.728 (0.041)	0.01238 (0.00046)	1.32007	4.86151
萧山鸡 Xiaoshan chicken	30	17	8	0.595 (0.101)	0.00389 (0.00123)	-1.81210^*	-1.25618
浙江 Zhejiang	89	29	19	0.800 (0.026)	0.01249 (0.00057)	0.73086	2.59771
河田鸡 (福建) Hetian chciken (Fujian)	59	29	20	0.887 (0.029)	0.01189 (0.00109)	-0.03561	-2.5954
惠阳胡须鸡 Huiyang bearded chicken	41	25	13	0.849 (0.033)	0.01231 (0.00083)	0.31439	0.41332
清远麻鸡 Qingyuan spotted chicken	97	32	25	0.808 (0.035)	0.01195 (0.00060)	0.09000	-3.46949
五华三黄鸡 Wuhua yellow chicken	89	21	13	0.857 (0.017)	0.01200 (0.00071)	1.48058	2.69746
杏花鸡 Xinghua chicken	36	26	13	0.879 (0.039)	0.00900 (0.00164)	-0.77683	-1.32623
阳山鸡 Yangshan chicken	36	22	11	0.835 (0.047)	0.01261 (0.00100)	0.79387	1.39084
中山沙栏鸡 Zhongshan shalan chicken	36	18	7	0.765 (0.051)	0.01155 (0.00097)	1.26962	4.61684
怀乡鸡 Huaixiang chicken	81	28	24	0.872 (0.025)	0.01023 (0.00106)	-0.07174	-5.06789
广东 Guangdong	416	49	61	0.877 (0.010)	0.01243 (0.00028)	-0.20442	-22.85323^**
广西麻鸡 Guangxi partridge chicken	20	22	10	0.832 (0.075)	0.01090 (0.00194)	-0.33564	-0.45343
霞烟鸡 Xiayan chicken	20	17	7	0.837 (0.048)	0.01072 (0.00147)	0.60216	2.04465
瑶鸡 Yao chicken	19	18	6	0.854 (0.041)	0.01239 (0.00126)	0.94892	3.59746
广西三黄鸡 Guangxi yellow chicken	30	24	10	0.561 (0.109)	0.00547 (0.00180)	-1.88476	-1.67216
广西 Guangxi	89	35	22	0.803 (0.036)	0.01104 (0.00078)	-0.53639	-2.60827
文昌鸡 (海南) Wenchang chicken (Hainan)	34	23	12	0.736 (0.076)	0.00994 (0.00154)	-0.28746	-0.42951
单倍型类群A Haplogroup A	198	42	43	0.742 (0.034)	0.00289 (0.00024)	-2.31919^**	-55.174^**
单倍型类群B Haplogroup B	632	61	79	0.718 (0.018)	0.00219 (n.d.)	-2.40914^**	-147.600^**
单倍型类群C Haplogroup C	237	21	21	0.552 (0.039)	0.00186 (0.00017)	-1.91201^*	-19.461^**
单倍型类群E Haplogroup E	210	17	21	0.757 (0.025)	0.00231 (0.00015)	-1.50947	-15.039^**
总计 Total	1283	101	169	0.903 (0.005)	0.01269 (n.d.)	-1.36487	-31.219^**

Table 2

Table 3

mtDNA D-loop haplotypes and their distribution in the 28 indigenous yellow-featherer chicken breeds from southern China"

¹⁾：单倍型数量及该品种或地区的独享型单倍型（括号数值） Numbers in this bracket indicate the private haplotypes to a given breed or region

项目 Item	单倍型数 No. of haplotypes	单倍型类群Haplogroup¹⁾
项目 Item	单倍型数 No. of haplotypes	A	B	C	D	E	G
固始鸡 Guishi chicken	24	5 (1)	6 (1)	6 (2)	1	5 (2)	1 (1)
正阳三黄鸡 Zhengyang yellow chicken	23	7 (4)	8 (3)	7 (2)		1
河南 Henan	41	10 (6)	11 (6)	12 (4)	1	6 (2)	1 (1)
淮北麻鸡 Huaibei partridge chicken	10	5 (2)	1	4
淮南麻黄鸡 Huainan yellow chicken	16	6 (4)	4 (2)	4	1	1
安徽 Anhui	22	10 (4)	4 (2)	6	1	1
洪山鸡 Hongshan chicken	7	2 (1)	4 (3)	1
江汉鸡 Jianhan chicken	7	3 (2)	1	1		2
郧阳大鸡 Yunyang da chicken	19	10 (6)	3 (1)	3		3
湖北 Hubei	28	13 (9)	6 (4)	4		5
桃源鸡 Taoyuan chicken	14	4 (2)	5 (1)	4		1
黄郎鸡 Huanglang chicken	20	4 (2)	10 (6)	4 (2)		2
东安鸡 Dongan chicken	10	2 (1)	3 (1)	1		4 (1)
湖南 Hunan	34	8 (5)	14 (9)	6 (2)		6 (1)
白耳黄鸡Baier yellow chicken	10	1	6 (3)	3 (1)
崇仁麻鸡 Chongren partridge chicken	9	2 (1)	3 (1)	2 (1)		2
宁都黄鸡 Ningdu yellow chicken	12	1	10 (1)		1 (1)
江西 Jiangxi Province	27	2 (1)	17 (7)	5 (2)	1 (1)	2
仙居鸡 Xianju chicken	9	3 (1)	4 (1)	1		1
萧山鸡 Xiaoshan chicken	8	2	5 (2)	1
浙江 Zhejiang	13	3 (2)	7 (3)	2		1
河田鸡 (福建) Hetian chciken (Fujian)	22	3 (2)	10 (5)	3		4
惠阳胡须鸡 Huiyang bearded chicken	13	3 (1)	2 (1)	2		6 (1)
清远麻鸡 Qingyuan spotted chicken	25	3 (1)	11 (6)	3		8 (4)
五华三黄鸡 Wuhua yellow chicken	13	1	6 (2)	2 (1)		4 (1)
杏花鸡 Xinghua chicken	13	3 (2)	7 (4)	2		1
阳山鸡 Yangshan chicken	11	2	3	1		5 (1)
中山沙栏鸡 Zhongshan shalan chicken	7	1	4 (2)	1		1
怀乡鸡 Huaixiang chicken	24	4 (1)	13 (2)	2 (1)		5
广东 Guangdong	61	9 (5)	31 (18)	6 (2)		15 (8)
广西麻鸡 Guangxi partridge chicken	10	3	4 (1)	2 (1)		1
霞烟鸡 Xiayan chicken	7	1	2 (1)		1 (1)	3
瑶鸡 Yao chicken	6	1	2 (1)	1		2
广西三黄鸡 Guangxi yellow chicken	10	1	7 (4)	1		1
广西 Guangxi	22	3	12 (7)	3 (1)	1 (1)	3
文昌鸡 (海南) Wenchang chicken (Hainan)	12	1	7 (2)	1		3
单倍型总数 Total No of haplotypes	169	43	79	22	3	21	1

Table 3

Fig. 1

Fig. 2

Table 4

Fig. 3

Fig. 4

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变异来源 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 variation (%)	固定指数 Fixation indices	P值 P-value
按省(区) In provinces
省(区)间Among provinces	9	221.727	0.02243	0.68	F_CT= 0.00677	0.30317
省(区)内群体间Among populations within provinces	18	373.839	0.40241	12.14	F_SC= 0.12222	0.00000
群体内Within populations	1255	3627.193	2.89019	87.18	F_ST= 0.12816	0.00000
总变异 Total vairiation	1282	4222.758	3.31503
按品种 In breeds
群体间Among populations	27	595.566	0.42201	12.74	F_ST= 0.12741	0.00000
群体内Within populations	1255	3627.193	2.89019	87.26
总变异 Total vairiation	1282

Genetic Diversity of Indigenous Yellow-Feathered Chickens in Southern China Inferred from Mitochondrial DNA D-Loop Region

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