基于线粒体DNA D-loop区的肉鸡品种遗传多样性和起源分析

doi:10.3864/j.issn.0578-1752.2021.24.012

Abstract

Abstract:

【Objective】 The purpose of this study was to investigate the genetic diversity and origin characteristics of the whole sequence of mitochondrial DNA D-loop region in chicken breeds (complete set line) with different growth rates, so as to provide a theoretical basis for breeding and traceability of broiler breeds. 【Method】 15 broiler breeds with different growth rates were used as research materials, including eight yellow-feathered broiler lines (5 medium-fast and 3 slow lines), two local chicken breeds (Gushi chicken and Tibetan chicken), two introduced chicken breeds (Recessive White and Anka), one white-feathered broiler (Ross 308), 817 hybrid broiler and one commercial layer line (Dawu Brown Eggshell Hens). Chicken blood was collected, and DNA was PCR amplified. The full sequences of mtDNA D-loop region of 683 individuals from 15 chicken breeds were sequenced, and the genetic diversity and haplotype characteristics of each chicken breed were analyzed using DnaSP 5.10 software. The genetic distance between breeds was calculated using MEGA 4.0 software, and then a phylogenetic tree was constructed between different haplotypes and the red original chicken. 【Result】The full sequence size of the D-loop region of 15 chicken breeds ranged from 1 231 to 1 232 bp, and individuals with sequence length of 1 231 bp had C-base deletion at 859 bp. 45 variant loci were detected in 683 individuals, which were combined into 53 haplotypes and could be divided into four haplotype groups, including A, B, C and E. Among them, the medium-fast broilers, 817 hybrid broilers and high-yielding laying hens were all haplotype E as the dominant haplotype (≥48.89%); the dominant haplotypes were B haplotypes for Hongguang black chickens, A haplotypes for Jinghai yellow chickens, and four haplotypes were relatively balanced for Xueshan chickens (the proportion of E haplotypes ≤38.46% for three chicken breeds); the haplotypes of local chicken breeds were A and C haplotypes for Gushi chickens and A and B haplotypes for Tibetan chickens. The genetic diversity of the 15 chicken breeds ranged from 0.496 to 0.853 for Hd and from 0.00146 to 0.00673 for Pi. The relatively rich genetic diversity was found in the Xinxing Dwarf Yellow Chicken, Xueshan Chicken, Jinghai Yellow Chicken and Ross 308; the relatively low genetic diversity was found in the Tibetan Chicken, the High Laying Chicken, the Anka Chicken, the Xinxing partridge Chicken No. 4 and the Xugang Yellow Chicken No. 1. The range of Kiumura two-parameter distance of 15 chicken breeds was 0.0016-0.0113, among which the intra-breed genetic distance of Ross 308 was the largest while the intra-breed genetic distance of 817 hybrid broiler and high-yielding chicken was the smallest; the inter-breed genetic distance was the largest between high-yielding chicken and Tibetan chicken, and the smallest between high-yielding chicken and 817 hybrid broiler; the genetic distance between medium-fast broiler was relatively small while the genetic distance between medium-fast broiler, slow-fast and local chicken breeds was relatively large; the genetic distance between Jinghai and local chicken breeds was relatively large. Cluster analysis showed that the haplotypes A, B, and gallus gallus spadiceus were clustered in one group. Haplotype E and gallus gallus murghi were clustered in another group. Haplotype C was clustered with four subspecies of jungle fowl, including gallus gallus murghi, gallus gallus spadiceus, gallus gallus gallus and gallus gallus bankiva. 【Conclusion】The genetic diversity of mitochondrial D-loop region varied among different chicken breeds; E haplotypes were strongly correlated with broiler growth rate, and E haplotypes were the dominant haplotypes in all medium and fast populations, while the proportion of E haplotypes in slow populations was less than 40%; the national chicken population had multiple red proto-chicken maternal origins, indicating that it was domesticated under neutral selection. The results of the study provided a theoretical basis for broiler breed selection and tracing as well as resource exploitation.

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

TANG XiuJun,FAN YanFeng,JIA XiaoXu,GE QingLian,LU JunXian,TANG MengJun,HAN Wei,GAO YuShi. Genetic Diversity and Origin Characteristics of Chicken Species Based on Mitochondrial DNA D-loop Region[J].Scientia Agricultura Sinica, 2021, 54(24): 5302-5315.

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Figures/Tables 8

Table 1

The place of origin and sample size of 15 chicken breeds"

品种 Breed	文中简称 Abbreviation	来源 Source	采样数 Sampling number
墟岗黄鸡1号 Xugang yellow chicken No.1	XGH	广东省鹤山市墟岗黄畜牧有限公司 Guangdong Heshan Xuganghuang Animal Husbandry Co. LTD	45
新广铁脚麻鸡 Xinguang tiejiaoma chicken	XGT	佛山市高明区新广农牧有限公司 Foshan Gaoming Xinguang Agriculture and Animal Husbandry Co. LTD	38
新兴麻鸡4号 Xinxing partridge chicken No.4	XXM	广东温氏南方家禽育种有限公司 Guangdong Wenshi South Poultry Breeding Co. LTD	55
良凤花鸡 Liangfeng hua chicken	LFH	广西南宁市良凤农牧有限责任公司 Guangxi Nanning Liangfeng Agriculture and Animal Husbandry Co. LTD	53
新兴矮脚黄鸡 Xinxing dwarf yellow chicken	XXA	广东温氏食品集团有限公司 Guangdong Wens Food Group Co. LTD	46
雪山鸡 Xueshan chicken	XS	江苏立华牧业股份有限公司 Jiangsu Lihua Animal Husbandry Co. LTD	39
京海黄鸡 Jinghai yellow chicken	JHH	江苏京海禽业集团有限公司 Jiangsu Jinghai Poultry Industry Group Co. LTD	40
鸿光黑鸡 Hongguang black chicken	HGH	广西鸿光农牧有限公司 Guangxi Hongguang Agriculture and Animal Husbandry Co. LTD	77
固始鸡 Gushi chicken	GS	国家级地方鸡种基因库（江苏） National Local Chicken Gene Bank (Jiangsu)	73
藏鸡 Tibetan chicken	Z	国家级地方鸡种基因库（江苏） National Local Chicken Gene Bank (Jiangsu)	38
隐性白羽鸡 Recessive White	YXB	国家级地方鸡种基因库（江苏） National Local Chicken Gene Bank (Jiangsu)	45
安卡鸡 Anka chicken	AK	国家级地方鸡种基因库（江苏） National Local Chicken Gene Bank (Jiangsu)	29
罗斯308 Rose 308	LS	国家家禽生产性能测定站 National Poultry production performance testing station	34
817杂交肉鸡 817 hybrid broiler	817	国家家禽生产性能测定站 National Poultry production performance testing station	32
高产蛋鸡 High-yielding layer	E	国家家禽生产性能测定站 National Poultry production performance testing station	39

Table 1

Table 2

The number of mtDNA D-loop region haplotypes in 15 chicken breeds"

单倍型 Haplotype	突变位点 Variable sites (bp)	总计 Total	单倍型类别 Haplotype category	品种 (个数) Breeds (number)
111
1112222222 2222222222 2333333333 3333344677 89022
3691112233 4444555688 9011234566 6669914819 42511
3791272589 0236269113 6605102401 2371976612 60245
D-NC007237 TTTAGTACGA CGCCACATGA CCTCGCGTTA CCTCGCCGGG CCTCG
Hap_1..C..C............A..T....A.........T......T.		82	E1	XGH(6), XGT(11), XXM(8), LFH(17), XXA(3), XS(9), JHH(3),AK(10),LS(15)
Hap_2.....C............A..T....A.........T......T.		159	E2	XGH(30), XGT(14),XXM(36),LFH(14), XXA(13), XS(6),YXB(19), AK(16), LS(1), 817(6), E(4)
Hap_3...........A.....C...T.........TC............		85	C1	XGH(5), XGT(12), XXM(5), LFH(2), XXA(7), XS(11),GS(28),YXB(14), LS(1)
Hap_4....A.......TT.T.CA..TCT..A..........A.A....A		27	B1	XGH(4), LFH(4), XXA(5), XS(4), YXB(2), AK(1), LS(7)
Hap_5....A.......TT.TGCA...CT..A.................A		1	B2	XGT(1)
Hap_6.C.....T.G..T..T.CA..TC...A..................		13	A1	XXM(3), LFH(2),XXA(7),AK(1)
Hap_7.....C............A..T....A.........TA.....T.		5	E3	XXM(3),YXB(2)
Hap_8..C..C............A..T....A........TT......T.		4	E4	LFH(4)
Hap_9.....C...........CA..T...TA.........T......T.		6	E5	LFH(6)
Hap_10....A.......TT.T.CA..TCT..A..........A.A...T.		4	B3	LFH(4)
Hap_11..C..C............A..T....A.........T..A...T.		6	E6	XXA(6)
Hap_12.C.....T....T..T.CA..TC...A..................		52	A2	XXA(4),XS(9),JHH(2),GS(37)
Hap_13.....C............A..T...TA.........T......T.		7	E7	XXA(1),817(6)
Hap_14 CC.....T....T..T.CA..TC...A..................		16	A3	JHH(3),Z(13)
Hap_15....A.......TTTT.CA..TCT..A.................A		3	B4	JHH(3)
单倍型 Haplotype	突变位点 Variable sites（bp）	总计 Total	单倍型类别 Haplotype category	品种 (个数) Breeds (number)
Hap_16.C.....T....T..T.CA..TC...A..........A.......		13	A4	JHH(13)
Hap_17....A.......TT.T.CA..T.T..A..........A......A		2	B5	JHH(2)
Hap_18....A.......TT.T.CA..TCT..A............A....A		7	B6	JHH(7)
Hap_19...........A.........T.........TC............		3	C2	JHH(3)
Hap_20.C..A..T....T..T.CA..TC...A..................		2	A5	JHH(2)
Hap_21.......... TA.....C...T.........TC............		2	C3	JHH(2)
Hap_22....A.......TT.T.CA..TCT..A............A T...A		20	B7	HGH(20)
Hap_23....A.......TT.T.CA..TCT..A............. T...A		23	B8	HGH(23)
Hap_24....A.......TT.T.CA..TCT..A..........A.. T...A		1	B9	HGH(1)
Hap_25.C.....T....T..T.CA..TC...A... T......... T....		4	A6	HGH(4)
Hap_26...........A.....C...T.........TC....... T....		7	C4	HGH(3),GS(4)
Hap_27....A.......TT.T.CAG.TCT..A............. T...A		2	B10	HGH(2)
Hap_28....A.......TT.TGCA...CT..A............A T...A		2	B11	HGH(2)
Hap_29....A.......TT.T.CA. TTCT..A............A T...A		3	B12	HGH(3)
Hap_30....A.......TT.T.CA..TCT..A.C..........A T...A		2	B13	HGH(2)
Hap_31....A........T.T.CA..TCT..A............A T...A		1	B14	HGH(1)
Hap_32.....C............A..T....AC........T... T..T.		1	E8	HGH(1)
Hap_33....A.......TT.T.CA..TCT..A..........A.A T...A		3	B15	HGH(3)
Hap_34...........A.....C...T.........TC....A.. T....		2	C5	HGH(2)
Hap_35....A.......TT.T.CA..TCT..A...........AA T...A		1	B16	HGH(1)
Hap_36.....C............A..T....A.........T... T..T.		4	E9	HGH(4)
Hap_37.C.....TA...T..T.CA..TC...A..........A.. T....		1	A7	HGH(1)
Hap_38....A.......TT.T.CA..TCT..A......T...... T...A		1	B17	HGH(1)
Hap_39.....C............A..T....A......A..T... T..T.		1	E10	HGH(1)
Hap_40.....C............A..T....A.........TA.. T..T.		2	E11	HGH(2)
Hap_41...G.......A.....C...T..A......TC............		1	C6	GS(1)
Hap_42...........A.....C...T.........TC........T...		2	C7	GS(1),AK(1)
Hap_43.C.....T....T..T.CA..TC...A..T...............		8	A8	GS(2),YXB(6)
Hap_44....A.......TT.T.CA. TTCT..A............A....A		24	B18	Z(24)
Hap_45....A.......TT.T.CA..TCT..A.................A		1	B19	Z(1)
Hap_46.C.....T....T..T.CA..TC...A................T.		1	A9	YXB(1)
Hap_47.....C............A..T....A.........T........		1	E12	YXB(1)
Hap_48.C.....T.G..T..T.CA..TC...A...............C..		7	A10	LS(7)
Hap_49....A.......TT.T.CA..TCT..A.......A..A.A....A		1	B20	LS(1)
Hap_50..C..C............A..T....A.......A.T......T.		1	E13	LS(1)
Hap_51.C.....T.G..T..T.CA..TC...A.......A.......C..		1	A11	LS(1)
Hap_52.....C............A..T..............TA.....T.		24	E14	817(13),E（11）
Hap_53.....CG...........A..T...TA.........T......T.		31	E15	817(7),E（24）

Table 2

Table 3

Table 4

Table 5

Fig. 1

Fig. 2

Fig. 3

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鸡种 Breed	总数 Total	单倍型个数Number of haplotypes (%)
鸡种 Breed	总数 Total	A	B	C	E
XGH	45	—	4(8.89%)	5(11.11%)	36(80.00%)
XGT	38	—	1(2.63%)	12(31.58%)	25(65.79%)
XXM	55	3(5.45%)	—	5(9.09%)	47(85.45%)
LFH	53	2(3.77%)	8(15.09%)	2(3.77%)	41(77.36%)
XXA	46	11(23.91%)	5(10.87%)	7(15.22%)	23(50.00%)
XS	39	9(23.08%)	4(10.26%)	11(28.21%)	15(38.46%)
JHH	40	20(50.00%)	12(30.00%)	5(12.50%)	3(7.50%)
HGH	77	5(6.49%)	59(76.62%)	5(6.49%)	8(10.39%)
GS	73	39(53.42%)	—	34(46.58%)	—
Z	38	13(34.21%)	25(65.79%)	—	—
YXB	45	7(15.56%)	2(4.44%)	14(31.11%)	22(48.89%)
AK	29	1(3.45%)	1(3.45%)	1(3.45%)	26(89.66%)
LS	34	8(23.53%)	8(23.53%)	1(2.94%)	17(50.00%)
817	32	—	—	—	32(100%)
E	39	—	—	—	39(100%)

品种 Breed	变异位点数 No. of variable sites	单倍型数 No. of haplotype	平均核苷酸差异 Average number of nucleotide differences (K)	核苷酸多样度 Nucleotide diversity (Pi)	单倍型多样度 Haplotype diversity (Hd)
XGH	19	4	4.0465	0.00329±0.00078	0.529±0.078
XGT	19	4	4.9644	0.00403±0.00053	0.698±0.026
XXM	17	5	2.8431	0.00231±0.00057	0.546±0.072
LFH	24	8	5.2438	0.00426±0.00066	0.810±0.032
XXA	23	8	7.4899	0.00608±0.00043	0.851±0.026
XS	21	5	7.6167	0.00619±0.00036	0.800±0.024
JHH	24	10	6.9372	0.00564±0.00057	0.853±0.039
HGH	30	19	5.1490	0.00418±0.00056	0.840±0.029
GS	15	6	5.2870	0.00429±0.00013	0.600±0.034
Z	9	3	4.1920	0.00340±0.00036	0.496±0.054
YXB	21	7	6.5920	0.00535±0.00045	0.718±0.043
AK	23	5	2.6700	0.00217±0.00088	0.594±0.065
LS308	24	8	8.2820	0.00673±0.00047	0.738±0.055
817	4	4	1.8468	0.00150±0.00009	0.740±0.041
E	4	3	1.8030	0.00146±0.00016	0.545±0.063
总Total	45	53	7.9552	0.00646±0.00011	0.901±0.006

品种 Breed	种内 Within breeds	XGH	XGT	XXM	LFH	XXA	XS	JHH	HGH	GS	Z	YXB	AK	LS308	817
XGH	0.0033	—
XGT	0.0041	0.0039	—
XXM	0.0023	0.0028	0.0035	—
LFH	0.0043	0.0039	0.0046	0.0035	—
XXA	0.0061	0.0052	0.0056	0.0049	0.0056	—
XS	0.0062	0.0056	0.0056	0.0054	0.0060	0.0062	—
JHH	0.0057	0.0079	0.0082	0.0079	0.0079	0.0071	0.0071	—
HGH	0.0042	0.0091	0.0098	0.0095	0.0090	0.0086	0.0086	0.0068	—
GS	0.0043	0.0074	0.0068	0.0072	0.0079	0.0067	0.0061	0.0061	0.0083	—
Z	0.0034	0.0094	0.0101	0.0098	0.0092	0.0083	0.0084	0.0058	0.0053	0.0075	—
YXB	0.0054	0.0048	0.0049	0.0045	0.0055	0.0059	0.0058	0.0074	0.0091	0.0062	0.0091	—
AK	0.0022	0.0028	0.0036	0.0023	0.0033	0.0050	0.0055	0.0080	0.0094	0.0076	0.0098	0.0047	—
LS308	0.0068	0.0060	0.0066	0.0058	0.0061	0.0066	0.0069	0.0073	0.0083	0.0077	0.0080	0.0069	0.0056	—
817	0.0015	0.0029	0.0038	0.0024	0.0036	0.0054	0.0060	0.0088	0.0104	0.0083	0.0110	0.0050	0.0023	0.0063	—
E	0.0015	0.0032	0.0042	0.0027	0.0039	0.0058	0.0064	0.0092	0.0107	0.0087	0.0113	0.0053	0.0026	0.0067	0.0016

Genetic Diversity and Origin Characteristics of Chicken Species Based on Mitochondrial DNA D-loop Region

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