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

• 研究报告:研究报告 • 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. 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
  • 通讯作者: 钟福生 E-mail:zfs@jyu.edu.cn
  • 作者简介:

    # 共同第一作者

  • 基金项目:
    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 Huang1, 2, Zheqi Yu1, Zhuoxian Weng1, 2, 3, Danlin He4, Zhenhua Yi4, Weina Li1, 2, Jiebo Chen1, 2, Xiquan Zhang4, Bingwang Du5, Fusheng Zhong1, 2, 3, *()   

  1. 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
  • Contact: Zhong Fusheng E-mail:zfs@jyu.edu.cn
  • About author:

    # Co-first authors

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

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

表1

本研究的样品信息(每个品种均取30个样本)"

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

表2

12种地方鸡mtDNA D-loop的单倍型及其在品种中的分布。*表示参考序列NC_007235对应的变异位点位置, 圆点表示与参考序列具有相同的碱基。"

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

表3

12个地方鸡品种的线粒体DNA D-loop遗传多样性统计。品种代号同表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

表4

12个鸡品种间的净遗传距离(上三角)和Kimura双参数距离(下三角)。品种代号同表1。"

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

图1

基于85种广东省和邻省家鸡线粒体DNA D-loop单倍型构建的邻接树"

图2

广东省和邻省12种地方鸡线粒体DNA D-loop单倍型的中介网络图。连接点数字表示核苷酸转换的位置; 圆的大小对应单倍型频率; 不同鸡品种用不同颜色标注。品种代号同表1。"

表5

家鸡主要进化枝的地理分布。a单倍型数量及该地区的独享型单倍型(括号数值); b不包括广东省家鸡的数量。"

地区
Region
个体数Individuals 单倍型a/个体数 Haplotypesa/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b
southern 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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