生物多样性 ›› 2019, Vol. 27 ›› Issue (6): 667-676.doi: 10.17520/biods.2019013

• 研究报告 • 上一篇    下一篇

利用线粒体COI基因揭示中国乌骨鸡遗传多样性和群体遗传结构

翁茁先1, 2, 3, 黄佳琼2, 张仕豪2, 余锴纯2, 钟福生1, 2, 3, 黄勋和2, 3, *(), 张彬1, *()   

  1. 1 湖南农业大学动物科学技术学院, 长沙 410128
    2 嘉应学院生命科学学院, 广东梅州 514015
    3 广东省五华三黄鸡科技创新中心, 广东梅州 514015
  • 收稿日期:2019-01-17 接受日期:2019-05-20 出版日期:2019-06-20
  • 通讯作者: 黄勋和,张彬 E-mail:hxh826@jyu.edu.cn;zhb8236@126.com
  • 基金项目:
    广东省公益研究与能力建设项目(2016A030303068);嘉应学院省市共建重点建设项目(嘉院[2017]27号)

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

Weng Zhuoxian1, 2, 3, Huang Jiaqiong2, Zhang Shihao2, Yu Kaichun2, Zhong Fusheng1, 2, 3, Huang Xunhe2, 3, *(), Zhang Bin1, *()   

  1. 1 College of Animal Science & Technology, Hunan Agricultural University, Changsha 410128
    2 School of Life Science, Jiaying University, Meizhou, Guangdong 514015
    3 Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, Meizhou, Guangdong 514015
  • Received:2019-01-17 Accepted:2019-05-20 Online:2019-06-20
  • Contact: Huang Xunhe,Zhang Bin E-mail:hxh826@jyu.edu.cn;zhb8236@126.com

全面了解中国乌骨鸡的遗传背景有利于保护和开发利用其种质资源。本研究测定了中国12个乌骨鸡品种线粒体细胞色素c氧化酶亚基I (cytochrome c oxidase subunit I, COI)基因, 比较分析其遗传多样性和群体遗传结构。255份乌骨鸡样品共检测到22个变异位点, 占分析位点的3.17%; 核苷酸多样性为0.00142-0.00339, 单倍型多样性为0.380-0.757, 其中略阳乌鸡核苷酸多样性最高, 德化黑鸡最低。检测到7个氨基酸变异位点, 来自6个品种共11个个体。定义了24种单倍型, 其中单倍型H1和H3为12个乌骨鸡品种共享, 出现频率分别为115次和64次; 盐津乌骨鸡单倍型数最多, 广西乌鸡最少。中性检验与错配分析显示实验种群未经历显著的群体扩张事件。分子变异分析显示81.06%的变异来自群体内; 品种间遗传距离为0.002-0.004, 品种间遗传分化系数Fst值为-0.035至0.594, 雪峰乌骨鸡与其他种群间的遗传分化程度最高。邻接树显示, 乌骨鸡未能独立形成分支, 不能从家鸡和红原鸡中有效区分开来。中国乌骨鸡中介网络图将24个单倍型分为3条进化主支, 呈现出一定的品种特异性, 由无量山乌骨鸡、云南盐津乌骨鸡和雪峰乌骨鸡组成单倍型H8、H9、H11、H12游离于这3条进化主支之外。增加其他家鸡和红原鸡COI基因的中介网络图主体结构与中国乌骨鸡的相同。结果表明中国乌骨鸡品种遗传多样性较低, 但品种间遗传分化显著, 可能是从当地家鸡中选育而来, 需要加强种质资源的保护。

关键词: 乌骨鸡, 线粒体COI基因, 遗传变异, 遗传分化

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 Fst 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

表1

本研究样品信息"

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

表2

12个乌骨鸡品种COI基因序列变异位点数、平均核苷酸差异、核苷酸多样性和单倍型多样性。品种代号同表1。"

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

表3

12个乌骨鸡品种线粒体COI基因的单倍型及其在不同品种的分布"

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

表4

COI基因编码的氨基酸变异及其在不同品种的分布。品种代号同表1。"

品种名
Breed
变异位点
Variation sites
氨基酸变异
Amino acid variation
变异数
Variation number



AP003321
0000122
1235124
9010875
YLTEVDI
竹乡鸡 ZX F...... 酪氨酸→苯丙氨酸 Tyrosine → Phenylalanine 3
竹乡鸡 ZX S...... 酪氨酸→丝氨酸 Tyrosine → Serine 1
竹乡鸡 ZX ..A.... 苏氨酸→丙氨酸 Threonine → Alanine 1
盐津乌骨鸡 YJ ..A.... 苏氨酸→丙氨酸 Threonine → Alanine 1
盐津乌骨鸡 YJ .VA.... 亮氨酸→缬氨酸, 苏氨酸→丙氨酸 Leucine → Valine, Threonine → Alanine 1
丝羽乌骨鸡 SK .....H. 天冬氨酸→组氨酸 Asparagine → Histidine 1
略阳乌鸡 LY ......V 异亮氨酸→缬氨酸 Isoleucine → Valine 1
江山乌骨鸡 JS ...K... 谷氨酸→赖氨酸 Glutamic acid → Lysine 1
余干乌骨鸡 YG ....E.. 缬氨酸→谷氨酸 Valine → Glutamic acid 1

表5

12个乌骨鸡品种的COI序列中性检验。品种代号同表1。"

品种名
Breed
Tajima’s D Fu’s Fs
D P Fs P
略阳乌鸡 LY 0.45768 0.70000 0.96375 0.68900
无量山乌骨鸡 WLS 0.12109 0.56400 0.49464 0.62700
盐津乌骨鸡 YJ -0.79944 0.25300 -1.69126 0.17200
竹乡鸡 ZX 0.99606 0.85100 -0.31381 0.45400
雪峰乌骨鸡 XF -0.76698 0.25300 0.57269 0.65900
江山乌骨鸡 JS 0.01119 0.54100 -0.25147 0.44900
丝羽乌骨鸡 SK -1.43529 0.07300 -1.92588 0.07000
余干乌骨鸡 YG 0.76262 0.79100 0.24173 0.59100
黄羽黑鸡 HY 0.15067 0.60000 0.87825 0.69200
德化黑鸡 DH -0.28222 0.43600 1.28651 0.75700
金湖乌凤鸡 JH 0.31722 0.67500 1.19223 0.77300
广西乌鸡 GX 1.81444 0.97700 3.86919 0.94800
平均 Average 0.11225 0.55950 0.44305 0.57342
方差 Squared deviation 0.87539 0.26761 1.50012 0.25155

图1

12个乌骨鸡品种错配分布"

图2

384只鸡的41个COI单倍型邻接树。R为红原鸡, B为乌骨鸡, D为家鸡, 数字表示样品数量。品种代号同表1。"

图3

COI基因中介网络图。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。(a)中国12种255只乌骨鸡个体的24个COI单倍型。(b) 384只鸡个体的41个COI单倍型中介网络图。"

表6

12种乌骨鸡种群遗传变异的分子变异分析"

变异起源
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 variance (%)
群体间 Among populations 11 52.622 0.18826 18.94
群体内 Within populations 243 195.743 0.805553 81.06
总变异 Total variation 254 248.365 0.99378 100

表7

12个乌骨鸡品种间Kiumura遗传双参数距离(上三角)和遗传分化系数(Fst) (下三角)。品种代号同表1。"

Breed LY WLS YJ ZX XF JS SK YG HY DH JH GX
LY 0.003 0.004 0.003 0.003 0.003 0.003 0.003 0.003 0.003 0.003 0.003
WLS 0.116* 0.003 0.003 0.004 0.004 0.002 0.002 0.003 0.002 0.003 0.003
YJ 0.189* 0.017 0.004 0.004 0.004 0.003 0.004 0.004 0.003 0.003 0.004
ZX -0.018 0.134* 0.207* 0.003 0.003 0.003 0.003 0.003 0.002 0.003 0.003
XF 0.231* 0.427* 0.433* 0.248* 0.004 0.004 0.003 0.004 0.004 0.003 0.002
JS 0.004 0.121* 0.196* -0.014 0.341* 0.002 0.003 0.003 0.003 0.002 0.003
SK 0.178* 0.192* 0.269* 0.134* 0.594* 0.074* 0.003 0.002 0.001 0.002 0.003
YG -0.035 0.170* 0.234* -0.011 0.158* 0.032 0.250* 0.003 0.002 0.003 0.002
HY 0.165* 0.204* 0.261* 0.120* 0.535* 0.051 0.079* 0.223* 0.002 0.002 0.004
DH 0.117 0.160* 0.243* 0.072 0.551* 0.011 -0.012 0.182* 0.044 0.002 0.003
JH 0.013 0.121* 0.206* -0.001 0.403* -0.033 0.445 0.546 0.067 -0.011 0.003
GX 0.054 0.305* 0.343* 0.089* 0.029 0.173* 0.441* -0.002 0.393* 0.383* 0.220*
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