Biodiversity Science ›› 2019, Vol. 27 ›› Issue (6): 667-676.doi: 10.17520/biods.2019013

• Original Papers • Previous Article     Next Article

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:2019-06-14
  • Huang Xunhe,Zhang Bin E-mail:hxh826@jyu.edu.cn;zhb8236@126.com

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

Table 1

Sample information of this study"

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

Table 2

The number of variable sites, average K (k), nucleotide diversity (π) and haplotype diversity (h) of COI gene in the 12 black-bone chicken breeds. Breed codes are the same as in Table 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

Table 3

COI haplotypes and their distributions in the 12 black-bone chicken breeds"

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

Table 4

Amino acid variation of COI gene and their distribution in these black-bone chicken breeds. Breed codes are the same as in Table 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

Table 5

Neutrality test in 12 breeds based on COI sequences. Breed codes are the same as in Table 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

Fig. 1

Mismatch distribution analysis of 12 black-bone chicken breeds"

Fig. 2

Neighbor-joining tree of 41 COI haplotypes deteced in the samples of 384 chickens. R, Red junglefowl; B, Black-bone chicken; D, Domestic chicken. Numbers represent the sample size. Breed codes are the same as in Table 1."

Fig. 3

Median-joining network based on COI gene. The links are labeled by the nucleotide positions to designate transitions. Cycle size is roughly proportional to the haplotype frequency, the breeds are indicated by different colors, breed codes are the same as in Table 1. (a) Median-joining network of 24 COI haplotypes deteced in the samples of 255 individuals of 12 Chinese black-bone breeds. (b) Median-joining network of 41 COI haplotypes deteced in the samples of 384 individuals."

Table 6

AMOVA analysis of genetic variation of 12 black-bone chicken breeds"

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

Table 7

K2P distance (above diagonal) and fixation index (Fst) (below diagonal) among 12 black-bone chicken breeds. Breed codes are the same as in Table 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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