Biodiv Sci ›› 2017, Vol. 25 ›› Issue (5): 540-548. DOI: 10.17520/biods.2017012
• Original Papers: Animal Diversity • Previous Articles Next Articles
Xiaoxu Jia, Xiujun Tang, Yanfeng Fan, Junxian Lu, Shenghai Huang, Qinglian Ge, Yushi Gao*(), Wei Han
Received:
2017-01-08
Accepted:
2017-04-10
Online:
2017-05-20
Published:
2017-06-06
Contact:
Gao Yushi
Xiaoxu Jia, Xiujun Tang, Yanfeng Fan, Junxian Lu, Shenghai Huang, Qinglian Ge, Yushi Gao, Wei Han. Genetic diversity of local chicken breeds in East China based on mitochondrial DNA D-loop region[J]. Biodiv Sci, 2017, 25(5): 540-548.
品种及代号 Breed and code | 原产地 Origin | 现有种群规模及采样 Population (sample size) | 经济用途 Economic use |
---|---|---|---|
安义瓦灰 Anyi Gray (AY) | 江西安义 Anyi, Jiangxi | 600,000 (30) | 肉蛋兼用 E & M |
白耳黄 Baier Yellow (BE) | 江西广丰 Guangfeng, Jiangxi | 20,000,000 (30) | 蛋用 E |
崇仁麻 Chongren Partridge (CP) | 江西崇仁 Chongren, Jiangxi | 52,000,000 (30) | 肉蛋兼用 E & M |
东乡绿壳 Dongxiang Blue-eggshell (DX) | 江西东乡 Dongxiang, Jiangxi | 200,000 (30) | 肉蛋兼用 E & M |
丝羽乌骨 Silkies (SL) | 江西泰和 Taihe, Jiangxi | 16,500,000 (30) | 肉药兼用 Med & M |
金湖乌凤 Jinhu Black-bone (JH) | 福建泰宁 Taining, Fujian | 160,000 (29) | 肉药兼用 Med & M |
仙居 Xianju (XJ) | 浙江仙居 Xianju, Zhejiang | 1,484,000 (30) | 蛋用 E |
琅琊 Langya (LY) | 山东日照 Rizhao, Shandong | 110,000 (30) | 肉蛋兼用 E & M |
寿光 Shouguang (SG) | 山东寿光 Shouguang, Shandong | 201,000 (30) | 肉蛋兼用 E & M |
狼山 Langshan (LS) | 江苏如东 Rudong, Jiangsu | 10,000 (20) | 肉蛋兼用 E & M |
鹿苑 Luyuan (LU) | 江苏张家港 Zhangjiagang, Jiangsu | 20,000 (30) | 肉蛋兼用 E & M |
Table 1 Sampling information about the 11 local chicken breeds. M, Meat; E, Egg; Med, Medical.
品种及代号 Breed and code | 原产地 Origin | 现有种群规模及采样 Population (sample size) | 经济用途 Economic use |
---|---|---|---|
安义瓦灰 Anyi Gray (AY) | 江西安义 Anyi, Jiangxi | 600,000 (30) | 肉蛋兼用 E & M |
白耳黄 Baier Yellow (BE) | 江西广丰 Guangfeng, Jiangxi | 20,000,000 (30) | 蛋用 E |
崇仁麻 Chongren Partridge (CP) | 江西崇仁 Chongren, Jiangxi | 52,000,000 (30) | 肉蛋兼用 E & M |
东乡绿壳 Dongxiang Blue-eggshell (DX) | 江西东乡 Dongxiang, Jiangxi | 200,000 (30) | 肉蛋兼用 E & M |
丝羽乌骨 Silkies (SL) | 江西泰和 Taihe, Jiangxi | 16,500,000 (30) | 肉药兼用 Med & M |
金湖乌凤 Jinhu Black-bone (JH) | 福建泰宁 Taining, Fujian | 160,000 (29) | 肉药兼用 Med & M |
仙居 Xianju (XJ) | 浙江仙居 Xianju, Zhejiang | 1,484,000 (30) | 蛋用 E |
琅琊 Langya (LY) | 山东日照 Rizhao, Shandong | 110,000 (30) | 肉蛋兼用 E & M |
寿光 Shouguang (SG) | 山东寿光 Shouguang, Shandong | 201,000 (30) | 肉蛋兼用 E & M |
狼山 Langshan (LS) | 江苏如东 Rudong, Jiangsu | 10,000 (20) | 肉蛋兼用 E & M |
鹿苑 Luyuan (LU) | 江苏张家港 Zhangjiagang, Jiangsu | 20,000 (30) | 肉蛋兼用 E & M |
单倍型 Haplotype | 变异位点 Variable sites | 单倍型在品种的分布(频率) Breeds (frequency) | 总计 Total |
---|---|---|---|
0000000000 0000000000 0000000000 0000111 1112222222 2222222222 3333333333 4677222 3690111122 3444445678 1134566679 4819112 3797027925 9012366101 0502813726 6612455 | |||
NC007235 | TTTACATCAC ACAGTTTCTA CTCAAACTAT CGGGCAA | ||
A1 | .C...G...T .....C.... .C........ .....G. | BE8, DX13, SL21, XJ8, LU17, LY2 | 69 |
A2 | .C.G.G...T .....C.... .C........ .....G. | SG8 | 8 |
A3 | .C...G...T .....C.... .C...T.... .....G. | LU6 | 6 |
A4 | .C...G...T .....C...G .C.......C .....GG | CP2 | 2 |
A5 | .C...G...T .....C.... .C.......C .....G. | SG5 | 5 |
A6 | .C...G...T G....C.... .C........ .....G. | JH1 | 1 |
A7 | .CC..G...T .....C.... .C......G. .....G. | LY1 | 1 |
A8 | .C...G...T .....CC... .C........ .....G. | SL2 | 2 |
A9 | .C...G...T .....C.... .C........ .A...G. | AY3 | 3 |
A10 | .C..TG...T .....C.... .C........ .A...G. | JH2 | 2 |
A11 | .C.......T .....C.... .C........ .....G. | LY1 | 1 |
B1 | .......... .......... .......... ....... | XJ1, AY7, CP10, DX4, LY2, SG9, LS20 | 53 |
B2 | C......... .......... .......... ....... | CP1 | 1 |
B3 | .......... .......... ..T....... ....... | SL7 | 7 |
B4 | ....T..... .......... .......... ....... | LY2 | 2 |
B5 | .......T.. .......T.. .......... ....... | LY1 | 1 |
B6 | .......... .......... .......... ...A... | XJ1, AY5, BE1, SG1, LY1 | 9 |
B7 | .......... ......C... .......... ...A... | BE4 | 4 |
B8 | .......... .......... .......... .A.A... | JH11, XJ2, BE1 | 14 |
B9 | .......... G......... ....G..... .A.A... | BE15 | 15 |
B10 | .......... .......... T......... .A..... | CP12 | 12 |
C1 | .....G.... ...ACCC..G TC.G..TC.. .....G. | XJ18, AY6, DX2, JH1, SG2 | 29 |
C2 | .....G.... ...ACCCT.G TC.G..TC.. .....G. | LY3 | 3 |
C3 | .....G.... .T.ACCC..G TC.G..TC.. .....G. | LY1 | 1 |
C4 | .....G.... .T.ACC...G TC.G..TC.. ..A..G. | LU1 | 1 |
C5 | .....G.... ...ACCCT.G TC....TC.. .....G. | AY2, LY1 | 3 |
C6 | .....G.... ...ACCCTCG TC....TC.. .....G. | CP1 | 1 |
C7 | .....G.... ...ACCC... TC.G..TC.. .....G. | BE1 | 1 |
C8 | .........T ..GACCC..G TC....TC.. .....G. | AY7 | 7 |
C9 | .......... ...ACCC..G TC....TC.. .....G. | LY1 | 1 |
E1 | .....GC... ....CCCT.. TC........ T...TG. | JH13, CP3, LY6, LU6 | 28 |
E2 | .....GC.G. ....CCCT.. TCT....... T...TG. | CP1 | 1 |
E3 | .....GC... ....CCCT.. TC.G...... TA..TG. | LY8 | 8 |
E4 | ..C..GC... ....CC.T.. TC........ T...TG. | DX11 | 11 |
E5 | ..C..GC... ....CCCT.. TC........ T...TG. | JH1, SG5 | 6 |
Table 2 Variable information and haplotype distribution of the 11 local chicken breeds. Dots (.) denote identity with the reference sequence (NC007235). Breed codes are the same as in Table 1.
单倍型 Haplotype | 变异位点 Variable sites | 单倍型在品种的分布(频率) Breeds (frequency) | 总计 Total |
---|---|---|---|
0000000000 0000000000 0000000000 0000111 1112222222 2222222222 3333333333 4677222 3690111122 3444445678 1134566679 4819112 3797027925 9012366101 0502813726 6612455 | |||
NC007235 | TTTACATCAC ACAGTTTCTA CTCAAACTAT CGGGCAA | ||
A1 | .C...G...T .....C.... .C........ .....G. | BE8, DX13, SL21, XJ8, LU17, LY2 | 69 |
A2 | .C.G.G...T .....C.... .C........ .....G. | SG8 | 8 |
A3 | .C...G...T .....C.... .C...T.... .....G. | LU6 | 6 |
A4 | .C...G...T .....C...G .C.......C .....GG | CP2 | 2 |
A5 | .C...G...T .....C.... .C.......C .....G. | SG5 | 5 |
A6 | .C...G...T G....C.... .C........ .....G. | JH1 | 1 |
A7 | .CC..G...T .....C.... .C......G. .....G. | LY1 | 1 |
A8 | .C...G...T .....CC... .C........ .....G. | SL2 | 2 |
A9 | .C...G...T .....C.... .C........ .A...G. | AY3 | 3 |
A10 | .C..TG...T .....C.... .C........ .A...G. | JH2 | 2 |
A11 | .C.......T .....C.... .C........ .....G. | LY1 | 1 |
B1 | .......... .......... .......... ....... | XJ1, AY7, CP10, DX4, LY2, SG9, LS20 | 53 |
B2 | C......... .......... .......... ....... | CP1 | 1 |
B3 | .......... .......... ..T....... ....... | SL7 | 7 |
B4 | ....T..... .......... .......... ....... | LY2 | 2 |
B5 | .......T.. .......T.. .......... ....... | LY1 | 1 |
B6 | .......... .......... .......... ...A... | XJ1, AY5, BE1, SG1, LY1 | 9 |
B7 | .......... ......C... .......... ...A... | BE4 | 4 |
B8 | .......... .......... .......... .A.A... | JH11, XJ2, BE1 | 14 |
B9 | .......... G......... ....G..... .A.A... | BE15 | 15 |
B10 | .......... .......... T......... .A..... | CP12 | 12 |
C1 | .....G.... ...ACCC..G TC.G..TC.. .....G. | XJ18, AY6, DX2, JH1, SG2 | 29 |
C2 | .....G.... ...ACCCT.G TC.G..TC.. .....G. | LY3 | 3 |
C3 | .....G.... .T.ACCC..G TC.G..TC.. .....G. | LY1 | 1 |
C4 | .....G.... .T.ACC...G TC.G..TC.. ..A..G. | LU1 | 1 |
C5 | .....G.... ...ACCCT.G TC....TC.. .....G. | AY2, LY1 | 3 |
C6 | .....G.... ...ACCCTCG TC....TC.. .....G. | CP1 | 1 |
C7 | .....G.... ...ACCC... TC.G..TC.. .....G. | BE1 | 1 |
C8 | .........T ..GACCC..G TC....TC.. .....G. | AY7 | 7 |
C9 | .......... ...ACCC..G TC....TC.. .....G. | LY1 | 1 |
E1 | .....GC... ....CCCT.. TC........ T...TG. | JH13, CP3, LY6, LU6 | 28 |
E2 | .....GC.G. ....CCCT.. TCT....... T...TG. | CP1 | 1 |
E3 | .....GC... ....CCCT.. TC.G...... TA..TG. | LY8 | 8 |
E4 | ..C..GC... ....CC.T.. TC........ T...TG. | DX11 | 11 |
E5 | ..C..GC... ....CCCT.. TC........ T...TG. | JH1, SG5 | 6 |
品种名 Breed | 样本量 sample size | 单倍型数 No. of haplotypes | 单倍型群(对应个体数) Haplogroup (number of individuals observed) | 单倍型多样度 Haplotype diversity (SD) | 核苷酸多样度 Nucleotide diversity (SD) | 平均核苷酸差异 Average number of nucleotide differences |
---|---|---|---|---|---|---|
安义瓦灰 AY | 30 | 6(A = 1; B = 2; C = 3) | A(3); B(12); C(15) | 0.837(0.027) | 0.00613(0.00140) | 7.540 |
白耳黄 BE | 30 | 6(A = 1; B = 4; C = 1) | A(8); B(21); C(1) | 0.680(0.066) | 0.00424(0.00133) | 5.218 |
崇仁麻 CP | 30 | 7(A = 1; B = 3; C = 1; E = 2) | A(2); B(23); C(1); E(4) | 0.736(0.054) | 0.00425(0.00178) | 5.232 |
东乡绿壳 DX | 30 | 4(A = 1; B = 1; C = 1; E = 1) | A(13); B(4); C(2); E(11) | 0.678(0.049) | 0.00457(0.00138) | 5.444 |
金湖乌凤 JH | 29 | 6(A = 2; B = 1; C = 1; E = 2) | A(3); B(11); C(1); E(14) | 0.670(0.057) | 0.00615(0.00174) | 7.571 |
丝羽乌骨 SL | 30 | 3(A = 2; B = 1) | A(23); B(7) | 0.467(0.087) | 0.00221(0.00075) | 2.720 |
仙居 XJ | 30 | 5(A = 1; B = 3; C = 1) | A(8); B(4); C(18) | 0.582(0.079) | 0.00492(0.00127) | 6.053 |
琅琊 LY | 30 | 13(A = 3; B = 4; C = 4; E = 2) | A(4); B(6); C(6); E(14) | 0.887(0.038) | 0.00647(0.00184) | 7.968 |
寿光 SG | 30 | 6(A = 2; B = 2; C = 1; E = 1) | A(13); B(10); C(2); E(5) | 0.805(0.035) | 0.00553(0.00165) | 6.805 |
狼山 LS | 20 | 1(B = 1) | B(20) | 0 | 0 | 0.000 |
鹿苑 LU | 30 | 3(A = 2; E = 1) | A(25); E(5) | 0.549(0.081) | 0.00237(0.00088) | 2.917 |
总计 All | 319 | 35(A = 11; B = 10; C = 9; E = 5) | (A = 100; B = 118; C = 47; E = 54) | 0.901(0.009) | 0.00573(0.000001) | 6.833 |
Table 3 Haplotype diversity (Hd), average number of differences (K) and nucleotide diversity (Pi) of the D-loop of mtDNA in 11 domestic chicken breeds. Breed codes are the same as in Table 1.
品种名 Breed | 样本量 sample size | 单倍型数 No. of haplotypes | 单倍型群(对应个体数) Haplogroup (number of individuals observed) | 单倍型多样度 Haplotype diversity (SD) | 核苷酸多样度 Nucleotide diversity (SD) | 平均核苷酸差异 Average number of nucleotide differences |
---|---|---|---|---|---|---|
安义瓦灰 AY | 30 | 6(A = 1; B = 2; C = 3) | A(3); B(12); C(15) | 0.837(0.027) | 0.00613(0.00140) | 7.540 |
白耳黄 BE | 30 | 6(A = 1; B = 4; C = 1) | A(8); B(21); C(1) | 0.680(0.066) | 0.00424(0.00133) | 5.218 |
崇仁麻 CP | 30 | 7(A = 1; B = 3; C = 1; E = 2) | A(2); B(23); C(1); E(4) | 0.736(0.054) | 0.00425(0.00178) | 5.232 |
东乡绿壳 DX | 30 | 4(A = 1; B = 1; C = 1; E = 1) | A(13); B(4); C(2); E(11) | 0.678(0.049) | 0.00457(0.00138) | 5.444 |
金湖乌凤 JH | 29 | 6(A = 2; B = 1; C = 1; E = 2) | A(3); B(11); C(1); E(14) | 0.670(0.057) | 0.00615(0.00174) | 7.571 |
丝羽乌骨 SL | 30 | 3(A = 2; B = 1) | A(23); B(7) | 0.467(0.087) | 0.00221(0.00075) | 2.720 |
仙居 XJ | 30 | 5(A = 1; B = 3; C = 1) | A(8); B(4); C(18) | 0.582(0.079) | 0.00492(0.00127) | 6.053 |
琅琊 LY | 30 | 13(A = 3; B = 4; C = 4; E = 2) | A(4); B(6); C(6); E(14) | 0.887(0.038) | 0.00647(0.00184) | 7.968 |
寿光 SG | 30 | 6(A = 2; B = 2; C = 1; E = 1) | A(13); B(10); C(2); E(5) | 0.805(0.035) | 0.00553(0.00165) | 6.805 |
狼山 LS | 20 | 1(B = 1) | B(20) | 0 | 0 | 0.000 |
鹿苑 LU | 30 | 3(A = 2; E = 1) | A(25); E(5) | 0.549(0.081) | 0.00237(0.00088) | 2.917 |
总计 All | 319 | 35(A = 11; B = 10; C = 9; E = 5) | (A = 100; B = 118; C = 47; E = 54) | 0.901(0.009) | 0.00573(0.000001) | 6.833 |
品种名 Breed | 品种内 Within breeds | 安义瓦灰 AY | 白耳黄 BE | 崇仁麻 CP | 东乡绿壳 DX | 金湖乌凤 JH | 丝羽乌骨 SL | 仙居 XJ | 琅琊 LY | 寿光 SG | 狼山 LS | 鹿苑 LU |
---|---|---|---|---|---|---|---|---|---|---|---|---|
安义瓦灰 AY | 0.0062 | |||||||||||
白耳黄 BE | 0.0043 | 0.0073 | ||||||||||
崇仁麻 CP | 0.0044 | 0.0066 | 0.0053 | |||||||||
东乡绿壳 DX | 0.0050 | 0.0073 | 0.0074 | 0.0066 | ||||||||
金湖乌凤 JH | 0.0062 | 0.0077 | 0.0072 | 0.0063 | 0.0064 | |||||||
丝羽乌骨 SL | 0.0022 | 0.0063 | 0.0053 | 0.0055 | 0.0046 | 0.0066 | ||||||
仙居 XJ | 0.0050 | 0.0060 | 0.0084 | 0.0077 | 0.0069 | 0.0079 | 0.0063 | |||||
琅琊 LY | 0.0065 | 0.0077 | 0.0088 | 0.0074 | 0.0065 | 0.0066 | 0.0072 | 0.0071 | ||||
寿光 SG | 0.0056 | 0.0069 | 0.0065 | 0.0060 | 0.0056 | 0.0068 | 0.0043 | 0.0070 | 0.0072 | |||
狼山 LS | 0.0000 | 0.0056 | 0.0035 | 0.0028 | 0.0061 | 0.0060 | 0.0040 | 0.0073 | 0.0075 | 0.0046 | ||
鹿苑 LU | 0.0032 | 0.0069 | 0.0068 | 0.0067 | 0.0046 | 0.0065 | 0.0031 | 0.0063 | 0.0066 | 0.0049 | 0.0061 |
Table 4 The interspecies and intraspecies mean genetic distance of the 11 chicken breeds calculated by Kimura-2-parameter model. Breed codes are the same as in Table 1.
品种名 Breed | 品种内 Within breeds | 安义瓦灰 AY | 白耳黄 BE | 崇仁麻 CP | 东乡绿壳 DX | 金湖乌凤 JH | 丝羽乌骨 SL | 仙居 XJ | 琅琊 LY | 寿光 SG | 狼山 LS | 鹿苑 LU |
---|---|---|---|---|---|---|---|---|---|---|---|---|
安义瓦灰 AY | 0.0062 | |||||||||||
白耳黄 BE | 0.0043 | 0.0073 | ||||||||||
崇仁麻 CP | 0.0044 | 0.0066 | 0.0053 | |||||||||
东乡绿壳 DX | 0.0050 | 0.0073 | 0.0074 | 0.0066 | ||||||||
金湖乌凤 JH | 0.0062 | 0.0077 | 0.0072 | 0.0063 | 0.0064 | |||||||
丝羽乌骨 SL | 0.0022 | 0.0063 | 0.0053 | 0.0055 | 0.0046 | 0.0066 | ||||||
仙居 XJ | 0.0050 | 0.0060 | 0.0084 | 0.0077 | 0.0069 | 0.0079 | 0.0063 | |||||
琅琊 LY | 0.0065 | 0.0077 | 0.0088 | 0.0074 | 0.0065 | 0.0066 | 0.0072 | 0.0071 | ||||
寿光 SG | 0.0056 | 0.0069 | 0.0065 | 0.0060 | 0.0056 | 0.0068 | 0.0043 | 0.0070 | 0.0072 | |||
狼山 LS | 0.0000 | 0.0056 | 0.0035 | 0.0028 | 0.0061 | 0.0060 | 0.0040 | 0.0073 | 0.0075 | 0.0046 | ||
鹿苑 LU | 0.0032 | 0.0069 | 0.0068 | 0.0067 | 0.0046 | 0.0065 | 0.0031 | 0.0063 | 0.0066 | 0.0049 | 0.0061 |
Fig. 2 Median network profile of the mtDNA D-loop haplotypes observed in the present study. The circle sizes are proportional of the haplotype frequencies. Different shades of the circles correspond to distinct populations. Breed codes are the same as in Table 1.
Fig. 3 Neighbor-joining tree based on mtDNA D-loop sequences. GGS, Gallus gallus spadiceus; GGJ, G. gallus jabouillei; GGG, G. gallus gallus; GGB, G. gallus bankiva; GGM, G. gallus murghi.
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