Biodiv Sci ›› 2020, Vol. 28 ›› Issue (6): 688-694. DOI: 10.17520/biods.2019307
• Original Papers: Animal Diversity • Previous Articles Next Articles
Gang Ren1,2,En Li1,Shiye Zhao3,Yanqiong Jiang3,Shasha Wang2,Sixian Tang3,*(),Huijian Hu2,*()
Received:
2019-09-27
Accepted:
2020-02-21
Online:
2020-06-20
Published:
2020-03-27
Contact:
Sixian Tang,Huijian Hu
Gang Ren, En Li, Shiye Zhao, Yanqiong Jiang, Shasha Wang, Sixian Tang, Huijian Hu. Correlation between color polymorphism and the MC1R gene of Lanius schach[J]. Biodiv Sci, 2020, 28(6): 688-694.
地点 Site | 色型 Morph | 数量 No. | 编号 ID |
---|---|---|---|
海丰县公平 Gongping, Haifeng County | 棕色型 Brown | 4 | Z1, Z2, Z3, Z4 |
黑色型 Black | 2 | HS1, HS2 | |
黑色白边型 White-remiged black | 4 | HB1, HB2, HB3, HB4 | |
海丰县联安 Lian’an, Haifeng County | 棕色型 Brown | 2 | Z5, Z6 |
黑色型 Black | 2 | HS3, HS4 | |
海丰县大湖 Dahu, Haifeng County | 棕色型 Brown | 3 | Z7, Z8, Z9 |
黑色型 Black | 3 | HS5, HS6, HS7 |
Table 1 Sampling information of Lanius schach
地点 Site | 色型 Morph | 数量 No. | 编号 ID |
---|---|---|---|
海丰县公平 Gongping, Haifeng County | 棕色型 Brown | 4 | Z1, Z2, Z3, Z4 |
黑色型 Black | 2 | HS1, HS2 | |
黑色白边型 White-remiged black | 4 | HB1, HB2, HB3, HB4 | |
海丰县联安 Lian’an, Haifeng County | 棕色型 Brown | 2 | Z5, Z6 |
黑色型 Black | 2 | HS3, HS4 | |
海丰县大湖 Dahu, Haifeng County | 棕色型 Brown | 3 | Z7, Z8, Z9 |
黑色型 Black | 3 | HS5, HS6, HS7 |
物种名 Species | 基因序列号 GenBank accession no. | 分类地位 Taxonomic status |
---|---|---|
蕉森莺 Coereba flaveola | AF362605.1 | 雀形目 Passeriformes 裸鼻雀科 Thraupidae |
红原鸡 Gallus gallus | NM_001031462.1 | 鸡形目 Galliformes 雉科 Phasianidae |
侏儒鸟 Lepidothrix coronata | XM_017816335.1 | 雀形目 Passeriformes 侏儒鸟科 Pipridae |
柠檬腰柳莺 Phylloscopus chloronotus | AY308751.1 | 雀形目 Passeriformes 莺科 Sylviidae |
Table 2 Reference genetic information used in primer design
物种名 Species | 基因序列号 GenBank accession no. | 分类地位 Taxonomic status |
---|---|---|
蕉森莺 Coereba flaveola | AF362605.1 | 雀形目 Passeriformes 裸鼻雀科 Thraupidae |
红原鸡 Gallus gallus | NM_001031462.1 | 鸡形目 Galliformes 雉科 Phasianidae |
侏儒鸟 Lepidothrix coronata | XM_017816335.1 | 雀形目 Passeriformes 侏儒鸟科 Pipridae |
柠檬腰柳莺 Phylloscopus chloronotus | AY308751.1 | 雀形目 Passeriformes 莺科 Sylviidae |
引物 ID | 引物序列 Primer sequence | 扩增片段长度 Amplified fragment length (bp) |
---|---|---|
1 | Upper 5′-AAYRCCAGYGAGGGCAACCA-3′ Lower 5′-CTACCAGGAGCACRKCACCAC-3′ | 903 |
2 | Upper 5′-GAGCCCTSGAAYRCCAGYGAG-3′ Lower 5′-KCACCACCTCCCGCAGCGTC-3′ | 898 |
3 | Upper 5′-GAGCCCTSGAAYGCCAGCGAG-3′ Lower 5′-GCACCACCTCCCGCAGCGTC-3′ | 898 |
Table 3 The primer for MC1R gene amplification of Lanius schach
引物 ID | 引物序列 Primer sequence | 扩增片段长度 Amplified fragment length (bp) |
---|---|---|
1 | Upper 5′-AAYRCCAGYGAGGGCAACCA-3′ Lower 5′-CTACCAGGAGCACRKCACCAC-3′ | 903 |
2 | Upper 5′-GAGCCCTSGAAYRCCAGYGAG-3′ Lower 5′-KCACCACCTCCCGCAGCGTC-3′ | 898 |
3 | Upper 5′-GAGCCCTSGAAYGCCAGCGAG-3′ Lower 5′-GCACCACCTCCCGCAGCGTC-3′ | 898 |
单倍型 | 变异位点 Variable sites | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Halotype | 41 | 45 | 63 | 69 | 85 | 88 | 119 | 134 | 219 | 237 |
1 | C | T | C | C | G | G | G | C | C | G |
H1 | . | T | . | . | . | . | . | . | . | . |
H2 | C | T | . | . | . | . | . | . | . | . |
H4 | C | T | . | . | . | . | . | . | . | . |
H3 | G | C | G | T | A | A | A | T | T | A |
243 | 268-303 | 321 | 333 | 359 | 362 | 375 | 378 | 379 | 381 | |
G | . | C | G | C | T | C | G | T | C | |
. | . | . | . | . | T | . | . | . | . | |
. | ─ | . | . | . | T | . | . | . | . | |
. | ─ | . | . | . | T | . | . | . | . | |
T | ─ | T | C | T | C | G | C | G | G | |
384 | 408 | 411 | 414 | 438 | 465 | 468 | 474 | 496 | 504 | |
G | T | C | G | C | C | G | C | G | G | |
. | . | . | . | . | . | . | . | . | . | |
. | . | . | . | . | . | . | . | . | . | |
. | . | . | . | . | . | . | . | . | . | |
T | C | T | T | T | G | C | G | A | A | |
513 | 527 | 529 | 535 | 552 | 556 | 579 | 623 | 628 | 675 | |
C | T | C | G | T | G | C | T | G | G | |
. | C | . | . | . | . | . | T | . | . | |
. | . | . | . | . | . | . | T | . | . | |
. | . | . | . | . | . | . | T | . | . | |
T | T | T | A | C | A | T | C | A | A | |
680 | 681 | 682 | 711 | 732 | 828 | 885 | 931 | |||
C | T | G | G | G | C | T | A | |||
. | . | . | . | . | . | . | . | |||
. | . | . | . | . | . | . | . | |||
. | . | . | . | . | . | . | . | |||
T | C | A | C | A | T | C | C |
Table 4 Variable sites of MC1R gene haplotypes in the Lanius schach
单倍型 | 变异位点 Variable sites | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Halotype | 41 | 45 | 63 | 69 | 85 | 88 | 119 | 134 | 219 | 237 |
1 | C | T | C | C | G | G | G | C | C | G |
H1 | . | T | . | . | . | . | . | . | . | . |
H2 | C | T | . | . | . | . | . | . | . | . |
H4 | C | T | . | . | . | . | . | . | . | . |
H3 | G | C | G | T | A | A | A | T | T | A |
243 | 268-303 | 321 | 333 | 359 | 362 | 375 | 378 | 379 | 381 | |
G | . | C | G | C | T | C | G | T | C | |
. | . | . | . | . | T | . | . | . | . | |
. | ─ | . | . | . | T | . | . | . | . | |
. | ─ | . | . | . | T | . | . | . | . | |
T | ─ | T | C | T | C | G | C | G | G | |
384 | 408 | 411 | 414 | 438 | 465 | 468 | 474 | 496 | 504 | |
G | T | C | G | C | C | G | C | G | G | |
. | . | . | . | . | . | . | . | . | . | |
. | . | . | . | . | . | . | . | . | . | |
. | . | . | . | . | . | . | . | . | . | |
T | C | T | T | T | G | C | G | A | A | |
513 | 527 | 529 | 535 | 552 | 556 | 579 | 623 | 628 | 675 | |
C | T | C | G | T | G | C | T | G | G | |
. | C | . | . | . | . | . | T | . | . | |
. | . | . | . | . | . | . | T | . | . | |
. | . | . | . | . | . | . | T | . | . | |
T | T | T | A | C | A | T | C | A | A | |
680 | 681 | 682 | 711 | 732 | 828 | 885 | 931 | |||
C | T | G | G | G | C | T | A | |||
. | . | . | . | . | . | . | . | |||
. | . | . | . | . | . | . | . | |||
. | . | . | . | . | . | . | . | |||
T | C | A | C | A | T | C | C |
T(U) | C | A | G | |
---|---|---|---|---|
H1 | 22.9 | 35.7 | 16.7 | 24.6 |
H2 | 23.1 | 35.7 | 16.7 | 24.5 |
H4 | 23.1 | 35.7 | 16.7 | 24.5 |
H3 | 22.7 | 36.2 | 16.8 | 24.2 |
均值 Average | 22.9 | 35.9 | 16.7 | 24.5 |
Table 5 The nucleotide frequencies of the halotypes (%) from MC1R gene sequences of Lanius schach
T(U) | C | A | G | |
---|---|---|---|---|
H1 | 22.9 | 35.7 | 16.7 | 24.6 |
H2 | 23.1 | 35.7 | 16.7 | 24.5 |
H4 | 23.1 | 35.7 | 16.7 | 24.5 |
H3 | 22.7 | 36.2 | 16.8 | 24.2 |
均值 Average | 22.9 | 35.9 | 16.7 | 24.5 |
单倍型 Halotype | 氨基酸变异位点 Amino acid variable sites | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
14 | 21 | 29 | 30 | 40 | 45 | 90-101 | 120 | 121 | 127 | |
1 | S | H | G | G | S | A | LAEMLFMLLLEH | T | L | F |
H1 | . | . | . | . | . | . | LAEMLFMLLLEH | . | L | . |
H2 | S | . | . | . | . | . | ─ | . | L | . |
H4 | S | . | . | . | . | . | ─ | . | L | . |
H3 | W | Q | S | S | N | V | ─ | M | P | V |
166 | 176 | 179 | 186 | 208 | 210 | 227 | 228 | 311 | ||
V | V | A | V | M | A | T | A | T | ||
. | . | . | . | M | . | . | . | . | ||
. | . | . | . | M | . | . | . | . | ||
. | . | . | . | M | . | . | . | . | ||
I | V | T | I | T | T | I | T | P |
Table 6 Variable sites of MC1R in the Lanius schach
单倍型 Halotype | 氨基酸变异位点 Amino acid variable sites | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
14 | 21 | 29 | 30 | 40 | 45 | 90-101 | 120 | 121 | 127 | |
1 | S | H | G | G | S | A | LAEMLFMLLLEH | T | L | F |
H1 | . | . | . | . | . | . | LAEMLFMLLLEH | . | L | . |
H2 | S | . | . | . | . | . | ─ | . | L | . |
H4 | S | . | . | . | . | . | ─ | . | L | . |
H3 | W | Q | S | S | N | V | ─ | M | P | V |
166 | 176 | 179 | 186 | 208 | 210 | 227 | 228 | 311 | ||
V | V | A | V | M | A | T | A | T | ||
. | . | . | . | M | . | . | . | . | ||
. | . | . | . | M | . | . | . | . | ||
. | . | . | . | M | . | . | . | . | ||
I | V | T | I | T | T | I | T | P |
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