新疆农业科学 ›› 2023, Vol. 60 ›› Issue (10): 2590-2600.DOI: 10.6048/j.issn.1001-4330.2023.10.030
• 农业装备工程与机械化·畜牧兽医 • 上一篇
韩丽云1,2(), 李艳艳2, 马云1, 虎红红1, 康小龙1, 郭殿芝2, 史远刚1()
收稿日期:
2022-12-28
出版日期:
2023-10-20
发布日期:
2023-11-01
通信作者:
史远刚(1962-),男,宁夏银川人,教授,博士,博士生导师,研究方向为动物遗传育种与繁殖,(E-mail)作者简介:
韩丽云(1989-),女,河北衡水人,硕士研究生,研究方向为动物遗传育种,(E-mail)18152307692@163.com
基金资助:
HAN Liyun1,2(), LI Yanyan2, MA Yun1, HU Honghong1, KANG Xiaolong1, GUO Dianzhi2, SHI Yuangang1()
Received:
2022-12-28
Online:
2023-10-20
Published:
2023-11-01
Correspondence author:
SHI Yuangang (1962-), male, native place :Yinchuan, Ningxia. professor, research field: animal genetics, breeding and reproduction,(E-mail)Supported by:
摘要:
【目的】 鉴定与牛体尺性状相关的基因,筛选PPARγ、MYF5和AGPAT5三个基因的SNP多态性,研究SNP突变对牛体尺性状的影响,为新疆褐牛的分子育种提供标记信息。【方法】 采用PCR-RFLP方法对新疆褐牛PPARγ、MYF5和AGPAT5基因的突变位点进行研究,通过单倍型法构建三个目标基因的单倍型块并统计不同单倍型的基因型频率。【结果】 三个基因的6个SNP位点对体尺性状均有显著影响,mRNA二级结构预测发现PPARγ-exon7(G74T)和AGPAT5-exon7(G72A)均导致mRNA二级结构和自由能发生改变,蛋白二级结构预测发现牛PPARγ基因外显子1和AGPAT5外显子7的2个SNP位点均为错义突变,改变氨基酸结构,但是蛋白质二级结构未发生改变;MYF5外显子1的SNP位点突变为同义突变,氨基酸及蛋白质二级结构均未发生改变。【结论】 筛选PPARγ、MYF5和AGPAT5基因的6个SNP位点,基因PPARγ、MYF5和AGPAT5与牛体尺性状的关系。
中图分类号:
韩丽云, 李艳艳, 马云, 虎红红, 康小龙, 郭殿芝, 史远刚. 新疆褐牛PPARγ、MYF5和AGPAT5基因SNP突变与体尺性状的关联分析[J]. 新疆农业科学, 2023, 60(10): 2590-2600.
HAN Liyun, LI Yanyan, MA Yun, HU Honghong, KANG Xiaolong, GUO Dianzhi, SHI Yuangang. A study of association analysis on gene PPARγ, MYF5 and AGPAT5 with body size traits in Xinjiang brown cattle[J]. Xinjiang Agricultural Sciences, 2023, 60(10): 2590-2600.
基因区域 Gene & SNP | 登陆号 Accession number | 引物序列 Primer sequence (5’-3’) | 扩增片段长度 Product length (bp) |
---|---|---|---|
PPARγ-exon7 | NM-181024.2 | F: AATGTGAGTCATTGGCTG | 417 |
R: GGTGTCAGATTTTTCCCTPHPH | |||
PPARγ-intron2 | F: CCCGATGGTTGCAGATTA | 1 842 | |
R: AGGCTCCACTTTGATTGC | |||
MYF5-exon1 | NM-174116.1 | F:GGCGTCTGCCCTTGTTA | 690 |
R: TTTGTAAAAGTTGGGAAG | |||
MYF5-intron1 | F: CTCTGATGGCATGGTAAG | 923 | |
R: CAGTAGACGATGTCAAAA | |||
AGPAT5-exon7 | NM_001075932.1 | F: GTAGGGAACTATGGGAGA | 771 |
R: CACTAACTGCAAAACAACA | |||
AGPAT5-intron3 | F: TCCCGCTGTATGGCAGTTA | 3 461 | |
R: CTGGAGTTCCTGCGTTGAT |
表1 引物序列
Tab.1 Primer sequence
基因区域 Gene & SNP | 登陆号 Accession number | 引物序列 Primer sequence (5’-3’) | 扩增片段长度 Product length (bp) |
---|---|---|---|
PPARγ-exon7 | NM-181024.2 | F: AATGTGAGTCATTGGCTG | 417 |
R: GGTGTCAGATTTTTCCCTPHPH | |||
PPARγ-intron2 | F: CCCGATGGTTGCAGATTA | 1 842 | |
R: AGGCTCCACTTTGATTGC | |||
MYF5-exon1 | NM-174116.1 | F:GGCGTCTGCCCTTGTTA | 690 |
R: TTTGTAAAAGTTGGGAAG | |||
MYF5-intron1 | F: CTCTGATGGCATGGTAAG | 923 | |
R: CAGTAGACGATGTCAAAA | |||
AGPAT5-exon7 | NM_001075932.1 | F: GTAGGGAACTATGGGAGA | 771 |
R: CACTAACTGCAAAACAACA | |||
AGPAT5-intron3 | F: TCCCGCTGTATGGCAGTTA | 3 461 | |
R: CTGGAGTTCCTGCGTTGAT |
图1 PCR扩增产物 注:M代表Marker,P1代表PPARγ-exon7,P2表示PPARγ-intron2,P3表示MYF5-exon1,P4表示MYF5-intron1,P5表示AGPAT5-exon7,P6表示AGPAT5-intron3。
Fig.1 Individual PCR product Note: M represents Marker, P1 represents PPARγ-Exon7, P2 represents PPARγ-Intron2, P3 represents MyF5-Exon1, P4 represents MyF5-Inintron1, P5 represents AGPAT5-Exon7, P6 represents AGPAT5-Inintron3
基因 Gene | SNP | 基因型 Genotype | 基因型 频率 Genotypic frequency | 等位基因 Allele | 等位基因 频率 Allele frequency | 纯合度 Homozy- gosity | 杂合度 Heterozy- gosity | 有效 等位 基因数 Effective number of alleles | PIC | 哈代-温伯格平衡 Hardy-weinberg equilibrium | |
---|---|---|---|---|---|---|---|---|---|---|---|
x2 | P | ||||||||||
PPARγ-extron7 | SNP1 | AA(84) | 0.85 | A | 0.92 | 0.86 | 0.14 | 1.16 | 0.13 | 0.66 | 0.42 |
AB(15) | 0.15 | B | 0.08 | ||||||||
BB (0) | 0 | ||||||||||
PPARγ-intron2 | SNP2 | AA(50) | 0.51 | A | 0.70 | 0.58 | 0.42 | 1.74 | 0.33 | 1.62 | 0.20 |
AB(37) | 0.37 | B | 0.30 | ||||||||
BB(1) | 0.12 | ||||||||||
MYF5-exon1 | SNP3 | AA(95) | 0.96 | A | 0.98 | 0.97 | 0.03 | 1.04 | 0.04 | 0.04 | 0.84 |
AB(4) | 0.04 | B | 0.02 | ||||||||
BB(0) | 0 | ||||||||||
MYF5-intron1 | SNP4 | AA(24) | 0.24 | A | 0.62 | 0.63 | 0.47 | 1.89 | 0.36 | 37.56 | <0.001 |
AB(75) | 0.76 | B | 0.38 | ||||||||
BB(0) | 0 | ||||||||||
AGPAT5-intron3 | SNP5 | AA(27) | 0.27 | A | 0.55 | 0.50 | 0.50 | 1.99 | 0.37 | 1.19 | 0.28 |
AB(54) | 0.55 | B | 0.46 | ||||||||
BB(18) | 0.18 | ||||||||||
AGPAT5-exon7 | SNP6 | AA(72) | 0.73 | A | 0.81 | 0.69 | 0.31 | 1.46 | 0.26 | 27.27 | <0.001 |
AB(15) | 0.15 | B | 0.19 | ||||||||
BB(12) | 0.12 |
表2 6个SNPs位点基因频率、基因型频率以及检验
Tab.2 Genotypic and allelic frequencies and Hardy-Weinberg equilibrium test of 6 SNPs
基因 Gene | SNP | 基因型 Genotype | 基因型 频率 Genotypic frequency | 等位基因 Allele | 等位基因 频率 Allele frequency | 纯合度 Homozy- gosity | 杂合度 Heterozy- gosity | 有效 等位 基因数 Effective number of alleles | PIC | 哈代-温伯格平衡 Hardy-weinberg equilibrium | |
---|---|---|---|---|---|---|---|---|---|---|---|
x2 | P | ||||||||||
PPARγ-extron7 | SNP1 | AA(84) | 0.85 | A | 0.92 | 0.86 | 0.14 | 1.16 | 0.13 | 0.66 | 0.42 |
AB(15) | 0.15 | B | 0.08 | ||||||||
BB (0) | 0 | ||||||||||
PPARγ-intron2 | SNP2 | AA(50) | 0.51 | A | 0.70 | 0.58 | 0.42 | 1.74 | 0.33 | 1.62 | 0.20 |
AB(37) | 0.37 | B | 0.30 | ||||||||
BB(1) | 0.12 | ||||||||||
MYF5-exon1 | SNP3 | AA(95) | 0.96 | A | 0.98 | 0.97 | 0.03 | 1.04 | 0.04 | 0.04 | 0.84 |
AB(4) | 0.04 | B | 0.02 | ||||||||
BB(0) | 0 | ||||||||||
MYF5-intron1 | SNP4 | AA(24) | 0.24 | A | 0.62 | 0.63 | 0.47 | 1.89 | 0.36 | 37.56 | <0.001 |
AB(75) | 0.76 | B | 0.38 | ||||||||
BB(0) | 0 | ||||||||||
AGPAT5-intron3 | SNP5 | AA(27) | 0.27 | A | 0.55 | 0.50 | 0.50 | 1.99 | 0.37 | 1.19 | 0.28 |
AB(54) | 0.55 | B | 0.46 | ||||||||
BB(18) | 0.18 | ||||||||||
AGPAT5-exon7 | SNP6 | AA(72) | 0.73 | A | 0.81 | 0.69 | 0.31 | 1.46 | 0.26 | 27.27 | <0.001 |
AB(15) | 0.15 | B | 0.19 | ||||||||
BB(12) | 0.12 |
基因 Gene | 基因型 Genotype | 体长 Length | 胸围 Bust | 胸宽 Chest width | 十字部高 Height at hip cross | 体重 Weight | |
---|---|---|---|---|---|---|---|
PPARγ-extron7 | SNP1 | AA | 128.97±1.16 | 158.22±0.89A | 43.30±0.48 | 122.32±0.63 | 300.21±3.86A |
AB | 129.11±1.28 | 162.07±0.99B | 42.79±0.51 | 122.37±0.71 | 311.76±4.42B | ||
P值 | 0.921 9 | 0.000 2 | 0.588 5 | 0.957 7 | 0.009 9 | ||
PPARγ-intron2 | SNP2 | AA | 128.11±1.15 | 160.60±0.88 | 43.43±0.48 | 122.42±0.63 | 313.72±3.87Aa |
AB | 130.42±1.20 | 161.33±0.94 | 42.79±0.51 | 122.21±0.67 | 396.63±4.11B | ||
BB | 128.59±1.49 | 158.51±1.15 | 43.21±0.63 | 122.42±0.82 | 307.61±5.02b | ||
P值 | 0.077 4 | 0.063 1 | 0.324 7 | 0.923 4 | 0.001 9 | ||
MYF5-exon1 | SNP3 | AA | 128.61±0.89 | 159.51±0.71 | 42.32±0.38 | 121.53±0.50 | 301.65±2.96 |
AB | 129.47±1.88 | 160.79±1.42 | 43.97±0.78 | 123.17±1.01 | 310.32±6.28 | ||
P值 | 0.681 8 | 0.421 8 | 0.061 2 | 0.147 9 | 0.208 7 | ||
MYF5-intron1 | SNP4 | AA | 128.93±1.24 | 159.89±0.97 | 42.59±0.53a | 122.75±0.69 | 301.65±2.96 |
AB | 129.15±1.06 | 160.40±0.80 | 43.70±0.44b | 121.95±0.57 | 310.32±6.28 | ||
P值 | 0.832 2 | 0.549 8 | 0.014 2 | 0.176 2 | 0.588 7 | ||
AGPAT5-intron3 | SNP5 | AA | 129.19±1.26 | 160.96±0.96A | 43.58±0.53A | 123.17±0.68 | 313.60±4.25A |
AB | 130.54±1.17a | 161.99±0.90A | 43.69±0.49A | 122.36±0.64 | 310.47±3.96A | ||
BB | 127.39±1.33b | 157.50±1.04B | 42.16±0.56B | 121.52±0.74 | 293.88±4.49B | ||
P值 | 0.039 5 | 0.001 7 | 0.008 6 | 0.088 0 | 0.000 3 | ||
AGPAT5-exon7 | SNP6 | AA | 128.81±1.18 | 161.35±0.91A | 42.92±0.50a | 123.06±0.65 | 301.86±3.97 |
AB | 130.02±1.29 | 162.91±0.98A | 44.14±0.54b | 122.86±0.69 | 311.17±4.38 | ||
BB | 128.30±1.55 | 156.18±1.22B | 42.36±0.62a | 121.12±0.86 | 304.89±5.21 | ||
P值 | 0.523 9 | 0.000 2 | 0.019 5 | 0.076 1 | 0.093 7 |
表3 目标基因6个SNPs位点与体尺性状的关联(最小二乘均值±标准误)
Tab.3 Effects of 6 SNPs on body size in Xinjiang cattle(LSE±SE)
基因 Gene | 基因型 Genotype | 体长 Length | 胸围 Bust | 胸宽 Chest width | 十字部高 Height at hip cross | 体重 Weight | |
---|---|---|---|---|---|---|---|
PPARγ-extron7 | SNP1 | AA | 128.97±1.16 | 158.22±0.89A | 43.30±0.48 | 122.32±0.63 | 300.21±3.86A |
AB | 129.11±1.28 | 162.07±0.99B | 42.79±0.51 | 122.37±0.71 | 311.76±4.42B | ||
P值 | 0.921 9 | 0.000 2 | 0.588 5 | 0.957 7 | 0.009 9 | ||
PPARγ-intron2 | SNP2 | AA | 128.11±1.15 | 160.60±0.88 | 43.43±0.48 | 122.42±0.63 | 313.72±3.87Aa |
AB | 130.42±1.20 | 161.33±0.94 | 42.79±0.51 | 122.21±0.67 | 396.63±4.11B | ||
BB | 128.59±1.49 | 158.51±1.15 | 43.21±0.63 | 122.42±0.82 | 307.61±5.02b | ||
P值 | 0.077 4 | 0.063 1 | 0.324 7 | 0.923 4 | 0.001 9 | ||
MYF5-exon1 | SNP3 | AA | 128.61±0.89 | 159.51±0.71 | 42.32±0.38 | 121.53±0.50 | 301.65±2.96 |
AB | 129.47±1.88 | 160.79±1.42 | 43.97±0.78 | 123.17±1.01 | 310.32±6.28 | ||
P值 | 0.681 8 | 0.421 8 | 0.061 2 | 0.147 9 | 0.208 7 | ||
MYF5-intron1 | SNP4 | AA | 128.93±1.24 | 159.89±0.97 | 42.59±0.53a | 122.75±0.69 | 301.65±2.96 |
AB | 129.15±1.06 | 160.40±0.80 | 43.70±0.44b | 121.95±0.57 | 310.32±6.28 | ||
P值 | 0.832 2 | 0.549 8 | 0.014 2 | 0.176 2 | 0.588 7 | ||
AGPAT5-intron3 | SNP5 | AA | 129.19±1.26 | 160.96±0.96A | 43.58±0.53A | 123.17±0.68 | 313.60±4.25A |
AB | 130.54±1.17a | 161.99±0.90A | 43.69±0.49A | 122.36±0.64 | 310.47±3.96A | ||
BB | 127.39±1.33b | 157.50±1.04B | 42.16±0.56B | 121.52±0.74 | 293.88±4.49B | ||
P值 | 0.039 5 | 0.001 7 | 0.008 6 | 0.088 0 | 0.000 3 | ||
AGPAT5-exon7 | SNP6 | AA | 128.81±1.18 | 161.35±0.91A | 42.92±0.50a | 123.06±0.65 | 301.86±3.97 |
AB | 130.02±1.29 | 162.91±0.98A | 44.14±0.54b | 122.86±0.69 | 311.17±4.38 | ||
BB | 128.30±1.55 | 156.18±1.22B | 42.36±0.62a | 121.12±0.86 | 304.89±5.21 | ||
P值 | 0.523 9 | 0.000 2 | 0.019 5 | 0.076 1 | 0.093 7 |
位点 Site | 单倍型 Haplt- type | 单倍型频率 Haplotype frequency | 体长 Length | 胸围 Bust | 胸宽 Chest width | 十字部高 Height at hip cross | 体重 Weight |
---|---|---|---|---|---|---|---|
PPARγ- exon7(74) -intron2 (133、170) | GGC | 0.417 7 | 129.51±0.82 | 161.81±0.81 | 43.51±0.48a | 122.23±0.61 | 304.67±3.02 |
GCC | 0.316 5 | 127.62±1.38 | 161.83±1.36 | 44.50±0.80A | 123.91±1.01a | 306.55±4.99 | |
GGT | 0.113 9 | 129.93±0.72 | 161.17±0.68 | 43.97±0.41A | 122.63±0.51 | 307.77±2.61 | |
GCT | 0.113 9 | 129.87±1.40 | 159.68±1.33 | 41.14±0.80Bb | 124.47±1.00a | 308.62±4.99 | |
TCT | 0.038 0 | 131.60±2.35 | 162.89±2.27 | 45.50±1.37A | 119.18±1.70b | 298.14±8.64 |
表 4 PPARγ-exon7(74)-intron2(133、170)与体尺性状的关联(最小二乘均值±标准误)
Tab.4 Effects of haplotype block PPARγ-exon7(74)-intron2(133、170) on body size traits in Xinjiang brown cattle (LSE±SE)
位点 Site | 单倍型 Haplt- type | 单倍型频率 Haplotype frequency | 体长 Length | 胸围 Bust | 胸宽 Chest width | 十字部高 Height at hip cross | 体重 Weight |
---|---|---|---|---|---|---|---|
PPARγ- exon7(74) -intron2 (133、170) | GGC | 0.417 7 | 129.51±0.82 | 161.81±0.81 | 43.51±0.48a | 122.23±0.61 | 304.67±3.02 |
GCC | 0.316 5 | 127.62±1.38 | 161.83±1.36 | 44.50±0.80A | 123.91±1.01a | 306.55±4.99 | |
GGT | 0.113 9 | 129.93±0.72 | 161.17±0.68 | 43.97±0.41A | 122.63±0.51 | 307.77±2.61 | |
GCT | 0.113 9 | 129.87±1.40 | 159.68±1.33 | 41.14±0.80Bb | 124.47±1.00a | 308.62±4.99 | |
TCT | 0.038 0 | 131.60±2.35 | 162.89±2.27 | 45.50±1.37A | 119.18±1.70b | 298.14±8.64 |
位点 Site | 单倍型 Haplt- type | 单倍型频率 Haplotype frequency | 体长 Length | 胸围 Bust | 胸宽 Chest width | 十字部高 Height at hip cross | 体重 Weight |
---|---|---|---|---|---|---|---|
MYF5- exon1(236) -intron1 (633) | CG | 0.021 9 | 129.43±2.91a | 170.47±2.87A | 46.45±1.65 | 121.64±2.03 | 349.81±1.24A |
TA | 0.252 7 | 128.31±0.88 | 161.60±0.83B | 44.50±0.48a | 120.64±0.59A | 300.99±3.31B | |
TG | 0.725 2 | 123.50±0.53b | 161.25±0.51B | 43.31±0.30b | 123.13±0.36B | 307.18±1.96B |
表5 MYF5-exon1(236)-intron1(633)与体尺性状的关联(最小二乘均值±标准误)
Tab.5 Effects of haplotype block MYF5-exon1(236)-intron1(633) on body size traits in Xinjiang brown cattle(LSE±SE)
位点 Site | 单倍型 Haplt- type | 单倍型频率 Haplotype frequency | 体长 Length | 胸围 Bust | 胸宽 Chest width | 十字部高 Height at hip cross | 体重 Weight |
---|---|---|---|---|---|---|---|
MYF5- exon1(236) -intron1 (633) | CG | 0.021 9 | 129.43±2.91a | 170.47±2.87A | 46.45±1.65 | 121.64±2.03 | 349.81±1.24A |
TA | 0.252 7 | 128.31±0.88 | 161.60±0.83B | 44.50±0.48a | 120.64±0.59A | 300.99±3.31B | |
TG | 0.725 2 | 123.50±0.53b | 161.25±0.51B | 43.31±0.30b | 123.13±0.36B | 307.18±1.96B |
位点 Site | 单倍型 Haplt- type | 单倍型频率 Haplotype frequency | 体长 Length | 胸围 Bust | 胸宽 Chest width | 十字部高 Height at hip cross | 体重 Weight |
---|---|---|---|---|---|---|---|
AGPAT5- exon7 (72、97)- intron3 (501、515、 550) | AAGGG | 0.062 5 | 133.25±2.14Aa | 160.43±2.15A | 45.41±1.10A | 116.57±1.30B | 316.37±8.14A |
AGCTT | 0.062 5 | 123.39±1.98B | 149.60±2.06B | 37.52±1.04B | 120.60±1.25A | 274.02±8.14C | |
ATGGG | 0.062 5 | 133.25±2.14Ab | 160.43±2.15A | 45.40±1.10A | 116.57±1.30B | 316.37±8.14A | |
GGGGG | 0.312 5 | 130.99±0.82Ab | 160.83±0.84Aa | 44.08±0.43Aa | 122.20±0.51A | 296.26±3.28B | |
GTCTT | 0.390 6 | 129.22±1.64b | 161.31±1.70A | 43.07±0.82Aa | 123.06±1.00A | 305.69±6.15B | |
GTGGG | 0.109 4 | 127.75±0.94Ab | 164.20±0.96Ab | 45.49±0.49b | 121.89±0.59A | 321.68±3.64A |
表6 AGPAT5-exon7(72、97)-intron3(501、515、550)与体尺性状的关联(最小二乘均值±标准误)
Tab.6 Effects of haplotype block AGPAT5-exon7(72、97)-intron3(501、515、550) on body size traits in brown cattle(LSE±SE)
位点 Site | 单倍型 Haplt- type | 单倍型频率 Haplotype frequency | 体长 Length | 胸围 Bust | 胸宽 Chest width | 十字部高 Height at hip cross | 体重 Weight |
---|---|---|---|---|---|---|---|
AGPAT5- exon7 (72、97)- intron3 (501、515、 550) | AAGGG | 0.062 5 | 133.25±2.14Aa | 160.43±2.15A | 45.41±1.10A | 116.57±1.30B | 316.37±8.14A |
AGCTT | 0.062 5 | 123.39±1.98B | 149.60±2.06B | 37.52±1.04B | 120.60±1.25A | 274.02±8.14C | |
ATGGG | 0.062 5 | 133.25±2.14Ab | 160.43±2.15A | 45.40±1.10A | 116.57±1.30B | 316.37±8.14A | |
GGGGG | 0.312 5 | 130.99±0.82Ab | 160.83±0.84Aa | 44.08±0.43Aa | 122.20±0.51A | 296.26±3.28B | |
GTCTT | 0.390 6 | 129.22±1.64b | 161.31±1.70A | 43.07±0.82Aa | 123.06±1.00A | 305.69±6.15B | |
GTGGG | 0.109 4 | 127.75±0.94Ab | 164.20±0.96Ab | 45.49±0.49b | 121.89±0.59A | 321.68±3.64A |
图14 PPARγ-exon7和AGPAT5-exon7 SNP位点突变前后RNA二级结构对比
Fig.14 Comparison of RNA secondary structure before and after mutation of SNP sites in PPARγ-exon7 and AGPAT5-exon7
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