A study of association analysis on gene PPARγ, MYF5 and AGPAT5 with body size traits in Xinjiang brown cattle

doi:10.6048/j.issn.1001-4330.2023.10.030

Abstract

Abstract:

【Objective】 To screen SNP polymorphisms in PPARγ, MYF5and AGPAT5 closely related to the regulation of muscle growth and development, lipid metabolism and meat quality, and reveal the effects of SNP mutations on body size traits in Xinjiang brown cattle.【Methods】 The mutation of gene PPARγ, MYF5 and AGPAT5 in Xinjiang brown cattle were screened by PCR-RFLP method.The haplotype blocks of the above three target genes were constructed by haplotype method, and the genotype frequencies of different haplotypes were counted.【Results】 SNP association analysis showed that six SNP loci of the three genes had structure PPARγ- Exon7 (g74t) and AGPAT5-exon7 (g72a) led to changes in mRNA secondary structure and free energy, and protein secondary structure prediction revealed that two SNPs in both exon 1 of PPARγand exon 7 of AGPAT5 were missense mutations, which could change amino acid, but no impact on protein secondary structure.【Conclusion】 In this study, six polymorphisms in PPARγ, MYF5, and AGPAT5 genes were screened, and through genotyping, association analysis and bioinformatics analysis, and marker AGPAT5, PPARγ, MYF5 and AGPAT5 determined the relationship with body size traits by information for molecular breeding of Xinjiang brown cattle.

Key words: Xinjiang brown cattle; PPARγ; MYF5; AGPAT5; body size

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。

关键词: 新疆褐牛, PPARγ, MYF5, AGPAT5, 体尺性状

CLC Number:

S826
S814

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.

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.

Figures/Tables 20

References 26

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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
PPARγ-exon7		R: GGTGTCAGATTTTTCCCTPHPH	417
PPARγ-intron2		F: CCCGATGGTTGCAGATTA	1 842
PPARγ-intron2		R: AGGCTCCACTTTGATTGC	1 842
MYF5-exon1	NM-174116.1	F:GGCGTCTGCCCTTGTTA	690
MYF5-exon1		R: TTTGTAAAAGTTGGGAAG	690
MYF5-intron1		F: CTCTGATGGCATGGTAAG	923
MYF5-intron1		R: CAGTAGACGATGTCAAAA	923
AGPAT5-exon7	NM_001075932.1	F: GTAGGGAACTATGGGAGA	771
AGPAT5-exon7		R: CACTAACTGCAAAACAACA	771
AGPAT5-intron3		F: TCCCGCTGTATGGCAGTTA	3 461
AGPAT5-intron3		R: CTGGAGTTCCTGCGTTGAT	3 461

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
PPARγ-exon7		R: GGTGTCAGATTTTTCCCTPHPH	417
PPARγ-intron2		F: CCCGATGGTTGCAGATTA	1 842
PPARγ-intron2		R: AGGCTCCACTTTGATTGC	1 842
MYF5-exon1	NM-174116.1	F:GGCGTCTGCCCTTGTTA	690
MYF5-exon1		R: TTTGTAAAAGTTGGGAAG	690
MYF5-intron1		F: CTCTGATGGCATGGTAAG	923
MYF5-intron1		R: CAGTAGACGATGTCAAAA	923
AGPAT5-exon7	NM_001075932.1	F: GTAGGGAACTATGGGAGA	771
AGPAT5-exon7		R: CACTAACTGCAAAACAACA	771
AGPAT5-intron3		F: TCCCGCTGTATGGCAGTTA	3 461
AGPAT5-intron3		R: CTGGAGTTCCTGCGTTGAT	3 461

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
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	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	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
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	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±0.89^A	43.30±0.48	122.32±0.63	300.21±3.86^A
		AB	129.11±1.28	162.07±0.99^B	42.79±0.51	122.37±0.71	311.76±4.42^B
		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±3.87^Aa
		AB	130.42±1.20	161.33±0.94	42.79±0.51	122.21±0.67	396.63±4.11^B
		BB	128.59±1.49	158.51±1.15	43.21±0.63	122.42±0.82	307.61±5.02^b
		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±0.53^a	122.75±0.69	301.65±2.96
		AB	129.15±1.06	160.40±0.80	43.70±0.44^b	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±0.96^A	43.58±0.53^A	123.17±0.68	313.60±4.25^A
		AB	130.54±1.17^a	161.99±0.90^A	43.69±0.49^A	122.36±0.64	310.47±3.96^A
		BB	127.39±1.33^b	157.50±1.04^B	42.16±0.56^B	121.52±0.74	293.88±4.49^B
		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±0.91^A	42.92±0.50^a	123.06±0.65	301.86±3.97
		AB	130.02±1.29	162.91±0.98^A	44.14±0.54^b	122.86±0.69	311.17±4.38
		BB	128.30±1.55	156.18±1.22^B	42.36±0.62^a	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