基因组和DNA甲基化组联合分析筛选猪肉质性状关键基因

doi:10.3864/j.issn.0578-1752.2024.07.014

Abstract

Abstract:

【Background】 The meat quality traits of pigs are important economic traits. Studying the molecular mechanisms that affect various meat quality traits and discovering key genes can guide genetic improvement of pigs and have significant implications for improving pork quality. Currently, those researches on meat-related mechanisms were mainly based on DNA genomics, while studies on DNA methylation related to meat quality traits, as well as integrated analysis of combining genomics and methylation, are scarce. 【Objective】 The potential key genes affecting pork meat quality were screened and identified by combined analysis of genome and DNA methylome, so as to provide a reference for the genetic improvement of pork quality. 【Method】 In this study, 28 meat quality traits of the ongissimus dorsi muscle of 140 Large White pigs were examined. Epigenome-wide association analysis (EWAS) and genome-wide association analysis (GWAS) were performed to identify CpG and SNP sites significantly associated with each trait. Subsequently, the conditional association analysis was performed by using SNPs as covariates on the significantly associated sites overlapping between GWAS and EWAS to further identify CpG sites with independent effects. Association analysis was then conducted to identify methylation quantitative trait loci (meQTL) by using the methylation levels of CpG sites as the dependent variable and SNPs as the independent variable. Finally, the cis-methylation quantitative trait loci (cis-meQTL) were used as instrumental variables for Mendelian randomization analysis to infer the causal relationship between cis-meQTL and phenotypes, while potential key genes at the loci were annotated and identified. 【Result】 (1) The significant associated sites were identified in the same genomic regions for the meat quality traits, namely yellowness value at slaughter 45 minutes postmortem (b_45min), drip loss (DL), and docosahexaenoic acid (C22:6n-3), by both EWAS and GWAS. (2) After conditional association analysis, seven CpG sites for b_45min and one CpG site for DL remained significant, while the three sites for C22:6n-3 were no longer significant after using SNPs as covariates, indicating that the significant associations of the seven CpG sites for b_45min and one CpG site for DL identified by EWAS were not influenced by nearby significant SNPs. (3) A total of ten meQTL were identified for the seven CpG sites for b_45min and one CpG site for DL, but the majority were trans-meQTL, with only one CpG site (SSC12:44 254 675 bp) identifying a cis-meQTL, suggesting that this site might be regulated by nearby SNPs. (4) Mendelian randomization analysis showed a causal relationship between the CpG site (SSC12:44 254 675 bp) and the b_45min phenotype. (5) annotation of the locus revealed that the nearest gene to the CpG site (SSC12:44 254 675 bp) and its cis-meQTL was NOS2, and the CpG site was located within the NOS2 gene. 【Conclusion】 Based on the integrated analysis of DNA methylation and genomics data, this study proposed that the NOS2 gene might be a key candidate gene for meat color traits. DNA methylation and SNP jointly regulated gene expression, thereby affecting the expression of genes related to meat color traits.

Key words: epigenome-wide association study (EWAS), genome-wide association study (GWAS), meat quality traits, DNA methylation, meQTL

ZHAO ZhenJian, WANG Kai, CHEN Dong, SHEN Qi, YU Yang, CUI ShengDi, WANG JunGe, CHEN ZiYang, YU ShiXin, CHEN JiaMiao, WANG XiangFeng, TANG GuoQing. Integrated Aanalysis of Genome and DNA Methylation for Screening Key Genes Related to Pork Quality Traits[J].Scientia Agricultura Sinica, 2024, 57(7): 1394-1406.

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References 58

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性状 Trait	GWAS关联 GWAS associations		EWAS关联 EWAS associations
性状 Trait	染色体SSC	位点或区域 Position or Region (bp)	SNP数量 Number of SNP	CpG位点 CpG site (bp)
b_45min	1	4049232	1	SSC1:4667485
b_45min	6	5191168-5483926	10	SSC6:4737404
b_45min	7	9770008-10877899	20	SSC7:10489621
b_45min	10	35692369	1	SSC10:36329538
b_45min	12	44218560	1	SSC12:44254675
b_45min	14	17744509-18820911	19	SSC14:17859513
b_45min	18	49231979-50010893	7	SSC18:48429425
b_45min	18	49231979-50010893	7	SSC18:50979305
DL	7	121791317	1	SSC7:120954182
C22:6n-3	4	101860069-103765886	146	SSC4:102796889
C22:6n-3	4	101860069-103765886	146	SSC4:103218200
C22:6n-3	4	101860069-103765886	146	SSC4:103552805

性状Trait	CpG位点 CpG site (bp)	染色体SSC	位置 Position (bp)	P value (EWAS)	P value (after correct)
b_45min	SSC1: 4667485	1	4667485	3.95E-9	3.95E-9
	SSC6: 4737404	6	4737404	7.59E-9	0.35
	SSC7: 10489621	7	10489621	1.53E-9	1.53E-9
	SSC10: 36329538	10	36329538	2.76E-13	2.76E-13
	SSC12: 44254675	12	44254675	5.45E-9	5.45E-9
	SSC14: 17859513	14	17859513	1.26E-9	1.26E-9
	SSC18: 48429425	18	48429425	1.06E-10	1.06E-10
	SSC18: 50979305	18	50979305	1.18E-9	1.18E-9
DL	SSC7: 120954182	7	120954182	7.79E-9	7.79E-9
C22:6n-3	SSC4: 102796889	4	102796889	1.32E-12	0.99
	SSC4: 103218200	4	103218200	3.32E-9	0.13
	SSC4: 103552805	4	103552805	1.32E-12	0.99

CpG位点 CpG site (bp)	甲基化数量性状位点 meQTL	顺式meQTL cis-meQTL	反式meQTL trans-meQTL	SNP
SSC1:4667485	0	0	0	0
SSC7:10489621	2	0	2	9
SSC10:36329538	0	0	0	0
SSC12:44254675	2	1	1	11
SSC14:17859513	2	0	2	46
SSC18:48429425	0	0	0	0
SSC18:50979305	3	0	3	345
SSC7:120954182	1	0	1	4

Integrated Aanalysis of Genome and DNA Methylation for Screening Key Genes Related to Pork Quality Traits

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