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Integrative Analysis of Metabolomic, Proteomic and Genomic Data to Reveal Functional Pathways and Candidate Genes for Drip Loss in Pigs

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ABSTRACT

The aim of this study was to integrate multi omics data to characterize underlying functional pathways and candidate genes for drip loss in pigs. The consideration of different omics levels allows elucidating the black box of phenotype expression. Metabolite and protein profiling was applied in Musculus longissimus dorsi samples of 97 Duroc × Pietrain pigs. In total, 126 and 35 annotated metabolites and proteins were quantified, respectively. In addition, all animals were genotyped with the porcine 60 k Illumina beadchip. An enrichment analysis resulted in 10 pathways, amongst others, sphingolipid metabolism and glycolysis/gluconeogenesis, with significant influence on drip loss. Drip loss and 22 metabolic components were analyzed as intermediate phenotypes within a genome-wide association study (GWAS). We detected significantly associated genetic markers and candidate genes for drip loss and for most of the metabolic components. On chromosome 18, a region with promising candidate genes was identified based on SNPs associated with drip loss, the protein “phosphoglycerate mutase 2” and the metabolite glycine. We hypothesize that association studies based on intermediate phenotypes are able to provide comprehensive insights in the genetic variation of genes directly involved in the metabolism of performance traits. In this way, the analyses contribute to identify reliable candidate genes.

No MeSH data available.


Overlapping SNPs at Sus scrofa chromosomes (SSC) 14, 17 and 18. GWAS procedures resulted in varying numbers of significant SNP (q ≤ 0.1) per trait. On some chromosomes there are overlapping SNPs with meaning for two traits. Drip loss measured in Musculus longissimus dorsi (LD) 24 h post-mortem (p.m.); Glycerone-p = dihydroxyacetone phosphate; PGAM2 = phosphoglycerate mutase 2 (muscle); FBPase = fructose-1,6-bisphosphatase 2; DG3P = d-glycerate-3-phosphate.
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ijms-17-01426-f001: Overlapping SNPs at Sus scrofa chromosomes (SSC) 14, 17 and 18. GWAS procedures resulted in varying numbers of significant SNP (q ≤ 0.1) per trait. On some chromosomes there are overlapping SNPs with meaning for two traits. Drip loss measured in Musculus longissimus dorsi (LD) 24 h post-mortem (p.m.); Glycerone-p = dihydroxyacetone phosphate; PGAM2 = phosphoglycerate mutase 2 (muscle); FBPase = fructose-1,6-bisphosphatase 2; DG3P = d-glycerate-3-phosphate.

Mentions: On several chromosomes we identified 126 (45) SNPs (QTL) which were significant for more than one trait. These SNPs are located on SSC 1, 7, 8, 14, 17 and 18. As presented in Figure 1 the most overlapping exists between metabolites hydroxypyruvic acid and succinic acid on SSC 14. Moreover, the overlapping on SSC 18 is of particular interest, because it indicates a metabolic process comprising glycine and phosphoglycerate mutase 2 (PGAM2) that influences drip loss (Figure 1). On SSC 7, there was only one overlapping SNP of glucose and fructose-6-phosphate (F6P). In contrast, on SSC 1 and 8, we indeed detected significant SNPs for two traits but the QTLs are located in distant chromosomal regions.


Integrative Analysis of Metabolomic, Proteomic and Genomic Data to Reveal Functional Pathways and Candidate Genes for Drip Loss in Pigs
Overlapping SNPs at Sus scrofa chromosomes (SSC) 14, 17 and 18. GWAS procedures resulted in varying numbers of significant SNP (q ≤ 0.1) per trait. On some chromosomes there are overlapping SNPs with meaning for two traits. Drip loss measured in Musculus longissimus dorsi (LD) 24 h post-mortem (p.m.); Glycerone-p = dihydroxyacetone phosphate; PGAM2 = phosphoglycerate mutase 2 (muscle); FBPase = fructose-1,6-bisphosphatase 2; DG3P = d-glycerate-3-phosphate.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5037705&req=5

ijms-17-01426-f001: Overlapping SNPs at Sus scrofa chromosomes (SSC) 14, 17 and 18. GWAS procedures resulted in varying numbers of significant SNP (q ≤ 0.1) per trait. On some chromosomes there are overlapping SNPs with meaning for two traits. Drip loss measured in Musculus longissimus dorsi (LD) 24 h post-mortem (p.m.); Glycerone-p = dihydroxyacetone phosphate; PGAM2 = phosphoglycerate mutase 2 (muscle); FBPase = fructose-1,6-bisphosphatase 2; DG3P = d-glycerate-3-phosphate.
Mentions: On several chromosomes we identified 126 (45) SNPs (QTL) which were significant for more than one trait. These SNPs are located on SSC 1, 7, 8, 14, 17 and 18. As presented in Figure 1 the most overlapping exists between metabolites hydroxypyruvic acid and succinic acid on SSC 14. Moreover, the overlapping on SSC 18 is of particular interest, because it indicates a metabolic process comprising glycine and phosphoglycerate mutase 2 (PGAM2) that influences drip loss (Figure 1). On SSC 7, there was only one overlapping SNP of glucose and fructose-6-phosphate (F6P). In contrast, on SSC 1 and 8, we indeed detected significant SNPs for two traits but the QTLs are located in distant chromosomal regions.

View Article: PubMed Central - PubMed

ABSTRACT

The aim of this study was to integrate multi omics data to characterize underlying functional pathways and candidate genes for drip loss in pigs. The consideration of different omics levels allows elucidating the black box of phenotype expression. Metabolite and protein profiling was applied in Musculus longissimus dorsi samples of 97 Duroc × Pietrain pigs. In total, 126 and 35 annotated metabolites and proteins were quantified, respectively. In addition, all animals were genotyped with the porcine 60 k Illumina beadchip. An enrichment analysis resulted in 10 pathways, amongst others, sphingolipid metabolism and glycolysis/gluconeogenesis, with significant influence on drip loss. Drip loss and 22 metabolic components were analyzed as intermediate phenotypes within a genome-wide association study (GWAS). We detected significantly associated genetic markers and candidate genes for drip loss and for most of the metabolic components. On chromosome 18, a region with promising candidate genes was identified based on SNPs associated with drip loss, the protein “phosphoglycerate mutase 2” and the metabolite glycine. We hypothesize that association studies based on intermediate phenotypes are able to provide comprehensive insights in the genetic variation of genes directly involved in the metabolism of performance traits. In this way, the analyses contribute to identify reliable candidate genes.

No MeSH data available.