Identification of a missense variant in the porcine <i>AGPAT</i> gene family associated with intramuscular fat content through whole‐genome sequencing

Molinero, Eduard; Pena, Ramona N.; Estany, J.; Ros‐Freixedes, Roger

doi:10.1111/age.13258

Cited by 6 publications

(3 citation statements)

References 88 publications

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“…AGPAT2 has been shown to play an important role in lipid metabolism in chickens [ 46 ]. AGPAT5 , on the other hand, is considered a potential genetic marker for excellent pork quality [ 48 ]. In a study conducted on cattle, AGPAT5 was found to be significantly correlated with pre-slaughter weight, carcass weight, and meat weight [ 49 ].…”

Section: Discussionmentioning

confidence: 99%

Weighted gene co-expression network analysis identified hub genes critical to fatty acid composition in Gushi chicken breast muscle

Zhai,

Zhao,

et al. 2023

BMC Genomics

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Background The composition and content of fatty acids in the breast muscle are important factors influencing meat quality. In this study, we investigated the fatty acid composition and content in the breast muscle of Gushi chickens at different developmental stages (14 weeks, 22 weeks, and 30 weeks). Additionally, we utilized transcriptomic data from the same tissue and employed WGCNA and module identification methods to identify key genes associated with the fatty acid composition in Gushi chicken breast muscle and elucidate their regulatory networks. Results Among them, six modules (blue, brown, green, light yellow, purple, and red modules) showed significant correlations with fatty acid content and metabolic characteristics. Enrichment analysis revealed that these modules were involved in multiple signaling pathways related to fatty acid metabolism, including fatty acid metabolism, PPAR signaling pathway, and fatty acid biosynthesis. Through analysis of key genes, we identified 136 genes significantly associated with fatty acid phenotypic traits. Protein–protein interaction network analysis revealed that nine of these genes were closely related to fatty acid metabolism. Additionally, through correlation analysis of transcriptome data, we identified 51 key ceRNA regulatory networks, including six central genes, 7 miRNAs, and 28 lncRNAs. Conclusion This study successfully identified key genes closely associated with the fatty acid composition in Gushi chicken breast muscle, as well as their post-transcriptional regulatory networks. These findings provide new insights into the molecular regulatory mechanisms underlying the flavor characteristics of chicken meat and the composition of fatty acids in the breast muscle.

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Section: Discussionmentioning

confidence: 99%

Weighted gene co-expression network analysis identified hub genes critical to fatty acid composition in Gushi chicken breast muscle

Zhai,

Zhao,

et al. 2023

BMC Genomics

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“…The DNA samples were submitted to the Centre Nacional d’Anàlisi Genòmica (CNAG-CRG, Barcelona, Spain) for whole-genome sequencing on a NovaSeq 6000 instrument (Illumina, San Diego, CA, USA) in paired-end mode, as described by Molinero et al . (2022).…”

Section: Methodsmentioning

confidence: 99%

Association between mitochondrial DNA copy number and production traits in pigs

Molinero,

Pena,

Estany

et al. 2024

Preprint

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Mitochondria are essential organelles in the regulation of cellular energetic metabolism. Mitochondrial DNA copy number (mtDNA_CN) can be used as a proxy for mitochondria number, size, and activity. The aims of our study are to evaluate the effect of mtDNA_CN and mitochondrial haploblocks on production traits in pigs, and to identify the genetic background of this cellular phenotype. We collected performance data of 234 pigs and extracted DNA from skeletal muscle. Whole-genome sequencing data was used to determine mtDNA_CN. We detected positive correlations of muscle mtDNA_CN with backfat thickness at 207 d (+0.14; p-value = 0.07), and negative correlations with carcase loin thickness (-0.14; p-value = 0.03). Pigs with less mtDNA_CN had greater loin thickness (+4.1 mm; p-value = 0.01) and lower backfat thickness (-1.1 mm; p-value = 0.08), which resulted in greater carcase lean percentage (+2.4%; p-value = 0.04) than pigs with high mtDNA_CN. These results support the hypothesis that a reduction of mitochondrial activity is associated with greater feed efficiency. Pork from pigs with less mtDNA_CN may also tend to have lower ultimate pH (correlation: +0.19; p-value < 0.01). We found no association of the most frequent mitochondrial haploblocks with mtDNA_CN or the production traits, but several genomic regions that harbour potential candidate genes with functions related to mitochondrial biogenesis and homeostasis were associated to mtDNA_CN. These regions provide new insights into the genetic background of this cellular phenotype but it is still uncertain if such associations translate into noticeable effects on the production traits.

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“…DNA extraction was carried out following a conventional phenol: chloroform protocol (Green & Sambrook, 2017) and used for single nucleotide polymorphism (SNP) genotyping with either the PorcineSNP60 v2 Genotyping BeadChip ( n = 138; Illumina, San Diego, CA, USA), the GGP Porcine HD Array ( n = 256; Illumina) porcine arrays or whole‐genome sequencing ( n = 262, of which 130 were also genotyped using a SNP array) on a NovaSeq 6000 instrument (Illumina) in paired‐end mode, as described by Molinero et al. (2022). SNPs from the SNP arrays that mapped to sex chromosomes or with minor allele frequency <0.05 were discarded from further analyses.…”

Section: Figurementioning

confidence: 99%

A novel QTL region for pH and meat color in Duroc pigs

Molinero,

Pena,

Estany

et al. 2024

Animal Genetics

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One of the most important processes that occur during the transformation of muscle to meat is the pH decline as a consequence of the post‐mortem metabolism of muscle tissue. Abnormal pH declines lead to pork defects such as pale, soft, and exudative meat. There is genetic variance for ultimate pH and the role of some genes on this phenotype is well established. After conducting a genome‐wide association study on ultimate pH using 526 purebred Duroc pigs, we identified associated regions on Sus scrofa chromosomes (SSC) 3, 8, and 15. Functional candidate genes in these regions included PRKAG3 and PHKG1. The SSC8 region, at 71.6 Mb, was novel and, although no candidate causative gene could be identified, it may have regulatory effects. Subsequent analysis on 828 pigs from the same population confirmed the impact of the three associated regions on pH and meat color. We detected no interaction between the three regions. Further investigations are necessary to unravel the functional significance of the novel genomic region at SSC8. These variants could be used as markers in marker‐assisted selection for improving meat quality.

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Identification of a missense variant in the porcine AGPAT gene family associated with intramuscular fat content through whole‐genome sequencing

Cited by 6 publications

References 88 publications

Weighted gene co-expression network analysis identified hub genes critical to fatty acid composition in Gushi chicken breast muscle

Weighted gene co-expression network analysis identified hub genes critical to fatty acid composition in Gushi chicken breast muscle

Association between mitochondrial DNA copy number and production traits in pigs

A novel QTL region for pH and meat color in Duroc pigs

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