An integration analysis based on genomic, transcriptomic and QTX information reveals credible candidate genes for fat‐related traits in pigs

Fu, Yuhua; Wang, L.; Tang, Zhonghui; Ding, Yin; Xu, Jing; Yu, Fan; Li, X.; Zhao, Shuhong; Liu, X.

doi:10.1111/age.12971

Cited by 4 publications

(4 citation statements)

References 53 publications

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“…FoxO1 promotes lipogenesis during porcine intramuscular preadipocyte differentiation by downregulating PDGFRα (Sun et al, 2017). A previous study showed that the PPARα gene is related to pig fat traits by incorporating transcriptome and genomic data (Fu et al, 2020). The downregulation of CPT2 can induce the suppression of fatty acid β‐oxidation to increase IMF accumulation (Fujiwara et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

Integrating genome‐wide association study with RNA‐seq revealed DBI as a good candidate gene for intramuscular fat content in Beijing black pigs

et al. 2022

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Increasing intramuscular fat (IMF) content can enhance the sensory quality of meat, including tenderness, juiciness, flavor, and color. Genome‐wide association study and RNA‐sequencing (RNA‐seq) analysis were used to identify candidate IMF genes in Beijing Black pigs, a popular species among consumers in northern China. Two and three single nucleotide polymorphisms were significantly associated with IMF in SSC13 and SSC15 respectively. Solute carrier family 4 member 7 (SLC4A7) on SSC13 and insulin induced gene 2 (INSIG2), coiled‐coil domain containing 93 (CCDC93), and diazepam binding inhibitor acyl‐CoA binding protein (DBI) on SSC15 are good candidate genes in this population. Furthermore, RNA‐seq analysis was performed between high and low IMF groups, and 534 differentially expressed genes were identified. In addition, based on differentially expressed genes, Kyoto Encyclopedia of Genes and Genomes analysis revealed that peroxisome proliferator‐activated receptors and FoxO signaling pathway pathways might contribute to IMF. Moreover, the DBI gene was identified as a candidate for IMF both by genome‐wide association study and RNA‐seq analysis, suggesting that it might be a crucial candidate gene for influencing IMF in Beijing Black pigs.

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Section: Discussionmentioning

confidence: 99%

Integrating genome‐wide association study with RNA‐seq revealed DBI as a good candidate gene for intramuscular fat content in Beijing black pigs

et al. 2022

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“…The most significant SNP found resides in a splice site in ACACA, which catalyzes the rate-limiting step in fatty acid biosynthesis through the carboxylation of acetyl CoA to malonyl-CoA. Gene expression levels and genetic markers of ACACA have been associated with fatness traits in pigs (Gallardo et al 2009;Eusebi et al 2017;Fu et al 2020;Pi orkowska et al 2020). Hypothalamic malonyl-CoA is implicated in food intake and (Schneider 2004;Zhuo et al 2014;McIlwraith & Belsham 2020) and human age at menarche (Speliotes et al 2010;Day et al 2015;Howard & Dunkel 2018).…”

Section: Discussionmentioning

confidence: 99%

Potential functional variants in AHR signaling pathways are associated with age at puberty in swine

et al. 2021

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Puberty in female pigs is defined as age at first estrus and gilts that have an earlier age at puberty are more likely to have greater lifetime productivity. Because age at puberty is predictive for sow longevity and lifetime productivity, but not routinely measured in commercial herds, it would be beneficial to use genomic or marker-assisted selection to improve these traits. A GWAS at the US Meat Animal Research Center (USMARC) identified several loci associated with age at puberty in pigs. Candidate genes in these regions were scanned for potential functional variants using sequence information from the USMARC swine population founder animals and public databases. In total, 135 variants (SNP and insertion/deletions) in 39 genes were genotyped in 1284 phenotyped animals from a validation population sired by Landrace and Yorkshire industry semen using the Agena MassArray system. Twelve variants in eight genes were associated with age at puberty (P < 0.005) with estimated additive SNP effects ranging from 1.6 to 5.3 days. Nine of these variants were non-synonymous coding changes in AHR, CYP1A2, OR2M4, SDCCAG8, TBC1D1 and ZNF608, two variants were deletions of one and four codons in aryl hydrocarbon receptor, AHR, and the most significant SNP was near an acceptor splice site in the acetyl-CoA carboxylase alpha, ACACA. Several of the loci identified have a physiological and a genetic role in sexual maturation in humans and other animals and are involved in AHR-mediated pathways. Further functional validation of these variants could identify causative mutations that influence age at puberty in gilts and possibly sow lifetime productivity.

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“…Other noteworthy genes in the study included Titin and TEK (angiopoietin-1 receptor known also as a tyrosine-protein kinase), which appeared to be under substantial multigene regulation and also were located close to significant splicing cis-regulatory SNP. In another study, Fu et al (2020) combined gene expression with GWAS and quantitative trait expression profiles to refine 180 candidate genes for fat-related traits down to just six, including known master regulators such as several PPARs (PPARG, PPARD and PPARA). New insights have been gained on the molecular pathways underpinning heterosis and its implications for growth, development and meat quality in sheep meat using RNA sequencing (Cheng et al, 2020).…”

Section: Genetic Regions and Gene Expression Associated With Meat Qua...mentioning

confidence: 99%

Current research and emerging tools to improve fresh red meat quality

Gagaoua

Duffy

Álvarez

et al. 2022

Irish Journal of Agricultural and Food Research

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A consumer’s decision to purchase red meat is guided by a combination of many interacting factors including safety, nutrition, sustainability and perception of healthiness along with a variety of sensory characteristics such as colour, marbling, tenderness, juiciness and flavour. Red meat quality is complex and influenced by many intrinsic and extrinsic factors, spanning the chain from breed/genetics through to the final end product with key influences coming from on-farm management and post-mortem processing. As a result of various factors, including consumer demands, the importance of both red meat quality and safety has in recent times come to the fore for the meat industry, with steps to meet these requirements having a large bearing on profitability. Therefore, a critical review of steps which can help control these traits is very important. Accordingly, several processing strategies were proposed at the research and industry level aiming to improve fresh red meat quality traits. This review summarises the current methods applied to improve fresh red meat quality and safety, including the advances in management and prediction tools for carcass and technological and sensory quality traits. These methods are also relevant to the safety and microbiological status of carcasses and meat produced, along with the recent developments in sensory analysis, which aim to understand the sensory properties of red meat and consumers responses. The potential of foodomics approaches is discussed under the topics of genomics, proteomics and metabolomics, which help our understanding of the underlying biological mechanisms behind the variation of sensory and technological quality traits and their use for the discovery of putative biomarkers. We further considered the current and emerging sequencing-based methods used to understand microbial community composition of fresh red meat.

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An integration analysis based on genomic, transcriptomic and QTX information reveals credible candidate genes for fat‐related traits in pigs

Cited by 4 publications

References 53 publications

Integrating genome‐wide association study with RNA‐seq revealed DBI as a good candidate gene for intramuscular fat content in Beijing black pigs

Integrating genome‐wide association study with RNA‐seq revealed DBI as a good candidate gene for intramuscular fat content in Beijing black pigs

Potential functional variants in AHR signaling pathways are associated with age at puberty in swine

Current research and emerging tools to improve fresh red meat quality

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