Study of candidate genes for glycolytic potential of porcine skeletal muscle: identification and analysis of mutations, linkage and physical mapping and association with meat quality traits in pigs

2003 ◽  
Vol 102 (1-4) ◽  
pp. 145-151 ◽  
Author(s):  
L. Fontanesi ◽  
R. Davoli ◽  
L. Nanni Costa ◽  
E. Scotti ◽  
V. Russo
Keyword(s):  
Skeletal Muscle ◽  
Candidate Genes ◽  
Meat Quality ◽  
Physical Mapping ◽  
Quality Traits ◽  
Meat Quality Traits ◽  
Glycolytic Potential

scholarly journals Genome-wide analysis of expression QTL (eQTL) and allele-specific expression (ASE) in pig muscle identifies candidate genes for meat quality traits

2020 ◽  
Vol 52 (1) ◽  
Author(s):  
Yan Liu ◽  
Xiaolei Liu ◽  
Zhiwei Zheng ◽  
Tingting Ma ◽  
Ying Liu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Meat Quality ◽  
Quality Traits ◽  
Q Value ◽  
Specific Expression ◽  
Allele Specific Expression ◽  
Meat Quality Traits ◽  
Genome Wide ◽  
A Genome ◽  
Allele Specific

Abstract Background Genetic analysis of gene expression level is a promising approach for characterizing candidate genes that are involved in complex economic traits such as meat quality. In the present study, we conducted expression quantitative trait loci (eQTL) and allele-specific expression (ASE) analyses based on RNA-sequencing (RNAseq) data from the longissimus muscle of 189 Duroc × Luchuan crossed pigs in order to identify some candidate genes for meat quality traits. Results Using a genome-wide association study based on a mixed linear model, we identified 7192 cis-eQTL corresponding to 2098 cis-genes (p ≤ 1.33e-3, FDR ≤ 0.05) and 6400 trans-eQTL corresponding to 863 trans-genes (p ≤ 1.13e-6, FDR ≤ 0.05). ASE analysis using RNAseq SNPs identified 9815 significant ASE-SNPs in 2253 unique genes. Integrative analysis between the cis-eQTL and ASE target genes identified 540 common genes, including 33 genes with expression levels that were correlated with at least one meat quality trait. Among these 540 common genes, 63 have been reported previously as candidate genes for meat quality traits, such as PHKG1 (q-value = 1.67e-6 for the leading SNP in the cis-eQTL analysis), NUDT7 (q-value = 5.67e-13), FADS2 (q-value = 8.44e-5), and DGAT2 (q-value = 1.24e-3). Conclusions The present study confirmed several previously published candidate genes and identified some novel candidate genes for meat quality traits via eQTL and ASE analyses, which will be useful to prioritize candidate genes in further studies.

scholarly journals An Integrative Analysis of Transcriptome and GWAS Data to Identify Potential Candidate Genes Influencing Meat Quality Traits in Pigs

2021 ◽  
Vol 12 ◽  
Author(s):  
Xianxian Liu ◽  
Junjie Zhang ◽  
Xinwei Xiong ◽  
Congying Chen ◽  
Yuyun Xing ◽  
...  
Keyword(s):  
Gene Expression ◽  
Candidate Genes ◽  
Meat Quality ◽  
Integrative Analysis ◽  
Potential Candidate ◽  
Quality Traits ◽  
Eqtl Mapping ◽  
Meat Quality Traits ◽  
Genome Wide ◽  
A Genome

Understanding the genetic factors behind meat quality traits is of great significance to animal breeding and production. We previously conducted a genome-wide association study (GWAS) for meat quality traits in a White Duroc × Erhualian F2 pig population using Illumina porcine 60K SNP data. Here, we further investigate the functional candidate genes and their network modules associated with meat quality traits by integrating transcriptomics and GWAS information. Quantitative trait transcript (QTT) analysis, gene expression QTL (eQTL) mapping, and weighted gene co-expression network analysis (WGCNA) were performed using the digital gene expression (DGE) data from 493 F2 pig’s muscle and liver samples. Among the quantified 20,108 liver and 23,728 muscle transcripts, 535 liver and 1,014 muscle QTTs corresponding to 416 and 721 genes, respectively, were found to be significantly (p < 5 × 10−4) correlated with 22 meat quality traits measured on longissiums dorsi muscle (LM) or semimembranosus muscle (SM). Transcripts associated with muscle glycolytic potential (GP) and pH values were enriched for genes involved in metabolic process. There were 42 QTTs (for 32 genes) shared by liver and muscle tissues, of which 10 QTTs represent GP- and/or pH-related genes, such as JUNB, ATF3, and PPP1R3B. Furthermore, a genome-wide eQTL mapping revealed a total of 3,054 eQTLs for all annotated transcripts in muscle (p < 2.08 × 10−5), including 1,283 cis-eQTLs and 1771 trans-eQTLs. In addition, WGCNA identified five modules relevant to glycogen metabolism pathway and highlighted the connections between variations in meat quality traits and genes involved in energy process. Integrative analysis of GWAS loci, eQTL, and QTT demonstrated GALNT15/GALNTL2 and HTATIP2 as strong candidate genes for drip loss and pH drop from postmortem 45 min to 24 h, respectively. Our findings provide valuable insights into the genetic basis of meat quality traits and greatly expand the number of candidate genes that may be valuable for future functional analysis and genetic improvement of meat quality.

162 Fetal Programming and Meat Quality

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 87-87
Author(s):  
Marcio Duarte ◽  
Mateus P Gionbelli
Keyword(s):  
Skeletal Muscle ◽  
Meat Quality ◽  
Fetal Programming ◽  
Maternal Nutrition ◽  
Muscle Fibers ◽  
Quality Traits ◽  
Intrauterine Development ◽  
Meat Quality Traits ◽  
Fetal Stage

Abstract For many years, variation in carcass and meat quality traits was thought to result from actions taken throughout the animals’ life after birth. However, the quantity and quality of meat obtained at slaughter are not always as good as expected. The past decade has increased the number of evidence of the effects of intrauterine development of skeletal muscle on animal performance that affects the carcass and meat quality traits. The so-called “Fetal Programming” concept sheds light on the biology of skeletal muscle development in meat animals, revealing that this development stage appears to be a pivotal moment to invest efforts aiming to improve animal productivity and the quality of meat. Because most, if not all, of the muscle fibers are formed prenatally in livestock species, the impairment of muscle fiber formation at this stage will limit the overall muscle mass deposition throughout postnatal life. Intramuscular adipocytes also start their formation at the fetal stage. As such, since the intramuscular fat depot has a lower deposition rate than other fat depots, enhancement of intramuscular adipogenesis during the fetal stage may increase marbling deposition postnatally. Muscle fibers, adipocytes, and fibroblasts, which contribute to connective tissue formation, are derived from the same pool of mesenchymal stem (MS) cells. Depending on the insult suffered during intrauterine development, their commitment may shift from myogenic towards adipogenic/fibrogenic lineage. So far, most of the evidence in livestock animals has shown that maternal nutrition during gestation is the main factor that influences the mechanisms underlying the commitment of the MS cells. Although the majority of these studies have shown the consequences of maternal nutrition on myogenesis, adipogenesis, and fibrogenesis, the epigenetic markers that cause the programming of MS cells to undergo to one lineage or another needs to be further investigated.

scholarly journals Exploring the lncRNAs Related to Skeletal Muscle Fiber Types and Meat Quality Traits in Pigs

Genes ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 883
Author(s):  
Rongyang Li ◽  
Bojiang Li ◽  
Aiwen Jiang ◽  
Yan Cao ◽  
Liming Hou ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Meat Quality ◽  
Muscle Fiber ◽  
Skeletal Muscle Fiber ◽  
Fiber Formation ◽  
Muscle Fiber Types ◽  
Fiber Types ◽  
Quality Traits ◽  
Meat Quality Traits ◽  
Non Coding Rnas

The alteration in skeletal muscle fiber is a critical factor affecting livestock meat quality traits and human metabolic diseases. Long non-coding RNAs (lncRNAs) are a diverse class of non-coding RNAs with a length of more than 200 nucleotides. However, the mechanisms underlying the regulation of lncRNAs in skeletal muscle fibers remain elusive. To understand the genetic basis of lncRNA-regulated skeletal muscle fiber development, we performed a transcriptome analysis to identify the key lncRNAs affecting skeletal muscle fiber and meat quality traits on a pig model. We generated the lncRNA expression profiles of fast-twitch Biceps femoris (Bf) and slow-twitch Soleus (Sol) muscles and identified the differentially expressed (DE) lncRNAs using RNA-seq and performed bioinformatics analyses. This allowed us to identify 4581 lncRNA genes among six RNA libraries and 92 DE lncRNAs between Bf and Sol which are the key candidates for the conversion of skeletal muscle fiber types. Moreover, we detected the expression patterns of lncRNA MSTRG.42019 in different tissues and skeletal muscles of various development stages. In addition, we performed a correlation analyses between the expression of DE lncRNA MSTRG.42019 and meat quality traits. Notably, we found that DE lncRNA MSTRG.42019 was highly expressed in skeletal muscle and its expression was significantly higher in Sol than in Bf, with a positive correlation with the expression of Myosin heavy chain 7 (MYH7) (r = 0.6597, p = 0.0016) and a negative correlation with meat quality traits glycolytic potential (r = −0.5447, p = 0.0130), as well as drip loss (r = −0.5085, p = 0.0221). Moreover, we constructed the lncRNA MSTRG.42019–mRNAs regulatory network for a better understanding of a possible mechanism regulating skeletal muscle fiber formation. Our data provide the groundwork for studying the lncRNA regulatory mechanisms of skeletal muscle fiber conversion, and given the importance of skeletal muscle fiber types in muscle-related diseases, our data may provide insight into the treatment of muscular diseases in humans.

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