A genome‐wide association analysis for carcass traits in a commercial Duroc pig population

Eusebi, Paulina G.; González-Prendes, Rayner; Quintanilla, Raquel; Tibau, J.; Cardoso, Tainã Figueiredo; Clop, Alex; Amills, Marcel

doi:10.1111/age.12545

Cited by 17 publications

(14 citation statements)

References 19 publications

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“…In general, most of the economic traits in commercial animals are quantitative and controlled by many genes with small effects ( Khatkar et al 2004 ). This quantitative genetics view is supported by most of the recent gene mapping researches, including the identification of selection signatures and genome-wide association studies (GWAS) ( Eusebi et al 2017 ; Ma et al 2018 ; Pritchard et al 2010 ; Ros-Freixedes et al 2014 ). Therefore, genomic selection has become the main method in genetic improvement in important economic traits ( Hayes et al 2009 ).…”

Section: Introductionmentioning

confidence: 96%

Genomic Analysis To Identify Signatures of Artificial Selection and Loci Associated with Important Economic Traits in Duroc Pigs

Ma¹,

Zhang²,

Zhang

et al. 2018

G3 Genes|Genomes|Genetics

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Identifying genetic basis of domestication and improvement in livestock contributes to our understanding of the role of artificial selection in shaping the genome. Here we used whole-genome sequencing and the genotyping by sequencing approach to detect artificial selection signatures and identify the associated SNPs of two economic traits in Duroc pigs. A total of 38 candidate selection regions were detected by combining the fixation index and the Composite Likelihood Ratio methods. Further genome-wide association study revealed seven associated SNPs that were related with intramuscular fat content and feed conversion ratio traits, respectively. Enrichment analysis suggested that the artificial selection regions harbored genes, such as MSTN, SOD2, MC5R and CD83, which are responsible for economic traits including lean muscle mass, fertility and immunization. Overall, this study found a series of candidate genes putatively associated with the breeding improvement of Duroc pigs and the polygenic basis of adaptive evolution, which can provide important references and fundamental information for future breeding programs.

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Section: Introductionmentioning

confidence: 96%

Genomic Analysis To Identify Signatures of Artificial Selection and Loci Associated with Important Economic Traits in Duroc Pigs

Ma¹,

Zhang²,

Zhang

et al. 2018

G3 Genes|Genomes|Genetics

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“…Genome-wide association study(GWAS) can provide preliminary results in genetic research on complex traits in animals. Many single nucleotide polymorphism (SNP) loci and qualitative trait loci(QTL) with strong statistical signi cance have been discovered [6][7][8][9]. GWAS has become a powerful tool for studying important economic traits of livestock and poultry and has promoted research on marker-assisted breeding.…”

Section: Introductionmentioning

confidence: 99%

Pathway-based analysis enables deeper mining of GWAS data on H/L in chickens

Wang¹,

Zhu²,

Wen³

et al. 2020

Preprint

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Background Heterophils are refers to white blood cells with phagocytosis and killing functions in the avian immune system, These cells identify and kill pathogenic microorganisms through precise regulatory mechanisms. As a simple index, the heterophil/lymphocyte ratio (H/L) in the blood reflects the immune system status of chickens. H/L is a complex trait affected by multiple genetic loci, but single nucleotide polymorphisms (SNPs) significantly associated with traits can usually explain only part of the phenotypic variation. Combining a genome-wide association study (GWAS) with pathway analysis can improve understanding of the biological pathways affecting traits. Our objective was to conduct a SNP- and pathway-based analysis to identify possible biological mechanisms involved in H/L traits. Methods GWAS for H/L was performed in 1,317 Cobb broilers to identify significant single nucleotide polymorphisms (SNPs) associated with H/L. Eight SNPs (P< 1/8,068) reached a significant level of association. The following results were obtained through a series of analyses, including pathway-based association analysis and analysis of the proportion of phenotypic variance explained by SNPs. Results On the basis of GWAS analysis results, one associated SNP (5% genome-wide significance (6.80E-6,0.05/8,068)) on GGA 1(chicken chromosome 1) and seven suggestively associated SNPs with a trend toward significance(1.24E-4, 1/8,068) on GGAs 1, 7, 13 and 19 were detected. The significant SNP on GGA 19 was in Complement C1q Binding Protein (C1QBP). The wild-type and mutant individuals showed significant differences in H/L at five loci (P< 0.05). According to the results of pathway-based analysis, nine associated pathways (P < 0.05) were identified, including small cell lung cancer, proteoglycans in cancer, sulfur relay system, pathways in cancer, gastric acid secretion and purine metabolism. By combining GWAS with pathway analysis, we found that all SNPs after QC explained 12.4% of the phenotypic variation in H/L and 53 SNPs associated with H/L explained as much as 9.7% of the phenotypic variation in H/L. Conclusions Our findings contribute to understanding of the genetic regulation of H/L and provide theoretical support.

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“…Phenotypes listed in Additional file 1: Table S1 were recorded in the 36 Duroc gilts. Meat quality traits were measured as described in [14,15]. Total muscle cholesterol content was determined following Cayuela et al [16], whereas intramuscular fatty acids content and composition were determined in accordance with previous reports [17].…”

Section: Animal Materials and Phenotypic Recordingmentioning

confidence: 99%

Co-expression network analysis predicts a key role of microRNAs in the adaptation of the porcine skeletal muscle to nutrient supply

Mármol-Sánchez

Ramayo-Caldas

Quintanilla

et al. 2020

J Animal Sci Biotechnol

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Background: The role of non-coding RNAs in the porcine muscle metabolism is poorly understood, with few studies investigating their expression patterns in response to nutrient supply. Therefore, we aimed to investigate the changes in microRNAs (miRNAs), long intergenic non-coding RNAs (lincRNAs) and mRNAs muscle expression before and after food intake. Results: We measured the miRNA, lincRNA and mRNA expression levels in the gluteus medius muscle of 12 gilts in a fasting condition (AL-T0) and 24 gilts fed ad libitum during either 5 h. (AL-T1, N = 12) or 7 h. (AL-T2, N = 12) prior to slaughter. The small RNA fraction was extracted from muscle samples retrieved from the 36 gilts and sequenced, whereas lincRNA and mRNA expression data were already available. In terms of mean and variance, the expression profiles of miRNAs and lincRNAs in the porcine muscle were quite different than those of mRNAs. Food intake induced the differential expression of 149 (AL-T0/AL-T1) and 435 (AL-T0/AL-T2) mRNAs, 6 (AL-T0/AL-T1) and 28 (AL-T0/AL-T2) miRNAs and none lincRNAs, while the number of differentially dispersed genes was much lower. Among the set of differentially expressed miRNAs, we identified ssc-miR-148a-3p, ssc-miR-22-3p and ssc-miR-1, which play key roles in the regulation of glucose and lipid metabolism. Besides, co-expression network analyses revealed several miRNAs that putatively interact with mRNAs playing key metabolic roles and that also showed differential expression before and after feeding. One case example was represented by seven miRNAs (ssc-miR-148a-3p, ssc-miR-151-3p, ssc-miR-30a-3p, ssc-miR-30e-3p, ssc-miR-421-5p, ssc-miR-493-5p and ssc-miR-503) which putatively interact with the PDK4 mRNA, one of the master regulators of glucose utilization and fatty acid oxidation. Conclusions: As a whole, our results evidence that microRNAs are likely to play an important role in the porcine skeletal muscle metabolic adaptation to nutrient availability.

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A genome‐wide association analysis for carcass traits in a commercial Duroc pig population

Cited by 17 publications

References 19 publications

Genomic Analysis To Identify Signatures of Artificial Selection and Loci Associated with Important Economic Traits in Duroc Pigs

Genomic Analysis To Identify Signatures of Artificial Selection and Loci Associated with Important Economic Traits in Duroc Pigs

Pathway-based analysis enables deeper mining of GWAS data on H/L in chickens

Co-expression network analysis predicts a key role of microRNAs in the adaptation of the porcine skeletal muscle to nutrient supply

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