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Tang S, Xin Y, Ma Y, Xu X, Zhao S, Cao J. Screening of Microbes Associated With Swine Growth and Fat Deposition Traits Across the Intestinal Tract. Front Microbiol 2020; 11:586776. [PMID: 33178171 PMCID: PMC7596661 DOI: 10.3389/fmicb.2020.586776] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/15/2020] [Indexed: 12/12/2022] Open
Abstract
Pigs, as one of the most common livestock species worldwide, are expected to have a fast growth rate and lower subcutaneous fatness but higher intramuscular fat ("marbling meat"). Nowadays, it is believed that not only host genetics but also its gut microbiomes can modulate farm animal phenotypes, however, many of the mechanisms remain elusive. We measured the body weight (BW), average daily gain (ADG), backfat thickness (BFT), and intramuscular fatness (IMF) of 91 Enshi pigs at 260 days of age, then genotyped each one individually using a 50K single nucleotide polymorphism array and performed 16S ribosomal RNA gene sequencing on 455 microbial samples from the jejunum, ileum, cecum, colon, and rectum. The microbial diversity showed notable spatial variation across the entire intestinal tract, with the cecum and colon having the highest α-diversity. The cecal and colonic microbiotas made greater contributions to BW and ADG and accounted for 22-37% of the phenotypic variance. The jejunal and cecal microbiotas contributed more (13-31%) to the BFT and IMF than the other segments. Finally, from cecum, colon, and jejunum, we identified eight microbial taxa that were significantly correlated with the target traits. The genera Alloprevotella and Ruminococcaceae UCG-005 were highly positively correlated with BW and ADG. The genera Prevotellaceae UCG-001 and Alistipes in the cecum and Clostridium sensu stricto 1 in the jejunum were highly positively correlated with BFT and IMF. The genera Stenotrophomonas, Sphaerochaeta, and Desulfovibrio were negatively associated with the mentioned traits. These findings could aid in developing strategies for manipulating the gut microbiota to alter production performance in pigs.
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Affiliation(s)
- Shi Tang
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production – Swine Breeding and Reproduction Innovation Platform, Huazhong Agricultural University, Wuhan, China
| | - Ying Xin
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production – Swine Breeding and Reproduction Innovation Platform, Huazhong Agricultural University, Wuhan, China
| | - Yunlong Ma
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production – Swine Breeding and Reproduction Innovation Platform, Huazhong Agricultural University, Wuhan, China
| | - Xuewen Xu
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production – Swine Breeding and Reproduction Innovation Platform, Huazhong Agricultural University, Wuhan, China
| | - Shuhong Zhao
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production – Swine Breeding and Reproduction Innovation Platform, Huazhong Agricultural University, Wuhan, China
| | - Jianhua Cao
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production – Swine Breeding and Reproduction Innovation Platform, Huazhong Agricultural University, Wuhan, China
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2
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Criado-Mesas L, Ballester M, Crespo-Piazuelo D, Castelló A, Fernández AI, Folch JM. Identification of eQTLs associated with lipid metabolism in Longissimus dorsi muscle of pigs with different genetic backgrounds. Sci Rep 2020; 10:9845. [PMID: 32555447 PMCID: PMC7300017 DOI: 10.1038/s41598-020-67015-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 05/29/2020] [Indexed: 12/14/2022] Open
Abstract
Intramuscular fat content and its fatty acid composition affect porcine meat quality and its nutritional value. The present work aimed to identify genomic variants regulating the expression in the porcine muscle (Longissimus dorsi) of 45 candidate genes for lipid metabolism and fatty acid composition in three experimental backcrosses based on the Iberian breed. Expression genome-wide association studies (eGWAS) were performed between the muscle gene expression values, measured by real-time quantitative PCR, and the genotypes of 38,426 SNPs distributed along all chromosomes. The eGWAS identified 186 eSNPs located in ten Sus scrofa regions and associated with the expression of ACSM5, ACSS2, ATF3, DGAT2, FOS and IGF2 (FDR < 0.05) genes. Two expression quantitative trait loci (eQTLs) for IGF2 and ACSM5 were classified as cis-acting eQTLs, suggesting a mutation in the same gene affecting its expression. Conversely, ten eQTLs showed trans-regulatory effects on gene expression. When the eGWAS was performed for each backcross independently, only three common trans-eQTL regions were observed, indicating different regulatory mechanisms or allelic frequencies among the breeds. In addition, hotspot regions regulating the expression of several genes were detected. Our results provide new data to better understand the functional regulatory mechanisms of lipid metabolism genes in muscle.
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Affiliation(s)
- Lourdes Criado-Mesas
- Departament de Genòmica Animal, Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain.
| | - Maria Ballester
- Departament de Genètica i Millora Animal, Institut de Recerca y Tecnologia Agraroalimentàries (IRTA), Caldes de Montbui, Spain
| | - Daniel Crespo-Piazuelo
- Departament de Genòmica Animal, Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, UAB, Bellaterra, Spain
| | - Anna Castelló
- Departament de Genòmica Animal, Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, UAB, Bellaterra, Spain
| | - Ana I Fernández
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Josep M Folch
- Departament de Genòmica Animal, Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, UAB, Bellaterra, Spain
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3
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Crespo-Piazuelo D, Criado-Mesas L, Revilla M, Castelló A, Fernández AI, Folch JM, Ballester M. Indel detection from Whole Genome Sequencing data and association with lipid metabolism in pigs. PLoS One 2019; 14:e0218862. [PMID: 31246983 PMCID: PMC6597088 DOI: 10.1371/journal.pone.0218862] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 06/11/2019] [Indexed: 12/15/2022] Open
Abstract
The selection in commercial swine breeds for meat-production efficiency has been increasing among the past decades, reducing the intramuscular fat content, which has changed the sensorial and technological properties of pork. Through processes of natural adaptation and selective breeding, the accumulation of mutations has driven the genetic divergence between pig breeds. The most common and well-studied mutations are single-nucleotide polymorphisms (SNPs). However, insertions and deletions (indels) usually represents a fifth part of the detected mutations and should also be considered for animal breeding. In the present study, three different programs (Dindel, SAMtools mpileup, and GATK) were used to detect indels from Whole Genome Sequencing data of Iberian boars and Landrace sows. A total of 1,928,746 indels were found in common with the three programs. The VEP tool predicted that 1,289 indels may have a high impact on protein sequence and function. Ten indels inside genes related with lipid metabolism were genotyped in pigs from three different backcrosses with Iberian origin, obtaining different allelic frequencies on each backcross. Genome-Wide Association Studies performed in the Longissimus dorsi muscle found an association between an indel located in the C1q and TNF related 12 (C1QTNF12) gene and the amount of eicosadienoic acid (C20:2(n-6)).
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Affiliation(s)
- Daniel Crespo-Piazuelo
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
- * E-mail:
| | - Lourdes Criado-Mesas
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
| | - Manuel Revilla
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Anna Castelló
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Ana I. Fernández
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Josep M. Folch
- Plant and Animal Genomics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB Consortium, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Maria Ballester
- Departament de Genètica i Millora Animal, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Caldes de Montbui, Spain
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Gol S, González-Prendes R, Bosch L, Tor M, Reixach J, Pena RN, Estany J. Linoleic acid metabolic pathway allows for an efficient increase of intramuscular fat content in pigs. J Anim Sci Biotechnol 2019; 10:33. [PMID: 31080594 PMCID: PMC6503358 DOI: 10.1186/s40104-019-0343-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/11/2019] [Indexed: 12/18/2022] Open
Abstract
Background Intramuscular fat (IMF) content is a relevant trait for high-quality meat products such as dry-cured ham, but increasing IMF has the undesirable correlated effect of decreasing lean growth. Thus, there is a need to find selection criteria for IMF independent from lean growth. In pigs, the proportion of linoleic (C18:2) and arachidonic (C20:4) acids decline with fat deposition and therefore they can be considered as indicators of fatness. The aim of this research was to estimate the genetic variation for C18:2 and C20:4 in IMF and their genetic correlations with IMF and lean growth traits, with the objective to assess their potential as specific biomarkers of IMF. The analysis was conducted using a full-pedigreed Duroc resource line with 91,448 records of body weight and backfat thickness (BT) at 180 days of age and 1371 records of fatty acid composition in the muscle gluteus medius. Results The heritability estimates for C18:2 and C20:4 in IMF, whether expressed in absolute (mg/g of muscle) or in relative (mg/g of fatty acid) terms, as well as for their ratio (C20:4/C18:2), were high (> 0.40), revealing that the C18:2 to C20:4 pathway is subjected to substantial genetic influence. Litter effects were not negligible, with values ranging from 8% to 15% of the phenotypic variance. The genetic correlations of C18:2 and C20:4 with IMF and BT were negative (- 0.75 to - 0.66, for IMF, and - 0.64 to - 0.36, for BT), if expressed in relative values, but almost null (- 0.04 to 0.07), if expressed in absolute values, except for C18:2 with IMF, which was highly positive (0.88). The ratio of C20:4 to C18:2 also displayed a stronger genetic correlation with IMF (- 0.59) than with BT (- 0.10). Conclusions The amount of C18:2 in muscle can be used as an IMF-specific biomarker. Selection for the absolute amount of C18:2 is expected to deliver a similar response outcome as selection for IMF at restrained BT. Further genetic analysis of the C18:2 metabolic pathway may provide new insights into differential fat deposition among adipose tissues and on candidate genes for molecular markers targeting specifically for one of them.
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Affiliation(s)
- Sofia Gol
- 1Department of Animal Science, Universitat de Lleida - Agrotecnio Center, 191 Rovira Roure, 25198 Lleida, Catalonia Spain
| | - Rayner González-Prendes
- 1Department of Animal Science, Universitat de Lleida - Agrotecnio Center, 191 Rovira Roure, 25198 Lleida, Catalonia Spain
| | - Lluís Bosch
- 2Department of Chemical, Agricultural and Food Technology Engineering, Universitat de Girona, Campus de Montilivi, 17071 Girona, Catalonia Spain
| | - Marc Tor
- 1Department of Animal Science, Universitat de Lleida - Agrotecnio Center, 191 Rovira Roure, 25198 Lleida, Catalonia Spain
| | - Josep Reixach
- Selección Batallé S.A., Av. Segadors s/n, 17421 Riudarenes, Catalonia Spain
| | - Ramona N Pena
- 1Department of Animal Science, Universitat de Lleida - Agrotecnio Center, 191 Rovira Roure, 25198 Lleida, Catalonia Spain
| | - Joan Estany
- 1Department of Animal Science, Universitat de Lleida - Agrotecnio Center, 191 Rovira Roure, 25198 Lleida, Catalonia Spain
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5
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González-Prendes R, Quintanilla R, Mármol-Sánchez E, Pena RN, Ballester M, Cardoso TF, Manunza A, Casellas J, Cánovas Á, Díaz I, Noguera JL, Castelló A, Mercadé A, Amills M. Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi muscles. BMC Genomics 2019; 20:170. [PMID: 30832586 PMCID: PMC6399881 DOI: 10.1186/s12864-019-5557-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 02/22/2019] [Indexed: 12/23/2022] Open
Abstract
Background Intramuscular fat (IMF) content and composition have a strong impact on the nutritional and organoleptic properties of porcine meat. The goal of the current work was to compare the patterns of gene expression and the genetic determinism of IMF traits in the porcine gluteus medius (GM) and longissimus dorsi (LD) muscles. Results A comparative analysis of the mRNA expression profiles of the pig GM and LD muscles in 16 Duroc pigs with available microarray mRNA expression measurements revealed the existence of 106 differentially expressed probes (fold-change > 1.5 and q-value < 0.05). Amongst the genes displaying the most significant differential expression, several loci belonging to the Hox transcription factor family were either upregulated (HOXA9, HOXA10, HOXB6, HOXB7 and TBX1) or downregulated (ARX) in the GM muscle. Differences in the expression of genes with key roles in carbohydrate and lipid metabolism (e.g. FABP3, ORMDL1 and SLC37A1) were also detected. By performing a GWAS for IMF content and composition traits recorded in the LD and GM muscles of 350 Duroc pigs, we identified the existence of one region on SSC14 (110–114 Mb) displaying significant associations with C18:0, C18:1(n-7), saturated and unsaturated fatty acid contents in both GM and LD muscles. Moreover, we detected several genome-wide significant associations that were not consistently found in both muscles. Further studies should be performed to confirm whether these associations are muscle-specific. Finally, the performance of an eQTL scan for 74 genes, located within GM QTL regions and with available microarray measurements of gene expression, made possible to identify 14 cis-eQTL regulating the expression of 14 loci, and six of them were confirmed by RNA-Seq. Conclusions We have detected significant differences in the mRNA expression patterns of the porcine LD and GM muscles, evidencing that the transcriptomic profile of the skeletal muscle tissue is affected by anatomical, metabolic and functional factors. A highly significant association with IMF composition on SSC14 was replicated in both muscles, highlighting the existence of a common genetic determinism, but we also observed the existence of a few associations whose magnitude and significance varied between LD and GM muscles. Electronic supplementary material The online version of this article (10.1186/s12864-019-5557-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rayner González-Prendes
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Rovira Roure 191, 25198, Lleida, Spain
| | - Emilio Mármol-Sánchez
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Ramona N Pena
- Departament de Ciència Animal, Universitat de Lleida-Agrotecnio Centre, 25198, Lleida, Spain
| | - Maria Ballester
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Rovira Roure 191, 25198, Lleida, Spain
| | - Tainã Figueiredo Cardoso
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,CAPES Foundation, Ministry of Education of Brazil, Brasilia, DF, 70.040-020, Brazil
| | - Arianna Manunza
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Joaquim Casellas
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Ángela Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
| | - Isabel Díaz
- Institute for Research and Technology in Food and Agriculture (IRTA), Tecnologia dels Aliments, 17121, Monells, Spain
| | - José Luis Noguera
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Rovira Roure 191, 25198, Lleida, Spain
| | - Anna Castelló
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Anna Mercadé
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Marcel Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain. .,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
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6
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Revilla M, Puig-Oliveras A, Crespo-Piazuelo D, Criado-Mesas L, Castelló A, Fernández AI, Ballester M, Folch JM. Expression analysis of candidate genes for fatty acid composition in adipose tissue and identification of regulatory regions. Sci Rep 2018; 8:2045. [PMID: 29391556 PMCID: PMC5794915 DOI: 10.1038/s41598-018-20473-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 01/16/2018] [Indexed: 02/07/2023] Open
Abstract
The aim of this work was to study the genetic basis of the backfat expression of lipid-related genes associated with meat quality traits in pigs. We performed a genome-wide association study with the backfat gene expression measured in 44 genes by qPCR and the PorcineSNP60 BeadChip genotypes in 115 Iberian x Landrace backcross animals. A total of 193 expression-associated SNPs located in 19 chromosomal regions were associated with expression levels of ACSM5, ELOVL6, FABP4, FADS2, and SLC27A4 genes. Three expression quantitative trail loci (eQTLs) corresponding to ACSM5, FABP4, and FADS2 were classified as cis-acting eQTLs, whereas the remaining 16 eQTLs have trans-regulatory effects. Remarkably, a SNP in the ACSM5 promoter region and a SNP in the 3′UTR region of FABP4 were the most associated polymorphisms with the ACSM5 and FABP4 expression levels, respectively. Moreover, relevant lipid-related genes mapped in the trans-eQTLs regions associated with the ACSM5, FABP4, FADS2, and SLC27A4 genes. Interestingly, a trans-eQTL hotspot on SSC13 regulating the gene expression of ELOVL6, ELOLV5, and SCD, three important genes implicated in the elongation and desaturation of fatty acids, was identified. These findings provide new data to further understand the functional regulatory mechanisms implicated in the variation of fatty acid composition in pigs.
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Affiliation(s)
- Manuel Revilla
- Animal Genomics Department, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Spain. .,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain.
| | - Anna Puig-Oliveras
- Animal Genomics Department, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain
| | - Daniel Crespo-Piazuelo
- Animal Genomics Department, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain
| | - Lourdes Criado-Mesas
- Animal Genomics Department, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain
| | - Anna Castelló
- Animal Genomics Department, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain
| | - Ana I Fernández
- Departamento de Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040, Madrid, Spain
| | - Maria Ballester
- Departament de Genètica i Millora Animal, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, 08140, Caldes de Montbui, Spain
| | - Josep M Folch
- Animal Genomics Department, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain
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7
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Ballester M, Ramayo-Caldas Y, Revilla M, Corominas J, Castelló A, Estellé J, Fernández AI, Folch JM. Integration of liver gene co-expression networks and eGWAs analyses highlighted candidate regulators implicated in lipid metabolism in pigs. Sci Rep 2017; 7:46539. [PMID: 28422154 PMCID: PMC5396199 DOI: 10.1038/srep46539] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 03/22/2017] [Indexed: 12/14/2022] Open
Abstract
In the present study, liver co-expression networks and expression Genome Wide Association Study (eGWAS) were performed to identify DNA variants and molecular pathways implicated in the functional regulatory mechanisms of meat quality traits in pigs. With this purpose, the liver mRNA expression of 44 candidates genes related with lipid metabolism was analysed in 111 Iberian x Landrace backcross animals. The eGWAS identified 92 eSNPs located in seven chromosomal regions and associated with eight genes: CROT, CYP2U1, DGAT1, EGF, FABP1, FABP5, PLA2G12A, and PPARA. Remarkably, cis-eSNPs associated with FABP1 gene expression which may be determining the C18:2(n-6)/C18:3(n-3) ratio in backfat through the multiple interaction of DNA variants and genes were identified. Furthermore, a hotspot on SSC8 associated with the gene expression of eight genes was identified and the TBCK gene was pointed out as candidate gene regulating it. Our results also suggested that the PI3K-Akt-mTOR pathway plays an important role in the control of the analysed genes highlighting nuclear receptors as the NR3C1 or PPARA. Finally, sex-dimorphism associated with hepatic lipid metabolism was identified with over-representation of female-biased genes. These results increase our knowledge of the genetic architecture underlying fat composition traits.
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Affiliation(s)
- Maria Ballester
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Campus UAB, Bellaterra, 08193, Barcelona, Spain
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (Consorci CSIC-IRTA-UAB-UB), Edifici CRAG, Campus UAB, Bellaterra, 08193, Barcelona, Spain
- IRTA, Genètica i Millora Animal, Torre Marimon, 08140 Caldes de Montbui, Spain
| | - Yuliaxis Ramayo-Caldas
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Campus UAB, Bellaterra, 08193, Barcelona, Spain
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (Consorci CSIC-IRTA-UAB-UB), Edifici CRAG, Campus UAB, Bellaterra, 08193, Barcelona, Spain
- Génétique Animale et Biologie Intégrative, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Manuel Revilla
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Campus UAB, Bellaterra, 08193, Barcelona, Spain
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (Consorci CSIC-IRTA-UAB-UB), Edifici CRAG, Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Jordi Corominas
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Campus UAB, Bellaterra, 08193, Barcelona, Spain
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (Consorci CSIC-IRTA-UAB-UB), Edifici CRAG, Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Anna Castelló
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Campus UAB, Bellaterra, 08193, Barcelona, Spain
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (Consorci CSIC-IRTA-UAB-UB), Edifici CRAG, Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Jordi Estellé
- Génétique Animale et Biologie Intégrative, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Ana I. Fernández
- Departamento de Mejora Genética Animal, INIA, Ctra. de la Coruña km. 7, 28040, Madrid, Spain
| | - Josep M. Folch
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Campus UAB, Bellaterra, 08193, Barcelona, Spain
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (Consorci CSIC-IRTA-UAB-UB), Edifici CRAG, Campus UAB, Bellaterra, 08193, Barcelona, Spain
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González-Prendes R, Quintanilla R, Cánovas A, Manunza A, Figueiredo Cardoso T, Jordana J, Noguera JL, Pena RN, Amills M. Joint QTL mapping and gene expression analysis identify positional candidate genes influencing pork quality traits. Sci Rep 2017; 7:39830. [PMID: 28054563 PMCID: PMC5215505 DOI: 10.1038/srep39830] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 11/29/2016] [Indexed: 12/28/2022] Open
Abstract
Meat quality traits have an increasing importance in the pig industry because of their strong impact on consumer acceptance. Herewith, we have combined phenotypic and microarray expression data to map loci with potential effects on five meat quality traits recorded in the longissimus dorsi (LD) and gluteus medius (GM) muscles of 350 Duroc pigs, i.e. pH at 24 hours post-mortem (pH24), electric conductivity (CE) and muscle redness (a*), lightness (L*) and yellowness (b*). We have found significant genome-wide associations for CE of LD on SSC4 (~104 Mb), SSC5 (~15 Mb) and SSC13 (~137 Mb), while several additional regions were significantly associated with meat quality traits at the chromosome-wide level. There was a low positional concordance between the associations found for LD and GM traits, a feature that reflects the existence of differences in the genetic determinism of meat quality phenotypes in these two muscles. The performance of an eQTL search for SNPs mapping to the regions associated with meat quality traits demonstrated that the GM a* SSC3 and pH24 SSC17 QTL display positional concordance with cis-eQTL regulating the expression of several genes with a potential role on muscle metabolism.
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Affiliation(s)
- Rayner González-Prendes
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui 08140, Spain
| | - Angela Cánovas
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Arianna Manunza
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Tainã Figueiredo Cardoso
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.,CAPES Foundation, Ministry of Education of Brazil, Brasilia D. F., Zip Code 70.040-020, Brazil
| | - Jordi Jordana
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - José Luis Noguera
- Animal Breeding and Genetics Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui 08140, Spain
| | - Ramona N Pena
- Department of Animal Science, University of Lleida - Agrotecnio Center, Lleida 25198, Spain
| | - Marcel Amills
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
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9
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Pegolo S, Cecchinato A, Casellas J, Conte G, Mele M, Schiavon S, Bittante G. Genetic and environmental relationships of detailed milk fatty acids profile determined by gas chromatography in Brown Swiss cows. J Dairy Sci 2015; 99:1315-1330. [PMID: 26709183 DOI: 10.3168/jds.2015-9596] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 10/24/2015] [Indexed: 01/11/2023]
Abstract
The aim of this study was to characterize the profile of 47 fatty acids, including conjugated linoleic acid (CLA), 13 fatty acid groups, and 5 Δ(9)-desaturation indices in milk samples from Brown Swiss cows. The genetic variation was assessed and the statistical relevance of the genetic background for each trait was evaluated using the Bayes factor test. The additive genetic, herd-date, and residual relationships were also estimated among all single fatty acids and groups of fatty acids. Individual milk samples were collected from 1,158 Italian Brown Swiss cows and a detailed analysis of fat percentages and milk fatty acid compositions was performed by gas chromatography. Bayesian animal models were used for (co)variance components estimation. Exploitable genetic variation was observed for most of the de novo synthesized fatty acids and saturated fatty acids, except for C4:0 and C6:0, whereas long-chain fatty acids and unsaturated fatty acids (including CLA) were mainly influenced by herd-date effects. Herd-date effect explained large portions of the total phenotypic variance for C18:2 cis-9,cis-12 (0.668), C18:3 cis-9,cis-12,cis-15 (0.631), and the biohydrogenation and elongation products of these fatty acids. The desaturation ratios showed higher heritability estimates than the individual fatty acids, except for CLA desaturation index (0.098). Among the medium-chain fatty acids, C12:0 had greater heritability than C14:0 (0.243 vs. 0.097, respectively). Both C14:0 and C16:0 showed negative additive genetic correlations with the main monounsaturated and polyunsaturated fatty acids of milk fat, suggesting that their synthesis in the mammary gland may be influenced by the presence of unsaturated fatty acids. No correlation was observed between C4:0 and the other short-chain fatty acids (except for C6:0), confirming the independence of C4:0 from de novo mammary fatty acid synthesis. Among the genetic correlations dealing with potentially beneficial fatty acids, C18:0 was positively correlated with vaccenic and rumenic acids and negatively with linoleic acid. Finally, fatty acids C6:0 through C14:0 showed relevant correlations due to unknown environmental effects, suggesting the potential existence of genetic variances in micro-environmental sensitivity. This study allowed us to acquire new knowledge about the genetic and the environmental relationships among fatty acids. Likewise, the existence of genetic variation for most of de novo synthetized fatty acids and saturated fatty acids was also observed. Overall, these results provide useful information to combine feeding with genetic selection strategies for obtaining a desirable milk fatty acids profile, depending on the origin of fatty acids in milk.
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Affiliation(s)
- S Pegolo
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro, Padova, Italy
| | - A Cecchinato
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro, Padova, Italy.
| | - J Casellas
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - G Conte
- Department of Agricolture, Food and Environment, Università di Pisa, Via del Borghetto, 80, 56124 Pisa, Italy
| | - M Mele
- Department of Agricolture, Food and Environment, Università di Pisa, Via del Borghetto, 80, 56124 Pisa, Italy
| | - S Schiavon
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro, Padova, Italy
| | - G Bittante
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro, Padova, Italy
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Ros-Freixedes R, Reixach J, Bosch L, Tor M, Estany J. Genetic correlations of intramuscular fat content and fatty acid composition among muscles and with subcutaneous fat in Duroc pigs1. J Anim Sci 2014; 92:5417-25. [DOI: 10.2527/jas.2014-8202] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- R. Ros-Freixedes
- Departament de Producció Animal – Agrotecnio Center, Universitat de Lleida, 191 Rovira Roure, 25198 Lleida, Catalonia, Spain
| | - J. Reixach
- Selección Batallé S.A., Av. Segadors s/n, 17421 Riudarenes, Spain
| | - L. Bosch
- Departament d'Enginyeria Química, Agrària i Tecnologia Agroalimentària, Universitat de Girona, Campus de Montilivi, 17071 Girona, Spain
| | - M. Tor
- Departament de Producció Animal – Agrotecnio Center, Universitat de Lleida, 191 Rovira Roure, 25198 Lleida, Catalonia, Spain
| | - J. Estany
- Departament de Producció Animal – Agrotecnio Center, Universitat de Lleida, 191 Rovira Roure, 25198 Lleida, Catalonia, Spain
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Manunza A, Casellas J, Quintanilla R, González-Prendes R, Pena RN, Tibau J, Mercadé A, Castelló A, Aznárez N, Hernández-Sánchez J, Amills M. A genome-wide association analysis for porcine serum lipid traits reveals the existence of age-specific genetic determinants. BMC Genomics 2014; 15:758. [PMID: 25189197 PMCID: PMC4164741 DOI: 10.1186/1471-2164-15-758] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 07/25/2014] [Indexed: 01/07/2023] Open
Abstract
Background The genetic determinism of blood lipid concentrations, the main risk factor for atherosclerosis, is practically unknown in species other than human and mouse. Even in model organisms, little is known about how the genetic determinants of lipid traits are modulated by age-specific factors. To gain new insights into this issue, we have carried out a genome-wide association study (GWAS) for cholesterol (CHOL), triglyceride (TRIG) and low (LDL) and high (HDL) density lipoprotein concentrations measured in Duroc pigs at two time points (45 and 190 days). Results Analysis of data with mixed-model methods (EMMAX, GEMMA, GenABEL) and PLINK showed a low positional concordance between trait-associated regions (TARs) for serum lipids at 45 and 190 days. Besides, the proportion of phenotypic variance explained by SNPs at these two time points was also substantially different. The four analyses consistently detected two regions on SSC3 (124 Mb, CHOL and LDL at 190 days) and SSC6 (135 Mb, CHOL and TRIG at 190 days) with highly significant effects on the porcine blood lipid profile. Moreover, we have found that SNP variation within SSC3, SSC6, SSC10, SSC13 and SSC16 TARs is associated with the expression of several genes mapping to other chromosomes and related to lipid metabolism. Conclusions Our data demonstrate that the effects of genomic determinants influencing lipid concentrations in pigs, as well as the amount of phenotypic variance they explain, are influenced by age-related factors. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-758) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Marcel Amills
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
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Ramayo-Caldas Y, Ballester M, Fortes MRS, Esteve-Codina A, Castelló A, Noguera JL, Fernández AI, Pérez-Enciso M, Reverter A, Folch JM. From SNP co-association to RNA co-expression: novel insights into gene networks for intramuscular fatty acid composition in porcine. BMC Genomics 2014; 15:232. [PMID: 24666776 PMCID: PMC3987146 DOI: 10.1186/1471-2164-15-232] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 03/21/2014] [Indexed: 12/19/2022] Open
Abstract
Background Fatty acids (FA) play a critical role in energy homeostasis and metabolic diseases; in the context of livestock species, their profile also impacts on meat quality for healthy human consumption. Molecular pathways controlling lipid metabolism are highly interconnected and are not fully understood. Elucidating these molecular processes will aid technological development towards improvement of pork meat quality and increased knowledge of FA metabolism, underpinning metabolic diseases in humans. Results The results from genome-wide association studies (GWAS) across 15 phenotypes were subjected to an Association Weight Matrix (AWM) approach to predict a network of 1,096 genes related to intramuscular FA composition in pigs. To identify the key regulators of FA metabolism, we focused on the minimal set of transcription factors (TF) that the explored the majority of the network topology. Pathway and network analyses pointed towards a trio of TF as key regulators of FA metabolism: NCOA2, FHL2 and EP300. Promoter sequence analyses confirmed that these TF have binding sites for some well-know regulators of lipid and carbohydrate metabolism. For the first time in a non-model species, some of the co-associations observed at the genetic level were validated through co-expression at the transcriptomic level based on real-time PCR of 40 genes in adipose tissue, and a further 55 genes in liver. In particular, liver expression of NCOA2 and EP300 differed between pig breeds (Iberian and Landrace) extreme in terms of fat deposition. Highly clustered co-expression networks in both liver and adipose tissues were observed. EP300 and NCOA2 showed centrality parameters above average in the both networks. Over all genes, co-expression analyses confirmed 28.9% of the AWM predicted gene-gene interactions in liver and 33.0% in adipose tissue. The magnitude of this validation varied across genes, with up to 60.8% of the connections of NCOA2 in adipose tissue being validated via co-expression. Conclusions Our results recapitulate the known transcriptional regulation of FA metabolism, predict gene interactions that can be experimentally validated, and suggest that genetic variants mapped to EP300, FHL2, and NCOA2 modulate lipid metabolism and control energy homeostasis in pigs.
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Affiliation(s)
- Yuliaxis Ramayo-Caldas
- Centre de Recerca en Agrigenòmica (CRAG), Consorci CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra 08193, Spain.
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Analysis of porcine adipose tissue transcriptome reveals differences in de novo fatty acid synthesis in pigs with divergent muscle fatty acid composition. BMC Genomics 2013; 14:843. [PMID: 24289474 PMCID: PMC3879068 DOI: 10.1186/1471-2164-14-843] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 11/25/2013] [Indexed: 01/18/2023] Open
Abstract
Background In pigs, adipose tissue is one of the principal organs involved in the regulation of lipid metabolism. It is particularly involved in the overall fatty acid synthesis with consequences in other lipid-target organs such as muscles and the liver. With this in mind, we have used massive, parallel high-throughput sequencing technologies to characterize the porcine adipose tissue transcriptome architecture in six Iberian x Landrace crossbred pigs showing extreme phenotypes for intramuscular fatty acid composition (three per group). Results High-throughput RNA sequencing was used to generate a whole characterization of adipose tissue (backfat) transcriptome. A total of 4,130 putative unannotated protein-coding sequences were identified in the 20% of reads which mapped in intergenic regions. Furthermore, 36% of the unmapped reads were represented by interspersed repeats, SINEs being the most abundant elements. Differential expression analyses identified 396 candidate genes among divergent animals for intramuscular fatty acid composition. Sixty-two percent of these genes (247/396) presented higher expression in the group of pigs with higher content of intramuscular SFA and MUFA, while the remaining 149 showed higher expression in the group with higher content of PUFA. Pathway analysis related these genes to biological functions and canonical pathways controlling lipid and fatty acid metabolisms. In concordance with the phenotypic classification of animals, the major metabolic pathway differentially modulated between groups was de novo lipogenesis, the group with more PUFA being the one that showed lower expression of lipogenic genes. Conclusions These results will help in the identification of genetic variants at loci that affect fatty acid composition traits. The implications of these results range from the improvement of porcine meat quality traits to the application of the pig as an animal model of human metabolic diseases.
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Stachowiak M, Nowacka-Woszuk J, Szydlowski M, Switonski M. The ACACA and SREBF1 genes are promising markers for pig carcass and performance traits, but not for fatty acid content in the longissimus dorsi muscle and adipose tissue. Meat Sci 2013; 95:64-71. [DOI: 10.1016/j.meatsci.2013.04.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 02/01/2013] [Accepted: 04/03/2013] [Indexed: 10/27/2022]
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15
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Casellas J, Vidal O, Pena RN, Gallardo D, Manunza A, Quintanilla R, Amills M. Genetics of serum and muscle lipids in pigs. Anim Genet 2013; 44:609-19. [DOI: 10.1111/age.12049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2013] [Indexed: 01/31/2023]
Affiliation(s)
- J. Casellas
- Departament de Ciència Animal i dels Aliments; Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
| | - O. Vidal
- Departament de Biologia; Universitat de Girona; Girona 17071 Spain
| | - R. N. Pena
- Departament de Producció Animal; Universitat de Lleida; Lleida 25198 Spain
| | - D. Gallardo
- Departament de Ciència Animal i dels Aliments; Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
| | - A. Manunza
- Department of Animal Genetics; Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB); Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
| | | | - M. Amills
- Department of Animal Genetics; Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB); Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
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16
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Melo C, Quintanilla R, Gallardo D, Zidi A, Jordana J, Díaz I, Pena RN, Amills M. Association analysis with lipid traits of 2 candidate genes (LRP12 and TRIB1) mapping to a SSC4 QTL for serum triglyceride concentration in pigs. J Anim Sci 2013; 91:1531-7. [PMID: 23408821 DOI: 10.2527/jas.2012-5517] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The performance of a genome scan for serum lipid traits at 45 and 190 d in 5 half-sib families of Duroc pigs allowed us to detect several pig chromosomal regions with significant effects on these phenotypes. In the current work, we aimed to refine the position of 1 chromosome 4 (SSC4) genome-wide significant QTL for serum triglyceride concentration at 190 d. Genotyping of 4 additional microsatellites allowed reduction of the 90% confidence interval of this QTL to the genomic interval between markers SW2409 and SW839. Sequencing experiments were performed to characterize the variability of 2 lipid-related genes, the lipoprotein receptor-related protein 12 (LRP12) and tribbles homolog 1 (TRIB1) loci, that map to this region. In this way, 2 (c.771A > G and c.1101A > G) and 1 (c.*156_157del) polymorphisms were identified at the LRP12 coding region and TRIB1 3' untranslated region, respectively. Association analyses between LRP12 and TRIB1 genotypes did not reveal any significant effect on serum lipid concentrations, suggesting that variation of these two loci does not explain the segregation of the SSC4 QTL. However, highly significant associations were observed for gluteus medius saturated fatty acid content (LRP12 c.1101A > G, P = 0.0006; TRIB1 c.*156_157del, P = 0.0003). In the light of these and other findings, the potential involvement of LRP12 and TRIB1 in muscle lipid metabolism deserves to be further explored.
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Affiliation(s)
- C Melo
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain
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17
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Cecchinato A, Cipolat-Gotet C, Casellas J, Penasa M, Rossoni A, Bittante G. Genetic analysis of rennet coagulation time, curd-firming rate, and curd firmness assessed over an extended testing period using mechanical and near-infrared instruments. J Dairy Sci 2013; 96:50-62. [DOI: 10.3168/jds.2012-5784] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 09/24/2012] [Indexed: 11/19/2022]
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Hernández-Sánchez J, Amills M, Pena RN, Mercadé A, Manunza A, Quintanilla R. Genomic architecture of heritability and genetic correlations for intramuscular and back fat contents in Duroc pigs. J Anim Sci 2012; 91:623-32. [PMID: 23230112 DOI: 10.2527/jas.2012-5270] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genetic parameters such as heritability and correlations of fat traits in a Duroc population were dissected using molecular markers. The heritabilities of intramuscular fat in 2 muscles, the gluteus medius and LM, and back fat were 0.54, 0.48, and 0.23, respectively. The genetic correlations were well estimated with standardized SNP effects, being 0.65 between intramuscular fat traits and ∼0.37 between any intramuscular fat trait and back fat. Genetic correlations were overestimated when ignoring molecular information. Twelve chromosomes showed additive genetic variance for intramuscular fat compared with 8 for back fat. Population structure was accommodated using 4 different models. The number of significant, P < 5 × 10(-5) (suggestive, P < 2 × 10(-3)), SNP varied across models and ranged from 0 to 4 (2 to 261) for intramuscular fat in the gluteus medius, from 0 to 57 (9 to 564) for intramuscular fat in the LM, and from 3 to 4 (22 to 168) for back fat. Several SNP showed significant deviations from an additive mode of action. Only 2 SNP significantly affected 2 traits simultaneously.
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Affiliation(s)
- J Hernández-Sánchez
- IRTA, Genètica i Millora Animal, 191 Av. Alcalde Rovira Roure, 25198 Lleida, Spain.
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Ros-Freixedes R, Reixach J, Tor M, Estany J. Expected genetic response for oleic acid content in pork1. J Anim Sci 2012; 90:4230-8. [DOI: 10.2527/jas.2011-5063] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Ramayo-Caldas Y, Mach N, Esteve-Codina A, Corominas J, Castelló A, Ballester M, Estellé J, Ibáñez-Escriche N, Fernández AI, Pérez-Enciso M, Folch JM. Liver transcriptome profile in pigs with extreme phenotypes of intramuscular fatty acid composition. BMC Genomics 2012; 13:547. [PMID: 23051667 PMCID: PMC3478172 DOI: 10.1186/1471-2164-13-547] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 10/08/2012] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND New advances in high-throughput technologies have allowed for the massive analysis of genomic data, providing new opportunities for the characterization of the transcriptome architectures. Recent studies in pigs have employed RNA-Seq to explore the transcriptome of different tissues in a reduced number of animals. The main goal of this study was the identification of differentially-expressed genes in the liver of Iberian x Landrace crossbred pigs showing extreme phenotypes for intramuscular fatty acid composition using RNA-Seq. RESULTS The liver transcriptomes of two female groups (H and L) with phenotypically extreme intramuscular fatty acid composition were sequenced using RNA-Seq. A total of 146 and 180 unannotated protein-coding genes were identified in intergenic regions for the L and H groups, respectively. In addition, a range of 5.8 to 7.3% of repetitive elements was found, with SINEs being the most abundant elements. The expression in liver of 186 (L) and 270 (H) lncRNAs was also detected. The higher reproducibility of the RNA-Seq data was validated by RT-qPCR and porcine expression microarrays, therefore showing a strong correlation between RT-qPCR and RNA-Seq data (ranking from 0.79 to 0.96), as well as between microarrays and RNA-Seq (r=0.72). A differential expression analysis between H and L animals identified 55 genes differentially-expressed between groups. Pathways analysis revealed that these genes belong to biological functions, canonical pathways and three gene networks related to lipid and fatty acid metabolism. In concordance with the phenotypic classification, the pathways analysis inferred that linolenic and arachidonic acids metabolism was altered between extreme individuals. In addition, a connection was observed among the top three networks, hence suggesting that these genes are interconnected and play an important role in lipid and fatty acid metabolism. CONCLUSIONS In the present study RNA-Seq was used as a tool to explore the liver transcriptome of pigs with extreme phenotypes for intramuscular fatty acid composition. The differential gene expression analysis showed potential gene networks which affect lipid and fatty acid metabolism. These results may help in the design of selection strategies to improve the sensorial and nutritional quality of pork meat.
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Affiliation(s)
- Yuliaxis Ramayo-Caldas
- Centre de Recerca en Agrigenòmica (CRAG), Consorci CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193, Spain
| | - Nuria Mach
- INRA, UMR 1313 Génétique Animale et Biologie Intégrative (GABI), Equipe Génétique Immunité Santé, Jouy-en-Josas, F-78352, France
- AgroParisTech, UMR 1313 GABI, Jouy-en-Josas, F-78352, France
- CEA, DSV/iRCM/SREIT/LREG, Jouy-en-Josas, F-78352, France
| | - Anna Esteve-Codina
- Centre de Recerca en Agrigenòmica (CRAG), Consorci CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193, Spain
| | - Jordi Corominas
- Centre de Recerca en Agrigenòmica (CRAG), Consorci CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193, Spain
| | - Anna Castelló
- Centre de Recerca en Agrigenòmica (CRAG), Consorci CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193, Spain
| | - Maria Ballester
- Centre de Recerca en Agrigenòmica (CRAG), Consorci CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193, Spain
| | - Jordi Estellé
- INRA, UMR 1313 Génétique Animale et Biologie Intégrative (GABI), Equipe Génétique Immunité Santé, Jouy-en-Josas, F-78352, France
- AgroParisTech, UMR 1313 GABI, Jouy-en-Josas, F-78352, France
- CEA, DSV/iRCM/SREIT/LREG, Jouy-en-Josas, F-78352, France
| | | | - Ana I Fernández
- Departamento de Mejora Genética Animal, INIA, Ctra. De la Coruña km. 7, Madrid, 28040, Spain
| | - Miguel Pérez-Enciso
- Centre de Recerca en Agrigenòmica (CRAG), Consorci CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193, Spain
- Institut Català de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Josep M Folch
- Centre de Recerca en Agrigenòmica (CRAG), Consorci CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
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Ramayo-Caldas Y, Mercadé A, Castelló A, Yang B, Rodríguez C, Alves E, Díaz I, Ibáñez-Escriche N, Noguera J, Pérez-Enciso M, Fernández A, Folch J. Genome-wide association study for intramuscular fatty acid composition in an Iberian × Landrace cross1. J Anim Sci 2012; 90:2883-93. [DOI: 10.2527/jas.2011-4900] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Y. Ramayo-Caldas
- Centre for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB-UB. Edifici CRAG, Campus Universitat Autonoma Barcelona. 08193 Bellaterra, Spain
| | - A. Mercadé
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autò noma de Barcelona. 08193 Bellaterra, Spain
| | - A. Castelló
- Centre for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB-UB. Edifici CRAG, Campus Universitat Autonoma Barcelona. 08193 Bellaterra, Spain
| | - B. Yang
- Centre for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB-UB. Edifici CRAG, Campus Universitat Autonoma Barcelona. 08193 Bellaterra, Spain
| | - C. Rodríguez
- Departamento de Mejora Genética Animal, INIA, Ctra. De la Coruña km. 7. 28040 Madrid, Spain
| | - E. Alves
- Departamento de Mejora Genética Animal, INIA, Ctra. De la Coruña km. 7. 28040 Madrid, Spain
| | - I. Díaz
- IRTA, Tecnologia dels Aliments. 17121 Monells, Spain
| | | | - J.L. Noguera
- IRTA, Genètica i Millora Animal. 25198 Lleida, Spain
| | - M. Pérez-Enciso
- Centre for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB-UB. Edifici CRAG, Campus Universitat Autonoma Barcelona. 08193 Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autò noma de Barcelona. 08193 Bellaterra, Spain
- ICREA, Passeig Lluis Companys. Barcelona, Spain
| | - A.I. Fernández
- Departamento de Mejora Genética Animal, INIA, Ctra. De la Coruña km. 7. 28040 Madrid, Spain
| | - J.M. Folch
- Centre for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB-UB. Edifici CRAG, Campus Universitat Autonoma Barcelona. 08193 Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autò noma de Barcelona. 08193 Bellaterra, Spain
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Cánovas A, Pena RN, Gallardo D, Ramírez O, Amills M, Quintanilla R. Segregation of regulatory polymorphisms with effects on the gluteus medius transcriptome in a purebred pig population. PLoS One 2012; 7:e35583. [PMID: 22545120 PMCID: PMC3335821 DOI: 10.1371/journal.pone.0035583] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 03/19/2012] [Indexed: 01/21/2023] Open
Abstract
Background The main goal of the present study was to analyse the genetic architecture of mRNA expression in muscle, a tissue with an outmost economic importance for pig breeders. Previous studies have used F2 crosses to detect porcine expression QTL (eQTL), so they contributed with data that mostly represents the between-breed component of eQTL variation. Herewith, we have analysed eQTL segregation in an outbred Duroc population using two groups of animals with divergent fatness profiles. This approach is particularly suitable to analyse the within-breed component of eQTL variation, with a special emphasis on loci involved in lipid metabolism. Methodology/Principal Findings GeneChip Porcine Genome arrays (Affymetrix) were used to determine the mRNA expression levels of gluteus medius samples from 105 Duroc barrows. A whole-genome eQTL scan was carried out with a panel of 116 microsatellites. Results allowed us to detect 613 genome-wide significant eQTL unevenly distributed across the pig genome. A clear predominance of trans- over cis-eQTL, was observed. Moreover, 11 trans-regulatory hotspots affecting the expression levels of four to 16 genes were identified. A Gene Ontology study showed that regulatory polymorphisms affected the expression of muscle development and lipid metabolism genes. A number of positional concordances between eQTL and lipid trait QTL were also found, whereas limited evidence of a linear relationship between muscle fat deposition and mRNA levels of eQTL regulated genes was obtained. Conclusions/Significance Our data provide substantial evidence that there is a remarkable amount of within-breed genetic variation affecting muscle mRNA expression. Most of this variation acts in trans and influences biological processes related with muscle development, lipid deposition and energy balance. The identification of the underlying causal mutations and the ascertainment of their effects on phenotypes would allow gaining a fundamental perspective about how complex traits are built at the molecular level.
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Affiliation(s)
| | - Ramona N. Pena
- IRTA, Genètica i Millora Animal, Lleida, Spain
- * E-mail: (RQ); (RP)
| | - David Gallardo
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Oscar Ramírez
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Marcel Amills
- Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
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Gallardo D, Pena RN, Quintanilla R, Ramírez O, Almuzara D, Noguera JL, Amills M. Quantitative trait loci analysis of a Duroc commercial population highlights differences in the genetic determination of meat quality traits at two different muscles. Anim Genet 2012; 43:800-4. [DOI: 10.1111/j.1365-2052.2012.02333.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2011] [Indexed: 11/28/2022]
Affiliation(s)
- D. Gallardo
- Departament de Ciència Animal i dels Aliments; Universitat Autònoma de Barcelona; 08193; Bellaterra; Spain
| | - R. N. Pena
- IRTA; Genètica i Millora Animal; 25198; Lleida; Spain
| | | | - O. Ramírez
- Departament de Ciència Animal i dels Aliments; Universitat Autònoma de Barcelona; 08193; Bellaterra; Spain
| | - D. Almuzara
- IRTA; Genètica i Millora Animal; 25198; Lleida; Spain
| | - J. L. Noguera
- IRTA; Genètica i Millora Animal; 25198; Lleida; Spain
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25
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Cecchinato A, De Marchi M, Penasa M, Casellas J, Schiavon S, Bittante G. Genetic analysis of beef fatty acid composition predicted by near-infrared spectroscopy1. J Anim Sci 2012; 90:429-38. [DOI: 10.2527/jas.2011-4150] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- A. Cecchinato
- Department of Animal Science, University of Padova, Viale dell'Università 16, 35020 Legnaro (PD), Italy
| | - M. De Marchi
- Department of Animal Science, University of Padova, Viale dell'Università 16, 35020 Legnaro (PD), Italy
| | - M. Penasa
- Department of Animal Science, University of Padova, Viale dell'Università 16, 35020 Legnaro (PD), Italy
| | - J. Casellas
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - S. Schiavon
- Department of Animal Science, University of Padova, Viale dell'Università 16, 35020 Legnaro (PD), Italy
| | - G. Bittante
- Department of Animal Science, University of Padova, Viale dell'Università 16, 35020 Legnaro (PD), Italy
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Quintanilla R, Pena RN, Gallardo D, Cánovas A, Ramírez O, Díaz I, Noguera JL, Amills M. Porcine intramuscular fat content and composition are regulated by quantitative trait loci with muscle-specific effects1. J Anim Sci 2011; 89:2963-71. [DOI: 10.2527/jas.2011-3974] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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Uddin MJ, Duy DN, Cinar MU, Tesfaye D, Tholen E, Juengst H, Looft C, Schellander K. Detection of quantitative trait loci affecting serum cholesterol, LDL, HDL, and triglyceride in pigs. BMC Genet 2011; 12:62. [PMID: 21752294 PMCID: PMC3146427 DOI: 10.1186/1471-2156-12-62] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Accepted: 07/13/2011] [Indexed: 11/10/2022] Open
Abstract
Background Serum lipids are associated with many serious cardiovascular diseases and obesity problems. Many quantitative trait loci (QTL) have been reported in the pig mostly for performance traits but very few for the serum lipid traits. In contrast, remarkable numbers of QTL are mapped for serum lipids in humans and mice. Therefore, the objective of this research was to investigate the chromosomal regions influencing the serum level of the total cholesterol (CT), triglyceride (TG), high density protein cholesterol (HDL) and low density protein cholesterol (LDL) in pigs. For this purpose, a total of 330 animals from a Duroc × Pietrain F2 resource population were phenotyped for serum lipids using ELISA and were genotyped by using 122 microsatellite markers covering all porcine autosomes for QTL study in QTL Express. Blood sampling was performed at approximately 175 days before slaughter of the pig. Results Most of the traits were correlated with each other and were influenced by average daily gain, slaughter date and age. A total of 18 QTL including three QTL with imprinting effect were identified on 11 different porcine autosomes. Most of the QTL reached to 5% chromosome-wide (CW) level significance including a QTL at 5% experiment-wide (GW) and a QTL at 1% GW level significance. Of these QTL four were identified for both the CT and LDL and two QTL were identified for both the TG and LDL. Moreover, three chromosomal regions were detected for the HDL/LDL ratio in this study. One QTL for HDL on SSC2 and two QTL for TG on SSC11 and 17 were detected with imprinting effect. The highly significant QTL (1% GW) was detected for LDL at 82 cM on SSC1, whereas significant QTL (5% GW) was identified for HDL/LDL on SSC1 at 87 cM. Chromosomal regions with pleiotropic effects were detected for correlated traits on SSC1, 7 and 12. Most of the QTL identified for serum lipid traits correspond with the previously reported QTL for similar traits in other mammals. Two novel QTL on SSC16 for HDL and HDL/LDL ratio and an imprinted QTL on SSS17 for TG were detected in the pig for the first time. Conclusion The newly identified QTL are potentially involved in lipid metabolism. The results of this work shed new light on the genetic background of serum lipid concentrations and these findings will be helpful to identify candidate genes in these QTL regions related to lipid metabolism and serum lipid concentrations in pigs.
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Affiliation(s)
- Muhammad Jasim Uddin
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, Bonn, Germany
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