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González-Prendes R, Derks MFL, Groenen MAM, Quintanilla R, Amills M. Assessing the relationship between the in silico predicted consequences of 97 missense mutations mapping to 68 genes related to lipid metabolism and their association with porcine fatness traits. Genomics 2023; 115:110589. [PMID: 36842749 DOI: 10.1016/j.ygeno.2023.110589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 01/29/2023] [Accepted: 02/21/2023] [Indexed: 02/26/2023]
Abstract
In general, the relationship between the predicted functional consequences of missense mutations mapping to genes known to be involved in human diseases and the severity of disease manifestations is weak. In this study, we tested in pigs whether missense single nucleotide polymorphisms (SNPs), predicted to have consequences on the function of genes related to lipid metabolism are associated with lipid phenotypes. Association analysis demonstrated that nine out of 72 nominally associated SNPs were classified as "highly" or "very highly consistent" in silico-predicted functional mutations and did not show association with lipid traits expected to be affected by inactivation of the corresponding gene. Although the lack of endophenotypes and the limited sample size of certain genotypic classes might have limited to some extent the reach of the current study, our data indicate that present-day bioinformatic tools have a modest ability to predict the impact of missense mutations on complex phenotypes.
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Affiliation(s)
- Rayner González-Prendes
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands.
| | - Martijn F L Derks
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, Institute of Agrifood Research and Technology (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain
| | - Marcel Amills
- 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, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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Mármol-Sánchez E, Luigi-Sierra MG, Castelló A, Guan D, Quintanilla R, Tonda R, Amills M. Variability in porcine microRNA genes and its association with mRNA expression and lipid phenotypes. Genet Sel Evol 2021; 53:43. [PMID: 33947333 PMCID: PMC8097994 DOI: 10.1186/s12711-021-00632-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 04/15/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Mature microRNAs (miRNAs) play an important role in repressing the expression of a wide range of mRNAs. The presence of polymorphic sites in miRNA genes and their corresponding 3'UTR binding sites can disrupt canonical conserved miRNA-mRNA pairings, and thus modify gene expression patterns. However, to date such polymorphic sites in miRNA genes and their association with gene expression phenotypes and complex traits are poorly characterized in pigs. RESULTS By analyzing whole-genome sequences from 120 pigs and wild boars from Europe and Asia, we identified 285 single nucleotide polymorphisms (SNPs) that map to miRNA loci, and 109,724 SNPs that are located in predicted 7mer-m8 miRNA binding sites within porcine 3'UTR. In porcine miRNA genes, SNP density is reduced compared with their flanking non-miRNA regions. By sequencing the genomes of five Duroc boars, we identified 12 miRNA SNPs that were subsequently genotyped in their offspring (N = 345, Lipgen population). Association analyses of miRNA SNPs with 38 lipid-related traits and hepatic and muscle microarray expression phenotypes recorded in the Lipgen population were performed. The most relevant detected association was between the genotype of the rs319154814 (G/A) SNP located in the apical loop of the ssc-miR-326 hairpin precursor and PPP1CC mRNA levels in the liver (q-value = 0.058). This result was subsequently confirmed by qPCR (P-value = 0.027). The rs319154814 (G/A) genotype was also associated with several fatty acid composition traits. CONCLUSIONS Our findings show a reduced variability of porcine miRNA genes, which is consistent with strong purifying selection, particularly in the seed region that plays a critical role in miRNA binding. Although it is generally assumed that SNPs mapping to the seed region are those with the most pronounced consequences on mRNA expression, we show that a SNP mapping to the apical region of ssc-miR-326 is significantly associated with hepatic mRNA levels of the PPP1CC gene, one of its predicted targets. Although experimental confirmation of such an interaction is reported in humans but not in pigs, this result highlights the need to further investigate the functional effects of miRNA polymorphisms that are located outside the seed region on gene expression in pigs.
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Affiliation(s)
- Emilio Mármol-Sánchez
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - María Gracia Luigi-Sierra
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Anna Castelló
- 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, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Dailu Guan
- 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), Torre Marimon, 08140, Caldes de Montbui, Spain
| | - Raul Tonda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Marcel Amills
- 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, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
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Mármol-Sánchez E, Quintanilla R, Luigi-Sierra MG, Amills M. An association analysis between a polymorphism in the SEC24A gene and lipid traits recorded in Duroc pigs. ITALIAN JOURNAL OF ANIMAL SCIENCE 2021. [DOI: 10.1080/1828051x.2021.1951129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Emilio Mármol-Sánchez
- Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Raquel Quintanilla
- Genètica i Millora Animal, Intitut de Recerca i Tecnologia Agroalimentàries (IRTA), Caldes de Montbui, Spain
| | - María Gracia Luigi-Sierra
- Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Marcel Amills
- Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
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Kumar M, Srivastav AK, Parmar D. Genetic analysis and epistatic interaction association of lipid traits in a C57xBalb/c F2 mice. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Mármol-Sánchez E, Luigi-Sierra MG, Quintanilla R, Amills M. Detection of homozygous genotypes for a putatively lethal recessive mutation in the porcine argininosuccinate synthase 1 (ASS1) gene. Anim Genet 2019; 51:106-110. [PMID: 31729055 DOI: 10.1111/age.12877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2019] [Indexed: 12/18/2022]
Abstract
The sequencing of the pig genome revealed the existence of homozygous individuals for a nonsense mutation in the argininosuccinate synthase 1 (ASS1) gene (rs81212146, c.944T>A, L315X). Paradoxically, an AA homozygous genotype for this polymorphism is expected to abolish the function of the ASS1 enzyme that participates in the urea cycle, leading to citrullinemia, hyperammonemia, coma and death. Sequencing of five Duroc boars that sired a population of 350 Duroc barrows revealed the segregation of the c.944T>A polymorphism, so we aimed to investigate its phenotypic consequences. Genotyping of this mutation in the 350 Duroc barrows revealed the existence of seven individuals homozygous (AA) for the nonsense mutation. These AA pigs had a normal weight despite the fact that mild citrullinemia often involves impaired growth. Sequencing of the region surrounding the mutation in TT, TA and AA individuals revealed that the A substitution in the second position of the codon (c.944T>A) is in complete linkage disequilibrium with a C replacement (c.943T>C) in the first position of the codon. This second mutation would compensate for the potentially damaging effect of the c.944T>A replacement. In fact, this is the most probable reason why pigs with homozygous AA genotypes at the 944 site of the ASS1 coding region are alive. Our results illustrate the complexities of predicting the consequences of nonsense mutations on gene function and phenotypes, not only because of annotation issues but also owing to the existence of genetic mechanisms that sometimes limit the penetrance of highly harmful mutations.
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Affiliation(s)
- E Mármol-Sánchez
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - M G Luigi-Sierra
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - R Quintanilla
- Animal Breeding and Genetics Programme, Institute for Research and Technology in Food and Agriculture (IRTA), Caldes de Montbui, 08140, Spain
| | - M Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
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Ramayo-Caldas Y, Mármol-Sánchez E, Ballester M, Sánchez JP, González-Prendes R, Amills M, Quintanilla R. Integrating genome-wide co-association and gene expression to identify putative regulators and predictors of feed efficiency in pigs. Genet Sel Evol 2019; 51:48. [PMID: 31477014 PMCID: PMC6721172 DOI: 10.1186/s12711-019-0490-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 08/19/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Feed efficiency (FE) has a major impact on the economic sustainability of pig production. We used a systems-based approach that integrates single nucleotide polymorphism (SNP) co-association and gene-expression data to identify candidate genes, biological pathways, and potential predictors of FE in a Duroc pig population. RESULTS We applied an association weight matrix (AWM) approach to analyse the results from genome-wide association studies (GWAS) for nine FE associated and production traits using 31K SNPs by defining residual feed intake (RFI) as the target phenotype. The resulting co-association network was formed by 829 SNPs. Additive effects of this SNP panel explained 61% of the phenotypic variance of RFI, and the resulting phenotype prediction accuracy estimated by cross-validation was 0.65 (vs. 0.20 using pedigree-based best linear unbiased prediction and 0.12 using the 31K SNPs). Sixty-eight transcription factor (TF) genes were identified in the co-association network; based on the lossless approach, the putative main regulators were COPS5, GTF2H5, RUNX1, HDAC4, ESR1, USP16, SMARCA2 and GTF2F2. Furthermore, gene expression data of the gluteus medius muscle was explored through differential expression and multivariate analyses. A list of candidate genes showing functional and/or structural associations with FE was elaborated based on results from both AWM and gene expression analyses, and included the aforementioned TF genes and other ones that have key roles in metabolism, e.g. ESRRG, RXRG, PPARGC1A, TCF7L2, LHX4, MAML2, NFATC3, NFKBIZ, TCEA1, CDCA7L, LZTFL1 or CBFB. The most enriched biological pathways in this list were associated with behaviour, immunity, nervous system, and neurotransmitters, including melatonin, glutamate receptor, and gustation pathways. Finally, an expression GWAS allowed identifying 269 SNPs associated with the candidate genes' expression (eSNPs). Addition of these eSNPs to the AWM panel of 829 SNPs did not improve the accuracy of genomic predictions. CONCLUSIONS Candidate genes that have a direct or indirect effect on FE-related traits belong to various biological processes that are mainly related to immunity, behaviour, energy metabolism, and the nervous system. The pituitary gland, hypothalamus and thyroid axis, and estrogen signalling play fundamental roles in the regulation of FE in pigs. The 829 selected SNPs explained 61% of the phenotypic variance of RFI, which constitutes a promising perspective for applying genetic selection on FE relying on molecular-based prediction.
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Affiliation(s)
- Yuliaxis Ramayo-Caldas
- 0000 0001 1943 6646grid.8581.4Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain
| | - Emilio Mármol-Sánchez
- grid.7080.fDepartment of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSCIC-IRTA-UAB-UB, Campus de LA Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Maria Ballester
- 0000 0001 1943 6646grid.8581.4Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain
| | - Juan Pablo Sánchez
- 0000 0001 1943 6646grid.8581.4Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain
| | - Rayner González-Prendes
- grid.7080.fDepartment of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSCIC-IRTA-UAB-UB, Campus de LA Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Marcel Amills
- grid.7080.fDepartment of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSCIC-IRTA-UAB-UB, Campus de LA Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- grid.7080.fDepartament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Raquel Quintanilla
- 0000 0001 1943 6646grid.8581.4Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain
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González-Prendes R, Mármol-Sánchez E, Quintanilla R, Castelló A, Zidi A, Ramayo-Caldas Y, Cardoso TF, Manunza A, Cánovas Á, Amills M. About the existence of common determinants of gene expression in the porcine liver and skeletal muscle. BMC Genomics 2019; 20:518. [PMID: 31234802 PMCID: PMC6591854 DOI: 10.1186/s12864-019-5889-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 06/07/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The comparison of expression QTL (eQTL) maps obtained in different tissues is an essential step to understand how gene expression is genetically regulated in a context-dependent manner. In the current work, we have compared the transcriptomic and eQTL profiles of two porcine tissues (skeletal muscle and liver) which typically show highly divergent expression profiles, in 103 Duroc pigs genotyped with the Porcine SNP60 BeadChip (Illumina) and with available microarray-based measurements of hepatic and muscle mRNA levels. Since structural variation could have effects on gene expression, we have also investigated the co-localization of cis-eQTLs with copy number variant regions (CNVR) segregating in this Duroc population. RESULTS The analysis of differential expresssion revealed the existence of 1204 and 1490 probes that were overexpressed and underexpressed in the gluteus medius muscle when compared to liver, respectively (|fold-change| > 1.5, q-value < 0.05). By performing genome scans in 103 Duroc pigs with available expression and genotypic data, we identified 76 and 28 genome-wide significant cis-eQTLs regulating gene expression in the gluteus medius muscle and liver, respectively. Twelve of these cis-eQTLs were shared by both tissues (i.e. 42.8% of the cis-eQTLs identified in the liver were replicated in the gluteus medius muscle). These results are consistent with previous studies performed in humans, where 50% of eQTLs were shared across tissues. Moreover, we have identified 41 CNVRs in a set of 350 pigs from the same Duroc population, which had been genotyped with the Porcine SNP60 BeadChip by using the PennCNV and GADA softwares, but only a small proportion of these CNVRs co-localized with the cis-eQTL signals. CONCLUSION Despite the fact that there are considerable differences in the gene expression patterns of the porcine liver and skeletal muscle, we have identified a substantial proportion of common cis-eQTLs regulating gene expression in both tissues. Several of these cis-eQTLs influence the mRNA levels of genes with important roles in meat (CTSF) and carcass quality (TAPT1), lipid metabolism (TMEM97) and obesity (MARC2), thus evidencing the practical importance of dissecting the genetic mechanisms involved in their expression.
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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, Bellaterra, 08193, Barcelona, Spain.,Departament de Producció Animal-Agrotecnio Center, Universitat de Lleida, 191 Rovira Roure, 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, Bellaterra, 08193, Barcelona, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140, Caldes de Montbui, Spain
| | - Anna Castelló
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Ali Zidi
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Yuliaxis Ramayo-Caldas
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Tainã Figueiredo Cardoso
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.,CAPES Foundation, Ministry of Education of Brazil, Brasilia D. F, Zip Code 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, Bellaterra, 08193, Barcelona, Spain
| | - Ángela Cánovas
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.,Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
| | - Marcel Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain. .,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
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Mármol-Sánchez E, Quintanilla R, Cardoso TF, Jordana Vidal J, Amills M. Polymorphisms of the cryptochrome 2 and mitoguardin 2 genes are associated with the variation of lipid-related traits in Duroc pigs. Sci Rep 2019; 9:9025. [PMID: 31227735 PMCID: PMC6588565 DOI: 10.1038/s41598-019-45108-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 05/24/2019] [Indexed: 01/06/2023] Open
Abstract
The genetic factors determining the phenotypic variation of porcine fatness phenotypes are still largely unknown. We investigated whether the polymorphism of eight genes (MIGA2, CRY2, NPAS2, CIART, ARNTL2, PER1, PER2 and PCK1), which display differential expression in the skeletal muscle of fasted and fed sows, is associated with the variation of lipid and mRNA expression phenotypes in Duroc pigs. The performance of an association analysis with the GEMMA software demonstrated that the rs330779504 SNP in the MIGA2 gene is associated with LDL concentration at 190 days (LDL2, corrected P-value = 0.057). Moreover, the rs320439526 SNP of the CRY2 gene displayed a significant association with stearic acid content in the longissimus dorsi muscle (LD C18:0, corrected P-value = 0.015). Both SNPs were also associated with the mRNA levels of the corresponding genes in the gluteus medius skeletal muscle. From a biological perspective these results are meaningful because MIGA2 protein plays an essential role in mitochondrial fusion, a process tightly connected with the energy status of the cell, while CRY2 is a fundamental component of the circadian clock. However, inclusion of these two SNPs in chromosome-wide association analyses demonstrated that they are not located at the peaks of significance for the two traits under study (LDL2 for rs330779504 and LD C18:0 for rs320439526), thus implying that these two SNPs do not have causal effects.
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Affiliation(s)
- Emilio Mármol-Sánchez
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Programme, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, Caldes de Montbui, Spain
| | - Taina F Cardoso
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain.,CAPES Foundation, Ministry of Education of Brazil, Brasilia, D. F., Brazil
| | - Jordi Jordana Vidal
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Marcel Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain. .,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain.
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9
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Bovo S, Mazzoni G, Bertolini F, Schiavo G, Galimberti G, Gallo M, Dall'Olio S, Fontanesi L. Genome-wide association studies for 30 haematological and blood clinical-biochemical traits in Large White pigs reveal genomic regions affecting intermediate phenotypes. Sci Rep 2019; 9:7003. [PMID: 31065004 PMCID: PMC6504931 DOI: 10.1038/s41598-019-43297-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 04/16/2019] [Indexed: 12/20/2022] Open
Abstract
Haematological and clinical-biochemical parameters are considered indicators of the physiological/health status of animals and might serve as intermediate phenotypes to link physiological aspects to production and disease resistance traits. The dissection of the genetic variability affecting these phenotypes might be useful to describe the resilience of the animals and to support the usefulness of the pig as animal model. Here, we analysed 15 haematological and 15 clinical-biochemical traits in 843 Italian Large White pigs, via three genome-wide association scan approaches (single-trait, multi-trait and Bayesian). We identified 52 quantitative trait loci (QTLs) associated with 29 out of 30 analysed blood parameters, with the most significant QTL identified on porcine chromosome 14 for basophil count. Some QTL regions harbour genes that may be the obvious candidates: QTLs for cholesterol parameters identified genes (ADCY8, APOB, ATG5, CDKAL1, PCSK5, PRL and SOX6) that are directly involved in cholesterol metabolism; other QTLs highlighted genes encoding the enzymes being measured [ALT (known also as GPT) and AST (known also as GOT)]. Moreover, the multivariate approach strengthened the association results for several candidate genes. The obtained results can contribute to define new measurable phenotypes that could be applied in breeding programs as proxies for more complex traits.
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Affiliation(s)
- Samuele Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - Gianluca Mazzoni
- Department of Health Technology, Technical University of Denmark (DTU), Lyngby, 2800, Denmark
| | - Francesca Bertolini
- National Institute of Aquatic Resources, Technical University of Denmark (DTU), Lyngby, 2800, Denmark
| | - Giuseppina Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - Giuliano Galimberti
- Department of Statistical Sciences "Paolo Fortunati", University of Bologna, Via delle Belle Arti 41, 40126, Bologna, Italy
| | - Maurizio Gallo
- Associazione Nazionale Allevatori Suini (ANAS), Via Nizza 53, 00198, Roma, Italy
| | - Stefania Dall'Olio
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy.
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10
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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] [MESH Headings] [Grants] [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.
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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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Cardoso TF, Quintanilla R, Castelló A, González-Prendes R, Amills M, Cánovas Á. Differential expression of mRNA isoforms in the skeletal muscle of pigs with distinct growth and fatness profiles. BMC Genomics 2018; 19:145. [PMID: 29444639 PMCID: PMC5813380 DOI: 10.1186/s12864-018-4515-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 01/31/2018] [Indexed: 01/03/2023] Open
Abstract
Background The identification of genes differentially expressed in the skeletal muscle of pigs displaying distinct growth and fatness profiles might contribute to identify the genetic factors that influence the phenotypic variation of such traits. So far, the majority of porcine transcriptomic studies have investigated differences in gene expression at a global scale rather than at the mRNA isoform level. In the current work, we have investigated the differential expression of mRNA isoforms in the gluteus medius (GM) muscle of 52 Duroc HIGH (increased backfat thickness, intramuscular fat and saturated and monounsaturated fatty acids contents) and LOW pigs (opposite phenotype, with an increased polyunsaturated fatty acids content). Results Our analysis revealed that 10.9% of genes expressed in the GM muscle generate alternative mRNA isoforms, with an average of 2.9 transcripts per gene. By using two different pipelines, one based on the CLC Genomics Workbench and another one on the STAR, RSEM and DESeq2 softwares, we have identified 10 mRNA isoforms that both pipelines categorize as differentially expressed in HIGH vs LOW pigs (P-value < 0.01 and ±0.6 log2fold-change). Only five mRNA isoforms, produced by the ITGA5, SEMA4D, LITAF, TIMP1 and ANXA2 genes, remain significant after correction for multiple testing (q-value < 0.05 and ±0.6 log2fold-change), being upregulated in HIGH pigs. Conclusions The increased levels of specific ITGA5, LITAF, TIMP1 and ANXA2 mRNA isoforms in HIGH pigs is consistent with reports indicating that the overexpression of these four genes is associated with obesity and metabolic disorders in humans. A broader knowledge about the functional attributes of these mRNA variants would be fundamental to elucidate the consequences of transcript diversity on the determinism of porcine phenotypes of economic interest. Electronic supplementary material The online version of this article (10.1186/s12864-018-4515-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tainã Figueiredo Cardoso
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.,CAPES Foundation, Ministry of Education of Brazil, Brasilia D.F, 70.040-020, Brazil
| | - Raquel Quintanilla
- Animal Breeding and Genetics Programme, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140, Caldes de Montbui, Spain
| | - Anna Castelló
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Rayner González-Prendes
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Marcel Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain. .,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.
| | - Ángela Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada.
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González-Prendes R, Quintanilla R, Amills M. Investigating the genetic regulation of the expression of 63 lipid metabolism genes in the pig skeletal muscle. Anim Genet 2017; 48:606-610. [DOI: 10.1111/age.12586] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2017] [Indexed: 01/22/2023]
Affiliation(s)
- R. González-Prendes
- Department of Animal Genetics; Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB); Campus de la Universitat Autònoma de Barcelona Bellaterra 08193 Spain
| | - R. Quintanilla
- Animal Breeding and Genetics Program; Institut de Recerca i Tecnologia Agroalimentàries (IRTA); Torre Marimon Caldes de Montbui 08140 Spain
| | - M. Amills
- Department of Animal Genetics; Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB); Campus de la Universitat Autònoma de Barcelona Bellaterra 08193 Spain
- Departament de Ciència Animal i dels Aliments; Facultat de Veterinària; Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
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RNA-seq based detection of differentially expressed genes in the skeletal muscle of Duroc pigs with distinct lipid profiles. Sci Rep 2017; 7:40005. [PMID: 28195222 PMCID: PMC5307323 DOI: 10.1038/srep40005] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/30/2016] [Indexed: 12/14/2022] Open
Abstract
We have used a RNA-seq approach to investigate differential expression in the skeletal muscle of swine (N = 52) with divergent lipid profiles i.e. HIGH (increased intramuscular fat and muscle saturated and monounsaturated fatty acid contents, higher serum lipid concentrations and fatness) and LOW pigs (leaner and with an increased muscle polyunsaturated fatty acid content). The number of mRNAs and non-coding RNAs (ncRNAs) expressed in the porcine gluteus medius muscle were 18,104 and 1,558, respectively. At the nominal level of significance (P-value ≤ 0.05), we detected 1,430 mRNA and 12 non-coding RNA (ncRNA) transcripts as differentially expressed (DE) in the gluteus medius muscle of HIGH vs LOW pigs. This smaller contribution of ncRNAs to differential expression may have biological and technical reasons. We performed a second analysis, that was more stringent (P-value ≤ 0.01 and fold-change ≥ 1.5), and only 96 and 0 mRNA-and ncRNA-encoding genes happened to be DE, respectively. The subset of DE mRNA genes was enriched in pathways related with lipid (lipogenesis and triacylglycerol degradation) and glucose metabolism. Moreover, HIGH pigs showed a more lipogenic profile than their LOW counterparts.
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Chański W, González-Prendes R, Castelló A, Jordana J, Manunza A, Quintanilla R, Amills M. An association analysis between a missense polymorphism at the pig PCSK9 gene and serum lipid and meat quality traits in Duroc pigs. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Ding YY, Zhang W, Zhang MQ, Fu K, Chen WP, Ding C, He XL, Zhang XD, Huang L, Yin ZJ. Functional and association studies of the cholesteryl ester transfer protein (CETP) gene in a Wannan Black pig model. Anim Genet 2015; 46:702-6. [PMID: 26477338 DOI: 10.1111/age.12370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2015] [Indexed: 10/22/2022]
Abstract
Some polymorphisms of the human CETP gene are causally and significantly associated with serum lipids levels; however, the information regarding this gene in pigs is sparse. To evaluate the effects of CETP on blood lipid traits and fat deposition in pig, porcine CETP tissue expression patterns were observed by quantitative real-time polymerase chain reaction (qPCR) first. High expression was detected in liver, spleen, gluteus medius (GM) muscle and backfat. A de novo polymorphism (AF333037:g.795C>T) in the intron 1 region of porcine CETP was identified. This polymorphism was further genotyped by direct sequencing of the PCR products of 390 Wannan Black pigs, a Chinese native breed population. Association analyses at 45 and 300 days of age revealed highly significant associations between CETP genotypes and serum lipid traits. Furthermore, this polymorphism was proved to be associated with differences in liver CETP mRNA levels: pigs at 300 days of age with the TT genotype had higher levels than did those with other genotypes (P = 0.021). Additionally, analysis at 300 days of age showed that GM CETP mRNA expression correlated positively with serum lipids levels as well as with carcass backfat thickness and intramuscular fat content in GM. These results indicate that CETP is involved in serum, adipose and muscle lipid metabolism in pigs. The mechanisms underlying such relationships and their functional implications are worthy of further research.
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Affiliation(s)
- Y Y Ding
- Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Department of Animal Science, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R., China
| | - W Zhang
- Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Department of Animal Science, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R., China
| | - M Q Zhang
- Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Department of Animal Science, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R., China
| | - K Fu
- Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Department of Animal Science, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R., China
| | - W P Chen
- Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Department of Animal Science, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R., China
| | - C Ding
- Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Department of Animal Science, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R., China
| | - X L He
- Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Department of Animal Science, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R., China
| | - X D Zhang
- Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Department of Animal Science, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R., China
| | - L Huang
- Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Department of Animal Science, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R., China
| | - Z J Yin
- Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Department of Animal Science, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, P. R., China
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16
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Yang H, Huang X, Zeng Z, Zhang W, Liu C, Fang S, Huang L, Chen C. Genome-Wide Association Analysis for Blood Lipid Traits Measured in Three Pig Populations Reveals a Substantial Level of Genetic Heterogeneity. PLoS One 2015; 10:e0131667. [PMID: 26121138 PMCID: PMC4488070 DOI: 10.1371/journal.pone.0131667] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 06/05/2015] [Indexed: 11/25/2022] Open
Abstract
Serum lipids are associated with myocardial infarction and cardiovascular disease in humans. Here we dissected the genetic architecture of blood lipid traits by applying genome-wide association studies (GWAS) in 1,256 pigs from Laiwu, Erhualian and Duroc × (Landrace × Yorkshire) populations, and a meta-analysis of GWAS in more than 2,400 pigs from five diverse populations. A total of 22 genomic loci surpassing the suggestive significance level were detected on 11 pig chromosomes (SSC) for six blood lipid traits. Meta-analysis of GWAS identified 5 novel loci associated with blood lipid traits. Comparison of GWAS loci across the tested populations revealed a substantial level of genetic heterogeneity for porcine blood lipid levels. We further evaluated the causality of nine polymorphisms nearby or within the APOB gene on SSC3 for serum LDL-C and TC levels. Of the 9 polymorphisms, an indel showed the most significant association with LDL-C and TC in Laiwu pigs. But the significant association was not identified in the White Duroc × Erhualian F2 resource population, in which the QTL for LDL-C and TC was also detected on SSC3. This indicates that population-specific signals may exist for the SSC3 QTL. Further investigations are warranted to validate this assumption.
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Affiliation(s)
- Hui Yang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Xiaochang Huang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Zhijun Zeng
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Wanchang Zhang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Chenlong Liu
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Shaoming Fang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Lusheng Huang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, 330045, Nanchang, China
| | - Congying Chen
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, 330045, Nanchang, China
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17
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Castelló A, Quintanilla R, Melo C, Gallardo D, Zidi A, Manunza A, Noguera JL, Tibau J, Jordana J, Pena RN, Amills M. Associations between pig adiponectin (ADIPOQ) genotype and serum lipid levels are modulated by age-specific modifiers. J Anim Sci 2014; 92:5367-73. [PMID: 25367522 DOI: 10.2527/jas.2014-8029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The adiponectin (ADIPOQ) locus is a positional and functional candidate gene for 2 porcine chromosome 13 (SSC13) QTL influencing cholesterol (CHOL) and low-density lipoprotein (LDL) concentrations in 190-d-old pigs. By sequencing 2.37 kb of the pig ADIPOQ cDNA, we have identified 1 c.*1512G>T 3' untranslated region polymorphism that has been genotyped in a Duroc pig commercial population with records for serum lipid levels at 45 and 190 d of age. Statistical analysis of the data have revealed significant associations between the ADIPOQ genotype and CHOL (P=0.0040) and LDL (P=0.0011) concentrations at 190 d but not at 45 d. In family 3, most of the SSC13 QTL effects on LDL levels at 190 d were explained by the ADIPOQ genotype. We also found an association with triglyceride levels at 45 d (P=0.0060) but not at 190 d. Measurement of allelic mRNA imbalance demonstrated that the G and T alleles are expressed at very similar levels in muscle and fat tissues, indicating that the c.*1512G>T polymorphism does not affect transcript abundance. As a whole, results obtained in the current work as well as previous data gathered in humans and pigs provide evidence that the magnitude of associations between blood lipid phenotypes and candidate loci genotypes may vary depending on the age of the individual, therefore suggesting the existence of dynamic genotype×environment interactions changing on a temporal scale.
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Affiliation(s)
- A Castelló
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain
| | - R Quintanilla
- IRTA, Genètica i Millora Animal, Torre Marimon, 08140 Caldes de Montbui, Spain
| | - C Melo
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain
| | - D Gallardo
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain
| | - A Zidi
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain
| | - A Manunza
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain
| | - J L Noguera
- IRTA, Genètica i Millora Animal, Torre Marimon, 08140 Caldes de Montbui, Spain
| | - J Tibau
- IRTA, Genètica i Millora Animal, Torre Marimon, 08140 Caldes de Montbui, Spain
| | - J Jordana
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain
| | - R N Pena
- Department of Animal Production, University of Lleida-Agrotecnio Center, 25198, Lleida, Spain
| | - M Amills
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain
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18
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Abstract
Current statistical approaches to investigate the nature and magnitude of transmission ratio distortion (TRD) are scarce and restricted to the most common experimental designs such as F2 populations and backcrosses. In this article, we describe a new Bayesian approach to check TRD within a given biallelic genetic marker in a diploid species, providing a highly flexible framework that can accommodate any kind of population structure. This model relies on the genotype of each offspring and thus integrates all available information from either the parents' genotypes or population-specific allele frequencies and yields TRD estimates that can be corroborated by the calculation of a Bayes factor (BF). This approach has been evaluated on simulated data sets with appealing statistical performance. As a proof of concept, we have also tested TRD in a porcine population with five half-sib families and 352 offspring. All boars and piglets were genotyped with the Porcine SNP60 BeadChip, whereas genotypes from the sows were not available. The SNP-by-SNP screening of the pig genome revealed 84 SNPs with decisive evidences of TRD (BF > 100) after accounting for multiple testing. Many of these regions contained genes related to biological processes (e.g., nucleosome assembly and co-organization, DNA conformation and packaging, and DNA complex assembly) that are critically associated with embryonic viability. The implementation of this method, which overcomes many of the limitations of previous approaches, should contribute to fostering research on TRD in both model and nonmodel organisms.
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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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Chen C, Yang B, Zeng Z, Yang H, Liu C, Ren J, Huang L. Genetic dissection of blood lipid traits by integrating genome-wide association study and gene expression profiling in a porcine model. BMC Genomics 2013; 14:848. [PMID: 24299188 PMCID: PMC4046658 DOI: 10.1186/1471-2164-14-848] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 11/19/2013] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Serum concentrations of total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C) and triglycerides (TG) are highly heritable traits that are used clinically to evaluate risk for cardiovascular disease in humans. In this study, we applied a genome-wide association study (GWAS) in 1,075 pigs from two populations and gene expression studies on 497 liver samples to dissect the genetic basis of serum lipids in a pig model. RESULTS We totally identified 8, 5, 2 and 3 genomic loci harboring 109 SNPs that were significantly associated with LDL-C, TC, TG and the ratio of HDL-C/LDL-C in two experimental populations, respectively. In the F2 population, the most prominent SNP was identified at the SSC3: 124,769,847 bp where APOB is the well-known candidate gene. However, in the Sutai population, the most number of significant SNPs was identified at SSC2: 64.97-82.22 Mb where LDLR was identified as the candidate gene. Furthermore, we firstly reported 4 novel genomic loci in pigs harboring the LDL-C-associated SNPs. We also observed obvious population heterogeneity in the two tested populations. Through whole-genome gene expression analysis, we detected 718 trait-correlated expressions. Many of these transcripts correspond to candidate genes for blood lipids in humans. The GWAS mapped 120 cis-eQTLs and 523 trans-eQTLs for these transcripts. One gene encoding the transcript gnl|UG|Ssc#S35330332 stands out to be an important candidate gene for LDL-C by an integrative analysis of GWAS, eQTL and trait-associated expression. CONCLUSIONS We identified the genomic regions or candidate genes associated with blood lipids by an integrative analysis of GWAS, QTT and eQTL mapping in pigs. The findings would benefit the further identification of the causative genes for blood lipid traits in both pigs and humans.
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Affiliation(s)
- Congying Chen
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Bin Yang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Zhijun Zeng
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Hui Yang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Chenlong Liu
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Jun Ren
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, 330045 Nanchang, China
| | - Lusheng Huang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, 330045 Nanchang, China
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21
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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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22
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Ramírez O, Quintanilla R, Varona L, Gallardo D, Díaz I, Pena R, Amills M. DECR1
and ME1
genotypes are associated with lipid composition traits in Duroc pigs. J Anim Breed Genet 2013; 131:46-52. [DOI: 10.1111/jbg.12035] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 02/27/2013] [Indexed: 11/29/2022]
Affiliation(s)
- O. Ramírez
- Departament de Ciència Animal i dels Aliments; Facultat de Veterinària; Universitat Autònoma de Barcelona; Bellaterra Spain
| | | | - L. Varona
- Genètica i Millora Animal; IRTA; Lleida Spain
| | - D. Gallardo
- Departament de Ciència Animal i dels Aliments; Facultat de Veterinària; Universitat Autònoma de Barcelona; Bellaterra Spain
| | - I. Díaz
- Centre de Tecnologia de la Carn (IRTA); Monells Spain
| | - R.N. Pena
- Genètica i Millora Animal; IRTA; Lleida Spain
| | - M. Amills
- Departament de Ciència Animal i dels Aliments; Facultat de Veterinària; Universitat Autònoma de Barcelona; Bellaterra Spain
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB); Universitat Autònoma de Barcelona; Bellaterra Spain
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23
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Pena RN, Gallardo D, Guàrdia MD, Reixach J, Arnau J, Amills M, Quintanilla R. Appearance, flavor, and texture attributes of pig dry-cured hams have a complex polygenic genomic architecture1. J Anim Sci 2013; 91:1051-8. [DOI: 10.2527/jas.2012-5458] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- R. N. Pena
- IRTA, Genètica i Millora Animal, 191 Av. Rovira Roure, 25198 Lleida, Spain
- Universitat de Lleida, Departament de Producció Animal, 191 Av. Rovira Roure, 25198 Lleida, Spain
| | - D. Gallardo
- Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - M. D. Guàrdia
- IRTA, Tecnologia dels Aliments, Finca Camps i Armet, 17121 Monells, Spain
| | - J. Reixach
- Selección Batallé SA, Av. Segadors s/n, 17421 Riudarenes, Spain
| | - J. Arnau
- IRTA, Tecnologia dels Aliments, Finca Camps i Armet, 17121 Monells, Spain
| | - M. Amills
- Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - R. Quintanilla
- IRTA, Genètica i Millora Animal, 191 Av. Rovira Roure, 25198 Lleida, Spain
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24
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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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25
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Moradi Marjaneh M, Martin ICA, Kirk EP, Harvey RP, Moran C, Thomson PC. QTL mapping of complex binary traits in an advanced intercross line. Anim Genet 2012; 43 Suppl 1:97-101. [PMID: 22742507 DOI: 10.1111/j.1365-2052.2012.02383.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
An advanced intercross line (AIL) is an easier and more cost-effective approach compared to recombinant inbred lines for fine mapping of quantitative trait loci (QTL) identified by F(2) designs. In an AIL, a complex binary trait can be mapped through analysis of either continuously distributed proxy traits for the liability of the binary trait or the liability itself, the latter presenting the greater statistical challenge. In another work, we successfully applied both approaches in an AIL to fine map previously identified QTL underlying anatomical parameters of the cardiac inter-atrial septum including patent foramen ovale. Here, we describe the statistical methods that we used to analyse complex binary traits in our AIL design. This is achieved using a likelihood-based method, with the expectation-maximisation algorithm allowing use of standard logistic regression methods for model fitting.
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Affiliation(s)
- M Moradi Marjaneh
- Victor Chang Cardiac Research Institute, Darlinghurst 2010, NSW, Australia
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26
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Functional and association studies on the pig HMGCR gene, a cholesterol-synthesis limiting enzyme. Animal 2012; 4:224-33. [PMID: 22443876 DOI: 10.1017/s1751731109991145] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
The 3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR) is the rate-limiting enzyme in the biosynthesis of cholesterol. We have studied the role of the HMGCR gene in pig lipid metabolism by means of expression and structural analysis. We describe here the complete coding region of this gene in pigs and report two synonymous single nucleotide polymorphisms in the coding region. We have, additionally, studied the association of one of these polymorphisms (HMGCR:c.807A>C) with several lipid deposition- and cholesterol-related traits in a half-sib population generated from a commercial Duroc line, showing in some families a positive relationship of HMGCR:c.807A allele with serum low-density lipoprotein (LDL)-bound cholesterol and triglyceride levels, and also with intramuscular fat (IMF) content of gluteus medius muscle. We have also assessed the expression levels in muscle and in liver from 68 Duroc individuals corresponding to the most extreme animals for the analysed traits. Liver HMGCR expression correlated negatively with the serum high-density lipoprotein (HDL) levels, carcass lean percentage and stearic acid content, while muscle expression correlated also negatively with the carcass lean percentage, stearic and linoleic acids content, but showed a positive correlation with the serum lipid cholesterol (HDL, LDL and total cholesterol), IMF and muscle oleic and palmitic fatty acid content. With this information, we have performed an association analysis of expression data with lipid metabolism phenotypic levels and the HMGCR genotype. The results indicate that HMGCR expression levels in muscle are different in the two groups of pigs with extreme values for fat deposition and total cholesterol levels, and also between animals with the different HMGCR genotypes.
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27
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28
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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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29
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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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30
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Yoo CK, Cho IC, Lee JB, Jung EJ, Lim HT, Han SH, Lee SS, Ko MS, Kang T, Hwang JH, Park YS, Park HB. QTL analysis of clinical-chemical traits in an F₂ intercross between Landrace and Korean native pigs. Physiol Genomics 2012; 44:657-68. [PMID: 22496488 DOI: 10.1152/physiolgenomics.00172.2011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Clinical-chemical traits are essential when examining the health status of individuals. The aim of this study was to identify quantitative trait loci (QTL) and the associated positional candidate genes affecting clinical-chemical traits in a reciprocal F(2) intercross between Landrace and Korean native pigs. Following an overnight fast, 25 serum phenotypes related to clinical-chemical traits (e.g., hepatic function parameters, renal function parameters, electrolyte, lipids) were measured in >970 F(2) progeny. All experimental samples were subjected to genotyping analysis using 165 microsatellite markers located across the genome. We identified eleven genome-wide significant QTL in six chromosomal regions (SSC 2, 7, 8, 13, 14, and 15) and 59 suggestive QTL in 17 chromosomal regions (SSC 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, and 18). We also observed significant effects of reciprocal crosses on some of the traits, which would seem to result from maternal effect, QTL on sex chromosomes, imprinted genes, or genetic difference in mitochondrial DNA. The role of genomic imprinting in clinical-chemical traits also was investigated. Genome-wide analysis revealed a significant evidence for an imprinted QTL in SSC4 affecting serum amylase levels. Additionally, a series of bivariate linkage analysis provided strong evidence that QTL in SSC 2, 13, 15, and 18 have a pleiotropic effect on clinical-chemical traits. In conclusion, our study detected both novel and previously reported QTL influencing clinical-chemical traits in pigs. The identified QTL together with the positional candidate genes identified here could play an important role in elucidating the genetic structure of clinical-chemical phenotype variation in humans and swine.
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Affiliation(s)
- Chae-Kyoung Yoo
- Animal Science Major, Division of Applied Life Science (Brain Korea 21 Program) Gyeongsang National University, Jinju, Korea
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31
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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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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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Tomás A, Ramírez O, Casellas J, Muñoz G, Sánchez A, Barragán C, Arqué M, Riart I, Óvilo C, Noguera JL, Amills M, Rodríguez C. Quantitative trait loci for fatness at growing and reproductive stages in Iberian × Meishan F(2) sows. Anim Genet 2011; 42:548-51. [PMID: 21906106 DOI: 10.1111/j.1365-2052.2010.02169.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
A considerable number of fatness QTL have been identified in growing pigs, but there is a lack of knowledge about the genetic architecture of this trait in gilts and sows. We have performed a genome scan, in 255 Iberian × Meishan F(2) sows, for backfat thickness (BF) at 150 (BF(150) ) and 210 (BF(210)) days of age, 30 days after conception (BF(30)) and 7-10 days before farrowing (BF(bf)). We have found one BF150 QTL in SSC6 (120 cM) that was highly significant (P < 0.001) at the chromosome-wide level and suggestive at the genome-wide level (P < 0.1). Ten additional chromosome-wide significant QTL were found for sow BF(150) (SSC1, SSC13), BF(210) (SSC6, SSC8, SSC15), BF(30) (SSC5, SSC6) and BF(bf) (SSC1, SSC6, SSC13). The location of several of the BF QTL varied depending on the growing and reproductive status of the sow, suggesting that part of these genetic effects may have a temporal pattern of phenotypic expression.
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Affiliation(s)
- A Tomás
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
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Casellas J, Noguera JL, Reixach J, Díaz I, Amills M, Quintanilla R. Bayes factor analyses of heritability for serum and muscle lipid traits in Duroc pigs1. J Anim Sci 2010; 88:2246-54. [DOI: 10.2527/jas.2009-2205] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Cánovas A, Quintanilla R, Amills M, Pena RN. Muscle transcriptomic profiles in pigs with divergent phenotypes for fatness traits. BMC Genomics 2010; 11:372. [PMID: 20540717 PMCID: PMC2894043 DOI: 10.1186/1471-2164-11-372] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 06/11/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Selection for increasing intramuscular fat content would definitively improve the palatability and juiciness of pig meat as well as the sensorial and organoleptic properties of cured products. However, evidences obtained in human and model organisms suggest that high levels of intramuscular fat might alter muscle lipid and carbohydrate metabolism. We have analysed this issue by determining the transcriptomic profiles of Duroc pigs with divergent phenotypes for 13 fatness traits. The strong aptitude of Duroc pigs to have high levels of intramuscular fat makes them a valuable model to analyse the mechanisms that regulate muscle lipid metabolism, an issue with evident implications in the elucidation of the genetic basis of human metabolic diseases such as obesity and insulin resistance. RESULTS Muscle gene expression profiles of 68 Duroc pigs belonging to two groups (HIGH and LOW) with extreme phenotypes for lipid deposition and composition traits have been analysed. Microarray and quantitative PCR analysis showed that genes related to fatty acid uptake, lipogenesis and triacylglycerol synthesis were upregulated in the muscle tissue of HIGH pigs, which are fatter and have higher amounts of intramuscular fat than their LOW counterparts. Paradoxically, lipolytic genes also showed increased mRNA levels in the HIGH group suggesting the existence of a cycle where triacylglycerols are continuously synthesized and degraded. Several genes related to the insulin-signalling pathway, that is usually impaired in obese humans, were also upregulated. Finally, genes related to antigen-processing and presentation were downregulated in the HIGH group. CONCLUSION Our data suggest that selection for increasing intramuscular fat content in pigs would lead to a shift but not a disruption of the metabolic homeostasis of muscle cells. Future studies on the post-translational changes affecting protein activity or expression as well as information about protein location within the cell would be needed to to elucidate the effects of lipid deposition on muscle metabolism in pigs.
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Affiliation(s)
- Angela Cánovas
- IRTA, Genètica i Millora Animal, 191 Av Alcalde Rovira Roure, 25198 Lleida, Spain
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Switonski M, Stachowiak M, Cieslak J, Bartz M, Grzes M. Genetics of fat tissue accumulation in pigs: a comparative approach. J Appl Genet 2010; 51:153-68. [DOI: 10.1007/bf03195724] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Current world literature. Curr Opin Lipidol 2010; 21:148-52. [PMID: 20616627 DOI: 10.1097/mol.0b013e3283390e49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Current world literature. Curr Opin Endocrinol Diabetes Obes 2010; 17:177-85. [PMID: 20190584 DOI: 10.1097/med.0b013e3283382286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Cánovas E, Quintanilla R, Badaoui B, Porredón C, Gallardo D, Pena R, Díaz I, Amills M. Pig HDL-binding protein (HDLBP) genotype is associated with intramuscular fat percentage. Livest Sci 2009. [DOI: 10.1016/j.livsci.2009.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Gallardo D, Quintanilla R, Varona L, Díaz I, Ramírez O, Pena RN, Amills M. Polymorphism of the pigacetyl-coenzyme A carboxylase αgene is associated with fatty acid composition in a Duroc commercial line. Anim Genet 2009; 40:410-7. [DOI: 10.1111/j.1365-2052.2009.01854.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Pena RN, Cánovas A, Varona∗ L, Díaz I, Gallardo D, Ramírez O, Noguera JL, Quintanilla R. Nucleotide Sequence and Association Analysis of Pig Apolipoprotein-B and LDL-Receptor Genes. Anim Biotechnol 2009; 20:110-23. [DOI: 10.1080/10495390902892518] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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A genome-wide scan for quantitative trait loci affecting serum glucose and lipids in a White Duroc × Erhualian intercross F2 population. Mamm Genome 2009; 20:386-92. [DOI: 10.1007/s00335-009-9190-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Accepted: 05/05/2009] [Indexed: 11/26/2022]
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