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Casto-Rebollo C, Argente MJ, García ML, Pena RN, Blasco A, Ibáñez-Escriche N. Selection for environmental variance shifted the gut microbiome composition driving animal resilience. Microbiome 2023; 11:147. [PMID: 37400907 DOI: 10.1186/s40168-023-01580-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/23/2023] [Indexed: 07/05/2023]
Abstract
BACKGROUND Understanding how the host's microbiome shapes phenotypes and participates in the host response to selection is fundamental for evolutionists and animal and plant breeders. Currently, selection for resilience is considered a critical step in improving the sustainability of livestock systems. Environmental variance (V E), the within-individual variance of a trait, has been successfully used as a proxy for animal resilience. Selection for reduced V E could effectively shift gut microbiome composition; reshape the inflammatory response, triglyceride, and cholesterol levels; and drive animal resilience. This study aimed to determine the gut microbiome composition underlying the V E of litter size (LS), for which we performed a metagenomic analysis in two rabbit populations divergently selected for low (n = 36) and high (n = 34) V E of LS. Partial least square-discriminant analysis and alpha- and beta-diversity were computed to determine the differences in gut microbiome composition among the rabbit populations. RESULTS We identified 116 KEGG IDs, 164 COG IDs, and 32 species with differences in abundance between the two rabbit populations studied. These variables achieved a classification performance of the V E rabbit populations of over than 80%. Compared to the high V E population, the low V E (resilient) population was characterized by an underrepresentation of Megasphaera sp., Acetatifactor muris, Bacteroidetes rodentium, Ruminococcus bromii, Bacteroidetes togonis, and Eggerthella sp. and greater abundances of Alistipes shahii, Alistipes putredinis, Odoribacter splanchnicus, Limosilactobacillus fermentum, and Sutterella, among others. Differences in abundance were also found in pathways related to biofilm formation, quorum sensing, glutamate, and amino acid aromatic metabolism. All these results suggest differences in gut immunity modulation, closely related to resilience. CONCLUSIONS This is the first study to show that selection for V E of LS can shift the gut microbiome composition. The results revealed differences in microbiome composition related to gut immunity modulation, which could contribute to the differences in resilience among rabbit populations. The selection-driven shifts in gut microbiome composition should make a substantial contribution to the remarkable genetic response observed in the V E rabbit populations. Video Abstract.
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Affiliation(s)
- Cristina Casto-Rebollo
- Institute for Animal Science and Technology, Universitat Politècnica de València, València, Spain
| | - María José Argente
- Centro de Investigación e Innovación Agroalimentaria Y Agroambiental (CIAGRO_UMH), Miguel Hernández University, Orihuela, 03312, Spain
| | - María Luz García
- Centro de Investigación e Innovación Agroalimentaria Y Agroambiental (CIAGRO_UMH), Miguel Hernández University, Orihuela, 03312, Spain
| | - Ramona Natacha Pena
- Departament de Ciència Animal, Universitat de Lleida-AGROTECNIO Center, Lleida, Catalonia, Spain
| | - Agustín Blasco
- Institute for Animal Science and Technology, Universitat Politècnica de València, València, Spain
| | - Noelia Ibáñez-Escriche
- Institute for Animal Science and Technology, Universitat Politècnica de València, València, Spain.
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Laghouaouta H, Fraile L, Suárez-Mesa R, Ros-Freixedes R, Estany J, Pena RN. A genome-wide screen for resilient responses in growing pigs. Genet Sel Evol 2022; 54:50. [PMID: 35787790 PMCID: PMC9251948 DOI: 10.1186/s12711-022-00739-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 06/21/2022] [Indexed: 11/18/2022] Open
Abstract
Background There is a growing interest to decipher the genetic background of resilience and its possible improvement through selective breeding. The objective of the present study was to provide new insights into the genetic make-up of resilience in growing pigs by identifying genomic regions and candidate genes associated with resilience indicators. Commercial Duroc pigs were challenged with an attenuated Aujeszky vaccine at 12 weeks of age. Two resilience indicators were used: deviation from the expected body weight at 16 weeks of age given the growth curve of non-vaccinated pigs (∆BW) and the increase in acute-phase protein haptoglobin at four days post-vaccination (∆HP). Genome-wide association analyses were carried out on 445 pigs, using genotypes at 41,165 single nucleotide polymorphisms (SNPs) and single-marker and Bayesian multiple-marker regression approaches. Results Genomic regions on pig chromosomes 2, 8, 9, 11 (∆BW) and 8, 9, 13 (∆HP) were found to be associated with the resilience indicators and explained high proportions of their genetic variance. The genomic regions that were associated explained 27 and 5% of the genetic variance of ∆BW and ∆HP, respectively. These genomic regions harbour promising candidate genes that are involved in pathways related to immune response, response to stress, or signal transduction (CD6, PTGDR2, IKZF1, RNASEL and MYD88), and growth (GRB10 and LCORL). Conclusions Our study identified novel genomic regions that are associated with two resilience indicators (∆BW and ∆HP) in pigs. These associated genomic regions harbour potential candidate genes involved in immune response and growth pathways, which emphasise the strong relationship between resilience and immune response. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-022-00739-1.
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Affiliation(s)
- Houda Laghouaouta
- Department of Animal Science, University of Lleida-Agrotecnio-CERCA Center, 25198, Lleida, Catalonia, Spain
| | - Lorenzo Fraile
- Department of Animal Science, University of Lleida-Agrotecnio-CERCA Center, 25198, Lleida, Catalonia, Spain
| | - Rafael Suárez-Mesa
- Department of Animal Science, University of Lleida-Agrotecnio-CERCA Center, 25198, Lleida, Catalonia, Spain
| | - Roger Ros-Freixedes
- Department of Animal Science, University of Lleida-Agrotecnio-CERCA Center, 25198, Lleida, Catalonia, Spain
| | - Joan Estany
- Department of Animal Science, University of Lleida-Agrotecnio-CERCA Center, 25198, Lleida, Catalonia, Spain
| | - Ramona Natacha Pena
- Department of Animal Science, University of Lleida-Agrotecnio-CERCA Center, 25198, Lleida, Catalonia, Spain.
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Abella G, Pagès-Bernaus A, Estany J, Pena RN, Fraile L, Plà-Aragonés LM. Using PRRSV-Resilient Sows Improve Performance in Endemic Infected Farms with Recurrent Outbreaks. Animals (Basel) 2021; 11:ani11030740. [PMID: 33800382 PMCID: PMC8001314 DOI: 10.3390/ani11030740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/03/2021] [Accepted: 03/05/2021] [Indexed: 01/01/2023] Open
Abstract
Simple Summary Porcine reproductive and respiratory syndrome (PRRS) is a viral disease responsible for huge economic losses to the pig industry. The selection of PRRSV resilient sows has been proposed as a strategy to control this disease. A simulation model was developed to test the differences in reproductive performance and economic outcome of resilient or susceptible sows under farm PRRSV endemic conditions with or without recurrent PRRSV outbreaks. The data from phenotyped sows came from a PRRSV-positive farm with 1500 sows that suffered a PRRSV outbreak that lasted 24 weeks within three years. The reproductive parameters were generally better for resilient than for susceptible sows in PRRSV-positive farms suffering recurrent PRRSV outbreaks. Consequently, the piglet production cost was lower for resilient than for susceptible sows in any condition but showed only significant differences in PRRSV endemic farms suffering recurrent outbreaks. Finally, the annual gross margin by sow is significantly better for resilient than for susceptible sows under endemic conditions with or without recurrent outbreaks. Thus, the selection of PRRSV resilient sows is always a profitable approach for producers supporting the control of this disease. Abstract The selection of porcine reproductive and respiratory syndrome (PRRS) resilient sows has been proposed as a strategy to control this disease. A discrete event-based simulation model was developed to mimic the outcome of farms with resilient or susceptible sows suffering recurrent PRRSV outbreaks. Records of both phenotypes were registered in a PRRSV-positive farm of 1500 sows during three years. The information was split in the whole period of observation to include a PRRSV outbreak that lasted 24 weeks (endemic/epidemic or En/Ep) or only the endemic phase (En). Twenty simulations were modeled for each farm: Resilient/En, Resilient/En_Ep, Susceptible/En, and Susceptible/En_Ep during twelve years and analyzed for the productive performance and economic outcome, using reference values. The reproductive parameters were generally better for resilient than for susceptible sows in the PRRSV En/Ep scenario, and the contrary was observed in the endemic case. The piglet production cost was always lower for resilient than for susceptible sows but showed only significant differences in the PRRSV En/Ep scenario. Finally, the annual gross margin by sow is significantly better for resilient than for susceptible sows for the PRRSV endemic (12%) and endemic/epidemic scenarios (17%). Thus, the selection of PRRSV resilient sows is a profitable approach for producers to improve disease control.
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Affiliation(s)
- Gloria Abella
- Department of Animal Science, University of Lleida, 25198 Lleida, Spain; (G.A.); (J.E.); (R.N.P.)
| | - Adela Pagès-Bernaus
- Department of Mathematics, University of Lleida, 25001 Lleida, Spain; (A.P.-B.); (L.M.P.-A.)
- Department of Business Administration, University of Lleida, 25001 Lleida, Spain
| | - Joan Estany
- Department of Animal Science, University of Lleida, 25198 Lleida, Spain; (G.A.); (J.E.); (R.N.P.)
- AGROTECNIO CERCA Center, 25198 Lleida, Spain
| | - Ramona Natacha Pena
- Department of Animal Science, University of Lleida, 25198 Lleida, Spain; (G.A.); (J.E.); (R.N.P.)
- AGROTECNIO CERCA Center, 25198 Lleida, Spain
| | - Lorenzo Fraile
- Department of Animal Science, University of Lleida, 25198 Lleida, Spain; (G.A.); (J.E.); (R.N.P.)
- AGROTECNIO CERCA Center, 25198 Lleida, Spain
- Correspondence: ; Tel.: +34-973702814
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Villaplana-Velasco A, Noguera JL, Pena RN, Ballester M, Muñoz L, González E, Tejeda JF, Ibáñez-Escriche N. Comparative Transcriptome Profile between Iberian Pig Varieties Provides New Insights into Their Distinct Fat Deposition and Fatty Acids Content. Animals (Basel) 2021; 11:ani11030627. [PMID: 33673436 PMCID: PMC7997154 DOI: 10.3390/ani11030627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 11/16/2022] Open
Abstract
The high deposition of intramuscular fat and the content of oleic fatty acid are characteristic of the Iberian pig. These two parameters present great variability and are differentiated amongst the varieties that make up the Iberian pig population. Although previous studies generated evidence for causal genes and polymorphisms associated to the adipogenic potential of the Iberian pig, there is little information about how genetic expression influences this trait's variability. The aim of this study was to analyses the expression profile between two varieties of Iberian pig (Torbiscal and Retinto) and their reciprocal crosses differentiated in their intramuscular fat (IMF) content and fatty acid (FA) composition in the Longissimus thoracis muscle using an RNA-seq approach. Our results corroborate that the Retinto variety is the fattiest amongst all studied varieties as its upregulated genes, such as FABP3 and FABP5, SLC27A1 and VEGFA among others, contribute to increasing adiposity. In its turn, Torbiscal pigs showed an upregulation of genes associated with the inhibition of fat deposition such as ADIPOQ and CPT1A. Further genetic variation analysis in these Iberian varieties showed relevant associations for SNP located within the differentially expressed genes with IMF and FA content. Thus, the differences found in the genetic architecture and the muscle transcriptome of these Iberian varieties might explain the variability in their fat content and composition and hence, their meat quality.
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Affiliation(s)
- Ana Villaplana-Velasco
- Genetics and Genomics, The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, Edinburgh EH25 9RG, UK;
- Centre for Medical Informatics, Usher Institute, The University of Edinburgh, 9 Little France Road, Edinburgh EH16 4UX, UK
| | | | - Ramona Natacha Pena
- Departament de Ciència Animal, Universitat de Lleida-Agrotecnio Center, 25198 Lleida, Spain;
| | - Maria Ballester
- Animal Breeding and Genetics Program, IRTA, Torre Marimon, 08140 Caldes de Montbui, Spain;
| | | | - Elena González
- Department of Animal Production and Food Science, Research University Institute of Agricultural Resources (INURA), Escuela de Ingenierías Agrarias, Universidad de Extremadura, 06007 Badajoz, Spain; (E.G.); (J.F.T.)
| | - Juan Florencio Tejeda
- Department of Animal Production and Food Science, Research University Institute of Agricultural Resources (INURA), Escuela de Ingenierías Agrarias, Universidad de Extremadura, 06007 Badajoz, Spain; (E.G.); (J.F.T.)
| | - Noelia Ibáñez-Escriche
- Department for Animal Science and Tecnology, Universistat Politécnica de València, 46022 Valencia, Spain
- Correspondence: ; Tel.: +34-963-877-438
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Laplana M, Estany J, Fraile LJ, Pena RN. Resilience Effects of SGK1 and TAP1 DNA Markers during PRRSV Outbreaks in Reproductive Sows. Animals (Basel) 2020; 10:E902. [PMID: 32456052 PMCID: PMC7278433 DOI: 10.3390/ani10050902] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/14/2020] [Accepted: 05/19/2020] [Indexed: 12/13/2022] Open
Abstract
The porcine reproductive and respiratory syndrome virus (PRRSV) is a major infectious stressor that causes serious health problems and productivity drops. Based on previous genome-wide analyses, we selected SGK1 and TAP1 as candidate genes for resilience, and genotyped three mutations, including a 3'UTR variant SGK1_rs338508371 and two synonymous variants TAP1_rs1109026889 and TAP1_rs80928141 in 305 Landrace × Large White sows. All polymorphisms affected the reproductive performance in the outbreak, but not during the endemic phase, thereby indicating a potential use of these markers for resilience. Moreover, some genotypes were associated with a stable performance across PRRSV phases. Thus, in the outbreak, the SGK1_rs338508371 AA sows had less piglets born alive (p < 0.0001) and more stillborns (p < 0.05) while other sows were able to keep their productivity. During the outbreak, TAP1_rs80928141 GG sows had less piglets born alive (p < 0.05) and both TAP1 polymorphisms influenced the number of mummies in an additive manner (p < 0.05). Remarkably, TAP1_rs80928141 AA sows had around one mummy more than GG sows (p < 0.01). Resilience to PRRSV could be improved by including the SGK1 and TAP1 markers in crossbreeding and/or selection schemes, as they contribute to maintaining a stable number of piglets born alive and lost, particularly mummies, despite the outbreak.
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Affiliation(s)
| | | | | | - Ramona Natacha Pena
- Departament de Ciència Animal, Universitat de Lleida–AGROTECNIO Centre, 25198 Lleida, Spain; (M.L.); (J.E.); (L.J.F.)
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Fraile L, Fernández N, Pena RN, Balasch S, Castellà G, Puig P, Estany J, Valls J. A probabilistic Poisson-based model to detect PRRSV recirculation using sow production records. Prev Vet Med 2020; 177:104948. [PMID: 32172020 DOI: 10.1016/j.prevetmed.2020.104948] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 02/29/2020] [Accepted: 03/04/2020] [Indexed: 11/17/2022]
Abstract
Porcine reproductive and respiratory syndrome (PRRS) is a viral disease associated with a decrease in the number of born alive piglets (NBA) and an increase in the number of lost piglets (NLP) per farrowing. Under practical conditions, it is critical to assess whether a farm is suffering PRRSV recirculation in the sow herd as soon as possible. The aim of this research work was to develop a new method to detect potential PRRSV recirculation in sow production farms. Sow reproductive performance records from one farm (farm T) were used to set up the method and records from ten additional farms (farms V1 to V10) were used for validation. A conditional Poisson model of NLP on NBA was proposed to fit the data. A three-step procedure was implemented to detect potential PRRSV recirculation: (i) computation of the maximum-likelihood estimates of the expected values of NBA and NLP in a PRRSV non-recirculating scenario; (ii) calculation, for each farrowing, of the p-value associated with the probability of jointly observing deviations towards decreased NBA and increased NLP. The detection of a potential PRRSV recirculation was based on (iii) the combined p-value resulting from weighing the p-values of the last N farrowings by the chi-square-inverse method. In order to gain specificity, a displacement on the expected non-recirculating NBA and NLP values was used for tuning purposes. With this approach, two PRRSV circulating periods were detected in farm T, which were confirmed with standard laboratorial diagnostic techniques. The method was subsequently validated in farms V1 to V10, where ten PRRSV-recirculating time episodes had been diagnosed. The method proposed here was able to detect the ten PRRSV recirculations using a relatively small set of contiguous farrowings, with only two mismatched weeks, one as a false negative, in farm V1, and one as a false positive, in farm V4. It is concluded that a conditional Poisson-based model of NLP on NBA can be a useful tool for routinely detecting PRRSV recirculation in sow herds.
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Affiliation(s)
- L Fraile
- Department of Animal Science, University of Lleida - Agrotecnio Center, Lleida, Spain.
| | - N Fernández
- Biostatistics and Epidemiology Unit, Biomedical Research Institute of Lleida (IRB Lleida), Lleida, Spain
| | - R N Pena
- Department of Animal Science, University of Lleida - Agrotecnio Center, Lleida, Spain
| | - S Balasch
- Department of Applied Statistics and Operational Research, Universitat Politècnica de Valencia, Valencia, Spain
| | - G Castellà
- Biostatistics and Epidemiology Unit, Biomedical Research Institute of Lleida (IRB Lleida), Lleida, Spain
| | - P Puig
- Department of Mathematics, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - J Estany
- Department of Animal Science, University of Lleida - Agrotecnio Center, Lleida, Spain
| | - J Valls
- Biostatistics and Epidemiology Unit, Biomedical Research Institute of Lleida (IRB Lleida), Lleida, Spain; Department of Mathematics, Universitat Autònoma de Barcelona, Barcelona, Spain
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González-Prendes R, Pena RN, Solé E, Seradj AR, Estany J, Ramayo-Caldas Y. Modulatory Effect of Protein and Carotene Dietary Levels on Pig gut Microbiota. Sci Rep 2019; 9:14582. [PMID: 31601914 PMCID: PMC6787051 DOI: 10.1038/s41598-019-51136-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 09/20/2019] [Indexed: 12/16/2022] Open
Abstract
In this study we investigated the impact of dietary protein and carotene levels on microbial functions and composition during the last month of purebred fattening Duroc pigs. Fecal microbiota was characterized using 16S ribosomal RNA sequencing at two points of live, 165 (T1) and 195 (T2) days. From 70 to 165 days of age, 32 pigs were divided into two groups fed either a standard-protein (SP) or a low-protein (LP) diet. In the last month (165-195 days), all pigs received a LP diet, either carotene-enriched (CE) or not (NC). Significant differences were observed between T1 and T2 at Amplicon Sequences Variants (ASVs), phylum and genus levels. In T1 group, Prevotella, Faecalibacterium and Treponema were the genera most influenced by dietary protein, together with predicted functions related with the degradation of protein. In contrast, the CE diet did not impact the microbiome diversity, although 160 ASVs were differentially abundant between CE and NC groups at T2. Weak stability of enterotype clusters across time-points was observed as consequence of medium-term dietary interventions. Our results suggest that during the last month of fattening, dietary protein have a stronger effect than carotenes on the modulation of the compositional and functional structure of the pig microbiota.
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Affiliation(s)
- Rayner González-Prendes
- Departament de Ciència Animal, Universitat de Lleida-Agrotecnio Centre, Lleida, 25198, Catalonia, Spain
- Animal Breeding and Genomics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Ramona Natacha Pena
- Departament de Ciència Animal, Universitat de Lleida-Agrotecnio Centre, Lleida, 25198, Catalonia, Spain
| | - Emma Solé
- Departament de Ciència Animal, Universitat de Lleida-Agrotecnio Centre, Lleida, 25198, Catalonia, Spain
| | - Ahmad Reza Seradj
- Departament de Ciència Animal, Universitat de Lleida-Agrotecnio Centre, Lleida, 25198, Catalonia, Spain
| | - Joan Estany
- Departament de Ciència Animal, Universitat de Lleida-Agrotecnio Centre, Lleida, 25198, Catalonia, Spain.
| | - Yuliaxis Ramayo-Caldas
- Animal Breeding and Genetics Program, IRTA, Torre Marimon, Caldes de Montbui, Catalonia, Spain
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Pena RN, Noguera JL, García-Santana MJ, González E, Tejeda JF, Ros-Freixedes R, Ibáñez-Escriche N. Five genomic regions have a major impact on fat composition in Iberian pigs. Sci Rep 2019; 9:2031. [PMID: 30765794 PMCID: PMC6375979 DOI: 10.1038/s41598-019-38622-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 12/18/2018] [Indexed: 12/22/2022] Open
Abstract
The adipogenic nature of the Iberian pig defines many quality attributes of its fresh meat and dry-cured products. The distinct varieties of Iberian pig exhibit great variability in the genetic parameters for fat deposition and composition in muscle. The aim of this work is to identify common and distinct genomic regions related to fatty acid composition in Retinto, Torbiscal, and Entrepelado Iberian varieties and their reciprocal crosses through a diallelic experiment. In this study, we performed GWAS using a high density SNP array on 382 pigs with the multimarker regression Bayes B method implemented in GenSel. A number of genomic regions showed strong associations with the percentage of saturated and unsaturated fatty acid in intramuscular fat. In particular, five regions with Bayes Factor >100 (SSC2 and SSC7) or >50 (SSC2 and SSC12) explained an important fraction of the genetic variance for miristic, palmitoleic, monounsaturated (>14%), oleic (>10%) and polyunsaturated (>5%) fatty acids. Six genes (RXRB, PSMB8, CHGA, ACACA, PLIN4, PLIN5) located in these regions have been investigated in relation to intramuscular composition variability in Iberian pigs, with two SNPs at the RXRB gene giving the most consistent results on oleic and monounsaturated fatty acid content.
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Affiliation(s)
- R N Pena
- Departament de Ciència Animal, Universitat de Lleida-Agrotecnio Center, 25198, Lleida, Spain
| | - J L Noguera
- IRTA, Genètica i Millora Animal, 25198, Lleida, Spain
| | | | - E González
- Tecnología de los alimentos, Universidad de Extremadura, 06006, Badajoz, Spain
| | - J F Tejeda
- Tecnología de los alimentos, Universidad de Extremadura, 06006, Badajoz, Spain
| | - R Ros-Freixedes
- Departament de Ciència Animal, Universitat de Lleida-Agrotecnio Center, 25198, Lleida, Spain.,The Roslin Institute, Edinburgh University, Easter Bush, EH25 9RG, UK
| | - N Ibáñez-Escriche
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022, Valencia, Spain.
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Estany J, Ros-Freixedes R, Tor M, Pena RN. TRIENNIAL GROWTH AND DEVELOPMENT SYMPOSIUM: Genetics and breeding for intramuscular fat and oleic acid content in pigs. J Anim Sci 2017; 95:2261-2271. [PMID: 28727022 DOI: 10.2527/jas.2016.1108] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The intramuscular fat (IMF) and oleic acid (OL) content have been favorably related to pork quality and human health. This influences the purchasing behavior of consumers and, therefore, also shifts the attention of breeding companies toward whether these traits are included into the breeding goal of the lines producing for high-valued markets. Because IMF and OL are unfavorably associated with lean content, a key economic trait, the real challenge for the industry is not simply to increase IMF and OL, but rather to come up with the right trade-off between them and lean content. In this paper we review the efforts performed to genetically improve IMF and OL, with particular reference to the research we conducted in a Duroc line aimed at producing high quality fresh and dry-cured pork products. Based on this research, we conclude that there are selection strategies that lead to response scenarios where IMF, OL, and lean content can be simultaneously improved. Such scenarios involve regular recording of IMF and OL, so that developing a cost-efficient phenotyping system for these traits is paramount. With the economic benefits of genomic selection needing further assessment in pigs, selection on a combination of pedigree-connected phenotypes and genotypes from a panel of selected genetic markers is presented as a suitable alternative. Evidence is provided supporting that at least a polymorphism in the leptin receptor and another in the stearoyl-CoA desaturase genes should be in that panel. Selection for IMF and OL results in an opportunity cost on lean growth. The extent to which it is affordable relies on the consumers' willingness to pay for premium products and on the cost to benefit ratio of alternative management strategies, such as specific dietary manipulations. How the genotype can influence the effect of the diet on IMF and OL remains a topic for further research.
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Henriquez-Rodriguez E, Pena RN, Seradj AR, Fraile L, Christou P, Tor M, Estany J. Carotenoid intake and SCD genotype exert complementary effects over fat content and fatty acid composition in Duroc pigs. J Anim Sci 2017; 95:2547-2557. [PMID: 28727051 DOI: 10.2527/jas.2016.1350] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Nutritional and genetic strategies are needed to enhance intramuscular fat (IMF) and MUFA content without altering carcass leanness. Dietary vitamin A restriction has been suggested to specifically promote IMF, whereas a polymorphism of the () gene has shown to specifically increase MUFA. The purpose of this study was to investigate the combined effects of provitamin A (PVA) carotenoid intake and genotype (>) on hepatic retinoid content and on the liver, muscle (LM and gluteus medius [GM]), and subcutaneous fat (SF) content and fatty acid composition. Following a split-plot design, 32 castrated Duroc pigs, half of each of the 2 homozygous genotypes (CC and TT), were subjected from 165 to 195 d of age to 2 finishing diets differing in the PVA carotenoid content (an enriched-carotene diet [C+] and a control diet [C-]). Both diets were identical except for the corn line used in the feed. The C+ was formulated with 20% of a carotenoid-fortified corn (M37W-Ph3) whereas the C- instead used 20% of its near isogenic M37W line, which did not contain PVA carotenoids. No vitamin A was added to the diets. The C- was estimated to provide, at most, 1,300 IU of vitamin A/kg and the C+ to supply an extra amount of at least 800 IU vitamin A/kg. Compared with the pigs fed the C-, pigs fed with C+ had 3-fold more retinoic acid ( < 0.01) and 4-fold more gene expression in the liver ( = 0.06). The diet did not affect performance traits and backfat thickness, but pigs fed the C+ had less fat (4.0 vs. 5.0%; = 0.07) and MUFA (18.3 vs. 22.5%; = 0.01) in the liver, less IMF (5.4 vs. 8.3%; = 0.04) in the GM, and more fat content (90.4 vs. 87.9%; = 0.09) and MUFA (48.0 vs. 46.6%; = 0.04) in SF. The TT genotype at the gene increased MUFA ( < 0.05) in all tissues (21.4 vs. 19.5% in the liver, 55.0 vs. 53.1% in the LM, 53.9 vs. 51.7% in the GM, and 48.0 vs. 46.7% in SF for TT and CC genotypes, respectively). Liver fat and MUFA content nonlinearly declined with liver all- retinoic acid, indicating a saturation point at relatively low all- retinoic acid content. The results obtained provide evidence for a complementary role between dietary PVA and genotype, in the sense that the TT pigs fed with a low-PVA diet are expected to show higher and more monounsaturated IMF without increasing total fat content.
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Henriquez-Rodriguez E, Bosch L, Tor M, Pena RN, Estany J. The effect of SCD and LEPR genetic polymorphisms on fat content and composition is maintained throughout fattening in Duroc pigs. Meat Sci 2016; 121:33-39. [PMID: 27240305 DOI: 10.1016/j.meatsci.2016.05.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 05/18/2016] [Accepted: 05/19/2016] [Indexed: 12/11/2022]
Abstract
The effects of the stearoyl-CoA desaturase (SCD; AY487830:g.2228T>C) and leptin receptor (LEPR; NM_001024587:g.1987C>T) polymorphisms on fat content and fatty acid (FA) composition were investigated throughout fattening. Samples of Longissimus thoracis (LT) and subcutaneous fat (SF) from 214 Duroc barrows were collected from 160days to slaughter age (220days) using a longitudinal design. Results indicated that the positive effect of the T allele at the SCD gene on monounsaturated FA and of the T allele at the LEPR gene on saturated FA are maintained throughout the growing-finishing period, both in LT and SF. In LEPR, however, compositional changes, particularly in SF, are a result of increased fatness. There is very limited evidence of genotype by age interaction, and thus it is concluded that the combined selection for the SCD T and LEPR C alleles is a good strategy to increase the MUFA/SFA ratio regardless of the age at slaughter.
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Affiliation(s)
- E Henriquez-Rodriguez
- Departament de Producció Animal, Universitat de Lleida-Agrotecnio Centre, Rovira Roure 191, 25198 Lleida, Spain
| | - L Bosch
- Departament de Producció Animal, Universitat de Lleida-Agrotecnio Centre, Rovira Roure 191, 25198 Lleida, Spain
| | - M Tor
- Departament de Producció Animal, Universitat de Lleida-Agrotecnio Centre, Rovira Roure 191, 25198 Lleida, Spain
| | - R N Pena
- Departament de Producció Animal, Universitat de Lleida-Agrotecnio Centre, Rovira Roure 191, 25198 Lleida, Spain
| | - J Estany
- Departament de Producció Animal, Universitat de Lleida-Agrotecnio Centre, Rovira Roure 191, 25198 Lleida, Spain.
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Gol S, Estany J, Fraile LJ, Pena RN. Expression profiling of the GBP1 gene as a candidate gene for porcine reproductive and respiratory syndrome resistance. Anim Genet 2015; 46:599-606. [PMID: 26358736 DOI: 10.1111/age.12347] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2015] [Indexed: 12/17/2022]
Abstract
A genomic region in pig chromosome 4 has been previously associated with higher viraemia levels and lower weight gain following porcine reproduction and respiratory syndrome virus (PRRSV) infection. The region includes the marker WUR1000125, a G>A polymorphism next to a putative polyadenylation site in the 3'-untranslated region (3'-UTR) of the guanylate-binding protein 1, interferon-induced (GBP1) gene. The protein encoded by GBP1 is a negative regulator of T-cell responses. We show here that GBP1 expression is lower in liver and tonsils of pigs carrying the WUR1000125-G allele due to differential allele expression (allele A expression is 1.9-fold higher than for allele G). We also show that the GBP1 gene has two active polyadenylation signals 421 bp apart and that polyadenylation usage is dependent on the WUR1000125 genotype. The distal site is the most prevalently used in all samples, but the presence of the A allele favours the generation of shorter transcripts from the proximal site. This is confirmed by a differential allele expression study in AG genotype liver and tonsil samples. The interaction between WUR1000125 and other mutations identified in the 5'- and 3'-UTR regions of this gene needs to be studied. In conclusion, our study indicates that the WUR1000125 mutation is associated with changes in the expression of the negative T-cell regulator GBP1 gene. However, the chromosome 4 locus for PRRSV viraemia levels and weight gain contains a cluster of four other GBP genes that remain to be studied as candidate genes for this QTL.
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Affiliation(s)
- S Gol
- Department of Animal Production, University of Lleida-Agrotecnio Center, 25198, Lleida, Spain
| | - J Estany
- Department of Animal Production, University of Lleida-Agrotecnio Center, 25198, Lleida, Spain
| | - L J Fraile
- Department of Animal Production, University of Lleida-Agrotecnio Center, 25198, Lleida, Spain
| | - R N Pena
- Department of Animal Production, University of Lleida-Agrotecnio Center, 25198, Lleida, Spain
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Balatskyi VN, Saienko AM, Pena RN, Buslyk TV, Gibolenko OS. [THE GENETIC DIVERSITY OF PIG BREEDS ON TEN PRODUCTION QUANTITATIVE TRAITS LOCI]. Tsitol Genet 2015; 49:26-37. [PMID: 26638494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Genetic structure of 11 pig breeds and lines of different origins and production specialization for 10 quantitative traits loci: RYR1, GH, IGF2, CTSL, CTSS, CTSB, CTSK, MC4R, ESR1 & PRLR was analyzed. The results allow us to suppose that the uniqueness of genetic structure of each breed is largely determined by features of the allelic structure of a number of loci. Breeds of different production specialization differ significantly for such QTL, as RYR1, MC4R, ESR1 and IGF2. However, we have found that the loci CTSB, CTSL, CTSK, CTSS and PRLR in most of investigated breeds showed similar distribution of alleles, significant genetic differentiation between breeds and within breeds for these loci is missing. The exception is the Large Black breed for the CTSB locus and Ukrainian steppe spotted breed for the CTSL locus. Also, it can be assumed that allelic structure of some of investigated loci are more connected with the origins of pig breeds than to the selection on production traits. This refers, for example, to the growth hormone gene, the using of which in marker assisted selection could be effective only in some populations. The genetic distance between breeds and lines was defined and the dendrogram of the genetic relationship was built. Breeds are grouped in connection with the production specialization, as well as by their origins.
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Henriquez-Rodriguez E, Tor M, Pena RN, Estany J. A polymorphism in the stearoyl-CoA desaturase gene promoter increases monounsaturated fatty acid content in dry-cured ham. Meat Sci 2015; 106:38-43. [PMID: 25875642 DOI: 10.1016/j.meatsci.2015.03.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 02/09/2015] [Accepted: 03/23/2015] [Indexed: 11/15/2022]
Abstract
Data on 125 dry-cured hams from purebred Duroc pigs were used to examine whether the favorable effect of the T allele in the promoter region of the stearoyl-CoA desaturase gene (AY487830:g.2228T>C) on monounsaturated fatty acid (MUFA) content in green ham is maintained after the curing process. It is shown that pigs carrying the T allele produced dry-cured hams with increased C16:1, C18:1n-9, C18:1n-7, and MUFA and decreased C18:0 and saturated fatty acid (SFA) content. The TT pigs had 1.39% more MUFA and 1.62% less SFA than the CC animals, while gilts had 0.74% more MUFA and 0.34% less SFA than barrows. The correlation between MUFA in green and dry-cured hams (n=53) was high (r=0.88), with TT pigs being more effective in retaining increased MUFA in green hams until the end of the curing period. It is concluded that increasing the presence of the T allele could have more impact than gender to produce hams with a high level of MUFA.
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Affiliation(s)
- E Henriquez-Rodriguez
- Departament de Producció Animal, Universitat de Lleida-Agrotecnio Centre, 191 Rovira Roure Ave, 25198 Lleida, Spain
| | - M Tor
- Departament de Producció Animal, Universitat de Lleida-Agrotecnio Centre, 191 Rovira Roure Ave, 25198 Lleida, Spain
| | - R N Pena
- Departament de Producció Animal, Universitat de Lleida-Agrotecnio Centre, 191 Rovira Roure Ave, 25198 Lleida, Spain
| | - J Estany
- Departament de Producció Animal, Universitat de Lleida-Agrotecnio Centre, 191 Rovira Roure Ave, 25198 Lleida, Spain.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Pena RN, Noguera JL, Casellas J, Díaz I, Fernández AI, Folch JM, Ibáñez-Escriche N. Transcriptional analysis of intramuscular fatty acid composition in the longissimus thoracis muscle of Iberian × Landrace back-crossed pigs. Anim Genet 2013; 44:648-60. [PMID: 23826865 DOI: 10.1111/age.12066] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2013] [Indexed: 11/29/2022]
Abstract
This study aimed at identifying differential gene expression conditional on the fatty acid profile of the longissimus thoracis (Lt) muscle, a prime cut of economic relevance for fresh and cured pork production. A population of 110 Iberian (25%) × Landrace (75%) back-crossed pigs was used, because these two breeds exhibit extreme profiles of intramuscular saturated fatty acid, monounsaturated fatty acid (MUFA) and polyunsaturated fatty acid (PUFA) contents. Total RNA from Lt muscle was individually hybridized to GeneChip Porcine Genome arrays (Affymetrix). A principal component analysis was performed with data from the 110 animals to select 40 extreme animals based on the total fatty acid profile and the MUFA composition (MAP). Comparison of global transcription levels between extreme fatty acid profile pigs (n = 40) resulted in 219 differentially expressed probes (false discovery rate <0.10). Gene ontology, pathway and network analysis indicated that animals with higher percentages of PUFA exhibit a shift toward a more oxidative muscular metabolism state, with a raise in mitochondria function (PPARGC1A, ATF2), fatty acid uptake and oxidation (FABP5, MGLL). On the other hand, 87 probes were differentially expressed between MUFA composition groups (n = 40; false discovery rate <0.10). In particular, muscles rich in n-7 MUFA expressed higher levels of genes involved in lipid metabolism (GLUL, CRAT, PLA2G15) and lower levels of fatty acid elongation genes (ELOVL5). Moreover, the chromosomal position of FABP5, PAQR3, MGLL, PPARGC1A, GLUL and ELOVL5 co-localized with very relevant QTL for fat deposition and composition described in the same resource population. This study represents a complementary approach to identifying genes underlying these QTL effects.
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Affiliation(s)
- R N Pena
- Genètica i Millora Animal, IRTA, 191 Av. Rovira Roure, 25198, Lleida, Spain; Departament de Producció Animal, ETSEA, Universitat de Lleida, 191 Av. Rovira Roure, 25198, Lleida, Spain
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Hernández-Sánchez J, Amills M, Pena RN, Mercadé A, Manunza A, Quintanilla R. Genomic architecture of heritability and genetic correlations for intramuscular and back fat contents in Duroc pigs. J Anim Sci 2012; 91:623-32. [PMID: 23230112 DOI: 10.2527/jas.2012-5270] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genetic parameters such as heritability and correlations of fat traits in a Duroc population were dissected using molecular markers. The heritabilities of intramuscular fat in 2 muscles, the gluteus medius and LM, and back fat were 0.54, 0.48, and 0.23, respectively. The genetic correlations were well estimated with standardized SNP effects, being 0.65 between intramuscular fat traits and ∼0.37 between any intramuscular fat trait and back fat. Genetic correlations were overestimated when ignoring molecular information. Twelve chromosomes showed additive genetic variance for intramuscular fat compared with 8 for back fat. Population structure was accommodated using 4 different models. The number of significant, P < 5 × 10(-5) (suggestive, P < 2 × 10(-3)), SNP varied across models and ranged from 0 to 4 (2 to 261) for intramuscular fat in the gluteus medius, from 0 to 57 (9 to 564) for intramuscular fat in the LM, and from 3 to 4 (22 to 168) for back fat. Several SNP showed significant deviations from an additive mode of action. Only 2 SNP significantly affected 2 traits simultaneously.
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Affiliation(s)
- J Hernández-Sánchez
- IRTA, Genètica i Millora Animal, 191 Av. Alcalde Rovira Roure, 25198 Lleida, Spain.
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Gallardo D, Amills M, Quintanilla R, Pena RN. Mapping and tissue mRNA expression analysis of the pig solute carrier 27A (SLC27A) multigene family. Gene 2012; 515:220-3. [PMID: 23219995 DOI: 10.1016/j.gene.2012.11.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Revised: 10/20/2012] [Accepted: 11/27/2012] [Indexed: 12/31/2022]
Abstract
Solute-carrier family 27A molecules are integral transmembrane proteins that play a fundamental role in the uptake of long-chain fatty acids into mammalian cells. Our goal was to characterize this multigene family in pigs. Chromosomal location of the six porcine SLC27A genes was determined by radiation hybrid mapping and indicated that the six genes map to six different chromosomal locations. Moreover, we analyzed SLC27A mRNA expression in six pig tissues by quantitative RT-PCR. While SLC27A1, SLC27A3 and SLC27A4 were expressed in most, if not all, analyzed tissues, SLC27A2, SLC27A5 and SLC27A6 were predominantly expressed in the liver. In general, pig and human SLC27A mRNA expression profiles were remarkably concordant, although important differences were observed for SLC27A1 and SLC27A6 mRNAs. Discrepancies between mRNA expression profiles have been observed even in closely related primate species, and they might reflect the acquisition of regulatory changes promoting evolutionary adaptation.
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Affiliation(s)
- D Gallardo
- Genètica i Millora Animal, IRTA, Lleida, 25198, Spain
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Pérez-Montarelo D, Fernández A, Folch JM, Pena RN, Ovilo C, Rodríguez C, Silió L, Fernández AI. Joint effects of porcine leptin and leptin receptor polymorphisms on productivity and quality traits. Anim Genet 2012; 43:805-9. [PMID: 22497241 DOI: 10.1111/j.1365-2052.2012.02338.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2011] [Indexed: 11/26/2022]
Abstract
Leptin signalling plays a fundamental role in growth, fatness and body composition. The aim of this study was to investigate the porcine LEP gene sequence in an Iberian × Landrace experimental cross to identify polymorphisms associated with productivity and quality traits. Because of the documented effects on these traits of the LEPR c.1987C>T polymorphism, the LEP and LEPR c.1987C>T polymorphisms and their interactions have been jointly investigated. The LEP gene sequencing has allowed the identification of 39 polymorphisms, eight of which are novel. Three intronic SNPs, LEP g.1382C>T, LEP g.1387C>T and LEP g.1723A>G, have been genotyped, and association analyses have been carried out. Analyses of LEP g.1387C>T, fully linked to LEP g.1382C>T, have revealed additive effects on live and carcass weights and dominant effects on several backfat thickness measurements. Novel effects of both LEP and LEPR polymorphisms on fatty acid composition in subcutaneous fat have been detected, probably mediated through the effects on fatness. The results reported here suggest that the T alleles of both LEP g.1387C>T and LEPR c.1987C>T, which are fixed in the Iberian pigs, would lead to an increase in growth, fatness and saturated fatty acid content in fat, which could be explained by an increased feed intake.
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Martínez-Giner M, Noguera JL, Balcells I, Alves E, Varona L, Pena RN. Expression study on the porcine PTHLH gene and its relationship with sow teat number. J Anim Breed Genet 2011; 128:344-53. [PMID: 21906180 DOI: 10.1111/j.1439-0388.2011.00925.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Teat number is an important trait in sows that should accompany the increase in litter size that has been achieved in the last decades through selection. We have previously identified a genome-wide significant QTL for teat number in porcine chromosome SSC5 by means of an experimental Meishan by Iberian F(2) intercross population. In the present report, we have studied the porcine parathyroid hormone-like hormone (PTHLH) gene, which maps to SSC5, as a candidate gene for this trait, as PTHLH is involved in nipple formation during embryogenesis and nipple development during pregnancy and lactation. We have found that porcine PTHLH gene is transcribed into three mRNA species differing in the 5'UTR region. Two of these variants are reported in pigs here for the first time: one was similar to variant 1 described in humans while the other, which was generated by the retention of two small introns, has not been identified before in any other species. In addition, mRNA expression profile for two of the mRNA variants was assessed in 19 pig tissues. Porcine PTHLH showed a widespread expression as it was present in all tested tissues and relative expression of each variant was tissue dependent. Finally, we have performed an association study between a non-synonymous mutation in the coding region of this gene and sow teat number. The PTHLH polymorphism was segregating in our Meishan by Iberian F(2) population at intermediate allelic frequencies. We compared here six different statistical models to choose the one with a better fit and a lower degree of complexity. However, despite the potential negative effect of the PTHLH mutation in the signal peptide of this protein, we did not detect any association between the PTHLH genotype and the sow teat number phenotype, concluding that the causal mutation of the observed QTL is very likely not related to this gene.
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Affiliation(s)
- M Martínez-Giner
- IRTA, Genètica i Millora Animal, Av Rovira Roure, Lleida, Spain.
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Estellé J, Mercadé A, Pérez-Enciso M, Pena RN, Silió L, Sánchez A, Folch JM. Evaluation of FABP2 as candidate gene for a fatty acid composition QTL in porcine chromosome 8. J Anim Breed Genet 2009; 126:52-8. [PMID: 19207930 DOI: 10.1111/j.1439-0388.2008.00754.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The objective of this work was to analyse the porcine Fatty acid binding protein 2, intestinal (FABP2) gene as a candidate gene for a fatty acid composition quantitative trait loci (QTL) previously described on porcine chromosome 8 in an Iberian by Landrace F(2) cross (IBMAP). Re-sequencing of the porcine FABP2 gene in three Iberian and eight Landrace parental animals resulted in the identification of three single-nucleotide polymorphisms, all of them localized in intron 1. The polymorphism FABP2:g.412T>C, localized in intron 1, and two additional microsatellites were genotyped in the IBMAP population in order to perform an association test of the FABP2 gene and to better define the QTL position previously described. Association analyses of the FABP2:g.412T>C with the fatty acid composition traits were not significant in simple association and marker-assisted association tests, suggesting that the FABP2 region sequenced is not responsible for the QTL. However, the addition of three new markers to the pedigree allowed us to define the S0144-SW61 marker interval as the most likely QTL position, facilitating the future study of other candidate genes for this QTL.
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Affiliation(s)
- J Estellé
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, Spain.
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Babula D, Ruminska M, Sadowski J, Folch JM, Pena RN, Coll A, Sánchez A, Kijas JMH, Andersson L, Kordiš D, Gubenšek F, Majdič G, Snoj T, Horvat A, Mrkun J, Kosec M, Cestnik V, Medrano JF, Johnson A, DePeters EJ, Isias A, Ursič M, Zabavnik J. Abstracts. Pflugers Arch 2000. [DOI: 10.1007/s004240000077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Abstract
Two new variants have been detected and characterized for the goat beta-lactoglobulin gene at the cDNA level and confirmed at the genomic level. The two polymorphisms are located on exon 7 of the gene. One of the polymorphic sites is produced by a single nucleotide substitution in position +4601, allowing a polymerase chain reaction--restriction fragment length polymorphism (PCR-RFLP) genotyping procedure to be developed using SacII restriction enzyme. The other polymorphic position contains a 10 bp long insertion at position +4641 that can be detected by capillary electrophoresis of the PCR product amplified with a fluorescent primer. The association of these two polymorphisms was also investigated, resulting in the description of two new alleles. Both of these contained the point mutation at the SacII site, with or without the 10 bp insertion at position +4641. The distribution of these new polymorphisms was studied in a population of males of four different goat breeds. The gene frequencies for these variants were similar in Spanish and French breeds.
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Affiliation(s)
- R N Pena
- Departament de Patologia i Producció Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, España
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Affiliation(s)
- M H Yahyaoui
- Departament de Patologia i Producció Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, Spain.
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Pena RN, Sánchez A, Coll A, Folch JM. Isolation, sequencing and relative quantitation by fluorescent-ratio PCR of feline beta-lactoglobulin I, II, and III cDNAs. Mamm Genome 1999; 10:560-4. [PMID: 10341085 DOI: 10.1007/s003359901044] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Beta-lactoglobulin (betaLG) is a whey protein found in the milk of most mammals, except those of humans and rodents. In ruminants, only one type of betaLG is expressed in milk, although the presence of pseudogenes has been reported. The milk of other mammals (dog, horse, dolphins) contains two types of betaLG: type I is related to ruminant betaLG, while type II has a strong similarity to the ruminant pseudogenes. The presence of three types of betaLG has been described only in cat milk. For the first time, we have cloned, sequenced, and characterized the three types of feline betaLG cDNAs from a mammary gland sample of a lactating cat. Since no specific probe could be easily used to differentiate them by Northern Blotting, we developed a new technique named Fluorescent-Ratio PCR (FR-PCR) in order to assess their level of expression during lactation. The relative amounts of each feline betaLG cDNA was quantified in two cats by capillary electrophoresis of the restricted RT-PCR product, labeled with fluorescent primers. We observed the same percentage of expression of the three betaLG genes in two cats. The differences of expression could be due to changes in the promoter and 3' non-coding region affecting the level of transcription and the mRNA stability. The FR-PCR technique was shown to be reproducible and accurate even for small percentage differences, being very useful when a small amount of sample is available.
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Affiliation(s)
- R N Pena
- Unitat de Genètica i Millora, Departament de Patologia i Producció Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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Abstract
Different levels of the major milk protein beta-lactoglobulin are found in evolutionarily related ruminant species: with sheep milk containing as much as three times the concentration in goat milk. In an attempt to understand why these differences exist, we have characterised, using DNaseI as a probe of structure, the chromatin surrounding the goat beta-lactoglobulin promoter and compared it to that of the sheep homologue. The goat gene displays a mammary-specific chromatin pattern, which is reformed on expressing goat beta-lactoglobulin transgenes. This implies that this chromatin structure is sequence dependent and suggests that it plays a role in regulating beta-lactoglobulin gene expression. This pattern differs from that seen on the ovine beta-lactoglobulin gene in lactating sheep mammary chromatin. Thus, even between highly related species, the transcriptional mechanisms regulating activity of a gene can differ.
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Affiliation(s)
- R N Pena
- Unitat de Genètica i Millora, Departament de Patologia i Producció Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.
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