1
|
Feng X, Pan C, Liu S, Hu H, Ma Y. Identification of core genes affecting IMF deposition in bovine. Anim Biotechnol 2023; 34:2887-2899. [PMID: 36137229 DOI: 10.1080/10495398.2022.2124167] [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] [Indexed: 11/01/2022]
Abstract
Intramuscular fat (IMF) content is an important economic factor in beef production. However, knowledge on the key factors controlling bovine IMF is limited. In this study, using weighted gene co-expression network analysis (WGCNA), nine modules were identified and the number of transcripts in these modules ranged from 36 to 3191. Two modules were found to be significantly associated with fat deposition and three genes (TCAP, MYH7, and TNNC1) were further identified by Protein-protein interaction (PPI), which may be the hub genes regulating bovine IMF deposition. In addition, considering the genetic variation, the PCK1 gene was found by functional enrichment analysis of overlapping genes, which was previously reported to be involved in IMF deposition. We noted that the core promoter region of buffalo PCK1 binds to transcription factors involved in lipid metabolism while cattle PCK1 binds transcription factors involved in muscle development. The results suggest that PCK1 participated in IMF deposition of buffalo and cattle in different ways. In summary, gene expression networks and new candidate genes associated with IMF deposition identified in this study. This would lay the foundation for further research into the molecular regulatory mechanisms underlying bovine IMF deposition.
Collapse
Affiliation(s)
- Xue Feng
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, China
| | - Cuili Pan
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, China
| | - Shuang Liu
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, China
| | - Honghong Hu
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, China
| | - Yun Ma
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| |
Collapse
|
2
|
Suárez-Mesa R, Ros-Freixedes R, Laghouaouta H, Pena RN, Hernández-Ortiz B, Rondón-Barragán I, Estany J. Identification of breed-specific genomic variants in Colombian Creole pig breeds by whole-genome sequencing. Trop Anim Health Prod 2023; 55:154. [PMID: 37041265 PMCID: PMC10089996 DOI: 10.1007/s11250-023-03557-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/29/2023] [Indexed: 04/13/2023]
Abstract
Dissecting genetic variation of local breeds is important for the success of conservation. In this research, we investigated the genomic variation of Colombian Creole (CR) pigs, with a focus on the breed-specific variants in the exonic region of 34 genes with reported effects on adaptive and economic traits. Seven individuals of each of the three CR breeds (CM, Casco de Mula; SP, San Pedreño; and ZU, Zungo) were whole-genome sequenced along with 7 Iberian (IB) pigs and 7 pigs of each of the four most used cosmopolitan (CP) breeds (Duroc, Landrace × Large White, and Pietrain). Molecular variability in CR (6,451,218 variants; from 3,919,242, in SP, to 4,648,069, in CM) was comparable to that in CP, but higher than in IB. For the investigated genes, SP pigs displayed less exonic variants (178) than ZU (254), CM (263), IB (200), and the individual CP genetic types (201 to 335). Sequence variation in these genes confirmed the resemblance of CR to IB and indicates that CR pigs, particularly ZU and CM, are not exempt from selective introgression of other breeds. A total of 50 exonic variants were identified as being potentially specific to CR, including a high-impact deletion in the intron between exons 15 and 16 of the leptin receptor gene, which was only found in CM and ZU. The identification of breed-specific variants in genes related to adaptive and economical traits can bolster the understanding of the role of gene-environment interactions on local adaptation and points the way for effective breeding and conservation of CR pigs.
Collapse
Affiliation(s)
- Rafael Suárez-Mesa
- Department of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain.
- Research Group in Immunobiology and Pathogenesis, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Barrio Santa Helena Parte Alta, Ibagué, Colombia.
| | - Roger Ros-Freixedes
- Department of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain
| | - Houda Laghouaouta
- Department of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain
| | - Ramona N Pena
- Department of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain
| | - Byron Hernández-Ortiz
- Research and Innovation Group in Animal Health and Welfare Germplasm Animal Bank, Agrosavia, Bogotá, 250047, Colombia
| | - Iang Rondón-Barragán
- Research Group in Immunobiology and Pathogenesis, Faculty of Veterinary Medicine and Zootechnics, University of Tolima, Barrio Santa Helena Parte Alta, Ibagué, Colombia
| | - Joan Estany
- Department of Animal Science, University of Lleida Agrotecnio-CERCA Center, 191 Rovira Roure, 25198, Lleida, Catalonia, Spain.
| |
Collapse
|
3
|
Proteomic and clinical biomarkers for acute mountain sickness in a longitudinal cohort. Commun Biol 2022; 5:548. [PMID: 35668171 PMCID: PMC9170681 DOI: 10.1038/s42003-022-03514-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 05/18/2022] [Indexed: 11/17/2022] Open
Abstract
Ascending to high-altitude by non-high-altitude natives is a well-suited model for studying acclimatization to extreme environments. Acute mountain sickness (AMS) is frequently experienced by visitors. The diagnosis of AMS mainly depends on a self-questionnaire, revealing the need for reliable biomarkers for AMS. Here, we profiled 22 AMS symptom phenotypes, 65 clinical indexes, and plasma proteomic profiles of AMS via a combination of proximity extension assay and multiple reaction monitoring of a longitudinal cohort of 53 individuals. We quantified 1069 proteins and validated 102 proteins. Via differential analysis, machine learning, and functional association analyses. We found and validated that RET played an important role in the pathogenesis of AMS. With high-accuracies (AUCs > 0.9) of XGBoost-based models, we prioritized ADAM15, PHGDH, and TRAF2 as protective, predictive, and diagnostic biomarkers, respectively. Our findings shed light on the precision medicine for AMS and the understanding of acclimatization to high-altitude environments. Potential acute mountain sickness diagnostic, predictive, protective biomarkers are established using plasma proteomic, clinical and symptom phenotype data with machine learning approaches in a longitudinal cohort of 53 individuals.
Collapse
|
4
|
Guo L, Wei C, Yi L, Yang W, Geng Z, Chen X. Transcriptional Insights into Key Genes and Pathways Underlying Muscovy Duck Subcutaneous Fat Deposition at Different Developmental Stages. Animals (Basel) 2021; 11:ani11072099. [PMID: 34359227 PMCID: PMC8300375 DOI: 10.3390/ani11072099] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/07/2021] [Accepted: 07/10/2021] [Indexed: 01/24/2023] Open
Abstract
Simple Summary Subcutaneous fat is an important factor affecting the meat quality and feed conversion rate of waterfowl. The current study compared the transcriptome data of Muscovy duck subcutaneous fat among three developmental stages, aiming at exploring the key regulatory genes for subcutaneous fat deposition. The results generated abundant candidate genes and pathways involving in subcutaneous fat deposition in Muscovy duck. This study provides an important reference for revealing the developmental mechanisms of subcutaneous fat in duck. Abstract Subcutaneous fat is a crucial trait for waterfowl, largely associated with meat quality and feed conversion rate. In this study, RNA-seq was used to identify differentially expressed genes of subcutaneous adipose tissue among three developmental stages (12, 35, and 66 weeks) in Muscovy duck. A total of 138 and 129 differentially expressed genes (DEGs) were identified between 35 and 12 weeks (wk), and 66 and 35 wk, respectively. Compared with 12 wk, subcutaneous fat tissue at 35 wk upregulated several genes related to cholesterol biosynthesis and fatty acid biosynthesis, including HSD17B7 and MSMO1, while it downregulated fatty acid beta-oxidation related genes, including ACOX1 and ACSL1. Notably, most of the DEGs (92.2%) were downregulated in 66 wk compared with 35 wk, consistent with the slower metabolism of aging duck. Protein network interaction and function analyses revealed GC, AHSG, FGG, and FGA were the key genes for duck subcutaneous fat from adult to old age. Additionally, the PPAR signaling pathway, commonly enriched between the two comparisons, might be the key pathway contributing to subcutaneous fat metabolism among differential developmental stages in Muscovy duck. These results provide several candidate genes and pathways potentially involved in duck subcutaneous fat deposition, expanding our understanding of the molecular mechanisms underlying subcutaneous fat deposition during development.
Collapse
|
5
|
Poklukar K, Čandek-Potokar M, Vrecl M, Batorek-Lukač N, Fazarinc G, Kress K, Stefanski V, Škrlep M. Adipose Tissue Gene Expression of Entire Male, Immunocastrated and Surgically Castrated Pigs. Int J Mol Sci 2021; 22:1768. [PMID: 33578947 PMCID: PMC7916650 DOI: 10.3390/ijms22041768] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/01/2021] [Accepted: 02/06/2021] [Indexed: 12/13/2022] Open
Abstract
Differences in adipose tissue deposition and properties between pig male sex categories, i.e., entire males (EM), immunocastrates (IC) and surgical castrates (SC) are relatively well-characterized, whereas the underlying molecular mechanisms are still not fully understood. To gain knowledge about the genetic regulation of the differences in adipose tissue deposition, two different approaches were used: RNA-sequencing and candidate gene expression by quantitative PCR. A total of 83 differentially expressed genes were identified between EM and IC, 15 between IC and SC and 48 between EM and SC by RNA-sequencing of the subcutaneous adipose tissue. Comparing EM with IC or SC, upregulated genes related to extracellular matrix dynamics and adipogenesis, and downregulated genes involved in the control of lipid and carbohydrate metabolism were detected. Differential gene expression generally indicated high similarity between IC and SC as opposed to EM, except for several heat shock protein genes that were upregulated in EM and IC compared with SC. The candidate gene expression approach showed that genes involved in lipogenesis were downregulated in EM compared with IC pigs, further confirming RNA-sequencing results.
Collapse
Affiliation(s)
- Klavdija Poklukar
- Agricultural Institute of Slovenia, Hacquetova ulica 17, 1000 Ljubljana, Slovenia; (K.P.); (M.Č.-P.); (N.B.-L.)
| | - Marjeta Čandek-Potokar
- Agricultural Institute of Slovenia, Hacquetova ulica 17, 1000 Ljubljana, Slovenia; (K.P.); (M.Č.-P.); (N.B.-L.)
- Faculty of Agriculture and Life Sciences, University of Maribor, Pivola 10, 2311 Hoče, Slovenia
| | - Milka Vrecl
- Institute of Preclinical Sciences, Veterinary Faculty, University of Ljubljana, Gerbičeva ulica 60, 1000 Ljubljana, Slovenia; (M.V.); (G.F.)
| | - Nina Batorek-Lukač
- Agricultural Institute of Slovenia, Hacquetova ulica 17, 1000 Ljubljana, Slovenia; (K.P.); (M.Č.-P.); (N.B.-L.)
| | - Gregor Fazarinc
- Institute of Preclinical Sciences, Veterinary Faculty, University of Ljubljana, Gerbičeva ulica 60, 1000 Ljubljana, Slovenia; (M.V.); (G.F.)
| | - Kevin Kress
- Behavioural Physiology of Livestock, Institute of Animal Science, University of Hohenheim, Garbenstrasse 17, 70599 Stuttgart, Germany; (K.K.); (V.S.)
| | - Volker Stefanski
- Behavioural Physiology of Livestock, Institute of Animal Science, University of Hohenheim, Garbenstrasse 17, 70599 Stuttgart, Germany; (K.K.); (V.S.)
| | - Martin Škrlep
- Agricultural Institute of Slovenia, Hacquetova ulica 17, 1000 Ljubljana, Slovenia; (K.P.); (M.Č.-P.); (N.B.-L.)
| |
Collapse
|
6
|
Huang J, Feng X, Zhu R, Guo D, Wei Y, Cao X, Ma Y, Shi D. Comparative transcriptome analysis reveals that PCK1 is a potential gene affecting IMF deposition in buffalo. BMC Genomics 2020; 21:710. [PMID: 33045988 PMCID: PMC7552535 DOI: 10.1186/s12864-020-07120-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 10/02/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND In China, although buffaloes are abundant, beef is mainly obtained from cattle, and this preference is mainly attributed to the low intramuscular fat (IMF) content of buffalo. Genetic factors are an important driver that affects IMF deposition. RESULTS To reveal the intrinsic factors responsible for the low IMF content of buffalo, mRNA expression patterns in muscle and adipose tissue between buffalo and cattle were characterized by RNA sequencing analysis. The IMF content in Nanyang cattle was higher than that in Xinyang buffalo. A total of 1566 mRNAs expressed in adipose tissue showed differential expression between the longissimus dorsi muscles of buffalo and cattle. Functional annotation suggested a difference in the glycolysis/gluconeogenesis pathway between the two species. The results of RT-qPCR analysis and gain-of-function experiments confirmed the positive association between the IMF content and phosphoenolpyruvate carboxykinase 1 (PCK1) expression in buffalo. In both mouse C2C12 cells and cultured bovine myocytes, the activity of the PCK1 promoter in buffalo is lower than that in cattle. However, in mouse 3T3-L1 adipocytes and cultured bovine adipocytes, the activity of PCK1 in buffalo promoter is higher than that in cattle. CONCLUSIONS These results indicate the important role of PCK1 in buffalo IMF deposition and illustrate the differences between buffalo and cattle promoter activity that drive PCK1 expression. This research helps to establish a foundation for further studies investigating IMF deposition in buffalo.
Collapse
Affiliation(s)
- Jieping Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, Guangxi, China. .,College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China.
| | - Xue Feng
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Ruirui Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, Guangxi, China
| | - Duo Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, Guangxi, China
| | - Yutong Wei
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Xiaodan Cao
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Yun Ma
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China.,School of Agriculture, Ningxia University, Yinchuan, 750021, Ningxia, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, Guangxi, China
| |
Collapse
|
7
|
Albuquerque A, Óvilo C, Núñez Y, Benítez R, López-Garcia A, García F, Félix MDR, Laranjo M, Charneca R, Martins JM. Comparative Transcriptomic Analysis of Subcutaneous Adipose Tissue from Local Pig Breeds. Genes (Basel) 2020; 11:E422. [PMID: 32326415 PMCID: PMC7231169 DOI: 10.3390/genes11040422] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/07/2020] [Accepted: 04/11/2020] [Indexed: 12/12/2022] Open
Abstract
When compared to modern lean-type breeds, Portuguese local Alentejano (AL) and Bísaro (BI) pig breeds present a high potential for subcutaneous and intramuscular fat (IMF) deposition which contributes for better meat quality. The aim of this work was to explore the genome function to better understand the underlying physiological mechanisms associated with body fat accretion. Dorsal subcutaneous fat samples were collected at slaughter from adult animals (n = 4 for each breed) with ~150 kg body weight. Total RNA was obtained and sequenced for transcriptome analysis using DESeq2. A total of 458 differentially expressed (DE) genes (q-value < 0.05) were identified, with 263 overexpressed in AL and 195 in BI. Key genes involved in de novo fatty acid biosynthesis, elongation and desaturation were upregulated in AL such as ACLY, FASN, ME1, ELOVL6 and SCD. A functional enrichment analysis of the DE genes was performed using Ingenuity Pathway Analysis. Cholesterol synthesis is suggested to be higher in AL via SREBF2, SCAP and PPARG, while lipolytic activity may be more active in BI through GH and AMPK signalling. Increased signalling of CD40 together with the predicted activation of INSIG1 and INSIG2 in BI suggests that this breed is more sensitive to insulin whereas the AL is less sensitive like the Iberian breed.
Collapse
Affiliation(s)
- André Albuquerque
- MED-Mediterranean Institute for Agriculture, Environment and Development, Instituto de Investigação e Formação Avançada & Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal;
| | - Cristina Óvilo
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain; (C.Ó.); (Y.N.); (R.B.); (A.L.-G.); (F.G.)
| | - Yolanda Núñez
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain; (C.Ó.); (Y.N.); (R.B.); (A.L.-G.); (F.G.)
| | - Rita Benítez
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain; (C.Ó.); (Y.N.); (R.B.); (A.L.-G.); (F.G.)
| | - Adrián López-Garcia
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain; (C.Ó.); (Y.N.); (R.B.); (A.L.-G.); (F.G.)
| | - Fabián García
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain; (C.Ó.); (Y.N.); (R.B.); (A.L.-G.); (F.G.)
| | - Maria do Rosário Félix
- MED & Departamento de Fitotecnia, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal;
| | - Marta Laranjo
- MED-Mediterranean Institute for Agriculture, Environment and Development, Instituto de Investigação e Formação Avançada & Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal;
| | - Rui Charneca
- MED & Departamento de Medicina Veterinária, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal;
| | - José Manuel Martins
- MED & Departamento de Zootecnia, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
| |
Collapse
|
8
|
Groß C, Derks M, Megens HJ, Bosse M, Groenen MAM, Reinders M, de Ridder D. pCADD: SNV prioritisation in Sus scrofa. Genet Sel Evol 2020; 52:4. [PMID: 32033531 PMCID: PMC7006094 DOI: 10.1186/s12711-020-0528-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/28/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND In animal breeding, identification of causative genetic variants is of major importance and high economical value. Usually, the number of candidate variants exceeds the number of variants that can be validated. One way of prioritizing probable candidates is by evaluating their potential to have a deleterious effect, e.g. by predicting their consequence. Due to experimental difficulties to evaluate variants that do not cause an amino-acid substitution, other prioritization methods are needed. For human genomes, the prediction of deleterious genomic variants has taken a step forward with the introduction of the combined annotation dependent depletion (CADD) method. In theory, this approach can be applied to any species. Here, we present pCADD (p for pig), a model to score single nucleotide variants (SNVs) in pig genomes. RESULTS To evaluate whether pCADD captures sites with biological meaning, we used transcripts from miRNAs and introns, sequences from genes that are specific for a particular tissue, and the different sites of codons, to test how well pCADD scores differentiate between functional and non-functional elements. Furthermore, we conducted an assessment of examples of non-coding and coding SNVs, which are causal for changes in phenotypes. Our results show that pCADD scores discriminate between functional and non-functional sequences and prioritize functional SNVs, and that pCADD is able to score the different positions in a codon relative to their redundancy. Taken together, these results indicate that based on pCADD scores, regions with biological relevance can be identified and distinguished according to their rate of adaptation. CONCLUSIONS We present the ability of pCADD to prioritize SNVs in the pig genome with respect to their putative deleteriousness, in accordance to the biological significance of the region in which they are located. We created scores for all possible SNVs, coding and non-coding, for all autosomes and the X chromosome of the pig reference sequence Sscrofa11.1, proposing a toolbox to prioritize variants and evaluate sequences to highlight new sites of interest to explain biological functions that are relevant to animal breeding.
Collapse
Affiliation(s)
- Christian Groß
- Delft Bioinformatics Lab, University of Technology Delft, 2600GA, Delft, The Netherlands. .,Bioinformatics Group, Wageningen University & Research, 6708 PB, Wageningen, The Netherlands.
| | - Martijn Derks
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Mirte Bosse
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Marcel Reinders
- Delft Bioinformatics Lab, University of Technology Delft, 2600GA, Delft, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University & Research, 6708 PB, Wageningen, The Netherlands
| |
Collapse
|
9
|
Zappaterra M, Luise D, Zambonelli P, Mele M, Serra A, Costa LN, Davoli R. Association study between backfat fatty acid composition and SNPs in candidate genes highlights the effect of FASN polymorphism in large white pigs. Meat Sci 2019; 156:75-84. [DOI: 10.1016/j.meatsci.2019.05.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/08/2019] [Accepted: 05/13/2019] [Indexed: 12/30/2022]
|
10
|
Breed, Diet, and Interaction Effects on Adipose Tissue Transcriptome in Iberian and Duroc Pigs Fed Different Energy Sources. Genes (Basel) 2019; 10:genes10080589. [PMID: 31382709 PMCID: PMC6723240 DOI: 10.3390/genes10080589] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/01/2019] [Accepted: 08/02/2019] [Indexed: 12/14/2022] Open
Abstract
In this study, we analyzed the effects of breed, diet energy source, and their interaction on adipose tissue transcriptome in growing Iberian and Duroc pigs. The study comprised 29 Iberian and 19 Duroc males, which were kept under identical management conditions except the nutritional treatment. Two isoenergetic diets were used with 6% high oleic sunflower oil (HO) or carbohydrates (CH) as energy sources. All animals were slaughtered after 47 days of treatment at an average live weight of 51.2 kg. Twelve animals from each breed (six fed each diet) were employed for ham subcutaneous adipose tissue RNA-Seq analysis. The data analysis was performed using two different bioinformatic pipelines. We detected 837 and 1456 differentially expressed genes (DEGs) according to breed, depending on the pipeline. Due to the strong effect of breed on transcriptome, the effect of the diet was separately evaluated in the two breeds. We identified 207 and 57 DEGs depending on diet in Iberian and Duroc pigs, respectively. A joint analysis of both effects allowed the detection of some breed–diet interactions on transcriptome, which were inferred from RNA-Seq and quantitative PCR data. The functional analysis showed the enrichment of functions related to growth and tissue development, inflammatory response, immune cell trafficking, and carbohydrate and lipid metabolism, and allowed the identification of potential regulators. The results indicate different effects of diet on adipose tissue gene expression between breeds, affecting relevant biological pathways.
Collapse
|
11
|
Muñoz M, Bozzi R, García F, Núñez Y, Geraci C, Crovetti A, García-Casco J, Alves E, Škrlep M, Charneca R, Martins JM, Quintanilla R, Tibau J, Kušec G, Djurkin-Kušec I, Mercat MJ, Riquet J, Estellé J, Zimmer C, Razmaite V, Araujo JP, Radović Č, Savić R, Karolyi D, Gallo M, Čandek-Potokar M, Fontanesi L, Fernández AI, Óvilo C. Diversity across major and candidate genes in European local pig breeds. PLoS One 2018; 13:e0207475. [PMID: 30458028 PMCID: PMC6245784 DOI: 10.1371/journal.pone.0207475] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 10/30/2018] [Indexed: 11/18/2022] Open
Abstract
The aim of this work was to analyse the distribution of causal and candidate mutations associated to relevant productive traits in twenty local European pig breeds. Also, the potential of the SNP panel employed for elucidating the genetic structure and relationships among breeds was evaluated. Most relevant genes and mutations associated with pig morphological, productive, meat quality, reproductive and disease resistance traits were prioritized and analyzed in a maximum of 47 blood samples from each of the breeds (Alentejana, Apulo-Calabrese, Basque, Bísara, Majorcan Black, Black Slavonian (Crna slavonska), Casertana, Cinta Senese, Gascon, Iberian, Krškopolje (Krškopoljski), Lithuanian indigenous wattle, Lithuanian White Old Type, Mora Romagnola, Moravka, Nero Siciliano, Sarda, Schwäbisch-Hällisches Schwein (Swabian Hall pig), Swallow-Bellied Mangalitsa and Turopolje). We successfully analyzed allelic variation in 39 polymorphisms, located in 33 candidate genes. Results provide relevant information regarding genetic diversity and segregation of SNPs associated to production and quality traits. Coat color and morphological trait-genes that show low level of segregation, and fixed SNPs may be useful for traceability. On the other hand, we detected SNPs which may be useful for association studies as well as breeding programs. For instance, we observed predominance of alleles that might be unfavorable for disease resistance and boar taint in most breeds and segregation of many alleles involved in meat quality, fatness and growth traits. Overall, these findings provide a detailed catalogue of segregating candidate SNPs in 20 European local pig breeds that may be useful for traceability purposes, for association studies and for breeding schemes. Population genetic analyses based on these candidate genes are able to uncover some clues regarding the hidden genetic substructure of these populations, as the extreme genetic closeness between Iberian and Alentejana breeds and an uneven admixture of the breeds studied. The results are in agreement with available knowledge regarding breed history and management, although largest panels of neutral markers should be employed to get a deeper understanding of the population's structure and relationships.
Collapse
Affiliation(s)
- María Muñoz
- Departamento Mejora Genética Animal, INIA, Madrid, Spain
| | | | - Fabián García
- Departamento Mejora Genética Animal, INIA, Madrid, Spain
| | - Yolanda Núñez
- Departamento Mejora Genética Animal, INIA, Madrid, Spain
| | - Claudia Geraci
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | | | | | | | | | - Rui Charneca
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal
| | - Jose M. Martins
- Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal
| | | | - Joan Tibau
- Programa de Genética y Mejora Animal, IRTA, Barcelona, Spain
| | - Goran Kušec
- University of Osijek, Faculty of Agrobiotechnical Sciences, Osijek, Croatia
| | | | | | - Juliette Riquet
- Génétique Physiologie et Système d’Elevage, INRA, Castanet-Tolosan, France
| | - Jordi Estellé
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Christoph Zimmer
- Bäuerliche Erzeugergemeinschaft Schwäbisch Hall, Schwäbisch Hall, Germany
| | - Violeta Razmaite
- Animal Science Institute, Lithuanian University of Health Sciences, Baisogala, Lithuania
| | - Jose P. Araujo
- Instituto Politecnico de Viana do Castelo, Viana do Castelo, Portugal
| | - Čedomir Radović
- Institute for Animal Husbandry-Pig Research Department, Belgrade-Zemun, Serbia
| | - Radomir Savić
- University of Belgrade, Faculty of agriculture, Belgrade-Zemun, Serbia
| | - Danijel Karolyi
- Department of animal science, Faculty of agriculture, University of Zagreb, Zagreb, Croatia
| | - Maurizio Gallo
- Associazione Nazionale Allevatori Suini (ANAS), Roma, Italy
| | | | - Luca Fontanesi
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy
| | | | - Cristina Óvilo
- Departamento Mejora Genética Animal, INIA, Madrid, Spain
| |
Collapse
|
12
|
Jiang Y, Tang S, Wang C, Wang Y, Qin Y, Wang Y, Zhang J, Song H, Mi S, Yu F, Xiao W, Zhang Q, Ding X. A genome-wide association study of growth and fatness traits in two pig populations with different genetic backgrounds. J Anim Sci 2018. [PMID: 29528397 DOI: 10.1093/jas/skx038] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Improvement in growth and fatness traits are the main objectives in pig all breeding programs. Tenth rib backfat thickness (10RIBBFT) and days to 100 kg (D100), which are good predictors of carcass lean content and growth rate, respectively, are economically important traits and also main breeding target traits in pigs. To investigate the genetic mechanisms of 10RIBBFT and D100 of pigs, we sampled 1,137 and 888 pigs from 2 Yorkshire populations of American and British origin, respectively, and conducted genome-wide association study (GWAS) through combined analysis and meta-analysis, to identify SNPs associated with 10RIBBFT and D100. A total of 11 and 7 significant SNPs were identified by combined analysis for 10RIBBFT and D100, respectively. And in meta-analysis, 8 and 7 significant SNPs were identified for 10RIBBFT and D100, respectively. Among them, 6 and 5 common significant SNPs in two analysis results were, respectively, identified associated with 10RIBBFT and D100, and correspondingly explained 2.09% and 0.52% of the additive genetic variance of 10RIBBFT and D100. Further bioinformatics analysis revealed 10 genes harboring or close to these common significant SNPs, 5 for 10RIBBFT and 5 for D100. In particular, Gene Ontology analysis highlighted 6 genes, PCK1, ANGPTL3, EEF1A2, TNFAIP8L3, PITX2, and PLA2G12, as promising candidate genes relevant with backfat thickness and growth. PCK1, ANGPTL3, EEF1A2, and TNFAIP8L3 could influence backfat thickness through phospholipid transport, regulation of lipid metabolic process through the glycerophospholipid biosynthesis and metabolism pathway, the metabolism of lipids and lipoproteins pathway. PITX2 has a crucial role in skeletal muscle tissue development and animal organ morphogenesis, and PLA2G12A plays a role in the lipid catabolic and phospholipid catabolic processes, which both are involved in the body weight pathway. All these candidate genes could directly or indirectly influence fat production and growth in Yorkshire pigs. Our findings provide novel insights into the genetic basis of growth and fatness traits in pigs. The candidate genes for D100 and 10RIBBFT are worthy of further investigation.
Collapse
Affiliation(s)
- Y Jiang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
| | - S Tang
- Beijing Station of Animal Husbandry, Beijing, P.R. China
| | - C Wang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
| | - Y Wang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
| | - Y Qin
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
| | - Y Wang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
| | - J Zhang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
| | - H Song
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
| | - S Mi
- Beijing LM Pig Breeding Technology Co., Ltd., Beijing, P.R. China
| | - F Yu
- Beijing Shunxin Agricultural Co., Ltd., Beijing, P.R. China
| | - W Xiao
- Beijing Station of Animal Husbandry, Beijing, P.R. China
| | - Q Zhang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
| | - X Ding
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
| |
Collapse
|
13
|
Latorre-Muro P, Baeza J, Armstrong EA, Hurtado-Guerrero R, Corzana F, Wu LE, Sinclair DA, López-Buesa P, Carrodeguas JA, Denu JM. Dynamic Acetylation of Phosphoenolpyruvate Carboxykinase Toggles Enzyme Activity between Gluconeogenic and Anaplerotic Reactions. Mol Cell 2018; 71:718-732.e9. [PMID: 30193097 PMCID: PMC6188669 DOI: 10.1016/j.molcel.2018.07.031] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 06/01/2018] [Accepted: 07/24/2018] [Indexed: 12/11/2022]
Abstract
Cytosolic phosphoenolpyruvate carboxykinase (PCK1) is considered a gluconeogenic enzyme; however, its metabolic functions and regulatory mechanisms beyond gluconeogenesis are poorly understood. Here, we describe that dynamic acetylation of PCK1 interconverts the enzyme between gluconeogenic and anaplerotic activities. Under high glucose, p300-dependent hyperacetylation of PCK1 did not lead to protein degradation but instead increased the ability of PCK1 to perform the anaplerotic reaction, converting phosphoenolpyruvate to oxaloacetate. Lys91 acetylation destabilizes the active site of PCK1 and favors the reverse reaction. At low energy input, we demonstrate that SIRT1 deacetylates PCK1 and fully restores the gluconeogenic ability of PCK1. Additionally, we found that GSK3β-mediated phosphorylation of PCK1 decreases acetylation and increases ubiquitination. Biochemical evidence suggests that serine phosphorylation adjacent to Lys91 stimulates SIRT1-dependent deacetylation of PCK1. This work reveals an unexpected capacity of hyperacetylated PCK1 to promote anaplerotic activity, and the intersection of post-translational control of PCK1 involving acetylation, phosphorylation, and ubiquitination.
Collapse
Affiliation(s)
- Pedro Latorre-Muro
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), BIFIIQFR (CSIC) Joint Unit, Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Josue Baeza
- Wisconsin Institute for Discovery and Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health-Madison, Madison, WI 53715, USA
| | - Eric A Armstrong
- Wisconsin Institute for Discovery and Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health-Madison, Madison, WI 53715, USA
| | - Ramón Hurtado-Guerrero
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), BIFIIQFR (CSIC) Joint Unit, Universidad de Zaragoza, 50018 Zaragoza, Spain; Fundación ARAID, Government of Aragón, Zaragoza, Spain
| | - Francisco Corzana
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006 Logroño, Spain
| | - Lindsay E Wu
- Department of Pharmacology, School of Medical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - David A Sinclair
- Department of Pharmacology, School of Medical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia; Department of Genetics, Paul F. Glenn Laboratories for the Biological Mechanisms of Aging, Harvard Medical School, Boston, MA 02115, USA
| | - Pascual López-Buesa
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), BIFIIQFR (CSIC) Joint Unit, Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - José A Carrodeguas
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), BIFIIQFR (CSIC) Joint Unit, Universidad de Zaragoza, 50018 Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; IIS Aragón, Zaragoza, Spain.
| | - John M Denu
- Wisconsin Institute for Discovery and Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health-Madison, Madison, WI 53715, USA; Morgridge Institute for Research, Madison, WI 53715, USA.
| |
Collapse
|
14
|
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] [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.
Collapse
|
15
|
Latorre P, Varona L, Burgos C, Carrodeguas JA, López-Buesa P. O-GlcNAcylation mediates the control of cytosolic phosphoenolpyruvate carboxykinase activity via Pgc1α. PLoS One 2017; 12:e0179988. [PMID: 28644880 PMCID: PMC5482481 DOI: 10.1371/journal.pone.0179988] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/07/2017] [Indexed: 11/19/2022] Open
Abstract
PGC1α is a coactivator of many transcription factors and cytosolic phosphoenolpyruvate carboxykinase (PCK1) is a key enzyme for gluconeogenesis. PGC1α interacts with the transcription factor PPARγ to stimulate PCK1 expression and thus de novo glucose synthesis. These proteins are not only important for central energy metabolism but also for supplying intermediates for other metabolic pathways, including lipidogenesis and protein synthesis and might therefore be important factors in the ethiopathogenesis of metabolic disorders like diabetes but also in other pathologies like cancer. Since polymorphisms in these proteins have been related to some phenotypic traits in animals like pigs and PGC1α G482S polymorphism increases fat deposition in humans, we have investigated the molecular basis of such effects focusing on a commonly studied polymorphism in pig Pgc1α, which changes a cysteine at position 430 (WT) of the protein to a serine (C430S). Biochemical analyses show that Pgc1α WT stimulates higher expression of human PCK1 in HEK293T and HepG2 cells. Paradoxically, Pgc1α WT is less stable than Pgc1α p.C430S in HEK293T cells. However, the study of different post-translational modifications shows a higher O-GlcNAcylation level of Pgc1α p.C430S. This higher O-GlcNAcylation level significantly decreases the interaction between Pgc1α and PPARγ demonstrating the importance of post-translational glycosylation of PGC1α in the regulation of PCK1 activity. This, furthermore, could explain at least in part the observed epistatic effects between PGC1α and PCK1 in pigs.
Collapse
Affiliation(s)
- Pedro Latorre
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), BIFIIQFR (CSIC) Joint Unit, Universidad de Zaragoza, Zaragoza, Spain
| | - Luis Varona
- Departamento de Anatomía, Embriología y Genética, Universidad de Zaragoza, Zaragoza, Spain
- Instituto Agroalimentario de Aragón (IA2), Zaragoza, Spain
| | - Carmen Burgos
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), BIFIIQFR (CSIC) Joint Unit, Universidad de Zaragoza, Zaragoza, Spain
| | - José A. Carrodeguas
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), BIFIIQFR (CSIC) Joint Unit, Universidad de Zaragoza, Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
- IIS Aragón, Zaragoza, Spain
| | - Pascual López-Buesa
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), BIFIIQFR (CSIC) Joint Unit, Universidad de Zaragoza, Zaragoza, Spain
| |
Collapse
|
16
|
Genetic Marker Discovery in Complex Traits: A Field Example on Fat Content and Composition in Pigs. Int J Mol Sci 2016; 17:ijms17122100. [PMID: 27983643 PMCID: PMC5187900 DOI: 10.3390/ijms17122100] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 12/06/2016] [Accepted: 12/07/2016] [Indexed: 12/11/2022] Open
Abstract
Among the large number of attributes that define pork quality, fat content and composition have attracted the attention of breeders in the recent years due to their interaction with human health and technological and sensorial properties of meat. In livestock species, fat accumulates in different depots following a temporal pattern that is also recognized in humans. Intramuscular fat deposition rate and fatty acid composition change with life. Despite indication that it might be possible to select for intramuscular fat without affecting other fat depots, to date only one depot-specific genetic marker (PCK1 c.2456C>A) has been reported. In contrast, identification of polymorphisms related to fat composition has been more successful. For instance, our group has described a variant in the stearoyl-coA desaturase (SCD) gene that improves the desaturation index of fat without affecting overall fatness or growth. Identification of mutations in candidate genes can be a tedious and costly process. Genome-wide association studies can help in narrowing down the number of candidate genes by highlighting those which contribute most to the genetic variation of the trait. Results from our group and others indicate that fat content and composition are highly polygenic and that very few genes explain more than 5% of the variance of the trait. Moreover, as the complexity of the genome emerges, the role of non-coding genes and regulatory elements cannot be disregarded. Prediction of breeding values from genomic data is discussed in comparison with conventional best linear predictors of breeding values. An example based on real data is given, and the implications in phenotype prediction are discussed in detail. The benefits and limitations of using large SNP sets versus a few very informative markers as predictors of genetic merit of breeding candidates are evaluated using field data as an example.
Collapse
|
17
|
Hidalgo J, Latorre P, Carrodeguas JA, Velázquez-Campoy A, Sancho J, López-Buesa P. Inhibition of Pig Phosphoenolpyruvate Carboxykinase Isoenzymes by 3-Mercaptopicolinic Acid and Novel Inhibitors. PLoS One 2016; 11:e0159002. [PMID: 27391465 PMCID: PMC4938538 DOI: 10.1371/journal.pone.0159002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 06/25/2016] [Indexed: 11/24/2022] Open
Abstract
There exist two isoforms of cytosolic phosphoenolpyruvate carboxykinase (PEPCK-C) in pig populations that differ in a single amino acid (Met139Leu). The isoenzymes have different kinetic properties, affecting more strongly the Km and Vmax of nucleotides. They are associated to different phenotypes modifying traits of considerable economic interest. In this work we use inhibitors of phosphoenolpyruvate carboxykinase activity to search for further differences between these isoenzymes. On the one hand we have used the well-known inhibitor 3-mercaptopicolinic acid. Its inhibition patterns were the same for both isoenzymes: a three-fold decrease of the Ki values for GTP in 139Met and 139Leu (273 and 873 μM, respectively). On the other hand, through screening of a chemical library we have found two novel compounds with inhibitory effects of a similar magnitude to that of 3-mercaptopicolinic acid but with less solubility and specificity. One of these novel compounds, (N'1-({5-[1-methyl-5-(trifluoromethyl)-1H-pyrazol-3-yl]-2-thienyl}methylidene)-2,4-dichlorobenzene-1-carbohydrazide), exhibited significantly different inhibitory effects on either isoenzyme: it enhanced threefold the apparent Km value for GTP in 139Met, whereas in 139Leu, it reduced it from 99 to 69 μM. The finding of those significant differences in the binding of GTP reinforces the hypothesis that the Met139Leu substitution affects strongly the nucleotide binding site of PEPCK-C.
Collapse
Affiliation(s)
- Jorge Hidalgo
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), BIFI-IQFR (CSIC) Joint Unit, Universidad de Zaragoza, Zaragoza, Spain
| | - Pedro Latorre
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), BIFI-IQFR (CSIC) Joint Unit, Universidad de Zaragoza, Zaragoza, Spain
| | - José Alberto Carrodeguas
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), BIFI-IQFR (CSIC) Joint Unit, Universidad de Zaragoza, Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
- IIS Aragón, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), BIFI-IQFR (CSIC) Joint Unit, Universidad de Zaragoza, Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
- IIS Aragón, Zaragoza, Spain
- Fundación ARAID, Government of Aragón, Zaragoza, Spain
| | - Javier Sancho
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), BIFI-IQFR (CSIC) Joint Unit, Universidad de Zaragoza, Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Zaragoza, Spain
- IIS Aragón, Zaragoza, Spain
| | - Pascual López-Buesa
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), BIFI-IQFR (CSIC) Joint Unit, Universidad de Zaragoza, Zaragoza, Spain
- * E-mail:
| |
Collapse
|
18
|
Escós M, Latorre P, Hidalgo J, Hurtado-Guerrero R, Carrodeguas JA, López-Buesa P. Kinetic and functional properties of human mitochondrial phosphoenolpyruvate carboxykinase. Biochem Biophys Rep 2016; 7:124-129. [PMID: 28955899 PMCID: PMC5613351 DOI: 10.1016/j.bbrep.2016.06.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/02/2016] [Accepted: 06/06/2016] [Indexed: 11/28/2022] Open
Abstract
The cytosolic form of phosphoenolpyruvate carboxykinase (PCK1) plays a regulatory role in gluconeogenesis and glyceroneogenesis. The role of the mitochondrial isoform (PCK2) remains unclear. We report the partial purification and kinetic and functional characterization of human PCK2. Kinetic properties of the enzyme are very similar to those of the cytosolic enzyme. PCK2 has an absolute requirement for Mn2+ ions for activity; Mg2+ ions reduce the Km for Mn2+ by about 60 fold. Its specificity constant is 100 fold larger for oxaloacetate than for phosphoenolpyruvate suggesting that oxaloacetate phosphorylation is the favored reaction in vivo. The enzyme possesses weak pyruvate kinase-like activity (kcat=2.7 s−1). When overexpressed in HEK293T cells it enhances strongly glucose and lipid production showing that it can play, as the cytosolic isoenzyme, an active role in glyceroneogenesis and gluconeogenesis. Purification of recombinant human PCK2 has been performed. Its kinetic behavior is very similar to that of human PCK1. PCK2 overexpression increases gluconeogenesis and glyceroneogenesis in cell cultures.
Collapse
Affiliation(s)
- Miriam Escós
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), BIFI-IQFR (CSIC) Joint Unit, Universidad de Zaragoza, 50009 Zaragoza, Aragón, Spain
| | - Pedro Latorre
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), BIFI-IQFR (CSIC) Joint Unit, Universidad de Zaragoza, 50009 Zaragoza, Aragón, Spain
| | - Jorge Hidalgo
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), BIFI-IQFR (CSIC) Joint Unit, Universidad de Zaragoza, 50009 Zaragoza, Aragón, Spain
| | - Ramón Hurtado-Guerrero
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), BIFI-IQFR (CSIC) Joint Unit, Universidad de Zaragoza, 50009 Zaragoza, Aragón, Spain.,Fundación ARAID, Gobierno de Aragón, Zaragoza, Spain
| | - José Alberto Carrodeguas
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), BIFI-IQFR (CSIC) Joint Unit, Universidad de Zaragoza, 50009 Zaragoza, Aragón, Spain.,Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain.,IIS Aragón, 50009 Zaragoza, Spain
| | - Pascual López-Buesa
- Departamento de Producción Animal y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), BIFI-IQFR (CSIC) Joint Unit, Universidad de Zaragoza, 50009 Zaragoza, Aragón, Spain
| |
Collapse
|