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Wang F, Cheng Y, Yin L, Liu S, Li X, Xie M, Li J, Chen J, Fu C. Dietary supplementation with ellagic acid improves the growth performance, meat quality, and metabolomics profile of yellow-feathered broiler chickens. Poult Sci 2024; 103:103700. [PMID: 38631231 PMCID: PMC11036095 DOI: 10.1016/j.psj.2024.103700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/18/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024] Open
Abstract
The aim of this research was to explore the effects of ellagic acid (EA) on growth performance, meat quality, and metabolomics profile of broiler chickens. 240 healthy yellow-feathered broilers were randomly divided into 4 groups (6 replicates/group and 10 broilers /replicate): 1) a standard diet (CON); 2) CON+0.01% EA; 3) CON+0.02% EA; 4) CON+0.04% EA. Compared with the CON group, dietary 0.02% EA increased linearly and quadratically the ADG and lowered F/G ratio from 29 to 56 d and from 1 to 56 d of age (P < 0.05). The EA groups had higher spleen index and showed linear and quadratic improve thymus index (P < 0.05). A total of 0.02% EA linearly and quadratically increased the leg muscle percentage and quadratically increased the breast muscle percentage (P < 0.05). Compared to the control diet, 0.02% EA decreased quadratically the L* and increased a* of breast muscle at 45 min postslaughter (P < 0.05), and quadratically decreased (P < 0.05) the b* and increased linearly and quadratically (P < 0.05) drip loss. Additionally, EA improved linearly and quadratically (P < 0.05) serum total protein concentration and reduced linearly and quadratically (P < 0.05) serum blood urea nitrogen concentration. A total of 0.02% EA quadratically increased catalase activity and decreased malondialdehyde concentration in breast muscle compared with the control diet (P < 0.05). 0.02% and 0.04% EA could linearly and quadratically increase (P < 0.05) the concentrations of histidine, leucine and essential amino acids (EAA), 0.02% EA could linearly and quadratically increase (P < 0.05) the concentrations of threonine, glutamate, and flavored amino acids in breast muscle. 0.02% EA linearly and quadratically improved the C20:3n6, C22:6n3, polyunsaturated fatty acid (PUFA) concentrations, and the ratio of PUFA to saturated fatty acids (SFA), but reduced the C16:0 and the SFA concentrations in breast muscle than the CON group (P < 0.05). The EA diet linearly increased (P = 0.035) and quadratically tended (P = 0.068) to regulate the C18:2n6c concentration of breast muscle. Metabolomics showed that alanine metabolism, aspartate and glutamate metabolism, arginine and proline metabolism, taurine and hypotaurine metabolism, and glycerophospholipid metabolism were the most differentially abundant. These results showed that EA supported moderate positive effects on growth performance, meat quality, and metabolomics profile of broilers.
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Affiliation(s)
- Fang Wang
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Ying Cheng
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Lichen Yin
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Shida Liu
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Xinrui Li
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Meizhu Xie
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Jiayang Li
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Jiashun Chen
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Chenxing Fu
- Animal Nutritional Genome and Germplasm Innovation Research Center, College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China.
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Wang H, Wang X, Li M, Sun H, Chen Q, Yan D, Dong X, Pan Y, Lu S. Genome-wide association study reveals genetic loci and candidate genes for meat quality traits in a four-way crossbred pig population. Front Genet 2023; 14:1001352. [PMID: 36814900 PMCID: PMC9939654 DOI: 10.3389/fgene.2023.1001352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 01/24/2023] [Indexed: 02/08/2023] Open
Abstract
Meat quality traits (MQTs) have gained more attention from breeders due to their increasing economic value in the commercial pig industry. In this genome-wide association study (GWAS), 223 four-way intercross pigs were genotyped using the specific-locus amplified fragment sequencing (SLAF-seq) and phenotyped for PH at 45 min post mortem (PH45), meat color score (MC), marbling score (MA), water loss rate (WL), drip loss (DL) in the longissimus muscle, and cooking loss (CL) in the psoas major muscle. A total of 227, 921 filtered single nucleotide polymorphisms (SNPs) evenly distributed across the entire genome were detected to perform GWAS. A total of 64 SNPs were identified for six meat quality traits using the mixed linear model (MLM), of which 24 SNPs were located in previously reported QTL regions. The phenotypic variation explained (PVE) by the significant SNPs was from 2.43% to 16.32%. The genomic heritability estimates based on SNP for six meat-quality traits were low to moderate (0.07-0.47) being the lowest for CL and the highest for DL. A total of 30 genes located within 10 kb upstream or downstream of these significant SNPs were found. Furthermore, several candidate genes for MQTs were detected, including pH45 (GRM8), MC (ANKRD6), MA (MACROD2 and ABCG1), WL (TMEM50A), CL (PIP4K2A) and DL (CDYL2, CHL1, ABCA4, ZAG and SLC1A2). This study provided substantial new evidence for several candidate genes to participate in different pork quality traits. The identification of these SNPs and candidate genes provided a basis for molecular marker-assisted breeding and improvement of pork quality traits.
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Affiliation(s)
- Huiyu Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China,Faculty of Animal Science, Xichang University, Xichang, Sichuan, China
| | - Xiaoyi Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Mingli Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Hao Sun
- Faculty of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qiang Chen
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Dawei Yan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Xinxing Dong
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yuchun Pan
- Faculty of Animal Science, Zhejiang University, Hangzhou, Zhejiang, China,*Correspondence: Yuchun Pan, ; Shaoxiong Lu,
| | - Shaoxiong Lu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, China,*Correspondence: Yuchun Pan, ; Shaoxiong Lu,
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Shin MG, Nuzhdin SV. Interspecific Sample Prioritization Can Improve QTL Detection With Tree-Based Predictive Models. Front Genet 2021; 12:684882. [PMID: 34552613 PMCID: PMC8450460 DOI: 10.3389/fgene.2021.684882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/09/2021] [Indexed: 11/16/2022] Open
Abstract
Due to increasing demand for new advanced crops, considerable efforts have been made to explore the improvement of stress and disease resistance cultivar traits through the study of wild crops. When both wild and interspecific hybrid materials are available, a common approach has been to study two types of materials separately and simply compare the quantitative trait locus (QTL) regions. However, combining the two types of materials can potentially create a more efficient method of finding predictive QTLs. In this simulation study, we focused on scenarios involving causal marker expression suppressed by trans-regulatory mechanisms, where the otherwise easily lost associated signals benefit the most from combining the two types of data. A probabilistic sampling approach was used to prioritize consistent genotypic phenotypic patterns across both types of data sets. We chose random forest and gradient boosting to apply the prioritization scheme and found that both facilitated the investigation of predictive causal markers in most of the biological scenarios simulated.
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Affiliation(s)
- Min-Gyoung Shin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Sergey V Nuzhdin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
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Zhao X, Wang C, Wang Y, Lin H, Wang H, Hu H, Wang J. Comparative gene expression profiling of muscle reveals potential candidate genes affecting drip loss in pork. BMC Genet 2019; 20:89. [PMID: 31791257 PMCID: PMC6889219 DOI: 10.1186/s12863-019-0794-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 11/22/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Drip loss is a key aspect of meat quality. Transcriptome profiles of muscle with divergent drip loss would offer important insight into the genetic factors responsible for the trait. In this study, drip loss and other meat quality traits of 28 purebred Duroc pigs were measured, muscles of these individuals were RNA sequenced, and eight individuals with extremely low and high drip loss were selected for analyzing their transcriptome differences and identifying potential candidate genes affecting drip loss. RESULTS As a result, 363 differentially expressed (DE) genes were detected in the comparative gene expression analysis, of which 239 were up-regulated and 124 were down-regulated in the low drip loss group. The DE genes were further filtered by correlation analysis between their expression and drip loss values in the 28 Duroc pigs measured and comparison of them with QTLs affecting drip loss. Consequently, of the 363 DE genes, 100 were identified as critical DE genes for drip loss. Functional analysis of these critical DE genes revealed some GO terms (extracellular matrix, cell adhesion mediated by integrin, heterotypic cell-cell adhesion), pathway (ECM-receptor interaction), and new potential candidate genes (TNC, ITGA5, ITGA11, THBS3 and CD44) which played an important role in regulating the variation of drip loss, and deserved to carry further studies to unravel their specific mechanism on drip loss. CONCLUSIONS Our study revealed some GO terms, pathways and potential candidate genes affecting drip loss. It provides crucial information to understand the molecular mechanism of drip loss, and would be of help for improving meat quality of pigs.
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Affiliation(s)
- Xueyan Zhao
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Cheng Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Yanping Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Haichao Lin
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Huaizhong Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Hongmei Hu
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Jiying Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
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González-Prendes R, Mármol-Sánchez E, Quintanilla R, Castelló A, Zidi A, Ramayo-Caldas Y, Cardoso TF, Manunza A, Cánovas Á, Amills M. About the existence of common determinants of gene expression in the porcine liver and skeletal muscle. BMC Genomics 2019; 20:518. [PMID: 31234802 PMCID: PMC6591854 DOI: 10.1186/s12864-019-5889-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 06/07/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The comparison of expression QTL (eQTL) maps obtained in different tissues is an essential step to understand how gene expression is genetically regulated in a context-dependent manner. In the current work, we have compared the transcriptomic and eQTL profiles of two porcine tissues (skeletal muscle and liver) which typically show highly divergent expression profiles, in 103 Duroc pigs genotyped with the Porcine SNP60 BeadChip (Illumina) and with available microarray-based measurements of hepatic and muscle mRNA levels. Since structural variation could have effects on gene expression, we have also investigated the co-localization of cis-eQTLs with copy number variant regions (CNVR) segregating in this Duroc population. RESULTS The analysis of differential expresssion revealed the existence of 1204 and 1490 probes that were overexpressed and underexpressed in the gluteus medius muscle when compared to liver, respectively (|fold-change| > 1.5, q-value < 0.05). By performing genome scans in 103 Duroc pigs with available expression and genotypic data, we identified 76 and 28 genome-wide significant cis-eQTLs regulating gene expression in the gluteus medius muscle and liver, respectively. Twelve of these cis-eQTLs were shared by both tissues (i.e. 42.8% of the cis-eQTLs identified in the liver were replicated in the gluteus medius muscle). These results are consistent with previous studies performed in humans, where 50% of eQTLs were shared across tissues. Moreover, we have identified 41 CNVRs in a set of 350 pigs from the same Duroc population, which had been genotyped with the Porcine SNP60 BeadChip by using the PennCNV and GADA softwares, but only a small proportion of these CNVRs co-localized with the cis-eQTL signals. CONCLUSION Despite the fact that there are considerable differences in the gene expression patterns of the porcine liver and skeletal muscle, we have identified a substantial proportion of common cis-eQTLs regulating gene expression in both tissues. Several of these cis-eQTLs influence the mRNA levels of genes with important roles in meat (CTSF) and carcass quality (TAPT1), lipid metabolism (TMEM97) and obesity (MARC2), thus evidencing the practical importance of dissecting the genetic mechanisms involved in their expression.
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Affiliation(s)
- Rayner González-Prendes
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.,Departament de Producció Animal-Agrotecnio Center, Universitat de Lleida, 191 Rovira Roure, 25198, Lleida, Spain
| | - Emilio Mármol-Sánchez
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140, Caldes de Montbui, Spain
| | - Anna Castelló
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Ali Zidi
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Yuliaxis Ramayo-Caldas
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Tainã Figueiredo Cardoso
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.,CAPES Foundation, Ministry of Education of Brazil, Brasilia D. F, Zip Code 70.040-020, Brazil
| | - Arianna Manunza
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Ángela Cánovas
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.,Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
| | - Marcel Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain. .,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
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González-Prendes R, Quintanilla R, Mármol-Sánchez E, Pena RN, Ballester M, Cardoso TF, Manunza A, Casellas J, Cánovas Á, Díaz I, Noguera JL, Castelló A, Mercadé A, Amills M. Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi muscles. BMC Genomics 2019; 20:170. [PMID: 30832586 PMCID: PMC6399881 DOI: 10.1186/s12864-019-5557-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 02/22/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Intramuscular fat (IMF) content and composition have a strong impact on the nutritional and organoleptic properties of porcine meat. The goal of the current work was to compare the patterns of gene expression and the genetic determinism of IMF traits in the porcine gluteus medius (GM) and longissimus dorsi (LD) muscles. RESULTS A comparative analysis of the mRNA expression profiles of the pig GM and LD muscles in 16 Duroc pigs with available microarray mRNA expression measurements revealed the existence of 106 differentially expressed probes (fold-change > 1.5 and q-value < 0.05). Amongst the genes displaying the most significant differential expression, several loci belonging to the Hox transcription factor family were either upregulated (HOXA9, HOXA10, HOXB6, HOXB7 and TBX1) or downregulated (ARX) in the GM muscle. Differences in the expression of genes with key roles in carbohydrate and lipid metabolism (e.g. FABP3, ORMDL1 and SLC37A1) were also detected. By performing a GWAS for IMF content and composition traits recorded in the LD and GM muscles of 350 Duroc pigs, we identified the existence of one region on SSC14 (110-114 Mb) displaying significant associations with C18:0, C18:1(n-7), saturated and unsaturated fatty acid contents in both GM and LD muscles. Moreover, we detected several genome-wide significant associations that were not consistently found in both muscles. Further studies should be performed to confirm whether these associations are muscle-specific. Finally, the performance of an eQTL scan for 74 genes, located within GM QTL regions and with available microarray measurements of gene expression, made possible to identify 14 cis-eQTL regulating the expression of 14 loci, and six of them were confirmed by RNA-Seq. CONCLUSIONS We have detected significant differences in the mRNA expression patterns of the porcine LD and GM muscles, evidencing that the transcriptomic profile of the skeletal muscle tissue is affected by anatomical, metabolic and functional factors. A highly significant association with IMF composition on SSC14 was replicated in both muscles, highlighting the existence of a common genetic determinism, but we also observed the existence of a few associations whose magnitude and significance varied between LD and GM muscles.
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Affiliation(s)
- Rayner González-Prendes
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Rovira Roure 191, 25198 Lleida, Spain
| | - Emilio Mármol-Sánchez
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Ramona N. Pena
- Departament de Ciència Animal, Universitat de Lleida-Agrotecnio Centre, 25198 Lleida, Spain
| | - Maria Ballester
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Rovira Roure 191, 25198 Lleida, Spain
| | - Tainã Figueiredo Cardoso
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- CAPES Foundation, Ministry of Education of Brazil, Brasilia, DF 70.040-020 Brazil
| | - Arianna Manunza
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Joaquim Casellas
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Ángela Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1 Canada
| | - Isabel Díaz
- Institute for Research and Technology in Food and Agriculture (IRTA), Tecnologia dels Aliments, 17121 Monells, Spain
| | - José Luis Noguera
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Rovira Roure 191, 25198 Lleida, Spain
| | - Anna Castelló
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Anna Mercadé
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Marcel Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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Velez-Irizarry D, Casiro S, Daza KR, Bates RO, Raney NE, Steibel JP, Ernst CW. Genetic control of longissimus dorsi muscle gene expression variation and joint analysis with phenotypic quantitative trait loci in pigs. BMC Genomics 2019; 20:3. [PMID: 30606113 PMCID: PMC6319002 DOI: 10.1186/s12864-018-5386-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 12/18/2018] [Indexed: 12/21/2022] Open
Abstract
Background Economically important growth and meat quality traits in pigs are controlled by cascading molecular events occurring during development and continuing throughout the conversion of muscle to meat. However, little is known about the genes and molecular mechanisms involved in this process. Evaluating transcriptomic profiles of skeletal muscle during the initial steps leading to the conversion of muscle to meat can identify key regulators of polygenic phenotypes. In addition, mapping transcript abundance through genome-wide association analysis using high-density marker genotypes allows identification of genomic regions that control gene expression, referred to as expression quantitative trait loci (eQTL). In this study, we perform eQTL analyses to identify potential candidate genes and molecular markers regulating growth and meat quality traits in pigs. Results Messenger RNA transcripts obtained with RNA-seq of longissimus dorsi muscle from 168 F2 animals from a Duroc x Pietrain pig resource population were used to estimate gene expression variation subject to genetic control by mapping eQTL. A total of 339 eQTL were mapped (FDR ≤ 0.01) with 191 exhibiting local-acting regulation. Joint analysis of eQTL with phenotypic QTL (pQTL) segregating in our population revealed 16 genes significantly associated with 21 pQTL for meat quality, carcass composition and growth traits. Ten of these pQTL were for meat quality phenotypes that co-localized with one eQTL on SSC2 (8.8-Mb region) and 11 eQTL on SSC15 (121-Mb region). Biological processes identified for co-localized eQTL genes include calcium signaling (FERM, MRLN, PKP2 and CHRNA9), energy metabolism (SUCLG2 and PFKFB3) and redox hemostasis (NQO1 and CEP128), and results support an important role for activation of the PI3K-Akt-mTOR signaling pathway during the initial conversion of muscle to meat. Conclusion Co-localization of eQTL with pQTL identified molecular markers significantly associated with both economically important phenotypes and gene transcript abundance. This study reveals candidate genes contributing to variation in pig production traits, and provides new knowledge regarding the genetic architecture of meat quality phenotypes. Electronic supplementary material The online version of this article (10.1186/s12864-018-5386-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Sebastian Casiro
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA
| | - Kaitlyn R Daza
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA
| | - Ronald O Bates
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA
| | - Nancy E Raney
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA
| | - Juan P Steibel
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA.,Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, 48824, USA
| | - Catherine W Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI, 48824, USA.
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9
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Wei W, Li B, Liu K, Jiang A, Dong C, Jia C, Chen J, Liu H, Wu W. Identification of key microRNAs affecting drip loss in porcine longissimus dorsi by RNA-Seq. Gene 2018; 647:276-282. [DOI: 10.1016/j.gene.2018.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 09/28/2017] [Accepted: 01/02/2018] [Indexed: 12/27/2022]
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10
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González-Prendes R, Quintanilla R, Amills M. Investigating the genetic regulation of the expression of 63 lipid metabolism genes in the pig skeletal muscle. Anim Genet 2017; 48:606-610. [DOI: 10.1111/age.12586] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2017] [Indexed: 01/22/2023]
Affiliation(s)
- R. González-Prendes
- Department of Animal Genetics; Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB); Campus de la Universitat Autònoma de Barcelona Bellaterra 08193 Spain
| | - R. Quintanilla
- Animal Breeding and Genetics Program; Institut de Recerca i Tecnologia Agroalimentàries (IRTA); Torre Marimon Caldes de Montbui 08140 Spain
| | - M. Amills
- Department of Animal Genetics; Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB); Campus de la Universitat Autònoma de Barcelona Bellaterra 08193 Spain
- Departament de Ciència Animal i dels Aliments; Facultat de Veterinària; Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
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Welzenbach J, Neuhoff C, Heidt H, Cinar MU, Looft C, Schellander K, Tholen E, Große-Brinkhaus C. Integrative Analysis of Metabolomic, Proteomic and Genomic Data to Reveal Functional Pathways and Candidate Genes for Drip Loss in Pigs. Int J Mol Sci 2016; 17:E1426. [PMID: 27589727 PMCID: PMC5037705 DOI: 10.3390/ijms17091426] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/12/2016] [Accepted: 08/22/2016] [Indexed: 01/21/2023] Open
Abstract
The aim of this study was to integrate multi omics data to characterize underlying functional pathways and candidate genes for drip loss in pigs. The consideration of different omics levels allows elucidating the black box of phenotype expression. Metabolite and protein profiling was applied in Musculus longissimus dorsi samples of 97 Duroc × Pietrain pigs. In total, 126 and 35 annotated metabolites and proteins were quantified, respectively. In addition, all animals were genotyped with the porcine 60 k Illumina beadchip. An enrichment analysis resulted in 10 pathways, amongst others, sphingolipid metabolism and glycolysis/gluconeogenesis, with significant influence on drip loss. Drip loss and 22 metabolic components were analyzed as intermediate phenotypes within a genome-wide association study (GWAS). We detected significantly associated genetic markers and candidate genes for drip loss and for most of the metabolic components. On chromosome 18, a region with promising candidate genes was identified based on SNPs associated with drip loss, the protein "phosphoglycerate mutase 2" and the metabolite glycine. We hypothesize that association studies based on intermediate phenotypes are able to provide comprehensive insights in the genetic variation of genes directly involved in the metabolism of performance traits. In this way, the analyses contribute to identify reliable candidate genes.
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Affiliation(s)
- Julia Welzenbach
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany.
| | - Christiane Neuhoff
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany.
| | - Hanna Heidt
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany.
- Institute for Organic Agriculture Luxembourg, Association sans but lucratif (A.S.B.L.), 13 Rue Gabriel Lippmann, L-5365 Munsbach, Luxembourg.
| | - Mehmet Ulas Cinar
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany.
- Department of Animal Science, Faculty of Agriculture, Erciyes University, Talas Bulvari No. 99, 38039 Kayseri, Turkey.
| | - Christian Looft
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany.
| | - Karl Schellander
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany.
| | - Ernst Tholen
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany.
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12
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Li B, Liu K, Weng Q, Li P, Wei W, Li Q, Chen J, Huang R, Wu W, Liu H. RNA-seq analysis reveals new candidate genes for drip loss in a Pietrain × Duroc × Landrace × Yorkshire population. Anim Genet 2016; 47:192-9. [DOI: 10.1111/age.12401] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2015] [Indexed: 12/29/2022]
Affiliation(s)
- Bojiang Li
- Department of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology; Nanjing Agricultural University; Nanjing 210095 China
| | - Kaiqing Liu
- Department of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology; Nanjing Agricultural University; Nanjing 210095 China
| | - Qiannan Weng
- Department of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology; Nanjing Agricultural University; Nanjing 210095 China
| | - Pinghua Li
- Department of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology; Nanjing Agricultural University; Nanjing 210095 China
| | - Wei Wei
- Department of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology; Nanjing Agricultural University; Nanjing 210095 China
| | - Qifa Li
- Department of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology; Nanjing Agricultural University; Nanjing 210095 China
| | - Jie Chen
- Department of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology; Nanjing Agricultural University; Nanjing 210095 China
| | - Ruihua Huang
- Department of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology; Nanjing Agricultural University; Nanjing 210095 China
| | - Wangjun Wu
- Department of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology; Nanjing Agricultural University; Nanjing 210095 China
| | - Honglin Liu
- Department of Animal Genetics, Breeding and Reproduction; College of Animal Science and Technology; Nanjing Agricultural University; Nanjing 210095 China
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13
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Copy number variation-based genome wide association study reveals additional variants contributing to meat quality in Swine. Sci Rep 2015; 5:12535. [PMID: 26234186 PMCID: PMC4522650 DOI: 10.1038/srep12535] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/02/2015] [Indexed: 01/26/2023] Open
Abstract
Pork quality is important both to the meat processing industry and consumers' purchasing attitude. Copy number variation (CNV) is a burgeoning kind of variants that may influence meat quality. In this study, a genome-wide association study (GWAS) was performed between CNVs and meat quality traits in swine. After false discovery rate (FDR) correction, a total of 8 CNVs on 6 chromosomes were identified to be significantly associated with at least one meat quality trait. All of the 8 CNVs were verified by next generation sequencing and six of them were verified by qPCR. Only the haplotype block containing CNV12 is adjacent to significant SNPs associated with meat quality, suggesting the effects of those CNVs were not likely captured by tag SNPs. The DNA dosage and EST expression of CNV12, which overlap with an obesity related gene Netrin-1 (Ntn1), were consistent with Ntn1 RNA expression, suggesting the CNV12 might be involved in the expression regulation of Ntn1 and finally influence meat quality. We concluded that CNVs may contribute to the genetic variations of meat quality beyond SNPs, and several candidate CNVs were worth further exploration.
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14
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Zhang R, Große-Brinkhaus C, Heidt H, Uddin MJ, Cinar MU, Tesfaye D, Tholen E, Looft C, Schellander K, Neuhoff C. Polymorphisms and expression analysis of SOX-6 in relation to porcine growth, carcass, and meat quality traits. Meat Sci 2015; 107:26-32. [PMID: 25935846 DOI: 10.1016/j.meatsci.2015.04.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 03/16/2015] [Accepted: 04/13/2015] [Indexed: 11/24/2022]
Abstract
The aim of the study was to investigate single nucleotide polymorphisms (SNPs) and expression of SOX-6 to support its candidacy for growth, carcass, and meat quality traits in pigs. The first SNP, rs81358375, was associated with pH 45 min post mortem in loin (pH1L), the thickness of backfat and side fat, and carcass length in Pietrain (Pi) population, and related with backfat thickness and daily gain in Duroc × Pietrain F2 (DuPi) population. The other SNP, rs321666676, was associated with meat colour in Pi population. In DuPi population, the protein, not mRNA, level of SOX-6 in high pH1L pigs was significantly less abundant compared with low pH1L pigs, where microRNAs targeting SOX-6 were also differently regulated. This paper shows that SOX-6 could be a potential candidate gene for porcine growth, carcass, and meat quality traits based on genetic association and gene expression.
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Affiliation(s)
- Rui Zhang
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.
| | - Christine Große-Brinkhaus
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.
| | - Hanna Heidt
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.
| | - Muhammad Jasim Uddin
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany; Department of Medicine, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh.
| | - Mehmet Ulas Cinar
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany; Faculty of Agriculture, Department of Animal Science, Erciyes University, 38039 Kayseri, Turkey.
| | - Dawit Tesfaye
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.
| | - Ernst Tholen
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.
| | - Christian Looft
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.
| | - Karl Schellander
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.
| | - Christiane Neuhoff
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, 53115 Bonn, Germany.
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15
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Kadarmideen HN. Genomics to systems biology in animal and veterinary sciences: Progress, lessons and opportunities. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.04.028] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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