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Palma-Granados P, Muñoz M, Delgado-Gutierrez MA, Óvilo C, Nuñez Y, Fernández-Barroso MA, Sánchez-Esquiliche F, Ramírez L, García-Casco JM. Candidate SNPs for meat quality and carcass composition in free-range Iberian pigs. Meat Sci 2024; 207:109373. [PMID: 37906998 DOI: 10.1016/j.meatsci.2023.109373] [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: 06/30/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 11/02/2023]
Abstract
Several genetic markers, previously associated with meat quality traits, have been proposed to be included in Iberian pig breeding programs. However, before being implemented, effects of these candidate SNPs on premium cuts' yield should be evaluated to avoid potential undesirable antagonistic effects. Therefore, the main goals of this study were to evaluate the effects of a set of 26 polymorphisms on premium cuts weights and to corroborate their effects on meat quality in a larger population. Phenotypic data of approximately 1550 Iberian pigs were recorded. The PRKAG3_rs319678464C and PRKAG3_rs1108399077G alleles were associated with an increase of shear force, water losses and color values and a reduction of average daily gain (ADG). The CAST_rs196949783G > A and ADIPOQ_rs3476515794T > G SNPs mainly affected IMF content, with this last SNP being the only one with significant effects on any of the carcass measures, specifically Longissimus thoracis et lumborum (LTL) weight. The ELOVL6_rs3473714672A, FASN_rs331694510A, MTTP_rs335896411C and ACACA_rs340781986C alleles were linked to a higher percentage of oleic acid and monounsaturated FA and a decrease in palmitic, palmitoleic and saturated FA. Besides, suggestive effects were observed between ELOVL6_rs3473714672A > G and ham and shoulder weights, and between MTTP_rs335896411T > C and LTL muscle weight. Finally, the NR6A1_rs326780270T allele was associated with a significant increase in ADG and tended to reduce the ham weight. The SNPs mapped to PRKAG3 (rs319678464G > C), ACACA, FASN and CAST genes could be implemented in breeding programs to improve meat quality traits without undesirable effects on carcass composition. The SNPs mapped to PRKAG3 (rs1108399077G > A) ELOVL6, MTTP and NR6A1 should continue to be tested in a larger number of animals.
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Affiliation(s)
- Patricia Palma-Granados
- Centro de I+D en Cerdo Ibérico, INIA-CSIC, Ctra. EX101 km 4,7, 06300 Zafra, Spain; Dpto. Mejora Genética Animal, INIA-CSIC, Ctra La Coruña km 7,5, 28040 Madrid, Spain.
| | - María Muñoz
- Dpto. Mejora Genética Animal, INIA-CSIC, Ctra La Coruña km 7,5, 28040 Madrid, Spain
| | - Miguel A Delgado-Gutierrez
- Centro de I+D en Cerdo Ibérico, INIA-CSIC, Ctra. EX101 km 4,7, 06300 Zafra, Spain; Dpto. Mejora Genética Animal, INIA-CSIC, Ctra La Coruña km 7,5, 28040 Madrid, Spain
| | - Cristina Óvilo
- Dpto. Mejora Genética Animal, INIA-CSIC, Ctra La Coruña km 7,5, 28040 Madrid, Spain
| | - Yolanda Nuñez
- Dpto. Mejora Genética Animal, INIA-CSIC, Ctra La Coruña km 7,5, 28040 Madrid, Spain
| | - Miguel A Fernández-Barroso
- Centro de I+D en Cerdo Ibérico, INIA-CSIC, Ctra. EX101 km 4,7, 06300 Zafra, Spain; Dpto. Mejora Genética Animal, INIA-CSIC, Ctra La Coruña km 7,5, 28040 Madrid, Spain
| | | | - Luisa Ramírez
- Sánchez Romero Carvajal Jabugo SA, Ctra. San Juan del Puerto, 21290 Huelva, Spain
| | - Juan M García-Casco
- Centro de I+D en Cerdo Ibérico, INIA-CSIC, Ctra. EX101 km 4,7, 06300 Zafra, Spain; Dpto. Mejora Genética Animal, INIA-CSIC, Ctra La Coruña km 7,5, 28040 Madrid, Spain
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Deng X, Zhang Y, Song G, Fu Y, Chen Y, Gao H, Wang Q, Jin Z, Yin Y, Xu K. Integrative Analysis of Transcriptomic and Lipidomic Profiles Reveals a Differential Subcutaneous Adipose Tissue Mechanism among Ningxiang Pig and Berkshires, and Their Offspring. Animals (Basel) 2023; 13:3321. [PMID: 37958077 PMCID: PMC10647668 DOI: 10.3390/ani13213321] [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: 08/18/2023] [Revised: 09/28/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Adipose tissue composition contributes greatly to the quality and nutritional value of meat. Transcriptomic and lipidomic techniques were used to investigate the molecular mechanisms of the differences in fat deposition in Ningxiang pigs, Berkshires and F1 offspring. Transcriptomic analysis identified 680, 592, and 380 DEGs in comparisons of Ningxiang pigs vs. Berkshires, Berkshires vs. F1 offspring, and Ningxiang pigs vs. F1 offspring. The lipidomic analysis screened 423, 252, and 50 SCLs in comparisons of Ningxiang pigs vs. Berkshires, Berkshires vs. F1 offspring, and Ningxiang pigs vs. F1 offspring. Lycine, serine, and the threonine metabolism pathway, fatty acid biosynthesis and metabolism-related pathways were significantly enriched in comparisons of Berkshires vs. Ningxiang pigs and Berkshires vs. F1 offspring. The DEGs (PHGDH, LOC110256000) and the SCLs (phosphatidylserines) may have a great impact on the glycine, serine, and the threonine metabolism pathway. Moreover, the DEGs (FASN, ACACA, CBR4, SCD, ELOV6, HACD2, CYP3A46, CYP2B22, GPX1, and GPX3) and the SCLs (palmitoleic acid, linoleic acid, arachidonic acid, and icosadienoic acid) play important roles in the fatty acid biosynthesis and metabolism of fatty acids. Thus, the difference in fat deposition among Ningxiang pig, Berkshires, and F1 offspring may be caused by differences in the expression patterns of key genes in multiple enriched KEGG pathways. This research revealed multiple lipids that are potentially available biological indicators and screened key genes that are potential targets for molecular design breeding. The research also explored the molecular mechanisms of the difference in fat deposition among Ningxiang pig, Berkshires, and F1 pigs, and provided an insight into selection for backfat thickness and the fat composition of adipose tissue for future breeding strategies.
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Affiliation(s)
- Xiaoxiao Deng
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China; (X.D.); (Y.F.); (Y.C.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Changsha 410125, China
| | - Yuebo Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410125, China
| | - Gang Song
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410125, China
| | - Yawei Fu
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China; (X.D.); (Y.F.); (Y.C.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Changsha 410125, China
| | - Yue Chen
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China; (X.D.); (Y.F.); (Y.C.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Changsha 410125, China
| | - Hu Gao
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410125, China
| | - Qian Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410125, China
| | - Zhao Jin
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410125, China
| | - Yulong Yin
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China; (X.D.); (Y.F.); (Y.C.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Changsha 410125, China
| | - Kang Xu
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China; (X.D.); (Y.F.); (Y.C.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Changsha 410125, China
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Yang M, Zhang R, Liu X, Shi G, Liu H, Wang L, Hou X, Shi L, Wang L, Zhang L. Integrating genome-wide association study with RNA-seq revealed DBI as a good candidate gene for intramuscular fat content in Beijing black pigs. Anim Genet 2023; 54:24-34. [PMID: 36305366 DOI: 10.1111/age.13270] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 10/04/2022] [Accepted: 10/08/2022] [Indexed: 01/07/2023]
Abstract
Increasing intramuscular fat (IMF) content can enhance the sensory quality of meat, including tenderness, juiciness, flavor, and color. Genome-wide association study and RNA-sequencing (RNA-seq) analysis were used to identify candidate IMF genes in Beijing Black pigs, a popular species among consumers in northern China. Two and three single nucleotide polymorphisms were significantly associated with IMF in SSC13 and SSC15 respectively. Solute carrier family 4 member 7 (SLC4A7) on SSC13 and insulin induced gene 2 (INSIG2), coiled-coil domain containing 93 (CCDC93), and diazepam binding inhibitor acyl-CoA binding protein (DBI) on SSC15 are good candidate genes in this population. Furthermore, RNA-seq analysis was performed between high and low IMF groups, and 534 differentially expressed genes were identified. In addition, based on differentially expressed genes, Kyoto Encyclopedia of Genes and Genomes analysis revealed that peroxisome proliferator-activated receptors and FoxO signaling pathway pathways might contribute to IMF. Moreover, the DBI gene was identified as a candidate for IMF both by genome-wide association study and RNA-seq analysis, suggesting that it might be a crucial candidate gene for influencing IMF in Beijing Black pigs.
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Affiliation(s)
- Man Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Run Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiance Liu
- Beijing Heiliu Animal Husbandry Technology Co, Ltd, Beijing, China
| | - Guohua Shi
- Beijing Heiliu Animal Husbandry Technology Co, Ltd, Beijing, China
| | - Hai Liu
- Beijing Heiliu Animal Husbandry Technology Co, Ltd, Beijing, China
| | - Ligang Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinhua Hou
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lijun Shi
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lixian Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Longchao Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Liu X, Tian W, Wang L, Zhang L, Liang J, Wang L. Integrated Analysis of Long Non-Coding RNA and mRNA to Reveal Putative Candidate Genes Associated with Backfat Quality in Beijing Black Pig. Foods 2022; 11:foods11223654. [PMID: 36429246 PMCID: PMC9689697 DOI: 10.3390/foods11223654] [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: 09/16/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/17/2022] Open
Abstract
Pigs' backfat quality has an important impact on the quality of pork and pork products and has a strong relationship with nutrition and sensory characteristics. This study aimed to identify the related candidate genes of backfat quality and to preliminary clarify the molecular regulatory mechanism underlying pig backfat quality phenotypes. Expression assessments of long non-coding RNA (lncRNA) and mRNA profiling in backfat from high-quality (firm and white) and low-quality (soft and yellow) Beijing Black pigs were performed by RNA sequencing. Significantly different expressions were observed in 610 protein-coding genes and 290 lncRNAs between the two groups. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway annotation showed that some candidate differentially expressed genes that participate in lipid-related pathways and pigmentation terms may play a role in backfat quality in pigs. The cis-target and trans-target genes were predicted to explore the regulatory function of lncRNAs, and integrative analyses of different expression lncRNAs targets and different expression genes were performed. The results showed the regulatory networks of lncRNA-mRNA related to backfat quality, and our study obtained strong candidate genes for backfat quality: ELOVL5, SCD, DGAT2, SLC24A5, and TYRP1, which were involved in fat metabolism, adipogenesis regulation, and pigmentation. To our knowledge, this study is the first to demonstrate the molecular genetic mechanisms of backfat quality in pigs, and these findings improve the current understanding of backfat quality mechanisms and provide a foundation for further studies.
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Affiliation(s)
- Xin Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Weilong Tian
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Ligang Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Longchao Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jing Liang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Lixian Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: ; Tel.: +86-010-62818771
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Liu M, Sun C, Zheng X, Zhou Q, Liu B, Zhou Y, Xu P, Liu B. Comparative Proteomic Analysis Revealed the Mechanism of Tea Tree Oil Targeting Lipid Metabolism and Antioxidant System to Protect Hepatopancreatic Health in Macrobrachium rosenbergii. Front Immunol 2022; 13:906435. [PMID: 35711420 PMCID: PMC9195101 DOI: 10.3389/fimmu.2022.906435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/02/2022] [Indexed: 11/15/2022] Open
Abstract
Tea tree oil (TTO) is a pure natural plant essential oil. The studies evaluated the hepatopancreas lipid metabolism and antioxidant efficacy of Macrobrachium rosenbergii fed with 0 (CT group) and 100 mg/kg TTO (TT group) by label-free quantification proteomic analysis. Compared to the CT group, the TT group improved growth performance and increased the survival rate after stress. Dietary TTO also decreased hemolymph AST and ALT activities and decreased hepatopancreatic vacuolation. At the same time, hepatopancreas lipids droplets and hemolymph lipids (TG, TC, LDL-C) were decreased, and the peroxidation products content (MDA, LPO, 4-HNE) was also decreased. In addition, the levels of hepatopancreas antioxidant enzymes (T-AOC, CAT, and SOD) were increased in the TT group. With proteomic analysis, a total of 151 differentially expressed proteins (DEPs) (99 up-regulated and 52 down-regulated) were identified in the hepatopancreas. Kyoto Encyclopedia of Genes and Genomes (KEGG) and protein-protein interaction analysis showed that the 16 DEPs have interactions, which are mainly involved in the pathways related to lipid metabolism (fatty acid biosynthesis, fatty acid metabolism, glycerophospholipid metabolism) and redox reaction (cytochrome P450 enzyme systems). Furthermore, the mRNA expression of 15 proteins followed the proteomic analysis with qRT-PCR validation. Pearson correlation analysis showed that fatty acids and glycerophospholipid metabolism-related proteins were highly correlated to peroxide content, glycerophospholipid metabolism, and cytochrome P450 system-related proteins (CYP1A1, GSTT1, GPX4) were highly correlated to AST and ALT. Additionally, GPX4 is closely related to peroxide content and antioxidant enzyme activity. Our results revealed that TTO plays a protective role in the hepatopancreas targeting the critical enzymes and antioxidant reactions in lipid metabolism. Provides a new perspective to elucidate the action path of TTO in protecting invertebrate hepatopancreas, highlights the influence of lipid metabolism on hepatopancreas health and the interaction between lipid metabolism and antioxidant system in the regulation of TTO.
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Affiliation(s)
- Mingyang Liu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Cunxin Sun
- Key Laboratory of Aquatic Animal Nutrition and Health, Freshwater Fisheries Research Center, Chinese Academy of Fishery Science, Wuxi, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Xiaochuan Zheng
- Key Laboratory of Aquatic Animal Nutrition and Health, Freshwater Fisheries Research Center, Chinese Academy of Fishery Science, Wuxi, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Qunlan Zhou
- Key Laboratory of Aquatic Animal Nutrition and Health, Freshwater Fisheries Research Center, Chinese Academy of Fishery Science, Wuxi, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Bo Liu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Yifan Zhou
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Pao Xu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
- Key Laboratory of Aquatic Animal Nutrition and Health, Freshwater Fisheries Research Center, Chinese Academy of Fishery Science, Wuxi, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
- *Correspondence: Pao Xu, ; Bo Liu,
| | - Bo Liu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
- Key Laboratory of Aquatic Animal Nutrition and Health, Freshwater Fisheries Research Center, Chinese Academy of Fishery Science, Wuxi, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
- *Correspondence: Pao Xu, ; Bo Liu,
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Mármol-Sánchez E, Luigi-Sierra MG, Castelló A, Guan D, Quintanilla R, Tonda R, Amills M. Variability in porcine microRNA genes and its association with mRNA expression and lipid phenotypes. Genet Sel Evol 2021; 53:43. [PMID: 33947333 PMCID: PMC8097994 DOI: 10.1186/s12711-021-00632-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 04/15/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Mature microRNAs (miRNAs) play an important role in repressing the expression of a wide range of mRNAs. The presence of polymorphic sites in miRNA genes and their corresponding 3'UTR binding sites can disrupt canonical conserved miRNA-mRNA pairings, and thus modify gene expression patterns. However, to date such polymorphic sites in miRNA genes and their association with gene expression phenotypes and complex traits are poorly characterized in pigs. RESULTS By analyzing whole-genome sequences from 120 pigs and wild boars from Europe and Asia, we identified 285 single nucleotide polymorphisms (SNPs) that map to miRNA loci, and 109,724 SNPs that are located in predicted 7mer-m8 miRNA binding sites within porcine 3'UTR. In porcine miRNA genes, SNP density is reduced compared with their flanking non-miRNA regions. By sequencing the genomes of five Duroc boars, we identified 12 miRNA SNPs that were subsequently genotyped in their offspring (N = 345, Lipgen population). Association analyses of miRNA SNPs with 38 lipid-related traits and hepatic and muscle microarray expression phenotypes recorded in the Lipgen population were performed. The most relevant detected association was between the genotype of the rs319154814 (G/A) SNP located in the apical loop of the ssc-miR-326 hairpin precursor and PPP1CC mRNA levels in the liver (q-value = 0.058). This result was subsequently confirmed by qPCR (P-value = 0.027). The rs319154814 (G/A) genotype was also associated with several fatty acid composition traits. CONCLUSIONS Our findings show a reduced variability of porcine miRNA genes, which is consistent with strong purifying selection, particularly in the seed region that plays a critical role in miRNA binding. Although it is generally assumed that SNPs mapping to the seed region are those with the most pronounced consequences on mRNA expression, we show that a SNP mapping to the apical region of ssc-miR-326 is significantly associated with hepatic mRNA levels of the PPP1CC gene, one of its predicted targets. Although experimental confirmation of such an interaction is reported in humans but not in pigs, this result highlights the need to further investigate the functional effects of miRNA polymorphisms that are located outside the seed region on gene expression in pigs.
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Affiliation(s)
- Emilio Mármol-Sánchez
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - María Gracia Luigi-Sierra
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Anna Castelló
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Dailu Guan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140, Caldes de Montbui, Spain
| | - Raul Tonda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain. .,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
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Nonneman D, Lents CA, Rempel LA, Rohrer GA. Potential functional variants in AHR signaling pathways are associated with age at puberty in swine. Anim Genet 2021; 52:284-291. [PMID: 33667011 DOI: 10.1111/age.13051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2021] [Indexed: 12/31/2022]
Abstract
Puberty in female pigs is defined as age at first estrus and gilts that have an earlier age at puberty are more likely to have greater lifetime productivity. Because age at puberty is predictive for sow longevity and lifetime productivity, but not routinely measured in commercial herds, it would be beneficial to use genomic or marker-assisted selection to improve these traits. A GWAS at the US Meat Animal Research Center (USMARC) identified several loci associated with age at puberty in pigs. Candidate genes in these regions were scanned for potential functional variants using sequence information from the USMARC swine population founder animals and public databases. In total, 135 variants (SNP and insertion/deletions) in 39 genes were genotyped in 1284 phenotyped animals from a validation population sired by Landrace and Yorkshire industry semen using the Agena MassArray system. Twelve variants in eight genes were associated with age at puberty (P < 0.005) with estimated additive SNP effects ranging from 1.6 to 5.3 days. Nine of these variants were non-synonymous coding changes in AHR, CYP1A2, OR2M4, SDCCAG8, TBC1D1 and ZNF608, two variants were deletions of one and four codons in aryl hydrocarbon receptor, AHR, and the most significant SNP was near an acceptor splice site in the acetyl-CoA carboxylase alpha, ACACA. Several of the loci identified have a physiological and a genetic role in sexual maturation in humans and other animals and are involved in AHR-mediated pathways. Further functional validation of these variants could identify causative mutations that influence age at puberty in gilts and possibly sow lifetime productivity.
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Affiliation(s)
- Dan Nonneman
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Clay A Lents
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Lea A Rempel
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - Gary A Rohrer
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
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Mármol-Sánchez E, Quintanilla R, Luigi-Sierra MG, Amills M. An association analysis between a polymorphism in the SEC24A gene and lipid traits recorded in Duroc pigs. ITALIAN JOURNAL OF ANIMAL SCIENCE 2021. [DOI: 10.1080/1828051x.2021.1951129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Emilio Mármol-Sánchez
- Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Raquel Quintanilla
- Genètica i Millora Animal, Intitut de Recerca i Tecnologia Agroalimentàries (IRTA), Caldes de Montbui, Spain
| | - María Gracia Luigi-Sierra
- Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Marcel Amills
- Centre de Recerca en Agrigenòmica (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
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Bakhtiarizadeh MR, Alamouti AA. RNA-Seq based genetic variant discovery provides new insights into controlling fat deposition in the tail of sheep. Sci Rep 2020; 10:13525. [PMID: 32782325 PMCID: PMC7419499 DOI: 10.1038/s41598-020-70527-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/27/2020] [Indexed: 01/09/2023] Open
Abstract
Genetic basis of fat deposition in sheep tail have not been completely elucidated yet. Understanding the genetic mechanisms controlling fat-tail size can improve breeding strategies to modulate fat deposition. RNA sequencing has made it possible to discover genetic variants that may underlie various phenotypic differences. Hence, to identify genetic variants that are important for describing different fat-tail phenotypes in sheep, RNA sequencing was used for single nucleotide polymorphism (SNP) calling in two Iranian sheep breeds (Lori-Bakhtiari, fat-tailed; n = 4, vs Zel, thin-tailed; n = 4). Using a stringent pipeline, a total of 112,344 known SNPs were genotyped, of which 30,550 and 42,906 SNPs were shared by at least two Lori-Bakhtiari and Zel, respectively. Comparing these SNPs showed 2,774 (including 209 missense and 25 deleterious SNPs) and 10,470 (including 1,054 missense and 116 deleterious SNPs) breed-specific SNPs in Lori-Bakhtiari and Zel sheep, respectively. Potential breed-specific SNPs were detected by considering those located in QTL regions associated with fatness or reported as important candidates in previous similar studies. Of the breed-specific SNPs, 724 and 2,905 were located in the QTL regions. Functional enrichment analysis of the affected genes revealed several enriched gene ontologies and KEGG pathways related to fat metabolism. Based on the results, several affected genes were proposed to be strongly linked with fat deposition such as DGAT2, ACSL1, ACACA, ADIPOQ, ACLY, FASN, CPT2, SCD, ADCY6, PER3, CSF1R, SLC22A4, GFPT1, CDS2, BMP6, ACSS2, ELOVL6, HOXA10 and FABP4. Moreover, several SNPs were found in the candidate genes related to fatty acid oxidation introducing them as promising candidates responsible for lower fat content in tail of Zel. Our findings provided new insights into the genetic mechanisms of fat deposition in sheep, which can serve to designing appropriate breeding programs.
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Affiliation(s)
| | - Ali A Alamouti
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
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Luo R, Zheng Z, Yang C, Zhang X, Cheng L, Su G, Bai C, Li G. Comparative Transcriptome Analysis Provides Insights into the Polyunsaturated Fatty Acid Synthesis Regulation of Fat-1 Transgenic Sheep. Int J Mol Sci 2020; 21:ijms21031121. [PMID: 32046209 PMCID: PMC7038019 DOI: 10.3390/ijms21031121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/30/2020] [Accepted: 02/04/2020] [Indexed: 11/16/2022] Open
Abstract
Transgenic technology has huge application potential in agriculture and medical fields, such as producing new livestock varieties with new valuable features and xenotransplantation. However, how an exogenous gene affects the host animal’s gene regulation networks and their health status is still poorly understood. In the current study, Fat-1 transgenic sheep were generated, and the tissues from 100-day abnormal (DAF_1) and normal (DAF_2) fetuses, postnatal lambs (DAF_4), transgenic-silencing (DAFG5), and -expressing (DAFG6) skin cells were collected and subjected to transcriptome sequencing, and their gene expression profiles were compared in multiple dimensions. The results were as follows. For DAF_1, its abnormal development was caused by pathogen invasion but not the introduction of the Fat-1 gene. Fat-1 expression down-regulated the genes related to the cell cycle; the NF-κB signaling pathway and the PI3K/Akt signaling pathway were down-regulated, and the PUFAs (polyunsaturated fatty acids) biosynthesis pathway was shifted toward the biosynthesis of high-level n-3 LC-PUFAs (long-chain PUFAs). Four key node genes, FADS2, PPARA, PRKACA, and ACACA, were found to be responsible for the gene expression profile shift from the Fat-1 transgenic 100-day fetus to postnatal lamb, and FADS2 may play a key role in the accumulation of n-3 LC-PUFAs in Fat-1 transgenic sheep muscle. Our study provides new insights into the FUFAs synthesis regulation in Fat-1 transgenic animals.
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Affiliation(s)
- Rongsong Luo
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (R.L.); (Z.Z.); (X.Z.); (L.C.); (G.S.); (G.L.)
| | - Zhong Zheng
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (R.L.); (Z.Z.); (X.Z.); (L.C.); (G.S.); (G.L.)
| | - Chunrong Yang
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China;
| | - Xiaoran Zhang
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (R.L.); (Z.Z.); (X.Z.); (L.C.); (G.S.); (G.L.)
| | - Lei Cheng
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (R.L.); (Z.Z.); (X.Z.); (L.C.); (G.S.); (G.L.)
- College of Innovation Technology, Inner Mongolia University, Hohhot 010070, China
| | - Guanghua Su
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (R.L.); (Z.Z.); (X.Z.); (L.C.); (G.S.); (G.L.)
| | - Chunling Bai
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (R.L.); (Z.Z.); (X.Z.); (L.C.); (G.S.); (G.L.)
- Correspondence: ; Tel.: +86-0471-5298-583
| | - Guangpeng Li
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (R.L.); (Z.Z.); (X.Z.); (L.C.); (G.S.); (G.L.)
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Evaluation of SCD, ACACA and FASN Mutations: Effects on Pork Quality and Other Production Traits in Pigs Selected Based on RNA-Seq Results. Animals (Basel) 2020; 10:ani10010123. [PMID: 31940936 PMCID: PMC7023423 DOI: 10.3390/ani10010123] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/07/2020] [Accepted: 01/10/2020] [Indexed: 12/20/2022] Open
Abstract
Simple Summary This study aimed to evaluate mutations within three candidate genes (SCD, ACACA, FASN) for their effects on fattening and slaughter characteristics, as well as meat quality traits, including intramuscular fat (IMF) level in pork. They were selected within differentially expressed genes activated in response to variable backfat content obtained using the RNA sequencing method. The RNA-seq analysis identifies mutations/SNPs located in the mRNA and could be a useful tool for prediction of genetic markers in farm animals. The results showed that selection for FASN A allele in Polish Large White pigs could lead to improved meat quality traits such as water exudation and meat colour. However, analysed polymorphisms showed only slight effects on fat metabolism and IMF content. Abstract In recent years, pig producers have struggled with the problem of low intramuscular fat levels in pork, which impacts palatability and ultimately meat quality. Reduced levels of intramuscular fat are likely the result of breeding objectives aimed at increasing lean meat content. In this study, three mutations within candidate genes for fat content (SCD, ACACA, and FASN) were selected, based on RNA-seq results and the relationship between polymorphisms in genes related to lipid metabolism, fattening and slaughter characteristics, as well as pork quality, including IMF level, were evaluated to identify selection markers. Moreover, their impact on gene expression was also examined. The PCR–RFLP (polymerase cha- in reaction – restriction fragments length) method was used to establish genotypes and effect sizes of potential genetic markers were estimated using a GLM model. It was identified that a FASN missense variant was positively associated with the expression level of this gene, which suggested its linkage with a mutation having a regulatory function. The association study indicated that the FASN missense variant may play a role in the determination of feed conversion and meat colour. In turn, a mutation in the ACACA gene showed a relationship with IMF content in the Puławska breed where the differences reached as much as 20%. We suggest considering all three mutations in further studies based on different pig populations due to the crucial role of SCD, ACACA, and FASN genes in lipid metabolism.
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Mármol-Sánchez E, Luigi-Sierra MG, Quintanilla R, Amills M. Detection of homozygous genotypes for a putatively lethal recessive mutation in the porcine argininosuccinate synthase 1 (ASS1) gene. Anim Genet 2019; 51:106-110. [PMID: 31729055 DOI: 10.1111/age.12877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2019] [Indexed: 12/18/2022]
Abstract
The sequencing of the pig genome revealed the existence of homozygous individuals for a nonsense mutation in the argininosuccinate synthase 1 (ASS1) gene (rs81212146, c.944T>A, L315X). Paradoxically, an AA homozygous genotype for this polymorphism is expected to abolish the function of the ASS1 enzyme that participates in the urea cycle, leading to citrullinemia, hyperammonemia, coma and death. Sequencing of five Duroc boars that sired a population of 350 Duroc barrows revealed the segregation of the c.944T>A polymorphism, so we aimed to investigate its phenotypic consequences. Genotyping of this mutation in the 350 Duroc barrows revealed the existence of seven individuals homozygous (AA) for the nonsense mutation. These AA pigs had a normal weight despite the fact that mild citrullinemia often involves impaired growth. Sequencing of the region surrounding the mutation in TT, TA and AA individuals revealed that the A substitution in the second position of the codon (c.944T>A) is in complete linkage disequilibrium with a C replacement (c.943T>C) in the first position of the codon. This second mutation would compensate for the potentially damaging effect of the c.944T>A replacement. In fact, this is the most probable reason why pigs with homozygous AA genotypes at the 944 site of the ASS1 coding region are alive. Our results illustrate the complexities of predicting the consequences of nonsense mutations on gene function and phenotypes, not only because of annotation issues but also owing to the existence of genetic mechanisms that sometimes limit the penetrance of highly harmful mutations.
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Affiliation(s)
- E Mármol-Sánchez
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - M G Luigi-Sierra
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - R Quintanilla
- Animal Breeding and Genetics Programme, Institute for Research and Technology in Food and Agriculture (IRTA), Caldes de Montbui, 08140, Spain
| | - M Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
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Mármol-Sánchez E, Quintanilla R, Jordana J, Amills M. An association analysis for 14 candidate genes mapping to meat quality quantitative trait loci in a Duroc pig population reveals that the ATP1A2 genotype is highly associated with muscle electric conductivity. Anim Genet 2019; 51:95-100. [PMID: 31633210 DOI: 10.1111/age.12864] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2019] [Indexed: 01/14/2023]
Abstract
In previous GWAS carried out in a Duroc commercial line (Lipgen population), we detected on pig chromosomes 3, 4 and 14 several QTL for gluteus medius muscle redness (GM a*), electric conductivity in the longissimus dorsi muscle (LD CE) and vaccenic acid content in the LD muscle (LD C18:1 n - 7), respectively. We have genotyped, in the Lipgen population, 19 SNPs mapping to 14 genes located within these QTL. Subsequently, association analyses have been performed. After correction for multiple testing, two SNPs in the TGFBRAP1 (rs321173745) and SELENOI (rs330820437) genes were associated with GM a*, whereas ACADSB (rs81449951) and GPR26 (rs343087568) genotypes displayed significant associations with LD vaccenic content. Moreover, the polymorphisms located at the ATP1A2 (rs344748241), ATP8B2 (rs81382410) and CREB3L4 (rs321278469 and rs330133789) genes showed significant associations with LD CE. We made a second round of association analyses including the SNPs mentioned above as well as other SNPs located in the chromosomes to which they map. After performing a correction for multiple testing, the only association that remained significant at the chromosome-wide level was that between the ATP1A2 genotype and LD CE. From a functional point of view, this association is meaningful because this locus encodes a subunit of the Na+ /K+ -ATPase responsible for maintaining an electrochemical gradient across the plasma membrane.
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Affiliation(s)
- E Mármol-Sánchez
- Department of Animal Genetics, Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - R Quintanilla
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, Caldes de Montbui, 08140, Spain
| | - J Jordana
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - M Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
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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]
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González-Prendes R, Mármol-Sánchez E, Quintanilla R, Castelló A, Zidi A, Ramayo-Caldas Y, Cardoso TF, Manunza A, Cánovas Á, Amills M. About the existence of common determinants of gene expression in the porcine liver and skeletal muscle. BMC Genomics 2019; 20:518. [PMID: 31234802 PMCID: PMC6591854 DOI: 10.1186/s12864-019-5889-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 06/07/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The comparison of expression QTL (eQTL) maps obtained in different tissues is an essential step to understand how gene expression is genetically regulated in a context-dependent manner. In the current work, we have compared the transcriptomic and eQTL profiles of two porcine tissues (skeletal muscle and liver) which typically show highly divergent expression profiles, in 103 Duroc pigs genotyped with the Porcine SNP60 BeadChip (Illumina) and with available microarray-based measurements of hepatic and muscle mRNA levels. Since structural variation could have effects on gene expression, we have also investigated the co-localization of cis-eQTLs with copy number variant regions (CNVR) segregating in this Duroc population. RESULTS The analysis of differential expresssion revealed the existence of 1204 and 1490 probes that were overexpressed and underexpressed in the gluteus medius muscle when compared to liver, respectively (|fold-change| > 1.5, q-value < 0.05). By performing genome scans in 103 Duroc pigs with available expression and genotypic data, we identified 76 and 28 genome-wide significant cis-eQTLs regulating gene expression in the gluteus medius muscle and liver, respectively. Twelve of these cis-eQTLs were shared by both tissues (i.e. 42.8% of the cis-eQTLs identified in the liver were replicated in the gluteus medius muscle). These results are consistent with previous studies performed in humans, where 50% of eQTLs were shared across tissues. Moreover, we have identified 41 CNVRs in a set of 350 pigs from the same Duroc population, which had been genotyped with the Porcine SNP60 BeadChip by using the PennCNV and GADA softwares, but only a small proportion of these CNVRs co-localized with the cis-eQTL signals. CONCLUSION Despite the fact that there are considerable differences in the gene expression patterns of the porcine liver and skeletal muscle, we have identified a substantial proportion of common cis-eQTLs regulating gene expression in both tissues. Several of these cis-eQTLs influence the mRNA levels of genes with important roles in meat (CTSF) and carcass quality (TAPT1), lipid metabolism (TMEM97) and obesity (MARC2), thus evidencing the practical importance of dissecting the genetic mechanisms involved in their expression.
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Affiliation(s)
- Rayner González-Prendes
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.,Departament de Producció Animal-Agrotecnio Center, Universitat de Lleida, 191 Rovira Roure, 25198, Lleida, Spain
| | - Emilio Mármol-Sánchez
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140, Caldes de Montbui, Spain
| | - Anna Castelló
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Ali Zidi
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Yuliaxis Ramayo-Caldas
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Tainã Figueiredo Cardoso
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.,CAPES Foundation, Ministry of Education of Brazil, Brasilia D. F, Zip Code 70.040-020, Brazil
| | - Arianna Manunza
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Ángela Cánovas
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.,Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
| | - Marcel Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain. .,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
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Mármol-Sánchez E, Quintanilla R, Cardoso TF, Jordana Vidal J, Amills M. Polymorphisms of the cryptochrome 2 and mitoguardin 2 genes are associated with the variation of lipid-related traits in Duroc pigs. Sci Rep 2019; 9:9025. [PMID: 31227735 PMCID: PMC6588565 DOI: 10.1038/s41598-019-45108-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 05/24/2019] [Indexed: 01/06/2023] Open
Abstract
The genetic factors determining the phenotypic variation of porcine fatness phenotypes are still largely unknown. We investigated whether the polymorphism of eight genes (MIGA2, CRY2, NPAS2, CIART, ARNTL2, PER1, PER2 and PCK1), which display differential expression in the skeletal muscle of fasted and fed sows, is associated with the variation of lipid and mRNA expression phenotypes in Duroc pigs. The performance of an association analysis with the GEMMA software demonstrated that the rs330779504 SNP in the MIGA2 gene is associated with LDL concentration at 190 days (LDL2, corrected P-value = 0.057). Moreover, the rs320439526 SNP of the CRY2 gene displayed a significant association with stearic acid content in the longissimus dorsi muscle (LD C18:0, corrected P-value = 0.015). Both SNPs were also associated with the mRNA levels of the corresponding genes in the gluteus medius skeletal muscle. From a biological perspective these results are meaningful because MIGA2 protein plays an essential role in mitochondrial fusion, a process tightly connected with the energy status of the cell, while CRY2 is a fundamental component of the circadian clock. However, inclusion of these two SNPs in chromosome-wide association analyses demonstrated that they are not located at the peaks of significance for the two traits under study (LDL2 for rs330779504 and LD C18:0 for rs320439526), thus implying that these two SNPs do not have causal effects.
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Affiliation(s)
- Emilio Mármol-Sánchez
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Programme, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, Caldes de Montbui, Spain
| | - Taina F Cardoso
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain.,CAPES Foundation, Ministry of Education of Brazil, Brasilia, D. F., Brazil
| | - Jordi Jordana Vidal
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Marcel Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain. .,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain.
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Identification and Expression Analysis of Long Noncoding RNAs in Fat-Tail of Sheep Breeds. G3-GENES GENOMES GENETICS 2019; 9:1263-1276. [PMID: 30787031 PMCID: PMC6469412 DOI: 10.1534/g3.118.201014] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Emerging evidence suggests that long non-coding RNAs (lncRNAs) participate in the regulation of a diverse range of biological processes. However, most studies have been focused on a few established model organisms and little is known about lncRNAs in fat-tail development in sheep. Here, the first profile of lncRNA in sheep fat-tail along with their possible roles in fat deposition were investigated, based on a comparative transcriptome analysis between fat-tailed (Lori-Bakhtiari) and thin-tailed (Zel) Iranian sheep breeds. Among all identified lncRNAs candidates, 358 and 66 transcripts were considered novel intergenic (lincRNAs) and novel intronic (ilncRNAs) corresponding to 302 and 58 gene loci, respectively. Our results indicated that a low percentage of the novel lncRNAs were conserved. Also, synteny analysis identified 168 novel lincRNAs with the same syntenic region in human, bovine and chicken. Only seven lncRNAs were identified as differentially expressed genes between fat and thin tailed breeds. Q-RT-PCR results were consistent with the RNA-Seq data and validated the findings. Target prediction analysis revealed that the novel lncRNAs may act in cis or trans and regulate the expression of genes that are involved in the lipid metabolism. A gene regulatory network including lncRNA-mRNA interactions were constructed and three significant modules were found, with genes relevant to lipid metabolism, insulin and calcium signaling pathway. Moreover, integrated analysis with AnimalQTLdb database further suggested six lincRNAs and one ilncRNAs as candidates of sheep fat-tail development. Our results highlighted the putative contributions of lncRNAs in regulating expression of genes associated with fat-tail development in sheep.
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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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19
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Pena RN, Noguera JL, García-Santana MJ, González E, Tejeda JF, Ros-Freixedes R, Ibáñez-Escriche N. Five genomic regions have a major impact on fat composition in Iberian pigs. Sci Rep 2019; 9:2031. [PMID: 30765794 PMCID: PMC6375979 DOI: 10.1038/s41598-019-38622-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 12/18/2018] [Indexed: 12/22/2022] Open
Abstract
The adipogenic nature of the Iberian pig defines many quality attributes of its fresh meat and dry-cured products. The distinct varieties of Iberian pig exhibit great variability in the genetic parameters for fat deposition and composition in muscle. The aim of this work is to identify common and distinct genomic regions related to fatty acid composition in Retinto, Torbiscal, and Entrepelado Iberian varieties and their reciprocal crosses through a diallelic experiment. In this study, we performed GWAS using a high density SNP array on 382 pigs with the multimarker regression Bayes B method implemented in GenSel. A number of genomic regions showed strong associations with the percentage of saturated and unsaturated fatty acid in intramuscular fat. In particular, five regions with Bayes Factor >100 (SSC2 and SSC7) or >50 (SSC2 and SSC12) explained an important fraction of the genetic variance for miristic, palmitoleic, monounsaturated (>14%), oleic (>10%) and polyunsaturated (>5%) fatty acids. Six genes (RXRB, PSMB8, CHGA, ACACA, PLIN4, PLIN5) located in these regions have been investigated in relation to intramuscular composition variability in Iberian pigs, with two SNPs at the RXRB gene giving the most consistent results on oleic and monounsaturated fatty acid content.
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Affiliation(s)
- R N Pena
- Departament de Ciència Animal, Universitat de Lleida-Agrotecnio Center, 25198, Lleida, Spain
| | - J L Noguera
- IRTA, Genètica i Millora Animal, 25198, Lleida, Spain
| | | | - E González
- Tecnología de los alimentos, Universidad de Extremadura, 06006, Badajoz, Spain
| | - J F Tejeda
- Tecnología de los alimentos, Universidad de Extremadura, 06006, Badajoz, Spain
| | - R Ros-Freixedes
- Departament de Ciència Animal, Universitat de Lleida-Agrotecnio Center, 25198, Lleida, Spain.,The Roslin Institute, Edinburgh University, Easter Bush, EH25 9RG, UK
| | - N Ibáñez-Escriche
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022, Valencia, Spain.
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20
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Zhang HM, Xia HL, Jiang HR, Mao YJ, Qu KX, Huang BZ, Gong YC, Yang ZP. Longissimus dorsi muscle transcriptomic analysis of Yunling and Chinese simmental cattle differing in intramuscular fat content and fatty acid composition. Genome 2018; 61:549-558. [PMID: 29883552 DOI: 10.1139/gen-2017-0164] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Intramuscular fat (IMF) content and fatty acid (FA) composition vary significantly across beef cattle breeds, which play an important role in taste and nutritional value. However, the molecular mechanisms underlying these phenotypic differences remain unknown. The present study compared meat quality traits between Yunling cattle and Chinese Simmental cattle. Yunling cattle showed a lower IMF content and proportion of monounsaturated fatty acids (MUFA), as well as higher proportions of saturated fatty acids (SFA), polyunsaturated fatty acids (PUFA), and short-chain fatty acids (sc-FA) in the longissimus dorsi (LD) muscle than Chinese Simmental cattle. To further identify the candidate genes and pathways responsible for these phenotypic differences, the transcriptome of LD muscle from the two breeds were measured using RNA-seq. A total of 1347 differentially expressed genes were identified. The major metabolic pathways that were differentially modulated were lipolysis and glycometabolism. Yunling cattle showed a higher expression of lipolysis genes (ALDH9A1, ACSL5, ACADM, ACAT2, ACOT2) and a lower expression of genes related to glycometabolism (PGM1, GALM, PGM1, GPI, LDHA). This research identified candidate genes and pathways for IMF content and FA composition in the LD muscle of beef cattle, which may facilitate the design of new selection strategies to improve meat quality.
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Affiliation(s)
- H M Zhang
- a Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China.,b Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - H L Xia
- a Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China.,b Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - H R Jiang
- a Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China.,b Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Y J Mao
- a Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China.,b Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - K X Qu
- c Yunnan Academy of Grassland and Animal Science, Kunming, Yunnan 650212, China
| | - B Z Huang
- c Yunnan Academy of Grassland and Animal Science, Kunming, Yunnan 650212, China
| | - Y C Gong
- d The Centre for the Analysis of Genome Evolution and Function (CAGEF), University of Toronto, Toronto, ON M5S 2J7, Canada
| | - Z P Yang
- a Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China.,b Joint International Research Laboratory of Agriculture & Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
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21
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Wang Y, Ma C, Sun Y, Li Y, Kang L, Jiang Y. Dynamic transcriptome and DNA methylome analyses on longissimus dorsi to identify genes underlying intramuscular fat content in pigs. BMC Genomics 2017; 18:780. [PMID: 29025412 PMCID: PMC5639760 DOI: 10.1186/s12864-017-4201-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 10/08/2017] [Indexed: 01/12/2023] Open
Abstract
Background The intramuscular fat content (IMF) refers to the amount of fat within muscles, including the sum of phospholipids mainly found in cell membranes, triglycerides and cholesterol, and is determined both by hyperplasia and hypertrophy of adipocyte during the development of pigs. The IMF content is an important economic trait that is genetically controlled by multiple genes. The Laiwu pig is an indigenous fatty pig breed distributed in North China, characterized by excessively higher level of IMF content (9%~12%), therefore, is suitable for the identification of genes controlling IMF variations. To identify genes underlying IMF deposition, we performed genome-wide transcriptome and methylome analyses on longissimus dorsi (LD) muscle in Laiwu pigs across four developmental stages. Results A total of 22,524 expressed genes were detected and 1158 differentially expressed genes (DEGs) were hierarchically clustered in the LD muscle over four developmental stages from 60 d to 400 d. These genes were significantly clustered into four temporal expression profiles, and genes participating in fat cell differentiation and lipid biosynthesis processes were identified. From 120 d to 240 d, the period with the maximum IMF deposition rate, the lipid biosynthesis related genes (FOSL1, FAM213B and G0S2), transcription factors (TFs) (EGR1, KLF5, SREBF2, TP53 and TWIST1) and enriched pathways (steroid biosynthesis and fatty acid biosynthesis) were revealed; and fat biosynthesis relevant genes showing differences in DNA methylation in gene body or intergenic region were detected, such as FASN, PVALB, ID2, SH3PXD2B and EGR1. Conclusions This study provides a comprehensive landscape of transcriptome of the LD muscle in Laiwu pigs ranging from 60 to 400 days old, and methylome of the LD muscle in 120 d and 240 d Laiwu pigs. A set of candidate genes and TFs involved in fat biosynthesis process were identified, which were probably responsible for IMF deposition. The results from this study would provide a reference for the identification of genes controlling IMF variation, and for exploring molecular mechanisms underlying IMF deposition in pigs. Electronic supplementary material The online version of this article (10.1186/s12864-017-4201-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuding Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, No. 61 Daizong Street, Taian, 271018, People's Republic of China.,Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
| | - Cai Ma
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, No. 61 Daizong Street, Taian, 271018, People's Republic of China
| | - Yi Sun
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, No. 61 Daizong Street, Taian, 271018, People's Republic of China
| | - Yi Li
- Central Hospital of Taian, Taian, 271018, People's Republic of China
| | - Li Kang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, No. 61 Daizong Street, Taian, 271018, People's Republic of China
| | - Yunliang Jiang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, No. 61 Daizong Street, Taian, 271018, People's Republic of China.
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22
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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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23
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Eusebi PG, González-Prendes R, Quintanilla R, Tibau J, Cardoso TF, Clop A, Amills M. A genome-wide association analysis for carcass traits in a commercial Duroc pig population. Anim Genet 2017; 48:466-469. [DOI: 10.1111/age.12545] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/28/2016] [Indexed: 11/27/2022]
Affiliation(s)
- P. G. Eusebi
- 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. 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
| | - J. Tibau
- IRTA - Food Technology; Animal Genetics Program; Finca Camps i Armet Monells Spain
| | - T. F. Cardoso
- Department of Animal Genetics; Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB); Campus de la Universitat Autònoma de Barcelona Bellaterra 08193 Spain
- CAPES Foundation; Ministry of Education of Brazil; Brasilia D. F. 70.040-020 Brazil
| | - A. Clop
- Department of Animal Genetics; Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB); Campus de la Universitat Autònoma de Barcelona Bellaterra 08193 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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24
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González-Prendes R, Quintanilla R, Cánovas A, Manunza A, Figueiredo Cardoso T, Jordana J, Noguera JL, Pena RN, Amills M. Joint QTL mapping and gene expression analysis identify positional candidate genes influencing pork quality traits. Sci Rep 2017; 7:39830. [PMID: 28054563 PMCID: PMC5215505 DOI: 10.1038/srep39830] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 11/29/2016] [Indexed: 12/28/2022] Open
Abstract
Meat quality traits have an increasing importance in the pig industry because of their strong impact on consumer acceptance. Herewith, we have combined phenotypic and microarray expression data to map loci with potential effects on five meat quality traits recorded in the longissimus dorsi (LD) and gluteus medius (GM) muscles of 350 Duroc pigs, i.e. pH at 24 hours post-mortem (pH24), electric conductivity (CE) and muscle redness (a*), lightness (L*) and yellowness (b*). We have found significant genome-wide associations for CE of LD on SSC4 (~104 Mb), SSC5 (~15 Mb) and SSC13 (~137 Mb), while several additional regions were significantly associated with meat quality traits at the chromosome-wide level. There was a low positional concordance between the associations found for LD and GM traits, a feature that reflects the existence of differences in the genetic determinism of meat quality phenotypes in these two muscles. The performance of an eQTL search for SNPs mapping to the regions associated with meat quality traits demonstrated that the GM a* SSC3 and pH24 SSC17 QTL display positional concordance with cis-eQTL regulating the expression of several genes with a potential role on muscle metabolism.
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Affiliation(s)
- Rayner González-Prendes
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui 08140, Spain
| | - Angela Cánovas
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Arianna Manunza
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Tainã Figueiredo Cardoso
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.,CAPES Foundation, Ministry of Education of Brazil, Brasilia D. F., Zip Code 70.040-020, Brazil
| | - Jordi Jordana
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - José Luis Noguera
- Animal Breeding and Genetics Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Torre Marimon, Caldes de Montbui 08140, Spain
| | - Ramona N Pena
- Department of Animal Science, University of Lleida - Agrotecnio Center, Lleida 25198, Spain
| | - Marcel Amills
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
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25
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Chański W, González-Prendes R, Castelló A, Jordana J, Manunza A, Quintanilla R, Amills M. An association analysis between a missense polymorphism at the pig PCSK9 gene and serum lipid and meat quality traits in Duroc pigs. Livest Sci 2016. [DOI: 10.1016/j.livsci.2016.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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26
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Association of NLK polymorphisms with intramuscular fat content and fatty acid composition traits in pigs. Meat Sci 2016; 118:61-5. [DOI: 10.1016/j.meatsci.2016.03.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 03/16/2016] [Accepted: 03/24/2016] [Indexed: 12/16/2022]
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27
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Li H, Wang H, Yu L, Wang M, Liu S, Sun L, Chen Q. Effects of supplementation of rumen-protected choline on growth performance, meat quality and gene expression in longissimus dorsi muscle of lambs. Arch Anim Nutr 2016; 69:340-50. [PMID: 26305383 DOI: 10.1080/1745039x.2015.1073001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
This study determined the effects of rumen-protected choline (RPC) on growth performance, blood lipids, meat quality and expression of genes involved in fatty-acid metabolism in young lambs. A total of 24 Dorper × Hu lambs (about 20 kg body weight) were kept in individual pens and fed diets with 0%, 0.25%, 0.50% and 0.75% RPC for 60 d. Supplementation of 0.25% RPC increased average daily gain of lambs, whereas treatments had no significant effect on feed intake. The pH values of meat were increased at 0.25% RPC and both, dripping loss and shear force of meat, were significantly decreased in RPC-supplemented lambs. No significant changes were observed for dressing percentage and intramuscular fat. RPC supplementations had no significant effect on the concentrations of triglycerides and cholesterols in serum, but the concentration of high-density lipoprotein was decreased at 0.50% RPC and that of low-density lipoprotein was increased at 0.75% RPC. In m. longissimus dorsi, the expressions of cluster of differentiation 36 (CD36), acetyl-CoA carboxylase (ACC) and fatty-acid synthase (FASN) genes were increased at 0.25% RPC. Supplementation of 0.75% RPC increased the expressions of lipoprotein lipase (LPL) and FASN genes, decreased the expression of ACC gene and had no effect on CD36 gene. The results of this study showed that supplementation of 0.25% RPC could promote growth performance of lambs and improve meat quality. This may be mediated by effects on blood lipid profiles and the metabolism of fatty acids in skeleton muscles. However, the beneficial effects of 0.25% RPC supplementation need to be validated with a larger number of animals. Higher doses, particularly 0.75% RPC, showed adverse effects on live weight gain and ACC expression.
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Affiliation(s)
- Huawei Li
- a College of Animal Science and Technology , Yangzhou University , Yangzhou , China
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28
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Benítez R, Núñez Y, Fernández A, Isabel B, Fernández AI, Rodríguez C, Barragán C, Martín-Palomino P, López-Bote C, Silió L, Óvilo C. Effects of dietary fat saturation on fatty acid composition and gene transcription in different tissues of Iberian pigs. Meat Sci 2014; 102:59-68. [PMID: 25549539 DOI: 10.1016/j.meatsci.2014.12.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 12/10/2014] [Accepted: 12/12/2014] [Indexed: 10/24/2022]
Abstract
The effect of two diets, respectively enriched with SFA (S) and PUFA (P), on FA tissue composition and gene expression was studied in fattened Iberian pigs. The FA composition of adipose, muscular and liver tissues was affected by dietary treatment. S group showed higher MUFA and MUFA/SFA ratio and lower PUFA and n-6/n-3 ratio than P group in all analyzed tissues. In muscle and liver the extracted lipids were separated into neutral lipids and polar lipid fractions which showed significantly different responses to the dietary treatment, especially in liver where no significant effect of diet was observed in NL fraction. The expression of six candidate genes related to lipogenesis and FA oxidation was analyzed by qPCR. In liver, stearoyl CoA desaturase (SCD), acetyl CoA carboxylase alpha (ACACA) and malic enzyme 1 (ME1) genes showed higher expression in S group. SCD, ACACA, ME1, and fatty acid synthase (FASN) gene expression levels showed a wide variation across the tested tissues, with much higher expression levels observed in adipose tissue than other tissues. Tissue FA profile and gene expression results support the deposition of dietary FA, the lipogenic effect of dietary saturated fat in liver and the employment of saturated dietary fat for endogenous synthesis of MUFA in all the analyzed tissues.
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Affiliation(s)
- R Benítez
- Departamento Mejora Genética Animal, INIA, Ctra. Coruña Km 7.5, 28040 Madrid, Spain.
| | - Y Núñez
- Departamento Mejora Genética Animal, INIA, Ctra. Coruña Km 7.5, 28040 Madrid, Spain.
| | - A Fernández
- Departamento Mejora Genética Animal, INIA, Ctra. Coruña Km 7.5, 28040 Madrid, Spain.
| | - B Isabel
- Departamento Producción Animal, Facultad de Veterinaria, UCM, 28040 Madrid, Spain.
| | - A I Fernández
- Departamento Mejora Genética Animal, INIA, Ctra. Coruña Km 7.5, 28040 Madrid, Spain.
| | - C Rodríguez
- Departamento Mejora Genética Animal, INIA, Ctra. Coruña Km 7.5, 28040 Madrid, Spain.
| | - C Barragán
- Departamento Mejora Genética Animal, INIA, Ctra. Coruña Km 7.5, 28040 Madrid, Spain.
| | - P Martín-Palomino
- Universidad Alfonso X El Sabio, Campus de Villanueva de la Cañada, Avda. de la Universidad 1, 28691 Villanueva de la Cañada, Madrid, Spain.
| | - C López-Bote
- Departamento Producción Animal, Facultad de Veterinaria, UCM, 28040 Madrid, Spain.
| | - L Silió
- Departamento Mejora Genética Animal, INIA, Ctra. Coruña Km 7.5, 28040 Madrid, Spain.
| | - C Óvilo
- Departamento Mejora Genética Animal, INIA, Ctra. Coruña Km 7.5, 28040 Madrid, Spain.
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29
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Castelló A, Quintanilla R, Melo C, Gallardo D, Zidi A, Manunza A, Noguera JL, Tibau J, Jordana J, Pena RN, Amills M. Associations between pig adiponectin (ADIPOQ) genotype and serum lipid levels are modulated by age-specific modifiers. J Anim Sci 2014; 92:5367-73. [PMID: 25367522 DOI: 10.2527/jas.2014-8029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The adiponectin (ADIPOQ) locus is a positional and functional candidate gene for 2 porcine chromosome 13 (SSC13) QTL influencing cholesterol (CHOL) and low-density lipoprotein (LDL) concentrations in 190-d-old pigs. By sequencing 2.37 kb of the pig ADIPOQ cDNA, we have identified 1 c.*1512G>T 3' untranslated region polymorphism that has been genotyped in a Duroc pig commercial population with records for serum lipid levels at 45 and 190 d of age. Statistical analysis of the data have revealed significant associations between the ADIPOQ genotype and CHOL (P=0.0040) and LDL (P=0.0011) concentrations at 190 d but not at 45 d. In family 3, most of the SSC13 QTL effects on LDL levels at 190 d were explained by the ADIPOQ genotype. We also found an association with triglyceride levels at 45 d (P=0.0060) but not at 190 d. Measurement of allelic mRNA imbalance demonstrated that the G and T alleles are expressed at very similar levels in muscle and fat tissues, indicating that the c.*1512G>T polymorphism does not affect transcript abundance. As a whole, results obtained in the current work as well as previous data gathered in humans and pigs provide evidence that the magnitude of associations between blood lipid phenotypes and candidate loci genotypes may vary depending on the age of the individual, therefore suggesting the existence of dynamic genotype×environment interactions changing on a temporal scale.
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Affiliation(s)
- A Castelló
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain
| | - R Quintanilla
- IRTA, Genètica i Millora Animal, Torre Marimon, 08140 Caldes de Montbui, Spain
| | - C Melo
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain
| | - D Gallardo
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain
| | - A Zidi
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain
| | - A Manunza
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain
| | - J L Noguera
- IRTA, Genètica i Millora Animal, Torre Marimon, 08140 Caldes de Montbui, Spain
| | - J Tibau
- IRTA, Genètica i Millora Animal, Torre Marimon, 08140 Caldes de Montbui, Spain
| | - J Jordana
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain
| | - R N Pena
- Department of Animal Production, University of Lleida-Agrotecnio Center, 25198, Lleida, Spain
| | - M Amills
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain
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Stachowiak M, Nowacka-Woszuk J, Szydlowski M, Switonski M. The ACACA and SREBF1 genes are promising markers for pig carcass and performance traits, but not for fatty acid content in the longissimus dorsi muscle and adipose tissue. Meat Sci 2013; 95:64-71. [DOI: 10.1016/j.meatsci.2013.04.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 02/01/2013] [Accepted: 04/03/2013] [Indexed: 10/27/2022]
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31
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Muñoz M, Fernández AI, Benítez R, Pena RN, Folch JM, Rodríguez MDC, Silió L, Alves E. Disentangling Two QTL on Porcine Chromosome 12 for Backfat Fatty Acid Composition. Anim Biotechnol 2013; 24:168-86. [DOI: 10.1080/10495398.2012.763130] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Casellas J, Vidal O, Pena RN, Gallardo D, Manunza A, Quintanilla R, Amills M. Genetics of serum and muscle lipids in pigs. Anim Genet 2013; 44:609-19. [DOI: 10.1111/age.12049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2013] [Indexed: 01/31/2023]
Affiliation(s)
- J. Casellas
- Departament de Ciència Animal i dels Aliments; Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
| | - O. Vidal
- Departament de Biologia; Universitat de Girona; Girona 17071 Spain
| | - R. N. Pena
- Departament de Producció Animal; Universitat de Lleida; Lleida 25198 Spain
| | - D. Gallardo
- Departament de Ciència Animal i dels Aliments; Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
| | - A. Manunza
- Department of Animal Genetics; Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB); Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
| | | | - M. Amills
- Department of Animal Genetics; Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB); Universitat Autònoma de Barcelona; Bellaterra 08193 Spain
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Ramírez O, Quintanilla R, Varona L, Gallardo D, Díaz I, Pena R, Amills M. DECR1
and ME1
genotypes are associated with lipid composition traits in Duroc pigs. J Anim Breed Genet 2013; 131:46-52. [DOI: 10.1111/jbg.12035] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 02/27/2013] [Indexed: 11/29/2022]
Affiliation(s)
- O. Ramírez
- Departament de Ciència Animal i dels Aliments; Facultat de Veterinària; Universitat Autònoma de Barcelona; Bellaterra Spain
| | | | - L. Varona
- Genètica i Millora Animal; IRTA; Lleida Spain
| | - D. Gallardo
- Departament de Ciència Animal i dels Aliments; Facultat de Veterinària; Universitat Autònoma de Barcelona; Bellaterra Spain
| | - I. Díaz
- Centre de Tecnologia de la Carn (IRTA); Monells Spain
| | - R.N. Pena
- Genètica i Millora Animal; IRTA; Lleida Spain
| | - M. Amills
- Departament de Ciència Animal i dels Aliments; Facultat de Veterinària; Universitat Autònoma de Barcelona; Bellaterra Spain
- Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB); Universitat Autònoma de Barcelona; Bellaterra Spain
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34
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Melo C, Gallardo D, Quintanilla R, Zidi A, Castelló A, Díaz I, Amills M, Pena R. An association analysis between polymorphisms of the pig solute carrier family 27A (SLC27A), member 1 and 4 genes and serum and muscle lipid traits. Livest Sci 2013. [DOI: 10.1016/j.livsci.2013.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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35
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Melo C, Quintanilla R, Gallardo D, Zidi A, Jordana J, Díaz I, Pena RN, Amills M. Association analysis with lipid traits of 2 candidate genes (LRP12 and TRIB1) mapping to a SSC4 QTL for serum triglyceride concentration in pigs. J Anim Sci 2013; 91:1531-7. [PMID: 23408821 DOI: 10.2527/jas.2012-5517] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The performance of a genome scan for serum lipid traits at 45 and 190 d in 5 half-sib families of Duroc pigs allowed us to detect several pig chromosomal regions with significant effects on these phenotypes. In the current work, we aimed to refine the position of 1 chromosome 4 (SSC4) genome-wide significant QTL for serum triglyceride concentration at 190 d. Genotyping of 4 additional microsatellites allowed reduction of the 90% confidence interval of this QTL to the genomic interval between markers SW2409 and SW839. Sequencing experiments were performed to characterize the variability of 2 lipid-related genes, the lipoprotein receptor-related protein 12 (LRP12) and tribbles homolog 1 (TRIB1) loci, that map to this region. In this way, 2 (c.771A > G and c.1101A > G) and 1 (c.*156_157del) polymorphisms were identified at the LRP12 coding region and TRIB1 3' untranslated region, respectively. Association analyses between LRP12 and TRIB1 genotypes did not reveal any significant effect on serum lipid concentrations, suggesting that variation of these two loci does not explain the segregation of the SSC4 QTL. However, highly significant associations were observed for gluteus medius saturated fatty acid content (LRP12 c.1101A > G, P = 0.0006; TRIB1 c.*156_157del, P = 0.0003). In the light of these and other findings, the potential involvement of LRP12 and TRIB1 in muscle lipid metabolism deserves to be further explored.
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Affiliation(s)
- C Melo
- Department of Animal Genetics, Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB), Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain
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36
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Structure and function of biotin-dependent carboxylases. Cell Mol Life Sci 2012; 70:863-91. [PMID: 22869039 DOI: 10.1007/s00018-012-1096-0] [Citation(s) in RCA: 258] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 07/07/2012] [Accepted: 07/09/2012] [Indexed: 12/14/2022]
Abstract
Biotin-dependent carboxylases include acetyl-CoA carboxylase (ACC), propionyl-CoA carboxylase (PCC), 3-methylcrotonyl-CoA carboxylase (MCC), geranyl-CoA carboxylase, pyruvate carboxylase (PC), and urea carboxylase (UC). They contain biotin carboxylase (BC), carboxyltransferase (CT), and biotin-carboxyl carrier protein components. These enzymes are widely distributed in nature and have important functions in fatty acid metabolism, amino acid metabolism, carbohydrate metabolism, polyketide biosynthesis, urea utilization, and other cellular processes. ACCs are also attractive targets for drug discovery against type 2 diabetes, obesity, cancer, microbial infections, and other diseases, and the plastid ACC of grasses is the target of action of three classes of commercial herbicides. Deficiencies in the activities of PCC, MCC, or PC are linked to serious diseases in humans. Our understanding of these enzymes has been greatly enhanced over the past few years by the crystal structures of the holoenzymes of PCC, MCC, PC, and UC. The structures reveal unanticipated features in the architectures of the holoenzymes, including the presence of previously unrecognized domains, and provide a molecular basis for understanding their catalytic mechanism as well as the large collection of disease-causing mutations in PCC, MCC, and PC. This review will summarize the recent advances in our knowledge on the structure and function of these important metabolic enzymes.
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The SNPs in the ACACA gene are effective on fatty acid composition in Holstein milk. Mol Biol Rep 2012; 39:8637-44. [PMID: 22718502 DOI: 10.1007/s11033-012-1718-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 06/06/2012] [Indexed: 10/28/2022]
Abstract
Fatty acid composition is an important economic trait for both dairy and beef cattle and controlled by genetic factors. Candidate genes controlling fatty acid composition may be found in fat synthesis and metabolism pathways. Acetyl-CoA carboxylase is the flux-determining enzyme in the regulation of fatty acid synthesis in animal tissues. One of two isozymes of this enzyme, acetyl-CoA carboxylase-α (ACACA), catalyses the first committed step of fatty acid synthesis in mammalian cytosol, leading to the biosynthesis of long-chain fatty acids. In the current study, the sequence comparison of the coding sequence (CDS) and two promoter regions (PIA and PIII) in bovine ACACA gene was performed between Japanese Black and Holstein cattle to detect nucleotide polymorphisms influencing fatty acid composition in milk and beef. Five single nucleotide polymorphisms (SNPs) were identified in the CDS region, 28 SNPs in the PIA region and three SNPs in the PIII region. Association study revealed that CCT/CCT type of PIII_#1, #2/PIA_#26 indicated a higher percentage of C14:0 in the milk of the Holstein cattle than CCT/GTC type (p = 0.050) and that a difference of the percentage of C16:0 was observed between CCT/CCT and GTC/GTC type (p = 0.023). CDS_#2 T/T type indicated a higher percentage of C18:0 than T/C type (p = 0.008). In addition, the Japanese Black cattle with CC/GT type of PIII_#1, #2 showed a higher percentage of C18:2 in the meat than those with GT/GT type (p = 0.025). Since PIII is the promoter specific to mammary gland during lactation, the altered expression of the ACACA gene owing to the SNPs in the PIII region may influence the fatty acid composition in the milk.
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38
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Cánovas A, Pena RN, Gallardo D, Ramírez O, Amills M, Quintanilla R. Segregation of regulatory polymorphisms with effects on the gluteus medius transcriptome in a purebred pig population. PLoS One 2012; 7:e35583. [PMID: 22545120 PMCID: PMC3335821 DOI: 10.1371/journal.pone.0035583] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 03/19/2012] [Indexed: 01/21/2023] Open
Abstract
Background The main goal of the present study was to analyse the genetic architecture of mRNA expression in muscle, a tissue with an outmost economic importance for pig breeders. Previous studies have used F2 crosses to detect porcine expression QTL (eQTL), so they contributed with data that mostly represents the between-breed component of eQTL variation. Herewith, we have analysed eQTL segregation in an outbred Duroc population using two groups of animals with divergent fatness profiles. This approach is particularly suitable to analyse the within-breed component of eQTL variation, with a special emphasis on loci involved in lipid metabolism. Methodology/Principal Findings GeneChip Porcine Genome arrays (Affymetrix) were used to determine the mRNA expression levels of gluteus medius samples from 105 Duroc barrows. A whole-genome eQTL scan was carried out with a panel of 116 microsatellites. Results allowed us to detect 613 genome-wide significant eQTL unevenly distributed across the pig genome. A clear predominance of trans- over cis-eQTL, was observed. Moreover, 11 trans-regulatory hotspots affecting the expression levels of four to 16 genes were identified. A Gene Ontology study showed that regulatory polymorphisms affected the expression of muscle development and lipid metabolism genes. A number of positional concordances between eQTL and lipid trait QTL were also found, whereas limited evidence of a linear relationship between muscle fat deposition and mRNA levels of eQTL regulated genes was obtained. Conclusions/Significance Our data provide substantial evidence that there is a remarkable amount of within-breed genetic variation affecting muscle mRNA expression. Most of this variation acts in trans and influences biological processes related with muscle development, lipid deposition and energy balance. The identification of the underlying causal mutations and the ascertainment of their effects on phenotypes would allow gaining a fundamental perspective about how complex traits are built at the molecular level.
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Affiliation(s)
| | - Ramona N. Pena
- IRTA, Genètica i Millora Animal, Lleida, Spain
- * E-mail: (RQ); (RP)
| | - David Gallardo
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Oscar Ramírez
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Marcel Amills
- Departament de Genètica Animal, Centre de Recerca en Agrigenòmica (CRAG), Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
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39
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Maharani D, Jung YK, Jo C, Jung WY, Nam KC, Seo KS, Lee SH, Lee JH. Evaluation of Three Candidate Genes Affecting Fatty Acid Composition in Pigs. Korean J Food Sci Anim Resour 2012. [DOI: 10.5851/kosfa.2012.32.1.6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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40
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Muñoz M, Alves E, Corominas J, Folch JM, Casellas J, Noguera JL, Silió L, Fernández AI. Survey of SSC12 Regions Affecting Fatty Acid Composition of Intramuscular Fat Using High-Density SNP Data. Front Genet 2012; 2:101. [PMID: 22303395 PMCID: PMC3262226 DOI: 10.3389/fgene.2011.00101] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 12/14/2011] [Indexed: 11/13/2022] Open
Abstract
Fatty acid composition is a critical aspect of pork because it affects sensorial and technological aspects of meat quality and it is relevant for human health. Previous studies identified significant QTLs in porcine chromosome 12 for fatty acid profile of back fat (BF) and intramuscular fat (IMF). In the present study, 374 SNPs mapped in SSC12 from the 60K Porcine SNP Beadchip were used. We have combined linkage and association analyses with expression data analysis in order to identify regions of SSC12 that could affect fatty acid composition of IMF in longissimus muscle. The QTL scan showed a region around the 60-cM position that significantly affects palmitic fatty acid and two related fatty acid indexes. The Iberian QTL allele increased the palmitic content (+2.6% of mean trait). This QTL does not match any of those reported in the previous study on fatty acid composition of BF, suggesting different genetic control acting at both tissues. The SNP association analyses showed significant associations with linolenic and palmitic acids besides several indexes. Among the polymorphisms that affect palmitic fatty acid and match the QTL region at 60 cM, there were three that mapped in the Phosphatidylcholine transfer protein (PCTP) gene and one in the Acetyl-CoA Carboxylase ∝ gene (ACACA). Interestingly one of the PCTP SNPs also affected significantly unsaturated and double bound indexes and the ratio between polyunsaturated/monounsaturated fatty acids. Differential expression was assessed on longissimus muscle conditional on the genotype of the QTL and on the most significant SNPs, according to the results obtained in the former analyses. Results from the microarray expression analyses, validated by RT-qPCR, showed that PCTP expression levels significantly vary depending on the QTL as well as on the own PCTP genotype. The results obtained with the different approaches point out the PCTP gene as a powerful candidate underlying the QTL for palmitic content.
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Affiliation(s)
- María Muñoz
- Departament Mejora Genética Animal, Instituto Nacional de Investigaciones Agrarias Madrid, Spain
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41
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Quintanilla R, Pena RN, Gallardo D, Cánovas A, Ramírez O, Díaz I, Noguera JL, Amills M. Porcine intramuscular fat content and composition are regulated by quantitative trait loci with muscle-specific effects1. J Anim Sci 2011; 89:2963-71. [DOI: 10.2527/jas.2011-3974] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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42
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Kim SW, Choi YI, Choi JS, Kim JJ, Choi BH, Kim TH, Kim KS. Porcine Fatty Acid Synthase Gene Polymorphisms Are Associated with Meat Quality and Fatty Acid Composition. Korean J Food Sci Anim Resour 2011. [DOI: 10.5851/kosfa.2011.31.3.356] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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43
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Maharani D, Jo CR, Jeon JT, Lee JH. Quantitative Trait Loci and Candidate Genes Affecting Fatty Acid Composition in Cattle and Pig. Korean J Food Sci Anim Resour 2011. [DOI: 10.5851/kosfa.2011.31.3.325] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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44
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Hu G, Wang S, Tian J, Chu L, Li H. Epistatic effect between ACACA and FABP2 gene on abdominal fat traits in broilers. J Genet Genomics 2011; 37:505-12. [PMID: 20816383 DOI: 10.1016/s1673-8527(09)60070-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Revised: 04/28/2010] [Accepted: 04/29/2010] [Indexed: 02/02/2023]
Abstract
Epistasis is generally defined as the interaction between two or more genes or their mRNA or protein products to influence a single trait. Experimental evidence suggested that epistasis could be important in the determination of the genetic architecture of complex traits in domestic animals. Acetyl-coenzyme A carboxylase alpha (ACACA) and fatty acid binding protein 2 (FABP2) are both key factors of lipogenesis and transport. They may play a crucial role in the weight variability of abdominal adipose tissue in the growing chicken. In this study, the polymorphisms of c.2292G>A in ACACA and c.-561A>C in FABP2 were detected among individuals from two broiler lines which were divergently selected for abdominal fat content. Epistasis between the two SNPs on abdominal fat weight (AFW) and abdominal fat percentage (AFP) was analyzed. The additive x additive epistatic components between these two SNPs were found significant or suggestively significant on both AFW and AFP in lean lines of the 9th and 10th generation; whereas, it was not significantly associated with either AFW or AFP in fat lines. At the same time, there were not any other significant epistatic components found in both generations or in both lines. Significant epistatic effects between these two SNPs found only in the lean lines could partly be due to the fact that the abdominal fat traits in these two experimental lines have been greatly modified by strong artificial selection. The results suggested that the epistasis mode may be different between the lean and fat chicken lines. Our results could be helpful in further understanding the genetic interaction between candidate genes contributing to phenotypic variation of abdominal fat content in broilers.
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Affiliation(s)
- Guo Hu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
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45
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Dervishi E, Serrano C, Joy M, Serrano M, Rodellar C, Calvo JH. The effect of feeding system in the expression of genes related with fat metabolism in semitendinous muscle in sheep. Meat Sci 2011; 89:91-7. [PMID: 21543161 DOI: 10.1016/j.meatsci.2011.04.003] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 04/05/2011] [Accepted: 04/06/2011] [Indexed: 12/30/2022]
Abstract
The effect of feeding system on the expression of LPL, ACACA, FASN, FABP4, DGAT1, SCD, CPT1B, PRKAA2, LEP, SREBP1, PPARG, PPARA and CEBPB genes in semitendinous muscle was studied. Forty-four single born male lambs of the Rasa Aragonesa breed, allocated to four different dietary treatments, were used: grazing alfalfa, grazing alfalfa with supplement for lambs, indoor lambs with grazing ewes and drylot. Significant differences were found in the expression of genes LPL, ACACA, FASN, FABP4, CPT1B and SCD. Genes related to adipogenesis (LPL, ACACA, FASN, FABP4, and SCD) are up-regulated in the intensive groups. In grazing groups CPT1B gene expression, related to β-oxidation process, is up-regulated. The relative expression of CPT1B was 1.54 fold higher in ALF+S, and 0.43 and 0.37 fold lower in IND- GRE and IND, respectively. The results support the hypothesis that changes in fatty acid profile due to feeding system implicate changes in the mRNA expression level of genes related with fat metabolism. Feeding strategy is an important tool to manipulate intramuscular fatty acid profile in meat through altering gene expression of enzymes related with fat metabolism.
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Affiliation(s)
- E Dervishi
- Unidad de Tecnología en Producción Animal, CITA, Zaragoza, Spain.
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46
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Cánovas A, Quintanilla R, Amills M, Pena RN. Muscle transcriptomic profiles in pigs with divergent phenotypes for fatness traits. BMC Genomics 2010; 11:372. [PMID: 20540717 PMCID: PMC2894043 DOI: 10.1186/1471-2164-11-372] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 06/11/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Selection for increasing intramuscular fat content would definitively improve the palatability and juiciness of pig meat as well as the sensorial and organoleptic properties of cured products. However, evidences obtained in human and model organisms suggest that high levels of intramuscular fat might alter muscle lipid and carbohydrate metabolism. We have analysed this issue by determining the transcriptomic profiles of Duroc pigs with divergent phenotypes for 13 fatness traits. The strong aptitude of Duroc pigs to have high levels of intramuscular fat makes them a valuable model to analyse the mechanisms that regulate muscle lipid metabolism, an issue with evident implications in the elucidation of the genetic basis of human metabolic diseases such as obesity and insulin resistance. RESULTS Muscle gene expression profiles of 68 Duroc pigs belonging to two groups (HIGH and LOW) with extreme phenotypes for lipid deposition and composition traits have been analysed. Microarray and quantitative PCR analysis showed that genes related to fatty acid uptake, lipogenesis and triacylglycerol synthesis were upregulated in the muscle tissue of HIGH pigs, which are fatter and have higher amounts of intramuscular fat than their LOW counterparts. Paradoxically, lipolytic genes also showed increased mRNA levels in the HIGH group suggesting the existence of a cycle where triacylglycerols are continuously synthesized and degraded. Several genes related to the insulin-signalling pathway, that is usually impaired in obese humans, were also upregulated. Finally, genes related to antigen-processing and presentation were downregulated in the HIGH group. CONCLUSION Our data suggest that selection for increasing intramuscular fat content in pigs would lead to a shift but not a disruption of the metabolic homeostasis of muscle cells. Future studies on the post-translational changes affecting protein activity or expression as well as information about protein location within the cell would be needed to to elucidate the effects of lipid deposition on muscle metabolism in pigs.
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Affiliation(s)
- Angela Cánovas
- IRTA, Genètica i Millora Animal, 191 Av Alcalde Rovira Roure, 25198 Lleida, Spain
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47
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Switonski M, Stachowiak M, Cieslak J, Bartz M, Grzes M. Genetics of fat tissue accumulation in pigs: a comparative approach. J Appl Genet 2010; 51:153-68. [DOI: 10.1007/bf03195724] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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48
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García-Fernández M, Gutiérrez-Gil B, Garcia-Gámez E, Arranz JJ. Identification of single nucleotide polymorphisms in the ovine acetyl-CoA carboxylase-alpha gene. Small Rumin Res 2010. [DOI: 10.1016/j.smallrumres.2009.12.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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