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Lorenzetti WR, Ibelli AMG, Peixoto JDO, Savoldi IR, Mores MAZ, de Souza Romano G, do Carmo KB, Ledur MC. The downregulation of genes encoding muscle proteins have a potential role in the development of scrotal hernia in pigs. Mol Biol Rep 2024; 51:822. [PMID: 39023774 DOI: 10.1007/s11033-024-09766-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 06/30/2024] [Indexed: 07/20/2024]
Abstract
BACKGROUND Testicular descent is a physiological process regulated by many factors. Eventually, disturbances in the embryological/fetal development path facilitate the occurrence of scrotal hernia, a congenital malformation characterized by the presence of intestinal portions within the scrotal sac due to the abnormal expansion of the inguinal ring. In pigs, some genes have been related to this anomaly, but the genetic mechanisms involved remain unclear. This study aimed to investigate the expression profile of a set of genes potentially involved with the manifestation of scrotal hernia in the inguinal ring tissue. METHODS AND RESULTS Tissue samples from the inguinal ring/canal of normal and scrotal hernia-affected male pigs with approximately 30 days of age were used. Relative expression analysis was performed using qPCR to confirm the expression profile of 17 candidate genes previously identified in an RNA-Seq study. Among them, the Myosin heavy chain 1 (MYH1), Desmin (DES), and Troponin 1 (TNNI1) genes were differentially expressed between groups and had reduced levels of expression in the affected animals. These genes encode proteins involved in the formation of muscle tissue, which seems to be important for increasing the resistance of the inguinal ring to the abdominal pressure, which is essential to avoid the occurrence of scrotal hernia. CONCLUSIONS The downregulation of muscular candidate genes in the inguinal tissue clarifies the genetic mechanisms involved with this anomaly in its primary site, providing useful information for developing strategies to control this malformation in pigs and other mammals.
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Affiliation(s)
- William Raphael Lorenzetti
- Programa de Pós-graduação em Zootecnia, Centro de Educação Superior do Oeste (CEO), Universidade do Estado de Santa Catarina, UDESC, Rua Beloni Trombeta Zanin 680E, Chapecó, Santa Catarina, 89815-630, Brazil
| | - Adriana Mércia Guaratini Ibelli
- Embrapa Suínos e Aves, Rodovia BR153, km 110, Distrito de Tamanduá, Caixa Postal: 321, Concórdia, Santa Catarina, 89715-899, Brazil
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Estadual do Centro-Oeste, Alameda Élio Antonio Dalla Vecchia, 838, Guarapuava, Paraná, 85040-167, Brazil
- Embrapa Pecuária Sudeste, Rodovia Washington Luiz, Km 234, São Carlos, São Paulo, 13560-970, Brazil
| | - Jane de Oliveira Peixoto
- Embrapa Suínos e Aves, Rodovia BR153, km 110, Distrito de Tamanduá, Caixa Postal: 321, Concórdia, Santa Catarina, 89715-899, Brazil
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Estadual do Centro-Oeste, Alameda Élio Antonio Dalla Vecchia, 838, Guarapuava, Paraná, 85040-167, Brazil
| | - Igor Ricardo Savoldi
- Programa de Pós-graduação em Zootecnia, Centro de Educação Superior do Oeste (CEO), Universidade do Estado de Santa Catarina, UDESC, Rua Beloni Trombeta Zanin 680E, Chapecó, Santa Catarina, 89815-630, Brazil
- Laudo laboratório Avícola, Rodovia BR-365, Morumbi, Uberlândia, Minas Gerais, 38407180, Brazil
| | - Marcos Antônio Zanella Mores
- Embrapa Suínos e Aves, Rodovia BR153, km 110, Distrito de Tamanduá, Caixa Postal: 321, Concórdia, Santa Catarina, 89715-899, Brazil
| | | | - Kamilla Bleil do Carmo
- Universidade do Contestado, Concórdia, Santa Catarina, Brazil
- Instituto Federal Catarinense, Rodovia SC 283, km 17, Concórdia, Santa Catarina, 89703-720, Brazil
| | - Mônica Corrêa Ledur
- Programa de Pós-graduação em Zootecnia, Centro de Educação Superior do Oeste (CEO), Universidade do Estado de Santa Catarina, UDESC, Rua Beloni Trombeta Zanin 680E, Chapecó, Santa Catarina, 89815-630, Brazil.
- Embrapa Suínos e Aves, Rodovia BR153, km 110, Distrito de Tamanduá, Caixa Postal: 321, Concórdia, Santa Catarina, 89715-899, Brazil.
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Jové-Juncà T, Crespo-Piazuelo D, González-Rodríguez O, Pascual M, Hernández-Banqué C, Reixach J, Quintanilla R, Ballester M. Genomic architecture of carcass and pork traits and their association with immune capacity. Animal 2024; 18:101043. [PMID: 38113634 DOI: 10.1016/j.animal.2023.101043] [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: 05/25/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023] Open
Abstract
Carcass and pork traits have traditionally been considered of prime importance in pig breeding programmes. However, the changing conditions in modern farming, coupled with antimicrobial resistance issues, are raising the importance of health and robustness-related traits. Here, we explore the genetic architecture of carcass and pork traits and their relationship with immunity phenotypes in a commercial Duroc pig population. A total of nine traits related to fatness, lean content and meat pH were measured at slaughter (∼190 d of age) in 378 pigs previously phenotyped (∼70 d of age) for 36 immunity-related traits, including plasma concentrations of immunoglobulins, acute-phase proteins, leukocytes subpopulations and phagocytosis. Our study showed medium to high heritabilities and strong genetic correlations between fatness, lean content and meat pH at 24 h postmortem. Genetic correlations were found between carcass and pork traits and white blood cells. pH showed strong positive genetic correlations with leukocytes and eosinophils, and strong negative genetic correlations with haemoglobin, haematocrit and cytotoxic T cell proportion. In addition, genome-wide association studies (GWASs) pointed out four significantly associated genomic regions for lean meat percentages in different muscles, ham fat, backfat thickness, and semimembranosus pH at 24 h. The functional annotation of genes located in these regions reported a total of 14 candidate genes, with BGN, DPP10, LEPR, LEPROT, PDE4B and SLC6A8 being the strongest candidates. After performing an expression GWAS for the expression of these genes in muscle, two signals were detected in cis for the BGN and SLC6A8 genes. Our results indicate a genetic relationship between carcass fatness, lean content and meat pH with a variety of immunity-related traits that should be considered to improve immunocompetence without impairing production traits.
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Affiliation(s)
- T Jové-Juncà
- Animal Breeding and Genetics Program, IRTA, Torre Marimon, 08140 Caldes de Montbui, Barcelona, Spain
| | - D Crespo-Piazuelo
- Animal Breeding and Genetics Program, IRTA, Torre Marimon, 08140 Caldes de Montbui, Barcelona, Spain
| | - O González-Rodríguez
- Animal Breeding and Genetics Program, IRTA, Torre Marimon, 08140 Caldes de Montbui, Barcelona, Spain
| | - M Pascual
- Animal Breeding and Genetics Program, IRTA, Torre Marimon, 08140 Caldes de Montbui, Barcelona, Spain
| | - C Hernández-Banqué
- Animal Breeding and Genetics Program, IRTA, Torre Marimon, 08140 Caldes de Montbui, Barcelona, Spain
| | - J Reixach
- Selección Batallé S.A., Av. dels Segadors s/n, 17421 Riudarenes, Girona, Spain
| | - R Quintanilla
- Animal Breeding and Genetics Program, IRTA, Torre Marimon, 08140 Caldes de Montbui, Barcelona, Spain
| | - M Ballester
- Animal Breeding and Genetics Program, IRTA, Torre Marimon, 08140 Caldes de Montbui, Barcelona, Spain.
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Genetic regulation and variation of expression of miRNA and mRNA transcripts in fetal muscle tissue in the context of sex, dam and variable fetal weight. Biol Sex Differ 2022; 13:24. [PMID: 35550009 PMCID: PMC9103043 DOI: 10.1186/s13293-022-00433-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/25/2022] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Impaired skeletal muscle growth in utero can result in reduced birth weight and pathogenesis of intrauterine growth restriction. Fetal and placental growth is influenced by many factors including genetic, epigenetic and environmental factors. In fact, the sex and genotype of the fetus itself, as well as the mother providing it with a suitable environment, influence the growth of the fetus. Hence, our goal was to decipher and elucidate the molecular pathways of developmental processes mediated by miRNAs and mRNAs in fetal muscle tissue in the context of sex, dam, and fetal weight. Therefore, we analyse the variation of miRNA and mRNA expression in relation to these factors. In addition, the coincidence of genetic regulation of these mRNAs and miRNAs, as revealed by expression quantitative trait loci (eQTL) analyses, with sex-, mother- and weight-associated expression was investigated. METHODS A three-generation pig F2 population (n = 118) based on reciprocal crossing of German Landrace (DL) and Pietrain (Pi) was used. Genotype information and transcriptomic data (mRNA and miRNA) from longissimus dorsi muscle (LDM) of pig fetuses sampled at 63 days post-conception (dpc) were used for eQTL analyses. RESULTS The transcript abundances of 13, 853, and 275 probe-sets were influenced by sex, dam and fetal weight at 63 dpc, respectively (FDR < 5%). Most of significant transcripts affected by sex were located on the sex chromosomes including KDM6A and ANOS1 or autosomes including ANKS1B, LOC100155138 and miR-153. The fetal muscle transcripts associated with fetal weight indicated clearer metabolic directions than maternally influenced fetal muscle transcripts. Moreover, coincidence of genetic regulation (eQTL) and variation in transcript abundance due to sex, dam and fetal weight were identified. CONCLUSIONS Integrating information on eQTL, sex-, dam- and weight-associated differential expression and QTL for fetal weight allowed us to identify molecular pathways and shed light on the basic biological processes associated with differential muscle development in males and females, with implications for adaptive fetal programming.
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Liu X, Zhang J, Xiong X, Chen C, Xing Y, Duan Y, Xiao S, Yang B, Ma J. An Integrative Analysis of Transcriptome and GWAS Data to Identify Potential Candidate Genes Influencing Meat Quality Traits in Pigs. Front Genet 2021; 12:748070. [PMID: 34745221 PMCID: PMC8567094 DOI: 10.3389/fgene.2021.748070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
Understanding the genetic factors behind meat quality traits is of great significance to animal breeding and production. We previously conducted a genome-wide association study (GWAS) for meat quality traits in a White Duroc × Erhualian F2 pig population using Illumina porcine 60K SNP data. Here, we further investigate the functional candidate genes and their network modules associated with meat quality traits by integrating transcriptomics and GWAS information. Quantitative trait transcript (QTT) analysis, gene expression QTL (eQTL) mapping, and weighted gene co-expression network analysis (WGCNA) were performed using the digital gene expression (DGE) data from 493 F2 pig's muscle and liver samples. Among the quantified 20,108 liver and 23,728 muscle transcripts, 535 liver and 1,014 muscle QTTs corresponding to 416 and 721 genes, respectively, were found to be significantly (p < 5 × 10-4) correlated with 22 meat quality traits measured on longissiums dorsi muscle (LM) or semimembranosus muscle (SM). Transcripts associated with muscle glycolytic potential (GP) and pH values were enriched for genes involved in metabolic process. There were 42 QTTs (for 32 genes) shared by liver and muscle tissues, of which 10 QTTs represent GP- and/or pH-related genes, such as JUNB, ATF3, and PPP1R3B. Furthermore, a genome-wide eQTL mapping revealed a total of 3,054 eQTLs for all annotated transcripts in muscle (p < 2.08 × 10-5), including 1,283 cis-eQTLs and 1771 trans-eQTLs. In addition, WGCNA identified five modules relevant to glycogen metabolism pathway and highlighted the connections between variations in meat quality traits and genes involved in energy process. Integrative analysis of GWAS loci, eQTL, and QTT demonstrated GALNT15/GALNTL2 and HTATIP2 as strong candidate genes for drip loss and pH drop from postmortem 45 min to 24 h, respectively. Our findings provide valuable insights into the genetic basis of meat quality traits and greatly expand the number of candidate genes that may be valuable for future functional analysis and genetic improvement of meat quality.
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Affiliation(s)
- Xianxian Liu
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Junjie Zhang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Xinwei Xiong
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Congying Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yuyun Xing
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yanyu Duan
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Shijun Xiao
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Bin Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Junwu Ma
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
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Johnsson M, Jungnickel MK. Evidence for and localization of proposed causative variants in cattle and pig genomes. Genet Sel Evol 2021; 53:67. [PMID: 34461824 PMCID: PMC8404348 DOI: 10.1186/s12711-021-00662-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 08/20/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND This paper reviews the localization of published potential causative variants in contemporary pig and cattle reference genomes, and the evidence for their causality. In spite of the difficulties inherent to the identification of causative variants from genetic mapping and genome-wide association studies, researchers in animal genetics have proposed putative causative variants for several traits relevant to livestock breeding. RESULTS For this review, we read the literature that supports potential causative variants in 13 genes (ABCG2, DGAT1, GHR, IGF2, MC4R, MSTN, NR6A1, PHGK1, PRKAG3, PLRL, RYR1, SYNGR2 and VRTN) in cattle and pigs, and localized them in contemporary reference genomes. We review the evidence for their causality, by aiming to separate the evidence for the locus, the proposed causative gene and the proposed causative variant, and report the bioinformatic searches and tactics needed to localize the sequence variants in the cattle or pig genome. CONCLUSIONS Taken together, there is usually good evidence for the association at the locus level, some evidence for a specific causative gene at eight of the loci, and some experimental evidence for a specific causative variant at six of the loci. We recommend that researchers who report new potential causative variants use referenced coordinate systems, show local sequence context, and submit variants to repositories.
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Affiliation(s)
- Martin Johnsson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07 Uppsala, Sweden
| | - Melissa K. Jungnickel
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG Scotland, UK
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Hodge MJ, de las Heras-Saldana S, Rindfleish SJ, Stephen CP, Pant SD. Characterization of Breed Specific Differences in Spermatozoal Transcriptomes of Sheep in Australia. Genes (Basel) 2021; 12:genes12020203. [PMID: 33573244 PMCID: PMC7912062 DOI: 10.3390/genes12020203] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/10/2021] [Accepted: 01/22/2021] [Indexed: 01/27/2023] Open
Abstract
Reduced reproductive efficiency results in economic losses to the Australian sheep industry. Reproductive success, particularly after artificial insemination, is dependent on a number of contributing factors on both ewe and ram sides. Despite considerable emphasis placed on characterising ewe side contributions, little emphasis has been placed on characterising ram side contributions to conception success. Over 14,000 transcripts are in spermatozoa of other species, which are transferred to the ova on fertilisation. These transcripts conceivably influence early embryonic development and whether conception is successful. Semen was collected (n = 45) across three breeds; Merino, Dohne, and Poll Dorset. Following collection, each ejaculate was split in two; an aliquot was assessed utilising Computer Assisted Semen Analysis (CASA) and the remaining was utilised for RNA extraction and subsequent next-generation sequencing. Overall, 754 differentially expressed genes were identified in breed contrasts and contrast between ejaculates of different quality. Downstream analysis indicated that these genes could play significant roles in a broad range of physiological functions, including maintenance of spermatogenesis, fertilisation, conception, embryonic development, and offspring production performance. Overall results provide evidence that the spermatozoal transcriptome could be a crucial contributing factor in improving reproductive performance as well as in the overall productivity and profitability of sheep industries.
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Affiliation(s)
- Marnie J. Hodge
- Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), Charles Sturt University, Wagga Wagga, NSW 2678, Australia; (M.J.H.); (C.P.S.)
- Apiam Animal Health, Apiam Genetic Services, Dubbo, NSW 2830, Australia;
| | - Sara de las Heras-Saldana
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia;
| | | | - Cyril P. Stephen
- Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), Charles Sturt University, Wagga Wagga, NSW 2678, Australia; (M.J.H.); (C.P.S.)
| | - Sameer D. Pant
- Graham Centre for Agricultural Innovation (Charles Sturt University and NSW Department of Primary Industries), Charles Sturt University, Wagga Wagga, NSW 2678, Australia; (M.J.H.); (C.P.S.)
- Correspondence:
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Rodrigues AFG, Ibelli AMG, Peixoto JDO, Cantão ME, de Oliveira HC, Savoldi IR, Souza MR, Mores MAZ, Carreño LOD, Ledur MC. Genes and SNPs Involved with Scrotal and Umbilical Hernia in Pigs. Genes (Basel) 2021; 12:genes12020166. [PMID: 33513662 PMCID: PMC7912685 DOI: 10.3390/genes12020166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/20/2021] [Accepted: 01/22/2021] [Indexed: 12/27/2022] Open
Abstract
Hernia is one of the most common defects in pigs. The most prevalent are the scrotal (SH), inguinal (IH) and umbilical (UH) hernias. We compared the inguinal ring transcriptome of normal and SH-affected pigs with the umbilical ring transcriptome of normal and UH-affected pigs to discover genes and pathways involved with the development of both types of hernia. A total of 13,307 transcripts was expressed in the inguinal and 13,302 in the umbilical ring tissues with 94.91% of them present in both tissues. From those, 35 genes were differentially expressed in both groups, participating in 108 biological processes. A total of 67 polymorphisms was identified in the inguinal ring and 76 in the umbilical ring tissue, of which 11 and 14 were novel, respectively. A single nucleotide polymorphism (SNP) with deleterious function was identified in the integrin α M (ITGAM) gene. The microtubule associated protein 1 light chain 3 γ (MAP1LC3C), vitrin (VIT), aggrecan (ACAN), alkaline ceramidase 2 (ACER2), potassium calcium-activated channel subfamily M α 1 (KCNMA1) and synaptopodin 2 (SYNPO2) genes are highlighted as candidates to trigger both types of hernia. We generated the first comparative study of the pig umbilical and inguinal ring transcriptomes, contributing to the understanding of the genetic mechanism involved with these two types of hernia in pigs and probably in other mammals.
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Affiliation(s)
- Ariene Fernanda Grando Rodrigues
- Programa de Pós-Graduação em Zootecnia, Departamento de Zootecnia, Centro de Educação Superior do Oeste (CEO), Universidade do Estado de Santa Catarina, UDESC, 89815-630 Chapecó, Brazil; (A.F.G.R.); (I.R.S.); (M.R.S.)
| | - Adriana Mércia Guaratini Ibelli
- Embrapa Suínos e Aves, Distrito de Tamanduá, 89715-899 Concórdia, Brazil; (A.M.G.I.); (J.d.O.P.); (M.E.C.); (M.A.Z.M.)
- Programa de Pós-Graduação em Ciências Veterinárias, Departamento de Ciências Veterinárias, Universidade Estadual do Centro-Oeste, 85015-430 Guarapuava, Brazil
| | - Jane de Oliveira Peixoto
- Embrapa Suínos e Aves, Distrito de Tamanduá, 89715-899 Concórdia, Brazil; (A.M.G.I.); (J.d.O.P.); (M.E.C.); (M.A.Z.M.)
- Programa de Pós-Graduação em Ciências Veterinárias, Departamento de Ciências Veterinárias, Universidade Estadual do Centro-Oeste, 85015-430 Guarapuava, Brazil
| | - Maurício Egídio Cantão
- Embrapa Suínos e Aves, Distrito de Tamanduá, 89715-899 Concórdia, Brazil; (A.M.G.I.); (J.d.O.P.); (M.E.C.); (M.A.Z.M.)
| | | | - Igor Ricardo Savoldi
- Programa de Pós-Graduação em Zootecnia, Departamento de Zootecnia, Centro de Educação Superior do Oeste (CEO), Universidade do Estado de Santa Catarina, UDESC, 89815-630 Chapecó, Brazil; (A.F.G.R.); (I.R.S.); (M.R.S.)
| | - Mayla Regina Souza
- Programa de Pós-Graduação em Zootecnia, Departamento de Zootecnia, Centro de Educação Superior do Oeste (CEO), Universidade do Estado de Santa Catarina, UDESC, 89815-630 Chapecó, Brazil; (A.F.G.R.); (I.R.S.); (M.R.S.)
- Programa de Pós-Graduação em Zootecnia, Departamento de Zootecnia, Universidade Federal do Rio Grande do Sul, UFRGS, 91540-000 Porto Alegre, Brazil
| | - Marcos Antônio Zanella Mores
- Embrapa Suínos e Aves, Distrito de Tamanduá, 89715-899 Concórdia, Brazil; (A.M.G.I.); (J.d.O.P.); (M.E.C.); (M.A.Z.M.)
| | | | - Mônica Corrêa Ledur
- Programa de Pós-Graduação em Zootecnia, Departamento de Zootecnia, Centro de Educação Superior do Oeste (CEO), Universidade do Estado de Santa Catarina, UDESC, 89815-630 Chapecó, Brazil; (A.F.G.R.); (I.R.S.); (M.R.S.)
- Embrapa Suínos e Aves, Distrito de Tamanduá, 89715-899 Concórdia, Brazil; (A.M.G.I.); (J.d.O.P.); (M.E.C.); (M.A.Z.M.)
- Correspondence: or ; Tel.: +55-49-3441-0411
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8
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Yuan Z, Sunduimijid B, Xiang R, Behrendt R, Knight MI, Mason BA, Reich CM, Prowse-Wilkins C, Vander Jagt CJ, Chamberlain AJ, MacLeod IM, Li F, Yue X, Daetwyler HD. Expression quantitative trait loci in sheep liver and muscle contribute to variations in meat traits. Genet Sel Evol 2021; 53:8. [PMID: 33461502 PMCID: PMC7812657 DOI: 10.1186/s12711-021-00602-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 01/08/2021] [Indexed: 11/10/2022] Open
Abstract
Background Variants that regulate transcription, such as expression quantitative trait loci (eQTL), have shown enrichment in genome-wide association studies (GWAS) for mammalian complex traits. However, no study has reported eQTL in sheep, although it is an important agricultural species for which many GWAS of complex meat traits have been conducted. Using RNA sequence data produced from liver and muscle from 149 sheep and imputed whole-genome single nucleotide polymorphisms (SNPs), our aim was to dissect the genetic architecture of the transcriptome by associating sheep genotypes with three major molecular phenotypes including gene expression (geQTL), exon expression (eeQTL) and RNA splicing (sQTL). We also examined these three types of eQTL for their enrichment in GWAS of multi-meat traits and fatty acid profiles. Results Whereas a relatively small number of molecular phenotypes were significantly heritable (h2 > 0, P < 0.05), their mean heritability ranged from 0.67 to 0.73 for liver and from 0.71 to 0.77 for muscle. Association analysis between molecular phenotypes and SNPs within ± 1 Mb identified many significant cis-eQTL (false discovery rate, FDR < 0.01). The median distance between the eQTL and transcription start sites (TSS) ranged from 68 to 153 kb across the three eQTL types. The number of common variants between geQTL, eeQTL and sQTL within each tissue, and the number of common variants between liver and muscle within each eQTL type were all significantly (P < 0.05) larger than expected by chance. The identified eQTL were significantly (P < 0.05) enriched in GWAS hits associated with 56 carcass traits and fatty acid profiles. For example, several geQTL in muscle mapped to the FAM184B gene, hundreds of sQTL in liver and muscle mapped to the CAST gene, and hundreds of sQTL in liver mapped to the C6 gene. These three genes are associated with body composition or fatty acid profiles. Conclusions We detected a large number of significant eQTL and found that the overlap of variants between eQTL types and tissues was prevalent. Many eQTL were also QTL for meat traits. Our study fills a gap in the knowledge on the regulatory variants and their role in complex traits for the sheep model.
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Affiliation(s)
- Zehu Yuan
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Grassland Agriculture Engineering Center, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China.,Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.,Institutes of Agricultural Science and Technology Development (Joint International Research Laboratory of Agriculture & Agri-Product Safety), Yangzhou University, Yangzhou, 225000, People's Republic of China
| | - Bolormaa Sunduimijid
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Ruidong Xiang
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.,Faculty of Veterinary & Agricultural Science, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ralph Behrendt
- Agriculture Victoria, Hamilton Centre, Hamilton, VIC, 3300, Australia
| | - Matthew I Knight
- Agriculture Victoria, Hamilton Centre, Hamilton, VIC, 3300, Australia
| | - Brett A Mason
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Coralie M Reich
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Claire Prowse-Wilkins
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Christy J Vander Jagt
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Amanda J Chamberlain
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Iona M MacLeod
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Fadi Li
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Grassland Agriculture Engineering Center, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Xiangpeng Yue
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Grassland Agriculture Engineering Center, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China.
| | - Hans D Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia. .,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia.
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9
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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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10
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Gòdia M, Reverter A, González-Prendes R, Ramayo-Caldas Y, Castelló A, Rodríguez-Gil JE, Sánchez A, Clop A. A systems biology framework integrating GWAS and RNA-seq to shed light on the molecular basis of sperm quality in swine. Genet Sel Evol 2020; 52:72. [PMID: 33292187 PMCID: PMC7724732 DOI: 10.1186/s12711-020-00592-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Genetic pressure in animal breeding is sparking the interest of breeders for selecting elite boars with higher sperm quality to optimize ejaculate doses and fertility rates. However, the molecular basis of sperm quality is not yet fully understood. Our aim was to identify candidate genes, pathways and DNA variants associated to sperm quality in swine by analysing 25 sperm-related phenotypes and integrating genome-wide association studies (GWAS) and RNA-seq under a systems biology framework. RESULTS By GWAS, we identified 12 quantitative trait loci (QTL) associated to the percentage of head and neck abnormalities, abnormal acrosomes and motile spermatozoa. Candidate genes included CHD2, KATNAL2, SLC14A2 and ABCA1. By RNA-seq, we identified a wide repertoire of mRNAs (e.g. PRM1, OAZ3, DNAJB8, TPPP2 and TNP1) and miRNAs (e.g. ssc-miR-30d, ssc-miR-34c, ssc-miR-30c-5p, ssc-miR-191, members of the let-7 family and ssc-miR-425-5p) with functions related to sperm biology. We detected 6128 significant correlations (P-value ≤ 0.05) between sperm traits and mRNA abundances. By expression (e)GWAS, we identified three trans-expression QTL involving the genes IQCJ, ACTR2 and HARS. Using the GWAS and RNA-seq data, we built a gene interaction network. We considered that the genes and interactions that were present in both the GWAS and RNA-seq networks had a higher probability of being actually involved in sperm quality and used them to build a robust gene interaction network. In addition, in the final network we included genes with RNA abundances correlated with more than four semen traits and miRNAs interacting with the genes on the network. The final network was enriched for genes involved in gamete generation and development, meiotic cell cycle, DNA repair or embryo implantation. Finally, we designed a panel of 73 SNPs based on the GWAS, eGWAS and final network data, that explains between 5% (for sperm cell concentration) and 36% (for percentage of neck abnormalities) of the phenotypic variance of the sperm traits. CONCLUSIONS By applying a systems biology approach, we identified genes that potentially affect sperm quality and constructed a SNP panel that explains a substantial part of the phenotypic variance for semen quality in our study and that should be tested in other swine populations to evaluate its relevance for the pig breeding sector.
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Affiliation(s)
- Marta Gòdia
- Animal Genomics Group, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Cerdanyola del Vallès, 08193, Barcelona, Catalonia, Spain
| | - Antonio Reverter
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
| | - Rayner González-Prendes
- Animal Breeding and Genomics, Wageningen University & Research, 6708PB, Wageningen, The Netherlands
| | - Yuliaxis Ramayo-Caldas
- Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140, Caldes de Montbui, Catalonia, Spain
| | - Anna Castelló
- Animal Genomics Group, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Cerdanyola del Vallès, 08193, Barcelona, Catalonia, Spain.,Unit of Animal Science, Department of Animal and Food Science, Autonomous University of Barcelona, Cerdanyola del Vallès, 08193, Barcelona, Catalonia, Spain
| | - Joan-Enric Rodríguez-Gil
- Unit of Animal Reproduction, Department of Animal Medicine and Surgery, Autonomous University of Barcelona, Cerdanyola del Vallès, 08193, Barcelona, Catalonia, Spain
| | - Armand Sánchez
- Unit of Animal Science, Department of Animal and Food Science, Autonomous University of Barcelona, Cerdanyola del Vallès, 08193, Barcelona, Catalonia, Spain
| | - Alex Clop
- Animal Genomics Group, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB, Cerdanyola del Vallès, 08193, Barcelona, Catalonia, Spain. .,Consejo Superior de Investigaciones Científicas (CSIC), 08003, Barcelona, Catalonia, Spain.
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11
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Cai C, Li M, Zhang Y, Meng S, Yang Y, Gao P, Guo X, Cao G, Li B. Comparative Transcriptome Analyses of Longissimus thoracis Between Pig Breeds Differing in Muscle Characteristics. Front Genet 2020; 11:526309. [PMID: 33329687 PMCID: PMC7717936 DOI: 10.3389/fgene.2020.526309] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 10/15/2020] [Indexed: 01/23/2023] Open
Abstract
The two breeds, Mashen (MS; a northern China breed) and Large White (LW; a western lean breed) pigs, show important phenotypic differences in growth, adaptability, intramuscular fat (IMF) content, and energy metabolism since early developmental stage. The main aim of this study was the evaluation of longissimus thoracis muscle transcriptome profile of both genetic types to identify genes, pathways responsible for their differentiated phenotype. Longissimus thoracis of MS and LW pigs were sampled at 0 day (early stage), 90 days (middle stage), and 180 days (later stage) after birth. A total of 3,487 differentially expressed genes (DEGs) were identified at the three time points. Sample clustering analysis revealed the slower growth rate of MS than LW pigs. Gene expression pattern analysis revealed that multicellular organism growth genes (GHSR, EZR, FOXS1, DRD2, SH3PXD2B, CSF1, and TSHR) were involved in the fast growth rate of LW pigs at early stage. Furthermore, DEGs (ACACA, ACSF3, OXSM, CBR4, and HSD17B8) functionally related to fatty acid synthesis revealed that IMF accumulation occurred around 90 and up to 180 days. These DEGs provided valuable resource to study the phenotypic difference in longissimus thoracis muscle between MS and LW pigs.
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Affiliation(s)
- Chunbo Cai
- College of Animal Science, Shanxi Agricultural University, Shanxi, China
| | - Meng Li
- College of Animal Science, Shanxi Agricultural University, Shanxi, China
| | - Yanwei Zhang
- College of Animal Science, Shanxi Agricultural University, Shanxi, China
| | - Shan Meng
- College of Animal Science, Shanxi Agricultural University, Shanxi, China
| | - Yang Yang
- College of Animal Science, Shanxi Agricultural University, Shanxi, China
| | - Pengfei Gao
- College of Animal Science, Shanxi Agricultural University, Shanxi, China
| | - Xiaohong Guo
- College of Animal Science, Shanxi Agricultural University, Shanxi, China
| | - Guoqing Cao
- College of Animal Science, Shanxi Agricultural University, Shanxi, China
| | - Bugao Li
- College of Animal Science, Shanxi Agricultural University, Shanxi, China
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12
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Lam S, Zeidan J, Miglior F, Suárez-Vega A, Gómez-Redondo I, Fonseca PAS, Guan LL, Waters S, Cánovas A. Development and comparison of RNA-sequencing pipelines for more accurate SNP identification: practical example of functional SNP detection associated with feed efficiency in Nellore beef cattle. BMC Genomics 2020; 21:703. [PMID: 33032519 PMCID: PMC7545862 DOI: 10.1186/s12864-020-07107-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 09/28/2020] [Indexed: 12/14/2022] Open
Abstract
Background Optimization of an RNA-Sequencing (RNA-Seq) pipeline is critical to maximize power and accuracy to identify genetic variants, including SNPs, which may serve as genetic markers to select for feed efficiency, leading to economic benefits for beef production. This study used RNA-Seq data (GEO Accession ID: PRJEB7696 and PRJEB15314) from muscle and liver tissue, respectively, from 12 Nellore beef steers selected from 585 steers with residual feed intake measures (RFI; n = 6 low-RFI, n = 6 high-RFI). Three RNA-Seq pipelines were compared including multi-sample calling from i) non-merged samples; ii) merged samples by RFI group, iii) merged samples by RFI and tissue group. The RNA-Seq reads were aligned against the UMD3.1 bovine reference genome (release 94) assembly using STAR aligner. Variants were called using BCFtools and variant effect prediction (VeP) and functional annotation (ToppGene) analyses were performed. Results On average, total reads detected for Approach i) non-merged samples for liver and muscle, were 18,362,086.3 and 35,645,898.7, respectively. For Approach ii), merging samples by RFI group, total reads detected for each merged group was 162,030,705, and for Approach iii), merging samples by RFI group and tissues, was 324,061,410, revealing the highest read depth for Approach iii). Additionally, Approach iii) merging samples by RFI group and tissues, revealed the highest read depth per variant coverage (572.59 ± 3993.11) and encompassed the majority of localized positional genes detected by each approach. This suggests Approach iii) had optimized detection power, read depth, and accuracy of SNP calling, therefore increasing confidence of variant detection and reducing false positive detection. Approach iii) was then used to detect unique SNPs fixed within low- (12,145) and high-RFI (14,663) groups. Functional annotation of SNPs revealed positional candidate genes, for each RFI group (2886 for low-RFI, 3075 for high-RFI), which were significantly (P < 0.05) associated with immune and metabolic pathways. Conclusion The most optimized RNA-Seq pipeline allowed for more accurate identification of SNPs, associated positional candidate genes, and significantly associated metabolic pathways in muscle and liver tissues, providing insight on the underlying genetic architecture of feed efficiency in beef cattle.
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Affiliation(s)
- S Lam
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road E, Guelph, Ontario, N1G2W1, Canada
| | - J Zeidan
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road E, Guelph, Ontario, N1G2W1, Canada
| | - F Miglior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road E, Guelph, Ontario, N1G2W1, Canada
| | - A Suárez-Vega
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road E, Guelph, Ontario, N1G2W1, Canada
| | - I Gómez-Redondo
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road E, Guelph, Ontario, N1G2W1, Canada.,Spanish National Institute for Agriculture and Food Research and Technology, Carretera de La Coruña, 28040, Madrid, Spain
| | - P A S Fonseca
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road E, Guelph, Ontario, N1G2W1, Canada
| | - L L Guan
- Department of Agriculture, Food & Nutritional Science, University of Alberta, Edmonton, Alberta, T6H 2P5, Canada
| | - S Waters
- Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, C15 PW93, Ireland
| | - A Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road E, Guelph, Ontario, N1G2W1, Canada.
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13
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Duarte-Delgado D, Dadshani S, Schoof H, Oyiga BC, Schneider M, Mathew B, Léon J, Ballvora A. Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes. BMC PLANT BIOLOGY 2020; 20:428. [PMID: 32938380 PMCID: PMC7493341 DOI: 10.1186/s12870-020-02616-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/19/2020] [Indexed: 05/17/2023]
Abstract
BACKGROUND Bread wheat is one of the most important crops for the human diet, but the increasing soil salinization is causing yield reductions worldwide. Improving salt stress tolerance in wheat requires the elucidation of the mechanistic basis of plant response to this abiotic stress factor. Although several studies have been performed to analyze wheat adaptation to salt stress, there are still some gaps to fully understand the molecular mechanisms from initial signal perception to the onset of responsive tolerance pathways. The main objective of this study is to exploit the dynamic salt stress transcriptome in underlying QTL regions to uncover candidate genes controlling salt stress tolerance in bread wheat. The massive analysis of 3'-ends sequencing protocol was used to analyze leave samples at osmotic and ionic phases. Afterward, stress-responsive genes overlapping QTL for salt stress-related traits in two mapping populations were identified. RESULTS Among the over-represented salt-responsive gene categories, the early up-regulation of calcium-binding and cell wall synthesis genes found in the tolerant genotype are presumably strategies to cope with the salt-related osmotic stress. On the other hand, the down-regulation of photosynthesis-related and calcium-binding genes, and the increased oxidative stress response in the susceptible genotype are linked with the greater photosynthesis inhibition at the osmotic phase. The specific up-regulation of some ABC transporters and Na+/Ca2+ exchangers in the tolerant genotype at the ionic stage indicates their involvement in mechanisms of sodium exclusion and homeostasis. Moreover, genes related to protein synthesis and breakdown were identified at both stress phases. Based on the linkage disequilibrium blocks, salt-responsive genes within QTL intervals were identified as potential components operating in pathways leading to salt stress tolerance. Furthermore, this study conferred evidence of novel regions with transcription in bread wheat. CONCLUSION The dynamic transcriptome analysis allowed the comparison of osmotic and ionic phases of the salt stress response and gave insights into key molecular mechanisms involved in the salt stress adaptation of contrasting bread wheat genotypes. The leveraging of the highly contiguous chromosome-level reference genome sequence assembly facilitated the QTL dissection by targeting novel candidate genes for salt tolerance.
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Affiliation(s)
| | - Said Dadshani
- INRES-Plant Breeding, University of Bonn, Bonn, Germany
| | - Heiko Schoof
- INRES-Crop Bioinformatics, University of Bonn, Bonn, Germany
| | | | | | - Boby Mathew
- INRES-Plant Breeding, University of Bonn, Bonn, Germany
| | - Jens Léon
- INRES-Plant Breeding, University of Bonn, Bonn, Germany
| | - Agim Ballvora
- INRES-Plant Breeding, University of Bonn, Bonn, Germany.
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14
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Huang Y, Feulner PGD, Eizaguirre C, Lenz TL, Bornberg-Bauer E, Milinski M, Reusch TBH, Chain FJJ. Genome-Wide Genotype-Expression Relationships Reveal Both Copy Number and Single Nucleotide Differentiation Contribute to Differential Gene Expression between Stickleback Ecotypes. Genome Biol Evol 2020; 11:2344-2359. [PMID: 31298693 PMCID: PMC6735750 DOI: 10.1093/gbe/evz148] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2019] [Indexed: 12/11/2022] Open
Abstract
Repeated and independent emergence of trait divergence that matches habitat differences is a sign of parallel evolution by natural selection. Yet, the molecular underpinnings that are targeted by adaptive evolution often remain elusive. We investigate this question by combining genome-wide analyses of copy number variants (CNVs), single nucleotide polymorphisms (SNPs), and gene expression across four pairs of lake and river populations of the three-spined stickleback (Gasterosteus aculeatus). We tested whether CNVs that span entire genes and SNPs occurring in putative cis-regulatory regions contribute to gene expression differences between sticklebacks from lake and river origins. We found 135 gene CNVs that showed a significant positive association between gene copy number and gene expression, suggesting that CNVs result in dosage effects that can fuel phenotypic variation and serve as substrates for habitat-specific selection. Copy number differentiation between lake and river sticklebacks also contributed to expression differences of two immune-related genes in immune tissues, cathepsin A and GIMAP7. In addition, we identified SNPs in cis-regulatory regions (eSNPs) associated with the expression of 1,865 genes, including one eSNP upstream of a carboxypeptidase gene where both the SNP alleles differentiated and the gene was differentially expressed between lake and river populations. Our study highlights two types of mutations as important sources of genetic variation involved in the evolution of gene expression and in potentially facilitating repeated adaptation to novel environments.
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Affiliation(s)
- Yun Huang
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, ROC
| | - Philine G D Feulner
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Switzerland
| | - Christophe Eizaguirre
- School of Biological and Chemical Sciences, Queen Mary University of London, United Kingdom
| | - Tobias L Lenz
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Erich Bornberg-Bauer
- Evolutionary Bioinformatics, Institute for Evolution and Biodiversity, Westfälische Wilhelms University, Münster, Germany
| | - Manfred Milinski
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Thorsten B H Reusch
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Germany
| | - Frédéric J J Chain
- Department of Biological Sciences, University of Massachusetts Lowell, USA
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15
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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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16
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Drag MH, Kogelman LJA, Maribo H, Meinert L, Thomsen PD, Kadarmideen HN. Characterization of eQTLs associated with androstenone by RNA sequencing in porcine testis. Physiol Genomics 2019; 51:488-499. [PMID: 31373884 DOI: 10.1152/physiolgenomics.00125.2018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Characterization of genetic variants affecting genome-wide gene expression levels (expression quantitative trait loci or eQTLs) in pig testes may improve our understanding of genetic architecture of boar taint (an animal welfare trait) and helps in genome-assisted or genomic selection programs. The aims of this study were to identify eQTLs associated with androstenone, to find candidate eQTLs for low androstenone, and to validate the top eQTL by reverse transcriptase quantitative PCR (RT-qPCR). Gene expression profiles were obtained by RNA sequencing in testis from Danish cross-bred pigs and genotype data by 80K single nucleotide polymorphism panel. A total of 262 eQTLs [false discovery rate (FDR) < 0.05] were identified by using two software packages: Matrix eQTL and Krux eQTL. Of these, 149 cis-acting eQTLs were significantly associated with androstenone concentrations and gene expression (FDR < 0.05). The eQTLs were associated with several genes of boar taint relevance including CYP1A2, CYB5D1, and SPHK2. One eQTL gene, AMPH, was differentially expressed (FDR < 0.05) and affected by chicory. Five candidate eQTLs associated with low androstenone concentrations were discovered, including the top eQTL associated with CYP1A2. RT-qPCR confirmed target gene expression to be significantly (P < 0.05) different based on eQTL genotypes. Furthermore, eQTLs were enriched as QTLs for 15 boar taint related traits from the PigQTLdb. This is the first study to report eQTLs in testes of commercial crossbred pigs used in pork production and to reveal genetic architecture of boar taint. Potential applications include development of a DNA test and in advanced genomic selection models for boar taint.
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Affiliation(s)
- Markus H Drag
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lisette J A Kogelman
- Department of Neurology, Danish Headache Center, Rigshospitalet Glostrup, Faculty of Health and Medical Sciences, University of Copenhagen, Glostrup, Denmark
| | - Hanne Maribo
- SEGES, Danish Pig Research Center, Copenhagen, Denmark
| | - Lene Meinert
- Danish Meat Research Institute (DMRI), Danish Technological Institute, Taastrup, Denmark
| | - Preben D Thomsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Haja N Kadarmideen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kgs. Lyngby, Denmark
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17
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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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19
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Ben-Arye T, Levenberg S. Tissue Engineering for Clean Meat Production. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2019. [DOI: 10.3389/fsufs.2019.00046] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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20
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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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Role of AMPK signalling pathway during compensatory growth in pigs. BMC Genomics 2018; 19:682. [PMID: 30223793 PMCID: PMC6142327 DOI: 10.1186/s12864-018-5071-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 09/11/2018] [Indexed: 12/25/2022] Open
Abstract
Background The molecular basis of compensatory growth in monogastric animals has not yet been fully explored. Herewith, in this study we aim to determine changes in the pig skeletal muscle transcriptome profile during compensatory growth following a feed restriction period. A RNA-Seq experiment was performed with a total of 24 females belonging to a Duroc commercial line. Half of the animals received either a restricted (RE) or ad libitum (AL) diet during the first fattening period (60–125 d of age). After that, all gilts were fed ad libitum for a further ~30 d until the age of ~155 d, when animals were slaughtered and samples of gluteus medius muscle were harvested to perform RNA-Seq analyses and intramuscular fat content determination. Results During the period following food restriction, RE animals re-fed ad libitum displayed compensatory growth, showed better feed conversion rate and tended to deposit more subcutaneous fat than AL fed animals. Animals were slaughtered in the phase of accelerated growth, when RE animals had not completely compensated the performance of AL group, showing lower live and carcass weights. At intramuscular level, RE gilts showed a higher content of polyunsaturated fatty acids during the compensatory growth phase. The comparison of RE and AL expression profiles allowed the identification of 86 (ǀlog2Fold-Changeǀ > 1, padj < 0.05) differentially expressed (DE) genes. A functional categorization of these DE genes identified AMPK Signaling as the most significantly enriched canonical pathway. This kinase plays a key role in the maintenance of energy homeostasis as well as in the activation of autophagy. Among the DE genes identified as components of AMPK Signaling pathway, five out of six genes were downregulated in RE pigs. Conclusions Animals re-fed after a restriction period exhibited a less oxidative metabolic profile and catabolic processes in muscle than animals fed ad libitum. The downregulation of autophagy observed in the skeletal muscle of pigs undergoing compensatory growth may constitute a mechanism to increase muscle mass thus ensuring an accelerated growth rate. These results reveal that the downregulation of AMPK Signaling plays an important role in compensatory growth in pigs. Electronic supplementary material The online version of this article (10.1186/s12864-018-5071-5) contains supplementary material, which is available to authorized users.
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Drag M, Hansen MB, Kadarmideen HN. Systems genomics study reveals expression quantitative trait loci, regulator genes and pathways associated with boar taint in pigs. PLoS One 2018; 13:e0192673. [PMID: 29438444 PMCID: PMC5811030 DOI: 10.1371/journal.pone.0192673] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 01/29/2018] [Indexed: 01/14/2023] Open
Abstract
Boar taint is an offensive odour and/or taste from a proportion of non-castrated male pigs caused by skatole and androstenone accumulation during sexual maturity. Castration is widely used to avoid boar taint but is currently under debate because of animal welfare concerns. This study aimed to identify expression quantitative trait loci (eQTLs) with potential effects on boar taint compounds to improve breeding possibilities for reduced boar taint. Danish Landrace male boars with low, medium and high genetic merit for skatole and human nose score (HNS) were slaughtered at ~100 kg. Gene expression profiles were obtained by RNA-Seq, and genotype data were obtained by an Illumina 60K Porcine SNP chip. Following quality control and filtering, 10,545 and 12,731 genes from liver and testis were included in the eQTL analysis, together with 20,827 SNP variants. A total of 205 and 109 single-tissue eQTLs associated with 102 and 58 unique genes were identified in liver and testis, respectively. By employing a multivariate Bayesian hierarchical model, 26 eQTLs were identified as significant multi-tissue eQTLs. The highest densities of eQTLs were found on pig chromosomes SSC12, SSC1, SSC13, SSC9 and SSC14. Functional characterisation of eQTLs revealed functions within regulation of androgen and the intracellular steroid hormone receptor signalling pathway and of xenobiotic metabolism by cytochrome P450 system and cellular response to oestradiol. A QTL enrichment test revealed 89 QTL traits curated by the Animal Genome PigQTL database to be significantly overlapped by the genomic coordinates of cis-acting eQTLs. Finally, a subset of 35 cis-acting eQTLs overlapped with known boar taint QTL traits. These eQTLs could be useful in the development of a DNA test for boar taint but careful monitoring of other overlapping QTL traits should be performed to avoid any negative consequences of selection.
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Affiliation(s)
- Markus Drag
- Section of Anatomy, Biochemistry and Physiology, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Mathias B. Hansen
- Section of Anatomy, Biochemistry and Physiology, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Haja N. Kadarmideen
- Section of Anatomy, Biochemistry and Physiology, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
- Section of Systems Genomics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, Lyngby, Denmark
- * E-mail:
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24
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Maroilley T, Lemonnier G, Lecardonnel J, Esquerré D, Ramayo-Caldas Y, Mercat MJ, Rogel-Gaillard C, Estellé J. Deciphering the genetic regulation of peripheral blood transcriptome in pigs through expression genome-wide association study and allele-specific expression analysis. BMC Genomics 2017; 18:967. [PMID: 29237423 PMCID: PMC5729405 DOI: 10.1186/s12864-017-4354-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 11/28/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Efforts to improve sustainability in livestock production systems have focused on two objectives: investigating the genetic control of immune function as it pertains to robustness and disease resistance, and finding predictive markers for use in breeding programs. In this context, the peripheral blood transcriptome represents an important source of biological information about an individual's health and immunological status, and has been proposed for use as an intermediate phenotype to measure immune capacity. The objective of this work was to study the genetic architecture of variation in gene expression in the blood of healthy young pigs using two approaches: an expression genome-wide association study (eGWAS) and allele-specific expression (ASE) analysis. RESULTS The blood transcriptomes of 60-day-old Large White pigs were analyzed by expression microarrays for eGWAS (242 animals) and by RNA-Seq for ASE analysis (38 animals). Using eGWAS, the expression levels of 1901 genes were found to be associated with expression quantitative trait loci (eQTLs). We recovered 2839 local and 1752 distant associations (Single Nucleotide Polymorphism or SNP located less or more than 1 Mb from expression probe, respectively). ASE analyses confirmed the extensive cis-regulation of gene transcription in blood, and revealed allelic imbalance in 2286 SNPs, which affected 763 genes. eQTLs and ASE-genes were widely distributed on all chromosomes. By analyzing mutually overlapping eGWAS results, we were able to describe putative regulatory networks, which were further refined using ASE data. At the functional level, genes with genetically controlled expression that were detected by eGWAS and/or ASE analyses were significantly enriched in biological processes related to RNA processing and immune function. Indeed, numerous distant and local regulatory relationships were detected within the major histocompatibility complex region on chromosome 7, revealing ASE for most class I and II genes. CONCLUSIONS This study represents, to the best of our knowledge, the first genome-wide map of the genetic control of gene expression in porcine peripheral blood. These results represent an interesting resource for the identification of genetic markers and blood biomarkers associated with variations in immunity traits in pigs, as well as any other complex traits for which blood is an appropriate surrogate tissue.
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Affiliation(s)
- T Maroilley
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
| | - G Lemonnier
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - J Lecardonnel
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - D Esquerré
- GenPhySE, INRA, INPT, ENVT, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Y Ramayo-Caldas
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - M J Mercat
- IFIP - Institut du porc/BIOPORC, La Motte au Vicomte, BP 35104, 35651, Le Rheu, France
| | - C Rogel-Gaillard
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
| | - J Estellé
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
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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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Gonen S, Battagin M, Johnston SE, Gorjanc G, Hickey JM. The potential of shifting recombination hotspots to increase genetic gain in livestock breeding. Genet Sel Evol 2017; 49:55. [PMID: 28676070 PMCID: PMC5496647 DOI: 10.1186/s12711-017-0330-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 06/26/2017] [Indexed: 01/01/2023] Open
Abstract
Background This study uses simulation to explore and quantify the potential effect of shifting recombination hotspots on genetic gain in livestock breeding programs. Methods We simulated three scenarios that differed in the locations of quantitative trait nucleotides (QTN) and recombination hotspots in the genome. In scenario 1, QTN were randomly distributed along the chromosomes and recombination was restricted to occur within specific genomic regions (i.e. recombination hotspots). In the other two scenarios, both QTN and recombination hotspots were located in specific regions, but differed in whether the QTN occurred outside of (scenario 2) or inside (scenario 3) recombination hotspots. We split each chromosome into 250, 500 or 1000 regions per chromosome of which 10% were recombination hotspots and/or contained QTN. The breeding program was run for 21 generations of selection, after which recombination hotspot regions were kept the same or were shifted to adjacent regions for a further 80 generations of selection. We evaluated the effect of shifting recombination hotspots on genetic gain, genetic variance and genic variance. Results Our results show that shifting recombination hotspots reduced the decline of genetic and genic variance by releasing standing allelic variation in the form of new allele combinations. This in turn resulted in larger increases in genetic gain. However, the benefit of shifting recombination hotspots for increased genetic gain was only observed when QTN were initially outside recombination hotspots. If QTN were initially inside recombination hotspots then shifting them decreased genetic gain. Discussion Shifting recombination hotspots to regions of the genome where recombination had not occurred for 21 generations of selection (i.e. recombination deserts) released more of the standing allelic variation available in each generation and thus increased genetic gain. However, whether and how much increase in genetic gain was achieved by shifting recombination hotspots depended on the distribution of QTN in the genome, the number of recombination hotspots and whether QTN were initially inside or outside recombination hotspots. Conclusions Our findings show future scope for targeted modification of recombination hotspots e.g. through changes in zinc-finger motifs of the PRDM9 protein to increase genetic gain in production species. Electronic supplementary material The online version of this article (doi:10.1186/s12711-017-0330-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Serap Gonen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK
| | - Mara Battagin
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK
| | - Susan E Johnston
- Institute of Evolutionary Biology, The University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK
| | - John M Hickey
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK.
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Park WB, An SM, Yu GE, Kwon S, Hwang JH, Park DH, Kang DG, Kim TW, Park HC, Ha J, Kim CW. The rs196952262 Polymorphism of the AGPAT5 Gene is Associated with Meat Quality in Berkshire Pigs. Korean J Food Sci Anim Resour 2017; 37:926-930. [PMID: 29725215 PMCID: PMC5932945 DOI: 10.5851/kosfa.2017.37.6.926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 11/26/2017] [Accepted: 11/30/2017] [Indexed: 12/02/2022] Open
Abstract
High-quality meat is of great economic importance to the pig industry. The 1-acylglycerol-3-phosphate-O-acyltransferase 5 (AGPAT5) enzyme converts lysophosphatidic acid to phosphatidic acid in the mitochondrial membrane. In this study, we found that the porcine AGPAT5 gene was highly expressed in muscle tissue, influencing meat characteristics, and we also identified a non-synonymous single-nucleotide polymorphism (nsSNP) (rs196952262, c.673 A>G) in the gene, associated with a change of isoleucine 225 to valine. The presence of this nsSNP was significantly associated with meat color (lightness), lower cooking loss, and lower carcass temperatures 1, 4, and 12 h after slaughter (items T1, T4, and T12 on the recognized quality scale, respectively), and tended to increase backfat thickness and the water-holding capacity. These results suggest that nsSNP (c.673A>G) of the AGPAT5 gene is a potential genetic marker of high meat quality in pigs.
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Affiliation(s)
- Woo Bum Park
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju 52725, Korea.,Dasan Pig Breeding Co., Namwon 55716, Korea
| | - Sang Mi An
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju 52725, Korea.,Dasan Pig Breeding Co., Namwon 55716, Korea
| | - Go Eun Yu
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju 52725, Korea.,Dasan Pig Breeding Co., Namwon 55716, Korea
| | - Seulgi Kwon
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju 52725, Korea.,Dasan Pig Breeding Co., Namwon 55716, Korea
| | - Jung Hye Hwang
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju 52725, Korea.,Dasan Pig Breeding Co., Namwon 55716, Korea
| | - Da Hye Park
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju 52725, Korea.,Dasan Pig Breeding Co., Namwon 55716, Korea
| | - Deok Gyeong Kang
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju 52725, Korea.,Dasan Pig Breeding Co., Namwon 55716, Korea
| | - Tae Wan Kim
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju 52725, Korea.,Dasan Pig Breeding Co., Namwon 55716, Korea
| | | | - Jeongim Ha
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju 52725, Korea.,Dasan Pig Breeding Co., Namwon 55716, Korea
| | - Chul Wook Kim
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju 52725, Korea.,Dasan Pig Breeding Co., Namwon 55716, Korea
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