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Ben-Jemaa S, Boussaha M, Mandonnet N, Bardou P, Naves M. Uncovering structural variants in Creole cattle from Guadeloupe and their impact on environmental adaptation through whole genome sequencing. PLoS One 2024; 19:e0309411. [PMID: 39186744 PMCID: PMC11346954 DOI: 10.1371/journal.pone.0309411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/12/2024] [Indexed: 08/28/2024] Open
Abstract
Structural variants play an important role in evolutionary processes. Besides, they constitute a large source of inter individual genetic variation that might represent a major factor in the aetiology of complex, multifactorial traits. Their importance in adaptation is becoming increasingly evident in literature. Yet, the characterization of the genomic landscape of structural variants in local breeds remains scarce to date. Herein, we investigate patterns and gene annotation of structural variants in the Creole cattle from Guadeloupe breed using whole genome sequences from 23 bulls representative of the population. In total, we detected 32821 ascertained SV defining 15258 regions, representing ~ 17% of the Creole cattle genome. Among these, 6639 regions have not been previously reported in the Database of Genomic Variants archive. Average number of structural variants detected per individual in the studied population is in the same order of magnitude of that observed in indicine populations and higher than that reported in taurine breeds. We observe an important within-individual variability where approximately half of the detected structural variants have low frequency (MAF < 0.25). Most of the detected structural variants (55%) occurred in intergenic regions. Genic structural variants overlapped with 7793 genes and the predicted effect of most of them is ranked as "modifier". Among the structural variants that were predicted to have a high functional impact on the protein, a 5.5 Kb in length, highly frequent deletion on chromosome 2, affects ALPI, a gene associated with the interaction between gut microbiota and host immune system. The 6639 newly identified structural variants regions include three deletions and three duplications shared by more than 80% of individuals that are significantly enriched for genes related to tRNA threonylcarbamoyladenosine metabolic process, important for temperature adaptation in thermophilic organisms, therefore suggesting a potential role in the thermotolerance of Creole cattle from Guadeloupe cattle to tropical climate. Overall, highly frequent structural variants that are specific to the Creole cattle population encompass olfactory receptor and immunity genes as well as genes involved in muscle tone, muscle development and contraction. Beyond mapping and characterizing structural variants in the Creole cattle from Guadeloupe breed, this study provides valuable information for a better understanding of the potential role of chromosomal rearrangements in adaptive traits in cattle.
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Affiliation(s)
- Slim Ben-Jemaa
- INRAE, ASSET, 97170, Petit-Bourg, France
- Institut National de la Recherche Agronomique de Tunisie, Laboratoire des Productions Animales et Fourragères, Université de Carthage, 2049, Ariana, Tunisia
| | - Mekki Boussaha
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | | | - Philippe Bardou
- GenPhySE, Université de Toulouse, INRA, Ecole Nationale Vétérinaire de Toulouse (ENVT), 31320, Castanet-Tolosan, France
- Sigenae, INRAE, 31320, Castanet-Tolosan, France
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Tian R, Mahmoodi M, Tian J, Esmailizadeh Koshkoiyeh S, Zhao M, Saminzadeh M, Li H, Wang X, Li Y, Esmailizadeh A. Leveraging Functional Genomics for Understanding Beef Quality Complexities and Breeding Beef Cattle for Improved Meat Quality. Genes (Basel) 2024; 15:1104. [PMID: 39202463 PMCID: PMC11353656 DOI: 10.3390/genes15081104] [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: 07/01/2024] [Revised: 08/17/2024] [Accepted: 08/19/2024] [Indexed: 09/03/2024] Open
Abstract
Consumer perception of beef is heavily influenced by overall meat quality, a critical factor in the cattle industry. Genomics has the potential to improve important beef quality traits and identify genetic markers and causal variants associated with these traits through genomic selection (GS) and genome-wide association studies (GWAS) approaches. Transcriptomics, proteomics, and metabolomics provide insights into underlying genetic mechanisms by identifying differentially expressed genes, proteins, and metabolic pathways linked to quality traits, complementing GWAS data. Leveraging these functional genomics techniques can optimize beef cattle breeding for enhanced quality traits to meet high-quality beef demand. This paper provides a comprehensive overview of the current state of applications of omics technologies in uncovering functional variants underlying beef quality complexities. By highlighting the latest findings from GWAS, GS, transcriptomics, proteomics, and metabolomics studies, this work seeks to serve as a valuable resource for fostering a deeper understanding of the complex relationships between genetics, gene expression, protein dynamics, and metabolic pathways in shaping beef quality.
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Affiliation(s)
- Rugang Tian
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (J.T.); (M.Z.); (H.L.); (X.W.); (Y.L.)
| | - Maryam Mahmoodi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman P.O. Box 76169-133, Iran; (M.M.); (S.E.K.); (M.S.); (A.E.)
| | - Jing Tian
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (J.T.); (M.Z.); (H.L.); (X.W.); (Y.L.)
| | - Sina Esmailizadeh Koshkoiyeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman P.O. Box 76169-133, Iran; (M.M.); (S.E.K.); (M.S.); (A.E.)
| | - Meng Zhao
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (J.T.); (M.Z.); (H.L.); (X.W.); (Y.L.)
| | - Mahla Saminzadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman P.O. Box 76169-133, Iran; (M.M.); (S.E.K.); (M.S.); (A.E.)
| | - Hui Li
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (J.T.); (M.Z.); (H.L.); (X.W.); (Y.L.)
| | - Xiao Wang
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (J.T.); (M.Z.); (H.L.); (X.W.); (Y.L.)
| | - Yuan Li
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (J.T.); (M.Z.); (H.L.); (X.W.); (Y.L.)
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman P.O. Box 76169-133, Iran; (M.M.); (S.E.K.); (M.S.); (A.E.)
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Carvalho Filho I, Arikawa LM, Mota LFM, Campos GS, Fonseca LFS, Fernandes Júnior GA, Schenkel FS, Lourenco D, Silva DA, Teixeira CS, Silva TL, Albuquerque LG, Carvalheiro R. Genome-wide association study considering genotype-by-environment interaction for productive and reproductive traits using whole-genome sequencing in Nellore cattle. BMC Genomics 2024; 25:623. [PMID: 38902640 PMCID: PMC11188527 DOI: 10.1186/s12864-024-10520-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 06/13/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND The genotype-by-environment interaction (GxE) in beef cattle can be investigated using reaction norm models to assess environmental sensitivity and, combined with genome-wide association studies (GWAS), to map genomic regions related to animal adaptation. Including genetic markers from whole-genome sequencing in reaction norm (RN) models allows us to identify high-resolution candidate genes across environmental gradients through GWAS. Hence, we performed a GWAS via the RN approach using whole-genome sequencing data, focusing on mapping candidate genes associated with the expression of reproductive and growth traits in Nellore cattle. For this purpose, we used phenotypic data for age at first calving (AFC), scrotal circumference (SC), post-weaning weight gain (PWG), and yearling weight (YW). A total of 20,000 males and 7,159 females genotyped with 770k were imputed to the whole sequence (29 M). After quality control and linkage disequilibrium (LD) pruning, there remained ∼ 2.41 M SNPs for SC, PWG, and YW and ∼ 5.06 M SNPs for AFC. RESULTS Significant SNPs were identified on Bos taurus autosomes (BTA) 10, 11, 14, 18, 19, 20, 21, 24, 25 and 27 for AFC and on BTA 4, 5 and 8 for SC. For growth traits, significant SNP markers were identified on BTA 3, 5 and 20 for YW and PWG. A total of 56 positional candidate genes were identified for AFC, 9 for SC, 3 for PWG, and 24 for YW. The significant SNPs detected for the reaction norm coefficients in Nellore cattle were found to be associated with growth, adaptative, and reproductive traits. These candidate genes are involved in biological mechanisms related to lipid metabolism, immune response, mitogen-activated protein kinase (MAPK) signaling pathway, and energy and phosphate metabolism. CONCLUSIONS GWAS results highlighted differences in the physiological processes linked to lipid metabolism, immune response, MAPK signaling pathway, and energy and phosphate metabolism, providing insights into how different environmental conditions interact with specific genes affecting animal adaptation, productivity, and reproductive performance. The shared genomic regions between the intercept and slope are directly implicated in the regulation of growth and reproductive traits in Nellore cattle raised under different environmental conditions.
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Affiliation(s)
- Ivan Carvalho Filho
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Leonardo M Arikawa
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Lucio F M Mota
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil.
| | - Gabriel S Campos
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Larissa F S Fonseca
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Gerardo A Fernandes Júnior
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G2W1, Canada
| | - Daniela Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA
| | - Delvan A Silva
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Caio S Teixeira
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Thales L Silva
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Lucia G Albuquerque
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
- National Council for Science and Technological Development, Brasilia, DF, 71605-001, Brazil
| | - Roberto Carvalheiro
- Department of Animal Science, School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
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Kuraz Abebe B, Wang J, Guo J, Wang H, Li A, Zan L. A review of the role of epigenetic studies for intramuscular fat deposition in beef cattle. Gene 2024; 908:148295. [PMID: 38387707 DOI: 10.1016/j.gene.2024.148295] [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: 10/26/2023] [Revised: 01/23/2024] [Accepted: 02/15/2024] [Indexed: 02/24/2024]
Abstract
Intramuscular fat (IMF) deposition profoundly influences meat quality and economic value in beef cattle production. Meanwhile, contemporary developments in epigenetics have opened new outlooks for understanding the molecular basics of IMF regulation, and it has become a key area of research for world scholars. Therefore, the aim of this paper was to provide insight and synthesis into the intricate relationship between epigenetic mechanisms and IMF deposition in beef cattle. The methodology involves a thorough analysis of existing literature, including pertinent books, academic journals, and online resources, to provide a comprehensive overview of the role of epigenetic studies in IMF deposition in beef cattle. This review summarizes the contemporary studies in epigenetic mechanisms in IMF regulation, high-resolution epigenomic mapping, single-cell epigenomics, multi-omics integration, epigenome editing approaches, longitudinal studies in cattle growth, environmental epigenetics, machine learning in epigenetics, ethical and regulatory considerations, and translation to industry practices from perspectives of IMF deposition in beef cattle. Moreover, this paper highlights DNA methylation, histone modifications, acetylation, phosphorylation, ubiquitylation, non-coding RNAs, DNA hydroxymethylation, epigenetic readers, writers, and erasers, chromatin immunoprecipitation followed by sequencing, whole genome bisulfite sequencing, epigenome-wide association studies, and their profound impact on the expression of crucial genes governing adipogenesis and lipid metabolism. Nutrition and stress also have significant influences on epigenetic modifications and IMF deposition. The key findings underscore the pivotal role of epigenetic studies in understanding and enhancing IMF deposition in beef cattle, with implications for precision livestock farming and ethical livestock management. In conclusion, this review highlights the crucial significance of epigenetic pathways and environmental factors in affecting IMF deposition in beef cattle, providing insightful information for improving the economics and meat quality of cattle production.
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Affiliation(s)
- Belete Kuraz Abebe
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China; Department of Animal Science, Werabe University, P.O. Box 46, Werabe, Ethiopia
| | - Jianfang Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Juntao Guo
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Hongbao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Anning Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China; National Beef Cattle Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China.
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Garcia IS, Silva-Vignato B, Cesar ASM, Petrini J, da Silva VH, Morosini NS, Goes CP, Afonso J, da Silva TR, Lima BD, Clemente LG, Regitano LCDA, Mourão GB, Coutinho LL. Novel putative causal mutations associated with fat traits in Nellore cattle uncovered by eQTLs located in open chromatin regions. Sci Rep 2024; 14:10094. [PMID: 38698200 PMCID: PMC11066111 DOI: 10.1038/s41598-024-60703-5] [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: 10/19/2023] [Accepted: 04/26/2024] [Indexed: 05/05/2024] Open
Abstract
Intramuscular fat (IMF) and backfat thickness (BFT) are critical economic traits impacting meat quality. However, the genetic variants controlling these traits need to be better understood. To advance knowledge in this area, we integrated RNA-seq and single nucleotide polymorphisms (SNPs) identified in genomic and transcriptomic data to generate a linkage disequilibrium filtered panel of 553,581 variants. Expression quantitative trait loci (eQTL) analysis revealed 36,916 cis-eQTLs and 14,408 trans-eQTLs. Association analysis resulted in three eQTLs associated with BFT and 24 with IMF. Functional enrichment analysis of genes regulated by these 27 eQTLs revealed noteworthy pathways that can play a fundamental role in lipid metabolism and fat deposition, such as immune response, cytoskeleton remodeling, iron transport, and phospholipid metabolism. We next used ATAC-Seq assay to identify and overlap eQTL and open chromatin regions. Six eQTLs were in regulatory regions, four in predicted insulators and possible CCCTC-binding factor DNA binding sites, one in an active enhancer region, and the last in a low signal region. Our results provided novel insights into the transcriptional regulation of IMF and BFT, unraveling putative regulatory variants.
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Affiliation(s)
- Ingrid Soares Garcia
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Bárbara Silva-Vignato
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Aline Silva Mello Cesar
- Department of Agroindustry, Food and Nutrition, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Juliana Petrini
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Vinicius Henrique da Silva
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Natália Silva Morosini
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Carolina Purcell Goes
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | | | - Thaís Ribeiro da Silva
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Beatriz Delcarme Lima
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Luan Gaspar Clemente
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | | | - Gerson Barreto Mourão
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Luiz Lehmann Coutinho
- Department of Animal Science, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil.
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Reis HBD, Carvalho ME, Espigolan R, Poleti MD, Ambrizi DR, Berton MP, Ferraz JBS, de Mattos Oliveira EC, Eler JP. Genome-Wide Association (GWAS) Applied to Carcass and Meat Traits of Nellore Cattle. Metabolites 2023; 14:6. [PMID: 38276296 PMCID: PMC10818672 DOI: 10.3390/metabo14010006] [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: 10/10/2023] [Revised: 11/14/2023] [Accepted: 11/22/2023] [Indexed: 01/27/2024] Open
Abstract
The meat market has enormous importance for the world economy, and the quality of the product offered to the consumer is fundamental for the success of the sector. In this study, we analyzed a database which contained information on 2470 animals from a commercial farm in the state of São Paulo, Brazil. Of this total, 2181 animals were genotyped, using 777,962 single-nucleotide polymorphisms (SNPs). After quality control analysis, 468,321 SNPs provided information on the number of genotyped animals. Genome-wide association analyses (GWAS) were performed for the characteristics of the rib eye area (REA), subcutaneous fat thickness (SFT), shear force at 7 days' ageing (SF7), and intramuscular fat (IMF), with the aid of the single-step genomic best linear unbiased prediction (ssGBLUP) method, with the purpose of identifying possible genomic windows (~1 Mb) responsible for explaining at least 0.5% of the genetic variance of the traits under analysis (≥0.5%). These genomic regions were used in a gene search and enrichment analyses using MeSH terms. The distributed heritability coefficients were 0.14, 0.20, 0.18, and 0.21 for REA, SFT, SF7, and IMF, respectively. The GWAS results indicated significant genomic windows for the traits of interest in a total of 17 chromosomes. Enrichment analyses showed the following significant terms (FDR ≤ 0.05) associated with the characteristics under study: for the REA, heat stress disorders and life cycle stages; for SFT, insulin and nonesterified fatty acids; for SF7, apoptosis and heat shock proteins (HSP27); and for IMF, metalloproteinase 2. In addition, KEGG (Kyoto encyclopedia of genes and genomes) enrichment analysis allowed us to highlight important metabolic pathways related to the studied phenotypes, such as the growth hormone synthesis, insulin-signaling, fatty acid metabolism, and ABC transporter pathways. The results obtained provide a better understanding of the molecular processes involved in the expression of the studied characteristics and may contribute to the design of selection strategies and future studies aimed at improving the productivity of Nellore cattle.
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Affiliation(s)
- Hugo Borges Dos Reis
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.E.C.); (M.D.P.); (J.B.S.F.)
| | - Minos Esperândio Carvalho
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.E.C.); (M.D.P.); (J.B.S.F.)
| | - Rafael Espigolan
- Department of Animal Science and Biological Sciences, Federal University of Santa Maria (UFSM), Av. Independencia, 3751, Palmeira das Missões 98300-000, RS, Brazil
| | - Mirele Daiana Poleti
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.E.C.); (M.D.P.); (J.B.S.F.)
| | - Dewison Ricardo Ambrizi
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.E.C.); (M.D.P.); (J.B.S.F.)
| | - Mariana Piatto Berton
- School of Agricultural and Veterinary Studies (FCAV), São Paulo State University, Jaboticabal 14884-900, SP, Brazil;
| | - José Bento Sterman Ferraz
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.E.C.); (M.D.P.); (J.B.S.F.)
| | - Elisângela Chicaroni de Mattos Oliveira
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.E.C.); (M.D.P.); (J.B.S.F.)
| | - Joanir Pereira Eler
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering (FZEA), University of Sao Paulo, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (M.E.C.); (M.D.P.); (J.B.S.F.)
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Buss CE, Afonso J, de Oliveira PSN, Petrini J, Tizioto PC, Cesar ASM, Gustani-Buss EC, Cardoso TF, Rovadoski GA, da Silva Diniz WJ, de Lima AO, Rocha MIP, Andrade BGN, Wolf JB, Coutinho LL, Mourão GB, de Almeida Regitano LC. Bivariate GWAS reveals pleiotropic regions among feed efficiency and beef quality-related traits in Nelore cattle. Mamm Genome 2023; 34:90-103. [PMID: 36463529 DOI: 10.1007/s00335-022-09969-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/16/2022] [Indexed: 12/07/2022]
Abstract
Feed-efficient cattle selection is among the most leading solutions to reduce cost for beef cattle production. However, technical difficulties in measuring feed efficiency traits had limited the application in livestock. Here, we performed a Bivariate Genome-Wide Association Study (Bi-GWAS) and presented candidate biological mechanisms underlying the association between feed efficiency and meat quality traits in a half-sibling design with 353 Nelore steers derived from 34 unrelated sires. A total of 13 Quantitative Trait Loci (QTL) were found explaining part of the phenotypic variations. An important transcription factor of adipogenesis in cattle, the TAL1 (rs133408775) gene located on BTA3 was associated with intramuscular fat and average daily gain (IMF-ADG), and a region located on BTA20, close to CD180 and MAST4 genes, both related to fat accumulation. We observed a low positive genetic correlation between IMF-ADG (r = 0.30 ± 0.0686), indicating that it may respond to selection in the same direction. Our findings contributed to clarifying the pleiotropic modulation of the complex traits, indicating new QTLs for bovine genetic improvement.
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Affiliation(s)
- Carlos Eduardo Buss
- Department of Genetic and Evolution, Federal University of São Carlos, São Carlos, São Paulo, Brazil
- Mindflow Genomics, Leuven, Flanders, Belgium
| | - Juliana Afonso
- Embrapa Southeast Cattle, Fazenda Canchim, Rodovia Washington Luiz, Km 234, S/N, São Carlos, São Paulo, Brazil
| | - Priscila S N de Oliveira
- Department of Genetic and Evolution, Federal University of São Carlos, São Carlos, São Paulo, Brazil
| | - Juliana Petrini
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | | | - Aline S M Cesar
- Department of Agroindustry, Food and Nutrition, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | - Emanuele Cristina Gustani-Buss
- Mindflow Genomics, Leuven, Flanders, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000, Leuven, Belgium
| | - Tainã Figueiredo Cardoso
- Embrapa Southeast Cattle, Fazenda Canchim, Rodovia Washington Luiz, Km 234, S/N, São Carlos, São Paulo, Brazil
| | - Gregori A Rovadoski
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | | | - Andressa Oliveira de Lima
- Division of Medical Genetics, Department of Genomics Science, University of Washington, Seattle, WA, USA
| | | | - Bruno Gabriel Nascimento Andrade
- Embrapa Southeast Cattle, Fazenda Canchim, Rodovia Washington Luiz, Km 234, S/N, São Carlos, São Paulo, Brazil
- Department of Computer Science, Munster Technological University/MTU, Cork, Ireland
| | - Jason B Wolf
- Department of Biology & Biochemistry, Milner Centre for Evolution Bath, University of Bath, Bath, BA2 7AY, UK
| | - Luiz Lehmann Coutinho
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | - Gerson Barreto Mourão
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
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8
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Bruscadin JJ, Cardoso TF, da Silva Diniz WJ, de Souza MM, Afonso J, Vieira D, Malheiros J, Andrade BGN, Petrini J, Ferraz JBS, Zerlotini A, Mourão GB, Coutinho LL, de Almeida Regitano LC. Differential Allele-Specific Expression Revealed Functional Variants and Candidate Genes Related to Meat Quality Traits in B. indicus Muscle. Genes (Basel) 2022; 13:genes13122336. [PMID: 36553605 PMCID: PMC9777870 DOI: 10.3390/genes13122336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/03/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Traditional transcriptomics approaches have been used to identify candidate genes affecting economically important livestock traits. Regulatory variants affecting these traits, however, remain under covered. Genomic regions showing allele-specific expression (ASE) are under the effect of cis-regulatory variants, being useful for improving the accuracy of genomic selection models. Taking advantage of the better of these two methods, we investigated single nucleotide polymorphisms (SNPs) in regions showing differential ASE (DASE SNPs) between contrasting groups for beef quality traits. For these analyses, we used RNA sequencing data, imputed genotypes and genomic estimated breeding values of muscle-related traits from 190 Nelore (Bos indicus) steers. We selected 40 contrasting unrelated samples for the analysis (N = 20 animals per contrasting group) and used a beta-binomial model to identify ASE SNPs in only one group (i.e., DASE SNPs). We found 1479 DASE SNPs (FDR ≤ 0.05) associated with 55 beef-quality traits. Most DASE genes were involved with tenderness and muscle homeostasis, presenting a co-expression module enriched for the protein ubiquitination process. The results overlapped with epigenetics and phenotype-associated data, suggesting that DASE SNPs are potentially linked to cis-regulatory variants affecting simultaneously the transcription and phenotype through chromatin state modulation.
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Affiliation(s)
- Jennifer Jessica Bruscadin
- Center of Biological Sciences and Health, Federal University of São Carlos, São Carlos 13560-000, SP, Brazil
- Embrapa Pecuária Sudeste, São Carlos 13560-000, SP, Brazil
| | | | | | | | - Juliana Afonso
- Embrapa Pecuária Sudeste, São Carlos 13560-000, SP, Brazil
| | - Dielson Vieira
- Embrapa Pecuária Sudeste, São Carlos 13560-000, SP, Brazil
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jessica Malheiros
- Federal University of Latin American Integration-UNILA, Foz do Iguaçu 85851-000, PR, Brazil
| | | | - Juliana Petrini
- Center for Functional Genomics, Department of Animal Science, 13400-000, University of São Paulo (ESALQ—USP), Piracicaba 13400-000, SP, Brazil
| | - José Bento Sterman Ferraz
- Department of Veterinary Medicine, University of São Paulo (FMVZ—USP), Pirassununga 13630-000, SP, Brazil
| | | | - Gerson Barreto Mourão
- Center for Functional Genomics, Department of Animal Science, 13400-000, University of São Paulo (ESALQ—USP), Piracicaba 13400-000, SP, Brazil
| | - Luiz Lehmann Coutinho
- Center for Functional Genomics, Department of Animal Science, 13400-000, University of São Paulo (ESALQ—USP), Piracicaba 13400-000, SP, Brazil
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9
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de Novais FJ, Yu H, Cesar ASM, Momen M, Poleti MD, Petry B, Mourão GB, Regitano LCDA, Morota G, Coutinho LL. Multi-omic data integration for the study of production, carcass, and meat quality traits in Nellore cattle. Front Genet 2022; 13:948240. [PMID: 36338989 PMCID: PMC9634488 DOI: 10.3389/fgene.2022.948240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 10/06/2022] [Indexed: 11/18/2022] Open
Abstract
Data integration using hierarchical analysis based on the central dogma or common pathway enrichment analysis may not reveal non-obvious relationships among omic data. Here, we applied factor analysis (FA) and Bayesian network (BN) modeling to integrate different omic data and complex traits by latent variables (production, carcass, and meat quality traits). A total of 14 latent variables were identified: five for phenotype, three for miRNA, four for protein, and two for mRNA data. Pearson correlation coefficients showed negative correlations between latent variables miRNA 1 (mirna1) and miRNA 2 (mirna2) (−0.47), ribeye area (REA) and protein 4 (prot4) (−0.33), REA and protein 2 (prot2) (−0.3), carcass and prot4 (−0.31), carcass and prot2 (−0.28), and backfat thickness (BFT) and miRNA 3 (mirna3) (−0.25). Positive correlations were observed among the four protein factors (0.45–0.83): between meat quality and fat content (0.71), fat content and carcass (0.74), fat content and REA (0.76), and REA and carcass (0.99). BN presented arcs from the carcass, meat quality, prot2, and prot4 latent variables to REA; from meat quality, REA, mirna2, and gene expression mRNA1 to fat content; from protein 1 (prot1) and mirna2 to protein 5 (prot5); and from prot5 and carcass to prot2. The relations of protein latent variables suggest new hypotheses about the impact of these proteins on REA. The network also showed relationships among miRNAs and nebulin proteins. REA seems to be the central node in the network, influencing carcass, prot2, prot4, mRNA1, and meat quality, suggesting that REA is a good indicator of meat quality. The connection among miRNA latent variables, BFT, and fat content relates to the influence of miRNAs on lipid metabolism. The relationship between mirna1 and prot5 composed of isoforms of nebulin needs further investigation. The FA identified latent variables, decreasing the dimensionality and complexity of the data. The BN was capable of generating interrelationships among latent variables from different types of data, allowing the integration of omics and complex traits and identifying conditional independencies. Our framework based on FA and BN is capable of generating new hypotheses for molecular research, by integrating different types of data and exploring non-obvious relationships.
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Affiliation(s)
- Francisco José de Novais
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Haipeng Yu
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Aline Silva Mello Cesar
- Department of Agri-Food Industry, Food and Nutrition, University of São Paulo, Piracicaba, Brazil
| | - Mehdi Momen
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Mirele Daiana Poleti
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Brazil
| | - Bruna Petry
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Gerson Barreto Mourão
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Gota Morota
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
- *Correspondence: Gota Morota, ; Luiz Lehmann Coutinho,
| | - Luiz Lehmann Coutinho
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
- *Correspondence: Gota Morota, ; Luiz Lehmann Coutinho,
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10
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Silva-Vignato B, Cesar ASM, Afonso J, Moreira GCM, Poleti MD, Petrini J, Garcia IS, Clemente LG, Mourão GB, Regitano LCDA, Coutinho LL. Integrative Analysis Between Genome-Wide Association Study and Expression Quantitative Trait Loci Reveals Bovine Muscle Gene Expression Regulatory Polymorphisms Associated With Intramuscular Fat and Backfat Thickness. Front Genet 2022; 13:935238. [PMID: 35991540 PMCID: PMC9386181 DOI: 10.3389/fgene.2022.935238] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
Understanding the architecture of gene expression is fundamental to unravel the molecular mechanisms regulating complex traits in bovine, such as intramuscular fat content (IMF) and backfat thickness (BFT). These traits are economically important for the beef industry since they affect carcass and meat quality. Our main goal was to identify gene expression regulatory polymorphisms within genomic regions (QTL) associated with IMF and BFT in Nellore cattle. For that, we used RNA-Seq data from 193 Nellore steers to perform SNP calling analysis. Then, we combined the RNA-Seq SNP and a high-density SNP panel to obtain a new dataset for further genome-wide association analysis (GWAS), totaling 534,928 SNPs. GWAS was performed using the Bayes B model. Twenty-one relevant QTL were associated with our target traits. The expression quantitative trait loci (eQTL) analysis was performed using Matrix eQTL with the complete SNP dataset and 12,991 genes, revealing a total of 71,033 cis and 36,497 trans-eQTL (FDR < 0.05). Intersecting with QTL for IMF, we found 231 eQTL regulating the expression levels of 117 genes. Within those eQTL, three predicted deleterious SNPs were identified. We also identified 109 eQTL associated with BFT and affecting the expression of 54 genes. This study revealed genomic regions and regulatory SNPs associated with fat deposition in Nellore cattle. We highlight the transcription factors FOXP4, FOXO3, ZSCAN2, and EBF4, involved in lipid metabolism-related pathways. These results helped us to improve our knowledge about the genetic architecture behind important traits in cattle.
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Affiliation(s)
- Bárbara Silva-Vignato
- Department of Animal Science, College of Agriculture “Luiz de Queiroz”, University of São Paulo, Piracicaba, Brazil
| | - Aline Silva Mello Cesar
- Department of Agroindustry, Food, and Nutrition, College of Agriculture “Luiz de Queiroz”, University of São Paulo, Piracicaba, Brazil
| | | | | | - Mirele Daiana Poleti
- College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Juliana Petrini
- Department of Animal Science, College of Agriculture “Luiz de Queiroz”, University of São Paulo, Piracicaba, Brazil
| | - Ingrid Soares Garcia
- Department of Animal Science, College of Agriculture “Luiz de Queiroz”, University of São Paulo, Piracicaba, Brazil
| | - Luan Gaspar Clemente
- Department of Animal Science, College of Agriculture “Luiz de Queiroz”, University of São Paulo, Piracicaba, Brazil
| | - Gerson Barreto Mourão
- Department of Animal Science, College of Agriculture “Luiz de Queiroz”, University of São Paulo, Piracicaba, Brazil
| | | | - Luiz Lehmann Coutinho
- Department of Animal Science, College of Agriculture “Luiz de Queiroz”, University of São Paulo, Piracicaba, Brazil
- *Correspondence: Luiz Lehmann Coutinho,
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11
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Du L, Li K, Chang T, An B, Liang M, Deng T, Cao S, Du Y, Cai W, Gao X, Xu L, Zhang L, Li J, Gao H. Integrating genomics and transcriptomics to identify candidate genes for subcutaneous fat deposition in beef cattle. Genomics 2022; 114:110406. [PMID: 35709924 DOI: 10.1016/j.ygeno.2022.110406] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/31/2022] [Accepted: 06/09/2022] [Indexed: 02/07/2023]
Abstract
Fat deposition is a complex economic trait regulated by polygenic genetic basis and environmental factors. Therefore, integrating multi-omics data to uncover its internal regulatory mechanism has attracted extensive attention. Here, we performed genomics and transcriptomics analysis to detect candidates affecting subcutaneous fat (SCF) deposition in beef cattle. The association of 770K SNPs with the backfat thickness captured nine significant SNPs within or near 11 genes. Additionally, 13 overlapping genes regarding fat deposition were determined via the analysis of differentially expressed genes and weighted gene co-expression network analysis (WGCNA). We then calculated the correlations of these genes with BFT and constructed their interaction network. Finally, seven biomarkers including ACACA, SCD, FASN, ACOX1, ELOVL5, HACD2, and HSD17B12 were screened. Notably, ACACA, identified by the integration of genomics and transcriptomics, was more likely to exert profound effects on SCF deposition. These findings provided novel insights into the regulation mechanism underlying bovine fat accumulation.
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Affiliation(s)
- Lili Du
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Keanning Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tianpeng Chang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bingxing An
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Mang Liang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tianyu Deng
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Sheng Cao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Tianjin Agricultural University, Tianjin 300000, China
| | - Yueying Du
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Qingdao Agricultural University, Shandong 266000, China
| | - Wentao Cai
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xue Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lupei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huijiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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12
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Schettini GP, Peripolli E, Alexandre PA, dos Santos WB, Pereira ASC, de Albuquerque LG, Baldi F, Curi RA. Transcriptome Profile Reveals Genetic and Metabolic Mechanisms Related to Essential Fatty Acid Content of Intramuscular Longissimus thoracis in Nellore Cattle. Metabolites 2022; 12:metabo12050471. [PMID: 35629975 PMCID: PMC9144777 DOI: 10.3390/metabo12050471] [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: 03/26/2022] [Revised: 05/05/2022] [Accepted: 05/16/2022] [Indexed: 02/05/2023] Open
Abstract
Beef is a source of essential fatty acids (EFA), linoleic (LA) and alpha-linolenic (ALA) acids, which protect against inflammatory and cardiovascular diseases in humans. However, the intramuscular EFA profile in cattle is a complex and polygenic trait. Thus, this study aimed to identify potential regulatory genes of the essential fatty acid profile in Longissimus thoracis of Nellore cattle finished in feedlot. Forty-four young bulls clustered in four groups of fifteen animals with extreme values for each FA were evaluated through differentially expressed genes (DEG) analysis and two co-expression methodologies (WGCNA and PCIT). We highlight the ECHS1, IVD, ASB5, and ERLIN1 genes and the TF NFIA, indicated in both FA. Moreover, we associate the NFYA, NFYB, PPARG, FASN, and FADS2 genes with LA, and the RORA and ELOVL5 genes with ALA. Furthermore, the functional enrichment analysis points out several terms related to FA metabolism. These findings contribute to our understanding of the genetic mechanisms underlying the beef EFA profile in Nellore cattle finished in feedlot.
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Affiliation(s)
- Gustavo Pimenta Schettini
- School of Agricultural and Veterinary Sciences, São Paulo State University, Jaboticabal 14884-900, SP, Brazil; (W.B.d.S.); (L.G.d.A.); (F.B.)
- Correspondence:
| | - Elisa Peripolli
- School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga 13635-900, SP, Brazil; (E.P.); (A.S.C.P.)
| | - Pâmela Almeida Alexandre
- Commonwealth Scientific and Industrial Research Organization, Agriculture & Food, St Lucia, QLD 4067, Australia;
| | - Wellington Bizarria dos Santos
- School of Agricultural and Veterinary Sciences, São Paulo State University, Jaboticabal 14884-900, SP, Brazil; (W.B.d.S.); (L.G.d.A.); (F.B.)
| | - Angélica Simone Cravo Pereira
- School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga 13635-900, SP, Brazil; (E.P.); (A.S.C.P.)
| | - Lúcia Galvão de Albuquerque
- School of Agricultural and Veterinary Sciences, São Paulo State University, Jaboticabal 14884-900, SP, Brazil; (W.B.d.S.); (L.G.d.A.); (F.B.)
| | - Fernando Baldi
- School of Agricultural and Veterinary Sciences, São Paulo State University, Jaboticabal 14884-900, SP, Brazil; (W.B.d.S.); (L.G.d.A.); (F.B.)
| | - Rogério Abdallah Curi
- School of Veterinary Medicine and Animal Science, São Paulo State University, Botucatu 18618-681, SP, Brazil;
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13
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Magnier J, Druet T, Naves M, Ouvrard M, Raoul S, Janelle J, Moazami-Goudarzi K, Lesnoff M, Tillard E, Gautier M, Flori L. The genetic history of Mayotte and Madagascar cattle breeds mirrors the complex pattern of human exchanges in Western Indian Ocean. G3 GENES|GENOMES|GENETICS 2022; 12:6523972. [PMID: 35137043 PMCID: PMC8982424 DOI: 10.1093/g3journal/jkac029] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/11/2022] [Indexed: 11/16/2022]
Abstract
Despite their central economic and cultural role, the origin of cattle populations living in Indian Ocean islands still remains poorly documented. Here, we unravel the demographic and adaptive histories of the extant Zebus from the Mayotte and Madagascar islands using high-density SNP genotyping data. We found that these populations are very closely related and both display a predominant indicine ancestry. They diverged in the 16th century at the arrival of European people who transformed the trade network in the area. Their common ancestral cattle population originates from an admixture between an admixed African zebu population and an Indian zebu that occurred around the 12th century at the time of the earliest contacts between human African populations of the Swahili corridor and Austronesian people from Southeast Asia in Comoros and Madagascar. A steep increase in the estimated population sizes from the beginning of the 16th to the 17th century coincides with the expansion of the cattle trade. By carrying out genome scans for recent selection in the two cattle populations from Mayotte and Madagascar, we identified sets of candidate genes involved in biological functions (cancer, skin structure, and UV-protection, nervous system and behavior, organ development, metabolism, and immune response) broadly representative of the physiological adaptation to tropical conditions. Overall, the origin of the cattle populations from Western Indian Ocean islands mirrors the complex history of human migrations and trade in this area.
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Affiliation(s)
- Jessica Magnier
- SELMET, University of Montpellier, CIRAD, INRAE, L’Institut Agro, Montpellier 34398, France
- CIRAD, UMR SELMET, Montpellier 34398, France
| | - Tom Druet
- Unit of Animal Genomics, GIGA-R, Faculty of Veterinary Medicine, University of Liège, Liège 4000, Belgium
| | | | | | | | - Jérôme Janelle
- SELMET, University of Montpellier, CIRAD, INRAE, L’Institut Agro, Montpellier 34398, France
- CIRAD, UMR SELMET, Saint-Pierre 97410, France
| | | | - Matthieu Lesnoff
- SELMET, University of Montpellier, CIRAD, INRAE, L’Institut Agro, Montpellier 34398, France
- CIRAD, UMR SELMET, Montpellier 34398, France
| | - Emmanuel Tillard
- SELMET, University of Montpellier, CIRAD, INRAE, L’Institut Agro, Montpellier 34398, France
- CIRAD, UMR SELMET, Saint-Pierre 97410, France
| | - Mathieu Gautier
- CBGP, INRAE, CIRAD, IRD, L’Institut Agro, University of Montpellier, Montferrier sur Lez 34988, France
| | - Laurence Flori
- SELMET, INRAE, CIRAD, L’Institut Agro, University of Montpellier, Montpellier 34398, France
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14
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Nguyen DV, Nguyen OC, Malau-Aduli AE. Main regulatory factors of marbling level in beef cattle. Vet Anim Sci 2021; 14:100219. [PMID: 34877434 PMCID: PMC8633366 DOI: 10.1016/j.vas.2021.100219] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/24/2021] [Accepted: 11/18/2021] [Indexed: 02/06/2023] Open
Abstract
The content of intramuscular fat (IMF), that determines marbling levels is considered as one of the vital factors influencing beef sensory quality including tenderness, juiciness, flavour and colour. The IMF formation in cattle commences around six months after conception, and continuously grows throughout the life of the animal. The accumulation of marbling is remarkably affected by genetic, sexual, nutritional and management factors. In this review, the adipogenesis and lipogenesis process regulated by various factors and genes during fetal and growing stages is briefly presented. We also discuss the findings of recent studies on the effects of breed, gene, heritability and gender on the marbling accumulation. Various research reported that feeding during pregnancy, concentrate to roughage ratios and the supplementation or restriction of vitamin A, C, and D are crucial nutritional factors affecting the formation and development of IMF. Castration and early weaning combined with high energy feeding are effective management strategies for improving the accumulation of IMF. Furthermore, age and weight at slaughter are also reviewed because they have significant effects on marbling levels. The combination of several factors could positively affect the improvement of the IMF deposition. Therefore, advanced strategies that simultaneously apply genetic, sexual, nutritional and management factors to achieve desired IMF content without detrimental impacts on feed efficiency in high-marbling beef production are essential.
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Affiliation(s)
- Don V. Nguyen
- National Institute of Animal Science, Bac Tu Liem, Hanoi 29909, Vietnam
- Faculty of Animal Science, Vietnam National University of Agriculture, Gia Lam, Hanoi 131000, Vietnam
| | - Oanh C. Nguyen
- Faculty of Animal Science, Vietnam National University of Agriculture, Gia Lam, Hanoi 131000, Vietnam
| | - Aduli E.O. Malau-Aduli
- Veterinary Sciences Discipline, College of Public Health, Medical and Veterinary Sciences, Division of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia
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15
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The Meat Quality Characteristics of Holstein Calves: The Story of Israeli 'Dairy Beef'. Foods 2021; 10:foods10102308. [PMID: 34681357 PMCID: PMC8534874 DOI: 10.3390/foods10102308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/12/2021] [Accepted: 09/23/2021] [Indexed: 01/06/2023] Open
Abstract
Global animal production systems are often criticized for their lack of sustainability and insufficient resilience to ensure food security. The ‘farm-to-fork’ approach aims at orienting food systems towards the creation of a positive environmental impact, nutritious, healthy, safe and sufficient foods, and fairer economic returns for primary producers. Many countries rely on an imported supply of live animals to fulfill their needs for fresh meat. In Israel, ~60% of the sources of fresh beef come from the import of live animals. In order to encourage sustainable beef production in Israel, the proportion of local beef should be raised at the expense of imported animals. However, for this to be achieved, the superior performance of local beef should be justified. The current study was conducted to compare between the meat quality characteristics of local (Israeli Holstein; N = 205) vs. imported (Australian; N = 169) animals. Generally, while the imported calves presented a higher dressing percentage (p < 0.0001), the local animals were characterized by tenderer meat (p < 0.0001), longer sarcomeres (p < 0.0001), higher a* color attributes and pH (p < 0.001), superior cooking (p = 0.002) and thawing loss (p < 0.0001), higher intra-muscular fat (IMF) content, and a higher PUFA proportion (p < 0.01 and p < 0.0001, respectively) and PUFA:SFA ratio. The findings shown herein may provide sound arguments for stakeholders and policy makers to facilitate sustainable local beef production in Israel.
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16
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Trevisoli PA, Moreira GCM, Boschiero C, Cesar ASM, Petrini J, Margarido GRA, Ledur MC, Mourão GB, Garrick D, Coutinho LL. A Missense Mutation in the MYBPH Gene Is Associated With Abdominal Fat Traits in Meat-Type Chickens. Front Genet 2021; 12:698163. [PMID: 34456973 PMCID: PMC8386115 DOI: 10.3389/fgene.2021.698163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/09/2021] [Indexed: 12/14/2022] Open
Abstract
Chicken is an important source of protein for human nutrition and a model system for growth and developmental biology. Although the genetic architecture of quantitative traits in meat-type chickens has been the subject of ongoing investigation, the identification of mutations associated with carcass traits of economic interest remains challenging. Therefore, our aim was to identify predicted deleterious mutation, which potentially affects protein function, and test if they were associated with carcass traits in chickens. For that, we performed a genome-wide association analysis (GWAS) for breast, thigh and drumstick traits in meat-type chickens and detected 19 unique quantitative trait loci (QTL). We then used: (1) the identified windows; (2) QTL for abdominal fat detected in a previous study with the same population and (3) previously obtained whole genome sequence data, to identify 18 predicted deleterious single nucleotide polymorphisms (SNPs) in those QTL for further association with breast, thigh, drumstick and abdominal fat traits. Using the additive model, a predicted deleterious SNP c.482C > T (SIFT score of 0.4) was associated (p-value < 0.05) with abdominal fat weight and percentage. This SNP is in the second exon of the MYBPH gene, and its allele frequency deviates from Hardy–Weinberg equilibrium. In conclusion, our study provides evidence that the c.482C > T SNP in the MYBPH gene is a putative causal mutation for fat deposition in meat-type chickens.
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Affiliation(s)
- Priscila Anchieta Trevisoli
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
| | - Gabriel Costa Monteiro Moreira
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
| | - Clarissa Boschiero
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
| | - Aline Silva Mello Cesar
- Agri-Food Industry, Food and Nutrition Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
| | - Juliana Petrini
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
| | | | | | - Gerson Barreto Mourão
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
| | - Dorian Garrick
- School of Agriculture, Massey University, Wellington, New Zealand
| | - Luiz Lehmann Coutinho
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
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17
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Amorim ST, Stafuzza NB, Kluska S, Peripolli E, Pereira ASC, Muller da Silveira LF, de Albuquerque LG, Baldi F. Genome-wide interaction study reveals epistatic interactions for beef lipid-related traits in Nellore cattle. Anim Genet 2021; 53:35-48. [PMID: 34407235 DOI: 10.1111/age.13124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2021] [Indexed: 11/27/2022]
Abstract
Gene-gene interactions cause hidden genetic variation in natural populations and could be responsible for the lack of replication that is typically observed in complex traits studies. This study aimed to identify gene-gene interactions using the empirical Hilbert-Schmidt Independence Criterion method to test for epistasis in beef fatty acid profile traits of Nellore cattle. The dataset contained records from 963 bulls, genotyped using a 777 962k SNP chip. Meat samples of Longissimus muscle, were taken to measure fatty acid composition, which was quantified by gas chromatography. We chose to work with the sums of saturated (SFA), monounsaturated (MUFA), polyunsaturated (PUFA), omega-3 (OM3), omega-6 (OM6), SFA:PUFA and OM3:OM6 fatty acid ratios. The SNPs in the interactions where P < 10 - 8 were mapped individually and used to search for candidate genes. Totals of 602, 3, 13, 23, 13, 215 and 169 candidate genes for SFAs, MUFAs, PUFAs, OM3s, OM6s and SFA:PUFA and OM3:OM6 ratios were identified respectively. The candidate genes found were associated with cholesterol, lipid regulation, low-density lipoprotein receptors, feed efficiency and inflammatory response. Enrichment analysis revealed 57 significant GO and 18 KEGG terms ( P < 0.05), most of them related to meat quality and complementary terms. Our results showed substantial genetic interactions associated with lipid profile, meat quality, carcass and feed efficiency traits for the first time in Nellore cattle. The knowledge of these SNP-SNP interactions could improve understanding of the genetic and physiological mechanisms that contribute to lipid-related traits and improve human health by the selection of healthier meat products.
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Affiliation(s)
- S T Amorim
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/no, Jaboticabal, CEP 14884-900, Brazil
| | - N B Stafuzza
- Instituto de Zootecnia - Centro de Pesquisa em Bovinos de Corte, Rodovia Carlos Tonanni, Km94, Sertãozinho, 14174-000, Brazil
| | - S Kluska
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/no, Jaboticabal, CEP 14884-900, Brazil
| | - E Peripolli
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/no, Jaboticabal, CEP 14884-900, Brazil
| | - A S C Pereira
- Faculdade de Zootecnia e Engenharia de Alimentos, Núcleo de Apoio à Pesquisa em Melhoramento Animal, Biotecnologia e Transgenia, Universidade de São Paulo, Rua Duque de Caxias Norte, 225, Pirassununga, CEP 13635-900, Brazil
| | - L F Muller da Silveira
- Faculdade de Zootecnia e Engenharia de Alimentos, Núcleo de Apoio à Pesquisa em Melhoramento Animal, Biotecnologia e Transgenia, Universidade de São Paulo, Rua Duque de Caxias Norte, 225, Pirassununga, CEP 13635-900, Brazil
| | - L G de Albuquerque
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/no, Jaboticabal, CEP 14884-900, Brazil
| | - F Baldi
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/no, Jaboticabal, CEP 14884-900, Brazil
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Genome-Wide Association Study for Fatty Acid Composition in American Angus Cattle. Animals (Basel) 2021; 11:ani11082424. [PMID: 34438882 PMCID: PMC8388739 DOI: 10.3390/ani11082424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/04/2021] [Accepted: 08/12/2021] [Indexed: 12/14/2022] Open
Abstract
Livestock is an important commodity playing a major role in the global economy. Red meat plays an important role in human life, as it is a good source of animal protein and energy. The fatty acid content of beef has been shown to impact the eating experience and nutritional value of beef. Therefore, this study aimed to identify genomic regions which can account for genetic variation in meat fatty acid content. Genotypes imputed to the Illumina BovineHD 770K BeadChip were used in this study. Thirty-six 1-Mb genomic regions with a posterior probability of inclusion (PPI) greater than 0.90 were identified to be associated with variation in the content of at least one fatty acid. The genomic regions (1Mb) which were associated with more than one fatty acid trait with high genetic variance and harbored good candidate genes were on Chromosome (Chr) 6 (fatty acid binding protein 2), Chr 19 (thyroid hormone receptor alpha, fatty acid synthase), Chr 26 (stearoyl-CoA desaturase), and Chr 29 (thyroid hormone responsive, fatty acid desaturase 2, and fatty acid desaturase 3). Further studies are required to identify the causal variants within the identified genomic regions. Findings from the present study will help to increase understanding of the variation in fatty acid content of beef and help to enhance selection for beef with improved fatty acid composition.
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19
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Twining CW, Bernhardt JR, Derry AM, Hudson CM, Ishikawa A, Kabeya N, Kainz MJ, Kitano J, Kowarik C, Ladd SN, Leal MC, Scharnweber K, Shipley JR, Matthews B. The evolutionary ecology of fatty-acid variation: Implications for consumer adaptation and diversification. Ecol Lett 2021; 24:1709-1731. [PMID: 34114320 DOI: 10.1111/ele.13771] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/20/2021] [Accepted: 04/09/2021] [Indexed: 12/20/2022]
Abstract
The nutritional diversity of resources can affect the adaptive evolution of consumer metabolism and consumer diversification. The omega-3 long-chain polyunsaturated fatty acids eicosapentaenoic acid (EPA; 20:5n-3) and docosahexaenoic acid (DHA; 22:6n-3) have a high potential to affect consumer fitness, through their widespread effects on reproduction, growth and survival. However, few studies consider the evolution of fatty acid metabolism within an ecological context. In this review, we first document the extensive diversity in both primary producer and consumer fatty acid distributions amongst major ecosystems, between habitats and amongst species within habitats. We highlight some of the key nutritional contrasts that can shape behavioural and/or metabolic adaptation in consumers, discussing how consumers can evolve in response to the spatial, seasonal and community-level variation of resource quality. We propose a hierarchical trait-based approach for studying the evolution of consumers' metabolic networks and review the evolutionary genetic mechanisms underpinning consumer adaptation to EPA and DHA distributions. In doing so, we consider how the metabolic traits of consumers are hierarchically structured, from cell membrane function to maternal investment, and have strongly environment-dependent expression. Finally, we conclude with an outlook on how studying the metabolic adaptation of consumers within the context of nutritional landscapes can open up new opportunities for understanding evolutionary diversification.
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Affiliation(s)
- Cornelia W Twining
- Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Limnological Institute, University of Konstanz, Konstanz-Egg, Germany
| | - Joey R Bernhardt
- Department of Biology, McGill University, Montréal, QC, Canada.,Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Alison M Derry
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC, Canada
| | - Cameron M Hudson
- Department of Fish Ecology and Evolution, Eawag, Center of Ecology, Evolution and Biochemistry, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Asano Ishikawa
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Naoki Kabeya
- Department of Marine Biosciences, Tokyo University of Marine Science and Technology (TUMSAT, Tokyo, Japan
| | - Martin J Kainz
- WasserCluster Lunz-Inter-university Center for Aquatic Ecosystems Research, Lunz am See, Austria
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Carmen Kowarik
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Sarah Nemiah Ladd
- Ecosystem Physiology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany
| | - Miguel C Leal
- ECOMARE and CESAM - Centre for Environmental and Marine Studies and Department of Biology, University of Aveiro, Aveiro, Portugal
| | - Kristin Scharnweber
- Department of Ecology and Genetics; Limnology, Uppsala University, Uppsala, Sweden.,University of Potsdam, Plant Ecology and Nature Conservation, Potsdam-Golm, Germany
| | - Jeremy R Shipley
- Max Planck Institute of Animal Behavior, Radolfzell, Germany.,Department of Fish Ecology and Evolution, Eawag, Center of Ecology, Evolution and Biochemistry, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Blake Matthews
- Department of Fish Ecology and Evolution, Eawag, Center of Ecology, Evolution and Biochemistry, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
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20
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Enhancing the Nutritional Value of Red Meat through Genetic and Feeding Strategies. Foods 2021; 10:foods10040872. [PMID: 33923499 PMCID: PMC8073878 DOI: 10.3390/foods10040872] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 12/20/2022] Open
Abstract
Consumption of red meat contributes to the intake of many essential nutrients in the human diet including protein, essential fatty acids, and several vitamins and trace minerals, with high iron content, particularly in meats with high myoglobin content. Demand for red meat continues to increase worldwide, particularly in developing countries where food nutrient density is a concern. Dietary and genetic manipulation of livestock can influence the nutritional value of meat products, providing opportunities to enhance the nutritional value of meat. Studies have demonstrated that changes in livestock nutrition and breeding strategies can alter the nutritional value of red meat. Traditional breeding strategies, such as genetic selection, have influenced multiple carcass and meat quality attributes relevant to the nutritional value of meat including muscle and fat deposition. However, limited studies have combined both genetic and nutritional approaches. Future studies aiming to manipulate the composition of fresh meat should aim to balance potential impacts on product quality and consumer perception. Furthermore, the rapidly emerging fields of phenomics, nutrigenomics, and integrative approaches, such as livestock precision farming and systems biology, may help better understand the opportunities to improve the nutritional value of meat under both experimental and commercial conditions.
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21
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Bruscadin JJ, de Souza MM, de Oliveira KS, Rocha MIP, Afonso J, Cardoso TF, Zerlotini A, Coutinho LL, Niciura SCM, de Almeida Regitano LC. Muscle allele-specific expression QTLs may affect meat quality traits in Bos indicus. Sci Rep 2021; 11:7321. [PMID: 33795794 PMCID: PMC8016890 DOI: 10.1038/s41598-021-86782-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 03/17/2021] [Indexed: 02/01/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) located in transcript sequences showing allele-specific expression (ASE SNPs) were previously identified in the Longissimus thoracis muscle of a Nelore (Bos indicus) population consisting of 190 steers. Given that the allele-specific expression pattern may result from cis-regulatory SNPs, called allele-specific expression quantitative trait loci (aseQTLs), in this study, we searched for aseQTLs in a window of 1 Mb upstream and downstream from each ASE SNP. After this initial analysis, aiming to investigate variants with a potential regulatory role, we further screened our aseQTL data for sequence similarity with transcription factor binding sites and microRNA (miRNA) binding sites. These aseQTLs were overlapped with methylation data from reduced representation bisulfite sequencing (RRBS) obtained from 12 animals of the same population. We identified 1134 aseQTLs associated with 126 different ASE SNPs. For 215 aseQTLs, one allele potentially affected the affinity of a muscle-expressed transcription factor to its binding site. 162 aseQTLs were predicted to affect 149 miRNA binding sites, from which 114 miRNAs were expressed in muscle. Also, 16 aseQTLs were methylated in our population. Integration of aseQTL with GWAS data revealed enrichment for traits such as meat tenderness, ribeye area, and intramuscular fat . To our knowledge, this is the first report of aseQTLs identification in bovine muscle. Our findings indicate that various cis-regulatory and epigenetic mechanisms can affect multiple variants to modulate the allelic expression. Some of the potential regulatory variants described here were associated with the expression pattern of genes related to interesting phenotypes for livestock. Thus, these variants might be useful for the comprehension of the genetic control of these phenotypes.
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Affiliation(s)
- Jennifer Jessica Bruscadin
- grid.411247.50000 0001 2163 588XPost-Graduation Program of Evolutionary Genetics and Molecular Biology, Center of Biological Sciences and Health, Federal University of São Carlos, São Carlos, SP Brazil
| | - Marcela Maria de Souza
- grid.34421.300000 0004 1936 7312Post-Doctoral Fellow, Department of Animal Science, Iowa State University, Ames, IA USA
| | - Karina Santos de Oliveira
- grid.411247.50000 0001 2163 588XPost-Graduation Program of Evolutionary Genetics and Molecular Biology, Center of Biological Sciences and Health, Federal University of São Carlos, São Carlos, SP Brazil
| | - Marina Ibelli Pereira Rocha
- grid.411247.50000 0001 2163 588XPost-Graduation Program of Evolutionary Genetics and Molecular Biology, Center of Biological Sciences and Health, Federal University of São Carlos, São Carlos, SP Brazil
| | - Juliana Afonso
- grid.11899.380000 0004 1937 0722Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, SP Brazil
| | - Tainã Figueiredo Cardoso
- grid.460200.00000 0004 0541 873XEmbrapa Pecuária Sudeste, P. O. Box 339, São Carlos, SP 13564-230 Brazil
| | - Adhemar Zerlotini
- grid.460200.00000 0004 0541 873XEmbrapa Informática Agropecuária, Campinas, SP Brazil
| | - Luiz Lehmann Coutinho
- grid.11899.380000 0004 1937 0722Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, SP Brazil
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22
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Multi-Omics Approach Reveals miR-SNPs Affecting Muscle Fatty Acids Profile in Nelore Cattle. Genes (Basel) 2021; 12:genes12010067. [PMID: 33419037 PMCID: PMC7825288 DOI: 10.3390/genes12010067] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/26/2020] [Accepted: 12/31/2020] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are key regulators of gene expression, potentially affecting several biological processes, whose function can be altered by sequence variation. Hence, the integration of single nucleotide polymorphisms (SNP) and miRNAs can explain individual differences in economic traits. To provide new insights into the effects of SNPs on miRNAs and their related target genes, we carried out a multi-omic analysis to identify SNPs in miRNA mature sequences (miR-SNPs) associated with fatty acid (FA) composition in the Nelore cattle. As a result, we identified 3 miR-SNPs in different miRNAs (bta-miR-2419-3p, bta-miR-193a-2, and bta-miR-1291) significantly associated with FA traits (p-value < 0.02, Bonferroni corrected). Among these, the rs110817643C>T, located in the seed sequence of the bta-miR-1291, was associated with different ω6 FAs, polyunsaturated FA, and polyunsaturated:saturated FA ratios. Concerning the other two miR-SNPs, the rs43400521T>C (located in the bta-miR-2419-3p) was associated with C12:0 and C18:1 cis-11 FA, whereas the rs516857374A>G (located in the bta-miR-193a-2) was associated with C18:3 ω6 and ratio of ω6/ω3 traits. Additionally, to identify potential biomarkers for FA composition, we described target genes affected by these miR-SNPs at the mRNA or protein level. Our multi-omics analysis outlines the effects of genetic polymorphism on miRNA, and it highlights miR-SNPs and target candidate genes that control beef fatty acid composition.
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Laghouaouta H, Sosa-Madrid BS, Zubiri-Gaitán A, Hernández P, Blasco A. Novel Genomic Regions Associated with Intramuscular Fatty Acid Composition in Rabbits. Animals (Basel) 2020; 10:ani10112090. [PMID: 33187110 PMCID: PMC7697864 DOI: 10.3390/ani10112090] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/08/2020] [Accepted: 11/09/2020] [Indexed: 12/19/2022] Open
Abstract
Intramuscular fat (IMF) content and its composition affect the quality of meat. Selection for IMF generated a correlated response on its fatty acid composition. The increase of IMF content is associated with an increase of its saturated (SFA) and monounsaturated (MUFA) fatty acids, and consequently a decrease of polyunsaturated fatty acids (PUFA). We carried out a genome wide association study (GWAS) for IMF composition on two rabbit lines divergently selected for IMF content, using a Bayes B procedure. Association analyses were performed using 475 individuals and 90,235 Single Nucleotide Polymorphisms (SNPs). The main objectives were to identify genomic regions associated with the IMF composition and to generate a list of candidate genes. Genomic regions associated with the intramuscular fatty acid composition were spread across different rabbit chromosomes (OCU). An important region at 34.0-37.9 Mb on OCU1 was associated with C14:0, C16:0, SFA, and C18:2n6, explaining 3.5%, 11.2%, 11.3%, and 3.2% of the genomic variance, respectively. Another relevant genomic region was found to be associated at 46.0-48.9 Mb on OCU18, explaining up to 8% of the genomic variance of MUFA/SFA. The associated regions harbor several genes related to lipid metabolism, such as SCD, PLIN2, and ERLIN1. The main genomic regions associated with the fatty acids were not previously associated with IMF content in rabbits. Nonetheless, MTMR2 is the only gene that was associated with both the IMF content and composition in rabbits. Our study highlighted the polygenic nature of the fatty acids in rabbits and elucidated its genetic background.
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24
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Amorim ST, Yu H, Momen M, de Albuquerque LG, Cravo Pereira AS, Baldi F, Morota G. An assessment of genomic connectedness measures in Nellore cattle. J Anim Sci 2020; 98:skaa289. [PMID: 32877515 PMCID: PMC7792904 DOI: 10.1093/jas/skaa289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 08/27/2020] [Indexed: 12/17/2022] Open
Abstract
An important criterion to consider in genetic evaluations is the extent of genetic connectedness across management units (MU), especially if they differ in their genetic mean. Reliable comparisons of genetic values across MU depend on the degree of connectedness: the higher the connectedness, the more reliable the comparison. Traditionally, genetic connectedness was calculated through pedigree-based methods; however, in the era of genomic selection, this can be better estimated utilizing new approaches based on genomics. Most procedures consider only additive genetic effects, which may not accurately reflect the underlying gene action of the evaluated trait, and little is known about the impact of non-additive gene action on connectedness measures. The objective of this study was to investigate the extent of genomic connectedness measures, for the first time, in Brazilian field data by applying additive and non-additive relationship matrices using a fatty acid profile data set from seven farms located in the three regions of Brazil, which are part of the three breeding programs. Myristic acid (C14:0) was used due to its importance for human health and reported presence of non-additive gene action. The pedigree included 427,740 animals and 925 of them were genotyped using the Bovine high-density genotyping chip. Six relationship matrices were constructed, parametrically and non-parametrically capturing additive and non-additive genetic effects from both pedigree and genomic data. We assessed genome-based connectedness across MU using the prediction error variance of difference (PEVD) and the coefficient of determination (CD). PEVD values ranged from 0.540 to 1.707, and CD from 0.146 to 0.456. Genomic information consistently enhanced the measures of connectedness compared to the numerator relationship matrix by at least 63%. Combining additive and non-additive genomic kernel relationship matrices or a non-parametric relationship matrix increased the capture of connectedness. Overall, the Gaussian kernel yielded the largest measure of connectedness. Our findings showed that connectedness metrics can be extended to incorporate genomic information and non-additive genetic variation using field data. We propose that different genomic relationship matrices can be designed to capture additive and non-additive genetic effects, increase the measures of connectedness, and to more accurately estimate the true state of connectedness in herds.
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Affiliation(s)
- Sabrina T Amorim
- Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias,
Departamento de Zootecnia, Via de acesso Prof. Paulo Donato Castellane, CEP
Jaboticabal, SP, Brazil
| | - Haipeng Yu
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and
State University, Blacksburg, VA
| | - Mehdi Momen
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and
State University, Blacksburg, VA
| | - Lúcia Galvão de Albuquerque
- Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias,
Departamento de Zootecnia, Via de acesso Prof. Paulo Donato Castellane, CEP
Jaboticabal, SP, Brazil
| | - Angélica S Cravo Pereira
- Universidade de São Paulo, Faculdade de Zootecnia e Engenharia de Alimentos,
Núcleo de Apoio à Pesquisa em Melhoramento Animal, Biotecnologia e
Transgenia, Rua Duque de Caxias Norte, CEP Pirassununga, SP, Brazil
| | - Fernando Baldi
- Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias,
Departamento de Zootecnia, Via de acesso Prof. Paulo Donato Castellane, CEP
Jaboticabal, SP, Brazil
| | - Gota Morota
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and
State University, Blacksburg, VA
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Raza SHA, Khan S, Amjadi M, Abdelnour SA, Ohran H, Alanazi KM, Abd El-Hack ME, Taha AE, Khan R, Gong C, Schreurs NM, Zhao C, Wei D, Zan L. Genome-wide association studies reveal novel loci associated with carcass and body measures in beef cattle. Arch Biochem Biophys 2020; 694:108543. [PMID: 32798459 DOI: 10.1016/j.abb.2020.108543] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/26/2020] [Accepted: 08/08/2020] [Indexed: 12/18/2022]
Abstract
Genomic selection has an essential role in the livestock economy by increasing selection productivity. Genomics provides a mechanism to increase the rate of genetic gain using marker-assisted selection. Various quantitative trait loci (QTL) associated with body, carcass and meat quality traits in beef cattle have been found. It is widely accepted that QTL traits in livestock species are regulated by several genes and factors from the environment. Genome-wide association studies (GWAS) are a powerful approach in identifying QTL and to establish genomic regions harboring the genes and polymorphisms associated with specific characteristics in beef cattle. Due to their impact on economic returns, growth, carcass and meat quality traits of cattle are frequently used as essential criteria in selection in breeding programs., GWAS has been used in beef cattle breeding and genetic program and some progress has been made. Furthermore, numerous genes and markers related to productivity traits in beef cattle have been found. This review summarizes the advances in the use of GWAS in beef cattle production and outlines the associations with growth, carcass, and meat quality.
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Affiliation(s)
- Sayed Haidar Abbas Raza
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
| | - Samiullah Khan
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan, 650201, China
| | - Motahareh Amjadi
- Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - Sameh A Abdelnour
- Department of Animal Production, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Hussien Ohran
- Department of Physiology, University of Sarajevo, Veterinary Faculty, Zmajaod Bosne 90, 71000, Sarajevo, Bosnia and Herzegovina
| | - Khalid M Alanazi
- Zoology Department, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Mohamed E Abd El-Hack
- Department of Poultry, Faculty of Agriculture, Zagazig University, Zagazig, 44511, Egypt
| | - Ayman E Taha
- Department of Animal Husbandry and Animal Wealth Development, Faculty of Veterinary Medicine, Alexandria University, Edfina, 22578, Egypt
| | - Rajwali Khan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Cheng Gong
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Nicola M Schreurs
- Animal Science, School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Chunping Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Dawei Wei
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China; National Beef Cattle Improvement Center, Northwest A&F University, Yangling, 712100, China.
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26
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Costa C, Rizzieri R, Melo G, Müller L, Estevan D, Pacheco R, Millen D, Pereira A, Zanatta M, Cappellozza B, Cervieri R, Martins C, Arrigoni M. Effects of fatty acid profile of supplements on intake, performance, carcass traits, meat characteristics, and meat sensorial analysis of feedlot Bos indicus bulls offered a high-concentrate diet. Transl Anim Sci 2020; 4:txaa142. [PMID: 33024942 PMCID: PMC7526738 DOI: 10.1093/tas/txaa142] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/17/2020] [Indexed: 12/24/2022] Open
Abstract
This experiment was designed to evaluate the effects of lipid source and fatty acid (FA) profile on intake, performance, carcass characteristics, expression of enzymes, and sensorial analysis of Bos indicus animals offered a high-concentrate diet. On day 0, 96 noncastrated animals were blocked by initial body weight (400 ± 19.3 kg), randomly allocated to 1 of 24 pens (4 animals/pen), and pens were randomly assigned to receive: 1) control: basal diet composed of whole cottonseed and corn germ as lipid substrates (CONT; n = 6), 2) calcium salts of fatty acids (CSFA) of soybean: CSFA of soybean oil as replacement for whole cottonseed and corn germ (calcium salts of soybean oil [CSSO]; n = 6), 3) CSFA-Blend: CSFA of palm, cottonseed, and soybean oil as replacement for whole cottonseed and corn germ (calcium salts of vegetable oils [CSVO]; n = 6), and 4) Mix: basal diet containing whole cottonseed, corn germ, and CSVO (MIXT; n = 6). Experiment lasted 108 d and performance, ultrasound measurements, as well as carcass characteristics were evaluated. Additionally, meat FA profile, expression of enzymes involved in lipid metabolism, and sensorial analysis were evaluated. No treatment effects were observed on performance variables, ultrasound, and carcass traits (P ≥ 0.22), whereas animals receiving CONT had a greater intake of C10:0, C16:0, C16:1 trans-9, C18:1 cis-9, C18:2, C18:3, total FA, monounsatured FA (MUFA), and polyunsaturated FA (PUFA) vs. CSSO and MIXT (P < 0.05). Conversely, intake ratios of saturated FA (SFA):MUFA and SFA:PUFA were all reduced for CONT vs. other treatments. Meat obtained from CONT animals had greater colorimetric (L*, a*, and b*) values vs. MIXT (P < 0.01). On meat FA profile, CONT increased C18:0 vs. supplementation with calcium salts (P < 0.02) and supplementation with CSSO yielded greater meat concentrations of C18:1 trans-10 and C18:2 CLA intermediates (P < 0.01). Expression of SREBP-1, SCD, and LPL was downregulated for CSSO (P < 0.05). For sensorial analysis, regular flavor was greater (P = 0.01) for CSSO vs. other treatments, but also greater aroma (P = 0.05) vs. CONT and CSVO. In summary, addition of different lipid sources with varying FA profiles into high-concentrate diets did not affect performance and carcass characteristics of B. indicus animals, but supplementation with calcium salts of soybean oil inhibited the mRNA expression of enzymes involved in lipid metabolism, whereas flavor and aroma were positively affected by this lipid source.
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Affiliation(s)
- Carolina Costa
- Faculdade de Medicina Veterinária e Zootecnia, Universidade Estadual Paulista, Botucatu, SP, Brazil
| | - Ramon Rizzieri
- Faculdade de Medicina Veterinária e Zootecnia, Universidade Estadual Paulista, Botucatu, SP, Brazil
| | - Gabriel Melo
- Faculdade de Medicina Veterinária e Zootecnia, Universidade Estadual Paulista, Botucatu, SP, Brazil
| | - Leonardo Müller
- Faculdade de Medicina Veterinária e Zootecnia, Universidade Estadual Paulista, Botucatu, SP, Brazil
| | - Daniela Estevan
- Faculdade de Medicina Veterinária e Zootecnia, Universidade Estadual Paulista, Botucatu, SP, Brazil
| | | | - Danilo Millen
- Faculdade de Ciências Agrárias e Tecnológicas, Universidade Estadual Paulista, Dracena, SP, Brazil
| | - Angélica Pereira
- Faculdade de Medicina Veterinaria e Zootecnia, Universidade de São Paulo, Pirassununga, SP, Brazil
| | - Mariana Zanatta
- Faculdade de Medicina Veterinaria e Zootecnia, Universidade de São Paulo, Pirassununga, SP, Brazil
| | | | | | - Cyntia Martins
- Faculdade de Medicina Veterinária e Zootecnia, Universidade Estadual Paulista, Botucatu, SP, Brazil
| | - Mário Arrigoni
- Faculdade de Medicina Veterinária e Zootecnia, Universidade Estadual Paulista, Botucatu, SP, Brazil
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Ribeiro DM, Salama AAK, Vitor ACM, Argüello A, Moncau CT, Santos EM, Caja G, de Oliveira JS, Balieiro JCC, Hernández-Castellano LE, Zachut M, Poleti MD, Castro N, Alves SP, Almeida AM. The application of omics in ruminant production: a review in the tropical and sub-tropical animal production context. J Proteomics 2020; 227:103905. [PMID: 32712373 DOI: 10.1016/j.jprot.2020.103905] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 06/25/2020] [Accepted: 07/16/2020] [Indexed: 02/08/2023]
Abstract
The demand for animal products (e.g. dairy and beef) in tropical regions is expected to increase in parallel with the public demand for sustainable practices, due to factors such as population growth and climate change. The necessity to increase animal production output must be achieved with better management and production technologies. For this to happen, novel research methodologies, animal selection and postgenomic tools play a pivotal role. Indeed, improving breeder selection programs, the quality of meat and dairy products as well as animal health will contribute to higher sustainability and productivity. This would surely benefit regions where resource quality and quantity are increasingly unstable, and research is still very incipient, which is the case of many regions in the tropics. The purpose of this review is to demonstrate how omics-based approaches play a major role in animal science, particularly concerning ruminant production systems and research associated to the tropics and developing countries. SIGNIFICANCE: Environmental conditions in the tropics make livestock production harder, compared to temperate regions. Due to global warming, the sustainability of livestock production will become increasingly problematic. The use of novel omics technologies could generate useful information to understand adaptation mechanisms of resilient breeds and/or species. The application of omics to tropical animal production is still residual in the currently available literature. With this review, we aim to summarize the most notable results in the field whilst encouraging further research to deal with the future challenges that animal production in the tropics will need to face.
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Affiliation(s)
- David M Ribeiro
- LEAF Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, University of Lisbon, Lisboa, Portugal
| | - Ahmed A K Salama
- Group of Research in Ruminants (G2R), Department of Animal and Food Science, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Ana C M Vitor
- CIISA - Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Av. da Universidade Técnica, Lisboa, Portugal
| | - Anastasio Argüello
- Animal Production and Biotechnology group, Institute of Animal Health and Food Safety, Universidad de Las Palmas de Gran Canaria, 35413 Arucas, Spain
| | - Cristina T Moncau
- FZEA - Faculty of Animal Science and Food Engineering, University of São Paulo, Avenida Duque de Caxias Norte - 225, 13635-900 Pirassununga, SP, Brazil
| | - Edson M Santos
- Departamento de Zootecnia, Centro de Ciências Agrárias, Universidade Federal da Paraíba, Areia, PB, Brazil
| | - Gerardo Caja
- Group of Research in Ruminants (G2R), Department of Animal and Food Science, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Juliana S de Oliveira
- Departamento de Zootecnia, Centro de Ciências Agrárias, Universidade Federal da Paraíba, Areia, PB, Brazil
| | - Júlio C C Balieiro
- FMVZ - School of Veterinary Medicine and Animal Science, University of São Paulo, Avenida Duque de Caxias Norte - 225, 13635-900 Pirassununga, SP, Brazil
| | | | - Maya Zachut
- Department of Ruminant Science, Institute of Animal Sciences Agricultural Research Organization/Volcani Center, Rishon Lezion 7505101, Israel
| | - Mirele D Poleti
- FZEA - Faculty of Animal Science and Food Engineering, University of São Paulo, Avenida Duque de Caxias Norte - 225, 13635-900 Pirassununga, SP, Brazil
| | - Noemi Castro
- Animal Production and Biotechnology group, Institute of Animal Health and Food Safety, Universidad de Las Palmas de Gran Canaria, 35413 Arucas, Spain
| | - Susana P Alves
- CIISA - Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Av. da Universidade Técnica, Lisboa, Portugal
| | - André M Almeida
- LEAF Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, University of Lisbon, Lisboa, Portugal.
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28
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de Souza MM, Zerlotini A, Rocha MIP, Bruscadin JJ, Diniz WJDS, Cardoso TF, Cesar ASM, Afonso J, Andrade BGN, Mudadu MDA, Mokry FB, Tizioto PC, de Oliveira PSN, Niciura SCM, Coutinho LL, Regitano LCDA. Allele-specific expression is widespread in Bos indicus muscle and affects meat quality candidate genes. Sci Rep 2020; 10:10204. [PMID: 32576896 PMCID: PMC7311436 DOI: 10.1038/s41598-020-67089-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/20/2020] [Indexed: 11/09/2022] Open
Abstract
Differences between the expression of the two alleles of a gene are known as allele-specific expression (ASE), a common event in the transcriptome of mammals. Despite ASE being a source of phenotypic variation, its occurrence and effects on genetic prediction of economically relevant traits are still unexplored in bovines. Furthermore, as ASE events are likely driven by cis-regulatory mutations, scanning them throughout the bovine genome represents a significant step to elucidate the mechanisms underlying gene expression regulation. To address this question in a Bos indicus population, we built the ASE profile of the skeletal muscle tissue of 190 Nelore steers, using RNA sequencing data and SNPs genotypes from the Illumina BovineHD BeadChip (770 K bp). After quality control, 820 SNPs showed at least one sample with ASE. These SNPs were widespread among all autosomal chromosomes, being 32.01% found in 3'UTR and 31.41% in coding regions. We observed a considerable variation of ASE profile among individuals, which highlighted the need for biological replicates in ASE studies. Functional analysis revealed that ASE genes play critical biological functions in the development and maintenance of muscle tissue. Additionally, some of these genes were previously reported as associated with beef production and quality traits in livestock, thus indicating a possible source of bias on genomic predictions for these traits.
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Affiliation(s)
- Marcela Maria de Souza
- Animal Biotechnology, Embrapa Pecuária Sudeste, São Carlos, SP, Brazil.,Post-graduate Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Adhemar Zerlotini
- Bioinformatic Multi-user Laboratory, Embrapa Informática Agropecuária, Campinas, SP, Brazil
| | - Marina Ibelli Pereira Rocha
- Animal Biotechnology, Embrapa Pecuária Sudeste, São Carlos, SP, Brazil.,Post-graduate Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Jennifer Jessica Bruscadin
- Animal Biotechnology, Embrapa Pecuária Sudeste, São Carlos, SP, Brazil.,Post-graduate Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Wellison Jarles da Silva Diniz
- Animal Biotechnology, Embrapa Pecuária Sudeste, São Carlos, SP, Brazil.,Post-graduate Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | | | | | - Juliana Afonso
- Animal Biotechnology, Embrapa Pecuária Sudeste, São Carlos, SP, Brazil.,Post-graduate Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | | | | | - Fabiana Barichello Mokry
- Animal Biotechnology, Embrapa Pecuária Sudeste, São Carlos, SP, Brazil.,Post-graduate Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
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Abstract
An experiment of divergent selection for intramuscular fat was carried out at Universitat Politècnica de València. The high response of selection in intramuscular fat content, after nine generations of selection, and a multidimensional scaling analysis showed a high degree of genomic differentiation between the two divergent populations. Therefore, local genomic differences could link genomic regions, encompassing selective sweeps, to the trait used as selection criterion. In this sense, the aim of this study was to identify genomic regions related to intramuscular fat through three methods for detection of selection signatures and to generate a list of candidate genes. The methods implemented in this study were Wright's fixation index, cross population composite likelihood ratio and cross population - extended haplotype homozygosity. Genomic data came from the 9th generation of the two populations divergently selected, 237 from Low line and 240 from High line. A high single nucleotide polymorphism (SNP) density array, Affymetrix Axiom OrcunSNP Array (around 200k SNPs), was used for genotyping samples. Several genomic regions distributed along rabbit chromosomes (OCU) were identified as signatures of selection (SNPs having a value above cut-off of 1%) within each method. In contrast, 8 genomic regions, harbouring 80 SNPs (OCU1, OCU3, OCU6, OCU7, OCU16 and OCU17), were identified by at least 2 methods and none by the 3 methods. In general, our results suggest that intramuscular fat selection influenced multiple genomic regions which can be a consequence of either only selection effect or the combined effect of selection and genetic drift. In addition, 73 genes were retrieved from the 8 selection signatures. After functional and enrichment analyses, the main genes into the selection signatures linked to energy, fatty acids, carbohydrates and lipid metabolic processes were ACER2, PLIN2, DENND4C, RPS6, RRAGA (OCU1), ST8SIA6, VIM (OCU16), RORA, GANC and PLA2G4B (OCU17). This genomic scan is the first study using rabbits from a divergent selection experiment. Our results pointed out a large polygenic component of the intramuscular fat content. Besides, promising positional candidate genes would be analysed in further studies in order to bear out their contributions to this trait and their feasible implications for rabbit breeding programmes.
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30
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Olivieri BF, Braz CU, Brito Lopes F, Peripolli E, Medeiros de Oliveira Silva R, Ruegger Pereira da Silva Corte R, Albuquerque LGD, Pereira ASC, Stafuzza NB, Baldi F. Differentially expressed genes identified through RNA-seq with extreme values of principal components for beef fatty acid in Nelore cattle. J Anim Breed Genet 2020; 138:80-90. [PMID: 32424857 DOI: 10.1111/jbg.12483] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/13/2020] [Accepted: 04/22/2020] [Indexed: 12/13/2022]
Abstract
The aim of this study was to identify differentially expressed genes (DEG) in the Longissimus thoracis muscle of Nelore cattle related to fatty acid (FA) profile through RNA sequencing and principal component analysis (PCA). Two groups of 10 animals each were selected containing PC1 and PC2 extreme DEG values (HIGH × LOW) for each FA group. The intramuscular fat (IMF) was compared between cluster groups by ANOVA, and only the sum of monounsaturated FA (MUFA) and ω3 showed significant differences (p < .05). Interestingly, the highest percentage (95%) of phenotypic variation explained by the sum of the first two PC was observed for ω3, which also displayed the lowest number of DEG (n = 1). The lowest percentage (59%) was observed for MUFA, which also revealed the largest number of DEG (n = 66). Since only MUFA and ω3 exhibited significant differences between cluster groups, we can conclude that the differences observed for the remaining groups are not due to the percentage of IMF. Several genes that have been previously associated with meat quality and FA traits were identified as DEG in this study. The functional analysis revealed one KEGG pathway and eight GO terms as significant (p < .05), in which we highlighted the purine metabolism, glycolytic process, adenosine triphosphate binding and bone development. These results strongly contribute to the knowledge of the biological mechanisms involved in meat FA profile of Nelore cattle.
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Affiliation(s)
- Bianca Ferreira Olivieri
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Jaboticabal, Brazil
| | - Camila Urbano Braz
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Jaboticabal, Brazil
| | - Fernando Brito Lopes
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Jaboticabal, Brazil.,Embrapa Cerrados, Brasilia, Brazil
| | - Elisa Peripolli
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Jaboticabal, Brazil
| | | | | | - Lucia Galvão de Albuquerque
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Jaboticabal, Brazil
| | - Angélica Simone Cravo Pereira
- Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Nutrição e Produção Animal, Universidade de São Paulo (USP), Pirassununga, Brazil
| | | | - Fernando Baldi
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Jaboticabal, Brazil
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31
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Proteome alterations associated with the oleic acid and cis-9, trans-11 conjugated linoleic acid content in bovine skeletal muscle. J Proteomics 2020; 222:103792. [PMID: 32335295 DOI: 10.1016/j.jprot.2020.103792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 04/09/2020] [Accepted: 04/19/2020] [Indexed: 12/18/2022]
Abstract
Oleic acid (OA) and cis-9, trans-11 conjugated linoleic acid (c9t11-CLA) are fatty acids found in beef with beneficial effects in human health. This study investigated differentially abundant proteins (DAPs) in skeletal muscle of bovines with extreme values of OA, and c9t11-CLA. For each one of the fatty acids, twenty muscle samples were divided into two groups (N = 10_High; N = 10_Low) and analyzed by high definition mass spectrometry. We identified 103 and 133 DAPs between the groups for each fatty acid. We found 64 and 45 up-regulated and 39 and 68 down-regulated proteins for OA and c9t11-CLA, respectively. Comparative analysis between proteomic and transcriptomic data revealed eight and ten genes with a consistent between mRNA expression levels and protein abundance for OA and c9t11-CLA, respectively. Unconventional myosin-Id (MYO1D), mineralocorticoid receptor (NR3C2), geranylgeranyl transferase type-2 subunit-alpha (RABGGTA), and uveal autoantigen with coiled-coil domains and ankyrin repeats (UACA) were found as putative candidate proteins for OA content. Fatty acid synthase (FASN), tubulin alpha-4A chain (TUBA4A), vinculin (VCL), NADH dehydrogenase 1 alpha subcomplex 5 (NDUFA5), and prefoldin subunit 6 (PFDN6) for c9t11-CLA. Our findings contribute to a deeper understanding of the molecular mechanisms behind the regulation of the OA and c9t11-CLA content in cattle skeletal muscle. SIGNIFICANCE: Questions about the association between meat intake and disease incidence in humans has driven animal scientist to pursue a better understanding of the biological processes associated with differences in the intramuscular fat composition. The beneficial effects of oleic acid and conjugated linoleic acid in human health have been demonstrated by improving the immune system and preventing atherosclerosis, different types of cancers, hypertension, and diabetes. Previous genome-wide association and gene expression studies identified genomic regions and differentially expressed genes associated with the fatty acid profile in skeletal muscle. In this work, differences were evaluated at the protein level. The use of a label-free quantitative proteomic approach, compared with muscle transcriptome results obtained by RNA-sequencing, allowed us to earn new insights into the variability in fatty acid deposition in skeletal muscle of farm animals. This study opens new avenues to explore the effect of the fatty acids in the skeletal muscle of livestock animals, which is associated with nutritional values of the meat, and perhaps to understand the mechanisms correlated with metabolic diseases in other species.
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32
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Lukić B, Ferenčaković M, Šalamon D, Čačić M, Orehovački V, Iacolina L, Curik I, Cubric-Curik V. Conservation Genomic Analysis of the Croatian Indigenous Black Slavonian and Turopolje Pig Breeds. Front Genet 2020; 11:261. [PMID: 32296459 PMCID: PMC7136467 DOI: 10.3389/fgene.2020.00261] [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] [Received: 05/06/2019] [Accepted: 03/05/2020] [Indexed: 12/19/2022] Open
Abstract
The majority of the nearly 400 existing local pig breeds are adapted to specific environments and human needs. The demand for large production quantities and the industrialized pig production have caused a rapid decline of many local pig breeds in recent decades. Black Slavonian pig and Turopolje pig, the latter highly threatened, are the two Croatian local indigenous breeds typically grown in extensive or semi-intensive systems. In order to guide a long-term breeding program to prevent the disappearance of these breeds, we analyzed their genetic diversity, inbreeding level and relationship with other local breeds across the world, as well as modern breeds and several wild populations, using high throughput genomic data obtained using the Illumina Infinium PorcineSNP60 v2 BeadChip. Multidimensional scaling analysis positioned Black Slavonian pigs close to the UK/North American breeds, while the Turopolje pig clustered within the Mediterranean breeds. Turopolje pig showed a very high inbreeding level (FROH>4Mb = 0.400 and FROH>8Mb = 0.332) that considerably exceeded the level of full-sib mating, while Black Slavonian pig showed much lower inbreeding (FROH>4Mb = 0.098 and FROH>8Mb = 0.074), indicating a planned mating strategy. In Croatian local breeds we identified several genome regions showing adaptive selection signals that were not present in commercial breeds. The results obtained in this study reflect the current genetic status and breeding management of the two Croatian indigenous local breeds. Given the small populations of both breeds, a controlled management activity has been implemented in Black Slavonian pigs since their commercial value has been recognized. In contrast, the extremely high inbreeding level observed in Turopolje pig argues for an urgent conservation plan with a long-term, diversity-oriented breeding program.
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Affiliation(s)
- Boris Lukić
- Department for Animal Production and Biotechnology, Faculty of Agrobiotechnical Sciences Osijek, J.J. Strossmayer University of Osijek, Osijek, Croatia
| | - Maja Ferenčaković
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Dragica Šalamon
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Mato Čačić
- Ministry of Agriculture, Zagreb, Croatia
| | | | - Laura Iacolina
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.,Department for Apiculture, Wildlife Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Vlatka Cubric-Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
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33
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Genomic regions associated with principal components for growth, visual score and reproductive traits in Nellore cattle. Livest Sci 2020. [DOI: 10.1016/j.livsci.2020.103936] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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34
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Naderi S, Moradi MH, Farhadian M, Yin T, Jaeger M, Scheper C, Korkuc P, Brockmann GA, König S, May K. Assessing selection signatures within and between selected lines of dual-purpose black and white and German Holstein cattle. Anim Genet 2020; 51:391-408. [PMID: 32100321 DOI: 10.1111/age.12925] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2020] [Indexed: 12/29/2022]
Abstract
The aim of this study was to detect selection signatures considering cows from the German Holstein (GH) and the local dual-purpose black and white (DSN) population, as well as from generated sub-populations. The 4654 GH and 261 DSN cows were genotyped with the BovineSNP50 Genotyping BeadChip. The geographical herd location was used as an environmental descriptor to create the East-DSN and West-DSN sub-populations. In addition, two further sub-populations of GH cows were generated, using the extreme values for solutions of residual effects of cows for the claw disorder dermatitis digitalis. These groups represented the most susceptible and most resistant cows. We used cross-population extended haplotype homozygosity methodology (XP-EHH) to identify the most recent selection signatures. Furthermore, we calculated Wright's fixation index (FST ). Chromosomal segments for the top 0.1 percentile of negative or positive XP-EHH scores were studied in detail. For gene annotations, we used the Ensembl database and we considered a window of 250 kbp downstream and upstream of each core SNP corresponding to peaks of XP-EHH. In addition, functional interactions among potential candidate genes were inferred via gene network analyses. The most outstanding XP-EHH score was on chromosome 12 (at 77.34 Mb) for DSN and on chromosome 20 (at 36.29-38.42 Mb) for GH. Selection signature locations harbored QTL for several economically important milk and meat quality traits, reflecting the different breeding goals for GH and DSN. The average FST value between GH and DSN was quite low (0.068), indicating shared founders. For group stratifications according to cow health, several identified potential candidate genes influence disease resistance, especially to dermatitis digitalis.
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Affiliation(s)
- S Naderi
- Institute of Animal Breeding and Genetics, Justus-Liebig University Giessen, Ludwigstr. 21b, Giessen, Germany
| | - M H Moradi
- Department of Animal Sciences, Arak University, Shahid Beheshti Street, Arak, Iran
| | - M Farhadian
- Department of Animal Science, University of Tabriz, 29 Bahman Boulevard, Tabriz, Iran
| | - T Yin
- Institute of Animal Breeding and Genetics, Justus-Liebig University Giessen, Ludwigstr. 21b, Giessen, Germany
| | - M Jaeger
- Institute of Animal Breeding and Genetics, Justus-Liebig University Giessen, Ludwigstr. 21b, Giessen, Germany
| | - C Scheper
- Institute of Animal Breeding and Genetics, Justus-Liebig University Giessen, Ludwigstr. 21b, Giessen, Germany
| | - P Korkuc
- Albrecht Daniel Thaer Institute for Agricultural and Horticultural Sciences, Humboldt University Berlin, Invalidenstr. 42, Berlin, D-10115, Germany
| | - G A Brockmann
- Albrecht Daniel Thaer Institute for Agricultural and Horticultural Sciences, Humboldt University Berlin, Invalidenstr. 42, Berlin, D-10115, Germany
| | - S König
- Institute of Animal Breeding and Genetics, Justus-Liebig University Giessen, Ludwigstr. 21b, Giessen, Germany
| | - K May
- Institute of Animal Breeding and Genetics, Justus-Liebig University Giessen, Ludwigstr. 21b, Giessen, Germany
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35
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Sosa‐Madrid BS, Hernández P, Blasco A, Haley CS, Fontanesi L, Santacreu MA, Pena RN, Navarro P, Ibáñez‐Escriche N. Genomic regions influencing intramuscular fat in divergently selected rabbit lines. Anim Genet 2020; 51:58-69. [PMID: 31696970 PMCID: PMC7004202 DOI: 10.1111/age.12873] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2019] [Indexed: 12/12/2022]
Abstract
Intramuscular fat (IMF) is one of the main meat quality traits for breeding programmes in livestock species. The main objective of this study was to identify genomic regions associated with IMF content comparing two rabbit populations divergently selected for this trait, and to generate a list of putative candidate genes. Animals were genotyped using the Affymetrix Axiom OrcunSNP Array (200k). After quality control, the data involved 477 animals and 93 540 SNPs. Two methods were used in this research: single marker regressions with the data adjusted by genomic relatedness, and a Bayesian multiple marker regression. Associated genomic regions were located on the rabbit chromosomes (OCU) OCU1, OCU8 and OCU13. The highest value for the percentage of the genomic variance explained by a genomic region was found in two consecutive genomic windows on OCU8 (7.34%). Genes in the associated regions of OCU1 and OCU8 presented biological functions related to the control of adipose cell function, lipid binding, transportation and localisation (APOLD1, PLBD1, PDE6H, GPRC5D and GPRC5A) and lipid metabolic processes (MTMR2). The EWSR1 gene, underlying the OCU13 region, is linked to the development of brown adipocytes. The findings suggest that there is a large component of polygenic effect behind the differences in IMF content in these two lines, as the variance explained by most of the windows was low. The genomic regions of OCU1, OCU8 and OCU13 revealed novel candidate genes. Further studies would be needed to validate the associations and explore their possible application in selection programmes.
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Affiliation(s)
- Bolívar S. Sosa‐Madrid
- Institute for Animal Science and TechnologyUniversitat Politècnica de València46022 ValenciaSpain
| | - Pilar Hernández
- Institute for Animal Science and TechnologyUniversitat Politècnica de València46022 ValenciaSpain
| | - Agustín Blasco
- Institute for Animal Science and TechnologyUniversitat Politècnica de València46022 ValenciaSpain
| | - Chris S. Haley
- MRC Human Genetics UnitMRC Institute of Genetics and Molecular MedicineUniversity of EdinburghCrewe Road, Edinburgh EH4 2XUUnited Kingdom
- Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothian EH25 9RGUnited Kingdom
| | - Luca Fontanesi
- Division of Animal SciencesDepartment of Agricultural and Food SciencesUniversity of Bologna40127 BolognaItaly
| | - María A. Santacreu
- Institute for Animal Science and TechnologyUniversitat Politècnica de València46022 ValenciaSpain
| | - Romi N. Pena
- Departament de Ciència AnimalUniversitat de Lleida–Agrotecnio CentreE-25198 LleidaCatalonia, Spain
| | - Pau Navarro
- MRC Human Genetics UnitMRC Institute of Genetics and Molecular MedicineUniversity of EdinburghCrewe Road, Edinburgh EH4 2XUUnited Kingdom
| | - Noelia Ibáñez‐Escriche
- Institute for Animal Science and TechnologyUniversitat Politècnica de València46022 ValenciaSpain
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Ventura RV, Brito LF, Oliveira GA, Daetwyler HD, Schenkel FS, Sargolzaei M, Vandervoort G, Fonseca e Silva F, Miller SP, Carvalho ME, Santana MHA, Mattos EC, Fonseca P, Eler JP, Ferraz JBS. A comprehensive comparison of high-density SNP panels and an alternative ultra-high-density panel for genomic analyses in Nellore cattle. ANIMAL PRODUCTION SCIENCE 2020. [DOI: 10.1071/an18305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
There is evidence that some genotyping platforms might not work very well for Zebu cattle when compared with Taurine breeds. In addition, the availability of panels with low to moderate number of overlapping markers is a limitation for combining datasets for genomic evaluations, especially when animals are genotyped using different SNP panels. In the present study, we compared the performance of medium- and high-density (HD) commercially available panels and investigated the feasibility of developing an ultra-HD panel (SP) containing markers from an Illumina (HD_I) and an Affymetrix (HD_A) panels. The SP panel contained 1123442 SNPs. After performing SNP pruning on the basis of linkage disequilibrium, HD_A, HD_I and SP contained 429624, 365225 and 658770 markers distributed across the whole genome. The overall mean proportion of markers pruned out per chromosome for HD_A, HD_I and SP was 15.17%, 43.18%, 38.63% respectively. The HD_I panel presented the highest mean number of runs-of-homozygosity segments per animal (45.48%, an increment of 5.11% compared with SP) and longer segments, on average (3057.95 kb per segment), than did both HD_A and SP. HD_I also showed the highest mean number of SNPs per run-of-homozygosity segment. Consequently, the majority of animals presented the highest genomic inbreeding levels when genotyped using HD_I. The visual examination of marker distribution along the genome illustrated uncovered regions among the different panels. Haplotype-block comparison among panels and the average haplotype size constructed on the basis of HD_A were smaller than those from HD_I. The average number of SNPs per haplotype was different between HD_A and HD_I. Both HD_A and HD_I panels achieved high imputation accuracies when used as the lower-density panels for imputing to SP. However, imputation accuracy from HD_A to SP was greater than was imputation from HD_I to SP. Imputation from one HD panel to the other is also feasible. Low- and medium-density panels, composed of markers that are subsets of both HD_A and HD_I panels, should be developed to achieve better imputation accuracies to both HD levels. Therefore, the genomic analyses performed in the present study showed significant differences among the SNP panels used.
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Feitosa FLB, Pereira ASC, Amorim ST, Peripolli E, Silva RMDO, Braz CU, Ferrinho AM, Schenkel FS, Brito LF, Espigolan R, de Albuquerque LG, Baldi F. Comparison between haplotype-based and individual snp-based genomic predictions for beef fatty acid profile in Nelore cattle. J Anim Breed Genet 2019; 137:468-476. [PMID: 31867831 DOI: 10.1111/jbg.12463] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 11/18/2019] [Accepted: 11/24/2019] [Indexed: 11/28/2022]
Abstract
The aim of this study was to evaluate the genomic predictions using the single-step genomic best linear unbiased predictor (ssGBLUP) method based on SNPs and haplotype markers associated with beef fatty acids (FAs) profile in Nelore cattle. The data set contained records from 963 Nelore bulls finished in feedlot (±90 days) and slaughtered with approximately 24 months of age. Meat samples from the Longissimus dorsi muscle were taken for FAs profile measurement. FAs were quantified by gas chromatography using a SP-2560 capillary column. Animals were genotyped with the high-density SNP panel (BovineHD BeadChip assay) containing 777,962 markers. SNPs with a minor allele frequency and a call rate lower than 0.05 and 0.90, respectively, monomorphic, located on sex chromosomes, and with unknown position were removed from the data set. After genomic quality control, a total of 469,981 SNPs and 892 samples were available for subsequent analyses. Missing genotypes were imputed and phased using the FImpute software. Haplotype blocks were defined based on linkage disequilibrium using the Haploview software. The model to estimate variance components and genetic parameters and to predict the genomic values included the random genetic additive effects, fixed effects of the contemporary group and the age at slaughter as a linear covariate. Accuracies using the haplotype-based approach ranged from 0.07 to 0.31, and those SNP-based ranged from 0.06 to 0.33. Regression coefficients ranged from 0.07 to 0.74 and from 0.08 to 1.45 using the haplotype- and SNP-based approaches, respectively. Despite the low to moderate accuracies for the genomic values, it is possible to obtain genetic progress trough selection using genomic information based either on SNPs or haplotype markers. The SNP-based approach allows less biased genomic evaluations, and it is more feasible when taking into account the computational and operational cost underlying the haplotypes inference.
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Affiliation(s)
- Fabieli Loise Braga Feitosa
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Universidade Estadual Paulista Júlio de Mesquita Filho, UNESP, Jaboticabal, Brazil
| | - Angélica Simone Cravo Pereira
- Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Nutrição e Produção Animal, Universidade de São Paulo, Pirassununga, Brazil
| | - Sabrina Thaise Amorim
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Universidade Estadual Paulista Júlio de Mesquita Filho, UNESP, Jaboticabal, Brazil
| | - Elisa Peripolli
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Universidade Estadual Paulista Júlio de Mesquita Filho, UNESP, Jaboticabal, Brazil
| | | | - Camila Urbano Braz
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Universidade Estadual Paulista Júlio de Mesquita Filho, UNESP, Jaboticabal, Brazil
| | - Adrielle Matias Ferrinho
- Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Nutrição e Produção Animal, Universidade de São Paulo, Pirassununga, Brazil
| | | | | | - Rafael Espigolan
- Faculdade de Zootecnia e Engenharia de Alimentos, Departamento de Medicina Veterinária, Universidade de São Paulo, Pirassununga, Brazil
| | - Lucia Galvão de Albuquerque
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Universidade Estadual Paulista Júlio de Mesquita Filho, UNESP, Jaboticabal, Brazil
| | - Fernando Baldi
- Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Universidade Estadual Paulista Júlio de Mesquita Filho, UNESP, Jaboticabal, Brazil
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Zhou J, Liu L, Chen CJ, Zhang M, Lu X, Zhang Z, Huang X, Shi Y. Genome-wide association study of milk and reproductive traits in dual-purpose Xinjiang Brown cattle. BMC Genomics 2019; 20:827. [PMID: 31703627 PMCID: PMC6842163 DOI: 10.1186/s12864-019-6224-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/24/2019] [Indexed: 01/01/2023] Open
Abstract
Background Dual-purpose cattle are more adaptive to environmental challenges than single-purpose dairy or beef cattle. Balance among milk, reproductive, and mastitis resistance traits in breeding programs is therefore more critical for dual-purpose cattle to increase net income and maintain well-being. With dual-purpose Xinjiang Brown cattle adapted to the Xinjiang Region in northwestern China, we conducted genome-wide association studies (GWAS) to dissect the genetic architecture related to milk, reproductive, and mastitis resistance traits. Phenotypic data were collected for 2410 individuals measured during 1995–2017. By adding another 445 ancestors, a total of 2855 related individuals were used to derive estimated breeding values for all individuals, including the 2410 individuals with phenotypes. Among phenotyped individuals, we genotyped 403 cows with the Illumina 150 K Bovine BeadChip. Results GWAS were conducted with the FarmCPU (Fixed and random model circulating probability unification) method. We identified 12 markers significantly associated with six of the 10 traits under the threshold of 5% after a Bonferroni multiple test correction. Seven of these SNPs were in QTL regions previously identified to be associated with related traits. One identified SNP, BovineHD1600006691, was significantly associated with both age at first service and age at first calving. This SNP directly overlapped a QTL previously reported to be associated with calving ease. Within 160 Kb upstream and downstream of each significant SNP identified, we speculated candidate genes based on functionality. Four of the SNPs were located within four candidate genes, including CDH2, which is linked to milk fat percentage, and GABRG2, which is associated with milk protein yield. Conclusions These findings are beneficial not only for breeding through marker-assisted selection, but also for genome editing underlying the related traits to enhance the overall performance of dual-purpose cattle.
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Affiliation(s)
- Jinghang Zhou
- School of Agriculture, Ningxia University, Yinchuan, China.,Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, USA
| | - Liyuan Liu
- School of Agriculture, Ningxia University, Yinchuan, China.,Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, USA
| | - Chunpeng James Chen
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, USA
| | - Menghua Zhang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Xin Lu
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, USA.
| | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China.
| | - Yuangang Shi
- School of Agriculture, Ningxia University, Yinchuan, China.
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Moreira GCM, Poleti MD, Pértille F, Boschiero C, Cesar ASM, Godoy TF, Ledur MC, Reecy JM, Garrick DJ, Coutinho LL. Unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach. BMC Genet 2019; 20:83. [PMID: 31694549 PMCID: PMC6836328 DOI: 10.1186/s12863-019-0783-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/11/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Feed efficiency and growth rate have been targets for selection to improve chicken production. The incorporation of genomic tools may help to accelerate selection. We genotyped 529 individuals using a high-density SNP chip (600 K, Affymetrix®) to estimate genomic heritability of performance traits and to identify genomic regions and their positional candidate genes associated with performance traits in a Brazilian F2 Chicken Resource population. Regions exhibiting selection signatures and a SNP dataset from resequencing were integrated with the genomic regions identified using the chip to refine the list of positional candidate genes and identify potential causative mutations. RESULTS Feed intake (FI), feed conversion ratio (FC), feed efficiency (FE) and weight gain (WG) exhibited low genomic heritability values (i.e. from 0.0002 to 0.13), while body weight at hatch (BW1), 35 days-of-age (BW35), and 41 days-of-age (BW41) exhibited high genomic heritability values (i.e. from 0.60 to 0.73) in this F2 population. Twenty unique 1-Mb genomic windows were associated with BW1, BW35 or BW41, located on GGA1-4, 6-7, 10, 14, 24, 27 and 28. Thirty-eight positional candidate genes were identified within these windows, and three of them overlapped with selection signature regions. Thirteen predicted deleterious and three high impact sequence SNPs in these QTL regions were annotated in 11 positional candidate genes related to osteogenesis, skeletal muscle development, growth, energy metabolism and lipid metabolism, which may be associated with body weight in chickens. CONCLUSIONS The use of a high-density SNP array to identify QTL which were integrated with whole genome sequence signatures of selection allowed the identification of candidate genes and candidate causal variants. One novel QTL was detected providing additional information to understand the genetic architecture of body weight traits. We identified QTL for body weight traits, which were also associated with fatness in the same population. Our findings form a basis for further functional studies to elucidate the role of specific genes in regulating body weight and fat deposition in chickens, generating useful information for poultry breeding programs.
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Affiliation(s)
| | - Mirele Daiana Poleti
- University of São Paulo (USP) / College of Animal Science and Food Engineering (FZEA), Pirassununga, São Paulo, Brazil
| | - Fábio Pértille
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900 Brazil
| | - Clarissa Boschiero
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900 Brazil
| | | | - Thaís Fernanda Godoy
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900 Brazil
| | | | - James M. Reecy
- Department of Animal Science, Iowa State University (ISU), Ames, Iowa, USA
| | - Dorian J. Garrick
- School of Agriculture, Massey University, Ruakura, Hamilton, New Zealand
| | - Luiz Lehmann Coutinho
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900 Brazil
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Sosa-Madrid BS, Santacreu MA, Blasco A, Fontanesi L, Pena RN, Ibáñez-Escriche N. A genomewide association study in divergently selected lines in rabbits reveals novel genomic regions associated with litter size traits. J Anim Breed Genet 2019; 137:123-138. [PMID: 31657065 DOI: 10.1111/jbg.12451] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 10/02/2019] [Accepted: 10/03/2019] [Indexed: 12/28/2022]
Abstract
Uterine capacity (UC), defined as the total number of kits from unilaterally ovariectomized does at birth, has a high genetic correlation with litter size. The aim of our research was to identify genomic regions associated with litter size traits through a genomewide association study using rabbits from a divergent selection experiment for UC. A high-density SNP array (200K) was used to genotype 181 does from a control population, high and low UC lines. Traits included total number born (TNB), number born alive (NBA), number born dead, ovulation rate (OR), implanted embryos (IE) and embryo, foetal and prenatal survivals at second parity. We implemented the Bayes B method and the associations were tested by Bayes factors and the percentage of genomic variance (GV) explained by windows. Different genomic regions associated with TNB, NBA, IE and OR were found. These regions explained 7.36%, 1.27%, 15.87% and 3.95% of GV, respectively. Two consecutive windows on chromosome 17 were associated with TNB, NBA and IE. This genomic region accounted for 6.32% of GV of TNB. In this region, we found the BMP4, PTDGR, PTGER2, STYX and CDKN3 candidate genes which presented functional annotations linked to some reproductive processes. Our findings suggest that a genomic region on chromosome 17 has an important effect on litter size traits. However, further analyses are needed to validate this region in other maternal rabbit lines.
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Affiliation(s)
| | - María Antonia Santacreu
- Institute for Animal Science and Technology, Universitat Politècnica de València, Valencia, Spain
| | - Agustín Blasco
- Institute for Animal Science and Technology, Universitat Politècnica de València, Valencia, Spain
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Bologna, Italy
| | - Romi Natacha Pena
- Departament de Ciència Animal, Universitat de Lleida-Agrotecnio Center, Lleida, Spain
| | - Noelia Ibáñez-Escriche
- Institute for Animal Science and Technology, Universitat Politècnica de València, Valencia, Spain
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41
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Afonso J, Coutinho LL, Tizioto PC, da Silva Diniz WJ, de Lima AO, Rocha MIP, Buss CE, Andrade BGN, Piaya O, da Silva JV, Lins LA, Gromboni CF, Nogueira ARA, Fortes MRS, Mourao GB, de Almeida Regitano LC. Muscle transcriptome analysis reveals genes and metabolic pathways related to mineral concentration in Bos indicus. Sci Rep 2019; 9:12715. [PMID: 31481722 PMCID: PMC6722098 DOI: 10.1038/s41598-019-49089-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 08/02/2019] [Indexed: 01/18/2023] Open
Abstract
Mineral content affects the biological processes underlying beef quality. Muscle mineral concentration depends not only on intake-outtake balance and muscle type, but also on age, environment, breed, and genetic factors. To unveil the genetic factors involved in muscle mineral concentration, we applied a pairwise differential gene expression analysis in groups of Nelore steers genetically divergent for nine different mineral concentrations. Here, based on significant expression differences between contrasting groups, we presented candidate genes for the genetic regulation of mineral concentration in muscle. Functional enrichment and protein-protein interaction network analyses were carried out to search for gene regulatory processes concerning each mineral. The core genetic regulation for all minerals studied, except Zn, seems to rest on interactions between components of the extracellular matrix. Regulation of adipogenesis-related pathways was also significant in our results. Antagonistic patterns of gene expression for fatty acid metabolism-related genes may explain the Cu and Zn antagonistic effect on fatty acid accumulation. Our results shed light on the role of these minerals on cell function.
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Affiliation(s)
- Juliana Afonso
- Department of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil
| | | | | | | | - Andressa Oliveira de Lima
- Department of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil
| | - Marina Ibelli Pereira Rocha
- Department of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil
| | - Carlos Eduardo Buss
- Department of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil
| | | | - Otávio Piaya
- Department of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil
| | | | - Laura Albuquerque Lins
- Animal Science department, Laboratory of Molecular Genetics. São Paulo State University, Jaboticabal, Brazil
| | | | | | - Marina Rufino Salinas Fortes
- School of Chemistry and Molecular Biosciences, Faculty of Sciences, The University of Queensland, Brisbane, Australia
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Moreira GCM, Salvian M, Boschiero C, Cesar ASM, Reecy JM, Godoy TF, Ledur MC, Garrick D, Mourão GB, Coutinho LL. Genome-wide association scan for QTL and their positional candidate genes associated with internal organ traits in chickens. BMC Genomics 2019; 20:669. [PMID: 31438838 PMCID: PMC6704653 DOI: 10.1186/s12864-019-6040-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 08/16/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Poultry breeding programs have been focused on improvement of growth and carcass traits, however, this has resulted in correlated changes in internal organ weights and increased incidence of metabolic disorders. These disorders can affect feed efficiency or even cause death. We used a high density SNP array (600 K, Affymetrix) to estimate genomic heritability, perform genome-wide association analysis, and identify genomic regions and positional candidate genes (PCGs) associated with internal organ traits in an F2 chicken population. We integrated knowledge of haplotype blocks, selection signature regions and sequencing data to refine the list of PCGs. RESULTS Estimated genomic heritability for internal organ traits in chickens ranged from low (LUNGWT, 0.06) to high (GIZZWT, 0.45). A total of 20 unique 1 Mb windows identified on GGA1, 2, 4, 7, 12, 15, 18, 19, 21, 27 and 28 were significantly associated with intestine length, and weights or percentages of liver, gizzard or lungs. Within these windows, 14 PCGs were identified based on their biological functions: TNFSF11, GTF2F2, SPERT, KCTD4, HTR2A, RB1, PCDH7, LCORL, LDB2, NR4A2, GPD2, PTPN11, ITGB4 and SLC6A4. From those genes, two were located within haplotype blocks and three overlapped with selection signature regions. A total of 13,748 annotated sequence SNPs were in the 14 PCGs, including 156 SNPs in coding regions (124 synonymous, 26 non-synonymous, and 6 splice variants). Seven deleterious SNPs were identified in TNFSF11, NR4A2 or ITGB4 genes. CONCLUSIONS The results from this study provide novel insights to understand the genetic architecture of internal organ traits in chickens. The QTL detection performed using a high density SNP array covered the whole genome allowing the discovery of novel QTL associated with organ traits. We identified PCGs within the QTL involved in biological processes that may regulate internal organ growth and development. Potential functional genetic variations were identified generating crucial information that, after validation, might be used in poultry breeding programs to reduce the occurrence of metabolic disorders.
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Affiliation(s)
| | - Mayara Salvian
- University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - Clarissa Boschiero
- University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - Aline Silva Mello Cesar
- University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - James M. Reecy
- Department of Animal Science, Iowa State University (ISU), Ames, Iowa USA
| | - Thaís Fernanda Godoy
- University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | | | - Dorian Garrick
- School of Agriculture, Massey University, Ruakura, Hamilton, New Zealand
| | - Gerson Barreto Mourão
- University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - Luiz L. Coutinho
- University of São Paulo (USP), Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
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de Oliveira PSN, Coutinho LL, Cesar ASM, Diniz WJDS, de Souza MM, Andrade BG, Koltes JE, Mourão GB, Zerlotini A, Reecy JM, Regitano LCA. Co-Expression Networks Reveal Potential Regulatory Roles of miRNAs in Fatty Acid Composition of Nelore Cattle. Front Genet 2019; 10:651. [PMID: 31354792 PMCID: PMC6637853 DOI: 10.3389/fgene.2019.00651] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 06/19/2019] [Indexed: 12/15/2022] Open
Abstract
Fatty acid (FA) content affects the sensorial and nutritional value of meat and plays a significant role in biological processes such as adipogenesis and immune response. It is well known that, in beef, the main FAs associated with these biological processes are oleic acid (C18:1 cis9, OA) and conjugated linoleic acid (CLA-c9t11), which may have beneficial effects on metabolic diseases such as type 2 diabetes and obesity. Here, we performed differential expression and co-expression analyses, weighted gene co-expression network analysis (WGCNA) and partial correlation with information theory (PCIT), to uncover the complex interactions between miRNAs and mRNAs expressed in skeletal muscle associated with FA content. miRNA and mRNA expression data were obtained from skeletal muscle of Nelore cattle that had extreme genomic breeding values for OA and CLA. Insulin and MAPK signaling pathways were identified by WGCNA as central pathways associated with both of these fatty acids. Co-expression network analysis identified bta-miR-33a/b, bta-miR-100, bta-miR-204, bta-miR-365-5p, bta-miR-660, bta-miR-411a, bta-miR-136, bta-miR-30-5p, bta-miR-146b, bta-let-7a-5p, bta-let-7f, bta-let-7, bta-miR 339, bta-miR-10b, bta-miR 486, and the genes ACTA1 and ALDOA as potential regulators of fatty acid synthesis. This study provides evidence and insights into the molecular mechanisms and potential target genes involved in fatty acid content differences in Nelore beef cattle, revealing new candidate pathways of phenotype modulation that could positively benefit beef production and human consumption.
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Affiliation(s)
| | - Luiz L Coutinho
- Department of Animal Science, University of São Paulo, Piracicaba, Brazil
| | - Aline S M Cesar
- Department of Agroindustry, Food and Nutrition, University of São Paulo, Piracicaba, Brazil
| | | | - Marcela M de Souza
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Bruno G Andrade
- Embrapa Pecuária Sudeste, Empresa Brasileira de Pesquisa Agropecuária, São Carlos, Brazil
| | - James E Koltes
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Gerson B Mourão
- Department of Agroindustry, Food and Nutrition, University of São Paulo, Piracicaba, Brazil
| | | | - James M Reecy
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Luciana C A Regitano
- Embrapa Pecuária Sudeste, Empresa Brasileira de Pesquisa Agropecuária, São Carlos, Brazil
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An B, Xia J, Chang T, Wang X, Xu L, Zhang L, Gao X, Chen Y, Li J, Gao H. Genome-wide association study reveals candidate genes associated with body measurement traits in Chinese Wagyu beef cattle. Anim Genet 2019; 50:386-390. [PMID: 31179577 DOI: 10.1111/age.12805] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2019] [Indexed: 01/08/2023]
Abstract
We performed a genome-wide association study to identify candidate genes for body measurement traits in 463 Wagyu beef cattle typed with the Illumina Bovine HD 770K SNP array. At the genome-wide level, we detected 18, five and one SNPs associated with hip height, body height and body length respectively. In total, these SNPs are within or near 11 genes, six of which (PENK, XKR4, IMPAD1, PLAG1, CCND2 and SNTG1) have been reported previously and five of which (CSMD3, LAP3, SYN3, FAM19A5 and TIMP3) are novel candidate genes that we found to be associated with body measurement traits. Further exploration of these candidate genes will facilitate genetic improvement in Chinese Wagyu beef cattle.
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Affiliation(s)
- B An
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China
| | - J Xia
- Institute of Basic Medical Science, Westlake Institute for Advanced Study, Hangzhou, 310000, China
| | - T Chang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China
| | - X Wang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China
| | - L Xu
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China
| | - L Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China
| | - X Gao
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China
| | - Y Chen
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China
| | - J Li
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China
| | - H Gao
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China
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Diniz WJS, Mazzoni G, Coutinho LL, Banerjee P, Geistlinger L, Cesar ASM, Bertolini F, Afonso J, de Oliveira PSN, Tizioto PC, Kadarmideen HN, Regitano LCA. Detection of Co-expressed Pathway Modules Associated With Mineral Concentration and Meat Quality in Nelore Cattle. Front Genet 2019; 10:210. [PMID: 30930938 PMCID: PMC6424907 DOI: 10.3389/fgene.2019.00210] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 02/26/2019] [Indexed: 12/14/2022] Open
Abstract
Meat quality is a complex trait that is influenced by genetic and environmental factors, which includes mineral concentration. However, the association between mineral concentration and meat quality, and the specific molecular pathways underlying this association, are not well explored. We therefore analyzed gene expression as measured with RNA-seq in Longissimus thoracis muscle of 194 Nelore steers for association with three meat quality traits (intramuscular fat, meat pH, and tenderness) and the concentration of 13 minerals (Ca, Cr, Co, Cu, Fe, K, Mg, Mn, Na, P, S, Se, and Zn). We identified seven sets of co-expressed genes (modules) associated with at least two traits, which indicates that common pathways influence these traits. From pathway analysis of module hub genes, we further found an over-representation for energy and protein metabolism (AMPK and mTOR signaling pathways) in addition to muscle growth, and protein turnover pathways. Among the identified hub genes FASN, ELOV5, and PDE3B are involved with lipid metabolism and were affected by previously identified eQTLs associated to fat deposition. The reported hub genes and over-represented pathways provide evidence of interplay among gene expression, mineral concentration, and meat quality traits. Future studies investigating the effect of different levels of mineral supplementation in the gene expression and meat quality traits could help us to elucidate the regulatory mechanism by which the genes/pathways are affected.
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Affiliation(s)
- Wellison J S Diniz
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil.,Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark.,Embrapa Pecuária Sudeste, Empresa Brasileira de Pesquisa Agropecuária, São Paulo, Brazil
| | - Gianluca Mazzoni
- Department of Health Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Luiz L Coutinho
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Priyanka Banerjee
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ludwig Geistlinger
- Embrapa Pecuária Sudeste, Empresa Brasileira de Pesquisa Agropecuária, São Paulo, Brazil.,Graduate School of Public Health and Health Policy, The City University of New York, New York, NY, United States
| | - Aline S M Cesar
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Francesca Bertolini
- Department of Aquaculture, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Juliana Afonso
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | | | - Polyana C Tizioto
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Haja N Kadarmideen
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Luciana C A Regitano
- Embrapa Pecuária Sudeste, Empresa Brasileira de Pesquisa Agropecuária, São Paulo, Brazil
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Wang Z, Zhu B, Niu H, Zhang W, Xu L, Xu L, Chen Y, Zhang L, Gao X, Gao H, Zhang S, Xu L, Li J. Genome wide association study identifies SNPs associated with fatty acid composition in Chinese Wagyu cattle. J Anim Sci Biotechnol 2019; 10:27. [PMID: 30867906 PMCID: PMC6399853 DOI: 10.1186/s40104-019-0322-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/14/2019] [Indexed: 12/29/2022] Open
Abstract
Background Fatty acids are important traits that affect meat quality and nutritive values in beef cattle. Detection of genetic variants for fatty acid composition can help to elucidate the genetic mechanism underpinning these traits and promote the improvement of fatty acid profiles. In this study, we performed a genome-wide association study (GWAS) on fatty acid composition using high-density single nucleotide polymorphism (SNP) arrays in Chinese Wagyu cattle. Results In total, we detected 15 and 8 significant genome-wide SNPs for individual fatty acids and fatty acid groups in Chinese Wagyu cattle, respectively. Also, we identified nine candidate genes based on 100 kb regions around associated SNPs. Four SNPs significantly associated with C14:1 cis-9 were embedded with stearoyl-CoA desaturase (SCD), while three SNPs in total were identified for C22:6 n-3 within Phospholipid scramblase family member 5 (PLSCR5), Cytoplasmic linker associated protein 1 (CLASP1), and Chymosin (CYM). Notably, we found the top candidate SNP within SCD can explain ~ 7.37% of phenotypic variance for C14:1 cis-9. Moreover, we detected several blocks with high LD in the 100 kb region around SCD. In addition, we found three significant SNPs within a 100 kb region showing pleiotropic effects related to multiple FA groups (PUFA, n-6, and PUFA/SFA), which contains BAI1 associated protein 2 like 2 (BAIAP2L2), MAF bZIP transcription factor F (MAFF), and transmembrane protein 184B (TMEM184B). Conclusions Our study identified several significant SNPs and candidate genes for individual fatty acids and fatty acid groups in Chinese Wagyu cattle, and these findings will further assist the design of breeding programs for meat quality in cattle.
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Affiliation(s)
- Zezhao Wang
- 1Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China.,2National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Bo Zhu
- 1Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Hong Niu
- 1Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Wengang Zhang
- 1Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Ling Xu
- 1Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Lei Xu
- 1Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China.,3Institute of Animal Husbandry and Veterinary Research, Anhui Academy of Agricultural Sciences, Hefei, 230031 China
| | - Yan Chen
- 1Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Lupei Zhang
- 1Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Xue Gao
- 1Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Huijiang Gao
- 1Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Shengli Zhang
- 2National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Lingyang Xu
- 1Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Junya Li
- 1Innovation Team of Cattle Genetic Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
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Leal-Gutiérrez JD, Elzo MA, Johnson DD, Hamblen H, Mateescu RG. Genome wide association and gene enrichment analysis reveal membrane anchoring and structural proteins associated with meat quality in beef. BMC Genomics 2019; 20:151. [PMID: 30791866 PMCID: PMC6385435 DOI: 10.1186/s12864-019-5518-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 02/07/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Meat quality related phenotypes are difficult and expensive to measure and predict but are ideal candidates for genomic selection if genetic markers that account for a worthwhile proportion of the phenotypic variation can be identified. The objectives of this study were: 1) to perform genome wide association analyses for Warner-Bratzler Shear Force (WBSF), marbling, cooking loss, tenderness, juiciness, connective tissue and flavor; 2) to determine enriched pathways present in each genome wide association analysis; and 3) to identify potential candidate genes with multiple quantitative trait loci (QTL) associated with meat quality. RESULTS The WBSF, marbling and cooking loss traits were measured in longissimus dorsi muscle from 672 steers. Out of these, 495 animals were used to measure tenderness, juiciness, connective tissue and flavor by a sensory panel. All animals were genotyped for 221,077 markers and included in a genome wide association analysis. A total number of 68 genomic regions covering 52 genes were identified using the whole genome association approach; 48% of these genes encode transmembrane proteins or membrane associated molecules. Two enrichment analysis were performed: a tissue restricted gene enrichment applying a correlation analysis between raw associated single nucleotide polymorphisms (SNPs) by trait, and a functional classification analysis performed using the DAVID Bioinformatic Resources 6.8 server. The tissue restricted gene enrichment approach identified eleven pathways including "Endoplasmic reticulum membrane" that influenced multiple traits simultaneously. The DAVID functional classification analysis uncovered eleven clusters related to transmembrane or structural proteins. A gene network was constructed where the number of raw associated uncorrelated SNPs for each gene across all traits was used as a weight. A multiple SNP association analysis was performed for the top five most connected genes in the gene-trait network. The gene network identified the EVC2, ANXA10 and PKHD1 genes as potentially harboring multiple QTLs. Polymorphisms identified in structural proteins can modulate two different processes with direct effect on meat quality: in vivo myocyte cytoskeletal organization and postmortem proteolysis. CONCLUSION The main result from the present analysis is the uncovering of several candidate genes associated with meat quality that have structural function in the skeletal muscle.
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Affiliation(s)
| | - Mauricio A. Elzo
- Department of Animal Sciences, University of Florida, Gainesville, FL USA
| | - D. Dwain Johnson
- Department of Animal Sciences, University of Florida, Gainesville, FL USA
| | - Heather Hamblen
- Department of Animal Sciences, University of Florida, Gainesville, FL USA
| | - Raluca G. Mateescu
- Department of Animal Sciences, University of Florida, Gainesville, FL USA
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Silva-Vignato B, Coutinho LL, Poleti MD, Cesar ASM, Moncau CT, Regitano LCA, Balieiro JCC. Gene co-expression networks associated with carcass traits reveal new pathways for muscle and fat deposition in Nelore cattle. BMC Genomics 2019; 20:32. [PMID: 30630417 PMCID: PMC6329100 DOI: 10.1186/s12864-018-5345-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 11/30/2018] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Positively correlated with carcass weight and animal growth, the ribeye area (REA) and the backfat thickness (BFT) are economic important carcass traits, which impact directly on producer's payment. The selection of these traits has not been satisfactory since they are expressed later in the animal's life and multigene regulated. So, next-generation technologies have been applied in this area to improve animal's selection and better understand the molecular mechanisms involved in the development of these traits. Correlation network analysis, performed by tools like WGCNA (Weighted Correlation Network Analysis), has been used to explore gene-gene interactions and gene-phenotype correlations. Thus, this study aimed to identify putative candidate genes and metabolic pathways that regulate REA and BFT by constructing a gene co-expression network using WGCNA and RNA sequencing data, to better understand genetic and molecular variations behind these complex traits in Nelore cattle. RESULTS The gene co-expression network analysis, using WGCNA, were built using RNA-sequencing data normalized by transcript per million (TPM) from 43 Nelore steers. Forty-six gene clusters were constructed, between them, three were positively correlated (p-value< 0.1) to the BFT (Green Yellow, Ivory, and Light Yellow modules) and, one cluster was negatively correlated (p-value< 0.1) with REA (Salmon module). The enrichment analysis performed by DAVID and WebGestalt (FDR 5%) identified eight Gene Ontology (GO) terms and three KEGG pathways in the Green Yellow module, mostly associated with immune response and inflammatory mechanisms. The enrichment of the Salmon module demonstrated 19 GO terms and 21 KEGG pathways, related to muscle energy metabolism, lipid metabolism, muscle degradation, and oxidative stress diseases. The Ivory and Light yellow modules have not shown significant results in the enrichment analysis. CONCLUSION With this study, we verified that inflammation and immune response pathways modulate the BFT trait. Energy and lipid metabolism pathways, highlighting fatty acid metabolism, were the central pathways associated with REA. Some genes, as RSAD2, EIF2AK2, ACAT1, and ACSL1 were considered as putative candidate related to these traits. Altogether these results allow us to a better comprehension of the molecular mechanisms that lead to muscle and fat deposition in bovine.
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Affiliation(s)
- Bárbara Silva-Vignato
- College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, 13418-900, Brazil.
| | - Luiz L Coutinho
- College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Mirele D Poleti
- College of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, 13635-900, Brazil
| | - Aline S M Cesar
- College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | | | - Júlio C C Balieiro
- College of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, SP, 13635-900, Brazil
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De Oliveira PSN, Coutinho LL, Tizioto PC, Cesar ASM, de Oliveira GB, Diniz WJDS, De Lima AO, Reecy JM, Mourão GB, Zerlotini A, Regitano LCA. An integrative transcriptome analysis indicates regulatory mRNA-miRNA networks for residual feed intake in Nelore cattle. Sci Rep 2018; 8:17072. [PMID: 30459456 PMCID: PMC6244318 DOI: 10.1038/s41598-018-35315-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/30/2018] [Indexed: 12/21/2022] Open
Abstract
Residual Feed Intake (RFI) is an economically relevant trait in beef cattle. Among the molecular regulatory mechanisms, microRNAs (miRNAs) are an important dimension in post-transcriptional regulation and have been associated with different biological pathways. Here, we performed differential miRNAs expression and weighted gene co-expression network analyses (WGCNA) to better understand the complex interactions between miRNAs and mRNAs expressed in bovine skeletal muscle and liver. MiRNA and mRNA expression data were obtained from Nelore steers that were genetically divergent for RFI (N = 10 [low RFI or feed efficient]; N = 10 [high RFI or feed inefficient]). Differentially expressed and hub miRNAs such as bta-miR-486, bta-miR-7, bta-miR15a, bta-miR-21, bta-miR 29, bta- miR-30b, bta-miR-106b, bta-miR-199a-3p, bta-miR-204, and bta-miR 296 may have a potential role in variation of RFI. Functional enrichment analysis of differentially expressed (DE) miRNA's target genes and miRNA-mRNA correlated modules revealed that insulin, lipid, immune system, oxidative stress and muscle development signaling pathways might potentially be involved in RFI in this population. Our study identified DE miRNAs, miRNA - mRNA regulatory networks and hub miRNAs related to RFI. These findings suggest a possible role of miRNAs in regulation of RFI, providing new insights into the potential molecular mechanisms that control feed efficiency in Nelore cattle.
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Affiliation(s)
| | - Luiz L Coutinho
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - Aline S M Cesar
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - Wellison J da S Diniz
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, 13565-905, Brazil
| | - Andressa O De Lima
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, SP, 13565-905, Brazil
| | - James M Reecy
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Gerson B Mourão
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
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Leal-Gutiérrez JD, Rezende FM, Elzo MA, Johnson D, Peñagaricano F, Mateescu RG. Structural Equation Modeling and Whole-Genome Scans Uncover Chromosome Regions and Enriched Pathways for Carcass and Meat Quality in Beef. Front Genet 2018; 9:532. [PMID: 30555508 PMCID: PMC6282042 DOI: 10.3389/fgene.2018.00532] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/22/2018] [Indexed: 12/11/2022] Open
Abstract
Structural equation models involving latent variables are useful tools for formulating hypothesized models defined by theoretical variables and causal links between these variables. The objectives of this study were: (1) to identify latent variables underlying carcass and meat quality traits and (2) to perform whole-genome scans for these latent variables in order to identify genomic regions and individual genes with both direct and indirect effects. A total of 726 steers from an Angus-Brahman multibreed population with records for 22 phenotypes were used. A total of 480 animals were genotyped with the GGP Bovine F-250. The single-step genomic best linear unbiased prediction method was used to estimate the amount of genetic variance explained for each latent variable by chromosome regions of 20 adjacent SNP-windows across the genome. Three types of genetic effects were considered: (1) direct effects on a single latent phenotype; (2) direct effects on two latent phenotypes simultaneously; and (3) indirect effects. The final structural model included carcass quality as an independent latent variable and meat quality as a dependent latent variable. Carcass quality was defined by quality grade, fat over the ribeye and marbling, while the meat quality was described by juiciness, tenderness and connective tissue, all of them measured through a taste panel. From 571 associated genomic regions (643 genes), each one explaining at least 0.05% of the additive variance, 159 regions (179 genes) were associated with carcass quality, 106 regions (114 genes) were associated with both carcass and meat quality, 242 regions (266 genes) were associated with meat quality, and 64 regions (84 genes) were associated with carcass quality, having an indirect effect on meat quality. Three biological mechanisms emerged from these findings: postmortem proteolysis of structural proteins and cellular compartmentalization, cellular proliferation and differentiation of adipocytes, and fat deposition.
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Affiliation(s)
| | - Fernanda M. Rezende
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States
- Faculdade de Medicina Veterinária, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | - Mauricio A. Elzo
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States
| | - Dwain Johnson
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States
| | - Francisco Peñagaricano
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, United States
| | - Raluca G. Mateescu
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States
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