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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 DOI: 10.1038/s41598-024-60703-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [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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de Andrade Pantoja MH, Poleti MD, de Novais FJ, Duarte KKS, Mateescu RG, Mourão GB, Coutinho LL, Fukumasu H, Titto CG. Skin transcriptomic analysis reveals candidate genes and pathways associated with thermotolerance in hair sheep. Int J Biometeorol 2024; 68:435-444. [PMID: 38147121 DOI: 10.1007/s00484-023-02602-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 11/10/2023] [Accepted: 12/09/2023] [Indexed: 12/27/2023]
Abstract
The skin plays an important role in thermoregulation. Identification of genes on the skin that contribute to increased heat tolerance can be used to select animals with the best performance in warm environments. Our objective was to identify candidate genes associated with the heat stress response in the skin of Santa Ines sheep. A group of 80 sheep assessed for thermotolerance was kept in a climatic chamber for 8 days at a stress level temperature of 36 °C (10 am to 04 pm) and a maintenance temperature of 28 °C (04 pm to 10 am). Two divergent groups, with seven animals each, were formed after ranking them by thermotolerance using rectal temperature. From skin biopsy samples, total RNA was extracted, quantified, and used for RNA-seq analysis. 15,989 genes were expressed in sheep skin samples, of which 4 genes were differentially expressed (DE; FDR < 0.05) and 11 DE (FDR 0.05-0.177) between the two divergent groups. These genes are involved in cellular protection against stress (HSPA1A and HSPA6), ribosome assembly (28S, 18S, and 5S ribosomal RNA), and immune response (IGHG4, GNLY, CXCL1, CAPN14, and SAA-4). The candidate genes and main pathways related to heat tolerance in Santa Ines sheep require further investigation to understand their response to heat stress in different climatic conditions and under solar radiation. It is essential to verify whether these genes and pathways are present in different breeds and to understand the relationship between heat stress and other genes identified in this study.
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Affiliation(s)
- Messy Hannear de Andrade Pantoja
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, 13635-900, Brazil
| | - Mirele Daiana Poleti
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, 13635-900, Brazil
| | - Francisco José de Novais
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, 13635-900, Brazil
| | - Kelly Kéffny Souza Duarte
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, 13635-900, Brazil
| | - Raluca G Mateescu
- Department of Animal Sciences, University of Florida, Gainesville, FL, USA
| | - Gerson Barreto Mourão
- Escola Superior de Agricultura Luiz de Queiroz Universidade de São Paulo, Av. Pádua Dias, 11, Piracicaba, São Paulo, Brazil
| | - Luiz Lehmann Coutinho
- Escola Superior de Agricultura Luiz de Queiroz Universidade de São Paulo, Av. Pádua Dias, 11, Piracicaba, São Paulo, Brazil
| | - Heidge Fukumasu
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, 13635-900, Brazil
| | - Cristiane Gonçalves Titto
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, 13635-900, Brazil.
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Pantoja MHDA, Novais FJD, Mourão GB, Mateescu RG, Poleti MD, Beline M, Monteiro CP, Fukumasu H, Titto CG. Exploring candidate genes for heat tolerance in ovine through liver gene expression. Heliyon 2024; 10:e25692. [PMID: 38370230 PMCID: PMC10869868 DOI: 10.1016/j.heliyon.2024.e25692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/24/2024] [Accepted: 01/31/2024] [Indexed: 02/20/2024] Open
Abstract
Thermotolerance has become an essential factor in the prevention of the adverse effects of heat stress, but it varies among animals. Identifying genes related to heat adaptability traits is important for improving thermotolerance and for selecting more productive animals in hot environments. The primary objective of this research was to find candidate genes in the liver that play a crucial role in the heat stress response of Santa Ines sheep, which exhibit varying levels of heat tolerance. To achieve this goal, 80 sheep were selected based on their thermotolerance and placed in a climate chamber for 10 days, during which the average temperature was maintained at 36 °C from 10 a.m. to 4 p.m. and 28 °C from 4 p.m. to 10 a.m. A subset of 14 extreme animals, with seven thermotolerant and seven non-thermotolerant animals based on heat loss (rectal temperature), were selected for liver sampling. RNA sequencing and differential gene expression analysis were performed. Thermotolerant sheep showed higher expression of genes GPx3, RGS6, GPAT3, VLDLR, LOC101108817, and EVC. These genes were mainly related to the Hedgehog signaling pathway, glutathione metabolism, glycerolipid metabolism, and thyroid hormone synthesis. These enhanced pathways in thermotolerant animals could potentially mitigate the negative effects of heat stress, conferring greater heat resistance.
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Affiliation(s)
- Messy Hannear de Andrade Pantoja
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, SP, 13635-900, Brazil
| | - Francisco José de Novais
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, SP, 13635-900, Brazil
| | - Gerson Barreto Mourão
- Escola Superior de Agricultura Luiz de Queiroz, Universidade São Paulo, Av. Pádua Dias, 11, Piracicaba, SP, 13418-900, Brazil
| | - Raluca G. Mateescu
- Department of Animal Science, University of Florida, Gainesville, FL, United States
| | - Mirele Daiana Poleti
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, SP, 13635-900, Brazil
| | - Mariane Beline
- Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061-0002, United States
| | - Camylla Pedrosa Monteiro
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, SP, 13635-900, Brazil
| | - Heidge Fukumasu
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, SP, 13635-900, Brazil
| | - Cristiane Gonçalves Titto
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Pirassununga, SP, 13635-900, Brazil
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Conteville LC, da Silva JV, Andrade BGN, Cardoso TF, Bruscadin JJ, de Oliveira PSN, Mourão GB, Coutinho LL, Palhares JCP, Berndt A, de Medeiros SR, Regitano LCDA. Rumen and fecal microbiomes are related to diet and production traits in Bos indicus beef cattle. Front Microbiol 2023; 14:1282851. [PMID: 38163076 PMCID: PMC10754987 DOI: 10.3389/fmicb.2023.1282851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/22/2023] [Indexed: 01/03/2024] Open
Abstract
Background Ruminants harbor a complex microbial community within their gastrointestinal tract, which plays major roles in their health and physiology. Brazil is one of the largest producers of beef in the world and more than 90% of the beef cattle herds are composed of pure and crossbred Nelore (Bos indicus). Despite its importance to the Brazilian economy and human feeding, few studies have characterized the Nelore microbiome. Therefore, using shotgun metagenomics, we investigated the impact of diet on the composition and functionality of the Nelore microbiome, and explored the associations between specific microbial taxa and their functionality with feed efficiency and methane emission. Results The ruminal microbiome exhibited significantly higher microbial diversity, distinctive taxonomic profile and variations in microbial functionality compared to the fecal microbiome, highlighting the distinct contributions of the microbiomes of these environments. Animals subjected to different dietary treatments exhibited significant differences in their microbiomes' archaeal diversity and in the abundance of 89 genera, as well as in the functions associated with the metabolism of components of each diet. Moreover, depending on the diet, feed-efficient animals and low methane emitters displayed higher microbial diversity in their fecal microbiome. Multiple genera were associated with an increase or decrease of the phenotypes. Upon analyzing the functions attributed to these taxa, we observed significant differences on the ruminal taxa associated with feed efficient and inefficient cattle. The ruminal taxa that characterized feed efficient cattle stood out for having significantly more functions related to carbohydrate metabolism, such as monosaccharides, di-/oligosaccharides and amino acids. The taxa associated with methane emission had functions associated with methanogenesis and the production of substrates that may influence methane production, such as hydrogen and formate. Conclusion Our findings highlight the significant role of diet in shaping Nelore microbiomes and how its composition and functionality may affect production traits such as feed efficiency and methane emission. These insights provide valuable support for the implementation of novel feeding and biotechnological strategies.
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Affiliation(s)
| | - Juliana Virginio da Silva
- Embrapa Southeast Livestock, São Carlos, Brazil
- Department of Genetics and Evolution, Federal University of São Carlos (UFSCar), São Carlos, Brazil
| | | | | | - Jennifer Jessica Bruscadin
- Embrapa Southeast Livestock, São Carlos, Brazil
- Department of Genetics and Evolution, Federal University of São Carlos (UFSCar), São Carlos, Brazil
| | - Priscila Silva Neubern de Oliveira
- Embrapa Southeast Livestock, São Carlos, Brazil
- Department of Genetics and Evolution, Federal University of São Carlos (UFSCar), São Carlos, Brazil
| | - Gerson Barreto Mourão
- Department of Animal Science, Center for Functional Genomics, University of São Paulo/ESALQ, Piracicaba, Brazil
| | - Luiz Lehmann Coutinho
- Department of Animal Science, Center for Functional Genomics, University of São Paulo/ESALQ, Piracicaba, Brazil
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Malheiros JM, Correia BSB, Ceribeli C, Bruscadin JJ, Diniz WJS, Banerjee P, da Silva Vieira D, Cardoso TF, Andrade BGN, Petrini J, Cardoso DR, Colnago LA, Bogusz Junior S, Mourão GB, Coutinho LL, Palhares JCP, de Medeiros SR, Berndt A, de Almeida Regitano LC. Ruminal and feces metabolites associated with feed efficiency, water intake and methane emission in Nelore bulls. Sci Rep 2023; 13:18001. [PMID: 37865691 PMCID: PMC10590413 DOI: 10.1038/s41598-023-45330-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023] Open
Abstract
The objectives of this study were twofold: (1) to identify potential differences in the ruminal and fecal metabolite profiles of Nelore bulls under different nutritional interventions; and (2) to identify metabolites associated with cattle sustainability related-traits. We used different nutritional interventions in the feedlot: conventional (Conv; n = 26), and by-product (ByPr, n = 26). Thirty-eight ruminal fluid and 27 fecal metabolites were significantly different (P < 0.05) between the ByPr and Conv groups. Individual dry matter intake (DMI), residual feed intake (RFI), observed water intake (OWI), predicted water intake (WI), and residual water intake (RWI) phenotypes were lower (P < 0.05) in the Conv group, while the ByPr group exhibited lower methane emission (ME) (P < 0.05). Ruminal fluid dimethylamine was significantly associated (P < 0.05) with DMI, RFI, FE (feed efficiency), OWI and WI. Aspartate was associated (P < 0.05) with DMI, RFI, FE and WI. Fecal C22:1n9 was significantly associated with OWI and RWI (P < 0.05). Fatty acid C14:0 and hypoxanthine were significantly associated with DMI and RFI (P < 0.05). The results demonstrated that different nutritional interventions alter ruminal and fecal metabolites and provided new insights into the relationship of these metabolites with feed efficiency and water intake traits in Nelore bulls.
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Affiliation(s)
| | | | - Caroline Ceribeli
- Institute of Chemistry, University of São Paulo/USP, São Carlos, São Paulo, Brazil
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | | | - Wellison J S Diniz
- Departament of Animal Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Priyanka Banerjee
- Departament of Animal Sciences, Auburn University, Auburn, AL, 36849, USA
| | | | | | - Bruno Gabriel Nascimento Andrade
- Embrapa Southeast Livestock, São Carlos, São Paulo, Brazil
- Computer Science Department, Munster Technological University, MTU/ADAPT, Cork, Ireland
| | - Juliana Petrini
- 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
| | - Luiz Lehmann Coutinho
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
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Bogdanski FA, Silveira RMF, Rovadoscki GA, Franzo V, Gervásio IC, Escobar DYO, Dauria BD, Meira AN, Mourão LMB, Coutinho LL, Pizzolante CC, de Moraes JE, Mourão GB. Genetic parameters for production, quality, and colors from eggs in Brazilian lineages of chickens. Trop Anim Health Prod 2023; 55:148. [PMID: 37020063 DOI: 10.1007/s11250-023-03554-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/29/2023] [Indexed: 04/07/2023]
Abstract
Genetic parameters were estimated for egg production, egg quality, and eggshell colors in eight lineages of Brazilian laying hens. Age at first egg (AFE), total egg production up to the 45th week (PROD), egg weight (EW), albumen height (AH), yolk color (YC), the Haugh units (HU), eggshell strength (ESS), eggshell thickness (EST), yolk weight (YW), eggshell weight (ESW), and eggshell color (L*, a*, and b*) were measured in 2030 eggs obtained from 645 laying hens. Variance components were estimated from a mixed animal model, which included the fixed effects of contemporary groups, cage location, and hen line, and the additive genetic, permanent environmental, and residual as random effects. In general, heritabilities were low to moderate (h2 = 0.11 to 0.48). Genetic correlations among eggshell quality traits were moderate to high (0.36 and 0.69). High genetic correlations were obtained between the eggshell color traits [rg = -0.90 (L* and a*); rg = -0.64 (L* and b*); and rg = 0.65 (a* and b*)]. Results suggest that EW is strongly correlated with ESW, but the genetic correlations between EW and ESS and between EW and EST were low. Genetic correlations between L* and eggshell quality traits were low to moderate, suggesting that L* has little or no relation with external egg quality. However, genetic correlations between a* and b* values and eggshell quality traits were high. The genetic correlations between eggshell color and eggshell quality traits were low, suggesting that the eggshell color does not influence external egg quality. Genetic correlations between PROD and egg quality traits were negative and varied between -0.42 and -0.05. This antagonistic relationship emphasizes the importance of adopting breeding schemes that allow the simultaneous genetic progress of these traits by considering their genetic correlation and economic relevance, such as the selection index.
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Affiliation(s)
- Fátima Auler Bogdanski
- Department of Animal Science, "Luiz de Queiroz" College Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Gregori Alberto Rovadoscki
- Department of Animal Science, "Luiz de Queiroz" College Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Vamilton Franzo
- Department of Animal Science, "Luiz de Queiroz" College Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Izally Carvalho Gervásio
- Department of Animal Science, "Luiz de Queiroz" College Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Daysi Ylder Orzuza Escobar
- Department of Animal Science, "Luiz de Queiroz" College Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Brayan Dias Dauria
- Department of Animal Science, "Luiz de Queiroz" College Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Ariana Nascimento Meira
- Department of Animal Science, "Luiz de Queiroz" College Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Luiz Lehmann Coutinho
- Department of Animal Science, "Luiz de Queiroz" College Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - José Evandro de Moraes
- Research Center of Diversified Animal Science, Instituto de Zootecnia, Nova Odessa, Brazil
| | - Gerson Barreto Mourão
- Department of Animal Science, "Luiz de Queiroz" College Agriculture, University of São Paulo, Piracicaba, Brazil.
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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da Silva BPM, Fanalli SL, Gomes JD, de Almeida VV, Fukumasu H, Freitas FAO, Moreira GCM, Silva-Vignato B, Reecy JM, Koltes JE, Koltes D, de Carvalho Balieiro JC, de Alencar SM, da Silva JPM, Coutinho LL, Afonso J, Regitano LCDA, Mourão GB, Luchiari Filho A, Cesar ASM. Brain fatty acid and transcriptome profiles of pig fed diets with different levels of soybean oil. BMC Genomics 2023; 24:91. [PMID: 36855067 PMCID: PMC9976441 DOI: 10.1186/s12864-023-09188-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 02/15/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND The high similarity in anatomical and neurophysiological processes between pigs and humans make pigs an excellent model for metabolic diseases and neurological disorders. Lipids are essential for brain structure and function, and the polyunsaturated fatty acids (PUFA) have anti-inflammatory and positive effects against cognitive dysfunction in neurodegenerative diseases. Nutrigenomics studies involving pigs and fatty acids (FA) may help us in better understanding important biological processes. In this study, the main goal was to evaluate the effect of different levels of dietary soybean oil on the lipid profile and transcriptome in pigs' brain tissue. RESULTS Thirty-six male Large White pigs were used in a 98-day study using two experimental diets corn-soybean meal diet containing 1.5% soybean oil (SOY1.5) and corn-soybean meal diet containing 3.0% soybean oil (SOY3.0). No differences were found for the brain total lipid content and FA profile between the different levels of soybean oil. For differential expression analysis, using the DESeq2 statistical package, a total of 34 differentially expressed genes (DEG, FDR-corrected p-value < 0.05) were identified. Of these 34 DEG, 25 are known-genes, of which 11 were up-regulated (log2 fold change ranging from + 0.25 to + 2.93) and 14 were down-regulated (log2 fold change ranging from - 3.43 to -0.36) for the SOY1.5 group compared to SOY3.0. For the functional enrichment analysis performed using MetaCore with the 34 DEG, four pathway maps were identified (p-value < 0.05), related to the ALOX15B (log2 fold change - 1.489), CALB1 (log2 fold change - 3.431) and CAST (log2 fold change + 0.421) genes. A "calcium transport" network (p-value = 2.303e-2), related to the CAST and CALB1 genes, was also identified. CONCLUSION The results found in this study contribute to understanding the pathways and networks associated with processes involved in intracellular calcium, lipid metabolism, and oxidative processes in the brain tissue. Moreover, these results may help a better comprehension of the modulating effects of soybean oil and its FA composition on processes and diseases affecting the brain tissue.
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Affiliation(s)
- Bruna Pereira Martins da Silva
- grid.11899.380000 0004 1937 0722Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Simara Larissa Fanalli
- grid.11899.380000 0004 1937 0722Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Julia Dezen Gomes
- grid.11899.380000 0004 1937 0722Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Vivian Vezzoni de Almeida
- grid.411195.90000 0001 2192 5801College of Veterinary Medicine and Animal Science, Federal University of Goiás, Goiânia, Goiás Brazil
| | - Heidge Fukumasu
- grid.11899.380000 0004 1937 0722Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Felipe André Oliveira Freitas
- grid.11899.380000 0004 1937 0722Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Bárbara Silva-Vignato
- grid.11899.380000 0004 1937 0722Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - James Mark Reecy
- grid.34421.300000 0004 1936 7312College of Agriculture and Life Sciences, Iowa State University, Ames, IA USA
| | - James Eugene Koltes
- grid.34421.300000 0004 1936 7312College of Agriculture and Life Sciences, Iowa State University, Ames, IA USA
| | - Dawn Koltes
- grid.34421.300000 0004 1936 7312College of Agriculture and Life Sciences, Iowa State University, Ames, IA USA
| | - Júlio Cesar de Carvalho Balieiro
- grid.11899.380000 0004 1937 0722School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Severino Matias de Alencar
- grid.11899.380000 0004 1937 0722Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Julia Pereira Martins da Silva
- grid.11899.380000 0004 1937 0722Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Luiz Lehmann Coutinho
- grid.11899.380000 0004 1937 0722Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Juliana Afonso
- grid.460200.00000 0004 0541 873XEmbrapa Pecuária Sudeste, São Carlos, São Paulo, Brazil
| | | | - Gerson Barreto Mourão
- grid.11899.380000 0004 1937 0722Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Albino Luchiari Filho
- grid.11899.380000 0004 1937 0722Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Aline Silva Mello Cesar
- Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil. .,Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil.
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9
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Salvian M, Silveira RMF, Petrini J, Rovadoscki GA, Iung LHDS, Ramírez-Díaz J, Carrara ER, Pertile SFN, Cassoli LD, Machado PF, Mourão GB. Heat stress on breeding value prediction for milk yield and composition of a Brazilian Holstein cattle population. Int J Biometeorol 2023; 67:347-354. [PMID: 36580141 DOI: 10.1007/s00484-022-02413-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 09/27/2022] [Accepted: 11/26/2022] [Indexed: 06/17/2023]
Abstract
Due to the high milk production of Holstein cows, many countries have chosen to import semen to improve local dairy herds. This strategy would be more effective if this semen was used in the same environment conditions in which the bulls were selected. If the effect of genotype by environment (G × E) interaction is not considered, the estimated breeding values (EBVs) may vary, potentially reducing the selection response. We evaluate the impact of heat stress on selection for milk yield and composition of Holstein cows using random regression models. To verify the interference of heat stress in milk yield (MY) and composition traits (fat, protein, total saturated, and total unsaturated fatty acids content in milk), temperature-humidity index (THI) on test-day milk records was used. The threshold value to divide the environments using test-day information from Brazilian Holstein cows was 72 units of THI, i.e., < 72 represented no heat stress and > 72 represented heat stress. Legendre polynomials of second-order (Leg 2) model and two lactation points (33 and 122 DIM) were used to estimate heritabilities and EBVs for five important dairy traits. The heritabilities of milk components and fatty acids were low (0.09-0.29), regardless of lactation period and degree of heat stress, with the exception of protein content (0.30-0.35). Fat content was the only milk component that was reduced according to the degree of heat stress and lactation period. The EBVs tended to decrease in heat stress conditions, thus animals with high genetic potential demonstrated evidence of G × E interaction. However, acclimatization of dairy cows to heat stress in the farm production systems may have been responsible for the low differences among genetic parameters and EBVs with and without heat stress found in this study.
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Affiliation(s)
- Mayara Salvian
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Av. Pádua Dias, 11. Piracicaba13.418-900, São Paulo, Brazil
| | - Robson Mateus Freitas Silveira
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Av. Pádua Dias, 11. Piracicaba13.418-900, São Paulo, Brazil
| | - Julina Petrini
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Av. Pádua Dias, 11. Piracicaba13.418-900, São Paulo, Brazil
| | - Gregori Alberto Rovadoscki
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Av. Pádua Dias, 11. Piracicaba13.418-900, São Paulo, Brazil
| | - Laiza Helena de Souza Iung
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Av. Pádua Dias, 11. Piracicaba13.418-900, São Paulo, Brazil
| | - Johanna Ramírez-Díaz
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Av. Pádua Dias, 11. Piracicaba13.418-900, São Paulo, Brazil
| | - Eula Regina Carrara
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Av. Pádua Dias, 11. Piracicaba13.418-900, São Paulo, Brazil
| | - Simone Fernanda Nedel Pertile
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Av. Pádua Dias, 11. Piracicaba13.418-900, São Paulo, Brazil
| | - Laerte Dagher Cassoli
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Av. Pádua Dias, 11. Piracicaba13.418-900, São Paulo, Brazil
| | - Paulo Fernando Machado
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Av. Pádua Dias, 11. Piracicaba13.418-900, São Paulo, Brazil
| | - Gerson Barreto Mourão
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Av. Pádua Dias, 11. Piracicaba13.418-900, São Paulo, Brazil.
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10
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Fanalli SL, da Silva BPM, Gomes JD, Durval MC, de Almeida VV, Moreira GCM, Silva-Vignato B, Afonso J, Freitas FAO, Reecy JM, Koltes JE, Koltes D, Garrick D, Correia de Almeida Regitano L, Balieiro JCDC, Mourão GB, Coutinho LL, Fukumasu H, de Alencar SM, Luchiari Filho A, Cesar ASM. RNA-seq transcriptome profiling of pigs' liver in response to diet with different sources of fatty acids. Front Genet 2023; 14:1053021. [PMID: 36816031 PMCID: PMC9936315 DOI: 10.3389/fgene.2023.1053021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 01/09/2023] [Indexed: 01/26/2023] Open
Abstract
Pigs (Sus scrofa) are an animal model for metabolic diseases in humans. Pork is an important source of fatty acids (FAs) in the human diet, as it is one of the most consumed meats worldwide. The effects of dietary inclusion of oils such as canola, fish, and soybean oils on pig gene expression are mostly unknown. Our objective was to evaluate FA composition, identify changes in gene expression in the liver of male pigs fed diets enriched with different FA profiles, and identify impacted metabolic pathways and gene networks to enlighten the biological mechanisms' variation. Large White male pigs were randomly allocated to one of three diets with 18 pigs in each; all diets comprised a base of corn and soybean meal to which either 3% of soybean oil (SOY), 3% canola oil (CO), or 3% fish oil (FO) was added for a 98-day trial during the growing and finishing phases. RNA sequencing was performed on the liver samples of each animal by Illumina technology for differential gene expression analyses, using the R package DESeq2. The diets modified the FA profile, mainly in relation to polyunsaturated and saturated FAs. Comparing SOY vs. FO, 143 differentially expressed genes (DEGs) were identified as being associated with metabolism, metabolic and neurodegenerative disease pathways, inflammatory processes, and immune response networks. Comparing CO vs. SOY, 148 DEGs were identified, with pathways related to FA oxidation, regulation of lipid metabolism, and metabolic and neurodegenerative diseases. Our results help explain the behavior of genes with differential expression in metabolic pathways resulting from feeding different types of oils in pig diets.
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Affiliation(s)
- Simara Larissa Fanalli
- Faculty of Animal Science and Food Engineering, (FZEA), University of São Paulo, São Paulo, Brazil
| | | | - Julia Dezen Gomes
- Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, Brazil
| | - Mariah Castro Durval
- Faculty of Animal Science and Food Engineering, (FZEA), University of São Paulo, São Paulo, Brazil
| | | | | | - Bárbara Silva-Vignato
- Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, Brazil
| | | | - Felipe André Oliveira Freitas
- Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, Brazil
| | - James Mark Reecy
- Animal Science Department, Iowa State University, Ames, IA, United States
| | | | - Dawn Koltes
- Animal Science Department, Iowa State University, Ames, IA, United States
| | - Dorian Garrick
- AL Rae Centre for Genetics and Breeding, Massey University, Hamilton, New Zealand
| | | | | | - Gerson Barreto Mourão
- Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, Brazil
| | - Luiz Lehmann Coutinho
- Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, Brazil
| | - Heidge Fukumasu
- Faculty of Animal Science and Food Engineering, (FZEA), University of São Paulo, São Paulo, Brazil
| | - Severino Matias de Alencar
- Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, Brazil
| | - Albino Luchiari Filho
- Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, Brazil
| | - Aline Silva Mello Cesar
- Faculty of Animal Science and Food Engineering, (FZEA), University of São Paulo, São Paulo, Brazil,Animal Science Department, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo, Piracicaba, Brazil,*Correspondence: Aline Silva Mello Cesar,
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11
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Afonso J, Shim WJ, Boden M, Salinas Fortes MR, da Silva Diniz WJ, de Lima AO, Rocha MIP, Cardoso TF, Bruscadin JJ, Gromboni CF, Nogueira ARA, Mourão GB, Zerlotini A, Coutinho LL, de Almeida Regitano LC. Repressive epigenetic mechanisms, such as the H3K27me3 histone modification, were predicted to affect muscle gene expression and its mineral content in Nelore cattle. Biochem Biophys Rep 2023; 33:101420. [PMID: 36654922 PMCID: PMC9841166 DOI: 10.1016/j.bbrep.2023.101420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/12/2022] [Accepted: 01/02/2023] [Indexed: 01/07/2023] Open
Abstract
Epigenetic repression has been linked to the regulation of different cell states. In this study, we focus on the influence of this repression, mainly by H3K27me3, over gene expression in muscle cells, which may affect mineral content, a phenotype that is relevant to muscle function and beef quality. Based on the inverse relationship between H3K27me3 and gene expression (i.e., epigenetic repression) and on contrasting sample groups, we computationally predicted regulatory genes that affect muscle mineral content. To this end, we applied the TRIAGE predictive method followed by a rank product analysis. This methodology can predict regulatory genes that might be affected by repressive epigenetic regulation related to mineral concentration. Annotation of orthologous genes, between human and bovine, enabled our investigation of gene expression in the Longissimus thoracis muscle of Bos indicus cattle. The animals under study had a contrasting mineral content in their muscle cells. We identified candidate regulatory genes influenced by repressive epigenetic mechanisms, linking histone modification to mineral content in beef samples. The discovered candidate genes take part in multiple biological pathways, i.e., impulse transmission, cell signalling, immunological, and developmental pathways. Some of these genes were previously associated with mineral content or regulatory mechanisms. Our findings indicate that epigenetic repression can partially explain the gene expression profiles observed in muscle samples with contrasting mineral content through the candidate regulators here identified.
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Affiliation(s)
| | - Woo Jun Shim
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia,Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Mikael Boden
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | | | | | - Andressa Oliveira de Lima
- Division of Medical Genetics, Department of Genome Sciences, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Marina Ibelli Pereira Rocha
- Post-graduation Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, São Paulo, Brazil
| | | | - Jennifer Jessica Bruscadin
- Post-graduation Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, São Paulo, Brazil
| | | | | | - Gerson Barreto Mourão
- Department of Agroindustry, Food and Nutrition, University of São Paulo/ESALQ, Piracicaba, Brazil
| | - Adhemar Zerlotini
- Bioinformatic Multi-user Laboratory, Embrapa Informática Agropecuária, Campinas, São Paulo, Brazil
| | - Luiz Lehmann Coutinho
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
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12
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Pantoja MHDA, Campos JCD, Almeida DHSD, Negrão JA, Mourão GB, Pereira AMF, Titto CG. Influence of successive heat waves on the thermoregulatory responses of pregnant and non-pregnant ewes. J Therm Biol 2023; 111:103420. [PMID: 36585085 DOI: 10.1016/j.jtherbio.2022.103420] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 07/22/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
The frequency of heat waves has increased over the last years, with an impact on animal production and health, including the death of animals. Therefore, the aim of this study was to evaluate the dynamics of thermoregulation and hormonal responses in non-pregnant and pregnant ewes exposed to successive heat waves. Twenty-four non-pregnant and 18 pregnant Santa Ines ewes with black coat color (live weight: 55 ± 9.03 kg; age: 60 months) were used. Weather variables such air temperature, relative humidity, and solar radiation were continuously recorded. The rectal and tympanic temperatures and respiratory rate were measured daily. Serum triiodothyronine (T3) and prolactin were evaluated during the heat wave and thermoneutral periods. The physiological variables were higher under the heat wave conditions and were related to the activation of the thermoregulatory system for maintaining homeothermy (P < 0.05). The core body temperature was higher during successive heat waves (P < 0.05), as was the tympanic temperature, which are both affected by changes in air temperature (P < 0.05). T3 and prolactin levels were not influenced by successive heat waves (P < 0.05) and rectal temperature and respiratory rate were highest in non-pregnant ewes (P < 0.05). Prolactin was not affected by temperature. The results indicate that the Santa Ines breed overcomes the thermal challenge during a heat wave without showing severe signs of thermal stress regardless of being pregnant or not.
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Affiliation(s)
- Messy Hannear de Andrade Pantoja
- Faculdade de Zootecnia e Engenharia de Alimentos/ Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Campus Fernando Costa, Pirassununga, SP, 13635-900, Brazil.
| | - Jessica Caetano Dias Campos
- Faculdade de Zootecnia e Engenharia de Alimentos/ Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Campus Fernando Costa, Pirassununga, SP, 13635-900, Brazil.
| | - Douglas Henrique Silva de Almeida
- Faculdade de Zootecnia e Engenharia de Alimentos/ Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Campus Fernando Costa, Pirassununga, SP, 13635-900, Brazil.
| | - João Alberto Negrão
- Faculdade de Zootecnia e Engenharia de Alimentos/ Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Campus Fernando Costa, Pirassununga, SP, 13635-900, Brazil.
| | - Gerson Barreto Mourão
- Escola Superior de Agricultura Luiz de Queiroz/ Universidade de São Paulo, Av. Pádua Dias, 11, Piracicaba, SP, 13418900, Brazil.
| | | | - Cristiane Gonçalves Titto
- Faculdade de Zootecnia e Engenharia de Alimentos/ Universidade de São Paulo, Av. Duque de Caxias Norte, 225, Campus Fernando Costa, Pirassununga, SP, 13635-900, Brazil.
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13
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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Salvian M, Moreira GCM, Silveira RMF, Reis ÂP, Dias D'auria B, Pilonetto F, Gervásio IC, Ledur MC, Coutinho LL, Spangler ML, Mourão GB. Estimation of breeding values using different densities of SNP to inform kinship in broiler chickens. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.105124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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15
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Bruscadin JJ, Cardoso TF, da Silva Diniz WJ, Afonso J, de Souza MM, Petrini J, Nascimento Andrade BG, da Silva VH, Ferraz JBS, Zerlotini A, Mourão GB, Coutinho LL, de Almeida Regitano LC. Allele-specific expression reveals functional SNPs affecting muscle-related genes in bovine. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 2022; 1865:194886. [DOI: 10.1016/j.bbagrm.2022.194886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 09/27/2022] [Accepted: 10/12/2022] [Indexed: 11/09/2022]
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16
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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de Souza TC, de Souza TC, da Cruz VAR, Mourão GB, Pedrosa VB, Rovadoscki GA, Coutinho LL, de Camargo GMF, Costa RB, de Carvalho GGP, Pinto LFB. Estimates of heritability and candidate genes for primal cuts and dressing percentage in Santa Ines sheep. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.105048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Landim AV, Peres MCR, Costa HHA, Silveira RMF, Costa AC, Parente MDOM, Mourão GB, McManus CM. Feeding restriction in the pre and postpartum period of hair ewes raised in the semi-arid region: implications on performance and carcass traits of the progeny. Trop Anim Health Prod 2022; 54:303. [DOI: 10.1007/s11250-022-03279-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 08/31/2022] [Indexed: 11/29/2022]
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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: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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Cardoso TF, Bruscadin JJ, Afonso J, Petrini J, Andrade BGN, de Oliveira PSN, Malheiros JM, Rocha MIP, Zerlotini A, Ferraz JBS, Mourão GB, Coutinho LL, Regitano LCA. EEF1A1 transcription cofactor gene polymorphism is associated with muscle gene expression and residual feed intake in Nelore cattle. Mamm Genome 2022; 33:619-628. [PMID: 35816191 DOI: 10.1007/s00335-022-09959-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 06/22/2022] [Indexed: 12/01/2022]
Abstract
Cis-acting effects of noncoding variants on gene expression and regulatory molecules constitute a significant factor for phenotypic variation in complex traits. To provide new insights into the impacts of single-nucleotide polymorphisms (SNPs) on transcription factors (TFs) and transcription cofactors (TcoF) coding genes, we carried out a multi-omic analysis to identify cis-regulatory effects of SNPs on these genes' expression in muscle and describe their association with feed efficiency-related traits in Nelore cattle. As a result, we identified one SNP, the rs137256008C > T, predicted to impact the EEF1A1 gene expression (β = 3.02; P-value = 3.51E-03) and the residual feed intake trait (β = - 3.47; P-value = 0.02). This SNP was predicted to modify transcription factor sites and overlaps with several QTL for feed efficiency traits. In addition, co-expression network analyses showed that animals containing the T allele of the rs137256008 SNP may be triggering changes in the gene network. Therefore, our analyses reinforce and contribute to a better understanding of the biological mechanisms underlying gene expression control of feed efficiency traits in bovines. The cis-regulatory SNP can be used as biomarker for feed efficiency in Nelore cattle.
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Affiliation(s)
- T F Cardoso
- Embrapa Southeast Livestock, São Carlos, SP, Brazil
| | - J J Bruscadin
- Program on Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | - J Afonso
- Embrapa Southeast Livestock, São Carlos, SP, Brazil
| | - J Petrini
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo/ESALQ, Piracicaba, SP, Brazil
| | - B G N Andrade
- Computer Science Department, Munster Technological University, MTU/ADAPT, Cork, Ireland
| | - P S N de Oliveira
- Program on Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | - J M Malheiros
- Federal University of Latin American Integration, Foz do Iguaçu, Paraná, Brazil
| | - M I P Rocha
- Program on Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, SP, Brazil
| | - A Zerlotini
- Embrapa Agricultural Informatics, Campinas, SP, Brazil
| | - J B S Ferraz
- Department of Veterinary Medicine, University of São Paulo/FZEA, Pirassununga, Brazil
| | - G B Mourão
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo/ESALQ, Piracicaba, SP, Brazil
| | - L L Coutinho
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo/ESALQ, Piracicaba, SP, Brazil
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Fanalli SL, da Silva BPM, Gomes JD, de Almeida VV, Freitas FAO, Moreira GCM, Silva-Vignato B, Afonso J, Reecy J, Koltes J, Koltes D, de Almeida Regitano LC, Garrick DJ, de Carvalho Balieiro JC, Meira AN, Freitas L, Coutinho LL, Fukumasu H, Mourão GB, de Alencar SM, Luchiari Filho A, Cesar ASM. Differential Gene Expression Associated with Soybean Oil Level in the Diet of Pigs. Animals (Basel) 2022; 12:ani12131632. [PMID: 35804531 PMCID: PMC9265114 DOI: 10.3390/ani12131632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/15/2022] [Accepted: 06/20/2022] [Indexed: 12/21/2022] Open
Abstract
Simple Summary Findings from the analysis of the pig transcriptome may help to better understand the biological mechanisms that can be modulated by the diet. Thus, the aim of this study was to identify the differentially expressed genes from the skeletal muscle and liver samples of pigs fed diets with two different levels of soybean oil (1.5 or 3%). The FA profile in the tissues was modified by the diet mainly related to monounsaturated (MUFA) and polyunsaturated (PUFA). This nutrigenomics study verified the effect of different levels of soybean oil in the pig diet on the transcriptome profile of skeletal muscle and liver, where the higher level of soybean oil added to the diet led to a higher expression of genes targeting biological processes related to lipid oxidation and consequently to metabolic diseases and inflammation. Abstract The aim of this study was to identify the differentially expressed genes (DEG) from the skeletal muscle and liver samples of animal models for metabolic diseases in humans. To perform the study, the fatty acid (FA) profile and RNA sequencing (RNA-Seq) data of 35 samples of liver tissue (SOY1.5, n = 17 and SOY3.0, n = 18) and 36 samples of skeletal muscle (SOY1.5, n = 18 and SOY3.0, n = 18) of Large White pigs were analyzed. The FA profile of the tissues was modified by the diet, mainly those related to monounsaturated (MUFA) and polyunsaturated (PUFA) FA. The skeletal muscle transcriptome analysis revealed 45 DEG (FDR 10%), and the functional enrichment analysis identified network maps related to inflammation, immune processes, and pathways associated with oxidative stress, type 2 diabetes, and metabolic dysfunction. For the liver tissue, the transcriptome profile analysis revealed 281 DEG, which participate in network maps related to neurodegenerative diseases. With this nutrigenomics study, we verified that different levels of soybean oil in the pig diet, an animal model for metabolic diseases in humans, affected the transcriptome profile of skeletal muscle and liver tissue. These findings may help to better understand the biological mechanisms that can be modulated by the diet.
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Affiliation(s)
- Simara Larissa Fanalli
- Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga 13635-900, SP, Brazil; (S.L.F.); (B.P.M.d.S.); (H.F.)
| | - Bruna Pereira Martins da Silva
- Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga 13635-900, SP, Brazil; (S.L.F.); (B.P.M.d.S.); (H.F.)
| | - Julia Dezen Gomes
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (J.D.G.); (F.A.O.F.); (B.S.-V.); (A.N.M.); (L.L.C.); (G.B.M.); (S.M.d.A.); (A.L.F.)
| | - Vivian Vezzoni de Almeida
- College of Veterinary Medicine and Animal Science, Federal University of Goiás, Goiânia 74690-900, GO, Brazil;
| | - Felipe André Oliveira Freitas
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (J.D.G.); (F.A.O.F.); (B.S.-V.); (A.N.M.); (L.L.C.); (G.B.M.); (S.M.d.A.); (A.L.F.)
| | | | - Bárbara Silva-Vignato
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (J.D.G.); (F.A.O.F.); (B.S.-V.); (A.N.M.); (L.L.C.); (G.B.M.); (S.M.d.A.); (A.L.F.)
| | - Juliana Afonso
- Embrapa Pecuária Sudeste, São Carlos 70770-901, SP, Brazil; (J.A.); (L.C.d.A.R.)
| | - James Reecy
- College of Agriculture and Life Sciences, Iowa State University, Ames, IA 50011, USA; (J.R.); (J.K.); (D.K.)
| | - James Koltes
- College of Agriculture and Life Sciences, Iowa State University, Ames, IA 50011, USA; (J.R.); (J.K.); (D.K.)
| | - Dawn Koltes
- College of Agriculture and Life Sciences, Iowa State University, Ames, IA 50011, USA; (J.R.); (J.K.); (D.K.)
| | | | - Dorian John Garrick
- AL Rae Centre for Genetics and Breeding, Massey University, Hamilton 3214, New Zealand;
| | | | - Ariana Nascimento Meira
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (J.D.G.); (F.A.O.F.); (B.S.-V.); (A.N.M.); (L.L.C.); (G.B.M.); (S.M.d.A.); (A.L.F.)
| | - Luciana Freitas
- DB Genética de Suínos, Patos de Minas 38706-000, MG, Brazil;
| | - Luiz Lehmann Coutinho
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (J.D.G.); (F.A.O.F.); (B.S.-V.); (A.N.M.); (L.L.C.); (G.B.M.); (S.M.d.A.); (A.L.F.)
| | - Heidge Fukumasu
- Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga 13635-900, SP, Brazil; (S.L.F.); (B.P.M.d.S.); (H.F.)
| | - Gerson Barreto Mourão
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (J.D.G.); (F.A.O.F.); (B.S.-V.); (A.N.M.); (L.L.C.); (G.B.M.); (S.M.d.A.); (A.L.F.)
| | - Severino Matias de Alencar
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (J.D.G.); (F.A.O.F.); (B.S.-V.); (A.N.M.); (L.L.C.); (G.B.M.); (S.M.d.A.); (A.L.F.)
| | - Albino Luchiari Filho
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (J.D.G.); (F.A.O.F.); (B.S.-V.); (A.N.M.); (L.L.C.); (G.B.M.); (S.M.d.A.); (A.L.F.)
| | - Aline Silva Mello Cesar
- Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga 13635-900, SP, Brazil; (S.L.F.); (B.P.M.d.S.); (H.F.)
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba 13418-900, SP, Brazil; (J.D.G.); (F.A.O.F.); (B.S.-V.); (A.N.M.); (L.L.C.); (G.B.M.); (S.M.d.A.); (A.L.F.)
- Correspondence:
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22
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Petrini J, Salgado RM, Rodriguez MAP, Machado PF, Mourão GB. Machine learning methods for the prediction of milk fatty acid content. INT J DAIRY TECHNOL 2022. [DOI: 10.1111/1471-0307.12877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Juliana Petrini
- Department of Animal Science University of São Paulo Piracicaba 13418‐900 Brazil
| | - Ricardo Menezes Salgado
- Department of Computer Science, Institute of Exact Sciences Federal University of Alfenas Alfenas 37130‐001 Brazil
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23
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Berton MP, da Silva RP, Banchero G, Mourão GB, Ferraz JBS, Schenkel FS, Baldi F. Genomic integration to identify molecular biomarkers associated with indicator traits of gastrointestinal nematode resistance in sheep. J Anim Breed Genet 2022; 139:502-516. [PMID: 35535437 DOI: 10.1111/jbg.12682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 04/21/2022] [Indexed: 12/19/2022]
Abstract
This study aimed to integrate GWAS and structural variants to propose possible molecular biomarkers related to gastrointestinal nematode resistance traits in Santa Inês sheep. The phenotypic records FAMACHA, haematocrit, white blood cell count, red blood cell count, haemoglobin, platelets and egg counts per gram of faeces were collected from 700 naturally infected animals, belonging to four Brazilian flocks. A total of 576 animals were genotyped using the Ovine SNP12k BeadChip and were imputed using a reference population with Ovine SNP50 BeadChip. The GWAS approaches were based on SNPs, haplotypes, CNVs and ROH. The overlapping between the significant genomic regions detected from all approaches was investigated, and the results were integrated using a network analysis. Genes related to the immune system were found, such as ABCB1, IL6, WNT5A and IRF5. Genomic regions containing candidate genes and metabolic pathways involved in immune responses, inflammatory processes and immune cells affecting parasite resistance traits were identified. The genomic regions, biological processes and candidate genes uncovered could lead to biomarkers for selecting more resilient sheep and improving herd welfare and productivity. The results obtained are the start point to identify molecular biomarkers related to indicator traits of gastrointestinal nematode resistance in Santa Inês sheep.
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Affiliation(s)
- Mariana Piatto Berton
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, Brazil
| | - Rosiane Pereira da Silva
- Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, Brazil
| | - Georgget Banchero
- Instituto Nacional de Investigación Agropecuária (INIA), Colonia, Uruguay
| | - Gerson Barreto Mourão
- Departamento de Zootecnia, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo/ESALQ, Piracicaba, Brazil
| | | | | | - Fernando Baldi
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Jaboticabal, Brazil
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24
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Bóscollo PP, Dauria BD, Portes JV, Petrini J, da Silva Lopes JE, Ladeira GC, Júnior LFS, Mourão GB. BIOECONOMIC SELECTION INDexes FOR terminal lamb systems in tropical conditions. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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Ladeira GC, Pilonetto F, Fernandes AC, Bóscollo PP, Dauria BD, Titto CG, Coutinho LL, E Silva FF, Pinto LFB, Mourão GB. CNV detection and their association with growth, efficiency and carcass traits in Santa Inês sheep. J Anim Breed Genet 2022; 139:476-487. [PMID: 35218589 DOI: 10.1111/jbg.12671] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 01/04/2022] [Accepted: 02/09/2022] [Indexed: 11/30/2022]
Abstract
Copy number variations (CNV) are an important source of genetic variation. CNV has been increasingly studied and frequently associated with diseases and productive traits in livestock animals. However, CNV-based genome-wide association studies (GWAS) in Santa Inês sheep, one of the principal sheep breeds in Brazil, have not yet been reported. Thus, the aim of this study was to investigate the association between CNV and growth, efficiency and carcass traits in sheep. The Illumina OvineSNP50 BeadChip array was used to detect CNV in 491 Santa Inês individuals. Then, CNV-based GWAS was performed with a linear mixed model approach considering a genomic relationship matrix, for ten traits: (1) growth: body weight at three (W3) and six (W6) months of age; (2) efficiency: residual feed intake (RFI) and feed efficiency (FE) and (3) carcass: external carcass length (ECL), leg length (LL), carcass yield (CY), commercial cuts weight (CCW), loin eye area (LEA) and subcutaneous fat thickness (SFT). We identified 1,167 autosomal CNV in 438 sheep, with 294 non-redundant CNV, ranging from 21.8 to 861.9 kb, merged into 216 distinct copy number variation regions (CNVRs). One significant CNV segment (pFDR -value<0.05) in OAR3 was associated with CY, while another significant CNV in OAR6 was associated with RFI. Additionally, another 5 CNV segments were considered relevant for investigation in the future studies. The significant segments overlapped 4 QTLs and spanned 8 genes, including the SPAST, TGFA and ADGRL3 genes, involved in cell differentiation and energy metabolism. Therefore, the results of the present study increase knowledge about CNV in sheep, their possible impacts on productive traits, and provide information for future investigations, being especially useful for those interested in structural variations in the sheep genome.
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Affiliation(s)
- Giovanni Coelho Ladeira
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, Brazil
| | - Fabrício Pilonetto
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, Brazil
| | - Anna Carolina Fernandes
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, Brazil
| | - Paola Pérez Bóscollo
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, Brazil
| | - Brayan Dias Dauria
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, Brazil
| | - Cristiane Gonçalves Titto
- Department of Animal Science, College of Animal Science and Food Engineering, University of São Paulo (FZEA/USP), Pirassununga, Brazil
| | - Luiz Lehmann Coutinho
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, Brazil
| | | | - Luís Fernando Batista Pinto
- Department of Animal Science, College of Veterinary Medicine and Animal Science, Federal University of Bahia, Salvador, Brazil
| | - Gerson Barreto Mourão
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ/USP), Piracicaba, Brazil
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26
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Dauria BD, Sigdel A, Petrini J, Bóscollo PP, Pilonetto F, Salvian M, Rezende FM, Pedrosa VB, Bittar CMM, Machado PF, Coutinho LL, Wiggans GR, Mourão GB. Genetic effects of heat stress on milk fatty acids in a Brazilian Holstein cattle. J Dairy Sci 2022; 105:3296-3305. [PMID: 35094861 DOI: 10.3168/jds.2021-20914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/13/2021] [Indexed: 11/19/2022]
Abstract
The present study aimed to estimate covariance components of milk fatty acids (FA) and to compare the genomic estimated breeding values under general and heat-stress effects. Data consisted of 38,762 test-day records from 6,344 Holstein cows obtained from May 2012 through January 2018 on 4 dairy herds from Brazil. Single-trait repeatability test-day models with random regressions as a function of temperature-humidity index values were used for genetic analyses. The models included contemporary groups, parity order (1-6), and days in milk classes as fixed effects, and general and thermotolerance additive genetic and permanent environmental as random effects. Notably, differences in heritability estimates between environments (general and heat stress) increased (0.03 to 0.06) for unsaturated FA traits, such as unsaturated, monounsaturated, and polyunsaturated, at higher heat-stress levels. In contrast, heritability estimated between environments for saturated FA traits, including saturated FA, palmitic acid (C16:0), and stearic acid (C18:0) did not observe significant differences between environments. In addition, our study revealed negative genetic correlations between general and heat-stress additive genetic effects (antagonistic effect) for the saturated FA, C16:0, C18:0, and C18:1, which ranged from -0.007 to -0.32. Spearman's ranking correlation between genomic estimated breeding values ranged from -0.27 to 0.99. Results indicated a moderate to strong interaction of genotype by the environment for most FA traits comparing a heat-stress environment with thermoneutral conditions. Our findings point out novel opportunities to explore the use of FA milk profile and heat-stress models.
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Affiliation(s)
- B D Dauria
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900, Brazil
| | - A Sigdel
- Department of Animal and Dairy Science, University of Wisconsin, Madison 53706
| | - J Petrini
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900, Brazil
| | - P P Bóscollo
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900, Brazil
| | - F Pilonetto
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900, Brazil
| | - M Salvian
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900, Brazil
| | - F M Rezende
- Department of Animal Sciences, University of Florida, Gainesville 32608
| | - V B Pedrosa
- Department of Animal Science, State University of Ponta Grossa, Ponta Grossa, PR 84030-900, Brazil
| | - C M M Bittar
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900, Brazil
| | - P F Machado
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900, Brazil
| | - L L Coutinho
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900, Brazil
| | - G R Wiggans
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350
| | - G B Mourão
- Department of Animal Science, University of São Paulo, Piracicaba, SP 13418-900, Brazil.
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Colonia SRR, Oliveira ADC, Pilonetto F, Dauria BD, Mourão GB, Machado PF, Nogueira DA, Beijo LA, Petrini J. Genetic parameters for milk yield, casein percentage, subclinical mastitis incidence and sexual precocity using Bayesian linear and threshold models. Anim Prod Sci 2022. [DOI: 10.1071/an20313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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Landim AV, Roriz ND, Silveira RMF, Vega WHO, Costa HHA, de Sousa LCO, Alves GC, Ferreira J, Mourão GB. Sheep meat production in the Brazilian semi-arid region: crossing between indigenous breeds. Trop Anim Health Prod 2021; 53:510. [PMID: 34628538 DOI: 10.1007/s11250-021-02947-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/23/2021] [Indexed: 10/20/2022]
Abstract
Investigations in the Brazilian semi-arid region evaluating the performance and carcass traits of sheep of indigenous breeds and their crossings have been performed; however, these studies use exotic breeds which produce precocious lambs with heavier carcasses, but not adapted to climatic conditions and the extensive production system, jeopardizing the sustainability of the sheep production system. We crossed between three indigenous breeds: Morada Nova (MN - maternal breed); Rabo Largo (RL - paternal breed), and Santa Inês (SI - paternal breed) with the objective of evaluating the effect of genotype and sex on the performance and carcass traits of purebred and crossbred animals. A total of 30 lambs, males and females, reared in a semi-intensive system were evaluated. Birth and weaning weights were 2.26 ± 0.53 and 7.31 ± 1.85, respectively. All lambs were slaughtered at 10 months of age. A completely randomized design in a 3 × 2 factorial scheme (three genotypes and two sexes) was used. Multivariate techniques were also performed to reduce group and discriminate variables. Birth and weaning weight were similar (P > 0.05) among genetic groups and sexes. The weight gain, carcass and morphometric trait characteristics, and the main commercial cuts were higher in crossbred lambs (P < 0.05). All indicators have discriminatory power between genotypes and sexes, but the carcass traits have a higher discriminatory power (P < 0.001). All genotypes, regardless of sex, have particular characteristics, i.e. MN × SI was characterized by greater forelimb and ham perimeters (P < 0.001), and the MN × RL by higher hot carcass weight and finish (P = 0.001). The cluster analysis and the heatmap plot revealed associations between SI and the size of cuts and RL with the cut commercial yield and the reduction in weight loss due to cooling. Our findings confirm the hypothesis that crossing between indigenous breeds represents an adequate alternative in sheep meat production systems in semi-arid regions. Finally, we encourage the use of indigenous breeds for sheep meat production with breed identity in order to favor the conservation of genetic resources and the sustainability of the production system.
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Affiliation(s)
- Aline Vieira Landim
- Department of Animal Science, State University of Acaraú Valley (UVA), Sobral, CE, 62040-370, Brazil
| | - Natan Donato Roriz
- Department of Animal Science, State University of Acaraú Valley (UVA), Sobral, CE, 62040-370, Brazil
| | - Robson Mateus Freitas Silveira
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo (USP), Av. Pádua Dias, 11, Piracicaba, SP, 13.418-900, Brazil.
| | | | | | | | - Genilson César Alves
- Department of Animal Science, State University of Acaraú Valley (UVA), Sobral, CE, 62040-370, Brazil
| | - Josiel Ferreira
- Department of Animal Science, Federal Rural University of the Semi-arid (UFERSA), Mossoró, RN, 59625-900, Brazil
| | - Gerson Barreto Mourão
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo (USP), Av. Pádua Dias, 11, Piracicaba, SP, 13.418-900, Brazil
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de Souza TC, de Souza TC, Mourão GB, Lehmann Coutinho L, Rovadoscki GA, Pedrosa VB, Costa RB, de Camargo GMF, de Carvalho GGP, Pinto LFB. Genome-wide association for plasma albumin concentration in sheep. Anim Genet 2021; 52:898-900. [PMID: 34590327 DOI: 10.1111/age.13144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/17/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Taiana Cortez de Souza
- Federal University of Bahia - 500, Av. Adhemar de Barros, Salvador, BA, 40170110, Brazil
| | | | | | | | | | - Victor Breno Pedrosa
- State University of Ponta Grossa - 4748, Av. General Carlos Cavalcanti, Ponta Grossa, PR, 84030900, Brazil
| | - Raphael Bermal Costa
- Federal University of Bahia - 500, Av. Adhemar de Barros, Salvador, BA, 40170110, Brazil
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Ramírez Toro EJ, Mourão GB, Martínez Sarmiento RA, Cerón-Muñoz MF. Genetic selection indices for growth traits in Blanco-Orejinegro cattle. Transl Anim Sci 2021; 5:txab133. [PMID: 34476348 PMCID: PMC8404612 DOI: 10.1093/tas/txab133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/09/2021] [Indexed: 11/30/2022] Open
Abstract
Selection indices are used in genetic improvement programs, with the purpose of selectins simultaneous for several economically important traits. The objective of this study was to construct equations for selection indices in the Blanco-Orejinegro (BON) breed and to determine the index that would generate the greatest genetic progress. The information used included birth weight (BW), body weights adjusted to 120, 240, 480, and 720 days old (W120, W240, W240, 480 and W720, respectively), age at first calving (AFC) and interval between first and second calving (IBC) estimated breeding values. Two Smith and Hazel indices were calculated using variances (I1) and literature (I2), with a part two indices designed using information from experts and breeders (I3 and I4). All the indices favored the reduction of weight at birth. The I1 focused mainly on W120 and I2, I3 and I4 focused on 720. In general, the estimated indices obtained similar reliability and expected genetic differences I1 generated a decrease in direct BW. I2 generated the largest increases in BW and AFC. I3 and I4 generated positive changes in growth and reproductive traits, with I3 generating the greatest genetic gains in the population, especially for W240.
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Affiliation(s)
- Edison J Ramírez Toro
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Nus Research Center, San Roque, Antioquia, Colombia.,GAMMA Research Group, Faculty of Agrarian Science, Universidad de Antioquia UdeA, Medellín, Colombia
| | | | - Rodrigo A Martínez Sarmiento
- Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Tibaitata Research Center, Mosquera, Cundinamarca, Colombia
| | - Mario F Cerón-Muñoz
- GAMMA Research Group, Faculty of Agrarian Science, Universidad de Antioquia UdeA, Medellín, Colombia
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Santos ACPD, Santos EM, Carvalho GGPD, Pinto LFB, Pina DS, Perazzo AF, Oliveira JSD, Mourão GB, Nascimento TVC, Cruz GFDL. Productive and metabolic parameters, carcass and meat characteristics of lambs fed sorghum silage treated with urea and Lactobacillus buchneri. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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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: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Carrara ER, Petrini J, Salvian M, de Oliveira HR, Rovadoscki GA, Iung LHDS, Miquilini M, Machado PF, Mourão GB. Genetic parameters for milk yield and quality traits of Brazilian Holstein cows as a function of temperature and humidity index. J Anim Breed Genet 2021; 138:643-654. [PMID: 34184799 DOI: 10.1111/jbg.12636] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/11/2021] [Accepted: 06/11/2021] [Indexed: 11/29/2022]
Abstract
Measurements of milk yield (MY), somatic cell score (SCS), percentage of fat (FP), protein (PP), lactose (LP), casein (CP) and percentage of palmitic (C16:0), stearic (C18:0), oleic (C18:1), total saturated (SFA), unsaturated (UFA), monounsaturated (MUFA) and polyunsaturated (PUFA) fatty acids in milk from 5,224 Holstein cows were evaluated as a function of a temperature and humidity index (THI). Legendre orthogonal polynomials from second to seventh order were tested. The best fit order for MY, PP and C18:0 was the third, whereas the second for all other traits. The heritability estimates decreased for MY (0.31 to 0.14), FP (0.28 to 0.16), LP (0.43 to 0.30), SCS (0.14 to 0.09), SFA (0.33 to 0.22) and C16:0 (0.31 to 0.26), whereas increased for CP (0.32 to 0.42), MUFA (0.08 to 0.13), UFA (0.07 to 0.11) and C18:1 (0.07 to 0.11) as the THI level increased. For PP, heritabilities (0.26 to 0.39) presented larger values in intermediate THI. For PUFA and C18:0, heritabilities were approximately constant (0.13 to 0.14 and 0.15, respectively). However, the greatest variations may have been the result of the limitations of Legendre polynomials at the extreme points of the curve, and the pattern of heritabilities curves was approximately constant for the evaluated traits. Spearman's rank correlations between breeding values in extreme THI levels were greater than 0.80 for all traits considering all animals, only cows and only bulls. When considering the top 1% and the top 50% animals (only cows, only bulls and all), Spearman correlations smaller than 0.70 were found, suggesting reranking of the animals. Although there was little variation in the variance components over THI, it is possible that there is no heat stress in the animals studied, because, on average, there was no great impact of the thermal load on the traits. One possible explanation is the use of herds with little climatic difference among herds, as well as the use of fans and sprinklers into the barns. However, the THI levels may be important factors in the selection process, as reranking of animals was verified.
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Affiliation(s)
| | - Juliana Petrini
- Department of Animal Science, University of São Paulo, Piracicaba, Brazil
| | - Mayara Salvian
- Department of Animal Science, University of São Paulo, Piracicaba, Brazil
| | - Hinayah Rojas de Oliveira
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Canada
| | | | | | - Marina Miquilini
- Department of Animal Science, University of São Paulo, Piracicaba, Brazil
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Malheiros JM, Correia BSB, Ceribeli C, Cardoso DR, Colnago LA, Junior SB, Reecy JM, Mourão GB, Coutinho LL, Palhares JCP, Berndt A, de Almeida Regitano LC. Comparative untargeted metabolome analysis of ruminal fluid and feces of Nelore steers (Bos indicus). Sci Rep 2021; 11:12752. [PMID: 34140582 PMCID: PMC8211696 DOI: 10.1038/s41598-021-92179-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 06/07/2021] [Indexed: 02/05/2023] Open
Abstract
We conducted a study to identify the fecal metabolite profile and its proximity to the ruminal metabolism of Nelore steers based on an untargeted metabolomic approach. Twenty-six Nelore were feedlot with same diet during 105 d. Feces and rumen fluid were collected before and at slaughter, respectively. The metabolomics analysis indicated 49 common polar metabolites in the rumen and feces. Acetate, propionate, and butyrate were the most abundant polar metabolites in both bio-samples. The rumen presented significantly higher concentrations of the polar compounds when compared to feces (P < 0.05); even though, fecal metabolites presented an accentuated representability of the ruminal fluid metabolites. All fatty acids present in the ruminal fluid were also observed in the feces, except for C20:2n6 and C20:4n6. The identified metabolites offer information on the main metabolic pathways (higher impact factor and P < 0.05), as synthesis and degradation of ketone bodies; the alanine, aspartate and glutamate metabolisms, the glycine, serine; and threonine metabolism and the pyruvate metabolism. The findings reported herein on the close relationship between the ruminal fluid and feces metabolic profiles may offer new metabolic information, in addition to facilitating the sampling for metabolism investigation in animal production and health routines.
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Affiliation(s)
| | | | - Caroline Ceribeli
- Chemistry Institute of São Carlos, University of São Paulo/USP, São Carlos, São Paulo, Brazil
| | | | | | - Stanislau Bogusz Junior
- Chemistry Institute of São Carlos, University of São Paulo/USP, São Carlos, São Paulo, Brazil
| | - James Mark Reecy
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Gerson Barreto Mourão
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
| | - Luiz Lehmann Coutinho
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, São Paulo, Brazil
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35
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de Souza TC, de Souza TC, Rovadoscki GA, Coutinho LL, Mourão GB, de Camargo GMF, Costa RB, de Carvalho GGP, Pedrosa VB, Pinto LFB. Genome-wide association for plasma urea concentration in sheep. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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da Silva Magalhães T, Santos EM, de Freitas Júnior JE, Santos SA, dos Santos Pina D, Cirne LGA, Pinto LFB, Mourão GB, dos Santos Soares FD, Leite LC, Ruiz Alba HD, Tosto MSL, de Carvalho GGP. Chitosan and cottonseed processing method association on carcass traits and meat quality of feedlot lambs. PLoS One 2020; 15:e0242822. [PMID: 33227032 PMCID: PMC7682818 DOI: 10.1371/journal.pone.0242822] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 11/10/2020] [Indexed: 11/18/2022] Open
Abstract
The objective of this study was to evaluate the effects of the association of cottonseed processing method with chitosan on carcass traits and meat quality of lambs finished in feedlot. Eighty lambs with an average body weight of 20.6 kg, with 04 months of age, were distributed in a completely randomized design, in a 2 x 2 factorial arrangement. The factors were represented by two cottonseed processing method (whole or ground) and two levels of chitosan (0 and 136 mg/kg BW). The association of cottonseed processing method with chitosan in the lamb diet did not affect (P>0.05) carcasses traits. The pH, color, cooking losses, shear force, and proximate composition of meat were also not affected (P>0.05) by the processing method of cottonseed or its association with chitosan in the lamb diets. There was an increase in palmitoleic (c9-C16:1; P = 0.01) and conjugated linoleic (P = 0.02) fatty acids when ground cottonseed was associated with chitosan. Ground cottonseed associated with chitosan increases the concentration of unsaturated fatty acids in the meat of feedlot lambs.
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Affiliation(s)
| | - Edson Mauro Santos
- Department of Animal Science, Federal University of Paraiba, Areia, Paraíba, Brazil
| | | | | | | | - Luis Gabriel Alves Cirne
- Institute of Biodiversity and Forestry, Federal University of Western Pará, Santarém, Pará, Brazil
| | | | - Gerson Barreto Mourão
- Department of Animal Science, University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Laudí Cunha Leite
- Department of Animal Science, Federal University of Recôncavo da Bahia, Cruz das Almas, Bahia, Brazil
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Sousa-Junior LPB, Meira AN, Azevedo HC, Muniz EN, Coutinho LL, Mourão GB, Leão AG, Pedrosa VB, Pinto LFB. Variants in myostatin and MyoD family genes are associated with meat quality traits in Santa Inês sheep. Anim Biotechnol 2020; 33:201-213. [PMID: 32633608 DOI: 10.1080/10495398.2020.1781651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Myostatin and MyoD family genes play vital roles in myogenesis and this study aimed to identify association of variants in MyoD1, MyoG, MyF5, MyF6, and MSTN genes with meat traits in Santa Inês sheep. A dataset with 44 variants and records of seven meat traits in 192 lambs (pH0, pH24, a*, b*, L*, tenderness assessed by shear force, and water-holding capacity) was used. Single-locus and haplotype association analyses were performed, and the significance threshold was established according to Bonferroni's method. Single-locus analysis revealed two associations at a Bonferroni level, where the variant c.935-185C > G in MyoD1 had an additive effect (-4.31 ± 1.08 N) on tenderness, while the variant c.464 + 185G > A in MyoG had an additive effect (-2.86 ± 0.64) on a*. Additionally, the haplotype replacement GT>AC in MSTN was associated with pH0 (1.26 ± 0.31), pH24 (1.07 ± 0.27), a* (-1.40 ± 0.51), and tenderness (3.83 ± 1.22 N), while the replacement GT > AG in MyoD1 was associated with pH0 (1.43 ± 0.26), pH24 (1.25 ± 0.22), b* (-1.06 ± 0.39), and tenderness (-4.13 ± 1.16 N). Our results have demonstrated that some variants in MyoG, MyF6, MyoD1, and MSTN can be associated with physicochemical meat traits in Santa Inês sheep.
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Affiliation(s)
| | | | | | | | | | | | - André Gustavo Leão
- Instituto de Ciências Agrárias e Tecnológicas, Universidade Federal de Mato Grosso, Rondonópolis, MT, Brazil
| | - Victor Breno Pedrosa
- Departamento de Zootecnia, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brazil
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Afonso J, Fortes MRS, Reverter A, Diniz WJDS, Cesar ASM, Lima AOD, Petrini J, de Souza MM, Coutinho LL, Mourão GB, Zerlotini A, Gromboni CF, Nogueira ARA, Regitano LCDA. Genetic regulators of mineral amount in Nelore cattle muscle predicted by a new co-expression and regulatory impact factor approach. Sci Rep 2020; 10:8436. [PMID: 32439843 PMCID: PMC7242321 DOI: 10.1038/s41598-020-65454-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 05/04/2020] [Indexed: 12/11/2022] Open
Abstract
Mineral contents in bovine muscle can affect meat quality, growth, health, and reproductive traits. To better understand the genetic basis of this phenotype in Nelore (Bos indicus) cattle, we analysed genome-wide mRNA and miRNA expression data from 114 muscle samples. The analysis implemented a new application for two complementary algorithms: the partial correlation and information theory (PCIT) and the regulatory impact factor (RIF), in which we included the estimated genomic breeding values (GEBVs) for the phenotypes additionally to the expression levels, originally proposed for these methods. We used PCIT to determine putative regulatory relationships based on significant associations between gene expression and GEBVs for each mineral amount. Then, RIF was adopted to determine the regulatory impact of genes and miRNAs expression over the GEBVs for the mineral amounts. We also investigated over-represented pathways, as well as pieces of evidences from previous studies carried in the same population and in the literature, to determine regulatory genes for the mineral amounts. For example, NOX1 expression level was positively correlated to Zinc and has been described as Zinc-regulated in humans. Based on our approach, we were able to identify genes, miRNAs and pathways not yet described as underlying mineral amount. The results support the hypothesis that extracellular matrix interactions are the core regulator of mineral amount in muscle cells. Putative regulators described here add information to this hypothesis, expanding the knowledge on molecular relationships between gene expression and minerals.
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Affiliation(s)
- Juliana Afonso
- Department of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil
| | - Marina Rufino Salinas Fortes
- School of Chemistry and Molecular Biosciences, Faculty of Sciences, The University of Queensland, Brisbane, Australia
| | - Antonio Reverter
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia
| | | | - Aline Silva Mello Cesar
- Department of Agroindustry, Food and Nutrition, University of São Paulo/ESALQ, Piracicaba, Brazil
| | - Andressa Oliveira de Lima
- Department of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil
| | - Juliana Petrini
- Department of Statistics, Institute of Exact Sciences, Federal University of Alfenas, Alfenas, Brazil
| | | | | | - Gerson Barreto Mourão
- Department of Agroindustry, Food and Nutrition, University of São Paulo/ESALQ, Piracicaba, Brazil
| | - Adhemar Zerlotini
- Bioinformatic Multi-user Laboratory, Embrapa Informática Agropecuária, Campinas, São Paulo, Brazil
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Bittar CMM, Gallo MP, Silva JT, de Paula MR, Poczynek M, Mourão GB. Gradual weaning does not improve performance for calves with low starter intake at the beginning of the weaning process. J Dairy Sci 2020; 103:4672-4680. [PMID: 32173018 DOI: 10.3168/jds.2019-17614] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/09/2020] [Indexed: 02/03/2023]
Abstract
The weaning process may cause intense stress for dairy calves, even when low volumes of liquid diet are fed. Management tools that increase the intake of solid feeds, such as gradual weaning, can provide better physiological and metabolic conditions through better ruminal development, leading to better adaptation to ruminant metabolism and aiding in stress mitigation. The objective of this study was to evaluate the effects of 2 weaning protocols and 2 levels of concentrate intake on the performance and physiological and behavioral variables related to stress in dairy calves. Thirty-six newborn male Holstein calves were used in a randomized block design with a 2 × 2 factorial arrangement: 2 weaning strategies, abrupt or gradual, and 2 levels of concentrate intake at 5 wk of age, high (>350 g/d) or low (≤350 g/d). Calves were equally managed until they were 5 wk of age and then grouped according to concentrate intake. Statistical analyzes were performed using the MIXED procedure of SAS software (SAS Institute Inc., Cary, NC), and no significant interaction was observed between studied factors (weaning method and starter intake level); therefore, we considered each factor separately and their interactions with age. The highest dry matter intake and concentration of β-hydroxybutyrate were recorded for animals with a high level of starter intake independent of the weaning method. Structural growth (cm/wk) and average daily gain were superior for calves with high starter intake, but weaning method had no effect. The gradual weaning protocol increased the time eating starter, regardless of the level of concentrate intake. Even animals with low concentrate intake that were weaned abruptly showed levels of cortisol and acid-soluble glycoprotein within normal physiological levels. Apparently, other factors besides the milk supply affect the starter intake level of calves in a conventional feeding program. The adoption of gradual weaning is not effective in improving performance when a calf has low intake 3 wk before weaning is complete, but it reduced vocalization on d 2 postweaning.
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Affiliation(s)
- C M M Bittar
- Department of Animal Science, University of Sao Paulo, Piracicaba, SP 13418900 Brazil.
| | - M P Gallo
- Department of Animal Science, University of Sao Paulo, Piracicaba, SP 13418900 Brazil
| | - J T Silva
- Department of Animal Science, University of Sao Paulo, Piracicaba, SP 13418900 Brazil
| | - M R de Paula
- Department of Animal Science, University of Sao Paulo, Piracicaba, SP 13418900 Brazil
| | - M Poczynek
- Department of Animal Science, University of Sao Paulo, Piracicaba, SP 13418900 Brazil
| | - G B Mourão
- Department of Animal Science, University of Sao Paulo, Piracicaba, SP 13418900 Brazil
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40
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Carrara ER, de Genova Gaya L, de Paiva JT, Petrini J, Salvian M, Rovadoscki GA, Chaves Zanetti Reis A, Machado PF, Barreto Mourão G. Impact of inbreeding on milk fatty acids of a Brazilian Holstein cattle. Anim Prod Sci 2020. [DOI: 10.1071/an19240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context
Reproductive technologies may either contribute to the increase of genetic gains or inbreeding levels in dairy cattle breeding programs and herds. In general, studies have evaluated the impacts of inbreeding on traditional traits, such as production and reproduction. However, studies on novel traits, such as milk fatty acids profile, are scarce in the literature.
Aim
We aimed to evaluate the impact of inbreeding levels on milk fatty acids profile measured in a Brazilian Holstein cattle population.
Methods
Monthly records of the percentages (%) of palmitic, stearic, oleic, total saturated, unsaturated, monounsaturated and polyunsaturated fatty acids in milk were collected from 2047 Holstein cows between May and December 2012. The pedigree file contained 7963 animals over seven generations. The inbreeding trend was evaluated by linear regression of inbreeding coefficients on generations. The inbreeding impacts on breeding and phenotypic values were evaluated by linear regression of breeding values and phenotypic values on generations respectively. Breeding values were obtained by a Bayesian approach based on an animal model that included the systematic effect of contemporary group, cubic effect of days in milk as a covariate, and the random direct additive genetic and animal permanent environmental effects.
Key results
The average inbreeding coefficient was 0.28% for all animals, and 1.39% for inbred animals. Inbreeding tended to increase 0.24% per generation (P-value <0.0001). The regression coefficients of phenotypic values on inbreeding were not significant for saturated, unsaturated, monounsaturated, palmitic, stearic and oleic fatty acids (P-values >0.18, 0.10, 0.16, 0.26, 0.51 and 0.09 respectively); whereas for polyunsaturated fatty acids, they were significant (P-value <0.04), with an increase of –0.000978% on phenotypic values for each 1% increase in inbreeding. The regression coefficients of breeding values on inbreeding were not significant for unsaturated, monounsaturated, polyunsaturated, stearic and oleic fatty acids (P-values >0.33, 0.78, 0.48, 0.32 and 0.07 respectively). However, they were significant for saturated and palmitic fatty acids (P-values <0.03 and 0.0001 respectively), presenting an increase of 0.000689% and 0.000283% respectively on breeding values for each 1% increase in inbreeding.
Conclusions
There was a significant increase in inbreeding coefficients over the studied generations; however, the impacts on both breeding and phenotypic values were small, when significant.
Implications
Our study may contribute to the understanding of how inbreeding levels may affect the fatty acids profile in a Brazilian Holstein cattle population, as well as encourage future research on this subject.
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Petrini J, Souza Iung LH, Petersen Rodriguez MA, Salvian M, Alberto Rovadoscki G, Colonia SRR, Cassoli LD, Lehmann Coutinho L, Fernando Machado P, Wiggans G, Mourão GB. Assessing the accuracy of prediction for milk fatty acids by using a small reference population of tropical Holstein cows. J Anim Breed Genet 2019; 136:453-463. [DOI: 10.1111/jbg.12434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 08/01/2019] [Accepted: 08/05/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Juliana Petrini
- Department of Animal Science University of São Paulo Piracicaba Brazil
- Department of Statistics, Institute of Exact Sciences Federal University of Alfenas Alfenas Brazil
| | | | | | - Mayara Salvian
- Department of Animal Science University of São Paulo Piracicaba Brazil
| | | | | | | | | | | | - George Wiggans
- Animal Genomics and Improvement Laboratory, Agricultural Research Service USDA Beltsville Maryland
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [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. Electronic supplementary material The online version of this article (10.1186/s12864-019-6040-3) contains supplementary material, which is available to authorized users.
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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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Salvian M, Mourão GB, Moreira GCM, Ledur MC, Coutinho LL, Spangler ML. 60 Re-ranking of estimated breeding values using different panel densities with ssGBLUP in broiler chickens. J Anim Sci 2019. [DOI: 10.1093/jas/skz122.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
The aim of this study was to compare the rank of estimated breeding values (EBV) for organs (heart, liver, lungs and gizzard) and carcass (breast, thigh and drumstick) traits using pedigree-based BLUP (PBLUP) and single-step genomic BLUP (ssGBLUP) models. A total of 1,453 chickens (703 males and 750 females) from a paternal broiler (TT) reference population belonging to the Poultry Breeding Program from Embrapa Swine and Poultry were genotyped with the Axiom® Genome-Wide Chicken Genotyping Array (Affymetrix) 600K SNP panel. Samples with a call rate lower than 90% were removed. A SNP quality control was applied for removing SNP with call rate lower than 98%, MAF lower than 2% and significant deviations from HWE (p-value < 10–7) leaving 370,608 SNP for further analysis. Estimated breeding values were predicted using the blupf90 family of programs whereby a series of bi-variate animal models that included sex and hatching as fixed effects were fitted. Heritability estimates for carcass and organ traits obtained through PBLUP varied from low (0.16) for lungs to moderate (0.34 to 0.47) for heart, liver, gizzard, breast, thigh and drumstick. The genomic heritability estimates through ssGBLUP varied from low (0.14) for lungs to moderate (0.30 to .041) for all other traits. Five subsets (5, 10, 20, 40 and 80% of SNP) were randomly selected from the full SNP set to determine the impact, in terms of EBV rank, of using reduced subsets of SNP to inform relationships among individuals. Although the 5% subset of SNP consistently had the lowest correlation with the full set of SNP, all correlations were greater than 0.995. Results suggest that a relatively limited proportion of SNP could be used to reliably predict EBV via ssGBLUP in this population.
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Iung LHS, Petrini J, Ramírez-Díaz J, Salvian M, Rovadoscki GA, Pilonetto F, Dauria BD, Machado PF, Coutinho LL, Wiggans GR, Mourão GB. Genome-wide association study for milk production traits in a Brazilian Holstein population. J Dairy Sci 2019; 102:5305-5314. [PMID: 30904307 DOI: 10.3168/jds.2018-14811] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 10/19/2018] [Indexed: 12/19/2022]
Abstract
Advances in the molecular area of selection have expanded knowledge of the genetic architecture of complex traits through genome-wide association studies (GWAS). Several GWAS have been performed so far, but confirming these results is not always possible due to several factors, including environmental conditions. Thus, our objective was to identify genomic regions associated with traditional milk production traits, including milk yield, somatic cell score, fat, protein and lactose percentages, and fatty acid composition in a Holstein cattle population producing under tropical conditions. For this, 75,228 phenotypic records from 5,981 cows and genotypic data of 56,256 SNP from 1,067 cows were used in a weighted single-step GWAS. A total of 46 windows of 10 SNP explaining more than 1% of the genetic variance across 10 Bos taurus autosomes (BTA) harbored well-known and novel genes. The MGST1 (BTA5), ABCG2 (BTA6), DGAT1 (BTA14), and PAEP (BTA11) genes were confirmed within some of the regions identified in our study. Potential novel genes involved in tissue damage and repair of the mammary gland (COL18A1), immune response (LTTC19), glucose homeostasis (SLC37A1), synthesis of unsaturated fatty acids (LTBP1), and sugar transport (SLC37A1 and MFSD4A) were found for milk yield, somatic cell score, fat percentage, and fatty acid composition. Our findings may assist genomic selection by using these regions to design a customized SNP array to improve milk production traits on farms with similar environmental conditions.
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Affiliation(s)
- L H S Iung
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo 13418900, Brazil
| | - J Petrini
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo 13418900, Brazil
| | - J Ramírez-Díaz
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo 13418900, Brazil
| | - M Salvian
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo 13418900, Brazil
| | - G A Rovadoscki
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo 13418900, Brazil
| | - F Pilonetto
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo 13418900, Brazil
| | - B D Dauria
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo 13418900, Brazil
| | - P F Machado
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo 13418900, Brazil
| | - L L Coutinho
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo 13418900, Brazil
| | - G R Wiggans
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350
| | - G B Mourão
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo 13418900, Brazil.
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Gonçalves TM, de Almeida Regitano LC, Koltes JE, Cesar ASM, da Silva Andrade SC, Mourão GB, Gasparin G, Moreira GCM, Fritz-Waters E, Reecy JM, Coutinho LL. Gene Co-expression Analysis Indicates Potential Pathways and Regulators of Beef Tenderness in Nellore Cattle. Front Genet 2018; 9:441. [PMID: 30344530 PMCID: PMC6182065 DOI: 10.3389/fgene.2018.00441] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 09/14/2018] [Indexed: 12/13/2022] Open
Abstract
Beef tenderness, a complex trait affected by many factors, is economically important to beef quality, industry, and consumer’s palatability. In this study, RNA-Seq was used in network analysis to better understand the biological processes that lead to differences in beef tenderness. Skeletal muscle transcriptional profiles from 24 Nellore steers, selected by extreme estimated breeding values (EBVs) for shear force after 14 days of aging, were analyzed and 22 differentially expressed transcripts were identified. Among these were genes encoding ribosomal proteins, glutathione transporter ATP-binding cassette, sub-family C (CFTR/MRP), member 4 (ABCC4), and synaptotagmin IV (SYT4). Complementary co-expression analyses using Partial Correlation with Information Theory (PCIT), Phenotypic Impact Factor (PIF) and the Regulatory Impact Factor (RIF) methods identified candidate regulators and related pathways. The PCIT analysis identified ubiquitin specific peptidase 2 (USP2), growth factor receptor-bound protein 10 (GBR10), anoctamin 1 (ANO1), and transmembrane BAX inhibitor motif containing 4 (TMBIM4) as the most differentially hubbed (DH) transcripts. The transcripts that had a significant correlation with USP2, GBR10, ANO1, and TMBIM4 enriched for proteasome KEGG pathway. RIF analysis identified microRNAs as candidate regulators of variation in tenderness, including bta-mir-133a-2 and bta-mir-22. Both microRNAs have target genes present in the calcium signaling pathway and apoptosis. PIF analysis identified myoglobin (MB), enolase 3 (ENO3), and carbonic anhydrase 3 (CA3) as potentially having fundamental roles in tenderness. Pathways identified in our study impacted in beef tenderness included: calcium signaling, apoptosis, and proteolysis. These findings underscore some of the complex molecular mechanisms that control beef tenderness in Nellore cattle.
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Affiliation(s)
| | | | - James E Koltes
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | | | - Sónia Cristina da Silva Andrade
- Department of Animal Science, University of São Paulo, Piracicaba, Brazil.,Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, Brazil
| | | | - Gustavo Gasparin
- Department of Animal Science, University of São Paulo, Piracicaba, Brazil
| | | | - Elyn Fritz-Waters
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - James M Reecy
- Department of Animal Science, Iowa State University, Ames, IA, United States
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Alvarenga AB, Rovadoscki GA, Petrini J, Coutinho LL, Morota G, Spangler ML, Pinto LFB, Carvalho GGP, Mourão GB. Linkage disequilibrium in Brazilian Santa Inês breed, Ovis aries. Sci Rep 2018; 8:8851. [PMID: 29892085 PMCID: PMC5995818 DOI: 10.1038/s41598-018-27259-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 05/25/2018] [Indexed: 11/13/2022] Open
Abstract
For genomic selection to be successful, there must be sufficient linkage disequilibrium between the markers and the causal mutations. The objectives of this study were to evaluate the extent of LD in ovine using the Santa Inês breed and to infer the minimum number of markers required to reach reasonable prediction accuracy. In total, 38,168 SNPs and 395 samples were used. The mean LD between adjacent marker pairs measured by r2 and |D′| were 0.166 and 0.617, respectively. LD values between adjacent marker pairs ranged from 0.135 to 0.194 and from 0.568 to 0.650 for r2 for |D′| across all chromosomes. The average r2 between all pairwise SNPs on each chromosome was 0.018. SNPs separated by between 0.10 to 0.20 Mb had an estimated average r2 equal to 0.1033. The identified haplotype blocks consisted of 2 to 21 markers. Moreover, estimates of average coefficients of inbreeding and effective population size were 0.04 and 96, respectively. LD estimated in this study was lower than that reported in other species and was characterized by short haplotype blocks. Our results suggest that the use of a higher density SNP panel is recommended for the implementation of genomic selection in the Santa Inês breed.
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Affiliation(s)
- Amanda Botelho Alvarenga
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, SP, Brazil
| | - Gregori Alberto Rovadoscki
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, SP, Brazil
| | - Juliana Petrini
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, SP, Brazil
| | - Luiz Lehmann Coutinho
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, SP, Brazil
| | - Gota Morota
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | | | | | | | - Gerson Barreto Mourão
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, SP, Brazil.
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Mattos FCSZ, Canavessi AMO, Wiltbank MC, Bastos MR, Lemes AP, Mourão GB, Susin I, Coutinho LL, Sartori R. Investigation of mechanisms involved in regulation of progesterone catabolism using an overfed versus underfed ewe-lamb model. J Anim Sci 2018; 95:5537-5546. [PMID: 29293746 DOI: 10.2527/jas2017.1719] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Alterations in progesterone (P4) catabolism due to high feed intake underlie some effects of nutrition on reproduction. Based on previous research, we hypothesized that high feed intake could potentially increase P4 catabolism, likely due to increased liver blood flow. However, there could also be an opposing action due to increased circulating insulin, which has been shown to inhibit hepatic expression of key enzymes involved in P4 catabolism. To test which effect would have the greatest impact on circulating P4 during a 1- and 2 -mo time frame, we used a noncyclic ewe model. The plane of nutrition was controlled, and effects on circulating insulin, P4 catabolism in response to exogenous P4, and steady state mRNA for key hepatic enzymes were evaluated. Twenty-four F Dorper × Santa Inês ewe lambs (5 mo old and approximately 25 kg BW) were used. After 14 d of adaptation, ewes were randomized into 2 groups: ad libitum fed (Ad), with intake of 3.8% DM/kg BW, or restricted feed intake (R), with 2% DM/kg BW, for 8 wk. At wk 4 and 8, ewes received an intravaginal P4 implant to evaluate P4 catabolism. As designed, Ad ewes had greater daily feed intake than R ewes (means of 1.8 [SE 0.03] and 0.6 kg/ewe [SE 0.01]; < 0.001) and greater weekly gain in BW (means of 1.7 [SE 0.12] vs. -0.1 kg/ewe [SE 0.03]; < 0.001). Mean circulating insulin of samples collected from -0.5 to 7 h after the start of feeding was over 5-fold greater in Ad ewes than in R ewes (least squares means of 8.2 [SE 0.93] vs. 1.5 μIU/mL [SE 0.16], respectively, at wk 4 and 12.0 [SE 1.02] vs. 2.2 μIU/mL [SE 0.18], respectively, at wk 8; < 0.001). Although both groups received the same P4 treatment, mean circulating P4 of samples collected from -0.5 to 7 h after feeding was much lower in Ad ewes than in R ewes (least squares means of 3.2 [SE 0.32] vs. 5.5 ng/mL [SE 0.32], respectively, at wk 4 and 2.8 [SE 0.28] vs. 5.2 ng/mL [SE 0.28], respectively, at wk 8; < 0.001) indicating much greater P4 catabolism in ewes with high feed intake. Unexpectedly, there was no effect of diet on hepatic mRNA concentrations for , , , or at wk 4 or 8 in spite of dramatically elevated insulin. Therefore, high energy/feed intake primarily increased P4 catabolism with no evidence for offsetting effects due to insulin-induced changes in hepatic P4 metabolizing enzymes.
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Geremia EV, Crestani S, Mascheroni JDC, Carnevalli RA, Mourão GB, da Silva SC. Sward structure and herbage intake of Brachiaria brizantha cv. Piatã in a crop-livestock-forestry integration area. Livest Sci 2018. [DOI: 10.1016/j.livsci.2018.03.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Rovadoscki GA, Pertile SFN, Alvarenga AB, Cesar ASM, Pértille F, Petrini J, Franzo V, Soares WVB, Morota G, Spangler ML, Pinto LFB, Carvalho GGP, Lanna DPD, Coutinho LL, Mourão GB. Estimates of genomic heritability and genome-wide association study for fatty acids profile in Santa Inês sheep. BMC Genomics 2018; 19:375. [PMID: 29783944 PMCID: PMC5963081 DOI: 10.1186/s12864-018-4777-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 05/10/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Despite the health concerns and nutritional importance of fatty acids, there is a relative paucity of studies in the literature that report genetic or genomic parameters, especially in the case of sheep populations. To investigate the genetic architecture of fatty acid composition of sheep, we conducted genome-wide association studies (GWAS) and estimated genomic heritabilities for fatty acid profile in Longissimus dorsi muscle of 216 male sheep. RESULTS Genomic heritability estimates for fatty acid content ranged from 0.25 to 0.46, indicating that substantial genetic variation exists for the evaluated traits. Therefore, it is possible to alter fatty acid profiles through selection. Twenty-seven genomic regions of 10 adjacent SNPs associated with fatty acids composition were identified on chromosomes 1, 2, 3, 5, 8, 12, 14, 15, 16, 17, and 18, each explaining ≥0.30% of the additive genetic variance. Twenty-three genes supporting the understanding of genetic mechanisms of fat composition in sheep were identified in these regions, such as DGAT2, TRHDE, TPH2, ME1, C6, C7, UBE3D, PARP14, and MRPS30. CONCLUSIONS Estimates of genomic heritabilities and elucidating important genomic regions can contribute to a better understanding of the genetic control of fatty acid deposition and improve the selection strategies to enhance meat quality and health attributes.
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Affiliation(s)
- G A Rovadoscki
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - S F N Pertile
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - A B Alvarenga
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - A S M Cesar
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - F Pértille
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - J Petrini
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - V Franzo
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - W V B Soares
- Institute of Zootechny (IZ), Nova Odessa, SP, Brazil
| | - G Morota
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | - M L Spangler
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | - L F B Pinto
- Department of Animal Science, Federal University of Bahia (UFBA), Salvador, BA, Brazil
| | - G G P Carvalho
- Department of Animal Science, Federal University of Bahia (UFBA), Salvador, BA, Brazil
| | - D P D Lanna
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - L L Coutinho
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil
| | - G B Mourão
- Department of Animal Science, University of São Paulo (USP) / Luiz de Queiroz College of Agriculture (ESALQ), Av. Pádua Dias, 11, ESALQ/USP, Piracicaba, São Paulo, 13418-900, Brazil.
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de Paula MR, Oltramari CE, Silva JT, Gallo MPC, Mourão GB, Bittar CMM. Intensive liquid feeding of dairy calves with a medium crude protein milk replacer: Effects on performance, rumen, and blood parameters. J Dairy Sci 2017; 100:4448-4456. [PMID: 28365119 DOI: 10.3168/jds.2016-10859] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 02/11/2017] [Indexed: 11/19/2022]
Abstract
The objective of this study was to evaluate the effects of different liquid-feeding systems using a medium crude protein milk replacer on performance, rumen, and blood parameters. Thirty newborn Holstein calves were blocked according to birth weight and date of birth, and randomly distributed to different liquid-feeding systems: conventional (4 L/d), intensive (8 L/d), or step-up/step-down (wk 1, 4 L/d; wk 2 to 6, 8 L/d; wk 7 and 8, 4 L/d). The commercial milk replacer (12.5% solids, 20.2% crude protein, 15.6% fat) was fed twice daily (0700 and 1700 h) until calves were weaned, at 8 wk of age. Calves were individually housed in wood hutches, with free access to water and starter concentrate, and to hay only after weaning. They were followed through 10 wk of age. Milk replacer and starter intake were inversely affected by feeding system. After weaning, starter intake and hay intake were similar among feeding systems. Total dry matter intake was higher during the liquid-feeding period for calves on the intensive system compared to calves on the conventional system, but conventional feeding resulted in the highest dry matter intake after weaning. Feed efficiency was similar among feeding systems before and after weaning. Average body weight and daily gain were not affected by feeding system before or after weaning. During liquid feeding, diarrhea occurrence was lower for calves on the conventional system; however, when calves on the step-up/step-down system were fed lower volumes of liquid feed, diarrhea occurrence was similar to that of calves on the conventional system. Plasma concentrations of β-hydroxybutyrate were higher for calves on the conventional system, reflecting starter intake. Rumen pH, short-chain fatty acids, and N-NH3 were not affected by feeding system. Feeding higher volumes of milk replacer with a medium crude protein content had no beneficial effect on the performance of calves up to 10 wk of age.
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Affiliation(s)
- M R de Paula
- Department of Animal Sciences, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, 13418-900, Brazil
| | - C E Oltramari
- Department of Animal Sciences, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, 13418-900, Brazil
| | - J T Silva
- Department of Animal Sciences, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, 13418-900, Brazil
| | - M P C Gallo
- Department of Animal Sciences, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, 13418-900, Brazil
| | - G B Mourão
- Department of Animal Sciences, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, 13418-900, Brazil
| | - C M M Bittar
- Department of Animal Sciences, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, 13418-900, Brazil.
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