Search

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.

Made available in DSpace on 2021-06-25T10:30:37Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-04-30 Global Change Institute, University of Queensland Institute for Molecular Bioscience, University Of Queensland Queensland Alliance for Agriculture and Food Innovation, University of Queensland Research Computing Centre, University of Queensland University of Queensland Centre for Natural Gas, University of Queensland School of Agriculture and Food Sciences, University of Queensland School of Pharmacy, University of Queensland Spermatogenesis relies on complex molecular mechanisms, essential for the genesis and differentiation of the male gamete. Germ cell differentiation starts at the testicular parenchyma and finishes in the epididymis, which has three main regions: head, body, and tail. RNA-sequencing data of the testicular parenchyma (TP), head epididymis (HE), and tail epididymis (TE) from four bulls (three biopsies per bull: 12 samples) were subjected to differential expression analyses, functional enrichment analyses, and co-expression analyses. The aim was to investigate the co-expression and infer possible regulatory roles for transcripts involved in the spermatogenesis of Bos indicus bulls. Across the three pairwise comparisons, 3,826 differentially expressed (DE) transcripts were identified, of which 384 are small RNAs. Functional enrichment analysis pointed to gene ontology (GO) terms related to ion channel activity, detoxification of copper, neuroactive receptors, and spermatogenesis. Using the regulatory impact factor (RIF) algorithm, we detected 70 DE small RNAs likely to regulate the DE transcripts considering all pairwise comparisons among tissues. The pattern of small RNA co-expression suggested that these elements are involved in spermatogenesis regulation. The 3,826 DE transcripts (mRNAs and small RNAs) were further subjected to co-expression analyses using the partial correlation and information theory (PCIT) algorithm for network prediction. Significant correlations underpinned the co-expression network, which had 2,216 transcripts connected by 158,807 predicted interactions. The larger network cluster was enriched for male gamete generation and had 15 miRNAs with significant RIF. The miRNA bta-mir-2886 showed the highest number of connections (601) and was predicted to down-regulate ELOVL3, FEZF2, and HOXA13 (negative co-expression correlations and confirmed with TargetScan). In short, we suggest that bta-mir-2886 and other small RNAs might modulate gene expression in the testis and epididymis, in Bos indicus cattle. Department of Production and Animal Health School of Veterinary Medicine São Paulo State University (UNESP) Department of Animal Science University of São Paulo/ESALQ School of Chemistry and Molecular Biosciences The University of Queensland Australian Institute for Bioengineering and Nanotechnology (AIBN) The University of Queensland CSIRO Agriculture and Food Queensland Bioscience Precinct Department of Production and Animal Health School of Veterinary Medicine São Paulo State University (UNESP)

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. Made available in DSpace on 2020-09-09T04:37:14Z (GMT). No. of bitstreams: 1 AP-Genetic-regulators-2020.pdf: 3953162 bytes, checksum: f7f057405a94ac732a64d0f4b4788219 (MD5) Previous issue date: 2020 Article: 8436.

Made available in DSpace on 2019-10-04T12:15:56Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-09-03 Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Mineral content affects the biological processes underlying beef quality. Muscle mineral concentration depends not only on intake-outtake balance and muscle type, but also on age, environment, breed, and genetic factors. To unveil the genetic factors involved in muscle mineral concentration, we applied a pairwise differential gene expression analysis in groups of Nelore steers genetically divergent for nine different mineral concentrations. Here, based on significant expression differences between contrasting groups, we presented candidate genes for the genetic regulation of mineral concentration in muscle. Functional enrichment and protein-protein interaction network analyses were carried out to search for gene regulatory processes concerning each mineral. The core genetic regulation for all minerals studied, except Zn, seems to rest on interactions between components of the extracellular matrix. Regulation of adipogenesis-related pathways was also significant in our results. Antagonistic patterns of gene expression for fatty acid metabolism-related genes may explain the Cu and Zn antagonistic effect on fatty acid accumulation. Our results shed light on the role of these minerals on cell function. Univ Fed Sao Carlos, Dept Evolutionary Genet & Mol Biol, Sao Carlos, SP, Brazil Univ Sao Paulo, Dept Anim Sci, ESALQ, Piracicaba, Brazil Embrapa Pecuaria Sudeste, Sao Carlos, SP, Brazil Univ Sao Paulo, Phys Inst Sao Carlos, Sao Carlos, SP, Brazil Sao Paulo State Univ, Anim Sci Dept, Lab Mol Genet, Jaboticabal, Brazil Bahia Fed Inst Educ Sci & Technol, Ilheus, Brazil Univ Queensland, Fac Sci, Sch Chem & Mol Biosci, Brisbane, Qld, Australia NGS Solucoes Genom, Rua Ajudante Albano 847, Piracicaba, SP, Brazil Sao Paulo State Univ, Anim Sci Dept, Lab Mol Genet, Jaboticabal, Brazil FAPESP: 2012/23638-8

Residual Feed Intake (RFI) is an economically relevant trait in beef cattle. Among the molecular regulatory mechanisms, microRNAs (miRNAs) are an important dimension in post-transcriptional regulation and have been associated with different biological pathways. Here, we performed differential miRNAs expression and weighted gene co-expression network analyses (WGCNA) to better understand the complex interactions between miRNAs and mRNAs expressed in bovine skeletal muscle and liver. MiRNA and mRNA expression data were obtained from Nelore steers that were genetically divergent for RFI (N = 10 [low RFI or feed efficient]; N = 10 [high RFI or feed inefficient]). Differentially expressed and hub miRNAs such as bta-miR-486, bta-miR-7, bta-miR15a, bta-miR-21, bta-miR 29, btamiR-30b, bta-miR-106b, bta-miR-199a-3p, bta-miR-204, and bta-miR 296 may have a potential role in variation of RFI. Functional enrichment analysis of differentially expressed (DE) miRNA?s target genes and miRNA?mRNA correlated modules revealed that insulin, lipid, immune system, oxidative stress and muscle development signaling pathways might potentially be involved in RFI in this population. Our study identified DE miRNAs, miRNA - mRNA regulatory networks and hub miRNAs related to RFI. These findings suggest a possible role of miRNAs in regulation of RFI, providing new insights into the potential molecular mechanisms that control feed efficiency in Nelore cattle. Made available in DSpace on 2018-12-22T23:31:58Z (GMT). No. of bitstreams: 1 APIntegrativeAdhemaretal.pdf: 1483055 bytes, checksum: 14efe405fca6e8d91642f5067590314b (MD5) Previous issue date: 2018-12-20 Article number: 17072. Na publicação: Adhemar Zerlotini, Luciana C. A. Regitano.

Residual feed intake (RFI), a measure of feed efficiency (FE), is defined as the difference between the observed and the predictable feed intake considering size and growth of the animal. It is extremely important to beef production systems due to its impact on the allocation of land areas to alternative agricultural production, animal methane emissions, food demand and cost of production. Global differential gene expression analysis between high and low RFI groups (HRFI and LRFI: less and more efficient, respectively) revealed 73 differentially expressed (DE) annotated genes in Longissimus thoracis (LT) muscle of Nelore steers. These genes are involved in the overrepresented pathways Metabolism of Xenobiotics by Cytochrome P450 and Butanoate and Tryptophan Metabolism. Among the DE transcripts were several proteins related to mitochondrial function and the metabolism of lipids. Our findings indicate that observed gene expression differences are primarily related to metabolic processes underlying oxidative stress. Genes involved in the metabolism of xenobiotics and antioxidant mechanisms were primarily down-regulated, while genes responsible for lipid oxidation and ketogenesis were up-regulated in HRFI group. By using LT muscle, this study reinforces our previous findings using liver tissue and reveals new genes and likely tissue-specific regulators playing key-roles in these processes.

Residual feed intake (RFI), a measure of feed efficiency (FE), is defined as the difference between the observed and the predictable feed intake considering size and growth of the animal. It is extremely important to beef production systems due to its impact on the allocation of land areas to alternative agricultural production, animal methane emissions, food demand and cost of production. Global differential gene expression analysis between high and low RFI groups (HRFI and LRFI: less and more efficient, respectively) revealed 73 differentially expressed (DE) annotated genes in Longissimus thoracis (LT) muscle of Nelore steers. These genes are involved in the overrepresented pathways Metabolism of Xenobiotics by Cytochrome P450 and Butanoate and Tryptophan Metabolism. Among the DE transcripts were several proteins related to mitochondrial function and the metabolism of lipids. Our findings indicate that observed gene expression differences are primarily related to metabolic processes underlying oxidative stress. Genes involved in the metabolism of xenobiotics and antioxidant mechanisms were primarily down-regulated, while genes responsible for lipid oxidation and ketogenesis were up-regulated in HRFI group. By using LT muscle, this study reinforces our previous findings using liver tissue and reveals new genes and likely tissue-specific regulators playing key-roles in these processes. Made available in DSpace on 2019-06-15T00:40:16Z (GMT). No. of bitstreams: 1 srep39493.pdf: 952515 bytes, checksum: 9755372b27a1436f18494890258e8707 (MD5) Previous issue date: 2016

In contrast to the Mendelian inheritance model, parental alleles can contribute unequally to gene expression, which may result in phenotypic variance among individuals and bias in the predicted additive effect of molecular markers associated with production traits. Given the need to understand the effects of allelic variation and parent-of-origin effects on the expression of genes with a commercial interest in cattle, we analyzed the expression of KCNJ11 (potassium inwardly rectifying channel, subfamily J, member 11), which was previously described as a functional candidate gene for meat tenderness. Allele-specific and parent-of-origin-dependent expression of this gene were assessed in bovine muscle using the rs379610823 single nucleotide polymorphism as a reference. Biallelic expression was observed; however, the T allele was expressed at significantly higher levels than the C allele. Furthermore, increased expression of KCNJ11 was found in animals harboring the maternal T allele. This study is the first to describe the differential allelic expression of bovine KCNJ11. Our findings are important for understanding the mechanisms that underlie the pattern of KCNJ11 expression and its potential impact on the phenotypic variation of meat tenderness in Nelore beef cattle. This reinforces the need for further investigation of allelic- and parent-of-origin expression deviation in genetic markers eligible for the selection of target traits.

Residual feed intake (RFI) can increase the profitability of producers, reduce methane emission and land allocation to livestock production. However, this trait has late and costly measurements. Identifying gene expression changes combined with polymorphisms that affect residual feed intake variation is important for identify target regulatory polymorphisms that can be used in animal breeding programs. Diverse studies performed by our research group in a Nellore population, such as genome-wide association (GWA), association weight matrix (AWM) and RNA-seq analysis of liver tissue have been pointed Prune homolog 2 (Drosophila) (PRUNE2) as a potential candidate gene influencing feed efficiency. For this reason, we select this gene for a more detailed analysis considering haplotypes consisting of SNPs presented in the Illumina Bovine HD Bead Chip.

Made available in DSpace on 2015-03-18T15:55:48Z (GMT). No. of bitstreams: 0 Previous issue date: 2014-10-27Bitstream added on 2015-03-18T16:28:35Z : No. of bitstreams: 1 WOS000345683300006.pdf: 2467299 bytes, checksum: f761fc9f00b520f876ff89ab7486ec68 (MD5) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Embrapa (Brazilian Agricultural Research Corporation) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Background: The development of linkage disequilibrium (LD) maps and the characterization of haplotype block structure at the population level are useful parameters for guiding genome wide association (GWA) studies, and for understanding the nature of non-linear association between phenotypes and genes. The elucidation of haplotype block structure can reduce the information of several single nucleotide polymorphisms (SNP) into the information of a haplotype block, reducing the number of SNPs in a coherent way for consideration in GWA and genomic selection studies.Results: The maximum average LD, measured by r(2) varied between 0.33 to 0.40 at a distance of < 2.5 kb, and the minimum average values of r(2) varied between 0.05 to 0.07 at distances ranging from 400 to 500 kb, clearly showing that the average r(2) reduced with the increase in SNP pair distances. The persistence of LD phase showed higher values at shorter genomic distances, decreasing with the increase in physical distance, varying from 0.96 at a distance of < 2.5 kb to 0.66 at a distance from 400 to 500 kb. A total of 78% of all SNPs were clustered into haplotype blocks, covering 1,57 Mb of the total autosomal genome size.Conclusions: This study presented the first high density linkage disequilibrium map and haplotype block structure for a composite beef cattle population, and indicates that the high density SNP panel over 700 k can be used for genomic selection implementation and GWA studies for Canchim beef cattle. Univ Fed Sao Carlos, Dept Genet & Evolut, BR-13565905 Sao Carlos, SP, Brazil Univ Estadual Paulista, Fac Ciencias Agr & Vet, Dept Ciencias Exatas, BR-14884900 Jaboticabal, SP, Brazil Embrapa Southeast Livestock, BR-13560970 Sao Carlos, SP, Brazil Univ Guelph, Ctr Genet Improvement Livestock, Guelph, ON N1G 2W1, Canada Embrapa Agr Informat, BR-13083886 Campinas, SP, Brazil Univ Fed Lavras, Dept Anim Sci, BR-3720000 Lavras, Brazil Embrapa Dairy Cattle, BR-36038330 Juiz De Fora, Brazil Univ Estadual Paulista, Fac Ciencias Agr & Vet, Dept Ciencias Exatas, BR-14884900 Jaboticabal, SP, Brazil CAPES: 02663/09-0 CNPq: 142053/2010-4 CAPES: 5285-11-9

Submitted by Vitor Silverio Rodrigues (vitorsrodrigues@reitoria.unesp.br) on 2014-05-27T11:29:39Z No. of bitstreams: 0Bitstream added on 2014-05-27T14:43:12Z : No. of bitstreams: 1 2-s2.0-84878424253.pdf: 263850 bytes, checksum: 92513d7e69697fb7a847cffcd6bba3d0 (MD5) Made available in DSpace on 2014-05-27T11:29:39Z (GMT). No. of bitstreams: 0 Previous issue date: 2013-06-05 Background: Meat quality involves many traits, such as marbling, tenderness, juiciness, and backfat thickness, all of which require attention from livestock producers. Backfat thickness improvement by means of traditional selection techniques in Canchim beef cattle has been challenging due to its low heritability, and it is measured late in an animal's life. Therefore, the implementation of new methodologies for identification of single nucleotide polymorphisms (SNPs) linked to backfat thickness are an important strategy for genetic improvement of carcass and meat quality.Results: The set of SNPs identified by the random forest approach explained as much as 50% of the deregressed estimated breeding value (dEBV) variance associated with backfat thickness, and a small set of 5 SNPs were able to explain 34% of the dEBV for backfat thickness. Several quantitative trait loci (QTL) for fat-related traits were found in the surrounding areas of the SNPs, as well as many genes with roles in lipid metabolism.Conclusions: These results provided a better understanding of the backfat deposition and regulation pathways, and can be considered a starting point for future implementation of a genomic selection program for backfat thickness in Canchim beef cattle. © 2013 Mokry et al.; licensee BioMed Central Ltd. Department of Genetics and Evolution Federal University of São Carlos, Rodovia Washington Luiz, km 235, Po Box 676, 13565-905 São Carlos Embrapa Agricultural Informatics, Avenida André Tosello, 209, Po Box 6041, 13083-886 Campinas Embrapa Southeast Livestock, Rodovia Washington Luiz, km 234 PO BOX 339, 13560-970 São Carlos Department of Animal Science Federal University of Lavras, Po Box 3037, 37200-00 Lavras Embrapa Dairy Cattle, Rua Eugênio do Nascimento, 610, 36038-330 Juiz de Fora Embrapa Southern Region Animal Husbandry, BR 153, km 603, PO BOX 242, 96401-970 Bagé Department of Exact Science São Paulo State University, Po Box 53453, 14884-900 Jaboticabal Department of Exact Science São Paulo State University, Po Box 53453, 14884-900 Jaboticabal

Background: Meat quality involves many traits, such as marbling, tenderness, juiciness, and backfat thickness, all of which require attention from livestock producers. Backfat thickness improvement by means of traditional selection techniques in Canchim beef cattle has been challenging due to its low heritability, and it is measured late in an animal?s life. Therefore, the implementation of new methodologies for identification of single nucleotide polymorphisms (SNPs) linked to backfat thickness are an important strategy for genetic improvement of carcass and meat quality. Results: The set of SNPs identified by the random forest approach explained as much as 50% of the deregressed estimated breeding value (dEBV) variance associated with backfat thickness, and a small set of 5 SNPs were able to explain 34% of the dEBV for backfat thickness. Several quantitative trait loci (QTL) for fat-related traits were found in the surrounding areas of the SNPs, as well as many genes with roles in lipid metabolism. Conclusions: These results provided a better understanding of the backfat deposition and regulation pathways, and can be considered a starting point for future implementation of a genomic selection program for backfat thickness in Canchim beef cattle.