Search

Feed efficiency helps to reduce environmental impacts from livestock production, improving beef cattle profitability. We identified potential biomarkers (hub genes) for feed efficiency, by applying co-expression analysis in Longissimus thoracis RNA-Seq data from 180 Nelore steers. Six co-expression modules were associated with six feed efficiency-related traits (p-value ≤ 0.05). Within these modules, 391 hub genes were enriched for pathways as protein synthesis, muscle growth, and immune response. Trait-associated transcription factors (TFs) ELF1, ELK3, ETS1, FLI1, and TCF4, were identified with binding sites in at least one hub gene. Gene expression of CCDC80, FBLN5, SERPINF1, and OGN was associated with multiple feed efficiency-related traits (FDR ≤ 0.05) and were previously related to glucose homeostasis, oxidative stress, fat mass, and osteoblastogenesis, respectively. Potential regulatory elements were identified, integrating the hub genes with previous studies from our research group, such as the putative cis-regulatory elements (eQTLs) inferred as affecting the PCDH18 and SPARCL1 hub genes related to immune system and adipogenesis, respectively. Therefore, our analyses contribute to a better understanding of the biological mechanisms underlying feed efficiency in bovine and the hub genes disclosed can be used as biomarkers for feed efficiency-related traits in Nelore cattle. Made available in DSpace on 2020-08-15T04:11:44Z (GMT). No. of bitstreams: 1 AP-Potential-biomarkers-2020.pdf: 6772400 bytes, checksum: b6d50a8237cd649b3e08ecc7fb04b44e (MD5) Previous issue date: 2020 Article 189. Na publicação: Luciana C. A. Regitano.

Fatty acid (FA) content affects the sensorial and nutritional value of meat and plays a significant role in biological processes such as adipogenesis and immune response. It is well known that, in beef, the main FAs associated with these biological processes are oleic acid (C18:1 cis9, OA) and conjugated linoleic acid (CLA-c9t11), which may have beneficial effects on metabolic diseases such as type 2 diabetes and obesity. Here, we performed differential expression and co-expression analyses, weighted gene co-expression network analysis (WGCNA) and partial correlation with information theory (PCIT), to uncover the complex interactions between miRNAs and mRNAs expressed in skeletal muscle associated with FA content. miRNA and mRNA expression data were obtained from skeletal muscle of Nelore cattle that had extreme genomic breeding values for OA and CLA. Insulin and MAPK signaling pathways were identified by WGCNA as central pathways associated with both of these fatty acids. Co-expression network analysis identified bta-miR-33a/b, bta-miR-100, bta-miR-204, bta-miR-365-5p, btamiR-660, bta-miR-411a, bta-miR-136, bta-miR-30-5p, bta-miR-146b, bta-let-7a-5p, bta-let-7f, bta-let-7, bta-miR 339, bta-miR-10b, bta-miR 486, and the genes ACTA1 and ALDOA as potential regulators of fatty acid synthesis. This study provides evidence and insights into the molecular mechanisms and potential target genes involved in fatty acid content differences in Nelore beef cattle, revealing new candidate pathways of phenotype modulation that could positively benefit beef production and human consumption. Made available in DSpace on 2019-07-25T01:02:05Z (GMT). No. of bitstreams: 1 APCoexpressionnetworks.pdf: 1517209 bytes, checksum: c6c99bbfd9721e2c08e0d765e8b03b88 (MD5) Previous issue date: 2019 Article 651. Na publicação: Adhemar Zerlotini, Luciana C.A. Regitano.

Genetic variations in genes involved in lipid storage, which also may interfere with important phenotypic traits such as intramuscular fat deposition in cattle, can represent useful markers in marker assisted selection programs. An important candidate gene is perilipin 2 (PLIN2) that plays a role in the capture of long chain fatty acids and in the formation and stabilization of lipid droplets in different tissues including muscle. As reported by our group, PLIN2 expression level was associated with trans-eQTL (expression quantitative loci distant of gene associated) at chr3: 87, 253, 086 in Nellore cattle, where animals with different genotypes showed different expression level of PLIN2 among the 193 animals and the co-expression analysis detected correlation with intramuscular fat, palmitoleic, oleic and linoleic acids. Then, the objective of this study was to identify and characterize polymorphisms present in the PLIN2 gene of Nellore cattle. To date, there is not much information on mutations in the PLIN2 gene in Bos indicus animals. A total of 134 single nucleotide polymorphisms (SNPs) were identified in the genomic region of PLIN2 gene and five of those are novel with a moderate impact. These SNPs may change the protein effectiveness and, after further association studies and functional validation, could be used as genomic markers in animal breeding program. Made available in DSpace on 2020-01-28T18:11:29Z (GMT). No. of bitstreams: 1 NovelPolymorphismsPLIN2.pdf: 433440 bytes, checksum: 6cc16bdaa51a68669c745c6c5bc70198 (MD5) Previous issue date: 2019 Na publicação: Luciana CA Regitano, Adhemar Zerlotini. gmr16039963.

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

Made available in DSpace on 2015-10-21T20:36:18Z (GMT). No. of bitstreams: 0 Previous issue date: 2015-03-25. Added 1 bitstream(s) on 2015-10-22T09:47:55Z : No. of bitstreams: 1 WOS000351994200001.pdf: 1431968 bytes, checksum: b7029239d0376eb8d710b1b564138694 (MD5) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Agriculture and Food Research Initiative Background: Efficiency of feed utilization is important for animal production because it can reduce greenhouse gas emissions and improve industry profitability. However, the genetic basis of feed utilization in livestock remains poorly understood. Recent developments in molecular genetics, such as platforms for genome-wide genotyping and sequencing, provide an opportunity to identify genes and pathways that influence production traits. It is known that transcriptional networks influence feed efficiency-related traits such as growth and energy balance. This study sought to identify differentially expressed genes in animals genetically divergent for Residual Feed Intake (RFI), using RNA sequencing methodology (RNA-seq) to obtain information from genome-wide expression profiles in the liver tissues of Nelore cattle.Results: Differential gene expression analysis between high Residual Feed Intake (HRFI, inefficient) and low Residual Feed Intake (LRFI, efficient) groups was performed to provide insights into the molecular mechanisms that underlie feed efficiency-related traits in beef cattle. A total of 112 annotated genes were identified as being differentially expressed between animals with divergent RFI phenotypes. These genes are involved in ion transport and metal ion binding; act as membrane or transmembrane proteins; and belong to gene clusters that are likely related to the transport and catalysis of molecules through the cell membrane and essential mechanisms of nutrient absorption. Genes with functions in cellular signaling, growth and proliferation, cell death and survival were also differentially expressed. Among the over-represented pathways were drug or xenobiotic metabolism, complement and coagulation cascades, NRF2-mediated oxidative stress, melatonin degradation and glutathione metabolism.Conclusions: Our data provide new insights and perspectives on the genetic basis of feed efficiency in cattle. Some previously identified mechanisms were supported and new pathways controlling feed efficiency in Nelore cattle were discovered. We potentially identified genes and pathways that play key roles in hepatic metabolic adaptations to oxidative stress such as those involved in antioxidant mechanisms. These results improve our understanding of the metabolic mechanisms underlying feed efficiency in beef cattle and will help develop strategies for selection towards the desired phenotype. University of Missouri Columbia, Division of Animal Sciences Universidade de São Paulo, Departamento de Zootecnia, Escola Superior de Agricultura Luiz de Queiroz Universidade Federal de São Carlos, Departamento de Genética e Evolução Universidade Estadual Paulista, Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal CNPq: 473091/2012-7 FAPESP: 2013/17778-4 FAPESP: 2014/13555-3 Agriculture and Food Research Initiative: 2011-68004-30214 Agriculture and Food Research Initiative: 2011-68004-30367 Agriculture and Food Research Initiative: 2013-68004-20364

Made available in DSpace on 2018-06-13T00:44:56Z (GMT). No. of bitstreams: 1 SP19768ID31945.pdf: 2157874 bytes, checksum: a42b73251d981e89dd4096746321057d (MD5) Previous issue date: 2009-12-14