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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)

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.

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.