RESUMO
BACKGROUND: Host resilience (HR) to parasites can affect the performance of animals. Therefore, the aim of this study was to present a detailed investigation of the genetic mechanisms of HR to ticks (TICK), gastrointestinal nematodes (GIN), and Eimeria spp. (EIM) in Nellore cattle that were raised under natural infestation and a prophylactic parasite control strategy. In our study, HR was defined as the slope coefficient of body weight (BW) when TICK, GIN, and EIM burdens were used as environmental gradients in random regression models. In total, 1712 animals were evaluated at five measurement events (ME) at an average age of 331, 385, 443, 498, and 555 days, which generated 7307 body weight (BW) records. Of the 1712 animals, 1075 genotyped animals were used in genome-wide association studies to identify genomic regions associated with HR. RESULTS: Posterior means of the heritability estimates for BW ranged from 0.09 to 0.54 across parasites and ME. The single nucleotide polymorphism (SNP)-derived heritability for BW at each ME ranged from a low (0.09 at ME.331) to a moderate value (0.23 at ME.555). Those estimates show that genetic progress can be achieved for BW through selection. Both genetic and genomic associations between BW and HR to TICK, GIN, and EIM confirmed that parasite infestation impacted the performance of animals. Selection for BW under an environment with a controlled parasite burden is an alternative to improve both, BW and HR. There was no impact of age of measurement on the estimates of genetic variance for HR. Five quantitative trait loci (QTL) were associated with HR to EIM but none with HR to TICK and to GIN. These QTL contain genes that were previously shown to be associated with the production of antibody modulators and chemokines that are released in the intestinal epithelium. CONCLUSIONS: Selection for BW under natural infestation and controlled parasite burden, via prophylactic parasite control, contributes to the identification of animals that are resilient to nematodes and Eimeria ssp. Although we verified that sufficient genetic variation existed for HR, we did not find any genes associated with mechanisms that could justify the expression of HR to TICK and GIN.
Assuntos
Estudo de Associação Genômica Ampla , Parasitos , Animais , Bovinos/genética , Estudo de Associação Genômica Ampla/veterinária , Locos de Características Quantitativas , Genótipo , Parasitos/genética , Peso Corporal/genéticaRESUMO
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.
Assuntos
Regulação da Expressão Gênica , Redes Reguladoras de Genes , MicroRNAs/metabolismo , Minerais/metabolismo , Músculo Esquelético/metabolismo , Fenótipo , RNA Mensageiro/metabolismo , Animais , Bovinos , Genoma , MicroRNAs/genética , RNA Mensageiro/genéticaRESUMO
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.
Assuntos
Perfilação da Expressão Gênica , Regulação da Expressão Gênica/fisiologia , Redes Reguladoras de Genes/fisiologia , Redes e Vias Metabólicas/fisiologia , Minerais/metabolismo , Músculo Esquelético/metabolismo , Animais , BovinosRESUMO
In this study, we aimed to provide a wet laboratory validation for a set of single nucleotide polymorphisms (SNP), which had been identified as candidate functional variants in silico. Genotyping for candidate SNP was performed in Brahman and Tropical Composite cattle. After quality control, 29 SNP were first investigated individually for their association with female reproductive traits and then used as a panel for genomic predictions. The reproductive traits studied were age at first corpus luteum (AGECL; days), post-partum anoestrus interval (PPAI; days), and a binary trait that described if the cow had ovulated before weaning the first calf or not (PW, 0-1). Single nucleotide polymorphisms in six genes (FOXA2, TRAF4, IRF2, IRF1, BPTF, and CPEB1) were found to be significantly associated with reproduction traits . The genomic prediction method used was BayesR, to accommodate the 29 new SNP and compare their performance with predictions based on 50K genotypes (Illumina SNP chip). When new SNP and PLAG1 mutation rs109231213 were included in the genomic predictions for female reproductive traits their accuracies improved. The best predictions were obtained by combining the new SNP and the 50K SNP using BayesR analysis, with a 4% improvement in accuracy. The proportion of the genetic variance explained by the new SNP together was 0.07 for AGECL, 0.03 for PPAI, and 0.02 for PW. It would be favourable to include these new SNP in future versions of bovine SNP chips to target selection for female reproductive traits. These new SNP are likely to improve genomic predictions for female reproductive traits in tropical beef cattle breeds, with varying degrees of Bos indicus content.(AU)
Assuntos
Animais , Feminino , Bovinos , Bovinos/genética , Puberdade/genética , Polimorfismo de Nucleotídeo Único/genética , Moldes Genéticos , Anestro/genéticaRESUMO
Understanding the genetic architecture of beef cattle growth cannot be limited simply to the genome-wide association study (GWAS) for body weight at any specific ages, but should be extended to a more general purpose by considering the whole growth trajectory over time using a growth curve approach. For such an approach, the parameters that are used to describe growth curves were treated as phenotypes under a GWAS model. Data from 1,255 Brahman cattle that were weighed at birth, 6, 12, 15, 18, and 24 months of age were analyzed. Parameter estimates, such as mature weight (A) and maturity rate (K) from nonlinear models are utilized as substitutes for the original body weights for the GWAS analysis. We chose the best nonlinear model to describe the weight-age data, and the estimated parameters were used as phenotypes in a multi-trait GWAS. Our aims were to identify and characterize associated SNP markers to indicate SNP-derived candidate genes and annotate their function as related to growth processes in beef cattle. The Brody model presented the best goodness of fit, and the heritability values for the parameter estimates for mature weight (A) and maturity rate (K) were 0.23 and 0.32, respectively, proving that these traits can be a feasible alternative when the objective is to change the shape of growth curves within genetic improvement programs. The genetic correlation between A and K was -0.84, indicating that animals with lower mature body weights reached that weight at younger ages. One hundred and sixty seven (167) and two hundred and sixty two (262) significant SNPs were associated with A and K, respectively. The annotated genes closest to the most significant SNPs for A had direct biological functions related to muscle development (RAB28), myogenic induction (BTG1), fetal growth (IL2), and body weights (APEX2); K genes were functionally associated with body weight, body height, average daily gain (TMEM18), and skeletal muscle development (SMN1). Candidate genes emerging from this GWAS may inform the search for causative mutations that could underpin genomic breeding for improved growth rates.