RESUMO

The beef cattle industry has experienced a shift driven by a market demand for healthier meat, cost efficiency and environmental sustainability in recent years. Consequently, there has been a growing focus on the fatty acids content and functions of meat in cattle breeding programmes. Besides, a deeper understanding of the biological mechanisms influencing the expression of different phenotypes related to fatty acid profiles is crucial. In this study, we aimed to identify Single-Nucleotide Variants (SNV) and Insertion/Deletion (InDels) DNA variants in candidate genes related to fatty acid profiles described in genomic, transcriptomic and proteomic studies conducted in beef cattle breeds. Utilizing whole-genome re-sequencing data from Brazilian locally adapted bovine breeds, namely Caracu and Pantaneiro, we identified SNVs and InDels associated with 23,947 genes. From these, we identified 318 candidate genes related to fatty acid profiles that contain variants. Subsequently, we select only genes with SNVs and InDels in their promoter, 5' UTR and coding region. Through the gene-biological process network, approximately 19 genes were highlighted. Furthermore, considering the studied trait and a literature review, we selected the main transcription factors (TF). Functional analysis via gene-TF network allowed us to identify the 30 most likely candidate genes for meat fatty acid profile in cattle. LIPE, MFSD2A and SREBF1 genes were highlighted in networks due to their biological importance. Further dissection of these genes revealed 15 new variants found in promoter regions of Caracu and Pantaneiro sequences. The gene networks facilitated a better functional understanding of genes and TF, enabling the identification of variants potentially related to the expression of candidate genes for meat fatty acid profiles in cattle.

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This study aimed to build gene-biological process networks with differentially expressed genes associated with economically important traits of Nelore cattle from 17 previous studies. The genes were clustered into three groups by evaluated traits: group 1, production traits; group 2, carcass traits; and group 3, meat quality traits. For each group, a gene-biological process network analysis was performed with the differentially expressed genes in common. For production traits, 37 genes were found in common, of which 13 genes were enriched for six Gene Ontology (GO) terms; these terms were not functionally grouped. However, the enriched GO terms were related to homeostasis, the development of muscles and the immune system. For carcass traits, four genes were found in common. Thus, it was not possible to functionally group these genes into a network. For meat quality traits, the analysis revealed 222 genes in common. CSRP3 was the only gene differentially expressed in all three groups. Non-redundant biological terms for clusters of genes were functionally grouped networks, reflecting the cross-talk between all biological processes and genes involved. Many biological processes and pathways related to muscles, the immune system and lipid metabolism were enriched, such as striated muscle cell development and triglyceride metabolic processes. This study provides insights into the genetic mechanisms of production, carcass and meat quality traits of Nelore cattle. This information is fundamental for a better understanding of the complex traits and could help in planning strategies for the production and selection systems of Nelore cattle.

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Cattle population history, breeding systems, and geographic subdivision may be reflected in runs of homozygosity (ROH), effective population size (N e), and linkage disequilibrium (LD) patterns. Thus, the assessment of this information has become essential to the implementation of genomic selection on purebred and crossbred cattle breeding programs. In this way, we assessed the genotype of 19 cattle breeds raised in Brazil belonging to taurine, indicine, synthetic crossbreds, and Iberian-derived locally adapted ancestries to evaluate the overall LD decay patterns, N e, ROH, and breed composition. We were able to obtain a general overview of the genomic architecture of cattle breeds currently raised in Brazil and other tropical countries. We found that, among the evaluated breeds, different marker densities should be used to improve the genomic prediction accuracy and power of genome-wide association studies. Breeds showing low N e values indicate a recent inbreeding, also reflected by the occurrence of longer ROH, which demand special attention in the matting schemes to avoid extensive inbreeding. Candidate genes (e.g., ABCA7, PENK, SPP1, IFNAR1, IFNAR2, SPEF2, PRLR, LRRTM1, and LRRTM4) located in the identified ROH islands were evaluated, highlighting biological processes involved with milk production, behavior, rusticity, and fertility. Furthermore, we were successful in obtaining the breed composition regarding the taurine and indicine composition using single-nucleotide polymorphism (SNP) data. Our results were able to observe in detail the genomic backgrounds that are present in each breed and allowed to better understand the various contributions of ancestor breeds to the modern breed composition to the Brazilian cattle.

RESUMO

We aimed to evaluate the random regression models that promote the best fit of residual variance predicting the breeding values of quail body weights and the sensitivity of its breeding values to the variations of different tryptophan:lysine ratios in the diets via reaction norms. A total of 1112 meat quails from LF1 and LF2 lines with 35 days of age were evaluated. During the period of 1 to 21 days of age, birds were fed with different tryptophan:lysine ratios (0.17, 0.20, 0.23, 0.26 and 0.29%) containing 2900 kcal ME/kg and 26.10% crude protein, followed by basal diet provided up to 35 days. The best model fit for residual variance was evaluated comparing heterogeneity (2, 3 and 4 classes) and homogeneity (1 class), including sex as fixed effect and the additive genetic effect as random. The second order Legendre polynomial was used to analyze the genotype x environment interaction using reaction norms. The model considering two classes of residual variance was the one that promoted the best fit of the data, being adopted to predict the breeding values. Thus, we observed changes in the sensitivity of the breeding values, characterized by the rearrangement of the breeding values, according to the different ratios of amino acids, suggesting the genotype x environment interaction.

Objetivou-se avaliar o modelo de regressão aleatória que promove o melhor ajuste da variância residual para a predição dos valores genéticos dos pesos corporais de codornas de corte e a sensibilidade dos seus valores genéticos às variações de diferentes relações triptofano:lisina. Foram avaliadas 1112 codornas de corte das linhagens LF1 e LF2, do nascimento aos 35 dias de idade. No período de 1 a 21 dias de idade as aves receberam alimentação com dietas de diferentes relações triptofano:lisina (0,17, 0,20, 0,23, 0,26 e 0,29%), contendo 2900 kcal EM/kg e 26,10% de proteína bruta, seguido pelo fornecimento de ração basal até os 35 dias. Foi avaliado o ajuste da variância residual comparando a homogeneidade (1 classe) e a heterogeneidade (2, 3 e 4 classes) incluindo o sexo como efeito fixo e o efeito genético aditivo como aleatório. O polinômio de Legendre de segunda ordem foi utilizado para a análise da interação genótipo x ambiente utilizando normas de reação. O modelo que considerou duas classes de variância residual foi o que promoveu o melhor ajuste dos dados e foi adotado para predição dos valores genéticos. Desta forma, foi observada alteração na sensibilidade dos valores genéticos, caracterizados pelo reordenamento dos valores genéticos, em função das diferentes relações estudadas, indicando a presença de interação genótipo x ambiente.

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RESUMO

We aimed to evaluate the random regression models that promote the best fit of residual variance predicting the breeding values of quail body weights and the sensitivity of its breeding values to the variations of different tryptophan:lysine ratios in the diets via reaction norms. A total of 1112 meat quails from LF1 and LF2 lines with 35 days of age were evaluated. During the period of 1 to 21 days of age, birds were fed with different tryptophan:lysine ratios (0.17, 0.20, 0.23, 0.26 and 0.29%) containing 2900 kcal ME/kg and 26.10% crude protein, followed by basal diet provided up to 35 days. The best model fit for residual variance was evaluated comparing heterogeneity (2, 3 and 4 classes) and homogeneity (1 class), including sex as fixed effect and the additive genetic effect as random. The second order Legendre polynomial was used to analyze the genotype x environment interaction using reaction norms. The model considering two classes of residual variance was the one that promoted the best fit of the data, being adopted to predict the breeding values. Thus, we observed changes in the sensitivity of the breeding values, characterized by the rearrangement of the breeding values, according to the different ratios of amino acids, suggesting the genotype x environment interaction.(AU)

Objetivou-se avaliar o modelo de regressão aleatória que promove o melhor ajuste da variância residual para a predição dos valores genéticos dos pesos corporais de codornas de corte e a sensibilidade dos seus valores genéticos às variações de diferentes relações triptofano:lisina. Foram avaliadas 1112 codornas de corte das linhagens LF1 e LF2, do nascimento aos 35 dias de idade. No período de 1 a 21 dias de idade as aves receberam alimentação com dietas de diferentes relações triptofano:lisina (0,17, 0,20, 0,23, 0,26 e 0,29%), contendo 2900 kcal EM/kg e 26,10% de proteína bruta, seguido pelo fornecimento de ração basal até os 35 dias. Foi avaliado o ajuste da variância residual comparando a homogeneidade (1 classe) e a heterogeneidade (2, 3 e 4 classes) incluindo o sexo como efeito fixo e o efeito genético aditivo como aleatório. O polinômio de Legendre de segunda ordem foi utilizado para a análise da interação genótipo x ambiente utilizando normas de reação. O modelo que considerou duas classes de variância residual foi o que promoveu o melhor ajuste dos dados e foi adotado para predição dos valores genéticos. Desta forma, foi observada alteração na sensibilidade dos valores genéticos, caracterizados pelo reordenamento dos valores genéticos, em função das diferentes relações estudadas, indicando a presença de interação genótipo x ambiente.(AU)

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Genetic diversity is one of the most important issues in studies on conservation of cattle breeds and endangered species. The objective of this study was to estimate the levels of genetic differentiation between locally adapted taurine (Bos taurus taurus) and zebu (Bos taurus indicus) breeds in Brazil, which were genotyped for more than 777,000 SNPs. The fixation index (F ST), principal component analysis (PCA), and Bayesian clustering were estimated. The F ST highlighted genetic differentiation between taurine and zebu breeds. The taurine lines, Caracu and Caracu Caldeano, had significant genetic differentiation (F ST close to 5%) despite their recent selection for different uses (meat and milk). This genetic variability can be used for conservation of locally adapted animals, as well as for breeding programs on zebu breeds. Introgression of zebu in locally adapted breeds was identified, especially in Curraleiro Pé-Duro breed. The Gyr breed, however, had low breed purity at genomic level due to its very heterogeneous mixing pattern.

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