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We report here the first complete mitochondria genome of Onchocerca volvulus from a focus outside of Africa. An O. volvulus mitogenome from the Brazilian Amazonia focus was obtained using a combination of high-throughput and Sanger sequencing technologies. Comparisons made between this mitochondrial genome and publicly available mitochondrial sequences identified 46 variant nucleotide positions and suggested that our Brazilian mitogenome is more closely related to Cameroon-origin mitochondria than West African-origin mitochondria. As well as providing insights into the origins of Latin American onchocerciasis, the Brazilian Amazonia focus mitogenome may also have value as an epidemiological resource.

This study was carried out to evaluate the effects of four levels of intensification of grazing systems: 1) degraded pasture - DP; 2) irrigated pasture with high stocking rate - IHS; 3) dryland pasture with high stocking rate - DHS; 4) dryland pasture with moderate stocking rate - DMS; on growth, muscle development and meat quality of Nellore steers (271±2.2kg of live body weight - BW; 15months old) during two consecutive periods (17 and 15months). The final BW, the average daily BW gain, the hot carcass weight and the dress percentage were greater (P<0.0001), and the ribeye area tended to be greater (P=0.085), in the intensified systems compared to the degraded system. Animals in all systems presented similar back fat. Muscle development increased with the intensification of the grazing systems and meat quality was not affected., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Young Nellore and crossbreed bulls were comparatively slaughtered to generate equation models for predicting the chemical composition of the empty body and carcass from the chemical composition of the Hankins and Howe section (; ). Data were collected from 236 animals from different genetic groups: Nellore, one-half Canchim + one-half Nellore, one-half Angus + one-half Nellore, and one-half Simmental + one-half Nellore, with 48 baseline animals (BW range from 218 to 433 kg) and 188 animals finished in the feedlot (BW range from 356 to 618 kg). The chemical composition prediction equation model was developed for all genetic groups using stepwise regression analysis. Across all animals, the percentages of water and ether extract in the HH section were highly correlated ( < 0.001) with the percentages in the carcass ( = 0.911 and = 0.901, respectively, for water content of the carcass [HOC] and = 0.921 and = 0.921, respectively, for ether extract content of the carcass [EEC]) and empty body ( = 0.937 and = 0.926, respectively, for water content of the empty body [HOEB] and = 0.935 and = 0.939, respectively, for ether extract content of the empty body [EEEB]). The best prediction models were for the traits of empty body weight, HOEB, EEEB, HOC, and EEC. Determination coefficients for predicting the dependent variables obtained from the carcass composition were lower than those obtained from the empty body composition. It was concluded that the chemical composition of the empty body and the carcass can be predicted from the composition of the HH section, using a general equation for different genetic groups.

Mate (Ilex paraguariensis A.St.-Hil.) is generally recognized as safe (GRAS status) and has a high content of alkaloids, saponins, and phenolic acids. Addition of mate extract to broilers feed has been shown to increase the oxidative stability of chicken meat, however, its effect on beef quality from animals supplemented with mate extract has not been investigated so far. Addition of extract of mate to a standard maize/soy feed at a level of 0.5, 1.0 or 1.5% w/w to the diet of feedlot for cattle resulted in increased levels of inosine monophosphate, creatine and carnosine in the fresh meat. The content of total conjugated linoleic acid increased in the meat as mate extract concentration was increased in the feed. The tendency to radical formation in meat slurries as quantified by EPR spin-trapping decreased as increasing mate extract addition to feed, especially after storage of the meat, indicating higher oxidative stability. Mate supplementation in the diet did not affect animal performance and carcass characteristics, but meat from these animals was more tender and consequently more accepted by consumers. Mate extract is shown to be a promising additive to feedlot diets for cattle to improve the oxidative stability, nutritive value and sensory quality of beef., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

The crossbreeding of two or more breeds from the Bos taurus and Bos indicus species is an alternative for obtaining high-quality meat from animals adapted to tropical climates. Quality and sensory attributes of beef, mainly its tenderness and flavour, are very important with regard to the consumer's point of view. This study aimed to evaluate the physico-chemical and sensory characteristics of crossbred young bulls and heifers, the offspring of Angus or Limousin bulls and 1/2 Angus + 1/2 Nellore or 1/2 Simental + 1/2 Nellore cows that were finished on feedlot or pasture. Meat quality traits (pH, colour, cooking loss, water holding capacity and shear force) and sensory parameters (characteristic beef aroma/flavour intensity, strange aroma/flavour intensity, tenderness and juiciness descriptive attributes, flavour, texture (tenderness) and overall acceptance) were evaluated. The genetic group had an effect on the beef pH, but it was not as relevant as the effect of the combination between the production system and the sex or genetic group, which affected many of the quality and sensory traits.

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.

Background: Lipids are a class of molecules that play an important role in cellular structure and metabolism in all cell types. In the last few decades, it has been reported that long-chain fatty acids (FAs) are involved in several biological functions from transcriptional regulation to physiological processes. Several fatty acids have been both positively and negatively implicated in different biological processes in skeletal muscle and other tissues. To gain insight into biological processes associated with fatty acid content in skeletal muscle, the aim of the present study was to identify differentially expressed genes (DEGs) and functional pathways related to gene expression regulation associated with FA content in cattle., Results: Skeletal muscle transcriptome analysis of 164 Nellore steers revealed no differentially expressed genes (DEGs, FDR 10%) for samples with extreme values for linoleic acid (LA) or stearic acid (SA), and only a few DEGs for eicosapentaenoic acid (EPA, 5 DEGs), docosahexaenoic acid (DHA, 4 DEGs) and palmitic acid (PA, 123 DEGs), while large numbers of DEGs were associated with oleic acid (OA, 1134 DEGs) and conjugated linoleic acid cis9 trans11 (CLA-c9t11, 872 DEGs). Functional annotation and functional enrichment from OA DEGs identified important genes, canonical pathways and upstream regulators such as SCD, PLIN5, UCP3, CPT1, CPT1B, oxidative phosphorylation mitochondrial dysfunction, PPARGC1A, and FOXO1. Two important genes associated with lipid metabolism, gene expression and cancer were identified as DEGs between animals with high and low CLA-c9t11, specifically, epidermal growth factor receptor (EGFR) and RNPS., Conclusion: Only two out of seven classes of molecules of FA studied were associated with large changes in the expression profile of skeletal muscle. OA and CLA-c9t11 content had significant effects on the expression level of genes related to important biological processes associated with oxidative phosphorylation, and cell growth, survival, and migration. These results contribute to our understanding of how some FAs modulate metabolism and may have protective health function.

The myogenic differentiation 1 gene (MYOD1) has a key role in skeletal muscle differentiation and composition through its regulation of the expression of several muscle-specific genes. We first used a general linear mixed model approach to evaluate the association of MYOD1 expression levels on individual beef tenderness phenotypes. MYOD1mRNA levels measured by quantitative polymerase chain reactions in 136 Nelore steers were significantly associated (P ≤ 0.01) with Warner-Bratzler shear force, measured on the longissimus dorsi muscle after 7 and 14 days of beef aging. Transcript abundance for the muscle regulatory gene MYOD1 was lower in animals with more tender beef. We also performed a co-expression network analysis using whole transcriptome sequence data generated from 30 samples of longissimus muscle tissue to identify genes that are potentially regulated by MYOD1. The effect of MYOD1 gene expression on beef tenderness may emerge from its function as an activator of muscle-specific gene transcription such as for the serum response factor (C-fos serum response element-binding transcription factor) gene (SRF), which determines muscle tissue development, composition, growth and maturation., (© 2016 Stichting International Foundation for Animal Genetics.)

Feed efficiency and carcass characteristics are late-measured traits. The detection of molecular markers associated with them can help breeding programs to select animals early in life, and to predict breeding values with high accuracy. The objective of this study was to identify polymorphisms in the functional and positional candidate gene NEUROD1 (neurogenic differentiation 1), and investigate their associations with production traits in reference families of Nelore cattle. A total of 585 steers were used, from 34 sires chosen to represent the variability of this breed. By sequencing 14 animals with extreme residual feed intake (RFI) values, seven single nucleotide polymorphisms (SNPs) in NEUROD1 were identified. The investigation of marker effects on the target traits RFI, backfat thickness (BFT), ribeye area (REA), average body weight (ABW), and metabolic body weight (MBW) was performed with a mixed model using the restricted maximum likelihood method. SNP1062, which changes cytosine for guanine, had no significant association with RFI or REA. However, we found an additive effect on ABW (P ≤ 0.05) and MBW (P ≤ 0.05), with an estimated allele substitution effect of -1.59 and -0.93 kg0.75, respectively. A dominant effect of this SNP for BFT was also found (P ≤ 0.010). Our results are the first that identify NEUROD1 as a candidate that affects BFT, ABW, and MBW. Once confirmed, the inclusion of this SNP in dense panels may improve the accuracy of genomic selection for these traits in Nelore beef cattle as this SNP is not currently represented on SNP chips.

Five hundred and seventy-five Nellore steers were evaluated for residual feed intake and residual feed intake and gain and their relationships between carcass, non-carcass and meat quality traits. RFI was measured by the difference between observed and predicted dry matter intake and RIG was obtained by the sum of -1*RFI and residual gain. Efficient and inefficient animals were classified adopting ±0.5 standard deviations from RFI and RIG mean. A mixed model was used including RFI or RIG and contemporary group as fixed effects, initial age as covariate and sire and experimental period as random effects, testing the significance of the regression slope for each evaluated trait. RIG was positively related to longissimus muscle area. Efficient-RFI animals had lower liver and internal fat proportions compared to inefficient-RFI animals. Efficient-RFI and efficient-RIG animals had 11.8% and 11.2% lower extracted intramuscular fat, compared to inefficient-RFI and inefficient-RIG animals, respectively. Efficient-RFI animals had tougher meat compared to inefficient-RFI animals., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

Background: Nelore is the major beef cattle breed in Brazil with more than 130 million heads. Genome-wide association studies (GWAS) are often used to associate markers and genomic regions to growth and meat quality traits that can be used to assist selection programs. An alternative methodology to traditional GWAS that involves the construction of gene network interactions, derived from results of several GWAS is the AWM (Association Weight Matrices)/PCIT (Partial Correlation and Information Theory). With the aim of evaluating the genetic architecture of Brazilian Nelore cattle, we used high-density SNP genotyping data (~770,000 SNP) from 780 Nelore animals comprising 34 half-sibling families derived from highly disseminated and unrelated sires from across Brazil. The AWM/PCIT methodology was employed to evaluate the genes that participate in a series of eight phenotypes related to growth and meat quality obtained from this Nelore sample., Results: Our results indicate a lack of structuring between the individuals studied since principal component analyses were not able to differentiate families by its sires or by its ancestral lineages. The application of the AWM/PCIT methodology revealed a trio of transcription factors (comprising VDR, LHX9 and ZEB1) which in combination connected 66 genes through 359 edges and whose biological functions were inspected, some revealing to participate in biological growth processes in literature searches., Conclusions: The diversity of the Nelore sample studied is not high enough to differentiate among families neither by sires nor by using the available ancestral lineage information. The gene networks constructed from the AWM/PCIT methodology were a useful alternative in characterizing genes and gene networks that were allegedly influential in growth and meat quality traits in Nelore cattle.

The objective of this study was to examine the relationship of efficiency indices with performance, heart rate, oxygen consumption, blood parameters, and estimated heat production (EHP) in Nellore steers. Eighteen steers were individually lot-fed diets of 2.7 Mcal ME/kg DM for 84 d. Estimated heat production was determined using oxygen pulse (OP) methodology, in which heart rate (HR) was monitored for 4 consecutive days. Oxygen pulse was obtained by simultaneously measuring HR and oxygen consumption during a 10- to 15-min period. Efficiency traits studied were feed efficiency (G:F) and residual feed intake (RFI) obtained by regression of DMI in relation to ADG and midtest metabolic BW (RFI). Alternatively, RFI was also obtained based on equations reported by the NRC's to estimate individual requirement and DMI (RFI calculated by the NRC [1996] equation [RFI]). The slope of the regression equation and its significance was used to evaluate the effect of efficiency indices (RFI, RFI, or G:F) on the traits studied. A mixed model was used considering RFI, RFI, or G:F and pen type as fixed effects and initial age as a covariate. For HR and EHP variables, day was included as a random effect. There was no relationship between efficiency indices and back fat depth measured by ultrasound or daily HR and EHP ( > 0.05). Because G:F is obtained in relation to BW, the slope of G:F was positive and significant ( < 0.05). Regardless of the method used, efficient steers had lower DMI ( < 0.05). The initial LM area was indirectly related to RFI and RFI ( < 0.05); however, the final muscle area was related to only RFI. Oxygen consumption per beat was not related to G:F; however, it was lower for RFI- and RFI-efficient steers, and consequently, oxygen volume (mL·min·kg) and OP (μL O·beat·kg) were also lower ( < 0.05). Blood parameters were not related to RFI and RFI ( > 0.05); however, G:F-efficient steers showed lower hematocrit and hemoglobin concentrations ( < 0.05). Differences in EHP between efficient and inefficient animals were not directly detected. Nevertheless, differences in oxygen consumption and OP were detected, indicating that the OP methodology may be useful to predict growth efficiency.

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.

Background: Beef cattle require dietary minerals for optimal health, production and reproduction. Concentrations of minerals in tissues are at least partly genetically determined. Mapping genomic regions that affect the mineral content of bovine longissimus dorsi muscle can contribute to the identification of genes that control mineral balance, transportation, absorption and excretion and that could be associated to metabolic disorders., Methods: We applied a genome-wide association strategy and genotyped 373 Nelore steers from 34 half-sib families with the Illumina BovineHD BeadChip. Genome-wide association analysis was performed for mineral content of longissimus dorsi muscle using a Bayesian approach implemented in the GenSel software., Results: Muscle mineral content in Bos indicus cattle was moderately heritable, with estimates ranging from 0.29 to 0.36. Our results suggest that variation in mineral content is influenced by numerous small-effect QTL (quantitative trait loci) but a large-effect QTL that explained 6.5% of the additive genetic variance in iron content was detected at 72 Mb on bovine chromosome 12. Most of the candidate genes present in the QTL regions for mineral content were involved in signal transduction, signaling pathways via integral (also called intrinsic) membrane proteins, transcription regulation or metal ion binding., Conclusions: This study identified QTL and candidate genes that affect the mineral content of skeletal muscle. Our findings provide the first step towards understanding the molecular basis of mineral balance in bovine muscle and can also serve as a basis for the study of mineral balance in other organisms.

Background: Feed efficiency is jointly determined by productivity and feed requirements, both of which are economically relevant traits in beef cattle production systems. The objective of this study was to identify genes/QTLs associated with components of feed efficiency in Nelore cattle using Illumina BovineHD BeadChip (770 k SNP) genotypes from 593 Nelore steers. The traits analyzed included: average daily gain (ADG), dry matter intake (DMI), feed-conversion ratio (FCR), feed efficiency (FE), residual feed intake (RFI), maintenance efficiency (ME), efficiency of gain (EG), partial efficiency of growth (PEG) and relative growth rate (RGR). The Bayes B analysis was completed with Gensel software parameterized to fit fewer markers than animals. Genomic windows containing all the SNP loci in each 1 Mb that accounted for more than 1.0% of genetic variance were considered as QTL region. Candidate genes within windows that explained more than 1% of genetic variance were selected by putative function based on DAVID and Gene Ontology., Results: Thirty-six QTL (1-Mb SNP window) were identified on chromosomes 1, 2, 3, 5, 6, 7, 8, 9, 10, 12, 14, 15, 16, 18, 19, 20, 21, 22, 24, 25 and 26 (UMD 3.1). The amount of genetic variance explained by individual QTL windows for feed efficiency traits ranged from 0.5% to 9.07%. Some of these QTL minimally overlapped with previously reported feed efficiency QTL for Bos taurus. The QTL regions described in this study harbor genes with biological functions related to metabolic processes, lipid and protein metabolism, generation of energy and growth. Among the positional candidate genes selected for feed efficiency are: HRH4, ALDH7A1, APOA2, LIN7C, CXADR, ADAM12 and MAP7., Conclusions: Some genomic regions and some positional candidate genes reported in this study have not been previously reported for feed efficiency traits in Bos indicus. Comparison with published results indicates that different QTLs and genes may be involved in the control of feed efficiency traits in this Nelore cattle population, as compared to Bos taurus cattle.

Background: Meat from Bos taurus and Bos indicus breeds are an important source of nutrients for humans and intramuscular fat (IMF) influences its flavor, nutritional value and impacts human health. Human consumption of fat that contains high levels of monounsaturated fatty acids (MUFA) can reduce the concentration of undesirable cholesterol (LDL) in circulating blood. Different feeding practices and genetic variation within and between breeds influences the amount of IMF and fatty acid (FA) composition in meat. However, it is difficult and costly to determine fatty acid composition, which has precluded beef cattle breeding programs from selecting for a healthier fatty acid profile. In this study, we employed a high-density single nucleotide polymorphism (SNP) chip to genotype 386 Nellore steers, a Bos indicus breed and, a Bayesian approach to identify genomic regions and putative candidate genes that could be involved with deposition and composition of IMF., Results: Twenty-three genomic regions (1-Mb SNP windows) associated with IMF deposition and FA composition that each explain ≥1% of the genetic variance were identified on chromosomes 2, 3, 6, 7, 8, 9, 10, 11, 12, 17, 26 and 27. Many of these regions were not previously detected in other breeds. The genes present in these regions were identified and some can help explain the genetic basis of deposition and composition of fat in cattle., Conclusions: The genomic regions and genes identified contribute to a better understanding of the genetic control of fatty acid deposition and can lead to DNA-based selection strategies to improve meat quality for human consumption.

Nellore beef cattle, a Bos indicus (Zebu) breed, is well adapted to tropical conditions and has allowed Brazil to become one of the largest producers of red meat. Nevertheless, B. indicus breeds are reported to have less tender meat than Bos taurus. This study was designed to identify genes associated with meat tenderness and thus provides important information for breeding programs. A group of 138 animals was evaluated for longissimus thoracis muscle shear force (SF). Animals with the highest and lowest SF values (six animals each) were then selected for protein abundance studies. Samples were subjected to two-dimensional gel electrophoresis (2-DE) followed by peptide sequencing through mass spectrometry (MS) to identify differentially expressed proteins associated with SF values. Seventeen differentially expressed spots were observed (p<0.05) between the two groups. The 13 proteins identified included structural proteins (alpha actin-1, MLC1, MLC3, MLC2F and tropomyosin), related to cell organization (HSPB1 and HSP70), metabolism (beta-LG, ACBD6 and Complex III subunit I) and some uncharacterized proteins. Results confirm the existence of differentially expressed proteins associated with SF, which can lead to a better understanding of mechanisms involved in meat tenderness., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

Calcium (Ca) and potassium (K) are essential nutrients in animal nutrition. Furthermore, the Ca content can influence meat tenderness because it is needed by the proteolytic system of calpains and calpastatins, major factors in postmortem tenderization of skeletal muscles. K content, which is needed for muscle contraction, can also affect meat tenderness. This study showed that K positively affects the Warner-Bratzler shear force (WBSF), measured at 14days of meat aging, which means that higher levels of K are related to lower meat tenderness. Additionally, a significant effect (P≤0.015) of a SNP in the calcium-activated neutral protease 1 (CAPN1) gene on Ca content was observed. Metal content in beef can affect not only nutritional values but also meat quality traits. Part of this effect may be related to variation in specific genes., (© 2013.)

The potassium inwardly rectifying channel, subfamily J, member 11 (KCNJ11) gene was investigated as a candidate for meat tenderness based on the effects reported on muscle for KCNJ11 gene knockout in rat models and its position in a quantitative trait locus (QTL) for meat tenderness in the bovine genome. Sequence variations in the KCNJ11 gene were described by sequencing six amplified fragments, covering almost the entire gene. We identified single nucleotide polymorphisms (SNP) and validated them by different approaches, taking advantage of simultaneous projects that are being developed with the same Nelore population. By sequencing the KCNJ11 in Nelore steers representing extreme phenotypes for Warner-Bratzler shear force (WBSF), it was possible to identify 22 SNPs. We validated two of the identified markers by genotyping the whole population (n = 460). Analysis of association between genotypes and WBSF values revealed a significant additive effect of a SNP at different meat aging times (P ≤ 0.05). In addition, an association between the expression levels of KCNJ11 and WBSF was found, with lower expression levels of KCNJ11 associated with more tender meat (P ≤ 0.05). The results showed that the KCNJ11 gene is a candidate mapped to a QTL for meat tenderness previously identified on BTA15 and may be useful to identify animals with genetic potential to produce tender meat. The effect of KCNJ11 observed on muscle is potentially due to changes in activity of KATP channels, which in turn influence the flow of potassium in the intracellular space, allowing establishment of the membrane potential necessary for muscle contraction.

Meat quality traits are economically important because they affect consumers' acceptance, which, in turn, influences the demand for beef. However, selection to improve meat quality is limited by the small numbers of animals on which meat tenderness can be evaluated due to the cost of performing shear force analysis and the resultant damage to the carcass. Genome wide-association studies for Warner-Bratzler shear force measured at different times of meat aging, backfat thickness, ribeye muscle area, scanning parameters [lightness, redness (a*), and yellowness] to ascertain color characteristics of meat and fat, water-holding capacity, cooking loss (CL), and muscle pH were conducted using genotype data from the Illumina BovineHD BeadChip array to identify quantitative trait loci (QTL) in all phenotyped Nelore cattle. Phenotype count for these animals ranged from 430 to 536 across traits. Meat quality traits in Nelore are controlled by numerous QTL of small effect, except for a small number of large-effect QTL identified for a*fat, CL, and pH. Genomic regions harboring these QTL and the pathways in which the genes from these regions act appear to differ from those identified in taurine cattle for meat quality traits. These results will guide future QTL mapping studies and the development of models for the prediction of genetic merit to implement genomic selection for meat quality in Nelore cattle.

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.

The ASAP1 gene is located in a QTL region for meat production traits and to access the role of the ASAP1 gene, the association between a SNP in this gene and production traits in beef cattle was studied. For this, about 270 steers of reference families of Nelore breed were used. The investigation of marker effects on the traits was performed using a mixed model under the restricted maximum likelihood method. Novel association of a SNP in the ASAP1 gene and shear force measured at 24 h post mortem (P≤0.0083) was described in this population of Nelore cattle. This polymorphism accounted for 1.13% of the total additive variance and 17.51% of total phenotypic variance of the trait, suggesting that this marker could be used in marker assisted selection., (Copyright © 2012 Elsevier Ltd. All rights reserved.)