A. N. Rosa

Identification of genomic regions associated with feed efficiency in Nelore cattle

BackgroundFeed 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.ResultsThirty-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.ConclusionsSome 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.

Peso adulto de matrizes em rebanhos de seleção da raça Nelore no Brasil

The main objective of this work was to evaluate the Nellore breed in Brazil with respect to the phenotypic and genetic variation of the mature size of cows. The observations were taken from 34 herds of eleven different beef cattle production regions in the country. There were considered cows of the horned and polled varieties, raised on pastures, from herds that had at least 50 cows. With these restrictions it was formed a general file with 6,867 cows with valid observations on mature weight (MW) and a genetic relationship matrix with 17,039 animals. Body weight, as indicator of the mature size, was defined as the first weight (kg) observed since the cows were from four through twelve years old. This weight was taken under one of three different conditions: normal, at the routine weighing, in April and October, according to the established schedule of the program, at parturition or at weaning of the calf. Data management and statistical analyses were carried out through the utilization of the Statistical Analysis System (SAS). Herd, year of birth, year of weighing, condition at weighing, season of weighing and the interactions year*season of birth and year*season of weighing were the most important sources of variation for MW. The overall mean for mature weight was 447 kg, with a coefficient of variation of 11%. The genetic analysis was carried out by the use of the Multiple Trait Derivative-Free Restricted Maximum Likelihood (MTDFREML) algorithm under an animal model. The 1,126 contemporary groups included cows from the same herd, born at the same year, weighted at the same year and season and at the same condition at weighing. The additive genetic (537.78 kg2), residual (1,553.22 kg2) and phenotypic (2,090.59 kg2) variance components provided a heritability estimate of 0.26, for MW. The predicted genetic breeding values varied from -41.9 through +61.4 kg, with accuracy ranging from 0 to 0.95.

Calcium and potassium content in beef: Influences on tenderness and associations with molecular markers in Nellore cattle

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.

Feed efficiency indexes and their relationships with carcass, non-carcass and meat quality traits in Nellore steers.

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.

Identification of KCNJ11 as a functional candidate gene for bovine meat tenderness

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.

Relationship of efficiency indices with performance, heart rate, oxygen consumption, blood parameters, and estimated heat production in Nellore steers.

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 NRCs 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.

A genome‐wide scan for selection signatures in Nellore cattle

Brazilian Nellore cattle (Bos indicus) have been selected for growth traits for over more than four decades. In recent years, reproductive and meat quality traits have become more important because of increasing consumption, exports and consumer demand. The identification of genome regions altered by artificial selection can potentially permit a better understanding of the biology of specific phenotypes that are useful for the development of tools designed to increase selection efficiency. Therefore, the aims of this study were to detect evidence of recent selection signatures in Nellore cattle using extended haplotype homozygosity methodology and BovineHD marker genotypes (>777,000 single nucleotide polymorphisms) as well as to identify corresponding genes underlying these signals. Thirty-one significant regions (P < 0.0001) of possible recent selection signatures were detected, and 19 of these overlapped quantitative trait loci related to reproductive traits, growth, feed efficiency, meat quality, fatty acid profiles and immunity. In addition, 545 genes were identified in regions harboring selection signatures. Within this group, 58 genes were associated with growth, muscle and adipose tissue metabolism, reproductive traits or the immune system. Using relative extended haplotype homozygosity to analyze high-density single nucleotide polymorphism marker data allowed for the identification of regions potentially under artificial selection pressure in the Nellore genome, which might be used to better understand autozygosity and the effects of selection on the Nellore genome.

Herdabilidade da habilidade de permanência no rebanho em fêmeas de bovinos da raça Canchim

Abstract€–€The€objective of this work was to evaluate the effectiveness of using the stayability of beef cows asselection criterion for the Canchim breed. Stayability was defined as the probability of a beef cow having threeor more parities up to 76€months of age, given that she have calved at least once and was older than 76€months.Binary coding, with€0 indicating failure and€1 indicating success, was defined for each cow. An alternativecoding, with four categories, used the values€0, 1, 2 and€3, respectively , for cows with less than three, three, fouror five parities up to 76€months of age. The analises were perfomed with a single-trait sire and maternal grandsiremodel. Gibbs sampling was used to estimate variance components and heritabilities. The estimated heritabilitywas€0.07 for the binary trait and€0.08 for the trait with the four categories. The results indicate small diferences inthe estimated heritability for the binary and four-category models. They also suggest that the stayability inCanchim breed presents low potential for response to selection.Index terms: reprodutive trait, beef cattle, treshold model, genetic parameters.

Estimativas de componentes de (co)variância para peso e escores visuais de conformação frigorífica em bovinos Nelore

The aim of this study was to estimate variance components, heritability and genetic correlation for slaughter conformation at weaning (SCW), slaughter conformation at yearling age (SCY), weaning weight (WW) and yearling age weight (YW) of Nellore cattle. A total of 6,397 records of all traits measured at weaning and at yearling age were used in the analysis. A multiple trait animal model which included the direct genetic additive, maternal genetic additive, maternal permanent environmental and residual random effects, as well as the fixed effect of contemporary group and the covariates age at calving (for weight and slaughter conformation at weaning and yearling age) and age at the evaluation time (slaughter conformation at weaning and yearling age) was proposed. The heritability estimates for SCW, SCY, WW and YW were, respectively, 0.13, 0.25, 0.22 and 0.29. Positive and high genetic correlations between body weight traits and visual evaluation traits suggested that direct selection for one trait results in positive indirect response in the remaining trait. Slaughter conformation trait can be selected at earlier age due to the high and positive genetic correlation between conformation scores at different age.

Genetic evaluation for large data sets by random regression models in Nellore cattle

Expected progeny differences (EPD) of Nellore cattle estimated by random regression model (RRM) and multiple trait model (MTM) were compared. Genetic evaluation data included 3,819,895 records of up nine sequential weights of 963,227 animals measured at ages ranging from one day (birth weight) to 733 days. Traits considered were weights at birth, ten to 110-day old, 102 to 202-day old, 193 to 293-day old, 283 to 383-day old, 376 to 476-day old, 551 to 651-day old, and 633 to 733-day old. Seven data samples were created. Because the parameters estimates biologically were better, two of them were chosen: one with 84,426 records and another with 72,040. Records preadjusted to a fixed age were analyzed by a MTM, which included the effects of contemporary group, age of dam class, additive direct, additive maternal, and maternal permanent environment. Analyses were carried out by REML, with five traits at a time. The RRM included the effects of age of animal, contemporary group, age of dam class, additive direct, permanent environment, additive maternal, and maternal permanent environment. Different degree of Legendre polynomials were used to describe random effects. MTM estimated covariance components and genetic parameters for weight at birth and sequential weights and RRM for all ages. Due to the fact that correlation among the estimates EPD from MTM and all the tested RM were not equal to 1.0, it is not possible to recommend RRM to genetic evaluation to large data sets.