The selection of beef cattle for feed efficiency (FE) traits is very important not only for productive and economic efficiency but also for reduced environmental impact of livestock. Considering that ...FE is multifactorial and expensive to measure, the aim of this study was to identify biological functions and regulatory genes associated with this phenotype.
Eight genes were differentially expressed between high and low feed efficient animals (HFE and LFE, respectively). Co-expression analyses identified 34 gene modules of which 4 were strongly associated with FE traits. They were mainly enriched for inflammatory response or inflammation-related terms. We also identified 463 differentially co-expressed genes which were functionally enriched for immune response and lipid metabolism. A total of 8 key regulators of gene expression profiles affecting FE were found. The LFE animals had higher feed intake and increased subcutaneous and visceral fat deposition. In addition, LFE animals showed higher levels of serum cholesterol and liver injury biomarker GGT. Histopathology of the liver showed higher percentage of periportal inflammation with mononuclear infiltrate.
Liver transcriptomic network analysis coupled with other results demonstrated that LFE animals present altered lipid metabolism and increased hepatic periportal lesions associated with an inflammatory response composed mainly by mononuclear cells. We are now focusing to identify the causes of increased liver lesions in LFE animals.
Cis
-acting effects of noncoding variants on gene expression and regulatory molecules constitute a significant factor for phenotypic variation in complex traits. To provide new insights into the ...impacts of single-nucleotide polymorphisms (SNPs) on transcription factors (TFs) and transcription cofactors (TcoF) coding genes, we carried out a multi-omic analysis to identify
cis
-regulatory effects of SNPs on these genes’ expression in muscle and describe their association with feed efficiency-related traits in Nelore cattle. As a result, we identified one SNP, the rs137256008C > T, predicted to impact the
EEF1A1
gene expression (
β
= 3.02;
P
-value = 3.51E-03) and the residual feed intake trait (
β
= − 3.47;
P-
value = 0.02). This SNP was predicted to modify transcription factor sites and overlaps with several QTL for feed efficiency traits. In addition, co-expression network analyses showed that animals containing the T allele of the rs137256008 SNP may be triggering changes in the gene network. Therefore, our analyses reinforce and contribute to a better understanding of the biological mechanisms underlying gene expression control of feed efficiency traits in bovines. The
cis
-regulatory SNP can be used as biomarker for feed efficiency in Nelore cattle.
The prenatal environment is recognized as crucial for the postnatal performance in cattle. In tropical regions, pregnant beef cows commonly experience nutritional restriction during the second half ...of the gestation period. Thus, the present study was designed to analyze the genotype by prenatal environment interaction (G × Epn) and to identify genomic regions associated with the level and response in growth and reproduction-related traits of beef cattle to changes in the prenatal environment. A reaction norm model was applied to data from two Nelore herds using the solutions of contemporary groups for birth weight as a descriptor variable of the gestational environment quality. A better gestational environment favored weights until weaning, scrotal circumference at yearling, and days to first calving of the offspring. The G × Epn was strong enough to result in heterogeneity of variance components and genetic parameters in addition to reranking of estimated breeding values and SNPs effects. Several genomic regions associated with the level of performance and specific responses of the animals to variations in the gestational environment were revealed, which harbor QTLs and can be exploited for selection purposes. Therefore, genetic evaluation models considering G × Epn and special management and nutrition care for pregnant cows are recommended.
Urban air pollution is a global concern impairing citizens' health, thus monitoring is a pressing need for city managers. City-wide networks for air pollution monitoring based on low-cost sensors are ...promising to provide real-time data with detail and scale never before possible. However, they still present limitations preventing their ubiquitous use. Thus, this study aimed to perform a post-deployment validation and calibration based on two step methods for ozone low-cost sensor of a city-wide network for air pollution and meteorology monitoring using low-cost sensors focusing on the main challenges. Four of the 23 data collection units (DCUs) of the UrbanSense network installed in Porto city (Portugal) with low-cost sensors for particulate matter (PM), carbon monoxide (CO), ozone (O3), and meteorological variables (temperature, relative humidity, luminosity, precipitation, and wind speed and direction) were evaluated. This study identified post-deployment challenges related to their validation and calibration. The preliminary validation showed that PM, CO and precipitation sensors recorded only unreliable data, and other sensors (wind speed and direction) very few data. A multi-step calibration strategy was implemented: inter-DCU calibration (1st step, for O3, temperature and relative humidity) and calibration with a reference-grade instrument (2nd step, for O3). In the 1st step, multivariate linear regression (MLR) resulted in models with better performance than non-linear models such as artificial neural networks (errors almost zero and R2 > 0.80). In the 2nd step, the calibration models using non-linear machine learning boosting algorithms, namely Stochastic Gradient Boosting Regressor (both with the default and post-tuning hyper-parameters), performed better than artificial neural networks and linear regression approaches. The calibrated O3 data resulted in a marginal improvement from the raw data, with error values close to zero, with low predictability (R2 ∼ 0.32). The lessons learned with the present study evidenced the need to redesign the calibration strategy. Thus, a novel multi-step calibration strategy is proposed, based on two steps (pre and post-deployment calibration). When performed cyclically and continuously, this strategy reduces the need for reference instruments, while probably minimising data drifts over time. More experimental campaigns are needed to collect more data and further improve calibration models.
Display omitted
•Air quality low-cost sensors still have some limitations concerning low accuracy.•Linear and non-linear models were used to validate and calibrate low-cost sensors data.•A two steps calibration method was adopted.•The models obtained for both calibration steps were satisfactory.
Zebu animals () are known to take longer to reach puberty compared with taurine animals (), limiting the supply of animals for harvest or breeding and impacting profitability. Genomic information can ...be a helpful tool to better understand complex traits and improve genetic gains. In this study, we performed a genomewide association study (GWAS) to identify genetic variants associated with reproductive traits in Nelore beef cattle. Heifer pregnancy (HP) was recorded for 1,267 genotyped animals distributed in 12 contemporary groups (CG) with an average pregnancy rate of 0.35 (±0.01). Disregarding one of these CG, the number of antral follicles (NF) was also collected for 937 of these animals, with an average of 11.53 (±4.43). The animals were organized in CG: 12 and 11 for HP and NF, respectively. Genes in linkage disequilibrium (LD) with the associated variants can be considered in a functional enrichment analysis to identify biological mechanisms involved in fertility. Medical Subject Headings (MeSH) were detected using the MESHR package, allowing the extraction of broad meanings from the gene lists provided by the GWAS. The estimated heritability for HP was 0.28 ± 0.07 and for NF was 0.49 ± 0.09, with the genomic correlation being -0.21 ± 0.29. The average LD between adjacent markers was 0.23 ± 0.01, and GWAS identified genomic windows that accounted for >1% of total genetic variance on chromosomes 5, 14, and 18 for HP and on chromosomes 2, 8, 11, 14, 15, 16, and 22 for NF. The MeSH enrichment analyses revealed significant ( < 0.05) terms associated with HP-"Munc18 Proteins," "Fucose," and "Hemoglobins"-and with NF-"Cathepsin B," "Receptors, Neuropeptide," and "Palmitic Acid." This is the first study in Nelore cattle introducing the concept of MeSH analysis. The genomic analyses contributed to a better understanding of the genetic control of the reproductive traits HP and NF and provide new selection strategies to improve beef production.
Scrotal circumference data from 47,605 Nellore young bulls, measured at around 18 mo of age (SC18), were analyzed simultaneously with 27,924 heifer pregnancy (HP) and 80,831 stayability (STAY) ...records to estimate their additive genetic relationships. Additionally, the possibility that economically relevant traits measured directly in females could replace SC18 as a selection criterion was verified. Heifer pregnancy was defined as the observation that a heifer conceived and remained pregnant, which was assessed by rectal palpation at 60 d. Females were exposed to sires for the first time at about 14 mo of age (between 11 and 16 mo). Stayability was defined as whether or not a cow calved every year up to 5 yr of age, when the opportunity to breed was provided. A Bayesian linear-threshold-threshold analysis via Gibbs sampler was used to estimate the variance and covariance components of the multitrait model. Heritability estimates were 0.42 ± 0.01, 0.53 ± 0.03, and 0.10 ± 0.01, for SC18, HP, and STAY, respectively. The genetic correlation estimates were 0.29 ± 0.05, 0.19 ± 0.05, and 0.64 ± 0.07 between SC18 and HP, SC18 and STAY, and HP and STAY, respectively. The residual correlation estimate between HP and STAY was -0.08 ± 0.03. The heritability values indicate the existence of considerable genetic variance for SC18 and HP traits. However, genetic correlations between SC18 and the female reproductive traits analyzed in the present study can only be considered moderate. The small residual correlation between HP and STAY suggests that environmental effects common to both traits are not major. The large heritability estimate for HP and the high genetic correlation between HP and STAY obtained in the present study confirm that EPD for HP can be used to select bulls for the production of precocious, fertile, and long-lived daughters. Moreover, SC18 could be incorporated in multitrait analysis to improve the prediction accuracy for HP genetic merit of young bulls.
The objective of this study was to evaluate the genetic relationship between postweaning weight gain (PWG), heifer pregnancy (HP), scrotal circumference (SC) at 18 months of age, stayability at 6 ...years of age (STAY) and finishing visual score at 18 months of age (PREC), and to determine the potential of these traits as selection criteria for the genetic improvement of growth and reproduction in Nellore cattle. The HP was defined as the observation that a heifer conceived and remained pregnant, which was assessed by rectal palpation at 60 days. The STAY was defined as whether or not a cow calved every year up to the age of 6 years, given that she was provided the opportunity to breed. The Bayesian linear-threshold analysis via the Gibbs sampler was used to estimate the variance and covariance components applying a multitrait model. Posterior mean estimates of direct heritability were 0.15 ± 0.00, 0.42 ± 0.02, 0.49 ± 0.01, 0.11 ± 0.01 and 0.19 ± 0.00 for PWG, HP, SC, STAY and PREC, respectively. The genetic correlations between traits ranged from 0.17 to 0.62. The traits studied generally have potential for use as selection criteria in genetic breeding programs. The genetic correlations between all traits show that selection for one of these traits does not imply the loss of the others.
The objective of the study presented here was to analyze the genetic relationships among heifer pregnancy (HP), age at first calving (AFC), stayability (STAY), average annual productivity of the cow, ...in kilograms of weaned calf per cow per year (PRODAM), postweaning weight gain (PWG), and hip height (HH) of Nelore females from 12 Brazilian herds. (Co)variance components were obtained by six-trait animal model using Gibbs sampling. The posterior mean of the heritability estimates were 0.37, 0.18, 0.19, 0.16, 0.21, and 0.37 for HP, AFC, STAY, PRODAM, PWG, and HH, respectively. In general, the genetic correlations were strong between traits related to reproduction, for example, −0.85 between HP and AFC, and 0.94 between STAY and PRODAM. Weak genetic correlations were obtained between reproductive and growth traits (absolute values ranging from 0.02 to 0.30). Although weak, the genetic correlations between PWG and reproductive traits were favorable, whereas the genetic correlations between HH and reproductive traits were close to zero and slightly unfavorable for HP, AFC, and STAY. An increase of HH is therefore expected to have little or no negative effect on the reproductive performance of females. The posterior mean of genetic correlation between PWG and HH was moderate (0.50). On the basis of the heritability, genetic correlation estimates, and time to obtain data, HP and PRODAM seems to show the best potential as selection criteria to improve the productive and reproductive performance of Nelore females. In principle, it is possible to select for increased PWG without compromising the reproduction of Nelore females. However, selection for PWG may result in an increase of female HH as a correlated response, a fact that could increase management costs in advanced generations of selection. In the light of the results, all traits studied here can be used as selection criteria and there is no strong evidence of genetic antagonism among traits related to reproduction and growth of Nelore females.
Genetic parameters, genetic trends, and genetic progress of carcass traits were estimated for 12,447 Nellore individuals from different Brazilian herds. The following carcass traits were analyzed: ...visual body scores of conformation (CONF), precocity (PREC), and muscularity (MUSC); rump width (RW) and rump length (RL), body size (frame); and ultrasound evaluation of ribeye area (REA), backfat thickness (BFT), and rump fat thickness (RFT). Heritability estimates (± SE) for CONF, PREC, and MUSC were 0.23 ± 0.02, 0.33 ± 0.03, and 0.31 ± 0.02, respectively. The heritability estimates (± SE) for RW, RL, and frame were 0.25 ± 0.05, 0.16 ± 0.04, and 0.31 ± 0.03, respectively. Ultrasound of the REA, BFT, and RFT presented mean heritability estimates (± SE) of 0.38 ± 0.03, 0.44 ± 0.04, and 0.47 ± 0.04, respectively. The visual body score of CONF had high genetic correlations with RW, RL, and frame (0.74 ± 0.09, 0.82 ± 0.08, and 0.83 ± 0.04, respectively), indicating a high association of CONF with the measurements related to body structure. The REA had no correlation with BFT and RFT (-0.09 ± 0.04 and -0.03 ± 0.04, respectively) and showed only a moderate genetic correlation with MUSC (0.39 ± 0.05). The BFT and RFT had moderate genetic correlations with PREC (0.36 ± 0.07 and 0.29 ± 0.07, respectively) and no correlation with frame (-0.02 ± 0.03 and 0.05 ± 0.05, respectively), suggesting that selection for frame had no effect on the subcutaneous fat content of the carcass. Low genetic trends and low genetic progress were obtained for REA (0.026 cm, 0.02%), BFT (0.0031 mm, 0.05%), and RFT (0.0013 mm, 0.02%), with no significant values of genetic progress detected throughout the studied period. The CONF, PREC, and MUSC presented high genetic trends (0.030 points, 0.030 points, and 0.029 points, respectively) and high genetic progress (0.60%, 0.56%, and 0.59%, respectively), indicating a significant genetic progress for these traits throughout the evaluated period. Carcass traits evaluated by ultrasound and visual body scores are eligible for selection and can be used in genetic improvement programs in Nellore cattle; however, visual body score selection for carcass traits can result in slower genetic progress for carcass quality when compared to selection performed by ultrasound.
Influences of inbreeding on daily milk yield (DMY), age at first calving (AFC), and calving intervals (CI) were determined on a highly inbred zebu dairy subpopulation of the Guzerat breed. Variance ...components were estimated using animal models in single-trait analyses. Two approaches were employed to estimate inbreeding depression: using individual increase in inbreeding coefficients or using inbreeding coefficients as possible covariates included in the statistical models. The pedigree file included 9,915 animals, of which 9,055 were inbred, with an average inbreeding coefficient of 15.2%. The maximum inbreeding coefficient observed was 49.45%, and the average inbreeding for the females still in the herd during the analysis was 26.42%. Heritability estimates were 0.27 for DMY and 0.38 for AFC. The genetic variance ratio estimated with the random regression model for CI ranged around 0.10. Increased inbreeding caused poorer performance in DMY, AFC, and CI. However, some of the cows with the highest milk yield were among the highly inbred animals in this subpopulation. Individual increase in inbreeding used as a covariate in the statistical models accounted for inbreeding depression while avoiding overestimation that may result when fitting inbreeding coefficients.
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