Genetic and phenotypic relationships of feeding behavior and temperament with performance, feed efficiency, ultrasound, and carcass merit of beef cattle

A review of the role of transcription factors in regulating adipogenesis and lipogenesis in beef cattle

In the past few decades, genomic selection and other refined strategies have been used to increase the growth rate and lean meat production of beef cattle. Nevertheless, the fast growth rates of cattle breeds are often accompanied by a reduction in intramuscular fat (IMF) deposition, impairing meat quality. Transcription factors play vital roles in regulating adipogenesis and lipogenesis in beef cattle. Meanwhile, understanding the role of transcription factors in regulating adipogenesis and lipogenesis in beef cattle has gained significant attention to increase IMF deposition and meat quality. Therefore, the aim of this paper was to provide a comprehensive summary and valuable insight into the complex role of transcription factors in adipogenesis and lipogenesis in beef cattle. This review summarizes the contemporary studies in transcription factors in adipogenesis and lipogenesis, genome-wide analysis of transcription factors, epigenetic regulation of transcription factors, nutritional regulation of transcription factors, metabolic signalling pathways, functional genomics methods, transcriptomic profiling of adipose tissues, transcription factors and meat quality and comparative genomics with other livestock species. In conclusion, transcription factors play a crucial role in promoting adipocyte development and fatty acid biosynthesis in beef cattle. They control adipose tissue formation and metabolism, thereby improving meat quality and maintaining metabolic balance. Understanding the processes by which these transcription factors regulate adipose tissue deposition and lipid metabolism will simplify the development of marbling or IMF composition in beef cattle.

Estimation of genetic parameters and single-step genome-wide association studies for eating time and rumination time in Holstein dairy cows

The aims of this study were to estimate genetic parameters and to identify genomic regions associated with eating time (ET) and rumination time (RUT) in Holstein dairy cows. Genetic correlations among ET, RUT, and milk yield traits were also estimated. The data were collected from 2019 to 2022 in 6 dairy herds located in the Walloon Region of Belgium. The dataset consisted of daily ET and RUT records on 284 Holstein cows, from which 41 cows had records only for the first parity (P1), 101 cows had records from both the first and second parities, and 142 cows had records only for the second parity (P2). The number of daily ET and RUT records in the P1 and P2 cows were 18,569 (on 142 cows) and 34,464 (on 243 cows), respectively. Data on 28,994 SNPs located on 29 Bos taurus autosomes (BTA) of 747 animals (435 males) were used. Random regression test-day models were used to estimate genetic parameters through the Bayesian Gibbs sampling method. The SNP solutions were estimated using a single-step genomic best linear unbiased prediction approach. The proportion of genetic variance explained by each 20-SNP sliding window (with an average size of 1.52 Mb) was calculated, and regions accounting for at least 1.0% of the total additive genetic variance were used to search for candidate genes. Mean (standard deviation; SD) averaged daily ET and RUT were 327.0 (85.66) and 559.4 (77.69) min/d for cows in P1 and 316.0 (82.24) and 574.2 (75.42) min/d for cows in P2, respectively. Mean (standard deviation; SD) heritability estimates for daily ET and RUT were 0.42 (0.09) and 0.45 (0.06) for cows in P1 and 0.45 (0.04) and 0.43 (0.02) for cows in P2, respectively. Mean (SD) daily genetic correlations between daily ET and RUT were 0.27 (0.07) for P1 and 0.34 (0.08) for P2. Genome-wide association analyses identified 6 genomic regions distributed over 5 chromosomes (BTA1, BTA4, BTA11, 2 regions of BTA14, and BTA17) associated with ET or RUT. The findings of this study increase our preliminary understanding of the genetic background of feeding behavior in dairy cows; however, larger datasets are needed to determine whether ET and RUT might have the potential to be used in selection programs.

Genome-wide association study between copy number variation and feeding behavior, feed efficiency, and growth traits in Nellore cattle

BACKGROUND

Feeding costs represent the largest expenditures in beef production. Therefore, the animal efficiency in converting feed in high-quality protein for human consumption plays a major role in the environmental impact of the beef industry and in the beef producers' profitability. In this context, breeding animals for improved feed efficiency through genomic selection has been considered as a strategic practice in modern breeding programs around the world. Copy number variation (CNV) is a less-studied source of genetic variation that can contribute to phenotypic variability in complex traits. In this context, this study aimed to: (1) identify CNV and CNV regions (CNVRs) in the genome of Nellore cattle (Bos taurus indicus); (2) assess potential associations between the identified CNVR and weaning weight (W210), body weight measured at the time of selection (WSel), average daily gain (ADG), dry matter intake (DMI), residual feed intake (RFI), time spent at the feed bunk (TF), and frequency of visits to the feed bunk (FF); and, (3) perform functional enrichment analyses of the significant CNVR identified for each of the traits evaluated.

RESULTS

A total of 3,161 CNVs and 561 CNVRs ranging from 4,973 bp to 3,215,394 bp were identified. The CNVRs covered up to 99,221,894 bp (3.99%) of the Nellore autosomal genome. Seventeen CNVR were significantly associated with dry matter intake and feeding frequency (number of daily visits to the feed bunk). The functional annotation of the associated CNVRs revealed important candidate genes related to metabolism that may be associated with the phenotypic expression of the evaluated traits. Furthermore, Gene Ontology (GO) analyses revealed 19 enrichment processes associated with FF.

CONCLUSIONS

A total of 3,161 CNVs and 561 CNVRs were identified and characterized in a Nellore cattle population. Various CNVRs were significantly associated with DMI and FF, indicating that CNVs play an important role in key biological pathways and in the phenotypic expression of feeding behavior and growth traits in Nellore cattle.

Calming Hungarian Grey Cattle in Headlocks Using Processed Nasal Vocalization of a Mother Cow

Sound analysis is an important field of research for improving precision livestock farming systems. If the information carried by livestock sounds is interpreted correctly, it could be used to improve management and welfare assessment in this field. Therefore, we hypothesized that the nasal vocalization of a mother cow could have a calming effect on conspecifics. The nasal vocalization in our study was recorded from a mother cow (not part of the test herd) while it was licking its day-old calf. The raw sound was analyzed, cleaned from noises, and the most representative vocalization was lengthened to two minutes. Thirty cows having calves were randomly selected from eighty Hungarian grey cattle cows. Two test days were selected, one week apart; the weather circumstances in both days were similar. The herd was collected in a paddock, and the test site (a restraining crate with a headlock) was 21 m away from them. The cows from the herd were gently moved to the restraining crate, and, after the installation of the headlock, Polar® heart rate monitors were fixed on the animals. The recording of the RR intervals was carried out for two minutes. On day one of the test, the processed nasal sound was played to every second cow during the heart rate monitoring. When the sound ended, the heart rate monitor was removed. On test day two, the sound and no sound treatments were switched among the participating cows. At the end of the measurement, the headlock was opened, letting the animals out voluntarily, and a flight test was performed along a 5 m distance. The time needed to pass the 5 m length was measured with a stopwatch and divided by the distance. The RR intervals were analyzed with the Kubios HRV Standard (ver. 3.5.0) software. The following data were recorded for the entire measurement: average and maximum heart rate; SD1 and SD2; pNN50; VLF, LF, and HF. The quasi-periodic signal detected in the sound analyses can hardly be heard, even when it is enhanced to the maximum. This can be considered a vibration probably caused by the basis of articulation, such as a vibration of the tongue, for example. The SD2/SD1 ratio (0.97 vs. 1.07 for the animals having no sound and sound played, respectively, p = 0.0110) and the flight speed (0.92 vs. 1.08 s/m for the animals having no sound and sound played, respectively, p = 0.0409) indicate that the sound treatment had a calming effect on the restrained cows. The day of the test did not influence any of the measured parameters; therefore, no effect of the routine was observed. The yes-no sequence of the sound treatment significantly reduced the pNN50 and flight speed values, suggesting a somewhat more positive association with the headlock and the effectiveness of the processed nasal sound. In conclusion, we have demonstrated that, by means of sound analyses, not only information about individuals and the herd can be gathered but that, with proper processing, the sound obtained can be used to improve animal welfare.

Using dynamic modelling to enhance the assessment of the beef water footprint

Current water footprint assessment methods make a meaningful assessment of livestock water consumption difficult as they are mainly static, thus poorly adaptable to understanding future water consumption and requirements. They lack the integration of fundamental ruminant nutrition and growth equations within a dynamic context that accounts for short- and long-term behaviour and time delays associated with economically significant beef-producing areas. The current study utilised the System Dynamics methodology to conceptualise a water footprint for beef cattle within a dynamic and mechanistic modelling framework. The problem of assessing the water footprint of beef cattle was articulated, and a dynamic hypothesis was formed to represent the Texas livestock water use system as the initial step in developing the Dynamic Beef Water Footprint model (DWFB). The dynamic hypothesis development resulted in three causal loop diagrams (CLD): cattle population, growth and nutrition, and the livestock water footprint, that captured the daily water footprint of beef (WFB). Simulations and sensitivity analysis from the hypothesised CLD structures indicated that the framework was able to capture the dynamic behaviour of the WFB system. These behaviours included key reinforcing and balancing feedback processes that drive the WFB. It is extremely difficult to identify policy interventions (i.e., management strategies) for complex systems, like the U.S. beef cattle system, because there are many actors (i.e., cow-calf, stocker, feedlot) and interrelated variables that have delayed effects within and across the supply chain. Identification and understanding of feedback processes driving water use over time will help to overcome policy resistance for more sustainable beef production. Thus, the causal loops identified in the current study provide a system-level insight for the drivers of the WFB within and across each major segment of the beef supply chain to address freshwater concerns more adequately. Further, the nutrient scenarios and sensitivity analysis revealed that the high versus low nutrient composition of pasture, hay, and concentrates resulted in a significant difference in the WFB (2 669 L/kg boneless beef, P < 0.05). The WFB was sensitive to changes in nutrient composition and specific water demand (m3/t) for each production phase, not only phases with high levels of concentrate feed use. As models evolve, there is potential for the DWFB to integrate precision livestock data, further improving quantification of the WFB, precision water-efficient strategies, and selection of water-efficient livestock.

Genomic Selection for Dairy Cattle Behaviour Considering Novel Traits in a Changing Technical Production Environment

Cow behaviour is a major factor influencing dairy herd profitability and is an indicator of animal welfare and disease. Behaviour is a complex network of behavioural patterns in response to environmental and social stimuli and human handling. Advances in agricultural technology have led to changes in dairy cow husbandry systems worldwide. Increasing herd sizes, less time availability to take care of the animals and modern technology such as automatic milking systems (AMSs) imply limited human-cow interactions. On the other hand, cow behaviour responses to the technical environment (cow-AMS interactions) simultaneously improve production efficiency and welfare and contribute to simplified "cow handling" and reduced labour time. Automatic milking systems generate objective behaviour traits linked to workability, milkability and health, which can be implemented into genomic selection tools. However, there is insufficient understanding of the genetic mechanisms influencing cow learning and social behaviour, in turn affecting herd management, productivity and welfare. Moreover, physiological and molecular biomarkers such as heart rate, neurotransmitters and hormones might be useful indicators and predictors of cow behaviour. This review gives an overview of published behaviour studies in dairy cows in the context of genetics and genomics and discusses possibilities for breeding approaches to achieve desired behaviour in a technical production environment.

Characterization of feed efficiency-related key signatures molecular in different cattle breeds

Feed efficiency is a major constraint in the beef industry and has a significant negative correlation with residual feed intake (RFI). RFI is widely used as a measure of feed efficiency in beef cattle and is independent of economic traits such as body weight and average daily gain. However, key traits with commonality or specificity among beef cattle breeds at the same level of RFI have not been reported. Accordingly, the present study hypothesized that signatures associated with feed efficiency would have commonality or specificity in the liver of cattle breeds at the same RFI level. By comparing and integrating liver transcriptome data, we investigated the critical signatures closely associated with RFI in beef cattle using weighted co-expression network analysis, consensus module analysis, functional enrichment analysis and protein network interaction analysis. The results showed that the consensus modules in Angus and Charolais cattle were negatively correlated, and four (turquoise, red, tan, yellow) were significantly positively correlated in Angus liver, while (turquoise, red) were significantly negatively correlated in Charolais liver. These consensus modules were found to be primarily involved in biological processes such as substance metabolism, energy metabolism and gene transcription, which may be one of the possible explanations for the difference in feed efficiency between the two beef breeds. This research also identified five key candidate genes, PLA2G12B, LCAT, MTTP, LCAT, ABCA1 and FADS1, which are closely associated with hepatic lipid metabolism. The present study has identified some modules, genes and pathways that may be the major contributors to the variation in feed efficiency among different cattle breeds, providing a new perspective on the molecular mechanisms of feed efficiency in beef cattle and a research basis for investigating molecular markers associated with feed efficiency in beef cattle.

Multi-breed host rumen epithelium transcriptome and microbiome associations and their relationship with beef cattle feed efficiency

Understanding host-microbial interactions in the rumen and its influence on desirable production traits may lead to potential microbiota manipulation or genetic selection for improved cattle feed efficiency. This study investigated the host transcriptome and its correlation with the rumen archaea and bacteria differential abundance of two pure beef cattle breeds (Angus and Charolais) and one composite beef hybrid (Kinsella) divergent for residual feed intake (RFI; low-RFI vs. high-RFI). Using RNA-Sequencing of rumen tissue and 16S rRNA gene amplicon sequencing, differentially expressed genes (FDR ≤ 0.05, |log2(Fold-change) >|2) and differentially abundant (p-value < 0.05) archaea and bacteria amplicon sequence variants (ASV) were determined. Significant correlations between gene expression and ASVs (p-value < 0.05) were determine using Spearman correlation. Interesting associations with muscle contraction and the modulation of the immune system were observed for the genes correlated with bacterial ASVs. Potential functional candidate genes for feed efficiency status were identified for Angus (CCL17, CCR3, and CXCL10), Charolais (KCNK9, GGT1 and IL6), and Kinsella breed (ESR2). The results obtained here provide more insights regarding the applicability of target host and rumen microbial traits for the selection and breeding of more feed efficient beef cattle.

Contemporary Knowledge on the Assessment of Temperament in Cattle and Its Impact on Production and Reproduction Including Some Immunological, Genetic and Metabolic Parameters

Temperament is associated with the well-being, health, production and reproduction of cattle. In order to increase the population of individuals with the desired temperament, its evaluation should be standardized and be made one of the obligatory elements of breeding and veterinary examination. A number of different tests are used for temperament assessment. In this article, the importance of temperament correlation with some metabolic, genetic, immunological, production and reproductive parameters have been shown, pointing at its influence on the economy and cattle handling. The most common methods for assessing the temperament of cattle are presented, including long-time scales of temperament assessment. At the same time, the relationship of the temperament of cattle with production efficiency, immunity and reproductive indicators has been shown, indicating that its correct assessment is an important aspect of the proper development of the herd and the associated economic growth.

Heritability and variance component estimation for feed and water intake behaviors of feedlot cattle

Feed and water intake are two important aspects of cattle production that greatly impact the profitability, efficiency, and sustainability of producers. Feed and, to a lesser degree, water intake have been studied previously; however, there is little research on their associated animal behaviors and there is a lack of standardized phenotypes for these behaviors. Feed and water intakes obtained with an Insentec system (Hokofarm Group, The Netherlands) from 830 crossbred steers were used to compute five intake behaviors for both feed and water: daily sessions (DS), intake rate (IR), session size (SS), time per session (TS), and session interval (SI). Variance components and heritabilities were estimated for each trait. Heritabilities for feed intake behaviors were 0.50 ± 0.12, 0.63 ± 0.12, 0.40 ± 0.13, 0.35 ± 0.12, and 0.60 ± 0.12 for DS, IR, SS, TS, and SI, respectively. Heritabilities for water intake behaviors were 0.56 ± 0.11, 0.88 ± 0.07, 0.70 ± 0.11, 0.54 ± 0.12, and 0.80 ± 0.10 for NS, IR, SS, TS, and SI, respectively. Daily dry matter intake (DDMI) and daily water intake (DWI) had heritabilities of 0.57 ± 0.11 and 0.44 ± 0.11. Phenotypic correlations varied between pairs of traits (-0.83 to 0.82). Genetic correlations between DDMI and feed intake behaviors were moderate to high, while genetic correlations between DWI and water intake behaviors were low to moderate. Several significant single nucleotide polymorphisms (SNP) were identified for the feed and water intake behaviors. Genes and previously reported quantitative trait loci near significant SNPs were evaluated. The results indicated that feed and water intake behaviors are influenced by genetic factors and are heritable, providing one additional route to evaluate or manipulate feed and water intake.

Behavioural Traits in Bos taurus Cattle, Their Heritability, Potential Genetic Markers, and Associations with Production Traits

Simple Summary

Cattle have the potential to seriously injure humans and cause damage to property. The risk of cattle reacting in a dangerous manner can be reduced through genetic selection for cattle which have a better temperament. A literature search was undertaken which returned papers which met the criteria of “Bovine”, “Genetics” and “Behaviour” or terms therein. Behavioural traits were grouped and their heritability, genomic associations and correlations with production traits examined. It was found that heritability estimates were more accurate in studies with large populations (n > 1000). Gene associations with behavioural traits were found on all chromosomes except for chromosome 13, with associated SNPs reported on all chromosomes except 5, 13, 17, 18 and 23. Generally, it was found that correlations between behaviour and production traits were low or negligible, suggesting that genetic improvement can be undertaken without negatively affecting production. There was variation between the results of the studies examined, and this underlines that any genetic study is population specific. Thus, to assess the heritability, genetic associations with production and genomic areas of interest for behavioural traits, a large-scale study of the population of interest would be required.

Abstract

People who work with cattle are at severe risk of serious injury due to the size and strength of the cattle. This risk can be minimised by breeding less dangerous cattle, which have a more favourable reaction to humans. This study provides a systematic review of literature pertaining to cattle genetics relating to behaviour. The review protocol was developed using the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) framework, with Population, Exposure and Outcome components identified as Bovine, Genetics and Behaviour respectively. Forty-nine studies were identified in the sifting and assigned non-exclusively to groups of heritability (22), genomic associations (13) and production traits related to behaviour (24). Behavioural traits were clustered into the following groups: “temperament, disposition and/ or docility”, “aggression”, “chute score”, “flight speed”, “milking temperament”, “non-restrained methods” and “restrained methods”. Fourteen papers reported high accuracy (Standard Error ≤ 0.05) estimates of heritability, the majority (n = 12) of these studies measured over 1000 animals. The heritability estimates were found to vary between studies. Gene associations with behavioural traits were found on all chromosomes except for chromosome 13, with associated SNPs reported on all chromosomes except 5, 13, 17, 18 and 23. Generally, it was found that correlations between behaviour and production traits were low or negligible. These studies suggest that additive improvement of behavioural traits in cattle is possible and would not negatively impact performance. However, the variation between studies demonstrates that the genetic relationships are population specific. Thus, to assess the heritability, genetic associations with production and genomic areas of interest for behavioural traits, a large-scale study of the population of interest would be required.

The Effects of Breed and Residual Feed Intake Divergence on the Abundance and Active Population of Rumen Microbiota in Beef Cattle

To assess the effects of residual feed intake (RFI) and breed on rumen microbiota, the abundance (DNA) and active population (RNA) of the total bacteria, archaea, protozoa, and fungi in the rumen of 96 beef steers from three different breeds (Angus (AN), Charolais (CH), and Kinsella Composite (KC)), and divergent RFIs (High vs Low), were estimated by measuring their respective maker gene copies using qRT-PCR. All experimental animals were kept under the same feedlot condition and fed with the same high-energy finishing diet. Rumen content samples were collected at slaughter and used for the extraction of genetic material (DNA and RNA) and further analysis. There was a significant difference (p < 0.01) between the marker gene copies detected for abundance and active populations for all four microbial groups. AN steers had a higher abundance of bacteria (p < 0.05) and a lower abundance of eukaryotes (protozoa and fungi, p < 0.05) compared to KC steers, while the abundance of protozoa (p < 0.05) in the AN cattle and fungi (p < 0.05) in the KC cattle were lower and higher, respectively, than those in the CH steers. Meanwhile, the active populations of bacteria, archaea, and protozoa in the KC steers were significantly lower than those in the AN and CH animals (p < 0.01). This work demonstrates that cattle breed can affect rumen microbiota at both the abundance and activity level. The revealed highly active protozoal populations indicate their important role in rumen microbial fermentation under a feedlot diet, which warrants further study.

Estimates of genetic parameters for feeding behavior traits and their associations with feed efficiency in Holstein cows

Residual feed intake (RFI) is commonly used to measure feed efficiency but individual intake recording systems are needed. Feeding behavior may be used as an indicator trait for feed efficiency using less expensive precision livestock farming technologies. Our goal was to estimate genetic parameters for feeding behavior and the genetic correlations with feed efficiency in Holstein cows. Data consisted of 75,877 daily feeding behavior records of 1,328 mid-lactation Holstein cows in 31 experiments conducted from 2009 to 2020 with an automated intake recording system. Feeding behavior traits included number of feeder visits per day, number of meals per day, duration of each feeder visit, duration of each meal, total duration of feeder visits, intake per visit, intake per meal [kg of dry matter (DM)], feeding rate per visit, and feeding rate per meal (kg of DM per min). The meal criterion was estimated as 26.4 min, which means that any pair of feeder visits separated by less than 26.4 min were considered part of the same meal. The statistical model included lactation and days in milk as fixed effects, and experiment-treatment, animal, and permanent environment as random effects. Genetic parameters for feeding behavior traits were estimated using daily records and weekly averages. Estimates of heritability for daily feeding behavior traits ranged from 0.09 ± 0.02 (number of meals; mean ± standard error) to 0.23 ± 0.03 (feeding rate per meal), with repeatability estimates ranging from 0.23 ± 0.01 (number of meals) to 0.52 ± 0.02 (number of feeder visits). Estimates of heritability for weekly averages of feeding behavior traits ranged from 0.19 ± 0.04 (number of meals) to 0.32 ± 0.04 (feeding rate per visit), with repeatability estimates ranging from 0.46 ± 0.02 (duration of each meal) to 0.62 ± 0.02 (feeding rate per visit and per meal). Most of the feeding behavior measures were strongly genetically correlated, showing that with more visits or meals per day, cows spend less time in each feeder visit or meal with lower intake per visit or meal. Weekly averages for feeding behavior traits were analyzed jointly with RFI and its components. Number of meals was genetically correlated with milk energy (0.48), metabolic body weight (-0.27), and RFI (0.19). Duration of each feeder visit and meal were genetically correlated with milk energy (0.43 and 0.44, respectively). Total duration of feeder visits per day was genetically correlated with DM intake (0.29), milk energy (0.62), metabolic body weight (-0.37), and RFI (0.20). Intake per visit and meal were genetically correlated with DM intake (0.63 and 0.87), milk energy (0.47 and 0.69), metabolic body weight (0.47 and 0.68), and RFI (0.31 and 0.65). Feeding rate was genetically correlated with DM intake (0.69), metabolic body weight (0.67), RFI (0.47), and milk energy (0.21). We conclude that measures of feeding behavior could be useful indicators of dairy cow feed efficiency, and individual cows that eat at a slower rate may be more feed efficient.

Effects of nutritional management regimen and residual feed intake (RFI) classification on RFI reranking and feeding behaviour for finishing beef steers

Over 2 years, 207 steers were fed an alfalfa/corn silage diet to determine growing phase (GP) residual feed intake (RFI) classification (low, medium, and high) for individual cattle. Steers were then allocated to two finishing management regimens (MR): MR 1 cattle gradually adjusted to an 84.7% concentrate (dry matter (DM) basis) diet; MR 2 included backgrounding on pasture before finishing using the same diet as MR 1 cattle. Treatment differences in growth performance were examined using GP and finishing phase (FP) RFI classifications. Based on GP RFI classification, FP average daily gain was greater in MR 2 cattle (P = 0.01) with no RFI classification differences for most FP performance traits. However, low-RFI steers had lower FP dry matter intake (DMI) and greater G:F (P ≤ 0.05) than high-RFI steers based on FP RFI classification. Low-RFI steers had fewer visits to the feeder with a lower eating rate than high-RFI steers in both production phases (P ≤ 0.05). Extensive RFI reranking occurred between production phases with 64.3% of steers changing RFI classification. Given extensive reranking in the present study, RFI classification was poorly repeatable between growing and finishing production phases when diverse diets are fed and does not accurately predict feed efficiency.

Phenotypic and genetic associations between feeding behavior and carcass merit in crossbred growing cattle

In growing cattle, the phenotypic and genetic relationships between feeding behavior and both live animal ultrasound measures and subsequent carcass merit are generally poorly characterized. The objective of the current study was to quantify the phenotypic and genetic associations between a plethora of feeding behavior traits with both pre-slaughter ultrasound traits and post-slaughter carcass credentials in crossbred Bos taurus cattle. Carcass data were available on 3,146 young bulls, steers, and heifers, of which 2,795 and 2,445 also had records for pre-slaughter ultrasound muscle depth and intramuscular fat percentage, respectively; a total of 1,548 steers and heifers had information on all of the feeding behavior, ultrasound, and carcass traits. Young bulls were fed concentrates, while steers and heifers were fed a total mixed ration. Feeding behavior traits were defined based on individual feed events or meal events (i.e., individual feed events grouped into meals). Animal linear mixed models were used to estimate (co)variance components. Phenotypic correlations between feeding behavior and both ultrasound and carcass traits were generally weak and not different from zero, although there were phenotypic correlations of 0.40, 0.26, and 0.37 between carcass weight and feeding rate, energy intake per feed event, and energy intake per meal, respectively. Genetically, cattle that had heavier carcass weights, better carcass conformation, or a higher dressing percentage fed for a shorter time per day (genetic correlations [±SE] of -0.46 ± 0.12, -0.39 ± 0.11, and -0.50 ± 0.10, respectively). Genetic correlations of 0.43 ± 0.12 and 0.68 ± 0.13 were estimated between dressing difference (i.e., differential between live weight pre-slaughter and carcass weight) and energy intake per feed event and energy intake per meal, respectively. Neither intramuscular fat percentage measured on live animals nor carcass fat score (i.e., a measure of subcutaneous fat cover of the carcass) was genetically associated with any of the feeding behavior traits. The genetic associations between some feeding behavior traits and both ultrasound and carcass traits herein suggested that indirect responses in the feeding behavior of growing cattle from selection for improved carcass merit would be expected. Such changes in feeding behavior patterns in cattle may be reduced by measuring and including feeding behavior in a multiple-trait selection index alongside carcass traits.

Genetic variability in the feeding behavior of crossbred growing cattle and associations with performance and feed efficiency

The objectives of the present study were to estimate genetic parameters for several feeding behavior traits in growing cattle, as well as the genetic associations among and between feeding behavior and both performance and feed efficiency traits. An additional objective was to investigate the use of feeding behavior traits as predictors of genetic merit for feed intake. Feed intake and live-weight data on 6,088 growing cattle were used of which 4,672 had ultrasound data and 1,548 had feeding behavior data. Feeding behavior traits were defined based on individual feed events or meal events (where individual feed events were grouped into meals). Univariate and bivariate animal linear mixed models were used to estimate (co)variance components. Heritability estimates (± SE) for the feeding behavior traits ranged from 0.19 ± 0.08 for meals per day to 0.61 ± 0.10 for feeding time per day. The coefficient of genetic variation per trait varied from 5% for meals per day to 22% for the duration of each feed event. Genetically heavier cattle, those with a higher daily energy intake (MEI), or those that grew faster had a faster feeding rate, as well as a greater energy intake per feed event and per meal. Better daily feed efficiency (i.e., lower residual energy intake) was genetically associated with both a shorter feeding time per day and shorter meal time per day. In a validation population of 321 steers and heifers, the ability of estimated breeding values (EBV) for MEI to predict (adjusted) phenotypic MEI was demonstrated; EBVs for MEI were estimated using multi-trait models with different sets of predictor traits such as liveweight and/or feeding behaviors. The correlation (± SE) between phenotypic MEI and EBV for MEI marginally improved (P < 0.001) from 0.64 ± 0.03 to 0.68 ± 0.03 when feeding behavior phenotypes from the validation population were included in a genetic evaluation that already included phenotypic mid-test metabolic live-weight from the validation population. This is one of the largest studies demonstrating that significant exploitable genetic variation exists in the feeding behavior of young crossbred growing cattle; such feeding behavior traits are also genetically correlated with several performance and feed efficiency metrics. Nonetheless, there was only a marginal benefit to the inclusion of time-related feeding behavior phenotypes in a genetic evaluation for MEI to improve the precision of the EBVs for this trait.

Exploring Biological Impacts of Prenatal Nutrition and Selection for Residual Feed Intake on Beef Cattle Using Omics Technologies: A Review

Approximately 70% of the cost of beef production is impacted by dietary intake. Maximizing production efficiency of beef cattle requires not only genetic selection to maximize feed efficiency (i.e., residual feed intake (RFI)), but also adequate nutrition throughout all stages of growth and development to maximize efficiency of growth and reproductive capacity, even during gestation. RFI as a measure of feed efficiency in cattle has been recently accepted and used in the beef industry, but the effect of selection for RFI upon the dynamics of gestation has not been extensively studied, especially in the context of fluctuating energy supply to the dam and fetus. Nutrient restriction during gestation has been shown to negatively affect postnatal growth and development as well as fertility of beef cattle offspring. This, when combined with the genetic potential for RFI, may significantly affect energy partitioning in the offspring and subsequently important performance traits. In this review, we discuss: 1) the importance of RFI as a measure of feed efficiency and how it can affect other economic traits in beef cattle; 2) the influence of prenatal nutrition on physiological phenotypes in calves; 3) the benefits of investigating the interaction of genetic selection for RFI and prenatal nutrition; 4) how metabolomics, transcriptomics, and epigenomics have been employed to investigate the underlying biology associated with prenatal nutrition, RFI, or their interactions in beef cattle; and 5) how the integration of omics information is adding a level of deeper understanding of the genetic architecture of phenotypic traits in cattle.

Influence of Stress Assessed through Infrared Thermography and Environmental Parameters on the Performance of Fattening Rabbits

Simple Summary

The aim of this study was to evaluate the impact of stress due to heat (temperature-humidity index; THI) or handling (human restraining), assessed using infrared thermography, on the performance parameters of rabbits of a Spanish Common breed. Thirty-nine rabbits weaned at the age of 28 days were analyzed during a 38-d fattening period at two times of the year: a cold period and a warm period. The rabbits’ stress due to handling was assessed by the temperature difference taken by infrared thermography in the inner ear of the animals, before and after being handled. In general, the productive results were low, since it was an unimproved rustic breed. The animals were more productive in the cold season as the values obtained for daily feed intake (DFI), average daily gain (ADG), total body weight (TBW), total feed intake (TFI) and total weight gain (TWG) were higher then, while the feed conversion ratio (FCR) was higher in the warm season. The greater the stress due to handling, the less efficient the animals were. It was therefore concluded that changes in animal welfare caused by the rabbits’ reactivity to both climatic and individual factors affect animal productivity.

Abstract

Rabbits often experience stress when they perceive certain stimuli, such as handling. The physiological response of animals to stress and temperament is associated with feeding efficiency, with those with the least capacity to react to stress showing the highest performance. The aim of this study was to evaluate the impact of stress due to heat (temperature-humidity index; THI) or handling, assessed using infrared thermography, on the performance parameters of rabbits of a Spanish Common breed. Thirty-nine rabbits were analyzed during a 38-d fattening period at two times of the year: a cold period and a warm period. The rabbits’ stress due to handling was assessed by the temperature difference taken in the inner ear, before and after being handled. The animals were more productive in the cold season. Temperature-humidity index significantly influenced average daily gain (ADG) and daily feed intake (DFI). Rabbits with higher levels of stress showed higher ADG, DFI and feed conversion ratio (FCR) values. The greater the stress due to handling, the less efficient the animals were. FCR increased with higher THI. It was concluded that changes in animal welfare caused by the rabbits’ reactivity to both climatic and individual factors affect animal productivity.

Predicting feed intake using modelling based on feeding behaviour in finishing beef steers

Current techniques for measuring feed intake in housed cattle are both expensive and time-consuming making them unsuitable for use on commercial farms. Estimates of individual animal intake are required for assessing production efficiency. The aim of this study was to predict individual animal intake using parameters that can be easily obtained on commercial farms including feeding behaviour, liveweight and age. In total, 80 steers were used, and each steer was allocated to one of two diets (40 per diet) which consisted of (g/kg; DM) forage to concentrate ratios of either 494:506 (MIXED) or 80:920 (CONC). Individual daily fresh weight intakes (FWI; kg/day) were recorded for each animal using 32 electronic feeders over a 56-day period, and individual DM intakes (DMI; kg/day) subsequently calculated. Individual feeding behaviour variables were calculated for each day of the measurement period from the electronic feeders and included: total number of visits to the feeder, total time spent at the feeder (TOTFEEDTIME), total time where feed was consumed (TIMEWITHFEED) and average length of time during each visit to the feeder. These feeding behaviour variables were chosen due to ease of obtaining from accelerometers. Four modelling techniques to predict individual animal intake were examined, based on (i) individual animal TOTFEEDTIME relative expressed as a proportion of the dietary group (GRP) and total GRP intake, (ii) multiple linear regression (REG) (iii) random forests (RF) and (iv) support vector regressor (SVR). Each model was used to predict CONC and MIXED diets separately, giving eight prediction models, (i) GRP_CONC, (ii) GRP_MIXED, (iii) REG_CONC, (iv) REG_MIXED, (v) RF_CONC, (vi) RF_MIXED, (vii) SVR_CONC and (viii) SVR_MIXED. Each model was tested on FWI and DMI. Model performance was assessed using repeated measures correlations (R²_RM) to capture the repeated nature of daily intakes compared with standard R², RMSE and mean absolute error (MAE). REG, RF and SVR models predicted FWI with R²_RM = 0.1–0.36, RMSE = 1.51–2.96 kg and MAE = 1.19–2.49 kg, and DMI with R²_RM = 0.13–0.19, RMSE = 1.15–1.61 kg and MAE = 0.9–1.28 kg. The GRP models predicted FWI with R²_RM = 0.42–0.49, RMSE = 2.76–3.88 kg and MAE = 2.46–3.47 kg, and DMI with R²_RM = 0.32–0.44, RMSE = 0.32–0.44 kg, MAE = 1.55–2.22 kg. Whilst more simplistic GRP models showed higher R²_RM than regression and machine learning techniques, these models had larger errors, likely due to individual feeding patterns not being captured. Although regression and machine learning techniques produced lower errors associated with individual intakes, overall precision of prediction was too low for practical use.

Adrenergic Tone as an Intermediary in the Temperament Syndrome Associated With Flight Speed in Beef Cattle

The temperament of farm animals can influence their resilience to everyday variations within the managed production environment and has been under strong direct and indirect selection during the course of domestication. A prominent objective measure used for assessing temperament in beef cattle is the behavioral flight response to release from confinement in a crush or chute. This behavioral measure, termed flight speed (also known as escape velocity) is associated with physiological processes including body temperature, feeding behavior, growth rate, carcass composition, immune function, and health outcomes. This review examines the functional links between this suite of traits and adrenergic activity of the sympathetic nervous system and the adrenomedullary hormonal system. It is suggested that flight speed is the behavioral aspect of an underlying “flightiness” temperament syndrome, and that elevated adrenergic tone in animals with a high level of flightiness (i.e., flighty animals) tunes physiological activities toward a sustained “fight or flight” defense profile that reduces productivity and the capacity to flourish within the production environment. Nonetheless, despite a common influence of adrenergic tone on this suite of traits, variation in each trait is also influenced by other regulatory pathways and by the capacity of tissues to respond to a range of modulators in addition to adrenergic stimuli. It is suggested that tuning by adrenergic tone is an example of homeorhetic regulation that can help account for the persistent expression of behavioral and somatic traits associated with the flight speed temperament syndrome across the life of the animal. At a population level, temperament may modulate ecological fit within and across generations in the face of environmental variability and change. Associations of flight speed with the psychological affective state of the animal, and implications for welfare are also considered. The review will help advance understanding of the developmental biology and physiological regulation of temperament syndromes.

A Systematic Review of Genomic Regions and Candidate Genes Underlying Behavioral Traits in Farmed Mammals and Their Link with Human Disorders

Simple Summary

This study is a comprehensive review of genomic regions associated with animal behavior in farmed mammals (beef and dairy cattle, pigs, and sheep) which contributes to a better understanding of the biological mechanisms influencing the target indicator trait and to gene expression studies by suggesting genes likely controlling the trait, and it will be useful in optimizing genomic predictions of breeding values incorporating biological information. Behavioral mechanisms are complex traits, genetically controlled by multiple genes spread across the whole genome. The majority of the genes identified in cattle, pigs, and sheep in association with a plethora of behavioral measurements (e.g., temperament, terrain use, milking speed, tail biting, and sucking reflex) are likely controlling stimuli reception (e.g., olfactory), internal recognition of stimuli (e.g., neuroactive ligand–receptor interaction), and body response to a stimulus (e.g., blood pressure, fatty acidy metabolism, hormone signaling, and inflammatory pathways). Six genes were commonly identified between cattle and pigs. About half of the genes for behavior identified in farmed mammals were also identified in humans for behavioral, mental, and neuronal disorders. Our findings indicate that the majority of the genes identified are likely controlling animal behavioral outcomes because their biological functions as well as potentially differing allele frequencies between two breed groups (subjectively) clustered based on their temperament characteristics.

Abstract

The main objectives of this study were to perform a systematic review of genomic regions associated with various behavioral traits in the main farmed mammals and identify key candidate genes and potential causal mutations by contrasting the frequency of polymorphisms in cattle breeds with divergent behavioral traits (based on a subjective clustering approach). A total of 687 (cattle), 1391 (pigs), and 148 (sheep) genomic regions associated with 37 (cattle), 55 (pigs), and 22 (sheep) behavioral traits were identified in the literature. In total, 383, 317, and 15 genes overlap with genomic regions identified for cattle, pigs, and sheep, respectively. Six common genes (e.g., NR3C2, PITPNM3, RERG, SPNS3, U6, and ZFAT) were found for cattle and pigs. A combined gene-set of 634 human genes was produced through identified homologous genes. A total of 313 out of 634 genes have previously been associated with behavioral, mental, and neurologic disorders (e.g., anxiety and schizophrenia) in humans. Additionally, a total of 491 candidate genes had at least one statistically significant polymorphism (p-value < 0.05). Out of those, 110 genes were defined as having polymorphic regions differing in greater than 50% of exon regions. Therefore, conserved genomic regions controlling behavior were found across farmed mammal species and humans.

Methane and carbon dioxide emissions and grazed forage intake from pregnant beef heifers previously classified for residual feed intake under drylot conditions

The objectives of this study were to quantify the effect of post-weaning residual feed intake (RFI) on subsequent grazed forage intake, methane (CH4), and carbon dioxide (CO2) emissions. Beef heifers classified for RFI adjusted for off-test backfat (RFIfat; 55 high and 56 low) at 9 mo of age were monitored 7 mo later for CH4 and CO2 emissions using the GreenFeed Emissions Monitoring system. About 56 of these heifers were also monitored as high and low RFIfat groups using open-path Fourier-transform infrared spectroscopy (OP-FTIR). Heifers were dosed with 1 kg of C32-labelled pellets once daily for 15 d, with twice daily fecal sampling the last 8 d to determine individual grazed forage intake using the n-alkane method. Low RFIfat pregnant heifers consumed less forage (10.25 vs. 10.81 kg dry matter d−1; P < 0.001), and emitted less daily CH4 (238.7 vs. 250.7 g d−1; P = 0.009) and CO2 (7578 vs. 8041 g d−1; P < 0.001) compared with high RFIfat animals. Results from the OP-FTIR further confirmed that low RFIfat heifers emitted 6.3% less (g d−1; P = 0.006) CH4 compared with their high RFIfat cohorts. Thus, selection for low RFIfat will decrease daily CH4 and CO2 emissions from beef cattle.

Genetic association among feeding behavior, feed efficiency, and growth traits in growing indicine cattle

This study aimed to estimate genetic parameters, including genomic data, for feeding behavior, feed efficiency, and growth traits in Nellore cattle. The following feeding behavior traits were studied (861 animals with records): time spent at the feed bunk (TF), duration of one feeding event (FD), frequency of visits to the bunk (FF), feeding rate (FR), and dry matter intake (DMI) per visit (DMIv). The feed efficiency traits (1,543 animals with records) included residual feed intake (RFI), residual weight gain (RWG), and feed conversion (FC). The growth traits studied were average daily gain (ADG, n = 1,543 animals) and selection (postweaning) weight (WSel, n = 9,549 animals). The (co)variance components were estimated by the maximum restricted likelihood method, fitting animal models that did (single-step genomic best linear unbiased prediction) or did not include (best linear unbiased prediction) genomic information in two-trait analyses. The direct responses to selection were calculated for the feed efficiency traits, ADG, and WSel, as well as the correlated responses in feed efficiency and growth by direct selection for shorter TF. The estimated heritabilities were 0.51 ± 0.06, 0.35 ± 0.06, 0.27 ± 0.07, 0.34 ± 0.06, and 0.33 ± 0.06 for TF, FD, FF, FR, and DMIv, respectively. In general, TF and FD showed positive genetic correlations with all feed efficiency traits (RFI, RWG, and FC), ADG, DMI, and WSel. Additionally, TF showed high and positive genetic and phenotypic correlations with RFI (0.71 ± 0.10 and 0.46 ± 0.02, respectively) and DMI (0.56 ± 0.09 and 0.48 ± 0.03), and medium to weak genetic correlations with growth (0.32 ± 0.11 with ADG and 0.14 ± 0.09 with WSel). The results suggest that TF is a strong indicator trait of feed efficiency, which exhibits high heritability and a weak positive genetic correlation with growth. In a context of a selection index, the inclusion of TF to select animals for shorter TF may accelerate the genetic gain in feed efficiency by reducing RFI but with zero or slightly negative genetic gain in growth traits.

Phenotypic and genetic correlations between feeding behaviours and feed efficiency in crossbred beef replacement females

The objectives of this study were to identify the phenotypic and genetic relationships and heritability (h2) of feeding behaviours (FB) in replacement beef females. Between 2005 and 2017, heifers (N = 1394) were tested for feed intake using an electronic feed bunk system. The various FB were feeding duration (DUR; min d−1), head down time (HD; min d−1), feeding frequency (FREQ; events d−1), time-to-bunk (TTB; min). Dry matter intake (DMI; kg d−1), and residual feed intake adjusted for off-test ultrasound back fat thickness (RFIFAT) were also reported. The h2 estimates for DUR, HD, FREQ, TTB, DMI, and RFIFAT were 0.25 ± 0.05, 0.26 ± 0.06, 0.27 ± 0.05, 0.29 ± 0.06, 0.26 ± 0.05, and 0.40 ± 0.07, respectively. These are the first h2 to be presented for these FB among developing replacement heifers on a high-forage diet.

Serum Metabolite Biomarkers for Predicting Residual Feed Intake (RFI) of Young Angus Bulls

Residual feed intake (RFI) is a feed efficiency measure commonly used in the livestock industry to identify animals that efficiently/inefficiently convert feed into meat or body mass. Selection for low-residual feed intake (LRFI), or feed efficient animals, is gaining popularity among beef producers due to the fact that LRFI cattle eat less and produce less methane per unit weight gain. RFI is a difficult and time-consuming measure to perform, and therefore a simple blood test that could distinguish high-RFI (HRFI) from LRFI animals (early on) would potentially benefit beef farmers in terms of optimizing production or selecting which animals to cull or breed. Using three different metabolomics platforms (nuclear magnetic resonance (NMR) spectrometry, liquid chromatography-tandem mass spectrometry (LC-MS/MS), and inductively coupled plasma mass spectrometry (ICP-MS)) we successfully identified serum biomarkers for RFI that could potentially be translated to an RFI blood test. One set of predictive RFI biomarkers included formate and leucine (best for NMR), and another set included C4 (butyrylcarnitine) and LysoPC(28:0) (best for LC-MS/MS). These serum biomarkers have high sensitivity and specificity (AUROC > 0.85), for distinguishing HRFI from LRFI animals. These results suggest that serum metabolites could be used to inexpensively predict and categorize bovine RFI values. Further validation using a larger, more diverse cohort of cattle is required to confirm these findings.

Large variability in feeding behavior among crossbred growing cattle

The purpose of this study was to define an extensive suite of feeding behavior traits in growing crossbred cattle and to investigate their phenotypic inter-relationships as well as relationships with other performance and efficiency traits. Time-series feeding behavior data, as well as feed intake and liveweight records, were available for 624 growing crossbred cattle, of which 445 were steers and 179 were heifers. Feeding behavior repeatability estimates were calculated using linear mixed models. Additionally, partial Spearman correlations were estimated among 14 feeding behavior traits, as well as between feeding behavior with both performance and feed efficiency traits, using residuals retained from linear mixed models. The marginal contribution of several feeding behavior traits to the variability in metabolizable energy intake (MEI) was also determined. Repeatability estimates of 0.57, 0.36, and 0.48 were calculated for the number of feed events per day, the total time spent feeding per day, and the feeding rate, respectively. Cattle that ate more frequently each day, ate at a faster rate and consumed less energy in each visit to the feed bunk. More efficient cattle fed less often per day and fed for a shorter duration per day; they also had a slower feeding rate and fed for longer in each visit to the feed bunk. Moreover, heavier cattle fed for a longer duration per day had a faster feeding rate, but fed less often per day; heavier animals also fed first in the pen after the fresh feed was offered. The number of feed events per day and feeding time per day together explained an additional 13.4 percentage points of the variability in MEI above that already explained by all of growth rate, liveweight, and backfat depth. The results from the present study suggest that several repeatable time-series-related feeding behavior traits, that are less resource intensive to measure, may have a role as useful predictor traits of important but relatively difficult to record traits, such as feed intake and efficiency.

Phenotypic and genetic correlations of beef replacement heifer feeding behaviour, feed intake and feed efficiency with cow performance and lifetime productivity

Objectives were to quantify the phenotypic (r_p ) and genetic (r_g ) correlations between early-life feeding behaviours, dry matter intake, and feed efficiency and measures of cow performance and lifetime productivity traits. Traits were measured on 1,145 crossbred replacement beef heifers and then on cows over parities one to four. Feeding event duration (FD) was phenotypically correlated with cow prebreeding body weight (PBWT; r_p 0.29-0.45), cow prebreeding back fat thickness (PBBF; r_p 0.35-0.49), progeny weaning weight (WW; r_p 0.09-0.31) and progeny birthweight (BW; r_p -0.06 to 0.17). Feeding event frequency (FF) was phenotypically correlated with PBBF (r_p 0.16-0.30). Dry matter intake (DMI) was phenotypically correlated with PBWT (r_p 0.16-0.20) and PBBF (r_p -0.22 to -0.05). Feeding event duration was genetically correlated with PBWT (r_g 0.38-0.41). Feeding event frequency was genetically correlated with PBWT (r_g -0.43 to -0.39). Dry matter intake was genetically correlated with PBWT (r_g -0.27 to 0.14). Days in herd (DIH) was phenotypically correlated with FD and DMI (r_p  = 0.12, 0.20, respectively). Lifetime productivity was phenotypically correlated with FD and FF (r_g  = 0.25, 0.22, respectively). Calving interval was phenotypically correlated with FD and FF (r_p  = -0.12, -0.14, respectively) and genetically correlated with FF (r_g  = -0.41). Due to moderate positive correlations with cow weight, caution would be required in selection to prevent an increase in mature cow size. Use of FF, FD, DMI and a measure of feed efficiency such as residual feed intake adjusted for back fat (RFI_FAT ) in a balanced selection index is recommended.

Temperament and performance of Nellore bulls classified for residual feed intake in a feedlot system

This study aimed to evaluate the performance in feedlot and temperament of Nellore bulls classified by residual feed intake. The residual feed intake was calculated as the difference between the observed and predicted dry matter intake. Bulls classified as low residual feed intake had lower dry matter intake (kg day-1) and dry matter intake (g kg-1 d-1) of body weight, and were more efficient in feed conversion ratio than those classified as medium and high. The average daily gain didn't differ among residual feed intake classes and was 1.69 kg day-1, 1.82 kg day-1 and 1.71 kg day-1 for bulls classified as low, medium, or high, respectively. The residual feed intake was positively associated with dry matter intake, feed conversion ratio and subcutaneous fat thickness. The subcutaneous fat thickness was lower in bulls classified as low residual feed intake than in those with medium and high. No differences were observed in flight speed and reactivity score among residual feed intake classes. Overall, we concluded that bulls classified as low residual feed intake consumed less dry matter than high, with no differences in average daily gain, temperamentand had better feed efficiency, albeit their subcutaneous fat thickness was lower.

Large-Scale Phenotyping of Livestock Welfare in Commercial Production Systems: A New Frontier in Animal Breeding

Genomic breeding programs have been paramount in improving the rates of genetic progress of productive efficiency traits in livestock. Such improvement has been accompanied by the intensification of production systems, use of a wider range of precision technologies in routine management practices, and high-throughput phenotyping. Simultaneously, a greater public awareness of animal welfare has influenced livestock producers to place more emphasis on welfare relative to production traits. Therefore, management practices and breeding technologies in livestock have been developed in recent years to enhance animal welfare. In particular, genomic selection can be used to improve livestock social behavior, resilience to disease and other stress factors, and ease habituation to production system changes. The main requirements for including novel behavioral and welfare traits in genomic breeding schemes are: (1) to identify traits that represent the biological mechanisms of the industry breeding goals; (2) the availability of individual phenotypic records measured on a large number of animals (ideally with genomic information); (3) the derived traits are heritable, biologically meaningful, repeatable, and (ideally) not highly correlated with other traits already included in the selection indexes; and (4) genomic information is available for a large number of individuals (or genetically close individuals) with phenotypic records. In this review, we (1) describe a potential route for development of novel welfare indicator traits (using ideal phenotypes) for both genetic and genomic selection schemes; (2) summarize key indicator variables of livestock behavior and welfare, including a detailed assessment of thermal stress in livestock; (3) describe the primary statistical and bioinformatic methods available for large-scale data analyses of animal welfare; and (4) identify major advancements, challenges, and opportunities to generate high-throughput and large-scale datasets to enable genetic and genomic selection for improved welfare in livestock. A wide variety of novel welfare indicator traits can be derived from information captured by modern technology such as sensors, automatic feeding systems, milking robots, activity monitors, video cameras, and indirect biomarkers at the cellular and physiological levels. The development of novel traits coupled with genomic selection schemes for improved welfare in livestock can be feasible and optimized based on recently developed (or developing) technologies. Efficient implementation of genetic and genomic selection for improved animal welfare also requires the integration of a multitude of scientific fields such as cell and molecular biology, neuroscience, immunology, stress physiology, computer science, engineering, quantitative genomics, and bioinformatics.

Characterization of feeding behavior traits in steers with divergent residual feed intake consuming a high-concentrate diet

The objective of this study was to examine the differences in feeding behavior patterns of steers with divergent phenotypes for residual feed intake (RFI). Three trials were conducted with 508 Angus-based composite crossbred steers (body weight [BW] = 309 ± 57 kg) fed a high-concentrate diet in pens equipped with electronic feed bunks (GrowSafe System). Initial and final carcass ultrasound measurements (intra-muscular fat, backfat depth, and rib-eye area) were collected on days 0 and 70, and BW measured at 14-d intervals. Individual dry matter intake (DMI) and feeding behavior traits were collected for 70 d, and RFI calculated as the residual from the regression of DMI on average daily gain (ADG) and mid-test BW0.75. Steers were ranked by RFI and assigned to low-, medium-, and high-RFI classes based on ± 0.5 SD from the mean RFI within the trial. The feeding behavior traits evaluated in this study included frequency and duration of bunk visit (BV) and meal events, head-down (HD) duration, mean meal length, time-to-bunk interval, the maximum nonfeeding interval, and the day-to-day variation of these traits, defined as the root mean squared error (RMSE) from linear regression of each trait on the day of trial. Additionally, three ratio traits were evaluated: BV events per meal, HD duration per BV event, and HD duration per meal event. Low-RFI (feed-efficient) steers consumed 16% less (P < 0.01) DMI, while BW and ADG were not different compared with high-RFI steers. Low-RFI steers had 18% fewer and 21% shorter (P < 0.01) BV events, and 11% fewer and 13% shorter (P < 0.01) meal events per day compared with high-RFI steers. Furthermore, low-RFI steers exhibited less (P < 0.05) day-to-day variance in DMI, as well as in frequency and duration of BV and meal events and HD duration compared with high-RFI steers. Differences in feeding behavior traits due to RFI were minimally affected by covariate adjustment for DMI, indicating that steers with divergent RFI have distinct feeding behavior patterns that are largely independent of differences in DMI. These results suggest that feeding behavior traits may be useful biomarkers for the prediction of feed efficiency in beef cattle.

Mitochondrial abundance and function in skeletal muscle and liver from Simmental beef cattle divergent for residual feed intake

Cellular mitochondrial function has been suggested to contribute to variation in feed efficiency (FE) among animals. The objective of this study was to determine mitochondrial abundance and activities of various mitochondrial respiratory chain complexes (complex I (CI) to complex IV (CIV)) in liver and muscle tissue from beef cattle phenotypically divergent for residual feed intake (RFI), a measure of FE. Individual DM intake (DMI) and growth were measured in purebred Simmental heifers (n = 24) and bulls (n = 28) with an initial mean BW (SD) of 372 kg (39.6) and 387 kg (50.6), respectively. All animals were offered concentrates ad libitum and 3 kg of grass silage daily, and feed intake was recorded for 70 days. Residuals of the regression of DMI on average daily gain (ADG), mid-test BW0.75 and backfat (BF), using all animals, were used to compute individual RFI coefficients. Animals were ranked within sex, by RFI into high (inefficient; top third of the population), medium (middle third of population) and low (efficient; bottom third of the population) terciles. Statistical analysis was carried out using the MIXED procedure of SAS v 9.3. Overall mean ADG (SD) and daily DMI (SD) for heifers were 1.2 (0.4) and 9.1 (0.5) kg, respectively, and for bulls were 1.8 (0.3) and 9.5 (1.02) kg, respectively. Heifers and bulls ranked as high RFI consumed 10% and 15% more (P < 0.05), respectively, than their low RFI counterparts. There was no effect of RFI on mitochondrial abundance in either liver or muscle (P > 0.05). An RFI × sex interaction was apparent for CI activity in muscle. High RFI animals had an increased activity (P < 0.05) of CIV in liver tissue compared to their low RFI counterparts; however, the relevance of that observation is not clear. Our data provide no clear evidence that cellular mitochondrial function within either skeletal muscle or hepatic tissue has an appreciable contributory role to overall variation in FE among beef cattle.

Characterization of water intake and water efficiency in beef cattle1,2

In the future, water may not be as readily available due to increases in competition from a growing human population, wildlife, and other agricultural sectors, making selection for water efficiency of beef cattle increasingly important. Substantial selection emphasis has recently been placed on feed efficiency in an effort to reduce production costs, but no emphasis has been placed on making cattle more water efficient due to lack of data. Thus, the objective of this study was to calculate water efficiency metrics for cattle and evaluate their relationship to growth, feed intake (FI), and feed efficiency. Individual daily FI and water intake (WI) records were collected on 578 crossbred steers over a 70-d test period. Animals with low water intake ate less feed, had lower gains, and were more water efficient (as defined by water to gain ratio, W/G, and residual water intake, RWI). However, the amount of water consumed by animals had minimal phenotypic relationship with feed efficiency (residual feed intake [RFI], R2 = 0.1050 and feed to gain ratio (F/G) ratio R2 = 0.0726). Cattle that had low DMI consumed less water, had lower gains, had lower RFI, and had higher F/G. The level of feed consumed had minimal relationship with water efficiency. WI, W/G, RWI, and ADG had moderate heritability estimates of 0.39, 0.39, 0.37, and 0.37, respectively. High heritability estimates were observed for DMI and RFI (0.67 and 0.65, respectively). Feed to gain had a low heritability estimate of 0.16. WI had a strong positive genetic correlation with W/G (0.99) and RWI (0.88), thus selecting for decreased WI should also make cattle more water efficient. The genetic correlation between WI and ADG was 0.05; thus, selecting for low WI cattle should have little effect on growth. There is a low to moderate genetic correlation between WI and DMI (0.34). RWI has a positive genetic correlation with W/G ratio (0.89) and F/G ratio (0.42) and is negatively genetically correlated with RFI (-0.57). Water to gain and F/G had a strong positive genetic correlation (0.68). RFI has a positive genetic correlation with W/G ratio (0.37) and F/G (0.88). Minimal antagonisms seem to be present between WI and ADG, although it should be noted that standard errors were large and often not significantly different from zero due to the small sample size. However, care should be taken to ensure that unintended changes do not occur in DMI or other production traits and incorporation of WI into a selection index would likely prove to be the most effective method for selection.

Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: II: carcass merit traits

BACKGROUND

Genome wide association studies (GWAS) were conducted on 7,853,211 imputed whole genome sequence variants in a population of 3354 to 3984 animals from multiple beef cattle breeds for five carcass merit traits including hot carcass weight (HCW), average backfat thickness (AFAT), rib eye area (REA), lean meat yield (LMY) and carcass marbling score (CMAR). Based on the GWAS results, genetic architectures of the carcass merit traits in beef cattle were elucidated.

RESULTS

The distributions of DNA variant allele substitution effects approximated a bell-shaped distribution for all the traits while the distribution of additive genetic variances explained by single DNA variants conformed to a scaled inverse chi-squared distribution to a greater extent. At a threshold of P-value < 10-5, 51, 33, 46, 40, and 38 lead DNA variants on multiple chromosomes were significantly associated with HCW, AFAT, REA, LMY, and CMAR, respectively. In addition, lead DNA variants with potentially large pleiotropic effects on HCW, AFAT, REA, and LMY were found on chromosome 6. On average, missense variants, 3'UTR variants, 5'UTR variants, and other regulatory region variants exhibited larger allele substitution effects on the traits in comparison to other functional classes. The amounts of additive genetic variance explained per DNA variant were smaller for intergenic and intron variants on all the traits whereas synonymous variants, missense variants, 3'UTR variants, 5'UTR variants, downstream and upstream gene variants, and other regulatory region variants captured a greater amount of additive genetic variance per sequence variant for one or more carcass merit traits investigated. In total, 26 enriched cellular and molecular functions were identified with lipid metabolisms, small molecular biochemistry, and carbohydrate metabolism being the most significant for the carcass merit traits.

CONCLUSIONS

The GWAS results have shown that the carcass merit traits are controlled by a few DNA variants with large effects and many DNA variants with small effects. Nucleotide polymorphisms in regulatory, synonymous, and missense functional classes have relatively larger impacts per sequence variant on the variation of carcass merit traits. The genetic architecture as revealed by the GWAS will improve our understanding on genetic controls of carcass merit traits in beef cattle.

Flight speed as an indicator of Zebu cattle growth performance and suitability to the feedlot environment

Context Studies assessing the relationship between cattle reactivity and growth performance, as well as suitability to the feedlot, in Zebu cattle are limited. Based on previous studies using Bos Taurus cattle, it is expected that reactivity measured at weaning could be used as a predictor of feedlot performance, and that cattle with greater flight speed (FS) would have reduced average daily gain (ADG). Aims The aims of this study were to (1) determine if FS (m/s) measured before entry into the feedlot could be used as a predictor of cattle performance, (2) evaluate the consistency of FS over time, and (3) determine when FS should be measured to best predict animal suitability to the feedlot. Methods A total of 54 Nellore and 40 Guzerat calves were assessed by using FS, which was collected at the time of (FS0) and 1 week after weaning (FS1), as well as on Day 28 (FS28), 56 (FS56) and 168 (FS168) after entry into the feedlot, and a FS average was calculated using FS28, FS56 and FS168 (FS28–168). Performance using ADG (kg/calf.day) was calculated for each animal over three periods: ADG1–28, ADG28–168 and ADG1–168. Bunk attendance (min/calf.day) was recorded over a 173-day feeding period. Key results The ADG28–168 was reduced by 0.14 kg/calf.day for each unit increase in FS0 (P &lt; 0.05). Both ADG28–168 and ADG1–168 were reduced by 0.02 kg/calf.day for each unit increase in FS1 (P ≤ 0.01), but neither FS0 nor FS1 was associated with ADG1–28 (P &gt; 0.10). A significant increase was observed between FS1 and FS28 (P &lt; 0.01), followed by a reduction in FS56 (P &lt; 0.01) and FS168 (P &lt; 0.01). Conclusion FS measured at or within 1 week of weaning has the potential to be used as an indicator of feedlot growth performance in Nellore and Guzerat cattle. Implications Although our results do not indicate the efficacy of FS as a predictor of early suitability of cattle to the feedlot, it does have the potential to support its recommendation as an indicator of overall feedlot growth performance in Nellore and Guzerat breeds.

Developing and validating a model to predict the dry matter intake of grazing lactating beef cows

Current techniques for measuring the dry matter intake (DMI) of grazing lactating beef cows are invasive, time consuming and expensive making them impractical for use on commercial farms. This study was undertaken to explore the potential to develop and validate a model to predict DMI of grazing lactating beef cows, which could be applied in a commercial farm setting, using non-invasive animal measurements. The calibration dataset used to develop the model was comprised of 94 measurements recorded on 106 beef or beef-dairy crossbred cows (maternal origin). The potential of body measurements, linear type scoring, grazing behaviour and thermal imaging to predict DMI in combination with known biologically plausible adjustment variables and energy sinks was investigated. Multivariable regression models were constructed for each independent variable using SAS PROC REG and contained milk yield, BW, parity, calving day and maternal origin (dairy or beef). Of the 94 variables tested, 32 showed an association with DMI (P < 0.25) upon multivariable analysis. These variables were incorporated into a backwards linear regression model using SAS PROC REG. Variables were retained in this model if P < 0.05. Five variables; width at pins, full body depth, ruminating mastications, central ligament and rump width score, were retained in the model in addition to milk yield, BW, parity, calving day and maternal origin. The inclusion of these variables in the model increased the predictability of DMI by 0.23 (R2 = 0.68) when compared to a model containing milk yield, BW, parity, calving day and maternal origin only. This model was applied to data recorded on an independent dataset; a herd of 60 lactating beef cows two years after the calibration study. The R2 for the validation was 0.59. Estimates of DMI are required for measuring feed efficiency. While acknowledging challenges in applicability, the findings suggest a model such as that developed in this study may be used as a tool to more easily and less invasively estimate DMI on large populations of commercial beef cows, and therefore measure feed efficiency.

Genetic variation in residual feed intake is associated with body composition, behavior, rumen, heat production, hematology, and immune competence traits in Angus cattle1

This experiment was to evaluate a suite of biological traits likely to be associated with genetic variation in residual feed intake (RFI) in Angus cattle. Twenty nine steers and 30 heifers bred to be divergent in postweaning RFI (RFIp) and that differed in midparent RFIp-EBV (RFIp-EBVmp) by more than 2 kg DMI/d were used in this study. A 1-unit (1 kg DM/d) decrease in RFIp-EBVmp was accompanied by a 0.08 kg (SE = 0.03; P < 0.05) increase in ADG, a 0.58 kg/d (0.17; P < 0.01) decrease in DMI, a 0.89 kg/kg (0.22; P < 0.001) decrease in FCR, and a 0.62 kg/d (0.12; P < 0.001) decrease in feedlot RFI (RFIf). Ultrasonically scanned depths of subcutaneous fat at the rib and rump sites, measured at the start and end of the RFI test, all had strong positive correlations with RFIp-EBVmp, DMI, and RFIf (all r values ≥0.5 and P < 0.001). Variation in RFIp-EBVmp was significantly correlated (P < 0.05) with flight speed (r = -0.32), number of visits to feed bins (r = 0.45), and visits to exhaled-emission monitors (r = -0.27), as well as the concentrations of propionate (r = -0.32) and valerate (r = -0.31) in rumen fluid, white blood cell (r = -0.51), lymphocyte (r = -0.43), and neutrophil (r = -0.31) counts in blood. RFIp-EBVmp was also correlated with the cellular immune response to vaccination (r = 0.25; P < 0.1) and heat production in fasted cattle (r = -0.46; P < 0.001). Traits that explained significant variation (P < 0.05) in DMI over the RFI test were midtest metabolic-BW (44.7%), rib fat depth at the end of test (an additional 18%), number of feeder visits (additional 5.7%), apparent digestibility of the ration by animals (additional 2.4%) and white blood-cell count (2.1%), and the cellular immune response to vaccine injection (additional 1.1%; P < 0.1), leaving ~23% of the variation in DMI unexplained. The same traits (BW excluded) explained 33%, 12%, 3.6%, 3.7%, and 3.1%, and together explained 57% of the variation in RFIf. This experiment showed that genetic variation in RFI was accompanied by variation in estimated body composition, behavior, rumen, fasted heat production, hematology, and immune competence traits, and that variation in feedlot DMI and RFIf was due to differences in BW, scanned fatness, and many other factors in these cattle fed ad libitum and able to display any innate differences in appetite, temperament, feeding behavior, and activity.

Digestibility contributes to between-animal variation in feed efficiency in beef cows

Residual feed intake (RFI) is an alternative measure of feed efficiency (FE) and is calculated as the difference between actual and expected feed intake. The biological mechanisms underlying animal-to-animal variation in FE are not well understood. The aim of this study was to investigate the digestive ability of beef cows selected for RFI divergence as heifers, using two contrasted diets. Fifteen 4-year-old beef cows were selected from a total of 69 heifers based on their RFI following the feedlot test. The selected heifers were ranked into high-RFI (+ 1.02 ± 0.28, n = 8) and low-RFI (-0.73 ± 0.28, n = 7), and a digestibility trial was performed after their first lactation. Both RFI groups were offered two different diets: 100% hay or a fattening diet which consisted of a DM basis of 67% whole-plant maize silage and 33% high starch concentrates over four experimental periods (two per diet). A diet effect was observed on feed intake and apparent digestibility, whereas no diet × RFI interaction was detected (P > 0.05). Intake and apparent digestibility were higher in cows fed the fattening diet than in those fed the hay diet (P < 0.0001). DM intake (DMI) and organic matter apparent digestibility (OMd) were repeatable and positively correlated between the two subsequent periods of measurements. For the hay and fattening diets, the repeatability between periods was r = 0.71 and r = 0.73 for DMI and r = 0.87 and r = 0.48 for OMd, respectively. Moreover, both intake (r = 0.55) and OMd (r = 0.54) were positively correlated (P < 0.05) between the hay and fattening diets. Significant differences between beef cows selected for divergence in RFI as heifers were observed for digestive traits (P < 0.05), DM and organic matter (OM) apparent digestibility being higher for low-RFI cows. Overall, this study showed that apparent digestibility contributes to between-animal variation in FE in beef cows.

Effects of temperament at feedlot arrival and breed type on growth efficiency, feeding behavior, and carcass value in finishing heifers

Objectives were to evaluate the effects of temperament at feedlot arrival and breed type on productivity, feed efficiency, feeding behavior, and carcass quality traits in finishing beef heifers, and to examine interactions between temperament and breed type. Heifers (Angus, Braford, Brangus, and Simbrah, N = 411, BW = 280 kg) were fed a high-grain diet (ME = 3.0 Mcal/kg DM) in pens equipped with electronic feed bunks. Quality grade (QG), yield grade (YG), and Warner-Bratzler shear (WBS) force values (day 1 and 14 postmortem) were evaluated. Relative exit velocity (REV) at feedlot arrival was used as a covariate in mixed models to assess the effects of temperament and interactions with breed type, with means compared at ±1 SD from the mean initial REV. Calm heifers (mean REV minus 1 SD) had 4% greater (P < 0.001) initial BW, 12% greater (P < 0.001) ADG, 8% greater (P < 0.001) DMI, and 4% greater (P < 0.02) G:F than heifers with excitable temperaments (mean REV plus 1 SD). A temperament × breed interaction was detected (P < 0.01) for residual feed intake (RFI). Braford heifers had a more (P < 0.05) negative REV covariate slope (-1.49 ± 0.65) than the other breeds, such that excitable Braford heifers had lower (P < 0.05) RFI than the other breeds with excitable temperaments. Temperament × breed interactions were observed (P < 0.001) for DMI per BW0.75 and bunk visit (BV) duration. Braford heifers had more (P < 0.05) negative REV covariate slopes for both traits than Angus, Brangus, and Simbrah heifers such that excitable Braford heifers consumed less (P < 0.05) DMI per BW0.75 and had less BV duration compared to excitable Angus and Brangus heifers. Calm heifers had 9% greater (P < 0.01) meal duration, and consumed meals that were 22% longer (P < 0.001) and 17% larger (P < 0.001) compared to excitable heifers. Calm heifers had 12% more (P < 0.001) BV events per meal then excitable heifers. Carcasses from calm heifers were 4% heavier (P < 0.05) and had 7% greater (P = 0.05) backfat (BF) depth and tended to have 4% greater (P = 0.07) USDA YG than carcasses from excitable heifers. Additionally, loin steaks from calm heifers had 8% lower (P < 0.05) WBS force than steaks from excitable heifers. Based on a carcass grid with discounts and premiums for HCW, QG, YG, and tenderness, calm heifers returned $62 more (P < 0.01) revenue per animal than excitable heifers. These results demonstrate that heifers with divergent phenotypes for temperament on feedlot arrival differ in their performance, feed efficiency, and feeding behavior patterns, as well as carcass quality and revenue.

Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle

BACKGROUND

The symbiotic rumen microbiota is essential for the digestion of plant fibers and contributes to the variation of production and health traits in ruminants. However, to date, the heritability of rumen microbial features and host genetic components associated with the rumen microbiota, as well as whether such genetic components are animal performance relevant, are largely unknown.

RESULTS

In the present study, we assessed rumen microbiota from a cohort of 709 beef cattle and showed that multiple factors including breed, sex, and diet drove the variation of rumen microbiota among animals. The diversity indices, the relative abundance of ~ 34% of microbial taxa (59 out of 174), and the copy number of total bacteria had a heritability estimate (h²) ≥ 0.15, suggesting that they are heritable elements affected by host additive genetics. These moderately heritable rumen microbial features were also found to be associated with host feed efficiency traits and rumen metabolic measures (volatile fatty acids). Moreover, 19 single nucleotide polymorphisms (SNPs) located on 12 bovine chromosomes were found to be associated with 14 (12 of them had h² ≥ 0.15) rumen microbial taxa, and five of these SNPs were known quantitative trait loci for feed efficiency in cattle.

CONCLUSIONS

These findings suggest that some rumen microbial features are heritable and could be influenced by host genetics, highlighting a potential to manipulate and obtain a desirable and efficient rumen microbiota using genetic selection and breeding. It could be a useful strategy to further improve feed efficiency and optimize rumen fermentation through targeting both cattle and their rumen microbiota.

Relationships between feeding behaviors and performance traits in slow-growing yellow broilers

This study was conducted to investigate the feeding behaviors of slow-growing yellow broilers and the relationships of feeding behaviors with performance traits. With the help of automatic recording systems in floor houses, feeding events from a pure line of slow-growing yellow broilers were recorded from 57 to 77 d of age. After data quality control, a total of 116,477 feeding records from 319 birds were used for analyses. Feeding behaviors including number of visits per day (18.74), feeding duration per day (71.17 min/d), feeding duration per visit (262.00 s/visit), feeding rate (2.19 g/min), and feed intake per visit (8.52 g/visit) were calculated according to feeding records. Correlation analyses and comparisons between divergent efficiency groups were performed to examine the relationships between feed efficiency and feeding behaviors. Absolute correlations between residual feed intake (RFI) and feeding behaviors (except for feed intake per visit) were significant but weak (r = 0.18 to 0.34, P < 0.05), whereas feed conversion ratio (FCR) was not significantly correlated with any feeding behaviors. All of the weight-associated traits were positively correlated with feeding rate and feed intake per visit (r = 0.19 to 0.25, P < 0.05). Compared with the inefficient birds with the 20% highest RFI or FCR (HRFI or HFCR), the efficient ones with the 20% lowest RFI or FCR (LRFI or LFCR) ate faster (P < 0.05), spent shorter eating duration (P < 0.05) and had similar feed intakes per visit (P > 0.05). However, number of visits per day and the feeding duration per day were lower in the LRFI group than in the HRFI group (P < 0.05) but were not significantly different between the LFCR and HFCR groups (P > 0.05). In summary, this study shows the feeding behaviors of group-housed slow-growing yellow broilers and observed that RFI has closer relationships with feeding behaviors than FCR does, and the selection for birds with improved RFI may result in fewer visits, shorter duration and faster feeding rate.

Integrating the RFID identification system for Charolaise breeding bulls with 3D imaging for virtual archive creation

The individual electronic identification (EID) of cattle based on RFID technology (134.2 kHz ISO standard 11784) will definitely enter into force in European countries as an official means of animal identification from July 2019. Integrating EID with 3D digital images of the animal would lead to the creation of a virtual archive of breeding animals for the evaluation and promotion of morphology associated with economic traits, strategic in beef cattle production. The genetically-encoded morphology of bulls and cows together with the expression in the phenotype were the main drivers of omic technologies of beef cattle production. The evaluation of bulls raised for reproduction is mainly based on the conformation and heritability of traits, which culminates in muscle mass and optimized carcass traits in the offspring destined to be slaughtered. A bottom-up approach by way of SWOT analysis of the current morphological and functional evaluation process for bulls revealed a technological gap. The innovation of the process through the use of smart technologies was tested in the field. The conventional 2D scoring system based on visual inspection by breed experts was carried out on a 3D model of the live animal, which was found to be a faithful reproduction of live animal morphology, thanks to the non significant variance (p > 0.05) of means of the somatic measures determined on the virtual 3D model and on the real bull. The four main groups composing the scoring system of bull morphology can easily be carried out on the 3D model. These are as follows: (1) Muscular condition; (2) Skeletal development; (3) Functional traits; (4) Breed traits. The 3D-Bull model derived from the Structure from Motion (SfM) algorithm displays a high tech profile for the evaluation of animal morphology in an upgraded system.

Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle

BACKGROUND

Microorganisms are responsible for fermentation within the rumen and have been reported to contribute to the variation in feed efficiency of cattle. However, to what extent the breed affects the rumen microbiome and its association with host feed efficiency is unknown. Here, rumen microbiomes of beef cattle (n = 48) from three breeds (Angus, Charolais, Kinsella composite hybrid) with high and low feed efficiency were explored using metagenomics and metatranscriptomics, aiming to identify differences between functional potentials and activities of same rumen microbiomes and to evaluate the effects of host breed and feed efficiency on the rumen microbiome.

RESULTS

Rumen metagenomes were more closely clustered together and thus more conserved among individuals than metatranscriptomes, suggesting that inter-individual functional variations at the RNA level were higher than those at the DNA level. However, while mRNA enrichment significantly increased the sequencing depth of mRNA and generated similar functional profiles to total RNA-based metatranscriptomics, it led to biased abundance estimation of several transcripts. We observed divergent rumen microbial composition (metatranscriptomic level) and functional potentials (metagenomic level) among three breeds, but differences in functional activity (metatranscriptomic level) were less apparent. Differential rumen microbial features (e.g., taxa, diversity indices, functional categories, and genes) were detected between cattle with high and low feed efficiency, and most of them were breed-specific.

CONCLUSIONS

Metatranscriptomes represent real-time functional activities of microbiomes and have the potential to better associate rumen microorganisms with host performances compared to metagenomics. As total RNA-based metatranscriptomics seem to avoid potential biases caused by mRNA enrichment and allow simultaneous use of rRNA for generation of compositional profiles, we suggest their use for linking the rumen microbiome with host phenotypes in future studies. However, if exploration of specific lowly expressed genes is desired, mRNA enrichment is recommended as it will enhance the resolution of mRNA. Finally, the differential microbial features observed between efficient and inefficient steers tended to be specific to breeds, suggesting that interactions between host breed genotype and the rumen microbiome contribute to the variations in feed efficiency observed. These breed-associated differences represent an opportunity to engineer specific rumen microbiomes through selective breeding of the hosts.

The effects of age and gender (bull vs steer) on the feeding behavior of young beef cattle fed grass silage

Objective

The objective of this study was to determine the effects of age and gender (bull vs steer) on feeding behavior parameters in young beef cattle fed grass silage.

Methods

The study was conducted on 180 young beef cattle at 7 to 18 mo of age. The experimental materials comprised 90 bulls produced by commercial crossing of Polish Holstein-Friesian cows with Charolais, Limousin and Hereford bulls (30 animals of each breed) and 90 steers of the same genotypes. The animals had ad libitum access to grass silage; the concentrate was fed separately, in feed stations. They received 28 g dry matter of concentrate per kg of metabolic body weight per day. Bunk visit data and silage intake for all experimental animals were recorded individually using the Roughage Intake Control system (5 feed bunks per 15 animals).

Results

Age and gender (bull vs steer) exerted significant effects on the feeding behavior of young beef cattle. The frequency of bunk visits and meal frequency decreased, whereas the feeding rate of silage, and the average duration and size of a single meal increased with age (p<0.01). Bunk attendance and meal frequency were higher (p<0.01) in steers than in bulls (49.1 vs 37.4 visits/d, and 8.63 vs 7.99 meals/d, respectively). Daily feeding time was longer in steers than in bulls (102.3 vs 100.3 min/d, respectively), but the feeding rate of silage was lower in steers, and their meals were smaller in size and shorter in duration (p<0.01). Daily silage dry matter intake was higher (p<0.01) in bulls than in steers (4.62 vs 4.47 kg/d, respectively).

Conclusion

The results of this study indicate that age and gender (bull vs steer) exerted significant effects on the feeding behavior of young beef cattle.

Chicken or the Egg: The Reciprocal Association Between Feeding Behavior and Animal Welfare and Their Impact on Productivity in Dairy Cows

Feeding behavior in dairy cattle has a significant impact on feed efficiency, which is important for increasing the profitability of livestock and, at the same time, reducing the environmental impact. Feeding behavior can be measured by feeding time, meal duration, meal frequency, feeding rate, and rumination time. Higher feed intake is related to lower feed efficiency; whereas, an increase in feeding time facilitates chewing, reduces feed particle size and increases its digestibility. More frequent and shorter meals are usually associated with a more efficient use of feed due to improvement of feed digestibility. Rumination time is positively associated with milk production. Impaired health is associated with variations in feeding behavior, which can be used to identify and predict some diseases such as ketosis, mastitis, or lameness. Changes in rumination time are also a reliable indicator of mastitis, lameness, ketosis, abomasal displacement, and the onset of calving. In addition to the cause-effect relationship between disease and changes in feeding behavior, there are also some cases in which changes in feeding behavior may lead to an increased risk of disease, as exemplified by the relationship of feeding rate with sub-acute ruminal acidosis. Feeding behavior is regulated by internal and external factors and some of them are relevant for animal welfare. The main welfare-associated factors influencing feeding behavior are social behavior and temperament, and environmental effects. Cattle are social animals and hierarchy has a notable impact on feeding behavior, especially when access to feed is limited. Competition for feed causes a reduction in the average feeding time but increases feeding rate. Excitable animals visit the feeder more often and spend less time per meal. High environmental temperature affects feeding behavior, as heat-stressed cattle change their feeding pattern by concentrating the feeding events in crepuscular hours, leading to an increased risk of sub-acute ruminal acidosis. In conclusion, feeding behavior is a determinant feature for improving efficiency, productivity and welfare of dairy cattle. Routine assessment of feeding behavior allows monitoring of health and production status of dairy cattle at the individual and farm level, which is a useful tool to optimize the management of livestock.