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Despite the multiple definitions currently used to express enteric methane emissions from ruminants, no consensus has been reached on the most appropriate definition. The objective of the present study was to explore alternative trait definitions reflecting animal-level differences in enteric methane emissions in growing cattle. It is likely that no single methane trait definition will be best suited to all intended use cases, but at least knowing the relationships between the different traits may help inform the selection process. The research aimed to understand the complex inter-relationships between traditional and novel methane traits and their association with performance traits across multiple breeds and sexes of cattle; also of interest was the extent of variability in daily enteric methane emissions independent of performance traits like feed intake, growth and liveweight. Methane and carbon dioxide data were collected using the Greenfeed system on 939 growing crossbred cattle from a commercial feedlot. Performance traits including feed intake, feeding behavior, liveweight, live animal ultrasound, subjectively scored skeletal and muscular traits, and slaughter data were also available. A total of 13 different methane traits were generated, including (average) daily methane production, 5 ratio traits and 7 residual methane (RMP) traits. The RMP traits were defined as methane production adjusted statistically for different combinations of the performance traits of energy intake, liveweight, average daily gain, and carcass weight; terms reflecting systematic effects were also included in the fixed effects linear models. Of the performance traits investigated, liveweight and energy intake individually explained more of the variability in methane production than growth rate or fat. All definitions of RMP were strongly phenotypically correlated with each other (>0.90) as well as with methane production itself (>0.86); the RMP traits were also moderately correlated with the methane ratio traits (>0.57). The dataset included heifers, steers, and bulls; bulls were either fed a total mixed ration or ad lib concentrates. When all sexes fed total mixed ration were compared, bulls, on average, emitted the most enteric methane per day of 269.53 g, while heifers and steers produced 237.54 and 253.26 g, respectively. Breed differences in the methane traits existed, with Limousins, on average, producing the least amount of methane of the breeds investigated. Herefords and Montbéliardes produced 124.50 g and 130.77 g more methane per day, respectively, than Limousins. The most efficient 10% of test-day records, as defined by daily methane independent of both energy intake and liveweight emitted, on average, 54.60 g/d less methane than animals that were average for daily methane independent of both energy intake and liveweight. This equates to 6.5 kg less methane production per animal over a 120-d finishing period for the same feed intake and liveweight.This study explores established and novel enteric methane trait definitions in growing crossbred cattle, aiming to unravel associations between various methane traits and economically important performance traits, while also quantifying inter-breed differences.Understanding the dynamics of livestock methane emissions is an important aspect to reducing agricultural greenhouse gas emissions. The present study focused on growing beef cattle, one of the primary sources of enteric methane in agriculture. Various definitions of enteric methane emissions were explored. Individual animal eructed methane and carbon dioxide spot measures were available from 939 crossbred cattle at a commercial feedlot. Performance data of feed intake, feeding behavior, liveweight, live animal ultrasound scans, and slaughter information were also available. Thirteen distinct methane traits were defined, categorized into daily methane production, ratio-based traits, and residual traits. All methane trait definitions were positively correlated with one another. Methane emissions varied across different cattle breeds and sexes fed total mixed ration, with bulls typically emitting 31 g more methane per day than heifers. The overall mean methane emission was 248.86 g/d with a standard deviation of 40.69 g. Of the breeds studied, Limousin cattle emitted the least methane, while Herefords and Montbéliardes produced 124.5 and 130.77 g more methane per day, respectively, than Limousins. Importantly, independent of breed, the most efficient 10% of cattle, when adjusted for the same feed intake and liveweight, produced 54.60 g less methane per day than the average of the animals tested. Over a 120-d feeding period, this equates to 6.5 kg less methane per animal.

Genetic selection has been identified as a promising approach for reducing enteric methane (CH4) emissions; a prerequisite for genetic evaluations; however, these are estimates of the necessary genetic parameters based on a population representative of where the genetic evaluations will be used. The objective of this study was, therefore, to derive genetic parameters for a series of definitions of CH4, carbon dioxide (CO2), and dry matter intake (DMI) as well as genetic correlations between CH4, CO2, and DMI in a bid to address the paucity of studies involving methane emissions measured in beef cattle using GreenFeed systems. Lastly, estimated breeding values (EBV) were generated for nine alternative definitions of CH4using the derived genetic parameters; the EBV were validated against both phenotypic performance (adjusted for non-genetic effects) and the Legarra and Reverter method comparing EBV generated for a subset of the dataset compared to EBV generated from the entire dataset. Individual animal CH4and CO2records were available from a population of 1,508 multi-breed growing beef cattle using 10 GreenFeed Emission Monitoring systems. Nine trait definitions for CH4and CO2were derived: individual spot measures, the average of all spot measures within a 3-h, 6-h, 12-h, 1-d, 5-d, 10-d, and 15-d period and the average of all spot measures across the full test period (20 to 114 d on test). Heritability estimates from 1,155 animals, for CH4, increased as the length of the averaging period increased and ranged from 0.09 ± 0.03 for the individual spot measures trait to 0.43 ± 0.11 for the full test average trait; a similar trend existed for CO2with the estimated heritability ranging from 0.17 ± 0.04 to 0.50 ± 0.11. Enteric CH4was moderately to strongly genetically correlated with DMI with a genetic correlation of 0.72 ± 0.02 between the spot measures of CH4and a 1-d average DMI. Correlations, adjusted for heritability, between the adjusted phenotype and (parental average) EBV ranged from 0.56 to 1.14 across CH4definitions and the slope between the adjusted phenotype and EBV ranged from 0.92 to 1.16 (expectation = 1). Validation results from the Legarra and Reverter regression method revealed a level bias of between −0.81 and −0.45, a dispersion bias of between 0.93 and 1.17, and ratio accuracy (ratio of the partial evaluation accuracies on whole evaluation accuracies) from 0.28 to 0.38. While EBV validation results yielded no consensus, CH4is a moderately heritable trait, and selection for reduced CH4is achievable.The aim of this research was to establish how much of the observed variability in enteric methane production and feed intake in growing cattle is attributable to the underlying genetic differences in these animals and if downstream genetic evaluations could be used to breed lower-emitting animals.Livestock production is a significant contributor to greenhouse gas emissions. Animal breeding programs have been proposed as a sustainable mitigation strategy to reduce enteric methane emissions in livestock production. Before creating a genetic evaluation for enteric methane production, it is important to estimate how much inter-animal genetic variability contributes to the observed differences in enteric methane production. The purpose of this study was to explore multiple enteric methane phenotypes and estimate how much phenotypic variation was due to genetic differences among 1,508 growing cattle of multiple breeds and crosses; also of interest was the extent of similarity in the genetic control of enteric methane, carbon dioxide, and feed intake (i.e., the genetic correlation) and to determine if selection of animals on the estimated genetic merit for methane emissions of their parents would manifest itself in differences in actual methane produced by those animals. Between 9% and 43% of the inter-animal differences in daily enteric methane production were due to differences in the genetic composition of those animals; the genetic control influencing methane production was similar to that of feed intake (i.e., a strong genetic correlation between methane emissions and feed intake of up to 0.72).

The importance of improving the efficiency of beef production systems using both genetic and management strategies has long been discussed. Despite the contribution of the mature beef herd to the overall cost of production in the sector as a whole, most strategies for improving (feed) efficiency have focused on the growing animal. The objective of the present study was to quantify the phenotypic and genetic variability in several novel measures that relate the weight of a calf to that of its dam and vice versa. Two novel residual traits, representing the deviation in calf weight relative to its expectation from the population based on its dam's weight (DIFFcalf) or the deviation in the weight of the dam relative to its expectation from the population based on its calf's weight (DIFFdam), were calculated while simultaneously accounting for some nuisance factors in a multiple regression model. Four supplementary traits were also calculated, namely, 1) the deviation in calf weight from its expectation expressed relative to the weight of the dam (DIFFcalf_ratio), 2) the deviation in dam weight from its expectation relative to the weight of the dam (DIFFdam_ratio), 3) DIFFcalf-DIFFdam, and 4) the simple ratio of calf weight to its dam's weight (RATIOcalfdam). Genetic and residual variance components for each of the 6 traits were estimated using animal-dam linear mixed models. The phenotypic SD for DIFFcalf was 42 kg and, when expressed relative to the weight of the dam (i.e., DIFFcalf_ratio), was 0.07. The genetic SD for DIFFcalf and DIFFcalf_ratio was 16.66 kg and 0.02, respectively. The direct and maternal heritability estimated for DIFFcalf was 0.28 (SE = 0.04) and 0.11 (SE = 0.02), respectively, and for DIFFcalf_ratio was 0.24 (SE = 0.04) and 0.17 (SE = 0.03), respectively. The genetic SD for DIFFdam was 47.09 kg; the direct heritability was 0.50 (SE = 0.03), and the dam repeatability was 0.75 (SE = 0.01). The genetic SD for RATIOcalfdam was 0.03; the direct and maternal heritability was 0.24 (SE = 0.04) and 0.24 (SE = 0.03), respectively. The suggested traits outlined in the present study provide useful metrics for benchmarking dam-calf efficiency; in addition, the genetic variability detected in these traits suggest genetic progress for more efficient dam-calf pairs is indeed possible.

Having access to early predictions of both the genetic merit and expected phenotypic performance of an individual or its progeny can contribute to more informed decision-making. The objective here was to evaluate the usefulness of routinely available subjectively scored linear conformation information on live animals to predict genetic merit for primal carcass cut yields of their relatives. Data on 6 muscular and 6 skeletal traits on 43,078 live animals were used; the weights of up to 14 primal cuts plus 3 groups of primal cuts of 31,827 cattle were also used. Genetic correlations between the linear scores and the primal cut weights were estimated using sire linear mixed models; correlations were estimated with or without phenotypic adjustment of the primal cut weights to a constant carcass weight. The genetic correlations between each of the muscular and skeletal linear type traits with each of the primal cut weights (not adjusted for carcass weight) were all positive with the exception of the correlations between both chest width and pelvic length with cuberoll. On average, the muscular type traits were more strongly correlated (on average 0.42) with the primal cut weights than the skeletal traits (on average 0.35). Moreover, the average of the genetic correlations between each of the 6 muscular traits with all 8 hindquarter traits was, on average, 10% to 18% stronger than the average of the genetic correlations between the same muscular traits with all 5 forequarter primal cuts. When adjusted for differences in carcass weight, the correlations between all linear scores and the carcass traits regressed to zero or became negative. The skeletal traits were, in general, weakly genetically correlated with the primal cuts adjusted to a common carcass weight. The average of the genetic correlation between the muscular type traits and the primal cuts adjusted for differences in carcass weight was only 0.09 with only 13 of the 84 pairwise correlations being stronger than 0.30; the genetic correlation between silverside with the muscular traits was all stronger than 0.30, whereas the majority of the muscular traits had a correlation stronger than 0.30 with the topside primal cut. In fact, the average of the genetic correlations between the topside and silverside cuts with all the muscular traits was 0.50 and 0.42, respectively, with none of the correlations being negative.

The objective of the present study was to quantify the genetic and non-genetic contributors to variability in both carcass dressing percentage and dressing difference (i.e., the difference between carcass weight and live weight immediately prior to slaughter) in young animals and cows. The datasets contained 18,479 young animals from 653 herds, and 2,887 cows from 665 herds. Live weight records within 7 d of slaughter and associated carcass weight were available for all animals. Association analyses were undertaken using linear mixed models with fixed effects for the model of young animals consisting of animal breed, days between the date of last recorded live weight and slaughter date, heterosis and recombination loss coefficients, dam parity, a 3-way interaction between whether the animal originated in a dairy or beef herd, animal sex, and age at slaughter, as well as a 2-way interaction between calendar year of slaughter and month of slaughter; contemporary group was included as a random effect. Fixed effects in the cow model were cow breed, the number of days between the date of last recorded live weight and slaughter date, heterosis and recombination loss coefficients, the number of days postcalving, parity of the cow, and a 2-way interaction between calendar year of slaughter and month of slaughter; contemporary group was included as a random effect. The mean dressing percentage (phenotypic standard deviation in parentheses) and dressing difference in young animals were 55.86% (3.21%) and 280.03 kg (41.44 kg), respectively. Steers had the heaviest dressing difference at 34.18 and 60.44 kg heavier than a 16-mo old bull and 22-mo old heifer, respectively. Dressing difference for 30-mo old Simmental steers (breed with heaviest dressing difference) was 41.66 kg heavier than 30-mo old Belgian Blue steers (breed with lightest dressing difference). The heritability of dressing percentage (0.48) and dressing difference (0.35) in young animals was relatively similar to each other, in contrast to dressing percentage (0.08) in cows which was considerably lower than dressing difference (0.28). Considerable genetic variability existed in dressing difference amongst young animals (genetic standard deviation of 15.03 kg), despite the near unity genetic correlation (0.93) between carcass weight and live weight. This therefore indicates that genetic selection for increased saleable product can be achieved by selecting for increased carcass weight while concurrently selecting for lighter animals although the opportunity is limited by the strong part-whole relationships that exists between carcass weight, live weight, and dressing difference.

Linear type traits describing the skeletal, muscular, and functional characteristics of an animal are routinely scored on live animals in both the dairy and beef cattle industries. Previous studies have demonstrated that genetic parameters for certain performance traits may differ between breeds; no study, however, has attempted to determine if differences exist in genetic parameters of linear type traits among breeds or sexes. Therefore, the objective of the present study was to determine if genetic covariance components for linear type traits differed among five contrasting cattle breeds, and to also investigate if these components differed by sex. A total of 18 linear type traits scored on 3,356 Angus (AA), 31,049 Charolais (CH), 3,004 Hereford (HE), 35,159 Limousin (LM), and 8,632 Simmental (SI) were used in the analysis. Data were analyzed using animal linear mixed models which included the fixed effects of sex of the animal (except in the investigation into the presence of sexual dimorphism), age at scoring, parity of the dam, and contemporary group of herd-date of scoring. Differences (P< 0.05) in heritability estimates, between at least two breeds, existed for 13 out of 18 linear type traits. Differences (P< 0.05) also existed between the pairwise within-breed genetic correlations among the linear type traits. Overall, the linear type traits in the continental breeds (i.e., CH, LM, SI) tended to have similar heritability estimates to each other as well as similar genetic correlations among the same pairwise traits, as did the traits in the British breeds (i.e., AA, HE). The correlation between a linear function of breeding values computed conditional on covariance parameters estimated from the CH breed with a linear function of breeding values computed conditional on covariance parameters estimated from the other breeds was estimated. Replacing the genetic covariance components estimated in the CH breed with those of the LM had least effect but the impact was considerable when the genetic covariance components of the AA were used. Genetic correlations between the same linear type traits in the two sexes were all close to unity (≥0.90) suggesting little advantage in considering these as separate traits for males and females. Results for the present study indicate the potential increase in accuracy of estimated breeding value prediction from considering, at least, the British breed traits separate to continental breed traits.

Rumen methanogenesis results in the loss of 6% to 10% of gross energy intake in cattle and globally is the single most significant source of anthropogenic methane (CH4) emissions. The purpose of this study was to analyze greenhouse gas traits recorded in a commercial feedlot unit to gain an understanding into the relationships between greenhouse gas traits and production traits. Methane and carbon dioxide (CO2) data recorded via multiple GreenFeed Emission Monitoring (GEM), systems as well as feed intake, live weight, ultrasound scanning data, and slaughter data were available on 1,099 animals destined for beef production, of which 648 were steers, 361 were heifers, and 90 were bulls. Phenotypic relationships between GEM emission measurements with feed intake, weight traits, muscle ultrasound data, and carcass traits were estimated. Utilization of GEM systems, daily patterns of methane output, and repeatability of GEM system measurements across averaging periods were also assessed. Methane concentrations varied with visit number, duration, and time of day of visit to the GEM system. Mean CH4and CO2varied between sex, with mean CH4of 256.1 g/day ± 64.23 for steers, 234.7 g/day ± 59.46 for heifers, and 156.9 g/day ± 55.98 for young bulls. A 10-d average period of GEM system measurements were required for steers and heifers to achieve a minimum repeatability of 0.60; however, higher levels of repeatability were observed in animals that attended the GEM system more frequently. In contrast, CO2emissions reached repeatability estimates >0.6 for steers and heifers in all averaging periods greater than 2-d, suggesting that cattle have a moderately consistent CO2emission pattern across time periods. Animals with heavier bodyweights were observed to have higher levels of CH4(correlation = 0.30) and CO2production (correlation = 0.61), and when assessing direct methane, higher levels of dry matter intake were associated with higher methane output (correlation = 0.31). Results suggest that reducing CH4can have a negative impact on growth and body composition of cattle. Methane ratio traits, such as methane yield and intensity were also evaluated, and while easy to understand and compare across populations, ratio traits are undesirable in animal breeding, due to the unpredictable level of response. Methane adjusted for dry matter intake and liveweight (Residual CH4) should be considered as an alternative emission trait when selecting for reduced emissions within breeding goals.This research aims to emphasize the need for a consistent protocol with regard to methane measurement and data handling and highlight the relationships between methane and production traits.Methane production from cattle digestion results in the loss of 6% to 10% of gross energy intake in cattle and globally is the single most significant source of anthropogenic methane (CH4) emissions. The purpose of this study was to analyze greenhouse gas traits recorded in a commercial feedlot unit to gain an understanding into the relationships between greenhouse gas traits and production traits of economic importance. Methane and carbon dioxide emissions recorded using Greenfeed systems were available on a total of 1,099 animals. In addition, performance indicators such as feed intake, live weight, ultrasound scanning data, and slaughter data were also available on all animals. Phenotypic repeatability of CH4ranged from 0.13 to 0.74, with a CH4repeatability of >0.6 achieved by both heifers and steers in 10-d measuring period. Due to the high repeatability of CH4measures, an accurate portrayal of CH4production can be observed from a 10-d measuring period when measures are averaged. Methane emission data were positively correlated with traits of economic importance. Phenotypically, animals with heavier body weights and greater feed intake had higher emissions.

Sexual dimorphism, the phenomenon whereby males and females of the same species are distinctive in some aspect of appearance or size, has previously been documented in cattle for traits such as growth rate and carcass merit using a quantitative genetics approach. No previous study in cattle has attempted to document sexual dimorphism at a genome level; therefore, the objective of the present study was to determine whether genomic regions associated with size and muscularity in cattle exhibited signs of sexual dimorphism. Analyses were undertaken on 10 linear-type traits that describe the muscular and skeletal characteristics of both males and females of five beef cattle breeds: 1,444 Angus (AA), 6,433 Charolais (CH), 1,129 Hereford, 8,745 Limousin (LM), and 1,698 Simmental. Genome-wide association analyses were undertaken using imputed whole-genome sequence data for each sex separately by breed. For each single-nucleotide polymorphism (SNP) that was segregating in both sexes, the difference between the allele substitution effect sizes for each sex, in each breed separately, was calculated. Suggestively (P≤ 1 × 10−5) sexually dimorphic SNPs that were segregating in both males and females were detected for all traits in all breeds, although the location of these SNPs differed by both trait and breed. Significantly (P≤ 1 × 10−8) dimorphic SNPs were detected in just three traits in the AA, seven traits in the CH, and three traits in the LM. The vast majority of all segregating autosomal SNPs (86% in AA to 94% in LM) had the same minor allele in both males and females. Differences (P≤ 0.05) in allele frequencies between the sexes were observed for between 36% (LM) and 66% (AA) of the total autosomal SNPs that were segregating in both sexes. Dimorphic SNPs were located within a number of genes related to muscularity and/or size including the NAB1, COL5A2, and IWS1genes on BTA2 that are located close to, and thought to be co-inherited with, the MSTNgene. Overall, sexual dimorphism exists in cattle at the genome level, but it is not consistent by either trait or breed.

Beef carcasses in Europe are classified on measures of carcass weight, conformation, and fat cover. These measurements provide the basis for payment to producers, with financial penalties for carcasses that do not conform to desirable characteristics. The objective of the present study was to identify animal-level factors associated with the achievement of a desirable carcass weight, conformation score, fat score, and age at harvest, as stipulated by Irish beef processors in accordance with the EUROP carcass classification system. The stipulated specifications were a EUROP conformation score =O=, a carcass weight between 270 and 380 kg, a EUROP fat score between 2+ and 4=, and an age at harvest = 30 mo. In the present study, 59% of cattle failed to achieve at least one of these desired specifications. The logit of the probability of achieving the desired specifications was estimated using multivariable logistic regression and carcass data from 4,717,989 cattle finished and harvested in Ireland between the years 2003 and 2017. In comparison to beef-origin carcasses and after accounting for breed differences, the likelihood of dairy-origin carcasses achieving the desired age, conformation, fat, and weight specifications was 0.97, 0.88, 1.14, and 1.05, respectively. In comparison to heifer carcasses, the odds ratio (OR) of bull and steer carcasses simultaneously achieving all of the desired specifications (i.e. the overall specification) was 0.35 and 0.95, respectively. Additionally, after accounting for breed differences, heifers from the dairy herd were half as likely as heifers from the beef herd to achieve the overall specification, whereas the odds of dairy-origin bulls (OR = 3.46) and steers (OR = 2.41) achieving the overall specification was greater than that of their respective beef-origin counterparts. Finally, cattle with a greater breed proportion of Angus were most likely to achieve the overall specification. Results from the present study could provide a deeper understanding as to why animals fail to achieve desirable carcass specifications and could be implemented into the management decisions made on farm to ensure that the supply of beef carcasses that achieve the desired metrics is maximized.

The objective of the present study was to estimate the genetic parameters associated with the achievement of desirable weight, conformation, and fat specifications, represented by a series of binary traits. The desired specifications were those stipulated by Irish beef processors, in accordance with the EUROP carcass grading system, and were represented by a carcass weight between 270 and 380 kg, a fat score between 2+ and 4= (between 6 and 11 on a 15-point scale), and a conformation score of O= or better (=5 on a 15-point scale). Using data from 58,868 beef carcasses, variance components were estimated using linear mixed models for these binary traits, as well as their underlying continuous measures. Heritability estimates for the continuous traits ranged from 0.63 to 0.73; heritability estimates for the binary traits ranged from 0.05 to 0.19. An additional trait was defined to reflect if all desired carcass specifications were met. All genetic correlations between this trait and the individual contributing binary traits were positive (0.38 to 0.87), while all genetic correlations between this trait and the continuous carcass measures were negative (-0.87 to -0.07). The genetic parameters estimated in the present study signify that potential exists to breed cattle that more consistently achieve desirable carcass metrics at harvest.

Reducing the incidence of both the degree of assistance required at calving, as well as the extent of perinatal mortality (PM) has both economic and societal benefits. The existence of heritable genetic variability in both traits signifies the presence of underlying genomic variability. The objective of the present study was to locate regions of the genome, and by extension putative genes and mutations, that are likely to be underpinning the genetic variability in direct calving difficulty (DCD), maternal calving difficulty (MCD), and PM. Imputed whole-genome single-nucleotide polymorphism (SNP) data on up to 8,304 Angus (AA), 17,175 Charolais (CH), 16,794 Limousin (LM), and 18,474 Holstein-Friesian (HF) sires representing 5,866,712 calving events from descendants were used. Several putative quantitative trait loci (QTL) regions associated with calving performance both within and across dairy and beef breeds were identified, although the majority were both breed- and trait-specific. QTL surrounding and encompassing the myostatin (MSTN) gene were associated (P < 5 × 10-8) with DCD and PM in both the CH and LM populations. The well-known Q204X mutation was the fifth strongest association with DCD in the CH population and accounted for 5.09% of the genetic variance in DCD. In contrast, none of the 259 segregating variants in MSTN were associated (P > × 10-6) with DCD in the LM population but a genomic region 617 kb downstream of MSTN was associated (P < 5 × 10-8). The genetic architecture for DCD differed in the HF population relative to the CH and LM, where two QTL encompassing ZNF613 on Bos taurus autosome (BTA)18 and PLAG1 on BTA14 were identified in the former. Pleiotropic SNP associated with all three calving performance traits were also identified in the three beef breeds; 5 SNP were pleiotropic in AA, 116 in LM, and 882 in CH but no SNP was associated with more than one trait within the HF population. The majority of these pleiotropic SNP were on BTA2 surrounding MSTN and were associated with both DCD and PM. Multiple previously reported, but also novel QTL, associated with calving performance were detected in this large study. These also included QTL regions harboring SNP with the same direction of allele substitution effect for both DCD and MCD thus contributing to a more effective simultaneous selection for both traits.