Across-country genetic evaluation of meat sheep from Ireland and the United Kingdom.

Genetic evaluations in sheep have proven to be an effective way of increasing farm profitability. Much research has previously been conducted on producing within-country genetic evaluations; however, to date, no across-country sheep genetic evaluations have been produced between Ireland and the UK. The objective of the present study was to examine the feasibility of an across-country genetic evaluation of live body weight and carcass composition traits for Texel sheep raised in Ireland and the UK. The benefit of genetic selection based on across-country genetic evaluations, in comparison with within-country genetic evaluations, was also quantified. Animal traits included early-life and postweaning live body weights, and muscle and fat depth ultrasound measurements. Irish and UK data were combined, common animals with progeny with records in both countries were identified and a series of bivariate analyses were performed separately for each trait to produce across-country genetic evaluations. Fixed effects included contemporary group, age at first lambing of the dam, parity of the dam (Ireland), dam age at lamb's birth (UK), a gender by age of the lamb interaction, a birth type by rearing type of the lamb interaction and country of birth of the lamb. Random effects included the animal additive genetic, dam maternal, litter common environment and residual effect. The model for postweaning weight, muscle depth and fat depth included only the animal additive genetic and litter common environmental random effects. Genetic correlations between the two countries ranged from 0.82 to 0.88 for the various traits. Across-country breeding values were estimated for all animals and response to selection was predicted using the top 10 and top 20 sires in both within- and across-country analyses for the two countries. Overall, results showed that rates of genetic gain could potentially increase from between 2.59% and 19.63% from selection based on across-country genetic evaluations compared to within-country evaluations alone. Across-country evaluations are feasible and would be of significant benefit to both the Irish and UK sheep industries. In order to realize these potential gains though, there would need to be a switch in emphasis by sheep breeders towards using objective traits as their primary selection criteria.

Genetic and economic benefits of foreign sire contributions to a domestic sheep industry; including an Ireland-New Zealand case study.

BACKGROUND: Importation of foreign genetics is a widely used genetic improvement strategy. However, even if the foreign genetic merit is currently greater than the domestic genetic merit, differences in foreign and domestic trends mean that the long-term competitiveness of an importation strategy cannot be guaranteed. Gene flow models are used to quantify the impact that a specific subpopulation, such as foreign genetics, can have over time on the genetic or economic benefit of a domestic industry. METHODS: We used a deterministic recursive gene flow model to predict the commercial performance of lambs born across various subpopulations. Numerous breeding strategies were evaluated by varying market share, proportions of rams selected for mating, genetic trend, superiority of foreign genetics over domestic genetics and frequency of importation. Specifically, an Ireland-New Zealand case study was simulated to quantify the potential gain that could be made by using foreign sire contributions (New Zealand) in a domestic sheep industry (Ireland). RESULTS: Genetic and economic gains were generated from alternative breeding strategies. The 'base scenario' (i.e. representing the current industry) predicted an average genetic merit value of €2.51 for lambs born and an annualised cumulative benefit of €45 million (m) after 20 years. Maximum genetic (€9.45 for lambs born) and economic (annualised cumulative benefit of €180 m after 20 years) benefits were achieved by implementing the 'PRO-intense-market scenario' which involved shifting market share away from conservative domestic breeders and reducing the proportion of rams that were selected for mating by progressive domestic breeders from the top 40% to the top 20%, without the use of any foreign genetics. The 'PROFOR scenario', which considered the use of foreign and progressive domestic genetics, predicted an average genetic merit value of €7.37 for lambs born and an annualised cumulative benefit of €144 m, after 20 years. CONCLUSIONS: Our results demonstrate that there is opportunity for a domestic industry to increase industry benefits without the use of foreign genetics but through an attempt to shift the market share away from conservative domestic breeders towards progressive domestic breeders. However, the importation and use of progressive foreign genetics may be an effective method to trigger a change in behaviour of conservative domestic breeders towards the use of progressive genetics.

Inter- and intra-reproducibility of genotypes from sheep technical replicates on Illumina and Affymetrix platforms.

BACKGROUND: Accurate genomic analyses are predicated upon access to accurate genotype input data. The objective of this study was to quantify the reproducibility of genotype data that are generated from the same genotype platform and from different genotyping platforms. METHODS: Genotypes based on 51,121 single nucleotide polymorphisms (SNPs) for 84 animals that were each genotyped on Illumina and Affymetrix platforms and for another 25 animals that were each genotyped twice on the same Illumina platform were compared. Genotypes based on 11,323 SNPs for an additional 21 animals that were genotyped on two different Illumina platforms by two different service providers were also compared. Reproducibility of the results was measured as the correlation between allele counts and as genotype and allele concordance rates. RESULTS: A mean within-animal correlation of 0.9996 was found between allele counts in the 25 duplicate samples that were genotyped on the same Illumina platform and varied from 0.9963 to 1.0000 per animal. The mean (minimum, maximum) genotype and allele concordance rates per animal between the 25 duplicate samples were equal to 0.9996 (0.9968, 1.0000) and 0.9993 (0.9937, 1.0000), respectively. The concordance rate between the two different Illumina platforms was also near 1. A mean within-animal correlation of 0.9738 was found between genotypes that were generated on the Illumina and Affymetrix platforms and varied from 0.9505 to 0.9812 per animal. The mean (minimum, maximum) within-animal genotype and allele concordance rates between the Illumina and Affymetrix platforms were equal to 0.9711 (0.9418, 0.9798) and 0.9845 (0.9695, 0.9889), respectively. The genotype concordance rate across all genotypes increased from 0.9711 to 0.9949 when the SNPs used were restricted to those with three high-resolution genotype clusters which represented 75.2% of the called genotypes. CONCLUSIONS AND IMPLICATIONS: Our results suggest that, regardless of the genotype platform or service provider, high genotype concordance rates are achieved especially if they are restricted to high-quality extracted DNA and SNPs that result in high-quality genotypes.

Methane output across life stages in sheep, how it differs from lambs to adult ewes using portable accumulation chambers.

Methane (CH4) produced from enteric fermentation is a potent greenhouse gas produced by ruminant animals. Multiple measurements are required across life stages to develop an understanding of how CH4 output changes throughout the animal's lifetime. The objectives of the current study were to estimate CH4 output across life stages in sheep and to investigate the relationship between CH4 output and dry matter (DM) intake (DMI). Data were generated on a total of 266 female Suffolk and Texel animals. Methane and carbon dioxide (CO2) output, estimated using portable accumulation chambers, and DMI, estimated using the n-alkane technique outdoors and using individual penning indoors, were quantified across the animal's life stage; as lambs (<12 mo), nulliparous hoggets (12 to 24 mo) and ewes (primiparous or greater; > 24 mo). Ewes were further classified as pregnant, lactating, and dry (non-pregnant and non-lactating). Multiple measurements were taken within and across the life stages of the same animals. A linear mixed model was used to determine if CH4 and CO2 output differed across life stages and using a separate linear mixed model the factors associated with CH4 output within each life stage were also investigated. Methane, CO2 output, and DMI differed by life stage (P < 0.05), with lactating ewes producing the greatest amount of CH4 (25.99 g CH4/d) and CO2 (1711.6 g CO2/d), while also having the highest DMI (2.18 kg DM/d). Methane output differed by live-weight of the animals across all life stages (P < 0.001). As ewe body condition score increased CH4 output declined (P < 0.05). Correlations between CH4 output measured across life stages ranged from 0.26 (SE 0.08; lambs and lactating ewes) to 0.59 (SE 0.06; hoggets and pregnant ewes), while correlations between CO2 output measured across life stages ranged from 0.12 (SE 0.06; lambs and hoggets) to 0.65 (SE 0.06; hoggets and lactating ewes). DMI was moderately correlated with CH4 (0.44; SE 0.04) and CO2 output (0.59; SE 0.03). Results from this study provide estimates of CH4 output across life stages in a pasture-based sheep production system and offer valuable information for the national inventory and the marginal abatement cost curve on the optimum time to target mitigation strategies.

Obtaining accurate estimates of methane (CH4) output across life stages is important to assess how CH4 output changes throughout the production cycle in pasture-based sheep production systems. This study investigated the factors associated with CH4 output at each life stage (lambs, hoggets, pregnant, lactating, and dry ewes), the relationship between CH4 output measured across life stages and the relationship between CH4 output and dry matter intake (DMI) in an Irish lowland sheep production system. Methane and carbon dioxide (CO2) output and DMI were measured on 266 purebred Suffolk and Texel females across their lifetime. Lactating ewes produced the highest CH4 and CO2 output, along with having the highest DMI. Across all life stages, CH4 output increased with increasing live weight while CH4 output decreased as body condition score increased. Weak to moderate relationships were found between CH4 output measured across life stages, with the strength of the relationship decreasing as the time between life stages increased. A positive relationship was found between DMI and CH4 output. Results from this study lead to the development of a profile of CH4 output across the production cycle of a pasture-based sheep system.

Investigating How Genetic Merit and Country of Origin Impact the Profitability of Grass-Based Sheep Production Systems.

The objective of this study was to simulate and assess the profitability of sheep production systems that varied in maternal genetic merit (high or low) and country of origin (New Zealand (NZ) or Ireland), using the Teagasc Lamb Production Model (TLPM). A production system study performed at Teagasc Athenry, Co. Galway, Ireland, from 2016 to 2019, inclusive, provided key animal performance input parameters, which were compared across three scenarios: high maternal genetic merit NZ (NZ), high maternal genetic merit Irish (High Irish) and low maternal genetic merit Irish (Low Irish). Prior to the beginning of the study ewes and rams were imported from New Zealand to Ireland in order to compare animals within the same management system. Ewes were selected based on the respective national maternal genetic indexes; i.e., either the New Zealand Maternal Worth (NZ group) or the €uro-star Replacement index (Irish groups). The TLPM was designed to simulate the impact of changes in physical and technical outputs (such as number of lambs, drafting rates and replacement rates) on a range of economic parameters including variable costs, fixed costs, gross margin and net profit. Results showed that total farm costs (variable and fixed) were similar across the three scenarios, driven by the similar number of ewes in each scenario. The number of lambs produced and the cost of production per lamb was 14.05 lambs per hectare for the NZ scenario at a cost of EUR 82.35 per lamb, 11.40 lambs per hectare for the High Irish scenario at a cost of EUR 101.42 per lamb and 11.00 lambs per hectare for the Low Irish scenario at a cost of EUR 105.72 per lamb. The net profit of the three scenarios was EUR 514, EUR 299, and EUR 258 per hectare, for the NZ, High Irish and Low Irish scenarios, respectively. Overall, the NZ scenario had a lower cost of production in comparison to either Irish group, while the High Irish scenario had a 14% greater net profit than the Low Irish scenario, equating to an additional EUR 41 per hectare net profit. Output from this simulation model reiterates the importance, for overall farm profitability, of maximising the number of lambs weaned per hectare, particularly through maximising income and diluting the total farm costs. To conclude, the use of high-maternal-genetic-merit animals, regardless of their country of origin impacts farm profitability.

Validation of maternal and terminal sheep breeding objectives using Irish field data.

Genetic evaluations provide producers with a tool to aid in breeding decisions and highlight the increase in performance achievable at the farm level through genetic gain. Despite this, large-scale validation of sheep breeding objectives using field data is lacking in the scientific literature. The objective of the present study was to evaluate the phenotypic differences for a range of economically important traits for animals divergent in genetic merit for the Irish national maternal and terminal sheep breeding objectives. A dataset of 17,356 crossbred ewes and 54,322 progeny differing in their maternal and terminal breeding index recorded in 139 commercial flocks was available. The association of the maternal index of the ewe or terminal index of the ram and a range of phenotypic performance traits, including lambing, lamb performance, ewe performance, and health traits, were undertaken. Ewes excelling on the maternal index had higher litter sizes and produced progeny with greater perinatal lamb survival, heavier live weights from birth to postweaning and reduced days to slaughter (P < 0.05). Ewe maternal index had no quantifiable impact on lambing ease, carcass conformation, or fat, the health status of the ewe or lamb, ewe barren rate, or ewe live weight. Lambs born to rams of superior terminal index produced heavier lambs from preweaning onwards, with a reduced day to slaughter (P < 0.05). Lambing traits, lamb health, and carcass characteristics of the progeny did not differ between sires stratified as low or high on the terminal index (P > 0.05). Results from this study highlight that selecting either ewes or rams of superior maternal or terminal attributes will result in an improvement on pertinent performance traits of the national sheep flock, resulting in greater flock productivity and profitability.

The impact of maternal genetic merit and country of origin on ewe reproductive performance, lambing performance, and ewe survival.

The objective of this study was to investigate the impact of the ewe's maternal genetic merit and country of origin [New Zealand (NZ) or Ireland] on ewe reproductive, lambing, and productivity traits. The study was performed over a 4-yr period (2016-2019) and consisted of three genetic groups: high maternal genetic merit (NZ), high maternal genetic merit Irish (High Irish), and low maternal genetic merit Irish (Low Irish) ewes. Each group contained 30 Suffolk and 30 Texel ewes, selected based on the respective national maternal genetic indexes; i.e., either the NZ Maternal Worth (NZ group) or the €uro-star Replacement index (Irish groups). The impact of maternal genetic merit on reproductive traits such as litter size; lambing traits such as gestation length, birth weight, lambing difficulty, mothering ability; and productivity traits such as the number of lambs born and weaned was analyzed using linear mixed models. For binary traits, the impact of maternal genetic merit on reproductive traits such as conception to first artificial insemination (AI) service; lambing traits such as dystocia and perinatal lamb mortality; and productivity traits such as ewe survival was analyzed using logistic regression. NZ ewes outperformed Low Irish ewes for conception to first AI (P < 0.05) and litter size (P = 0.05). Irish ewes were more likely to suffer from dystocia [6.84 (High Irish) and 8.25 (Low Irish) times] compared to NZ ewes (P < 0.001); birth weight and perinatal mortality did not differ between groups (P > 0.05). Lambs born from NZ ewes were 4.67 [95% confidence interval (CI): 1.89-11.55; P < 0.001] and 6.54 (95% CI: 2.56-16.71; P<0.001) times more likely to stand up and suckle unassisted relative to lambs born from High or Low Irish ewes, respectively. NZ and High Irish ewes had a greater number of lambs born and weaned throughout the duration of the study compared to their Low Irish counterparts (P<0.001). NZ ewes tended to be more likely to survive from one year to the next compared with Low Irish ewes (P=0.07). Irish ewes of high maternal genetic merit outperformed their low counterparts in total number of lambs born and weaned per ewe, but performance did not differ across other traits investigated. This highlights the importance of continuous development of the Irish maternal sheep index to ensure favorable improvements in reproductive, lambing, and productivity traits at the farm level. Overall, results demonstrate the suitability of NZ genetics in an Irish production system.

The impact of genetic merit on ewe performance and efficiency parameters.

The aim of this study was to investigate the impact of ewe genetic merit on ewe performance and efficiency parameters. The study consisted of three genetic merit groups (New Zealand [NZ], High Irish, and Low Irish) and ran from 2016 to 2019, inclusive. Each genetic merit group contained 30 purebred Suffolk and 30 purebred Texel ewes, which were selected based on their maternal genetic indexes in their country of origin, namely Ireland (€uro-star Replacement index) or New Zealand (New Zealand Maternal worth). Ewe body condition score (BCS), ewe body weight (BW), milk yield, milk composition, dry matter intake (DMI), and efficiency parameters were all analyzed using linear mixed models. Ewe BW was similar across all genetic merit groups at each time point (P > 0.05). In comparison to both High and Low Irish ewes, NZ ewes had a higher BCS at mating, mid-pregnancy, lambing, week 10 post-lambing (PL, P < 0.05). Ewe BW change was similar across genetic merit groups, except between mating and mid-pregnancy where ewe BW loss was greater for NZ ewes than Irish ewes (P < 0.05) and between weeks 6 PL and 10 PL, where NZ ewes gained BW and High and Low Irish ewes lost BW (P < 0.01). Ewe milk yield, milk fat, total solids, and gross energy content were superior for milk produced by NZ ewes at week 6 PL in comparison to milk produced by High Irish and Low Irish ewes (P < 0.01). NZ ewes produced a greater quantity of milk solids/kg of BW at week 6 PL compared with High Irish ewes (P < 0.01), whereas Low Irish ewes did not differ from either NZ or High Irish (P > 0.05). Low Irish ewes had a greater daily DMI than High Irish ewes in late lactation (week 10 PL, P < 0.05) and had a greater DMI/kg of ewe BW compared with the High Irish ewes at the same time point (P < 0.05). NZ ewes weaned a litter BW equivalent to 60.4% of their mating BW, which was more than the Low Irish ewes who weaned 57.1% of the ewe's BW at mating (P < 0.01), whereas the High Irish ewes did not differ from either the NZ or Low Irish ewes at 59.3% of the ewe's BW at mating (P > 0.05). This study presents a range of parameters across ewes of high and low genetic merit, demonstrating the ability to achieve gains through selection of animals of high genetic merit. Sheep producers should consider genetic indexes as a tool to assist in the decision-making process of selecting replacement ewes and/or breeding rams, once satisfied the animal is correct, and meeting the breeding objectives of the system.

Investigation of intra-day variability of gaseous measurements in sheep using portable accumulation chambers.

Portable accumulation chambers (PAC) enable short-term spot measurements of gaseous emissions including methane (CH4), carbon dioxide (CO2), and oxygen (O2) consumption from small ruminants. To date the differences in morning and evening gaseous measurements in the PAC have not been investigated. The objectives of this study were to investigate: 1) the optimal measurement time in the PAC, 2) the appropriate method of accounting for the animal's size when calculating the animal's gaseous output, and 3) the intra-day variability of gaseous measurements. A total of 12 ewe lambs (c. 10 to 11 months of age) were randomly selected each day from a cohort of 48 animals over nine consecutive days. Methane emissions from the 12 lambs were measured in 12 PAC during two measurement runs daily, AM (8 to 10 h) and PM (14 to 16 h). Animals were removed from Perennial ryegrass silage for at least 1 h prior to measurements in the PAC and animals were assigned randomly to each of the 12 chambers. Methane (ppm) concentration, O2 and CO2 percentage were measured at 5 time points (T1 = 0.0 min, T2 = 12.5 min, T3 = 25.0 min, T4 = 37.5 min, and T5 = 50.0 min from entry of the first animal into the first chamber) using an Eagle 2 monitor. The correlation between time points T5-T1 (i.e., 50 min minus 0 min after entry of the animal to the chamber) and T4-T1 was 0.95, 0.92, and 0.77 for CH4, O2, and CO2, respectively (P < 0.01). The correlation between CH4 and CO2 output and O2 consumption, calculated with live-weight and with body volume was 0.99 (P < 0.001). The correlation between the PAC measurement recorded on the same animal in the AM and PM measurement runs was 0.73. Factors associated with CH4 production included: day and time of measurement, the live-weight of the animal and the hourly relative humidity. Results from this study suggest that the optimal time for measuring an animal's gaseous output in the PAC is 50 min, that live-weight should be used in the calculation of gaseous output from an animal and that the measurement of an animal's gaseous emissions in either the AM or PM does not impact on the ranking of animals when gaseous emissions are measured using the feeding and measurement protocol outlined in the present study.

Repeatability of gaseous measurements across consecutive days in sheep using portable accumulation chambers.

Portable accumulation chambers (PACs) enable gaseous emissions from small ruminants to be measured over a 50-min period; to date, however, the repeatability of consecutive days of measurement in the PAC has not been investigated. The objectives of this study were 1) to investigate the repeatability of consecutive days of gaseous measurements in the PAC, 2) to determine the number of days required to achieve precise gaseous measurements, and 3) to develop a prediction equation for gaseous emissions in sheep. A total of 48 ewe lambs (c. 10 to 11 mo of age) were randomly divided into four measurement groups each day, for 17 consecutive days. Gaseous measurements were conducted between 0800 and 1200 hours daily. Animals were removed from perennial ryegrass silage for at least 1 h before measurements in the PAC, and animals were assigned randomly to each of the 12 chambers. Methane (CH4; ppm) concentration, oxygen (O2; %), and carbon dioxide (CO2; %) were measured at three time points (0, 25, and 50 min after entry of the first animal into the first chamber). To quantify the effect of animal and day variation on gaseous emissions, between-animal, between-day, and error variances were calculated for each gaseous measurement using a linear mixed model. The number of days required to gain a certain precision (defined as the 95% confidence interval range) for each gaseous measurement was also calculated. For all three gases, the between-day variance (39% to 40%) accounted for a larger proportion of total variance compared with between-animal variance, while the repeatability of 17 consecutive days of measurement was 0.36, 0.31, and 0.23 for CH4, CO2, and O2, respectively. Correlations between consecutive days of measurement were strong for all three gases; the strongest correlation between day 1 and the remaining days for CH4, CO2, and O2 was 0.71 (days 1 and 6), 0.77 (days 1 and 2), and 0.83 (days 1 and 5), respectively. A high level of precision was achieved when gaseous measurements from PAC were taken over three consecutive days. The prediction equation overestimated gaseous production for all three gases: the correlations between actual and predicted gaseous output ranged from 0.67 to 0.71, with the r2 ranging from 0.45 to 0.71. The results from this study will aid the refinement of the protocol for the measurement of gaseous emissions in sheep using the PAC.

Validation of a beef cattle maternal breeding objective based on a cross-sectional analysis of a large national cattle database.

Despite the importance of validating any technology prior to recommendation for use, few studies exist in the scientific literature which have demonstrated the superior performance of high-ranking animals in a given total merit index; this is especially true for maternal cattle selection indexes. The objective of the present study was to demonstrate the impact of the Irish total merit maternal-based index and provide the benefits of using the Irish total merit maternal-based beef index as part of a breeding policy. The validation exercise was undertaken using 269,407 records (which included the cow's own records and her progeny records) from 92,300 females differing in a total merit index for maternal value; a comparison was also made with the Irish terminal index. Association analyses were undertaken within the framework of linear and threshold mixed models; the traits analyzed were fertility (e.g., calving interval), slaughter (e.g., harvest weight), live weight (e.g., weaning weight), and producer-recorded traits (e.g., docility). All traits were analyzed with the maternal index and terminal index fitted as covariate(s) separately. Depending on the independent variable analyzed, the other fixed effects included: parity of cow, heterosis and recombination loss of cow and/or progeny, gender of progeny, and the estimated breeding value of the sire; contemporary group was included as a random effect. The results demonstrate the effectiveness of using total merit indexes to improve performance in a whole range of different traits, despite the often antagonistic genetic correlations among traits that underpin the index. Cows excelling on the maternal index had less calving difficulty, superior fertility performance, lighter carcasses, and live weight, as well as being more easily managed. Additionally, progeny of higher maternal index cows were lighter at birth and more docile albeit with a small impact on slaughter traits. In contrast, higher terminal index cows had more calving difficulty, compromised fertility and had heavier carcasses themselves as well as their progeny. While the differences in phenotypic performance between groups on maternal index was, in most instances, relatively small, the benefits are: (1) expected to be greater when more genetically extreme groups of animals are evaluated and (2) expected to accumulate over time given the cumulative and permanent properties of breeding schemes.

Carcass and efficiency metrics of beef cattle differ by whether the calf was born in a dairy or a beef herd.

Beef originates from the progeny of either dairy or beef dams. The objective of the present study was to identify contributing factors to the differences in the carcass merit of progeny from both dam types. This goal was achieved using slaughter records from 16,414 bucket-reared dairy animals (DXD), 5,407 bucket-reared dairy-beef animals (BXD), 42,102 suckle-reared animals from a beef × dairy F1 cross dam (BXF1), and 93,737 suckle-reared animals from a beef × beef cow (BXB). Linear mixed models were used to quantify the least squares means for carcass characteristics in the various progeny genotypes. Nuisance fixed effects adjusted for in the models were: animal heterosis and recombination loss, dam parity, age at slaughter, and contemporary group; age at slaughter was replaced as an independent variable with both carcass weight and carcass fat score where the dependent variable was age at slaughter. In a follow-up analysis, models were re-analyzed where the genetic merit of the sire was adjusted for; a further analysis set the genetic merit of the dam for the dependent variable to be identical for both the dairy and beef dams. The final analysis adjusted to a common sire and dam genetic merit facilitating the estimation of just differences in early-life rearing strategies. Irrespective of the genetic merit of the sire and dam, animals originating from beef herds had heavier and more conformed carcasses. BXB animals had a 67 kg heavier carcass, with a conformation score (scale 1 [poor] to 15 [excellent]) of 5 units greater compared with DXD animals. When the genetic merit of all dams was set to be equal, BXB animals were heavier and better conformed than BXD animals. When the genetic merit for both the sire and dam were set to be equal, carcasses of the BXB animals were 15 kg heavier, with a 0.69 unit superior conformation score compared with the DXD animals; this difference is due to early life experiences. In conclusion, the majority of the inferiority in carcass metrics of calves from dairy herds compared with beef herds is due to differences in the genetic merit of the parents. Nevertheless, even after adjusting the parents to the same genetic merit, progeny from dairy herds were still inferior to their contemporaries born in beef herds, due most likely to the persistence of early life experiences.

Genetic and nongenetic factors associated with the fate of maiden ewe lambs: slaughtered without ever lambing versus retained for breeding.

The decision on which ewe lamb to retain versus which to sell is likely to vary by producer based on personal preference. What is not known, however, is if any commonality exists among producers in the characteristics of ewe lambs that influence their eventual fate. The objective of the present study was to determine what genetic and nongenetic factors associate with the fate of maiden ewe lambs. The fate of each ewe lamb born in the present study was defined as either subsequently: 1) having lambed in the flock, or 2) was slaughtered without any recorded lambing event. A total of 9,705 ewe lamb records from 41 crossbred flocks were used. The logit of the odds of the ewe lamb being retained for lambing was modeled using logistic regression. Variance components were then estimated for the binary trait representing the fate of the ewe lamb using animal linear and threshold mixed models. The genetic correlations between fate of the ewe lamb and preweaning, weaning, or postweaning liveweight were also estimated. From the edited data set, 45% of ewe lambs born entered the mature flock as ewes. Ewe lambs reared as singles, with greater levels of heterosis but lower levels of recombination loss, born to dams that lambed for the first time as hoggets, with greater breed proportion of the Belclare, Suffolk, Texel, and Llyen breeds were more likely (P < 0.001) to eventually lamb in the flock than be slaughtered without ever lambing. Irrespective of the age of the animal when weighed, heavier ewe lambs were more likely to eventually lamb (P < 0.001). The genetic SD and direct heritability of fate of the ewe lamb estimated in the univariate linear model was 26.58 percentage units and 0.31 (SE = 0.03), respectively; the heritability was 0.30 when estimated using the threshold model. The corresponding direct heritability of fate of the ewe lamb estimated in the bivariate analyses with liveweight ranged from 0.29 (SE = 0.03; preweaning weight) to 0.35 (SE = 0.04; postweaning weight). The genetic correlations estimated between fate of the ewe lamb and the liveweight traits were weak to moderate but strengthened as the age of the ewe lamb at weighing increased. Results from this study provide an understanding of the factors producers consider when selecting females for retention versus slaughter which may form useful parameters in the development of a decision support tool to identify suitable ewe lambs for retention.

Phenotypic factors associated with lamb live weight and carcass composition measurements in an Irish multi-breed sheep population.

Understanding the phenotypic factors that affect lamb live weight and carcass composition is imperative to generating accurate genetic evaluations and further enables implementation of functional management strategies. This study investigated phenotypic factors affecting live weight across the growing season and traits associated with carcass composition in lambs from a multibreed sheep population. Four live weight traits and two carcass composition traits were considered for analysis namely; birth, preweaning, weaning, and postweaning weight, and ultrasound muscle depth and fat depth. A total of 427,927 records from 159,492 lambs collected from 775 flocks between the years 2016 and 2019, inclusive were available from the Irish national sheep database. Factors associated with live weight and carcass composition were determined using linear mixed models. The heaviest birth, preweaning, and weaning weights were associated with single born lambs (P < 0.001), however by postweaning, there was no difference observed in the weights of single and twin born lambs (P > 0.01). Breed class affected lamb live weight and carcass composition with terminal lambs weighing heaviest and having greater muscle depth than all other breed classes investigated (P < 0.001). Lambs born to first parity dams were consistently lighter, regardless of time of weighing (P < 0.001), while dams lambing for the first time as ewe lambs produced lighter lambs than those lambing for the first time as hoggets (P < 0.001). Greater heterosis coefficients (i.e., >90% and ≤100%) resulted in heavier lambs at weaning compared with lambs with lower levels of heterosis coefficients (P < 0.001). A heterosis coefficient class <10% resulted in lambs with greater muscle depth while recombination loss of <10% increased ultrasound fat depth (P < 0.001). Results from this study highlight the impact of multiple animal level factors on lamb live weight and carcass composition which will enable more accurate bio-economic models and genetic evaluations going forward.

Using the difference in actual and expected calf liveweight relative to its dam liveweight as a statistic for interherd and intraherd benchmarking and genetic evaluations1.

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.

Infrared thermography as a tool to detect hoof lesions in sheep.

Lameness has a major negative impact on sheep production. The objective of this study was to 1) quantify the repeatability of sheep hoof temperatures estimated using infrared thermography (IRT); 2) determine the relationship between ambient temperature, sheep hoof temperature, and sheep hoof health status; and 3) validate the use of IRT to detect infection in sheep hooves. Three experiments (a repeatability, exploratory, and validation experiment) were conducted over 10 distinct nonconsecutive days. In the repeatability experiment, 30 replicate thermal images were captured from each of the front and back hooves of nine ewes on a single day. In the exploratory experiment, hoof lesion scores, locomotion scores, and hoof thermal images were recorded every day from the same cohort of 18 healthy ewes in addition to a group of lame ewes, which ranged from one to nine ewes on each day. Hoof lesion and locomotion scores were blindly recorded by three independent operators. In the validation experiment, all of the same procedures from the exploratory experiment were applied to a new cohort of 40 ewes across 2 d. The maximum and average temperature of each hoof was extracted from the thermal images. Repeatability of IRT measurements was assessed by partitioning the variance because of ewe and error using mixed models. The relationship between ambient temperature, hoof temperature, and hoof health status was quantified using mixed models. The percentage of hooves correctly classified as healthy (i.e., specificity) and infected (i.e., sensitivity) was calculated for a range of temperature thresholds. Results showed that a small-to-moderate proportion of the IRT-estimated temperature variability in a given hoof was due to error (1.6% to 20.7%). A large temperature difference (8.5 °C) between healthy and infected hooves was also detected. The maximum temperature of infected hooves was unaffected by ambient temperature (P > 0.05), whereas the temperature of healthy hooves was associated with ambient temperature. The best sensitivity (92%) and specificity (91%) results in the exploratory experiment were observed when infected hooves were defined as having a maximum hoof temperature ≥9 °C above the average of the five coldest hooves in the flock on that day. When the same threshold was applied to the validation dataset, a sensitivity of 77% and specificity of 78% was achieved, indicating that IRT could have the potential to detect infection in sheep hooves.

Investigation of the relationship between udder quarter somatic cell count and udder skin surface temperature of dairy cows measured by infrared thermography.

The objective of the present study was to quantify the relationship between udder skin surface temperature (USST) and somatic cell count (SCC) in lactating dairy cows. Data were recorded on the same 14 Holstein-Friesian cows, at evening (15:00 to 16:00) milking every day over a 2-mo period. Surface temperature measurements of all udders were extracted from thermal images. After imaging, milk was extracted from each quarter and analyzed for SCC. Environmental and cow-related factors (i.e., ambient temperature, humidity, rainfall, wind speed, distance walked to the parlor, number of days since the udder was shaved, parity, and stage of lactation) were recorded on each day of the experiment. A large array of descriptive temperature parameters (DTP) were extracted from every udder image including temperature-based (e.g., maximum, average and minimum USST), pixel count-based, and textural-based DTPs. Several different analytical methods were tested in an attempt to relate any given DTP to SCC; this included investigating the relationship between USST and the log transform of SCC (i.e., somatic cell score; SCS). The temperature range within each udder was also compared with the natural log of the range in SCC of the respective quarters. In a separate analysis, the temperature difference between each DTP and its respective daily baseline (i.e., average of the 5 lowest values of that DTP across the herd) was compared with SCS. Finally, the association between environmental and cow-related factors with each DTP was investigated to create prediction models for each DTP, the residuals of which were compared with SCC. Results from the present study indicate that the correlation between any DTP and SCS was weak (range of -0.16 to 0.19) and so could not be used to identify quarters with high SCC. Although some alternative measures had a significant relationship with SCS, again, the correlation was too weak for practical use on its own. Maximum and average USST could be predicted with a root mean square error of 0.23 and 0.35 °C, respectively, although the residuals from the prediction model could not be used to identify animals with high SCC. This suggests that infrared thermography alone could not be used as a real-time automated tool to detect high SCC for dairy cows in a pasture-based system.

A novel measure of ewe efficiency for breeding and benchmarking purposes.

Ewe efficiency has traditionally been defined as the ratio of litter weight to ewe weight; given the statistical properties of ratio traits, an alternative strategy is proposed in the present study. The concept of using the deviation in performance of an animal from the population norm has grown in popularity as a measure of animal-level efficiency. The objective of the present study was to define novel measures of efficiency for sheep, which considers the combined weight of a litter of lambs relative to the weight of their dam, and vice versa. Two novel traits, representing the deviation in total litter weight at 40 d (DEV40L) or weaning (DEVweanL), were calculated as the residuals of a statistical model, with litter weight as the dependent variable and with the fixed effects of litter rearing size, contemporary group, and ewe weight. The deviation in ewe weight at 40-d postlambing (DEV40E) or weaning (DEVweanE) was derived using a similar approach but with ewe weight and litter weight interchanged as the dependent variable. Variance components for each trait were estimated by first deriving the litter or ewe weight deviation phenotype and subsequently estimating the variance components. The phenotypic SD in DEV40L and DEVweanL was 8.46 and 15.37 kg, respectively; the mean litter weight at 40 d and weaning was 30.97 and 47.68 kg, respectively. The genetic SD and heritability for DEV40L was 2.65 kg and 0.12, respectively. For DEVweanL, the genetic SD and heritability was 4.94 kg and 0.13, respectively. The average ewe weight at 40-d postlambing and at weaning was 66.43 and 66.87 kg, respectively. The genetic SD and heritability for DEV40E was 4.33 kg and 0.24, respectively. The heritability estimated for DEVweanE was 0.31. The traits derived in the present study may be useful not only for phenotypic benchmarking of ewes within flock on performance but also for benchmarking flocks against each other; furthermore, the extent of genetic variability in all traits, coupled with the fact that the data required to generate these novel phenotypes are usually readily available, signals huge potential within sheep breeding programs.