Post-slaughter alimentary tract measures were collected from eight-month-old ram lambs during routine culling of sheep divergently selected for methane yield. Measures from 142 and 132 lambs from the high and low methane lines respectively were collected over five years. Low CH4 animals had lighter reticulo-rumen full, empty and contents weights (P<0.05), but tended to have longer rumen papillae (P=0.06). Preliminary heritability estimates for reticulo-rumen components and papillae traits were significantly different from zero, ranging from 0.09 to 0.25. Results validate earlier findings that differences in the anatomical characteristics of the alimentary tract are associated with methane emissions and suggest that there is a significant host genetic component, warranting further investigation.

Global agreements in place to reduce methane emissions in livestock are a potential threat to food security. Successful but independent breeding strategies for improved production and lower methane are in place. The unanswered questions are whether these strategies can be combined and how they impact one another, physically and economically. The New Zealand economy is largely dependent on pastoral agriculture from grazing ruminants. The sheep industry produces ∼20 million lamb carcasses for export each year primarily from grass. Methane emitted from the fermentation of forage by grazing ruminants accounts for one-third of all New Zealand’s greenhouse gas emissions. Here, we use sheep selection lines bred for divergent methane production and large numbers of their relatives to determine the genetic and phenotypic correlations between enteric methane emissions, carcass yield, and meat quality. The primary objectives were to determine whether previously shown physiological differences between methane selection lines (differing by ∼12% in methane) result in a negative impact on meat production and quality by measuring close relatives. The results show no negative effects of breeding for lowered methane on meat and carcass quality. Gross methane emissions were highly correlated with liveweight and measures of carcass weight and negatively correlated with dressing-out percentage and fat yield (GR). Trends were similar but not significant for methane yield (g CH4/kg DMI). Preliminary evidence, to date, shows that breeding for low methane may result in animals with higher lean yields that are economically favorable even before carbon costs and environmental benefits are taken into account. These benefits were seen in animals measured for methane on fixed intakes and require validation on intakes that are allowed to vary.

Residual energy (or feed) intake (REI) is one measure of feed efficiency, and is an estimate of whether an animal is consuming more or less energy for its biological outcomes than predicted. To date, little research has been conducted in sheep, and a multi-year trial is underway to generate data for New Zealand maternal breeds, firstly targeting growing lambs. Data required to estimate REI includes daily feed intake and live weight information from which growth rate can be calculated. A key to data collection for the trait of REI is to determine the test length required to accurately estimate REI. A dataset was available on approximately 600 growing maternal breed lambs from 3 cohorts that were measured for daily feed intake of lucerne pellets for a period of 42 days (after 14 days adjustment), with live weight measured twice weekly during the test period. The full dataset was subsetted to simulate reduced test lengths and environmental variance was calculated for each cohort-data subset. Additionally the correlation between the REI estimates from the reduced length datasets and the full dataset was also estimated. The results suggested that the variance of all traits stabilised within 21 to 28 days, and a correlation of greater than 0.90 existed between the estimates made on the data collected in 21 days versus the complete 42 day dataset. These results suggest that the environmental variances stabilises quicker in lamb studies than in beef studies which require a minimum of 56 to 70 days’ worth of data.

Selection lines of sheep with low and high CH yield (g/kg DMI; CH/DMI) are being developed on the basis of feeding pelleted alfalfa hay at 2.0 times maintenance ME requirements in respiration chambers, but their divergence under predominant grazing conditions, as in New Zealand, is not known. The objectives of this study were to determine CH emissions and rumen fermentation characteristics in sheep from low and high CH/DMI selection lines while grazing pasture. Two grazing experiments were conducted with 42 selection line ewes in March 2013 (Exp. 1) and 98 selection line progeny ewe hoggets in October/November 2014 (Exp. 2), with CH emissions estimated by the SF tracer technique and DMI estimated by titanium oxide in combination with natural long-chain -alkanes. Total daily CH production (g/d) was similar between high and low CH/DMI selection line sheep in Exp. 1 and lower for low CH/DMI progeny compared with high CH/DMI progeny in Exp. 2 ( < 0.05). The CH/DMI tended to be 20% lower for low CH/DMI line sheep compared with high CH/DMI selection line sheep in Exp. 1 ( < 0.10) and was 15% lower for the low CH/DMI line in Exp. 2 ( < 0.01). Total VFA concentration and concentrations (m) of acetate, butyrate, and isobutyrate plus isovalerate were lower ( < 0.05) for low CH/DMI line sheep compared with high CH/DMI selection line sheep in both experiments. The current study indicates that differences in CH/DMI and VFA concentrations in selection line sheep, previously established on alfalfa pellets, are also present to a similar magnitude when grazing pasture.

AIMS: To explore and validate the utility of rumen endoscopy for collection of rumen papillae for gene expression measurement. METHODS: Four adult Coopworth ewes were fasted for either 4 or 24 hours. Animals were sedated, placed in a dorsally recumbent position at 45 degrees with the head upright, and an endoscope inserted via a tube inserted into the mouth. Biopsies of rumen papillae were taken from the ventral surface of the rumen atrium under visual guidance. Two biopsies were collected from one of the animals that had been fasted for 4 hours, and three from one of the animals that had been fasted for 24 hours. Video of the rumen atrium and reticulum was also collected. The animals recovered uneventfully. Biopsies were subsequently used for extraction and sequencing of mRNA. RESULTS: The ventral surface of the rumen atrium was accessible after 4 hours off pasture, but a larger region was accessible after 24 hours of fasting. Sedation allowed access for endoscope use for around 5 to 10 minutes after which increased saliva flow was noted. Rumen papillae biopsies were easily collected, with samples from a variety of sites collected in the ∼10 minute time window. High quality RNA was obtained for stranded mRNA sequencing. Of the resulting reads, 69–70% mapped uniquely to version 3.1 of the ovine genome, and 48–49% to a known gene. The rumen mRNA profiles were consistent with a previously reported study. CONCLUSIONS: This method for obtaining rumenal tissue was found to be rapid and resulted in no apparent short or long term effects on the animal. High quality RNA was successfully extracted and amplified from the rumen papillae biopsies, indicating that this technique could be used for future gene expression studies. The use of rumen endoscopy could be extended to collection of a variety of rumen and reticulum anatomical measurements and deposition and retrieval of small sensors from the rumen. Rumen endoscopy offers an attractive and cost effective approach to repeated rumen biopsies compared with serial slaughter or use of cannulated animals.

Globally, ruminants are the most important source of emission of methane (CH4). Animal-to-animal variation in CH4 emission has genetic basis (Pinares-Patino et al., 2011), hence offering a potential mitigation avenue through animal breeding. However, for this approach to progress to practical application a rapid and reliable method of ranking animals for their CH4 emissions is required. Microbial fermentation of feed in the rumen produces volatile fatty acids (VFA), hydrogen (H2), carbon dioxide (CO2), ammonia and heat. A last step in the process is the reduction of CO2 to CH4 by Archaea using H2 as a source of energy. Formation of both acetic and butyric acids is accompanied by the production of H2 and CO2, whereas propionic production involves a net uptake of H2, hence VFA profiles may be used to predict CH4 emission rates (Benchaar et al., 2001). This controlled study conducted with sheep explored the relationship between rumen VFA and CH4 emission.

An analysis was undertaken to investigate how lamb autumn live weight breeding values could be calculated from fixed carcass weight progeny tests (e.g. lambs slaughtered at monthly intervals at a threshold carcass weight). Analysis of growth rate is problematic for this progeny test design as the slaughter groups may experience vastly different environmental conditions, both within and between years. Variance components were estimated from an animal model using restricted maximum likelihood (REML) on data from 11,411 Coopworth progeny records and 126 Coopworth sires. The dataset contained records of weaning weight and live weight at four, five and six months of age (LW4, LW5 and LW6, respectively) collected from 1995 to 2004 in a flock run at Woodlands Research Station. The multivariate mixed linear model included lamb birth day deviation as a covariate, sex of lamb, birth rearing rank, age of dam and live weight contemporary group as fixed effects, and sire as a random effect. The WWT model also had dam fitted as a random effect to give WWT direct and maternal effects (WWTd and WWTm). The analysis was then repeated, but with animals records removed from the dataset once they achieved a threshold weight of 31 and 27kg for ram and ewe lambs, respectively, on data prior to or following linear scaling by contemporary group mean. The heritabilities estimated from the full dataset for WWTd, WWTm, LW4, LW5 and LW6 were 0.30±0.03, 0.04±0.01, 0.49±0.02, 0.49±0.02 and 0.51±0.02, respectively. These traits were highly correlated with both phenotypic and genetic correlations between the direct traits ranging from 84 to 99%. The same analysis on the two culled datasets resulted in only minor changes the variance components. The correlation between sire breeding values for autumn live weight (LW6) estimated from the full and the two culled datasets were 98.8% for both models. Autumn live weight breeding values can be accurately estimated from datasets which include progressive culling if a multivariate live weight analysis is undertaken, and data from all animals measured at each date are used.

Livestock breeding programmes have created resistant (R) and susceptible (S) sheep that differ in their ability to control parasites through their immune function but potentially also their grazing behaviour (i.e. parasite avoidance). Using the Perendale genetic lines, we tested the hypothesis that R-sheep avoid parasites more effectively, reducing their parasite exposure/challenge, compared with S-sheep. However, in grazing systems, parasite-rich areas are also forage rich, suggesting that parasite avoidance behaviours are associated with nutritional penalties. We first created a naturally heterogeneous sward structure of gaps and tussocks and then used focal behavioural observations to quantify the sward selection of R- and S-sheep. Tussock swards were more nitrogen rich (41%), offered increased forage intake rates (32%) and contained 17 times more parasite larvae than gap swards. All the animals avoided grazing the tussock swards. However, the R-sheep grazed the tussock swards to a lesser degree than the S-sheep. We conclude that selection for genetic resistance has resulted in animals that, despite being well armed to fight parasitism through improved immune function, adopt parasite avoidance strategies with associated nutritional disadvantages. This experiment highlights the role of host behaviour in the control of parasitism and suggests that animals can be bred to avoid disease.

The East Friesian (EF) breed was imported into New Zealand and released to the industry in 1996. Few reports exist on the performance of EF crosses in New Zealand. This paper reports on results from EF sires mated to Coopworth ewes in the APEX Coopworth sire referencing scheme. A total of 30 EF sires were used in nine flocks of the 17 APEX member flocks to produce 3,478 EF x Coopworth progeny in the 1996 and 1997 birth years. These animals were compared with about 26,000 of their pure Coopworth contemporaries. Estimated breeding values (EBV’s) from a multitrait animal model BLUP were used to compare weaning weight, live weight at eight months, fleece weight at 12 months, and four measures of host resistance to internal parasites. The EF sires had significantly higher EBV’s for weaning weight (+1.94 kg; P O.O5). There was significant overlap in the range of EBV’s between the two sire breeds for all traits examined suggesting that selection decisions should be based on individual sire benefits rather than breed of origin.

The identification of a quantitative trait locus (QTL) affecting host resistance to internal parasites in sheep would aid selection for this trait. The MHC locus, located on chromosome 20 of sheep is a candidate region for such a QTL and has been associated with faecal egg count (FEC) in both Scottish Blackface and Soay sheep. Five Fl sires were produced by crossing divergent Romney lines selected for FEC. Nine hundred progeny from these sires were measured for host resistance and the extremes genotyped at 4 polymorphic loci on this chromosome. The four loci were evenly spread over the chromosome and included a marker within the MIX. Analysis provided little evidence for host resistance QTL on this chromosome. This suggests that QTL in the MHC locus are unlikely to have contributed significantly to the observed divergence in the parental lines.

Half-sib heritability estimates were derived from ewe lamb progeny of the Woodlands Romney selection project. Ultrasonic subcutaneous fat depths (C) were. measured with a Delphi probe at 5,6,8 and 14 months of age. Heritability estimates at each age were 0.3 1 (SE!&.12), 0.45 (0.1 l), 0.29 (0.06) and 0.28 (0.09) respectively. A Toshiba Sonolayer SAL-22A B-mode ultrasonic scanner was used to measure muscle width (A), depth (B) and GR tissue depth at 14months of age and resultant heritability estimates were 0.07 (0.05), 0.26 (0.09) and 0.39 (0.1 1), respectively. Genetic correlations among ultrasonic fat depths at different ages ranged from 0.81-0.95 (SE 0.06-0.12) with higher values for those of closer temporal separation. Phenotypic correlations were consistently about 0.3 below the corresponding genetic correlations. Ultrasonic GR had a high heritability estimate and a high genetic correlation with fat depth at 14months of 0.84 (0.08), but its genetic correlations with fat depths at earlier ages, were lower ranging from 0.55 to 0.72. The genetic correlation of hogget fleece weight with fat depth at 8 months of age was 0.09 (0.15), and thegenetic correlation between 8 month liveweight and fat depth was 0.38 (0.13); similarrelationships were found for fat depths measured at other ages. The heritability estimate for muscle depth B was moderate and close to that reported for carcass measurements. In contrast, the estimate for muscle width A was lower than reports from carcass measurements prehaps reflecting limitations in the ultrasonic technology used. The results indicate that ultrasonic measurements are useful selection criteria in breeding programmes to alter carcass traits.