Comparison of greenhouse gas emissions from sheep measured using both respiration and portable accumulation chambers.

Methane (CH4) is a potent gas produced by ruminants, and new measurement techniques are required to generate large datasets suitable for genetic analysis. One such technique are portable accumulation chambers (PAC), a short-term sampling method. The objectives of the current study were to explore the relationship between CH4 and carbon dioxide (CO2) output measured using both PAC and respiration chambers (RC) in growing lambs, and separately investigate the relationship among CH4, CO2 and measured ad libitum DM intake (DMI). Methane, CO2 and DMI were measured on 30 Suffolk and 30 Texel ewe lambs (age 253 ± 12 days) using the RC and PAC sequentially. The experiment was conducted over a 14-day period, with DMI measured from days 1 to 14; measurements in RC were conducted from days 10 to 12, while measurements in PAC were taken twice, the day immediately prior to the lambs entering the RC (day 9; PAC Pre-RC) and on the day lambs exited the RC (day 13; PAC Post-RC). Greater CH4 and CO2 output was measured in the RC than in the PAC (P < 0.01); similarly mean CH4 yield was greater when measured in the RC (15.39 ± 0.452 g CH4/kg DMI) compared to PAC (8.01 ± 0.767 g CH4/kg DMI). A moderate correlation of 0.37 was found between CH4 output measured in PAC Pre-RC and the RC, the corresponding regression coefficient of CH4 output measured in the RC regressed on CH4 output measured in PAC Pre-RC was close to unity (0.74; SE 0.224). The variance of CH4 and CO2 output within the measurement technique did not differ from each other (P > 0.05). Moderate to strong correlations were found between CH4 and CO2 per kg of live weight and CH4 and CO2 yield. Results from this study highlight the suitability of PAC as a ranking tool to rank animals based on their gaseous output when compared to the RC. However, repeated measurements separated by several days may be beneficial if precise rankings are required. Given the close to unity regression coefficient of CH4 output measured in the RC regressed on CH4 output measured in PAC Pre-RC suggests that PAC could also be potentially used to estimate absolute CH4 output; however, further research is required to substantiate this claim. When DMI is unknown, CH4 and CO2 per kg of live weight are a suitable alternative to the measurement of CH4 and CO2 yield.

Potential of in-plant intramuscular fat predictions to enable sheep breeders to incorporate consumer preferences in breeding programmes.

The inclusion of eating quality traits in sheep genetic improvement programmes is desirable. Intramuscular fat (IMF) plays a key role in ensuring consumer satisfaction when eating lamb, but genetic progress for IMF is constrained by a lack of routine data collection. This study investigated the potential for IMF predictor traits to substitute for measured IMF in genetic improvement programmes. Carcass and predicted IMF (near-infrared estimated IMF and marbling score) data were available on 10,113 New Zealand lambs, 1678 of which also had measured chemical IMF on a slice of M. longissimus lumborum on which the predictions of IMF had been made. Genetic antagonisms were observed between carcass lean traits and IMF. The genetic correlation between the predictors and measured IMF approached one, indicating that predictors of IMF can be used in genetic improvement programmes. Through using selection indexes, simultaneous increases in IMF and the existing terminal selection index are possible, provided all traits are measured. This study highlights the importance and potential of predicted IMF to achieve genetic improvement in traits of importance to consumers.

Can we have our steak and eat it: The impact of breeding for lowered environmental impact on yield and meat quality in sheep.

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.

Using genotyping-by-sequencing to predict gender in animals.

Gender assignment errors are common in some animal species and lead to inaccuracies in downstream analyses. Procedures for detecting gender misassignment are available for array-based SNP data but are still being developed for genotyping-by-sequencing (GBS) data. In this study, we describe a method for using GBS data to predict gender using X and Y chromosomal SNPs. From a set of 1286 X chromosomal and 23 Y chromosomal deer (Cervus sp.) SNPs discovered from GBS sequence reads, a prediction model was built using a training dataset of 422 Red deer and validated using a test dataset of 868 Red deer and Wapiti deer. Prediction was based on the proportion of heterozygous genotypes on the X chromosome and the proportion of non-missing genotypes on the Y chromosome observed in each individual. The concordance between recorded gender and predicted gender was 98.6% in the training dataset and 99.3% in the test dataset. The model identified five individuals across both datasets with incorrect recorded gender and was unable to predict gender for another five individuals. Overall, our method predicted gender with a high degree of accuracy and could be used for quality control in gender assignment datasets or for assigning gender when unrecorded, provided a suitable reference genome is available.

Development of an in situ procedure to evaluate the reticulo-rumen morphology of sheep selected for divergent methane emissions.

Published studies have shown that methane yield (g CH4/kg dry matter) from sheep is positively correlated with the size (volume and surface area) of the reticulo-rumen (RR) and the weight of its contents. However, the relationship between CH4 yield and RR shape has not been investigated. In this work, shape analysis has been performed on a data set of computerised tomography (CT) scans of the RR from sheep having high and low CH4 yields (n=20 and n=17, respectively). The three-dimensional geometries of the RRs were reconstructed from segmented scan data and split into three anatomical regions. An iterative fitting technique combining radial basis functions and principal component (PC) fitting was used to create a set of consistent landmarks which were then used as variables in a PC analysis to identify shape variation within the data. Significant size differences were detected for regions corresponding to the dorsal and ventral compartments between sheep with high and low CH4 yields. When the analysis was repeated after scaling the geometries to remove the effect of size, there was no significant shape variation correlating with CH4 yield. The results have demonstrated the feasibility of CT-based computational shape determination for studying the morphological characteristics of the RR and indicate that size, but not shape correlates with CH4 yield in sheep.

Heritability of ram mating success in multi-sire breeding situations.

Multi-sire mating of a mob of ewes is commonly used in commercial sheep production systems. However, ram mating success (defined as the number of lambs sired by an individual) can vary between rams in the mating group. If this trait was repeatable and heritable, selection of rams capable of siring larger numbers of lambs could reduce the number of rams required for mating and ultimately lead to increased genetic gain. However, genetic correlations with other productive traits, such as growth and female fertility, could influence the potential for ram mating success to be used as a selection trait. In order to investigate this trait, parentage records (including accuracy of sire assignment) from 15 commercial ram breeding flocks of various breeds were utilised to examine the repeatability and heritability of ram mating success in multi-sire mating groups. In addition, genetic and phenotypic correlations with growth and female fertility traits were estimated using ASReml. The final model used for the ram mating success traits included age of the ram and mating group as fixed effects. Older rams (3+years old) had 15% to 20% greater mating success than younger rams (1 or 2 years of age). Increasing the stringency of the criteria for inclusion of both an individual lamb, based on accuracy of sire assignment, or a whole mating group, based on how many lambs had an assigned sire, increased repeatability and heritability estimates of the ram mating success traits examined. With the most stringent criteria employed, where assignment of sire accuracy was >0.95 and the total number of lambs in the progeny group that failed to have a sire assigned was<0.05, repeatability and heritability for loge(number of lambs) was 0.40±0.09 and 0.26±0.12, respectively. For proportion of lambs sired, repeatability and heritability were both 0.30±0.09. The two ram mating traits (loge(nlamb) and proportion) were highly correlated, both phenotypically and genetically (0.88±0.01 and 0.94±0.06, respectively). Both phenotypic and genetic correlations between ram mating success and growth and other female fertility traits were low and non-significant. In conclusion, there is scope to select rams capable of producing high numbers of progeny and thus increase selection pressure on rams to increase genetic gain.

Ovine keratome: identification, localisation and genomic organisation of keratin and keratin-associated proteins.

Wool is composed primarily of proteins belonging to the keratin family. These include the keratins and keratin-associated proteins (KAPs) that are responsible for the structural and mechanical properties of wool fibre. Although all human keratin and KAP genes have been annotated, many of their ovine counterparts remain unknown and even less is known about their genomic organisation. The aim of this study was to use a combinatory approach including comprehensive cDNA and de novo genomic sequencing to identify ovine keratin and KAP genes and their genomic organisation and to validate the keratins and KAPs involved in wool production using ovine expressed sequence tag (EST) libraries and proteomics. The number of genes and their genomic organisation are generally conserved between sheep, cattle and human, despite some unique features in the sheep. Validation by protein mass spectrometry identified multiple keratins (types I and II), epithelial keratins and KAPs. However, 15 EST-derived genes, including one type II keratin and 14 KAPs, were identified in the sheep genome that were not present in the NCBI gene set, providing a significant increase in the number of keratin genes mapped on the sheep genome.

An ovine hepatorenal fibrocystic model of a Meckel-like syndrome associated with dysmorphic primary cilia and TMEM67 mutations.

Meckel syndrome (MKS) is an inherited autosomal recessive hepatorenal fibrocystic syndrome, caused by mutations in TMEM67, characterized by occipital encephalocoele, renal cysts, hepatic fibrosis, and polydactyly. Here we describe an ovine model of MKS, with kidney and liver abnormalities, without polydactyly or occipital encephalocoele. Homozygous missense p.(Ile681Asn; Ile687Ser) mutations identified in ovine TMEM67 were pathogenic in zebrafish phenotype rescue assays. Meckelin protein was expressed in affected and unaffected kidney epithelial cells by immunoblotting, and in primary cilia of lamb kidney cyst epithelial cells by immunofluorescence. In contrast to primary cilia of relatively consistent length and morphology in unaffected kidney cells, those of affected cyst-lining cells displayed a range of short and extremely long cilia, as well as abnormal morphologies, such as bulbous regions along the axoneme. Putative cilia fragments were also consistently located within the cyst luminal contents. The abnormal ciliary phenotype was further confirmed in cultured interstitial fibroblasts from affected kidneys. These primary cilia dysmorphologies and length control defects were significantly greater in affected cells compared to unaffected controls. In conclusion, we describe abnormalities involving primary cilia length and morphology in the first reported example of a large animal model of MKS, in which we have identified TMEM67 mutations.

Characterization of an X-chromosomal non-mosaic monosomy (59, X0) dairy heifer detected using routinely available single nucleotide polymorphism genotype data.

Evidence exists from a range of species on the impact of karyotype abnormalities on reproductive performance. Despite this, cytogenetic analyses of cattle, especially females, are not routinely undertaken. Genome-wide single nucleotide polymorphism (SNP) genotype data are now, however, routinely being generated in many species globally at a relatively low cost. The objective of the present study was to evaluate the potential of routinely available SNP genotype data to identify sex-chromosome aberrations using X chromosome monosomy 59,X0 as a case study for illustration. A single 2.5-yr old Holstein-Friesian heifer was detected with a mean allelic intensity of SNP on the X chromosome almost 17 standard deviations less than the mean of other genotyped females ( = 103,326). Following cytogenetic analysis (10 replicates by karyotyping and a further 140 by FISH), the female was deduced to be a non-mosaic 59,X0. The female had never produced a calf and, although gross examination revealed no physical abnormalities, she was smaller in size than expected based on her breed and age. Given the age of the animal at slaughter, the uterus and uterine tubes appeared immature and inactive. The oviduct appeared normal while the single ovary present contained a markedly reduced number of follicles. There was, however, some evidence of prior ovulation and formation of corpora lutea. The approach proposed in the present study to identify allosome aneuploidy from routinely available genotype data can be used to screen for such abnormalities at no additional cost to the breeder or producer.

Ovine rumen papillae biopsy via oral endoscopy; a rapid and repeatable method for serial sampling.

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.

Anaesthesia-associated hypersensitivity reactions: seven years' data from a British bi-specialty clinic.

Our bi-specialty clinic was established to systematically investigate patients with suspected peri-operative hypersensitivity reactions. Four hundred and ten patients were studied; 316 following an intra-operative reaction ('postoperative' group) and 94 with a previous history of reaction, referred before undergoing anaesthesia ('pre-operative' group). In the postoperative group, 173 (54.7%) were diagnosed with IgE-mediated reactions: 65 (37.6%) to neuromuscular blocking drugs; 54 (31.2%) antibiotics; 15 (8.7%) chlorhexidine and 12 (6.9%) patent blue dye. Reactions were severe in 114 patients (65.9%). All reactions to patent blue dye were severe. We identified IgE sensitisation in 22 (13.2%) cases with isolated mucocutaneous reactions. Only 173 (54.7%) patients had serum tryptase samples taken. Referrers' suspected causal agent was confirmed in only 37.2% of patients. Of 94 patients reviewed 'pre-operatively', 29 (30.8%) were diagnosed with IgE-mediated hypersensitivity reactions, reinforcing the importance of investigating this group of patients. Knowledge of the range of causative agents identified in our study should guide the investigation of suspected peri-operative hypersensitivity reactions.

Genetic analysis and genomic selection of stayability and productive life in New Zealand ewes.

Genetic parameters for ewes were estimated for stayability (STAY) and productive life (Prodlife). Records from 658,871 animals from 241 seed stock or ram breeder flocks and one research flock were used to estimate parameters for ram breeder flock STAY and Prodlife. These flocks would have a culling policy based on criteria typical of a commercial enterprise, but including culls based on knowledge such as estimated breeding values. A subset of 35,688 of these animals from 4 ram breeder and one research flock was used to infer the animals that might be culled based on the perspective of a commercial flock as these flocks recorded reasons for culling. These data were used to estimate parameters for commercial flock STAY and Prodlife. Heritability for ram breeder flock STAY until age 3 to 6 yr ranged from 0.07 to 0.09. The heritability of commercial flock STAY was similar in yr 5 and 6, but lower at 0.05 (age 3) and 0.07 (age 4). Heritability of Prodlife for ram breeder flock and commercial flock was respectively 0.10 and 0.13. The genetic correlations between ram breeder flock STAY and commercial flock STAY ranged from 0.20 to 0.99. Both STAY and Prodlife were most correlated genetically with the trait number of lambs born, at about 0.4, and to a lesser degree, live weight up to the age of 12 mo for the traits analyzed with lower genetic correlations estimated for the commercial flocks. Live weight at 18 mo and fleece weight had little or no correlation with STAY and Prodlife. From the data set used to estimate genetic parameters from a ram breeder flock, 4,330 animals were genotyped with the Illumina OvineSNP50 BeadChip and the genotypes used to develop genomic predictions via genomic best linear unbiased prediction. The animals used in the training data set were multibreed, but were heavily Romney breed based. The genomic prediction accuracy for ram breeder flock STAY, according to breed, was dependent on sample size and ranged from 0.4 to 0.44 for Romney and 0.26 to 0.4 for Coopworth. Accuracies for Perendale and Composites, for which sample sizes were less, were more variable. This study has derived genetic parameters for STAY and Prodlife and investigated genomic predictions for these traits. As these traits are of low heritability, sex limited and expressed late in life genomic selection will be useful.

Animal board invited review: genetic possibilities to reduce enteric methane emissions from ruminants.

Measuring and mitigating methane (CH4) emissions from livestock is of increasing importance for the environment and for policy making. Potentially, the most sustainable way of reducing enteric CH4 emission from ruminants is through the estimation of genomic breeding values to facilitate genetic selection. There is potential for adopting genetic selection and in the future genomic selection, for reduced CH4 emissions from ruminants. From this review it has been observed that both CH4 emissions and production (g/day) are a heritable and repeatable trait. CH4 emissions are strongly related to feed intake both in the short term (minutes to several hours) and over the medium term (days). When measured over the medium term, CH4 yield (MY, g CH4/kg dry matter intake) is a heritable and repeatable trait albeit with less genetic variation than for CH4 emissions. CH4 emissions of individual animals are moderately repeatable across diets, and across feeding levels, when measured in respiration chambers. Repeatability is lower when short term measurements are used, possibly due to variation in time and amount of feed ingested prior to the measurement. However, while repeated measurements add value; it is preferable the measures be separated by at least 3 to 14 days. This temporal separation of measurements needs to be investigated further. Given the above issue can be resolved, short term (over minutes to hours) measurements of CH4 emissions show promise, especially on systems where animals are fed ad libitum and frequency of meals is high. However, we believe that for short-term measurements to be useful for genetic evaluation, a number (between 3 and 20) of measurements will be required over an extended period of time (weeks to months). There are opportunities for using short-term measurements in standardised feeding situations such as breath 'sniffers' attached to milking parlours or total mixed ration feeding bins, to measure CH4. Genomic selection has the potential to reduce both CH4 emissions and MY, but measurements on thousands of individuals will be required. This includes the need for combined resources across countries in an international effort, emphasising the need to acknowledge the impact of animal and production systems on measurement of the CH4 trait during design of experiments.

Genome-wide DNA methylation analysis: no evidence for stable hemimethylation in the sheep muscle genome.

The importance of maintaining DNA methylation patterns and faithful transmission of these patterns during cell division to ensure appropriate gene expression has been known for many decades now. It has largely been assumed that the symmetrical nature of CpG motifs, the most common site for DNA methylation in mammals, together with the presence of maintenance methylases able to methylate newly synthesised DNA, ensures that there is concordance of methylation on both strands. However, although this assumption is compelling in theory, little experimental evidence exists that either supports or refutes this assumption. Here, we have undertaken a genome-wide single-nucleotide resolution analysis to determine the frequency with which hemimethylated CpG sites exist in sheep muscle tissue. Analysis of multiple independent samples provides strong evidence that stably maintained hemimethylation is a very rare occurrence, at least in this tissue. Given the rarity of stably maintained hemimethylation, next-generation sequencing data from both DNA strands may be carefully combined to increase the accuracy with which DNA methylation can be measured at single-nucleotide resolution.

Estimates of genetic parameters for breech strike and potential indirect indicators in sheep.

AIM: To determine flystrike incidence, and estimate genetic parameters and potential indicator traits to reduce breech strike susceptibility in Romney sheep in New Zealand. METHODS: Seventeen Romney-based flocks, on 11 farms from throughout New Zealand, were enrolled in a case-control study in 2009/10 and 2010/11. Farmers observed lambs with flystrike and recorded dag score, breech bareness score and flystrike location for each lamb. Flystrike location was classed as breech, body, belly, shoulders, head or feet. Paternity of lambs was determined from tissue samples collected from lambs and all potential sires on farms. Control lambs without flystrike were selected by matching birth year, flock and sex. Due to the majority of strike occurring in the breech, genetic parameters for breech strike were explored. Dag score and breech bareness were investigated as indirect indicators of breech strike. Heritabilities and genetic and phenotypic correlations were estimated for breech strike, dag score and breech bareness using an animal model. RESULTS: For the 2009/10 season, 484 cases of flystrike were recorded with mean incidence rate per farm of 1.76 (min 0.47, max 2.95)%. For the 2010/11 season, 352 cases were recorded with a mean incidence rate per farm of 2.54 (min 0.43, max 8.18)%. Over both years 694/792 (88%) cases of flystrike occurred on the breech. Heritability on the observed scale for breech strike was 0.32 (SE 0.10). Heritabilities for dag score and breech bareness were 0.23 (SE 0.09) and 0.35 (SE 0.11), respectively. Breech strike had a high positive genetic correlation with dag score (0.71) and a low negative genetic correlation with breech bareness (-0.17). Breech strike had a high phenotypic correlation with dag score (0.62) and negative phenotypic correlation with breech bareness (-0.06). CONCLUSIONS: The high genetic and phenotypic correlations between breech strike and dag score makes dag score a viable option for indirect selection for breech strike resistance in Romney sheep in New Zealand. The heritability, genetic and phenotypic correlations require validation in other dual-purpose breeds, before breeding values for breech strike can be implemented, for use throughout the New Zealand sheep industry.

Genetic parameters for predicted methane production and laser methane detector measurements.

Enteric ruminant methane is the most important greenhouse gas emitted from the pastoral agricultural systems. Genetic improvement of livestock provides a cumulative and permanent impact on performance, and using high-density SNP panels can increase the speed of improvement for most traits. In this study, a data set of 1,726 dairy cows, collected since 1990, was used to calculate a predicted methane emission (PME) trait from feed and energy intake and requirements based on milk yield, live weight, feed intake, and condition score data. Repeated measurements from laser methane detector (LMD) data were also available from 57 cows. The estimated heritabilities for PME, milk yield, DMI, live weight, condition score, and LMD data were 0.13, 0.25, 0.11, 0.92, 0.38, and 0.05, respectively. There was a high genetic correlation between DMI and PME. No SNP reached the Bonferroni significance threshold for the PME traits. One SNP was within the 3 best SNP for PME at wk 10, 20, 30, and 40. Genomic prediction accuracies between dependent variable and molecular breeding value ranged between 0.26 and 0.30. These results are encouraging; however, more work is required before a PME trait can be implemented in a breeding program.

Genomic prediction of breeding values in the New Zealand sheep industry using a 50K SNP chip.

The aim of genomic prediction is to predict breeding value from genomic data. We describe the development of genomic prediction equations and accuracies for molecular breeding values (MBV) for industry use, focusing on the methodology used to deal with predictions for the New Zealand sheep population structure. This is made up of a mixture of pure and crossbred animals, but principally Romney based. In particular, we used pedigree-based EBV for 8 traits (weaning weight as a direct effect, weaning weight as a maternal effect, live weight at 8 mo, live weight at 12 mo, greasy fleece weight at 12 mo, lamb fleece weight, adult fleece weight, and number of lambs born) and Illumina OvineSNP50 BeadChip genotypes from 13,420 animals to investigate BLUP with different genomic relationship matrices (GRM) based on SNP markers and to investigate varying sets of older animals (training sets) to predict the MBV of younger animals (validation sets). The GRM tested included modifications to account for allele frequency differences between breeds, rescaling so that the mean GRM is equal to the mean of the traditional pedigree numerator relationship matrix A: , and combining of the GRM with A: using a convex combination with a weight estimated by maximizing a conditional restricted likelihood. We found that these modifications were beneficial and recommend using a breed-adjusted GRM combined with A: . Training data sets with Romney, Coopworth, and Perendale animals all together usually predicted better than using just a pure breed training data set for all traits. But predictions for the breed Perendale were more accurate with a Perendale training set for 3 of the 8 traits. We concluded that using a mixed-breed training set for all combinations of traits and breeds was best but advise that increasing the number of Perendale animals genotyped should be a priority to increase the MBV accuracies obtained for that breed.

Towards genomic selection for facial eczema disease tolerance in the New Zealand sheep industry.

Pithomycotoxicosis, more commonly known as facial eczema (FE), is a liver disease that occurs predominantly in New Zealand because of its toxigenic Pithomyces chartarum strains. The first reported case was in sheep in 1887. Since the 1930s, a number of studies have been conducted in an attempt to mitigate the problems FE has on the sheep and dairy industries. The research in these studies included work on fungicide and biological control of the saprophytic fungus, use of different pasture plants to inhibit fungal growth, stock management with respect to pasture fungal spore counts and the use of zinc prophylaxis on animals. The finding that there was a genetic basis in FE sensitivity in sheep prompted research for a genetic approach to mitigation in the form of a diagnostic DNA test for susceptibility to the disease. Recently, we have used the Illumina OvineSNP50 BeadChip to develop a genome-enabled prediction approach to screen for FE-tolerant sheep. Our current best genomic prediction for FE is for the Romney breed and has an accuracy of 0.38. This prediction accuracy is not as high as the individual accuracy gained by an artificial challenge test (0.64). However, it has the advantage of being a non-invasive test and can be provided as part of genomic testing for other traits at minimal cost.

Genetic relationships between dagginess, breech bareness, and wool traits in New Zealand dual-purpose sheep.

Genetic and phenotypic parameters were estimated for dagginess, breech, wool, and fiber traits from approximately 29,500 progeny born in 2009 and 2010 in New Zealand dual-purpose ram breeding sheep flocks. Dagginess is adherence of fecal matter to the wool, and this study investigates the genetic and phenotypic correlations between dagginess and breech and wool traits. Estimates for heritability were moderate (0.21 to 0.44) for the following traits: dag score at 3 and 8 mo (DAG3, DAG8), breech bareness, wool length, wool bulk (BULK), mean fiber diameter, mean fiber diameter SD, mean fiber diameter CV, curvature (CURV), weaning weight at 3 mo, and autumn BW. Heritability estimates for fleece weight at 12 mo and proportion of medullated fibers were high (0.49 and 0.53, respectively). Dag score at 3 mo and DAG8 had low genetic and phenotypic correlations with all traits. Breech bareness had positive genetic and phenotypic correlations with CURV and BULK and mostly negative genetic correlations with all other wool traits. In summary the quantity and attributes of wool were not primary causative factors in fecal accumulation, leaving fecal consistency and composition as the major factors.

Heritability estimates of methane emissions from sheep.

The objective of this study was to determine the genetic parameters of methane (CH4) emissions and their genetic correlations with key production traits. The trial measured the CH4 emissions, at 5-min intervals, from 1225 sheep placed in respiration chambers for 2 days, with repeat measurements 2 weeks later for another 2 days. They were fed in the chambers, based on live weight, a pelleted lucerne ration at 2.0 times estimated maintenance requirements. Methane outputs were calculated for g CH4/day and g CH4/kg dry matter intake (DMI) for each of the 4 days. Single trait models were used to obtain estimates of heritability and repeatability. Heritability of g CH4/day was 0.29 ± 0.05, and for g CH4/kg DMI 0.13 ± 0.03. Repeatability between measurements 14 days apart were 0.55 ± 0.02 and 0.26 ± 0.02, for the two traits. The genetic and phenotypic correlations of CH4 outputs with various production traits (weaning weight, live weight at 8 months of age, dag score, muscle depth and fleece weight at 12 months of age) measured in the first year of life, were estimated using bivariate models. With the exception of fleece weight, correlations were weak and not significantly different from zero for the g CH4/kg DMI trait. For fleece weight the phenotypic and genetic correlation estimates were -0.08 ± 0.03 and -0.32 ± 0.11 suggesting a low economically favourable relationship. These results indicate that there is genetic variation between animals for CH4 emission traits even after adjustment for feed intake and that these traits are repeatable. Current work includes the establishment of selection lines from these animals to investigate the physiological, microbial and anatomical changes, coupled with investigations into shorter and alternative CH4 emission measurement and breeding value estimation techniques; including genomic selection.