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.

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.

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.

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.

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.

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.

Consistent divergence times and allele sharing measured from cross-species application of SNP chips developed for three domestic species

Recent advances in technology facilitated development of large sets of genetic markers for many taxa, though most often model or domestic organisms. Cross-species application of genomic technologies may allow for rapid marker discovery in wild relatives of taxa with well-developed resources. We investigated returns from cross-species application of three commercially available SNP chips (the OvineSNP50, BovineSNP50 and EquineSNP50 BeadChips) as a function of divergence time between the domestic source species and wild target species. Across all three chips, we observed a consistent linear decrease in call rate (~1.5% per million years), while retention of polymorphisms showed an exponential decay. These results will allow researchers to predict the expected amplification rate and polymorphism of cross-species application for their taxa of interest, as well as provide a resource for estimating divergence times.

Generation of a preliminary bovine gene atlas, using expression clustering to annotate gene function

Genes whose products function in a common biological process are often co-regulated. When regulation occurs at the transcriptional level, co-expressed genes can be detected globally by expression arrays or by sequencing non-normalized cDNA libraries. We examined bovine gene expression in 27 tissues using non-normalized cDNA library sequencing. Contigs were generated from expressed sequence tags whose sequences overlapped. Contigs containing a minimum of five expressed sequence tags were ordered via a hierarchical clustering process, where the distance between the contigs represents their expression pattern similarity across tissues. Gene ontology terms associated with the genes in each cluster showed that co-clustered genes encoded proteins involved in a common biological process. This process can be used to annotate genes of unknown function in the cluster. Gene expression was compared between bovine and human tissues; there were significant correlations between species for each tissue, with the exception of thyroid and placenta. Tissues were also clustered based on the genes they express; tissues with similar physiological functions clustered closely. Based on this information, we generated the first preliminary gene atlas of the bovine genome. Genes with similar expression patterns were clustered, and genes with a common function co-clustered. This method can be used to annotate genes of unknown function in the bovine genome.

Investigations into the GDF8 g+6723G-A polymorphism in New Zealand Texel sheep

This work investigated effects of carrying 0, 1, or 2 copies of the A allele resulting from the g+6723G-A transition in growth differentiation factor gene (GDF8) in New Zealand Texel-cross sheep at different lamb ages and carcass weights. Two Texel-cross sires carrying 1 copy of the A allele were mated to approximately 200 ewes carrying 0, 1, or 2 copies of the A allele. A total of 187 progeny were generated and genotyped to determine whether they were carrying 0, 1, or 2 copies of the A allele. The progeny were assigned to 1 of 4 slaughter groups balanced for the 3 genotypes, sex, and sire. The 4 groups were slaughtered commercially when their average BW (across all progeny in the slaughter group) reached 33, 40, 43, and 48 kg, respectively. Measurements of BW, and carcass dimensions and yield were made on all animals using Viascan (a commercial 2-dimensional imaging system that estimates lean content of the carcass as a percentage of total carcass weight). Additional measurements were made on the fourth slaughter group, which was computed tomography scanned at each slaughter time point to obtain 4 serial measures of lean and fat as estimated from the computed tomography images. The A allele did not have an effect on any BW traits. The A allele was associated with increased muscle and decreased fat across the variety of measures of muscling and fat, explaining between 0.2 and 1.1 of a residual SD unit. Estimates for an additive effect were significant and were positive for muscle and negative for fat traits. No dominance effect estimates (positive or negative) were significant. There was no significant interaction between A allele number and carcass weight or slaughter group for any trait. This is the first systematic study of the effect of the A allele copy number over a range of carcass weights (13 to 20 kg) and ages and results suggest the size of the effect across these endpoints is proportionately the same. Testing for the A allele therefore offers breeders the potential to improve rates of genetic gain for lean-meat yield across most production systems.

Growth hormone and ghrelin receptor genes are differentially expressed between genetically lean and fat selection lines of sheep

The objective of this study was to determine whether differences in mRNA levels of key pituitary genes that regulate GH production, pituitary development, and growth were present and/or associated with divergent body composition phenotypes observed between sheep from genetically divergent lean and fat selection lines. Real-time PCR transcription profiles for pituitary specific transcription factor 1, prophet of pit1, GH, GH receptor, GH secretagogue receptor, GHRH receptor, leptin receptor, and somatostatin receptors 1 and 2 were determined in pituitary tissue. There was a difference in the amount of both GH (P < 0.001) and GH secretagogue receptor (P < 0.001) mRNA between the selection lines (5 females and 5 males per line; 20 wk of age); the lean line had greater abundance than the fat line, irrespective of which endogenous control gene was used. The results obtained for GHRH receptor were equivocal but suggestive; there were greater GHRH receptor mRNA levels (P < 0.001) in the lean line using beta-2-microglobulin as the endogenous control but not when hypoxanthine phosphoribosyltransferase and glyceraldehyde-3-phosphate dehydrogenase were used. No difference in pituitary specific transcription factor 1, prophet of pit1, GH receptor, leptin receptor, or somatostatin receptors 1 and 2 mRNA concentration was observed between the lines. The greater abundance of GH mRNA in the pituitary somatotropes from genetically lean animals appears to be associated with increased levels of GH secretagogue receptor mRNA and possibly GHRH receptor mRNA. This suggests that the difference in GH secretion between the lines may be due to differences in the afferent signals, such as ghrelin and/or GHRH, arising from the hypothalamus, or as a result of differential pituitary sensitivity to these hormones.

Distribution of prion protein genotypes in breeds of sheep in New Zealand

AIM

To use an established high through-put genotyping procedure to gain an estimate of the frequency of alleles of the prion protein (PrP) gene in some common sheep breeds in New Zealand.

METHODS

Using a genotyping procedure based on matrix-assisted laser desorption ionisation-time of flight (MALDI-TOF), DNA samples from 3,024 sheep from New Zealand, including breeds such as Romney, Texel, Coopworth, Merino and mixed breed, were isolated, genotyped and the results analysed.

RESULTS

The 15 scrapie genotypes commonly reported, and derived from the five commonly reported allelic variants (ARR, ARQ, AHQ, ARH and VRQ), were all observed in the samples analysed. The estimates were indicative of the frequencies in the population of alleles present in breeds of sheep in New Zealand. There was a significant difference between the frequencies of alleles between breeds, but the ARQ, followed by the ARR allele, were, except in Carwell sheep, the most common alleles present.

CONCLUSION

This study gave an indication of the percentages of PrP gene alleles in sheep in New Zealand, including data previously unreported from breeds in this country. It is of interest because of the relatively large size of the sheep population in New Zealand compared with many countries, and it provides some useful information on the genetic susceptibility or resistance of the sheep population in New Zealand to scrapie. The frequencies of the alleles can be different for an individual breed compared between countries.

Genetically resistant sheep avoid parasites to a greater extent than do susceptible sheep

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.

A QTL study of growth and body shape in the inter-species hybrid of Père David's deer (Elaphurus davidianus) and red deer (Cervus elaphus)

An interspecies deer hybrid resource population developed from a cross of Père David's and red deer was used to detect QTL that account for species differences. A genome scan, coupled with composite interval mapping, was conducted to search for QTL controlling body measurements at pre-pubescent age (6 months of age) and puberty (15 months of age) in this interspecies hybrid. Five linkage groups that harbour QTL affecting morphology were identified. A joint-traits analysis was used to search for putative pleiotropic QTL on four of these linkage groups, and three were significantly associated with pleiotropic QTL for nose width and foot length (metacarpal and phalanges), which collectively accounted for 29-58% of the phenotypic difference between the two deer species. This study suggests that a few loci with large pleiotropic effects may be responsible for species-specific differences in growth and structure-related traits.

Comparative mapping of sheep chromosome 2q

Sheep chromosome 2q (OAR2q), which is homologous with human chromosome 2q (HSA2q), and cattle chromosome 2 (BTA2), is known to contain several loci contributing to carcass traits. However, the chromosomal rearrangements differentiating these chromosomes among the three species have not yet been determined and thus precise correspondences between the locations of sheep and human genes are not known. Twenty-six genes from HSA2q (2q21.1-->2q36) have been assigned to OAR2q by genetic linkage mapping to refine this area of the sheep genome. Seventy-six genes were initially selected from HSA2q. Sixty-eight percent of the PCR primer sets designed for these genes amplified successfully in sheep, and 34% amplified polymorphic products. Part of the proximal arm of OAR2q was found to be inverted compared with HSA2q. The breakpoint has been localised near the growth differentiation factor 8 gene (GDF8), spanning 380 kb between the positions of the hypothetical protein (FLJ20160) (HSA2:191008944-191075046) and glutaminase (GLS) (HSA2:191453847-191538510) (Build36.1).

Meat quality traits were unaffected by a quantitative trait locus affecting leg composition traits in Texel sheep

A QTL affecting leg muscle and fat traits has been identified within the New Zealand Texel population. The QTL maps to a region on OAR 2 with a two-marker haplotype test established at markers BULGE20 and BM81124. These markers encompass the likely position of Growth Differentiation Factor 8 (GDF8). The pleiotropic effects of this QTL on meat quality traits are tested. Objective measures of meat quality including pH, color (L*, a*, and b*), and tenderness (as assessed by Warner-Bratzler shear force measurements) were assessed on longissimus and semi-membranosus muscles of 540 progeny from six Texel sires. Four of these sires were subsequently identified as segregating for leg muscle and fat traits. For these segregating sires, comparison of progeny that had inherited the favorable haplotype from their sire with those that had received the alternate haplotype revealed no significant differences in the meat quality traits assessed. This finding suggests that the muscling QTL does not have pleiotropic effects on meat quality. A general scan for meat quality QTL was carried out using genotype data for eight markers from FCB128 to RM356 flanking 122cM of OAR 2 using Haley-Knott regression. This analysis revealed two QTL for a single sire. A QTL detected in the region of Marker INRA40 for color L* mapped to a site close to the muscling QTL, but there was evidence to suggest it is at a distinct locus. The QTL in the region of Marker RM356 might map distal to Marker RM356, as no peak was observed. This QTL, which seems to affect pH, color a*, color b*, and Warner-Bratzler shear measurements, requires further characterization.

Breeding sheep in New Zealand that are less reliant on anthelmintics to maintain health and productivity

Breeding sheep that are less reliant on the use of anthelmintics to maintain acceptable health and productivity is one of several options that may assist farmers to manage the growing anthelmintic-resistance problem in New Zealand and meet consumer demands to minimise drug usage in livestock. Although it has been known for many years that genetic factors contribute to the ability of sheep to cope with roundworm challenge, attempts to selectively breed for such factors have occurred only recently. Two host traits, 'resistance' and 'resilience', are thought to be involved in limiting the deleterious effects of roundworms on the health and productivity of sheep, and the associated need for treatment with anthelmintics. Over the last decade, considerable advances have been made in our understanding of the feasibility and implications of breeding for these traits under practical conditions. The experimental breeding lines developed as part of this research are now proving to be a valuable resource for further work directed at identifying genes and/or genetic markers associated with host resistance and understanding the mechanisms of host immunity to nematode parasites in ruminants. This review provides an up-to-date summary of the results of research in this field, with particular reference to dual-purpose sheep in New Zealand, and describes how this information is being applied in practical breeding programmes.

A directed search in the region of GDF8 for quantitative trait loci affecting carcass traits in Texel sheep1

A directed search for QTL affecting carcass traits was carried out in the region of growth differentiation factor 8 (GDF8, also known as myostatin) on ovine chromosome 2 in seven Texel-sired half-sib families totaling 927 progeny. Weights were recorded at birth, weaning, ultrasound scanning, and slaughter. Ultrasonic measures of LM cross-sectional dimensions and s.c. fat above the LM were made, with the same measurements made on the LM after slaughter. Following slaughter, linear measurements of carcass length and width were made on all carcasses, and legs and loins from 540 lambs were dissected. Genotyping was carried out using eight microsatellite markers from FCB128 to RM356 on OAR 2 and analyzed using Haley-Knott regression. There was no evidence for QTL for growth rates or linear carcass traits. There was some evidence for QTL affecting LM dimensions segregating in some sire families, although it was not consistent between ultrasound and carcass measures of the same traits. There was strong and consistent evidence for a QTL affecting muscle and fat traits in the leg that mapped between markers BM81124 and BULGE20 for the four sires that were heterozygous in this region, but not for the three sires that were homozygous. The size of the effect varied across the four sires, ranging from 0.5 to 0.9 of an adjusted SD for weight-adjusted leg muscle traits, and ranging from 0.6 to 1.2 of an adjusted SD for weight-adjusted leg fat traits. The clearest effect shown was for multivariate analysis combining all leg muscle and fat traits analyzed across sires, where the -log(10) probability was 14. Animals carrying the favorable haplotype had 3.3% more muscle and 9.9% less fat in the leg relative to animals carrying other haplotypes. There was evidence for a second peak in the region of marker TEXAN2 for one sire group. It seems that a QTL affecting muscle and fat traits exists within the New Zealand Texel population, and it maps to the region of GDF8 on OAR2.

Molecular and bioinformatic strategies for gene discovery for meat traits: a reverse genetics approach

The identification of genes that influence meat quality and meat yield has relevance for several livestock species. Candidate genes include those involved in the biochemical pathways controlling muscle differentiation, growth and development. Mutations in one such gene, myostatin, have previously been reported to have dramatic effects on muscle phenotype in cattle. Here we report a screening strategy for the discovery of novel mutations in 10 genes involved in muscle development using single-stand conformation polymorphism gels and DNA sequencing. Several novel mutations, both non-synonymous and synonymous were discovered, and some of these may alter gene function. In addition, we also conducted a meta-analysis of published quantitative trait loci from cattle, sheep, pigs and mice, identifying those muscle development genes most likely to contribute to variation in muscle traits within species. From this strategy we found several genes that map into regions that are part of the extended muscle development pathway.

Understanding the relationship between the inbreeding coefficient and multilocus heterozygosity: theoretical expectations and empirical data

Geneticists have been interested in inbreeding and inbreeding depression since the time of Darwin. Two alternative approaches that can be used to measure how inbred an individual is involve the use of pedigree records to estimate inbreeding coefficients or molecular markers to measure multilocus heterozygosity. However, the relationship between inbreeding coefficient and heterozygosity has only rarely been investigated. In this paper, a framework to predict the relationship between the two variables is presented. In addition, microsatellite genotypes at 138 loci spanning all 26 autosomes of the sheep genome were used to investigate the relationship between inbreeding coefficient and multilocus heterozygosity. Multilocus heterozygosity was only weakly correlated with inbreeding coefficient, and heterozygosity was not positively correlated between markers more often than expected by chance. Inbreeding coefficient, but not multilocus heterozygosity, detected evidence of inbreeding depression for morphological traits. The relevance of these findings to the causes of heterozygosity--fitness correlations is discussed and predictions for other wild and captive populations are presented.

Bone density in sheep: genetic variation and quantitative trait loci localisation

Bone density (BD) is an important factor in osteoporotic fracture risk in humans. However, BD is a complex trait confounded by environmental influences and polygenic inheritance. Sheep provide a potentially useful model for studying differences in BD, as they provide a means of circumventing complex environmental factors and are a similar weight to humans. The aims of this study were to establish whether there is genetic variation in BD in sheep and then to localise quantitative trait loci (QTLs) associated with this variation. We also aimed to evaluate the relationship between fat and muscle body components and BD in sheep. Results showed that there was significant (P < 0.01) genetic variation among Coopworth sheep sires for BD. This genetic difference was correlated (P < 0.01) with body weight and muscle mass. A number of QTLs exceeding the suggestive threshold were identified (nine in total). Of these, two (chromosomes 1, P < 0.05; chromosome 24, P < 0.01) were significant using genome-wide permutation significance thresholds (2000 iterations). The position of the QTL on chromosome 24 coincided with a number of other body composition QTLs, indicating possible pleiotropic effects or the presence of multiple genes affecting body composition at that site. This study shows that sheep are potentially a useful model for studying the genetics of BD.

Linkage disequilibrium in domestic sheep

The last decade has seen a dramatic increase in the number of livestock QTL mapping studies. The next challenge awaiting livestock geneticists is to determine the actual genes responsible for variation of economically important traits. With the advent of high density single nucleotide polymorphism (SNP) maps, it may be possible to fine map genes by exploiting linkage disequilibrium between genes of interest and adjacent markers. However, the extent of linkage disequilibrium (LD) is generally unknown for livestock populations. In this article microsatellite genotype data are used to assess the extent of LD in two populations of domestic sheep. High levels of LD were found to extend for tens of centimorgans and declined as a function of marker distance. However, LD was also frequently observed between unlinked markers. The prospects for LD mapping in livestock appear encouraging provided that type I error can be minimized. Properties of the multiallelic LD coefficient D' were also explored. D' was found to be significantly related to marker heterozygosity, although the relationship did not appear to unduly influence the overall conclusions. Of potentially greater concern was the observation that D' may be skewed when rare alleles are present. It is recommended that the statistical significance of LD is used in conjunction with coefficients such as D' to determine the true extent of LD.

Highly prolific Booroola sheep have a mutation in the intracellular kinase domain of bone morphogenetic protein IB receptor (ALK-6) that is expressed in both oocytes and granulosa cells

The Booroola fecundity gene (FecB) increases ovulation rate and litter size in sheep and is inherited as a single autosomal locus. The effect of FecB is additive for ovulation rate (increasing by about 1.6 corpora lutea per cycle for each copy) and has been mapped to sheep chromosome 6q23-31, which is syntenic to human chromosome 4q21-25. Bone morphogenetic protein IB (BMP-IB) receptor (also known as ALK-6), which binds members of the transforming growth factor-beta (TGF-beta) superfamily, is located in the region containing the FecB locus. Booroola sheep have a mutation (Q249R) in the highly conserved intracellular kinase signaling domain of the BMP-IB receptor. The mutation segregated with the FecB phenotype in the Booroola backcross and half-sib flocks of sheep with no recombinants. The mutation was not found in individuals from a number of sheep breeds not derived from the Booroola strain. BMPR-IB was expressed in the ovary and in situ hybridization revealed its specific location to the oocyte and the granulosa cell. Expression of mRNA encoding the BMP type II receptor was widespread throughout the ovary. The mutation in BMPR-IB found in Booroola sheep is the second reported defect in a gene from the TGF-beta pathway affecting fertility in sheep following the recent discovery of mutations in the growth factor, GDF9b/BMP15.

Genetic characterisation of protective vaccine responses in sheep using multi-valent Dichelobacter nodosus vaccines

Protective vaccine responses to nine distinct serogroups of Dichelobacter nodosus (serogroups A-I) can be readily measured by serogroup-specific K-agglutinating antibody titres. On the basis of a large quantitative genetic experiment (1200 progeny from 129 sire groups), it was shown that variation in antibody responses following vaccination with a multi-valent pilus antigen D. nodosus vaccine (serogroups A-I) is, in part, under genetic control and thus heritable. Based on the genetic relationships between antibody responses to all nine antigens, results suggested that both genes for a broad-based and genes for serogroup-specific response contributed to genetic variation in vaccine response. Furthermore, preliminary data in 389 progeny showed that polymorphism within the ovine major histocompatibility (MHC) based on serological classification accounted for a significant proportion of the variation in vaccine responses. In subsequent experimentation, we examined the importance of genetic polymorphism within the ovine MHC, and the possibility of genes outside the MHC for their involvement in antigen-specific and broad-based vaccine response. Within two large half sib families(131, and 143 progeny), four MHC haplotypes were investigated and found to be associated with differential antibody responses to six out of eight distinct vaccine-antigens presented to the host in a multi-valent vaccine. The model used here shows how well characterised immunogens, quantitative genetic experimentation, and molecular gene mapping tools can be used to unravel genetic differences in host responses to commercial vaccines.

Catalase gene is associated with facial eczema disease resistance in sheep

Facial eczema (FE) is a hepatogenous photosensitization disease of ruminant animals, particularly in sheep which vary widely in their susceptibility to the disease. The liver damage is caused by the mycotoxin, sporidesmin. There is evidence that the toxicity of sporidesmin is due to its ability to generate 'active oxygen' species. We evaluated the catalase gene, which encodes an enzyme with antioxidant functions, as a candidate for determining the susceptibility of sheep to the disease. Two microsatellite markers, OarSHP3 and OarSHP4, which flank the sheep catalase gene, were isolated from a Yeast Artificial Chromosome (YAC) clone. These markers mapped the catalase locus by linkage to ovine chromosome 15. Eleven informative markers spaced throughout chromosome 15, inclusive of the catalase marker OarSHP4, gave no significant linkage with the disease traits when analysed in four outcross resource pedigrees. However, OarSHP3 and OarSHP4 allele frequencies showed significant differences between FE resistant and susceptible selection-lines. Comparison of sequences of catalase cDNAs from sheep of resistant and susceptible lines showed only two silent mutations. A single nucleotide polymorphisms (KP1) in exon 6 of the catalase gene also showed significant differences in allele frequencies between the selection lines. The lack of evidence for linkage in outcross pedigrees, but the significant association in the genetic lines, implies that catalase is involved in determining the susceptibility of sheep to facial eczema, and that the candidate gene's effect is probably recessive or minor.

The physiological effects of natural variation in growth hormone gene copy number in ram lambs

The effects of natural variation in the number of copies of the growth hormone (GH) gene on growth parameters, plasma GH profiles, and the response to GHRH challenge were compared in Coopworth ram lambs from selection lines differing in body composition and GH levels. Different genotypes at the GH locus carried two, three, or four copies of the GH gene and GH secretion was studied under ad libitum feeding conditions and in the fasted state. There were no significant effects of GH genotype on any parameters of growth or body composition. Basal serum GH concentration, GH pulse frequency, and GH pulse amplitude differed significantly with selection line and fasting, but did not differ significantly between the GH genotypes. Significant differences of subtle nature were found between the GH genotypes in their responsiveness to GHRH. For the ad libitum-fed Lean selection line animals, the first GHRH challenge resulted in a higher mean maximum response for GH1/GH1 than GH2/GH2 (P < 0.05). Between the first and the second challenges there was a decrease in maximum response for the GH1/GH1 genotype and an increase for the GH2/GH2 genotype (P < 0.05 for GH genotype main effect). The differences between GH genotypes in response to GHRH challenge suggest that polymorphism in the number of GH gene copies in sheep may have physiological implications for the function of the GH axis, which may be manifested in growing lambs only under specific genotype-environment combinations.

Exclusion probabilities for pedigree testing farm animals

Pedigree testing, using genetic markers, may be undertaken for a variety of situations, of which the classical paternity testing is only one. This has not always been made clear in the literature. Exclusion probabilities associated with various testing situations, including the use of autosomal or X-linked codominant marker systems with any number of alleles, are presented. These formulae can be used to determine the appropriate exclusion probability for the situation being investigated. One such situation is where sire groups of progeny are to be verified without knowledge of the dams' genotypes, in which case the classical paternity exclusion probability is too high, and if used may result in an optimistic declaration about the progeny that have not been excluded. On the other hand, if mating pairs are known then incorrect progeny can be excluded at a higher rate than suggested by paternity exclusion calculations. The formulae also assist in determining the usefulness of X-linked markers, particularly if the pedigree checks involve progeny of only one sex. A system of notation that is useful for the algebraic manipulation of genetic probabilities, including exclusion probabilities as presented here, is also given.

Early stages of myogenesis in a large mammal: formation of successive generations of myotubes in sheep tibialis cranialis muscle

The generation of myotubes was studied in the tibialis cranialis muscle in the sheep hindlimb from the earliest stage of primary myotube formation until a stage shortly before muscle fascicles began to segregate. Primary myotubes were first seen on embryonic day 32 (E32) and reached their maximum number by E38. Small numbers of secondary myotubes were first identified at E38, and secondary myotube numbers continued to increase during the period of study. The ratio of adult muscle fibre to primary myotube numbers was approximately 70:1, making it seem unlikely that every later generation myotube used a primary myotube as scaffold for its formation, as described in small mammals. By E62, some secondary myotubes were supporting the formation of a third generation of myotubes. Experiments with diffusible dye markers showed that primary myotubes extended from tendon to tendon of the muscle, whereas most adult fibres ran for only part of the muscle length, terminating with myo-myonal attachments to other muscle fibres in a series arrangement. Acetylcholinesterase (AChE) and acetylcholine receptor (AChR) aggregations appeared in multiple bands across the muscle shortly after formation of the primary generation of myotubes was complete. The number of bands and their pattern of distribution across the muscle as they were first formed was the same as in the adult. Primary myotubes teased from early muscles had multiple focal AChE and AChR deposits regularly spaced along their lengths. We suggest that the secondary generation of myotubes forms at endplate sites in a series arrangement along the length of single primary myotubes, and that tertiary and possibly later generations of myotubes in their turn use the earlier generation myofibres as a scaffold. Although the fundamental cellular mechanisms appear to be similar, the process of muscle fibre generation in large mammalian muscles is more complex than that described from previous studies in small laboratory rodents.

Myosin heavy chain composition of single fibres and their origins and distribution in developing fascicles of sheep tibialis cranialis muscles

The myosin heavy chain (MHC) composition of single muscle fibres in developing sheep tibialis cranialis muscles was examined immunohistochemically with monoclonal antibodies to MHC isozymes. Data were collected with conventional microscopy and computerized image analysis from embryonic day (E) 76 to postnatal day (PN) 20, and from adult animals. At E76, 23% of the young myofibres stained for slow-twitch MHC. The number of these fibres considerably exceeded the number of primary and secondary myotubes. By E100, smaller fibres, negative for slow-twitch MHC, encircled each fibre from the initial population to form rosettes. A second population of small fibres appeared in the unoccupied spaces between rosettes. Small fibres, whether belonging to rosettes or not, did not initially express slow-twitch MHC, expressing mainly neonatal myosin instead. These small fibres then diverged into three separate groups. In the first group most fibres transiently expressed adult fast myosin (maximal at E110-E120), but in the adult expressed slow myosin. This transformation to the slow MHC phenotype commenced at E110, was nearing completion by 20 postnatal days, and was responsible for approximately 60% of the adult slow twitch fibre population. In the other two groups expression of adult fast MHC was maintained, and in the adult they accounted for 14% (IIa MHC) and 17% (IIb MHC) of the total fibre numbers. We conclude that muscle fibre formation in this large muscle involves at least three generations of myotube. Secondary myotubes are generated on a framework of primary myotubes and both populations differentiate into the young myofibres which we observed at E76 to form rosettes. Tertiary myotubes, in turn, appear in the spaces between rosettes and along the borders of fascicles, using the outer fibres of rosettes as scaffolds.

Infertility due to bilateral ovarian hypoplasia in sheep homozygous (FecXI FecXI) for the Inverdale prolificacy gene located on the X chromosome

Ewes heterozygous (I+) for the Inverdale prolificacy gene (FecXI) located on the X chromosome have ovulation rates about 1.0 units higher than noncarriers. The purpose of this study was to examine the reproductive performance of ewes that were either heterozygous or homozygous (II) carriers of the Inverdale gene. Carrier rams (I) were mated with heterozygous ewes (I+) to produce females, half of which were expected to be I+ and half II. The 59 female progeny were examined by laparoscopy at 8 mo or 1.5 yr of age; 48% were found to have nonfunctional "streak" ovaries, which were about one eighth the volume of normal ovaries and showed no sign of follicular activity. There were four examples of full sib pairs where within each pair one had normal ovaries and the other had streak ovaries. Since these streak ovaries have not been observed in ewes known to be I+ or noncarriers (++), it is concluded that this condition is associated with animals homozygous for the Inverdale gene.

Evidence for the presence of a major gene influencing ovulation rate on the X chromosome of sheep

In a flock of highly prolific Romney ewes obtained from industry flocks, one ewe (A281), with a production record of 33 lambs born in 11 lambings, produced a number of female descendants with high ovulation rates. The mode of inheritance of this trait was determined in a series of four progeny tests of male descendants of this ewe. The first progeny test produced strong evidence for a new major gene affecting ovulation rate in this family line; this finding was supported by two subsequent progeny tests. The fourth progeny test was designed to test the hypothesis that this gene is carried on the X chromosome. The results showed that six sons of a carrier ram did not inherit the gene, but it was passed on to three of his five maternal grandsons. This finding, together with evidence of genetic segregation in the progeny of carrier females, demonstrates for the first time the presence of a major gene for prolificacy specifically located on the X chromosome. The effect of the gene is to increase ovulation rate by about one additional egg per ewe.

Neural control of the sequence of expression of myosin heavy chain isoforms in foetal mammalian muscles

The expression of myosin isoforms was studied during development of calf muscles in foetal and neonatal rats, using monoclonal antibodies against slow, embryonic and neonatal isoforms of myosin heavy chain (MHC). Primary myotubes had appeared in all prospective rat calf muscles by embryonic day 16 (E16). On both E16 and E17, primary myotubes in all muscles with the exception of soleus stained for slow, embryonic and neonatal MHC isoforms; soleus did not express neonatal MHC. In earlier stages of muscle formation staining for the neonatal isoform was absent or faint. Secondary myotubes were present in all muscles by E18, and these stained for both embryonic and neonatal MHCs, but not slow. In mixed muscles, primary myotubes destined to differentiate into fast muscle fibres began to lose expression of slow MHC, and primary myotubes destined to become slow muscle fibres began to lose expression of neonatal MHC. This pattern was further accentuated by E19, when many primary myotubes stained for only one of these two isoforms. Chronic paralysis or denervation from E15 or earlier did not disrupt the normal sequence of maturation of primary myotubes up until E18, but secondary myotubes did not form. By E19, however, most primary myotubes in aneural or paralyzed tibialis anterior muscles had lost expression of slow MHC and expressed only embryonic and neonatal MHCs. Similar changes occurred in other muscles, except for soleus which never expressed neonatal MHC, as in controls. Paralysis or denervation commencing later than E15 did not have these effects, even though it was initiated well before the period of change in expression of MHC isoforms. In this case, some secondary myotubes appeared in treated muscles. Paralysis initiated on E15, followed by recovery 2 days later so that animals were motile during the period of change in expression of MHC isoforms, was as effective as full paralysis. These experiments define a critical period (E15-17) during which foetuses must be active if slow muscle fibres are to differentiate during E19-20. We suggest that changes in expression of MHC isoforms in primary myotubes depend on different populations of myoblasts fusing with the myotubes, and that the normal sequence of appearance of these myoblasts has a stage-dependent reliance on active innervation of foetal muscles. A critical period of nerve-dependence for these myoblasts occurs several days before their action can be noted.