Perspectives on Future Protein Production

An increasing world population, rising affluence, urbanization, and changing eating habits are all contributing to the diversification of protein production. Protein is a building block of life and is an essential part of a healthy diet, providing amino acids for growth and repair. The challenges and opportunities for production of protein-rich foods from animals (meat, dairy, and aquaculture), plant-based sources (pulses), and emerging protein sources (insects, yeast, and microalgae) are discussed against the backdrop of palatability, nutrition, and sustainability.

Net protein contribution and enteric methane production of pasture and grain-finished beef cattle supply chains

Ruminant red meat production systems around the world often include a grain feeding phase. The role of red meat in the food system is therefore often discussed in terms of the food vs feed debate, as well as invoking the comparatively poor feed conversion efficiency of ruminants and climate impacts from enteric methane. The concept of net protein contribution (NPC) incorporates the quality attributes of protein produced by livestock systems into estimates of the efficiency of production systems. We applied the NPC method to two Australian beef supply chains, i) Grass-fed and ii) Grain-finished beef, using an established model of ruminant grazing systems (GrassGro®) and these are reflective of beef production systems in other countries. The beef supply chains evaluated did not compete with humans for protein. The Grain-finished beef supply chain, while positively contributing to human protein requirements (NPC value 1.96), had markedly lower NPC values than the Grass-fed system (NPC value 1 597). However, Grass-fed beef production systems have a higher methane intensity than the Grain-finished supply chain. The two examples of pasture-based beef production systems examined provide a positive net protein contribution to human food supply, even with extended periods of finishing on grain-based diets. This is achieved by ruminant grazing on pastures converting low-quality forage into high value human edible protein. The efficiency of protein production varies according to the system design, and other considerations such as land use and enteric methane production are elements that need consideration in the overall assessment of the production footprint.

ImmuneDEX: a strategy for the genetic improvement of immune competence in Australian Angus cattle

In animal breeding and genetics, the ability to cope with disease, here defined as immune competence (IC), with minimal detriment to growth and fertility is a desired objective which addresses both animal production and welfare considerations. However, defining and objectively measuring IC phenotypes using testing methods which are practical to apply on-farm has been challenging. Based on previously described protocols, we measured both cell-mediated immune response (Cell-IR) and antibody-mediated immune response (Ab-IR) and combined these measures to determine an animal's IC. Using a population of 2,853 Australian Angus steers and heifers, we compared 2 alternative methods to combine both metrics into a single phenotype to be used as a tool for the genetic improvement of IC. The first method, named ZMEAN, is obtained by taking the average of the individual metrics after subjecting each to a Z-score standardization. The second, ImmuneDEX (IDEX), is a weighted average that considers the correlation between Cell-IR and Ab-IR, as well as the difference in ranking of individuals by each metric, and uses these as weights in the averaging. Both simulation and real data were used to understand the behavior of ZMEAN and IDEX. To further ascertain the relationship between IDEX and other traits of economic importance, we evaluated a range of traits related to growth, feedlot performance, and carcass characteristics. We report estimates of heritability of 0.31 ± 0.06 for Cell-IR, 0.42 ± 0.06 for Ab-IR, 0.42 ± 0.06 for ZMEAN and 0.370 ± 0.06 for IDEX, as well as a unity genetic correlation (rg) between ZMEAN and IDEX. While a moderately positive rg was estimated between Cell-IR and Ab-IR (rg = 0.33 ± 0.12), strongly positive estimates were obtained between IDEX and Cell-IR (rg = 0.80 ± 0.05) and between IDEX and Ab-IR (rg = 0.85 ± 0.04). We obtained a moderately negative rg between IC traits and growth including an rg = -0.38 ± 0.14 between IDEX and weaning weight, and negligible with carcass fat measurements, including an rg = -0.03 ± 0.12 between IDEX and marbling. Given that breeding with a sole focus on production might inadvertently increase susceptibility to disease and associated antibiotic use, our analyses suggest that ImmuneDEX will provide a basis to breed animals that are both highly productive and with an enhanced ability to resist disease.

Associations between immune competence phenotype and feedlot health and productivity in Angus cattle

Genetic strategies aimed at improving general immune competence (IC) have the potential to reduce the incidence and severity of disease in beef production systems, with resulting benefits of improved animal health and welfare and reduced reliance on antibiotics to prevent and treat disease. Implementation of such strategies first requires that methodologies be developed to phenotype animals for IC and demonstration that these phenotypes are associated with health outcomes. We have developed a methodology to identify IC phenotypes in beef steers during the yard weaning period, which is both practical to apply on-farm and does not restrict the future sale of tested animals. In the current study, a total of 838 Angus steers, previously IC phenotyped at weaning, were categorized as low (n = 98), average (n = 653), or high (n = 88) for the IC phenotype. Detailed health and productivity data were collected on all steers during feedlot finishing, and associations between IC phenotype, health outcomes, and productivity were investigated. A favorable association between IC phenotype and number of mortalities during feedlot finishing was observed with higher mortalities recorded in low IC steers (6.1%) as compared with average (1.2%, P < 0.001) or high (0%, P = 0.018) IC steers. Disease incidence was numerically highest in low IC steers (15.3 cases/100 animals) and similar in average IC steers (10.1 cases/100 animals) and high IC steers (10.2 cases/100 animals); however, differences between groups were not significant. No significant influence of IC phenotype on average daily gain was observed, suggesting that selection for improved IC is unlikely to incur a significant penalty to production. The potential economic benefits of selecting for IC in the feedlot production environment were calculated. Health-associated costs were calculated as the sum of lost production costs, lost capital investment costs, and disease treatment costs. Based on these calculations, health-associated costs were estimated at AUS$103/head in low IC steers, AUS$25/head in average IC steers, and AUS$4/head in high IC steers, respectively. These findings suggest that selection for IC has the potential to reduce mortalities during feedlot finishing and, as a consequence, improve the health and welfare of cattle in the feedlot production environment and reduce health-associated costs incurred by feedlot operators.

A low-density SNP genotyping panel for the accurate prediction of cattle breeds

Genomic tools to better define breed composition in agriculturally important species have sparked scientific and commercial industry interest. Knowledge of breed composition can inform multiple scientifically important decisions of industry application including DNA marker-assisted selection, identification of signatures of selection, and inference of product provenance to improve supply chain integrity. Genomic tools are expensive but can be economized by deploying a relatively small number of highly informative single-nucleotide polymorphisms (SNP) scattered evenly across the genome. Using resources from the 1000 Bull Genomes Project we established calibration (more stringent quality criteria; N = 1,243 cattle) and validation (less stringent; N = 864) data sets representing 17 breeds derived from both taurine and indicine bovine subspecies. Fifteen successively smaller panels (from 500,000 to 50 SNP) were built from those SNP in the calibration data that increasingly satisfied 2 criteria, high differential allele frequencies across the breeds as measured by average Euclidean distance (AED) and high uniformity (even spacing) across the physical genome. Those SNP awarded the highest AED were in or near genes previously identified as important signatures of selection in cattle such as LCORL, NCAPG, KITLG, and PLAG1. For each panel, the genomic breed composition (GBC) of each animal in the validation dataset was estimated using a linear regression model. A systematic exploration of the predictive accuracy of the various sized panels was then undertaken on the validation population using 3 benchmarking approaches: (1) % error (expressed relative to the estimated GBC made from over 1 million SNP), (2) % breed misassignment (expressed relative to each individual's breed recorded), and (3) Shannon's entropy of estimated GBC across the 17 target breeds. Our analyses suggest that a panel of just 250 SNP represents an adequate balance between accuracy and cost-only modest gains in accuracy are made as one increases panel density beyond this point.

ImmuneDEX: updated genomic estimates of genetic parameters and breeding values for Australian Angus cattle

Context Immune competence is a proxy trait for general disease resistance and is based on combined measures of an animal’s ability to mount both a cell-mediated immune response (Cell-IR) and an antibody-mediated immune response (Ab-IR). On the basis of previously described arithmetic, we combined these measures into a single proxy trait for immune competence, named ImmuneDEX (IDEX). Aims Using a population of 3715 Australian Angus steers (n = 2395) and heifers (n = 1320) with genotypes for 45 364 single-nucleotide polymorphisms, we provide the latest genomic estimates of heritability and genetic correlations for IDEX and the components Cell-IR and Ab-IR immune competence phenotypes. Accuracy and bias of genomic predictions of breeding values are also presented and discussed. Methods Measures of Cell-IR, Ab-IR and IDEX were analysed jointly in a tri-variate genomic restricted maximum-likelihood model that contained the fixed effects of contemporary group with 80 levels, the linear covariates of age at measurement and change in skin thickness at control site, and the random polygenic (genomic estimated breeding value, GEBV) and residual effects. Following Method LR procedures, we estimate accuracy, bias and dispersion of genomic predictions using a cross-validation scheme based on five year-of-birth cohorts. Key results We report genomic restricted maximum-likelihood model estimates of heritability of 0.247 ± 0.040 for Cell-IR, 0.326 ± 0.059 for Ab-IR, 0.275 ± 0.046 for IDEX. While a small positive genetic correlation (rg) was estimated between Cell-IR and Ab-IR (rg = 0.138 ± 0.095), strongly positive estimates were obtained between IDEX and Cell-IR (rg = 0.740 ± 0.044) and between IDEX and Ab-IR (rg = 0.741 ± 0.036). Averaged across the five validation sets, the accuracy of GEBV for Cell-IR, Ab-IR and IDEX was 0.405, 0.443 and 0.411 respectively. Also, some significant bias or dispersion can be expected depending on the cohort used as the validation population. Conclusions Consistent with previous findings, immune competence phenotypes are moderately heritable and accurate GEBV can be generated to allow the selection of cattle with an improved ability to mount a general immune response. Implications Our analyses suggest that ImmuneDEX will provide a tool to underpin long-term genetic strategies aimed at improving the immune competence of Australian Angus cattle in production systems, which, in turn, is expected to reduce the incidence of disease and our reliance on antibiotics to treat disease.

Exploring genomic approaches to fast-track genetic gains in breechstrike resistance in Merino sheep

Context Breech flystrike is a costly trait to measure. Industry investment into genetic solutions for breech flystrike has resulted in the availability of estimated breeding values for indicator traits, such as breech wrinkle, breech cover and dag. However, selection is based on indicator traits rather than breech flystrike itself, and genetic gains could be enhanced through genomic selection approaches. Aim This study investigated whether genomic approaches based on major genes, such as marker-assisted selection, or genomic selection based on genomic breeding values, would be the most efficient application of genomic information to enhance genetic gains for breech flystrike resistance. Methods The analysis comprised 1535 sheep of the Merino Breeding for Breech Flystrike Resistance Resource flocks from New South Wales and Western Australia with high density genotypes (actual and imputed). A genome-wide association study was conducted on breech flystrike and its indicator traits, namely, breech wrinkle, dag and breech cover. The study also estimated genomic breeding values and their accuracy. Key results The SNP associations found in this study did not point to the existence of few genes with major effects on breech flystrike resistance or its indicator traits. Throughout the genome, associations of small effect were found, which enabled the estimation of genomic breeding values. However, these were of low accuracy, as expected for the size of the dataset. Conclusion Genomic prediction of breeding values for breech flystrike resistance is a feasible tool for applying genomic technology in the Merino industry. Implications A reference population of appropriate size needs to be established for this difficult-to-measure trait, and a dispersed reference population could be an effective option.

Ultra-small SNP panels to uniquely identify individuals in thousands of samples

Context Genomic profiles are the only information source that can uniquely identify an individual but have not yet been strongly considered in the context of paddock to plate traceability due to the lack of value proposition. Aim The aim of this study was to define the minimum number of single nucleotide polymorphisms (SNP) required to distinguish a unique genotype profile for each individual sample within a large given population. At the same time, ad hoc approaches were explored to reduce SNP density, and therefore, the size of the dataset to improve computing efficiency and storage requirements while maintaining informativeness to distinguish individuals. Methods Data for this study included two datasets. One included 78 411 high-density SNP genotypes from commercial Angus cattle and the other 2107 from a research data (1000-bull genome data). In a stepwise approach, different-size SNP panels were explored, with the last step being a successive removal resulting in the smallest set of SNPs that still produced the maximum number of unique genotypes. Key results First study that has demonstrated for large datasets, that ultra-small SNP panels with 20–23 SNPs can generate unique genotypes for up to ~80 000 individuals, allowing for 100% matching accuracy. Conclusions Ultra-small SNP panels could provide an efficient method to approach the large-scale task of the traceability of beef products through the beef supply chain. Implications Genomic tools could enhance supply-chain traceability.

Dentition can predict maturity in young Merino sheep

Context A unique population of Merino sheep recorded for a range of production and reproduction traits presented an opportunity to calculate sire variation in dentition which may indicate maturity and influence marketing and selection decisions. A change in the definition of ‘lamb’ in the Australian sheep industry warranted an investigation of the relationship between production, reproduction and dentition. Aims To assess the variation in timing of dentition changes in Merino sheep and determine whether there are associations with key production and reproduction traits. Methods A population of 2150 pedigree-recorded Merino sheep were studied to analyse the sire variation in progeny for a range of dentition changes and production and reproduction traits. Dentition phenotypes included the age animals started to lose the deciduous lamb teeth, the age when one permanent incisor was in wear and the amount of time between these two events. Production records included bodyweight, fat and muscle traits. Reproduction records from the female progeny included the outcome of pregnancy scanning after the first joining opportunity. Sire variation for the age dentition changed was analysed. The effect of progeny age at hogget categorisation on production and reproduction was analysed. Key results Progeny that were heavier, fatter and with higher muscle measurements matured earlier. Female progeny were more likely to be pregnant if classed as hoggets earlier in life. Conclusions Dentition records provided useful indicators of maturity in Merino sheep in this study and can be used to inform decisions regarding the timing of marketing options and the likelihood of success when assessing female progeny for suitability to join at ~18 months of age. Implications Merino sires can exhibit a wide range of variation with respect to the age at which their progeny will mature, as indicated by their dentition. If animals are heavier at an earlier age, they are more likely to mature earlier, which has to be considered when planning nutritional requirements for growing out young male progeny, and females could be more successful as young breeders. Dentition is a useful tool to indicate maturity in young Merino sheep.

In silico validation of pooled genotyping strategies for genomic evaluation in Angus cattle

In this study, we aimed to assess the value of genotyping DNA pools as a strategy to generate accurate and cost-effective genomic estimated breeding values (GEBV) of sires in multi-sire mating systems. In order to do that, we used phenotypic records of 2,436 Australian Angus cattle from 174 sires, including yearling weight (YWT; N = 1,589 records), coat score (COAT; N = 2,026 records), and Meat Standards Australia marbling score (MARB; N = 1,304 records). Phenotypes were adjusted for fixed effects and age at measurement and pools of 2, 5, 10, 15, 20, and 25 animals were explored. Pools were created either by phenotype or at random. When pools were created at random, 10 replicates were examined to provide a measure of sampling variation. The relative accuracy of each pooling strategy was measured by the Pearson correlation coefficient between the sire's GEBV with pooled progeny and the GEBV using individually genotyped progeny. Random pools allow the computation of sire GEBV that are, on average, moderately correlated (i.e., r > 0.5 at pool sizes [PS] ≤ 10) with those obtained without pooling. However, for pools assigned at random, the difference between the best and the worst relative accuracy obtained out of the 10 replicates was as high as 0.41 for YWT, 0.36 for COAT, and 0.61 for MARB. This uncertainty associated with the relative accuracy of GEBV makes randomly assigning animals to pools an unreliable approach. In contrast, pooling by phenotype allowed the estimation of sires' GEBV with a relative accuracy ≥ 0.9 at PS < 10 for all three phenotypes. Moreover, even with larger PS, the lowest relative accuracy obtained was 0.88 (YWT, PS = 20). In agreement with results using simulated data, we conclude that pooling by phenotype is a robust approach to implementing genomic evaluation using commercial herd data, and PS larger than 10 individuals can be considered.

Repeatabilities, heritabilities and correlations of methane and feed intake of sheep in respiration and portable chambers

Context Knowledge of genetic and phenotypic variation and the accuracy of different measurement techniques is needed to successfully reduce livestock methane (CH4) emissions. Aims To estimate repeatabilities, heritabilities and genetic correlations of respiration-chamber (RC) and portable accumulation-chamber (PAC) measurements using two different protocols but the same management and feeding conditions. Methods Australian Information Nucleus Flock ewes were measured in seven test-batches. The 510 ewes were removed from pasture and habituated to chaffed alfalfa and cereal hay at 1.5–1.6 times maintenance. Methane was measured in RC for two 22-h periods approximately 14 days apart, and 40 min in PAC, either immediately after removal from individual pens (with feed as described above, PAC0), or 1-h after withdrawing feed (PAC1). There were up to 48 PAC0 tests per day (at 0930 hours, 1100 hours, 1230 hours, 1400 hours in 12 PAC) and 24 PAC1 tests per day (at 1100 hours and 1300 hours). Test methods (RC, PAC0, PAC1) were analysed as different traits in a multi-trait repeated-measures model. Key results Before adjustment for liveweight (Lwt) or feed intake (FI), CH4 was highly repeatable (RC 78%, PAC0 83%, PAC1 82%), with heritabilities of 39–55%, permanent environmental (PE) animal variances 23–43% of phenotypic variances (Vp), high genetic correlations between methods (98–100%), and lower PE correlations (44–58%). A second PAC test on the same day decreased CH4 by 8–12% compared with the ewe’s first test that day. Heritabilities of FI from 0800 hours until the test was complete (FIOD) were 16–17% (PAC) and 25% (RC) before adjusting for Lwt, with high PE variances (PAC 67–73%, RC 41% of Vp). FI in the previous 24 h was highly heritable and much less variable than was FIOD in the RC, suggesting that testing introduced additional variation by disrupting feeding patterns. After adjusting CH4 for Lwt, FIOD and FI in the previous 24 h and Lwt, some additive genetic variation remained, averaging 17% of Vp. Multivariate models of CH4 and FI, fitting a single animal term (representing genetic+PE variation) showed high animal correlations between FI and CH4, namely, 90–95% before, and 86–95% after adjusting for Lwt. Conclusions PAC measurements are heritable and highly correlated with RC measurements under similar management conditions. The high genetic and animal correlations of PAC CH4 and FI imply that CH4 is a useful proxy for FI of grazing animals.

Immune competence traits assessed during the stress of weaning are heritable and favorably genetically correlated with temperament traits in Angus cattle1

Selection for production traits with little or no emphasis on health-related traits has the potential to increase susceptibility to disease in food-producing animals. A possible genetic strategy to mitigate such effects is to include both production and health traits in the breeding objective when selecting animals. For this to occur, reliable methodologies are required to assess beneficial health traits, such as the immune capacity of animals. We describe here a methodology to assess the immune competence of beef cattle which is both practical to apply on farm and does not restrict the future sale of tested animals. The methodology also accommodates variation in prior vaccination history of cohorts of animals being tested. In the present study, the immune competence phenotype of 1,100 Angus calves was assessed during yard weaning. Genetic parameters associated with immune competence traits were estimated and associations between immune competence, temperament, and stress-coping ability traits were investigated. Results suggested that immune competence traits, related to an animal's ability to mount both antibody and cell-mediated immune responses, are moderately heritable (h2 = 0.32 ± 0.09 and 0.27 ± 0.08, respectively) and favorably genetically correlated with the temperament trait, flight time (r = 0.63 ± 0.31 and 0.60 ± 0.29 with antibody and cell-mediated immune responses, respectively). Development of methodologies to assess the immune competence phenotype of beef cattle is a critical first step in the establishment of genetic selection strategies aimed at improving the general disease resistance of beef herds. Strategies aimed at reducing the incidence of disease in beef cattle are expected to significantly improve animal health and welfare, reduce reliance on the use of antibiotics to treat disease, and reduce disease-associated costs incurred by producers.

Quantification of differences in resistance to gastrointestinal nematode infections in sheep using a multivariate blood parameter

Breeding for resistance to gastrointestinal nematodes (GIN) in sheep relies largely on the use of worm egg counts (WEC) to identify animals that are able to resist infection. As an alternative to such measures of parasite load we aimed to develop a method to identify animals showing resistance to GIN infection based on the impact of the infection on blood parameters. We hypothesized that blood parameters may provide a measure of infection level with a blood-feeding parasite through perturbation of red blood cell parameters due to feeding behaviour of the parasite, and white blood cell parameters through the mounting of an immune response in the host animal. We measured a set of blood parameters in 390 sheep that had been exposed to an artificial regime of repeated challenges with Trichostrongylus colubriformis followed by Haemonchus contortus. A simple analysis revealed strong relationships between single blood parameters and WECs with correlation coefficients -0.54 to -0.60. We then used more complex multi-variate methods based on supervised classifier models (including Bayesian Network) as well as regression models (Lasso and Elastic Net) to study the relationships between WECs and blood parameters, and derived algorithms describing the relationships. The ability of these algorithms to classify sheep GIN resistance status was tested using the WEC and blood parameters collected from a different group of 418 sheep that had acquired natural infections of H. contortus from pasture. We identified the most resistant and most susceptible animals (10% percentiles) of this group based on WECs, and then compared the identities of these animals to the identities of animals that were predicted to be most resistant and most susceptible by our algorithms. The models showed varying abilities to predict susceptible and resistant sheep, with up to 65% of the most susceptible animals and 30% of the most resistant animals identified by the Elastic Net model algorithms. The prediction algorithms derived from female sheep data performed better than those for male sheep in some cases, with the predicted animals accounting for up to 50-60% of the actual resistant and susceptible female animals. Heritability values were calculated for blood parameters and the aggregate trait descriptions defined by the novel prediction algorithms. The aggregate trait descriptions were moderately heritable and may therefore be suitable for use in genetic selection strategies. The present study indicates that multivariate models based on blood parameter data showed some ability to predict the resistance status of sheep to infection with H. contortus.

Variation in methane production over time and physiological state in sheep

Livestock produce 10% of the total CO2-equivalent greenhouse gases in Australia, predominantly as methane from rumen fermentation. Genetic selection has the potential to reduce emissions and be adopted in Australian grazing systems. Developing a breeding objective for reduced methane emissions requires information about heritability, genetic relationships, when best to measure the trait and knowledge of the annual production of methane. Among- and within-animal variation in methane production, methane yield and associated traits were investigated, so as to determine the optimal time of measurement and the relationship between that measurement and the total production of methane. The present study measured 96 ewes for methane production, liveweight, feed intake, rumen volume and components, and volatile fatty acid (VFA) production and composition. Measurements were recorded at three ages and different physiological states, including growing (12 months), dry and pregnant (21 months) and dry (non-pregnant, non-lactating; 28 months of age). The single biggest determinant of methane production was feed intake, but there were additional effects of age, proportion of propionate to (acetate+butyrate) in rumen VFA, total VFA concentration and CO2 flux. Rumen volume and pregnancy status also significantly affected methane production. Methane production, CO2 flux, liveweight, feed intake and rumen volume had high repeatability (&gt;65%), but repeatability of methane yield and VFA traits were low (&lt;20%). There were no interactions between sire and age (or pregnancy status) for methane traits. This suggests that methane could be measured at any time in the production cycle. However, because MY is reduced during pregnancy, it might be best to measure methane traits in dry ewes (neither pregnant nor lactating).

Ewe culling and retention strategies to increase reproductive rates in Merino sheep

The present empirical study of data from three Merino resource flocks of varying genetic backgrounds run in different environments investigated the impact of various selection strategies aimed at culling poor performers (‘passengers’) or retaining good doers (‘performers’) longer, or both, on the flock reproductive performance. Four strategies were investigated and applied either individually or in combination, to quantify their impact on the litter size, rearing type and breeding efficiency (number of lambs weaned per ewe per year) of the whole flock. The main benefit from implementing any of the strategies was a decrease in the proportion of dry ewes in each flock (1–7%). There was little difference between the single strategies of culling twice-dry ewes or culling ewes that twice lambed and lost their lambs. When retaining a cohort of older ewes, it was more efficient to select these on the basis of their lifetime reproductive performance. There was only a marginal benefit gained by combining strategies and, in some cases, a single strategy was still better in terms of breeding efficiency. Commercial producers can improve the reproductive rate of these flocks by culling twice-dry ewes on the basis of their pregnancy scan data.

Genetic and phenotypic parameters for reproduction, production and bodyweight traits in Australian fine-wool Merino sheep

The present study estimated phenotypic and genetic relationships between wool production, reproduction and bodyweight traits in Australian fine-wool Merino sheep. The data for the study originated from the CSIRO Fine Wool Project, Armidale, Australia. Data on wool characteristics, measured at ~10 and 22 months of age, bodyweight and several reproduction traits across consecutive lambing opportunities were analysed. The genetic correlations were moderately negative between fibre diameter measured as yearling and adult, and lamb survival (rg = –0.34 ± 0.15 and rg = –0.28 ± 0.14 respectively) and total number of lambs weaned (rg = –0.32 ± 0.21 and rg = –0.40 ± 0.21 respectively). The genetic correlations of yearling and adult greasy and clean fleece weights with number of lambs weaned and fecundity showed moderately to highly negative relationships and a moderately negative correlation with the number of fetuses at pregnancy scanning. Phenotypic correlations between reproduction and wool production traits were estimated to be zero, with the exception of bodyweight showing low to moderate positive phenotypic correlations with total number of lambs born and weaned. Genetic variances were generally low for the reproduction traits and resulted in low heritability estimates (from h2 = 0.03 ± 0.01 to h2 = 0.12 ± 0.13), with the exception of total number of lambs born (h2 = 0.25 ± 0.03). The study indicated that parameter estimation and trait definition of lifetime reproduction records require careful consideration and more work in this area is required.

One-hour portable chamber methane measurements are repeatable and provide useful information on feed intake and efficiency

Feed intake (FI), live weight (LW), and ADG were recorded over 31 d in ninety-six 12-month-old ewes (progeny of 4 sires) given ad libitum access to chaffed lucerne/cereal hay. Methane (CH) and CO emissions of each ewe were measured for 40 to 60 min in portable accumulation chambers (PAC) and in respiration chambers (RC) over 22 h. Testing in RC increased the variability of FI on the test day and depressed the amount eaten from an average of 1,384 to 1,062 g/d; FI depression increased by 0.63 ± 0.24 percentage points for every kilogram of additional LW. Repeatabilities of PAC measurements were 0.76 (CH) and 0.81 (CO). After adjusting for LW and ADG, repeatabilities were 0.47 (PAC CH) and 0.43 (PAC CO). Daily FI measurements had similar repeatability (0.76 before and 0.42 after adjustment for LW and ADG). The PAC measurements were highly correlated with mean 31-d FI ( = 0.81 for both CH and CO). After adjustment for LW and ADG, PAC measurements were moderately correlated with residual feed intake (RFI; = 0.37 for CH, 0.31 for CO). The CH:CO ratio was also significantly correlated with mean 31-d FI ( = 0.52). After most of the ewes had given birth and raised lambs, repeat PAC measurements were available for 91 of the ewes at 2 years of age (with ad libitum access to the same feed). Correlations with the 2012 PAC measurements were 0.64 (CH) and 0.75 (CO). After adjusting 2014 PAC measurements for LW, correlations with RFI in 2012 were 0.34 (CH) and 0.33 (CO), with a clear relationship between sire means for RFI in 2012 and PAC CH adjusted for LW in 2014. These results suggest that PAC tests under similar feeding conditions are repeatable over an extended time period and can provide useful information on FI and feed efficiency as well as methane emissions. Analyses of RC measurements might need to consider FI depression.

Estimating the genetic merit of sires by using pooled DNA from progeny of undetermined pedigree

Background

DNA-based predictions for hard-to-measure production traits hold great promise for selective breeding programs. DNA pooling might provide a cheap genomic approach to use phenotype data from commercial flocks which are commonly group-mated with parentage unknown. This study on sheep explores if genomic breeding values for stud sires can be estimated from genomic relationships that were obtained from pooled DNA in combination with phenotypes from commercial progeny.

Methods

Phenotypes used in this study were categorical data. Blood was pooled strategically aiming at even pool sizes and within sex and phenotype category. A hybrid genomic relationship matrix was constructed relating pools to sires. This matrix was used to determine the contribution of sires to each of the pools and therefore phenotype category by using a simple regression approach. Genomic breeding values were also estimated using the hybrid genomic relationship matrix.

Results

We demonstrated that, using pooled DNA, the genetic performance of sires can be illustrated as their contribution to phenotype categories and can be expressed as a regression coefficient. Genomic estimated breeding values for sires were equivalent to the regression coefficients and are a commonly used industry tool.

Conclusions

Genotyping of DNA from pooled biological samples offers a cheap method to link phenotypic information from commercial production animals to the breeding population and can be turned into information on the genetic value of stud sires for traits that cannot be measured in the stud environment.

Impact of young ewe fertility rate on risk and genetic gain in sheep-breeding programs using genomic selection

Genomic selection could be useful in sheep-breeding programs, especially if rams and ewes are first mated at an earlier age than is the current industry practice. However, young-ewe (1 year old) fertility rates are known to be lower and more variable than those of mature ewes. The aim of the present study was to evaluate how young-ewe fertility rate affects risk and expected genetic gain in Australian sheep-breeding programs that use genomic information and select ewes and rams at different ages. The study used stochastic simulation to model different flock age structures and young-ewe fertility levels with and without genomic information for Merino and maternal sheep-breeding programs. The results from 10 years of selection were used to compare breeding programs on the basis of the mean and variation in genetic gain. Ram and ewe age, availability of genomic information on males and young-ewe fertility level all significantly (P &lt; 0.05) affected expected genetic gain. Higher young-ewe fertility rates significantly increased expected genetic gain. Low fertility rate of young ewes (10%) resulted in net genetic gain similar to not selecting ewes until they were 19 months old and did not increase breeding-program risk, as the likelihood of genetic gain being lower than the range of possible solutions from a breeding program with late selection of both sexes was zero. Genomic information was of significantly (P &lt; 0.05) more value for 1-year-old rams than for 2-year-old rams. Unless genomic information was available, early mating of rams offered no greater gain in Merino breeding programs and increased breeding-program risk. It is concluded that genomic information decreases the risk associated with selecting replacements at 7 months of age. Genetic progress is unlikely to be adversely affected if fertility levels above 10% can be achieved. Whether the joining of young ewes is a viable management decision for a breeder will depend on the fertility level that can be achieved in their young ewes and on other costs associated with the early mating of ewes.

Linkage disequilibrium over short physical distances measured in sheep using a high-density SNP chip

The extent of linkage disequilibrium (LD) between genetic loci has implications for both association studies and the accuracy of genomic prediction. To characterise the persistence of LD in diverse sheep breeds, two SNP genotyping platforms were used. First, existing SNP genotypes from 63 breeds obtained using the ovine SNP50 BeadChip (49,034 loci) were used to estimate LD decay in populations with contrasting levels of genetic diversity. Given the paucity of marker pairs separated by short physical distances on the SNP50 BeadChip, genotyping was subsequently performed for four breeds using the recently developed ovine HD BeadChip that assays approximately 600,000 SNPs with an average genomic spacing of 5 kb. This facilitated a highly accurate estimate of LD over short genomic distances (<30 kb) and revealed LD varies considerably between sheep breeds. Further, sheep appear to contain generally lower levels of LD than do other domestic species, likely a reflection of aspects of their past population history.

Genetic and phenotypic parameters between yearling, hoggetand adult reproductive performance and age of first oestrus in sheep

The aims of this study were to quantify the relationship between age of first oestrus and yearling reproductive performance in maternal-cross ewes in the Information Nucleus Flock data and to estimate genetic and phenotypic correlations between early and later reproductive performance defined as three ages, yearling, hogget and adult in both Merino and maternal-cross ewes. Information on 2218 yearling records, 2047 hogget records and 910 age of first oestrus records were used in the analysis of maternal-cross ewes, whereas 3286 hogget and 2518 adult reproductive records were used in analysis of Merino ewes. Heritability estimates for yearling reproductive performance in maternal-cross ewes ranged from 0.08 ± 0.09 for ewe fecundity to 0.16 ± 0.05 for number of lambs born and were generally higher than hogget heritability estimates for both maternal-cross and Merino ewes. Age at first oestrus was found to have a low heritability, 0.02 with standard errors of 0.07 and 0.06 with and without weight fitted as a covariate. Genetic correlations between age at first oestrus with and without weight fitted as a covariate and yearling reproductive performance were positive, ranging from 0.07 ± 0.49 with lamb survival to 0.94 ± 0.39 with number of lambs born, which was unexpected. Correlations between traits from the same age class were high in both breed groups. Genetic correlations between yearling and hogget performance in maternal-cross ewes were generally lower than one, ranging from 0.46 ± 0.68 for lamb survival and 0.79 ± 0.50 for fertility suggesting that yearling and later reproductive performance are related but genetically different traits. In Merino ewes, the genetic correlations between hogget and adult performance followed a similar pattern. The small number of records in this study generated high standard errors for estimates, which restricts the conclusions that can be drawn. Overall, this study supports current practice used by ‘Sheep Genetics’, the Australian genetic evaluation system for sheep, in considering yearling reproductive performance as a trait separate from later parities for genetic evaluation purposes.

Descriptive statistics of data: understanding the data set and phenotypes of interest

A good understanding of the design of an experiment and the observational data that have been collected as part of the experiment is a key pre-requisite for correct and meaningful preparation of field data for further analysis. In this chapter, I provide a guideline of how an understanding of the field data can be gained, preparation steps that arise as a consequence of the experimental or data structure, and how to fit a linear model to extract data for further analysis.

Chromosomal differences between European and North American Atlantic salmon discovered by linkage mapping and supported by fluorescence in situ hybridization analysis

Background

Geographical isolation has generated a distinct difference between Atlantic salmon of European and North American Atlantic origin. The European Atlantic salmon generally has 29 pairs of chromosomes and 74 chromosome arms whereas it has been reported that the North American Atlantic salmon has 27 chromosome pairs and an NF of 72. In order to predict the major chromosomal rearrangements causing these differences, we constructed a dense linkage map for Atlantic salmon of North American origin and compared it with the well-developed map for European Atlantic salmon.

Results

The presented male and female genetic maps for the North American subspecies of Atlantic salmon, contains 3,662 SNPs located on 27 linkage groups. The total lengths of the female and male linkage maps were 2,153 cM and 968 cM respectively, with males characteristically showing recombination only at the telomeres. We compared these maps with recently published SNP maps from European Atlantic salmon, and predicted three chromosomal reorganization events that we then tested using fluorescence in situ hybridization (FISH) analysis. The proposed rearrangements, which define the differences in the karyotypes of the North American Atlantic salmon relative to the European Atlantic salmon, include the translocation of the p arm of ssa01 to ssa23 and polymorphic fusions: ssa26 with ssa28, and ssa08 with ssa29.

Conclusions

This study identified major chromosomal differences between European and North American Atlantic salmon. However, while gross structural differences were significant, the order of genetic markers at the fine-resolution scale was remarkably conserved. This is a good indication that information from the International Cooperation to Sequence the Atlantic salmon Genome, which is sequencing a European Atlantic salmon, can be transferred to Atlantic salmon from North America.

Estimating the effect of SNP genotype on quantitative traits from pooled DNA samples

Background

Studies to detect associations between DNA markers and traits of interest in humans and livestock benefit from increasing the number of individuals genotyped. Performing association studies on pooled DNA samples can provide greater power for a given cost. For quantitative traits, the effect of an SNP is measured in the units of the trait and here we propose and demonstrate a method to estimate SNP effects on quantitative traits from pooled DNA data.

Methods

To obtain estimates of SNP effects from pooled DNA samples, we used logistic regression of estimated allele frequencies in pools on phenotype. The method was tested on a simulated dataset, and a beef cattle dataset using a model that included principal components from a genomic correlation matrix derived from the allele frequencies estimated from the pooled samples. The performance of the obtained estimates was evaluated by comparison with estimates obtained using regression of phenotype on genotype from individual samples of DNA.

Results

For the simulated data, the estimates of SNP effects from pooled DNA are similar but asymptotically different to those from individual DNA data. Error in estimating allele frequencies had a large effect on the accuracy of estimated SNP effects. For the beef cattle dataset, the principal components of the genomic correlation matrix from pooled DNA were consistent with known breed groups, and could be used to account for population stratification. Correctly modeling the contemporary group structure was essential to achieve estimates similar to those from individual DNA data, and pooling DNA from individuals within groups was superior to pooling DNA across groups. For a fixed number of assays, pooled DNA samples produced results that were more correlated with results from individual genotyping data than were results from one random individual assayed from each pool.

Conclusions

Use of logistic regression of allele frequency on phenotype makes it possible to estimate SNP effects on quantitative traits from pooled DNA samples. With pooled DNA samples, genotyping costs are reduced, and in cases where trait records are abundant this approach is promising to obtain SNP associations for marker-assisted selection.

Design and phenotyping procedures for recording wool, skin, parasite resistance, growth, carcass yield and quality traits of the SheepGENOMICS mapping flock

A major aim of the research program known as SheepGENOMICS was to deliver DNA markers for commercial breeding programs. To that end, a resource flock was established, comprehensively phenotyped and genotyped with DNA markers. The flock of nearly 5000 sheep, born over two consecutive years, was extensively phenotyped, with more than 100 recorded observations being made on most of the animals. This generated more than 460 000 records over 17 months of gathering information on each animal. Here, we describe the experimental design and sample-collection procedures, and provide a summary of the basic measurements taken. Data from this project are being used to identify collections of genome markers for estimating genomic breeding values for new sheep industry traits.

Accuracy of estimated genomic breeding values for wool and meat traits in a multi-breed sheep population

Estimated breeding values for the selection of more profitable sheep for the sheep meat and wool industries are currently based on pedigree and phenotypic records. With the advent of a medium-density DNA marker array, which genotypes ~50 000 ovine single nucleotide polymorphisms, a third source of information has become available. The aim of this paper was to determine whether this genomic information can be used to predict estimated breeding values for wool and meat traits. The effects of all single nucleotide polymorphism markers in a multi-breed sheep reference population of 7180 individuals with phenotypic records were estimated to derive prediction equations for genomic estimated breeding values (GEBV) for greasy fleece weight, fibre diameter, staple strength, breech wrinkle score, weight at ultrasound scanning, scanned eye muscle depth and scanned fat depth. Five hundred and forty industry sires with very accurate Australian sheep breeding values were used as a validation population and the accuracies of GEBV were assessed according to correlations between GEBV and Australian sheep breeding values . The accuracies of GEBV ranged from 0.15 to 0.79 for wool traits in Merino sheep and from –0.07 to 0.57 for meat traits in all breeds studied. Merino industry sires tended to have more accurate GEBV than terminal and maternal breeds because the reference population consisted mainly of Merino haplotypes. The lower accuracy for terminal and maternal breeds suggests that the density of genetic markers used was not high enough for accurate across-breed prediction of marker effects. Our results indicate that an increase in the size of the reference population will increase the accuracy of GEBV.

Genetic resistance to growth of Lucilia cuprina larvae in Merino sheep

Cutaneous myiasis (fly strike), caused by Lucilia cuprina, is a major ectoparasitic infection of sheep. Previous research has identified contributions of body conformation, wool characteristics and resistance to bacterial dermatoses to resistance to fly strike. This paper investigates whether genetic variation occurs amongst sheep in growth of larvae on skin. Mixed sex Merino sheep in 27 half-sibling groups were challenged with freshly hatched Lucilia cuprina larvae, and survival and growth of larvae were measured after 50 h. Growth but not survival of larvae had moderate heritability (0.29 ± 0.22), comparable to that seen for resistance to nematode parasites in sheep. Phenotypic correlations between resistance to larval growth and wool traits, skin wheal response to intradermal injection of larval excretory secretory products and resistance to internal parasites were negligible; however, there was a significant negative phenotypic correlation with fleece rot score after exposure of sheep to simulated rain at a time independent to that of measurement of larval growth. Larval growth was negatively correlated with peripheral blood eosinophil numbers measured either before or after larval challenge. In addition, larval growth in vitro on serum collected from challenged sheep was moderately associated with larval growth in vivo. A search for quantitative trait loci (QTL) for larval survival and growth was conducted in data from 94 half-sibling progeny of a Merino × Romney sire backcrossed to Merino ewes. Potential QTL for larval growth were identified on chromosome 11 and for larval survival on chromosome 18, although phenotyping greater numbers of sheep and a higher marker density on these chromosomes is necessary to confirm the result. We conclude that this study has identified a novel level of resistance of Merino sheep to growth of L. cuprina larvae that may be mediated in part through actions of anti-larval factors in serum and eosinophils. Further studies are required to establish the impact of growth retardation on the severity of systemic responses of sheep to fly strike and on the biology of adult flies.

Factors influencing the efficiency of a marker-assisted introgression programme in Merino sheep

This study investigated a marker-assisted introgression programme in Australian Merino sheep. The goal was to introgress an allele with a large negative effect on fibre diameter into a Merino flock possessing medium average fibre diameter. The influence of two factors was explored: the strategy used to select animals from the purebred and backcross line for backcrossing purposes and the use of selection on background markers to accelerate the return to the purebred line's genome. The results were compared to introgression based on EBVs only. Introgression using EBVs only produced almost the same response in the dollar index as marker-based introgression methods. However, this study did not account for some of the costs associated with implementing the programmes, including the costs of phenotyping and genotyping. Given that the cost of measuring fibre diameter is low, it was concluded that introgression on EBVs only would be the preferred method since the marginal profit of marker-assisted introgression would not be large enough to cover the additional cost of genotyping. In marker-assisted introgression, reciprocal crossing of male and female selection candidates from the backcross and the purebred line was the most advantageous strategy from a practical and profit point of view. Selection for background markers was less profitable in this study than recovering the donor genome by selection on phenotype.

Adjusting worm egg counts for faecal moisture in sheep

The number of eggs from gastrointestinal nematodes per gram of faeces (worm egg count WEC) is commonly used to determine the need for anti-parasite treatments and the breeding value of animals when selecting for worm resistance. Diarrhoea increases faecal moisture and may dilute the number of worm eggs observed. To quantify this effect, egg counts in sheep at pasture were simulated by dosing 15 animals with chromic oxide particles. The simulated WEC diminished as faecal moisture increased. When faeces were dried, simulated WEC per unit dry matter was not influenced by the amount of faecal moisture present prior to drying. The results suggest that adjustment for faecal moisture may provide an improved estimate of FEC. Drying faeces to calculate the WEC per unit dry matter would provide such an adjustment but may not be practical for industry application. In the past, the CSIRO McMaster Laboratory has used an adjustment factor developed by Gordon based on the classification of faecal consistency derived from the morphology of faeces. To examine the utility of an adjustment factor based on faecal consistency score (FCS), the relationships between FCS and simulated WEC and dry matter were examined. Dry matter and simulated WEC exhibited an exponential decline as FCS increased. The relationship between FCS and dry matter was further examined in 368 samples collected over 12 months from sheep at pasture, where it was observed that dry matter showed a linear decline as FCS increased. Adjustment factors based on dry matter were similar to those proposed by Gordon however adjustment factors predicted from simulated WEC diverged from the remainder for FCS>4. As no samples scored FCS 5 in the study of simulated FEC, the adjustment factors based on the larger study that included samples with FCS 5 was therefore considered more robust. Adjustment factors were given by the equation: WEC(estimated)=(WEC(observed)/(34.21-5.15 FCS))x29.06. This equation estimates for samples with FCS>1 the WEC that would be expected if the samples were FCS 1, the faecal consistency score for normal faeces. The impact of adjustment of observed WEC for faecal moisture predicted by FCS on decision points for treatment and on estimated breeding values requires further examination.

Quantitative trait loci for internal nematode resistance in sheep: a review

Internal nematode resistance in sheep has a large impact on the economy of sheep industries. Selection for nematode resistance in sheep breeding schemes would help to reduce the direct and indirect cost of parasitism to these industries. However, this is not widely practiced because of the difficulty of measuring parasite resistance or correlated indirect selection criteria. The identification of genes or linked markers that have a significant association with the variance of indicator traits of internal nematode resistance in sheep would facilitate the inclusion of nematode resistance in sheep breeding operations. This review summarises findings reported in the literature of quantitative trait loci for internal nematode resistance in sheep. Issues relating to the analytical and phenotypic complexity of nematode resistance are discussed in the context of the findings of quantitative trait loci for nematode resistance published to date.

Metastatic choriocarcinoma in a postmenopausal woman

Trophoblastic disease is usually related to pregnancy and occurs in about 1 in 1300 pregnancies in Western countries. Since the advent of methotrexate therapy, trophoblastic tumors have become one of the most curable malignancies. Trophoblastic disease can develop independently of gestation, but this is very rare. We report the unusual case of a 58-year-old woman who had a metastatic choriocarcinoma 6 years after menopause and 29 years after her last pregnancy. The tumor proved to be primarily resistant to monochemotherapy and developed chemoresistance to three different polychemotherapeutic regimens. Eleven months after the diagnosis of uterine choriocarcinoma the patient died from advanced metastatic disease.

[The advantages of CO2 laser use in treatment of cervix dysplasia]

We use two kinds of laser treatment, namely, laser vaporisation and laser excision conisation. Laser vaporisation is a widely used method of localised ablative treatment based on both histologically confirmed cervical intraepithelial neoplasia and clear colposcopic visualisation of the upper limit of the lesion. Laser excision conisation is performed, if cervical intraepithelial neoplasia reaches the endocervix, being out of colposcopic view, and the squamocolumnar junction is localised in the endocervical canal. 116 patients with cervical intraepithelial neoplasia were treated with the CO2 laser. 81 (70%) were subjected to laser vaporisation, 35 (30%) to laser excision conisation. Intraoperative bleeding was rarely seen. After laser vaporisation, no complications were observed, but laser excision conisation complications occurred in one patient who developed postoperative cervical stenosis, and in another patient, who had postoperative bleeding requiring surgical examination. Follow-up with colposcopy and cytologic smears was carried out every 6 months. Recurrence of disease 6 months or later after laser treatment was seen in 6 patients (7.4%) after laser vaporisation and in 2 patients (5.7%) after laser excision conisation. This report shows the advantages of the carbon dioxide laser in comparison to cold knife conisation in the treatment of cervical intraepithelial neoplasia.