Browsing by Department "Animal Genetics and Breeding Unit"

For multivariate, single-step genomic best linear unbiased prediction analyses fitting a breeding value model, it is often assumed that the proportions of total genetic variance accounted for by genomic markers and residual polygenic effects are the same for all traits. Different covariance matrices for the two types of genetic effects are readily taken into account by fitting them separately. However, this can lead to slow convergence rates in iterative solution schemes. We propose an alternative computing strategy which – exploiting a canonical transformation – allows for trait-specific covariances whilst directly fitting total genetic effects only. Its effects on convergence rates and gains in accuracy and bias of genomic evaluation compared to analyses assuming proportionality of covariance matrices are examined using a small simulation study. Results show comparatively little improvement in accuracies but worthwhile reductions in overdispersion of predicted genetic merits for genotyped individuals without phenotypes.

Genomic selection is becoming a standard tool in livestock breeding programs, particularly for traits that are hard to measure. Accuracy of genomic selection can be improved by increasing the quantity and quality of data and potentially by improving analytical methods. Adding genotypes and phenotypes from additional breeds or crosses often improves the accuracy of genomic predictions but requires specific methodology. A model was developed to incorporate breed composition estimated from genotypes into genomic selection models. This method was applied to age at puberty data in female beef cattle (as estimated from age at first observation of a corpus luteum) from a mix of Brahman and Tropical Composite beef cattle. In this dataset, the new model incorporating breed composition did not increase the accuracy of genomic selection. However, the breeding values exhibited slightly less bias (as assessed by deviation of regression of phenotype on genomic breeding values from the expected value of 1). Adding additional Brahman animals to the Tropical Composite analysis increased the accuracy of genomic predictions and did not affect the accuracy of the Brahman predictions.

Accuracy of predicted breeding values (PBV) for low heritability traits may be increased in early generations by exploiting the information available in correlated traits. We compared the accuracy of PBV for 10 correlated traits with low to medium narrow-sense heritability (h²) in a genetically diverse field pea (Pisum sativum L.) population after univariate or multivariate linear mixed model (MLMM) analysis with pedigree information. In the contra-season, we crossed and selfed S₁ parent plants, and in the main season we evaluated spaced plants of S₀ cross progeny and S₂₊ (S₂ or higher) self progeny of parent plants for the 10 traits. Stem strength traits included stem buckling (SB) (h² = 0.05), compressed stem thickness (CST) (h² = 0.12), internode length (IL) (h² = 0.61) and angle of the main stem above horizontal at first flower (EAngle) (h² = 0.46). Significant genetic correlations of the additive effects occurred between SB and CST (0.61), IL and EAngle (−0.90) and IL and CST (−0.36). The average accuracy of PBVs in S₀ progeny increased from 0.799 to 0.841 and in S₂₊ progeny increased from 0.835 to 0.875 in univariate vs MLMM, respectively. An optimized mating design was constructed with optimal contribution selection based on an index of PBV for the 10 traits, and predicted genetic gain in the next cycle ranged from 1.4% (SB), 5.0% (CST), 10.5% (EAngle) and −10.5% (IL), with low achieved parental coancestry of 0.12. MLMM improved the potential genetic gain in annual cycles of early generation selection in field pea by increasing the accuracy of PBV.

Background Hoof structure and health are essential for the welfare and productivity of beef cattle. Therefore, we assessed the genetic and genomic background of foot score traits in American (US) and Australian (AU) Angus cattle and investigated the feasibility of performing genomic evaluations combining data for foot score traits recorded in US and AU Angus cattle. The traits evaluated were foot angle (FA) and claw set (CS). In total, 109,294 and ~1.12 million animals had phenotypic and genomic information, respectively. Four sets of analyses were performed: (1) genomic connectedness between US and AU Angus cattle populations and population structure, (2) estimation of genetic parameters, (3) single-step genomic prediction of breeding values, and (4) single-step genome-wide association studies for FA and CS.

Results There was no clear genetic differentiation between US and AU Angus populations. Similar heritability estimates (FA: 0.22–0.24 and CS: 0.22–0.27) and moderate-to-high genetic correlations between US and AU foot scores (FA: 0.61 and CS: 0.76) were obtained. A joint-genomic prediction using data from both populations outperformed within-country genomic evaluations. A genomic prediction model considering US and AU datasets as a single population performed similarly to the scenario accounting for genotype-by-environment interactions (i.e., multiple-trait model considering US and AU records as different traits), even though the genetic correlations between countries were lower than 0.80. Common signifcant genomic regions were observed between US and AU for FA and CS. Signifcant single nucleotide polymorphisms were identifed on the Bos taurus (BTA) chromosomes BTA1, BTA5, BTA11, BTA13, BTA19, BTA20, and BTA23. The candidate genes identified were primarily from growth factor gene families, including FGF12 and GDF5, which were previously associated with bone structure and repair.

Conclusions This study presents comprehensive population structure and genetic and genomic analyses of foot scores in US and AU Angus cattle populations, which are essential for optimizing the implementation of genomic selection for improved foot scores in Angus cattle breeding programs. We have also identified candidate genes associated with foot scores in the largest Angus cattle populations in the world and made recommendations for genomic evaluations for improved foot score traits in the US and AU.

The genetic basis of polled or horned phenotypes in beef cattle is now well documented, however horned animals will continue to be born in the national herd for some time. Animal welfare will continue to be compromised due to the need to dehorn animals with horn buds. While scurs don’t necessarily require removal, the inability to distinguish between horned or scurred animals at the age of dehorning mean they are dehorned nonetheless. Targeted breeding of polled herds in industry is increasing with genetic poll tests available, but without understanding the genetic basis of scurs, horn buds and thus dehorning practices will remain. The difficulty in identifying the genetic basis of scurs remains the lack of a reference population with accurate phenotypes, driven largely by the difficulty in phenotypinghorns and scurs at usual dehorning age. This paper describes the challenges and preliminary results of a phenotyping project using the Southern Multibreed project herd, which will form a reference population with poll/horn/scur phenotypes, accompanied by full pedigree recording and genomics data.

571 females from six beef breeds (Angus, Brahman, Charolais, Hereford, Shorthorn and Wagyu) from the first cohort of the Southern MultiBreed project were recorded for fertility traits at different physiological stages up until their second mating. Traits included age at puberty, days to calving and days to return to oestrus following first calving. Sire least-square means for these traits were used to examine relationships between traits. There was a strong positive relationship between age at puberty and days to calving, indicating that sires whose progeny reached puberty at a later age also conceived and calved later. There was a weaker positive relationship between age at puberty and return to oestrus indicating that sires whose progeny reached puberty at a later age also took longer to return to oestrus after the birth of their first calf. A weak negative relationship between days to calving and return to oestrus indicates that sires whose progeny calved later in the calving season exhibited a quicker return to oestrus. The nature of the relationship between these two traits was unexpected given previous studies, and further analyses once data from other years/cohorts is available will be required to gain confidence in the nature of the relationships between these three traits.

This AgGuide, Products of the hive, is about more than honey production. The complex behaviour of bees results in other products such as wax, pollen, propolis, royal jelly and, for older bees, bee venom. There is a range of possibilities for beekeepers to consider when it comes to overall profitability of keeping honey bees.

This book has been compiled for experienced beekeepers to give them ideas about how they might diversify their income from beekeeping activities. It has also been written for those who have a general interest and fascination with the art and pleasure of beekeeping. It includes an account of increased knowledge about the bioactivity of honey.