Including genomic information in the genetic evaluation of production and reproduction traits in South African Merino sheep

Genomic selection (GS) has become common in sheep breeding programmes in Australia, New Zealand, France and Ireland but requires validation in South Africa (SA). This study aimed to compare the predictive ability, bias and dispersion of pedigree BLUP (ABLUP) and single-step genomic BLUP (ssGBLUP) for production and reproduction traits in South African Merinos. Animals in this study originated from five research and five commercial Merino flocks and included between 54,072 and 79,100 production records for weaning weight (WW), yearling weight (YW), fibre diameter (FD), clean fleece weight (CFW) and staple length (SL). For reproduction traits, the dataset included 58,744 repeated records from 17,268 ewes for the number of lambs born (NLB), number of lambs weaned (NLW) and the total weight weaned (TWW). The single-step relationship matrix, H, was calculated using PreGS90 software combining 2811 animals with medium density (~50 K) genotypes and the pedigree of 88,600 animals. Assessment was based on single-trait analysis using ASREML V4.2 software. The accuracy of prediction was evaluated according to the 'LR-method' by a cross-validation design. Validation candidates were assigned according to Scenario I: born after a certain time point; and Scenario II: born in a particular flock. In Scenario I, the genotyping rate for the reference population between 2006 and the 2013 cut-off point approached 7% of animals with phenotypes and 20% of their sires. For reproduction traits, about 20% of ewes born between 2006 and 2011 cut-off were genotyped, along with 15% of their sires. Genotyping rates in the validation set of Scenario I were 3.7% (production) and 11.4% (reproduction) for candidates and 35% of their sires. Sires were allowed to have progeny in both the reference and validation set. In Scenario I, ssGBLUP increased the accuracy of prediction for all traits except NLB, ranging between +8% (0.62-0.67) for FD and +44% (0.36-0.52) for WW. This showed a promising gain in accuracy despite a modestly sized reference population. In the 'across flock validation' (Scenario II), overall accuracy was lower, but with greater differences between ABLUP and ssGBLUP ranging between +17% (0.12-0.14) for TWW and +117% (0.18-0.39) for WW. There was little indication of severe bias, but some traits were prone to over dispersion and the use of genomic information did not improve this. These results were the first to validate the benefit of genomic information in South African Merinos. However, because production traits are moderately heritable and easy to measure at an early age, future research should be aimed at best exploiting GS methods towards genetic prediction of sex-limited and/or lowly heritable traits such as NLW. GS methods should be combined with dedicated efforts to increase genetic links between sectors and improved phenotyping by commercial flocks.

Genetics of the phenotypic evolution in sheep: a molecular look at diversity-driving genes

BACKGROUND

After domestication, the evolution of phenotypically-varied sheep breeds has generated rich biodiversity. This wide phenotypic variation arises as a result of hidden genomic changes that range from a single nucleotide to several thousands of nucleotides. Thus, it is of interest and significance to reveal and understand the genomic changes underlying the phenotypic variation of sheep breeds in order to drive selection towards economically important traits.

REVIEW

Various traits contribute to the emergence of variation in sheep phenotypic characteristics, including coat color, horns, tail, wool, ears, udder, vertebrae, among others. The genes that determine most of these phenotypic traits have been investigated, which has generated knowledge regarding the genetic determinism of several agriculturally-relevant traits in sheep. In this review, we discuss the genomic knowledge that has emerged in the past few decades regarding the phenotypic traits in sheep, and our ultimate aim is to encourage its practical application in sheep breeding. In addition, in order to expand the current understanding of the sheep genome, we shed light on research gaps that require further investigation.

CONCLUSIONS

Although significant research efforts have been conducted in the past few decades, several aspects of the sheep genome remain unexplored. For the full utilization of the current knowledge of the sheep genome, a wide practical application is still required in order to boost sheep productive performance and contribute to the generation of improved sheep breeds. The accumulated knowledge on the sheep genome will help advance and strengthen sheep breeding programs to face future challenges in the sector, such as climate change, global human population growth, and the increasing demand for products of animal origin.

Genetic parameters of breech strike, neck wrinkles, dags and breech cover over the lifetime of crutched Merino ewes in a Mediterranean environment

Aims This study was undertaken to estimate the genetic parameters of breech strike and its indicator traits over the lifetime of crutched Merino ewes in a Mediterranean environment. Methods Breech strike records were collected on 3993 ewes over their lifetime where they were annually crutched. The ewes were scored at different times of the year for neck wrinkle, dag score and breech cover over their lifetime. A total of 13 577 breech strike records from birth up to 5 years of age were generated between 2006 and 2017. Face cover was only scored mid-year. Mixed model methodologies were used to estimate the genetic parameters of the different traits at different ages. Key results Breech strike was heritable (h2) and repeatable (t) on the observed scale (h2 = 0.07 ± 0.01; t = 0.13 ± 0.01), and as a binary trait on a logistic scale (h2 = 0.51 ± 0.10; t = 0.68 ± 0.10). Breech strike was genetically positively correlated across ages. Positive genetic correlations were found between breech strike and the indicator traits of neck wrinkle, face cover, breech cover and dags. Neck wrinkle and face cover, as well as breech cover and dag scored at different times of the year, were heritable and repeatable. Although high genetic correlations were found between different ages for neck wrinkle and post-shearing breech cover, these traits are not genetically the same traits at different ages. However, breech cover scored mid-year, before shearing and after shearing are genetically the same trait. The genetic relationship between dag at different ages is unclear as a moderate positive genetic correlation (rg = 0.25 ± 0.12) was found between hoggets and 2-year-old ewes, whereas a moderate negative correlation (rg = –0.30 ± 0.14) was found between 3- and 4-year-old ewes. The genetic correlations amongst the dag traits in older age groups were not significantly different from zero. Conclusions Breech strike and its indicator traits (i.e. neck wrinkle, breech cover, face cover and dags) were all heritable. Breech strike appears to be genetically strongly correlated across ages, however, the correlations had large standard errors. It was positively correlated with the indicator traits. Moderate to strong genetic correlations were found between ages for neck wrinkle and for breech cover. Dags, however, were poorly correlated across ages, indicating that dags are not genetically the same trait in mature ewes at different ages. Implications This study shows that selecting ewes for low breech strike, and for reduced neck wrinkle, lower breech cover and less dags will reduce breech strike in mature Merino ewes in future generations. However, as the phenotypic correlations were relatively low, culling ewes on these indicator traits will result in little gain in the current generation. It appears that dags at different ages is not genetically the same trait. Thus the benefit of selecting or culling ewes on dags will not be carried over to subsequent ages.

Modelling of breech strike risk and protective efficacy of mulesing in adult Merino sheep

Context Mulesing provides a high degree of protection against beech strike, but wool producers need to be able to predict the level of risk of flystrike if they cease mulesing. Aims To use data from trials of mulesed and unmulesed sheep to estimate the distribution of adult breech scores (wrinkle, breech cover and dag) from mean flock values, and use those scores to estimate the risk of breech strike in Merino sheep flocks. Methods Breech scores and breech strike from flocks with comparable mulesed and unmulesed sheep were examined using logistic functions to relate breech scores in mulesed sheep to those in unmulesed sheep, and to estimate the risk of breech strike in sheep for any given combination of breech scores. Key results Functions are given to estimate whole flock adult breech wrinkle and breech cover using combinations of the breech traits that are available. Unmulesed Merino sheep have a 6-fold increased risk of breech strike compared with mulesed sheep under the same conditions. There were increased relative risks of breech strike of 2.0 for each unit increase in dag score, 2.2 for each unit increase in breech wrinkle score and 1.7 for each unit increase in breech cover score. Mulesing reduced each of these risk factors, but had an additional 3.2-fold benefit independent of these factors. Adult breech wrinkle was most reliably estimated from neck wrinkle or from marking breech wrinkle (before mulesing). Breech cover was estimated from face cover, or from marking breech cover. The risk of breech strike if adult sheep were to be left unmulesed in a commercial flock was predicted using a centred log ratio transformation to estimate the distribution of dag scores in the unmulesed sheep, given the actual distribution in the mulesed flock. If the distribution was not known, then the mean dag score of the mulesed sheep could be used to estimate the distribution of dag scores in unmulesed sheep using a 2/3 power function to transform the mean dag score. Conclusions A flock of unmulesed sheep would need to lower breech wrinkle, breech cover and dag scores by 0.5 for each score to achieve a comparable level of risk of breech strike in mulesed sheep. Implications The use of the model will allow wool producers to selectively breed for sheep with lower risk of breech strike, while continuing to mules the sheep as long as it is necessary to do so. They will be able to estimate what the risk of strike would be if they cease mulesing, due to the proportion of sheep with potentially high wrinkle score, high breech cover or high dag scores at any stage of their breeding program.

Are breech strike, dags and breech wrinkle genetically the same trait in crutched, uncrutched and mulesed Merino sheep?

Breech strike is caused by the infestation of maggots from Lucilia cuprina on the skin of susceptible sheep. Crutching and mulesing modify the potential expression of breech strike, because crutched and mulesed sheep have a lower risk of being struck than uncrutched sheep. The inheritance of and genetic correlations among breech strike from birth to hogget shearing, and dags (breech soiling) and skin wrinkles scored at yearling age were estimated in unmulesed and crutched, unmulesed and uncrutched, and in mulesed and uncrutched Merino sheep to determine whether these traits were genetically the same under these three husbandry systems. The heritability estimates of breech strike in uncrutched, crutched and mulesed sheep were very similar (0.11 ± 0.02, 0.09 ± 0.02 and 0.08 ± 0.05 respectively). Breech strike in uncrutched sheep is genetically strongly correlated with breech strike in crutched sheep (0.80 ± 0.16). The genetic correlation between breech strike in uncrutched and in mulesed sheep was high (0.98 ± 0.40), but the high standard error makes this estimate unreliable. Dags and wrinkles are genetically moderately to strongly correlated with breech strike, which confirms that they are indicator traits for breech strike. Dags in uncrutched sheep was genetically strongly correlated with dags in mulesed sheep (0.84 ± 0.11). Breech wrinkle in uncrutched and crutched sheep, and tail wrinkle in mulesed sheep were not genetically strongly correlated with each other, as the correlations varied between zero and 0.48 (±0.18). The key outcome from this study indicates that all breech strike, wrinkle and dag data in mulesed, crutched or uncrutched flocks may be used in future to estimate a breeding value directly for breech strike.

Sheep death and loss of production associated with flystrike in mature Merino and crossbred ewes

In eight well-managed Australian Merino and crossbred sheep flocks the adult ewes were monitored frequently for flystrike. Occurrences of flystrike and severity of strike scores were recorded, whereas bodyweights and condition scores were recorded regularly across two wool production and reproduction cycles. In these unmulesed flocks, 17% of Merino and 5% of crossbred ewes were struck, with 2% of those struck dead within 7 days of detection of the strike. For those adult ewes that survived the immediate period of the strike, the rate of loss over the following year was slightly greater than for ewes that were never struck, particularly for those with a high severity strike. Flystrike also contributed to losses of up to 2.7 (Merino ewes) and 5.2 (crossbred ewes) kg of bodyweight, and 0.3 condition score units at the time of the strike. Bodyweights were still 2 kg lower by 3 months after the strike occurred for Merinos, although condition scores returned to average levels. For ewes struck between mating and lambing, flystrike was associated with significant losses of lambs. Flystrike at severity level 1 (light) had only minor effects on wool production, but severity score 3 (heavy) reduced clean fleece weight.

FlyBoss: a web-based flystrike information and decision support system

The FlyBoss system consists of comprehensive information on flystrike management and control, programs for assisting decision making, and sortable lists of products for preventing and treating flystrike. Readily accessible, up-to-date, best-practice information on flystrike is essential for effective, humane and economic management of flystrike by Australian wool producers, particularly those who are phasing out mulesing and those looking to adopt optimal insecticidal fly-control strategies. FlyBoss provides information on breeding and management to reduce flystrike susceptibility, effective methods of treating existing flystrike and flystrike prevention programs. The FlyBoss decision aids, which are based on simulation models and incorporate local weather data and sheep susceptibility factors, can assist sheep farmers who wish to optimise sheep management, chemical treatment and non-chemical options to minimise the risk of flystrike. FlyBoss also contains comprehensive information on fly biology, sheep and environmental factors associated with flystrike and information on appropriate chemicals for various situations. FlyBoss draws on expertise from organisations throughout Australia to provide the sheep industry with easily accessible, current and locally targeted information on flystrike management. The present report briefly describes the development of FlyBoss and associated workshops and provides an overview of current recommendations for the control and prevention of flystrike.