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The present work presents physical laboratory measurements of surface elevation and pore water pressures in a fine sand bed under bichromatic waves in a large‐scale laboratory experiment. This was done at three cross‐shore locations in the swash zone, with pressures being measured at different depths in the bed. The measurements show that the pore pressure signal decays and shifts with increased depth. These measurements are used to validate a practical model, based on the theory of Yamamoto et al. (1978, https://doi.org/10.1017/S0022112078003006) and Guest and Hay (2017, https://doi.org/10.1002/2016JC012257). The model corresponds well with the measurements (nRMSE < 0.2 and R2 > 0.95 for most probes) and shows that a frequency‐based model can reproduce the pressures in the bed, despite the bed being exposed during dry periods. Furthermore, the model provides the opportunity to calculate pressure gradients, both throughout the bed and at the bed surface. These modeled pressure gradients at the bed surface show that the vertical pressure gradient can have an important impact on the Shields parameter, thereby influencing sediment transport. Plain Language Summary: When waves run up and down the beach they can influence the pressure in the sand. In this work, we have measured pressures in the beach at different depths. A difference in pressure at different depths can lead to forces on the sand particles which make it easier or harder for the sand to move. The results show that at deep locations, the pressure varies slowly and a little later compared with pressures close to the beach surface. We also calculated the pressures with a model, which could predict the measured pressures very well. The model also shows that large differences in pressure exist at the bed surface. Key Points: New field‐scale laboratory measurements of pore pressures in the swash zone in a fine sand bed have been conductedAn analytical model based on Fourier decomposition models the pore pressures and gradients wellThe vertical pressure gradient can have an important impact on the Shields parameter, thereby influencing sediment transport [ABSTRACT FROM AUTHOR]

Model Predictive Control (MPC) of Urban Drainage Systems (UDS) has been established as a cost‐effective method to reduce pollution. However, the operation of large UDS (containing over 20 actuators) can only be optimized by oversimplifying the UDS dynamics, potentially leading to a decrease in performance and reduction in users' trust, thus inhibiting widespread implementation of MPC procedures. A Heuristic And Predictive Policy (HAPPy) was set up, relying on the dynamic selection of the actuators with the highest impact on the UDS functioning and optimizing those in real‐time. The remaining actuators follow a pre‐set heuristic procedure. The HAPPy procedure was applied to two separate UDS in Rotterdam with the control objective being the minimization of overflow volume in each of the two cases. Results obtained show that the level of impact of the actuators on the UDS functioning changes during an event and can be predicted using a Random Forest algorithm. These predictions can be used to provide near‐global optimal actuator settings resulting in the performance of the HAPPy procedure that is comparable to a full‐MPC control and outperforming heuristic control procedures. The number of actuators selected to obtain near‐global optimal settings depends on the UDS and rainfall characteristics showing an asymptotic real‐time control (RTC) performance as the number of actuators increases. The HAPPy procedure showed different RTC dynamics for medium and large rainfall events, with the former showing a higher level of controllability than the latter. For medium events, a relatively small number of actuators suffices to achieve the potential performance improvement. Key Points: The relative impact of actuators on the performance of real‐time control strategies changes during and in‐between eventsDynamically selecting actuators for optimization can ensure near‐global optimal control for urban drainage systemsUsing random forest algorithms, the most influential actuators can be selected in real‐time [ABSTRACT FROM AUTHOR]

Dr Helen Newton-Turner introduced a powerful model of bringing science into practice by working closely with breeders and the wider industry. This collaboration model has led to considerable achievements in genetic improvement in the Australian animal industries, with efficient genetic evaluation systems being implemented, providing a platform to achieve well defined breeding objectives and the introduction of new technologies such as genomic selection. The same model can be used to foster future development to achieve sustainable further improvements, allowing further technologies such as functional genomics to be used where they add value. This paper was prepared by Professor Julius van der Werf, the 2021 recipient of the Helen Newton-Turner Medal. Julius was awarded the medal for his outstanding contribution to genetic improvement of Australian livestock. [ABSTRACT FROM AUTHOR]

Context: Coping with high levels of cold stress should be beneficial to survival of lambs, given the high mortality rate associated with severe winter storms. The Elsenburg Merino selection experiment involved divergent selection for reproduction. Phenotypic results comparing the positively selected H-Lines and negatively selected L-Lines suggested that cold-stress adaption could have contributed to the favourable genetic trends for survival of H-Line lambs. However, observing the genetic merit of better adapted animals depends on the presence of cold stress at the time of recording. A genotype by environment component (G × E) could, thus, be important when assessing survival/mortality phenotypes. Aim: This study proposed the genetic analysis of this possible G × E component and compared the H- and L-Lines in this regard. Methods: The sire model allowed the use of progeny phenotypes for neonatal mortality recorded during different levels of cold stress, and the possible G × E could be investigated through the reaction-norm approach. Genetic parameters were evaluated as random regression components by implementing a Gibbs sampling approach. A data set of 5723 individual lamb records was analysed as the progeny of 213 sires. Results: A modelled G × E component played an important role in mortality outcomes, with the mean estimate (and 95% confidence interval) for the slope ( σ s b 2 = 0.113 [ 0.0019 – 0.28 ] AN22464_IE1.gif) only marginally smaller than the corresponding estimate for the intercept ( σ s a 2 = 0.124 [ 0.003 – 0.26 ] AN22464_IE2.gif). The reaction-norm model showed a higher heritability (h 2 ± posterior standard deviation) for mortality at 3 days of age during high cold-stress (0.22 ± 0.16 at ~1100 KJm−2h−1) than during mild (0.13 ± 0.10 at ~960 KJm−2h−1) conditions, suggesting a greater ability to discriminate between sires at increasing stress levels. Conclusions: Failure to account for this G × E component putatively contributes to the low h 2 commonly reported for survival traits. The higher h 2 at increased levels of cold stress could have played an important part in the higher survival of the H-Line progeny, who were better at coping with cold, wet and windy conditions. Implications: Larger studies representing a wider environmental trajectory are recommended. This should be very feasible since cold stress can be derived from commonly available weather-station data. Animals better adapted to cope with cold stress conditions should have higher survival rates, but the merit of these animals would not be visible under mild conditions. Accounting for the level of cold stress in the earliest days after birth allows for new ways to evaluate the genetic merit of survival or mortality traits. Cold-stress adaption is likely to have been an important part of the very favourable survival rate of the Elsenburg Merino H-Line. [ABSTRACT FROM AUTHOR]

Urban areas are constantly developing and thereby affect the local water cycle. Real‐time control (RTC) strategies are used to operate urban drainage systems optimally during these transitions. This paper aims to develop a methodology to study the impacts of common gradual changes occurring in the urban environment (densification of the urban area and implementation of blue‐green infrastructure), forming cumulative transitions, on the functioning of real‐time optimization procedures. A new generic methodology, relying on a comprehensive evaluation strategy based on three indicators assessing the continued optimal performance of RTC was proposed. This methodology was applied to two urban drainage catchments in Eindhoven and Rotterdam using both probabilistic and projected transitional paths. Based on the results obtained it can be noted that the performances of the RTC procedures were not strongly affected by the modeled transitions although the relative performance compared to the maximum performance potential decreases significantly with the large‐scale implementation of blue‐green infrastructure, indicating that the revision of RTC procedures could improve the sewer system functioning further. The relative performance loss associated with the modeled transitions was higher for model predictive control compared to heuristic RTC procedures for one case study and vice versa for the other. Continuous re‐evaluation of the RTC strategy is, therefore, an important but overlooked part of the implementation of RTC procedures. Key Points: Urban transitions are modeled to assess the effect on optimal control (RTC) efficacyStrong divergence from optimality was associated with SUDS implementationLong‐term implementation of RTC should include a regular re‐evaluation of the strategy [ABSTRACT FROM AUTHOR]

Coursework masters degrees in Australia have experienced rapid, decentralised growth since deregulation at the end of the 1980s. The result is an extraordinarily high level of diversity and some confusion as to standards, strategic positioning, purpose and educational approaches. Throughout this period of growth, a sense that large-scale (often distance-education based) collaboration between universities and with industry would be beneficial has not always led to successful outcomes. Using a new collaborative, industry-funded postgraduate coursework program as a case study, this paper describes the issues that decision-makers need to address and evaluates the challenges and benefits of the coursework masters in higher education. The outcomes of industry surveys, student interviews and action research suggest that postgraduate coursework can facilitate technology transfer and aid capacity building, through mechanisms similar to "mode 2" research. With some additional systems to ensure sustainability and standards, this could position coursework masters to be uniquely valuable nationally.

Context: Genetic evaluation of Australian sheep is conducted for millions of animals for more than 100 traits. Currently, the Australian sheep genetic-analysis software (OVIS) applies a pre-adjustment of phenotype for fixed effects rather than fitting all fixed and random effects jointly in a linear mixed model to estimate breeding values. However, the current correction factors might be outdated and potential interactions among fixed effects not accounted for, which could lead to bias in estimated breeding values (EBVs). Aims: This study aimed to assess whether correction factors used in OVIS for early bodyweights recorded in meat sheep breeds are appropriate, so as to explore whether the pre-adjustment method is still suitable and how this compares with a linear mixed model, and to estimate the significance of interactions between fixed effects. Methods: Correlations between EBVs from different models and regression slopes from forward prediction were calculated, using weaning-weight data on 365 956 White Suffolk and 370 649 Poll Dorset sheep and post-weaning weight data on 292 538 White Suffolk and 303 864 Poll Dorset sheep. Key results: The current OVIS procedure resulted in regression slopes of progeny performance on sire EBVs (averaged over breeds) of 0.37 and 0.35 for weaning and post-weaning weights respectively. Updated pre-adjustment factors improved the regression slopes to 0.40 and 0.38 respectively. Analysis with a linear mixed model produced significantly better regression slopes than did pre-adjustment (0.47 and 0.44 respectively). Further, regression slopes obtained from the linear mixed model with flock by sex by age interaction averaged over breeds were 0.48 for weaning and 0.46 for post-weaning weight respectively, which was a moderate improvement over the current OVIS model. Including a flock by sex by age interaction produced significantly better improvement in Poll Dorset sheep and modest improvement in White Suffolk sheep than did linear mixed model without interaction. Conclusions: Using a linear mixed model with a flock by sex by age interaction significantly improves the utility of estimated breeding values for weaning and post-weaning weight in predicting the performance of future progeny. Implications: To account for systematic environmental effects, a linear mixed model should be used in OVIS to jointly estimate the fixed effects and EBVs. Genetic evaluation of Australian sheep is conducted for millions of animals for more than 100 traits. Prediction of genetic merit of animals includes correcting observed phenotypes for environmental effects to allow fair genetic comparisons among animals, and is conducted by using old sheep data solutions because it was hard to fit these effects in each analysis. In the current scenario with more computing power, fitting all effects together and accounting for flock by sex by age interaction improves the utility of the model in predicting the performance of future progeny for weight traits. [ABSTRACT FROM AUTHOR]

Context. Genotype by environment interaction or sire re-ranking between measurements of methane emission in different environments or from using different measurement protocols can affect the efficiency of selection strategies to abate methane emission. Aim. This study tested the hypothesis that measurements of methane emission from grazing sheep under field conditions, where the feed intake is unknown, are genetically correlated to measurements in a controlled environment where feed intake is known. Methods. Data on emission of methane and carbon dioxide and uptake of oxygen were measured using portable accumulation chambers from 499 animals in a controlled environment in New South Wales and 1382 animals in a grazing environment in Western Australia were analysed. Genetic linkage between both environments was provided by 140 sires with progeny in both environments. Multi-variate animal models were used to estimate genetic parameters for the three gas traits corrected for liveweight. Genetic groups were fitted in the models to account for breed differences. Genetic correlations between the field and controlled environments for the three traits were estimated using bivariate models. Key results. Animals in the controlled environment had higher methane emission compared to the animals in the field environment (37.0 ± s.d 9.3 and 35.3 ± s.d 9.4 for two protocols vs 12.9 ± s.d 5.1 and 14.6 ± s.d 4.8 mL/min for lambs and ewes (±s.d); P < 0.05) but carbon dioxide emission and oxygen uptake did not significantly differ. The heritability estimates for methane emission, carbon dioxide emission and oxygen uptake were 0.15, 0.06 and 0.11 for the controlled environment and 0.17, 0.27 and 0.35 for the field environment. The repeatability for the traits in the controlled environment ranged from 0.51 to 0.59 and from 0.24 to 0.38 in the field environment. Genetic correlations were high (0.85-0.99) but with high standard errors. Conclusion. Methane emission phenotypes measured using portable accumulation chambers in grazing sheep can be used in genetic evaluation to estimate breeding values for genetic improvement of emission related traits. The combined measurement protocol-environment did not lead to re-ranking of sires. Implication. These results suggest that both phenotypes could be used in selection for reduced methane emission in grazing sheep. However, this needs to be consolidated using a larger number of animals and sires with larger progeny groups in different environments. [ABSTRACT FROM AUTHOR]

Context. Improving meat quality traits such as marbling is a well established breeding objective for many beef producers. More recently, the inclusion of feed efficiency is being considered. The main driving factors being the direct feed cost, as well as consumer concerns related to environmental sustainability of beef production. Aims. The main aim of this study was to examine modifying the definition of residual feed intake (RFI), by including an adjustment for intramuscular fat (IMF). The secondary aim was to further understand the genetic relationships between feed intake and a range of carcass traits. Methods. Using a population of 4034 Australian Angus animals, feed intake and carcass traits, along with pedigree and fixed effects, were analysed. This included the calculation of three definitions of RFI, being the standard definition, accounting for average daily gain and metabolic mid-weight, and two amended versions accounting for ultrasound IMF (RFIu), or carcass IMF (RFIi). Variance components, heritabilities, and genetic and phenotypic correlations were estimated and compared. Key results. All three definitions of RFI were moderately heritable (0.30-0.32) and highly correlated, both genetically (0.99) and phenotypically (0.99). Unfavourable genetic correlations were observed between RFI and carcass IMF (CIMF), and between RFIu and CIMF at 0.29 and 0.24 respectively. Similarly, there were unfavourable genetic correlations between RFI and ultrasound IMF (UIMF), between RFIi and UIMF, and between RFIu and UIMF at 0.30, 0,21 and 0.23 respectively. Conclusions. RFI can be redefined to account for traits, other than average daily gain and metabolic mid-weight, such as IMF. However due to limitations of phenotypic linear regression, and only small amounts of variation in feed intake being explained by the IMF traits, the redefinition of RFI was a suboptimal approach to breeding candidate selection. Furthermore, the present study confirmed the challenges with selecting for both feed efficiency and meat quality traits as they are generally genetically antagonist. Implications. For beef cattle breeding programs, the investigation of alternative selection approaches is warranted. This may include further understanding the genetic correlations among traits in the breeding objective and, according to their economic value, optimally weighting the related estimated breeding value. [ABSTRACT FROM AUTHOR]

The improvement of carcass traits is an important breeding objective in beef cattle breeding programs. The most common way of selecting for improvement in carcass traits is via indirect selection using ultrasound scanning of selection candidates which are submitted to genetic evaluation programs. Two systems used to analyze ultrasound images to predict carcass traits are the Pie Medical Esaote Aquila (PIE) and Central Ultrasound Processing (CUP). This study compared the ability of the two systems to predict carcass traits for genetic evaluation in Australian Angus cattle. Genetic and phenotypic parameters were estimated using data from 1,648 Angus steers which were ultrasound scanned twice with both systems, first at feedlot entry and then following 100 d in the feedlot. The traits interpreted from ultrasound scanning included eye muscle area (EMA), rib fat (RIB) rump fat (RUMP), and intramuscular fat (IMF). Abattoir carcass data were collected on all steers following the full feedlot feeding period of 285 d. For all ultrasound scan traits, CUP resulted in higher phenotypic and genetic variances compared to the PIE. For IMF, CUP had higher heritability at feedlot intake (0.51 for CUP compared to 0.37 for PIE) and after 100 d feeding (0.54 for CUP compared to 0.45 PIE). CUP predicted IMF also tended to have stronger correlations with the breeding objective traits of carcass IMF and marbling traits, both genetically (ranging from 0.59 to 0.75 for CUP compared to 0.45–0.63 for PIE) and phenotypically (ranging from 0.27 to 0.43 for CUP compared to 0.19–0.28 for PIE). Ultrasound scan EMA was the only group of traits in which the heritabilities were higher for PIE (0.52 for PIE compared to 0.40 for CUP at feedlot intake and 0.46 for PIE compared to 0.43 for CUP at 100 d of feeding), however with similar relationships to the breeding objective carcass EMA observed. For subcutaneous fat traits of ultrasound RIB and RUMP, the heritabilites and genetic correlations to the related carcass traits were similar, with the exception being the higher heritability observed for CUP predicted RUMP at feedlot intake at 0.52 compared to 0.38 for PIE. The results from this study indicates that the CUP system, compared to PIE, provides an advantage for genetic evaluation of carcass traits in Angus cattle, particularly for the IMF and associated marbling traits. [ABSTRACT FROM AUTHOR]

1. Genetic (co)variances and parameters between body weights (BW) across the growth trajectory were estimated using a univariate random regression (RR) animal model. The effect of growth rates (GH) on age at first egg (AFE) and egg weight at first egg (EWFE) were explored using a series of univariate and bivariate analyses. 2. Body weights were taken from Thai native chickens at hatch day to 168 days of age. The model included interactions between age with hatch nested within year and sex as fixed effects, and random effects of direct additive genetic, direct permanent environmental, maternal genetic and maternal permanent environmental effects. All random effects were fitted as regressions to animals' age via quadratic Legendre polynomials and fitting six classes of residual variances was identified as an optimal variance structure to estimate parameters. 3. Genetic and phenotypic variances for BW increased with increasing age. Estimated heritabilities for direct additive (h2a) and maternal genetic (h2m) effects on BW traits ranged from 0.34 to 0.54, and 0.04 to 0.06, respectively. Estimated variance ratios for direct (c2ape) and maternal permanent environmental (c2mpe) effects ranged from 0.19 to 0.48 and 0.10 to 0.12, respectively. Estimated correlations between weights at different ages were high for all random effects. 4. Estimated h2a for six GH traits ranged from 0.06 to 0.28, while for AFE and EWFE these were 0.24 and 0.16, respectively. Estimated h2m and c2mpe were low for GH. Estimated genetic correlations between GH and AFE ranged from −0.22 to 0.02 and, between GH and EWFE, ranged from −0.05 to 0.40. These estimates suggested that selecting high GH chickens at 28 days of age can be expected to reduce AFE and to increase EWFE. [ABSTRACT FROM AUTHOR]

The present study assessed the effectiveness and cost–benefit of several genotyping strategies for breeding poll Merino sheep in a closed nucleus with different initial allele frequencies and assuming a single-gene responsible for the horn or poll phenotype. We assumed that selection was based on phenotypes or genotypes for a single gene conferring polledness via a complete-dominance model. Under such a model, a complete fixation of the 'polled allele' (P) requires genotyping of the ewe-selection candidates. Testing a higher proportion of female candidates resulted in a faster fixation of the P-allele. Fixation ranged from 1 year of selection with a high starting P-allele frequency of 0.9, to 7 years for low starting P-allele frequencies of 0.3. When premiums of AU$50 or AU$100 were paid for rams with a PP genotype, breeding for PP genotypes was not profitable when the starting P-allele frequency was below 0.7. If the starting allele frequency was above 0.7, net profitability was positive over 10 years when premiums of AU$200 were paid for known PP-genotype rams. While fixing the P-allele, genetic gain for production traits was slowed down in the first 5 years of selection by up to 23% and 3% for initial P allele-frequencies of 0.3 and 0.9 respectively. Lost genetic gain due to fixing the P-allele, which can never be recovered in a closed nucleus, incurred 200–800% higher costs than the DNA testing costs. Rates of genetic gain recovered to pre-P-allele selection level rates of genetic gain once the P-allele was fixed. Testing a maximum of 25% ewe-selection candidates was the least expensive strategy across all starting allele frequencies and premiums. To avoid large losses of genetic gain in a closed nucleus with low P-allele starting frequencies, opening the nucleus should be considered to increase starting P-allele frequencies and also to potentially increase rates of genetic gain to offset the economic loss caused by P-selection. Australian Merino sheep can be bred with horns or without (polled). There is evidence suggesting polled rams are becoming more desirable due to increased welfare standards for both the individual sheep and their human handlers. As such there is indication that ram buyers will pay a premium for polled rams at present. This paper investigates breeding strategies to infuse the poll gene into a flock and the cost–benefit to the ram breeder. [ABSTRACT FROM AUTHOR]

Body weight and body measurements are commonly used to represent growth and measured at several growth stages in beef cattle. Those economically important traits should be genetically improved. To achieve breeding programs, genetic parameters are prerequisite, as they are needed for designing and predicting outcomes of breeding programs, as well as estimating of breeding values. (Co)variance components were estimated for BW and body measurements on Brahman cattle born between 1990 and 2016 from 17 research herds across Thailand. The traits measured were BW, heart girth (GR), hip height (HH) and body length (BL) and were measured at birth, 200 days, 400 days and 600 days of age. The number of records varied between traits from 18 890 for birth BW to 876 for GR at 600 days. Estimation of variance components was performed using restricted maximum likelihood using univariate and multivariate animal models. Pre-weaning traits were influenced by genetic and/or permanent environmental effects of the dam, except for BL. Heritability estimates from birth to 600 days of age ranged from 0.28±0.01 to 0.50±0.06 for BW, 0.27±0.01 to 0.43±0.09 for GR, 0.28±0.01 to 0.58±0.08 for HH and 0.34±0.01 to 0.51±0.08 for BL using univariate analysis. Heritability estimates for the traits studied increased with age. A similar trend was observed for the phenotypic and genetic correlations between subsequent BW and body measurements. A positive correlation was observed between different traits measured at a similar age, ranging from 0.22±0.01 to 0.72±0.01 for the phenotypic correlation and 0.25±0.04 to 0.97±0.11 for the genetic correlation. Also, a positive correlation was observed for similar traits across different age classes ranging from 0.07±0.03 to 0.76±0.02 for the phenotypic correlation and 0.24±0.11 to 0.92±0.05 for the genetic correlation. Therefore, all correlations between body measurements at the same age and across age classes were positive. The results show the potential improvement of growth traits in Brahman cattle, and those traits can be improved simultaneously under the same breeding program. [ABSTRACT FROM AUTHOR]

The data used in the present study consisted of 24 535 worm egg count records on sheep observed from 63 to 560 days of age under conditions of the natural challenge of trichostrongylid species. Records were extracted from the Information Nucleus Flock database of the Australia Sheep Cooperative Research Centre program from 2007 to 2011. Records were observed at various ages and subdivided into weaning (W, ~3 months), post-weaning (P, ~4 months), yearling (Y, ~12 months) and hogget (H, ~18 months) age stages and were used to investigate genetic variation at different age stages in univariate analyses and estimate genetic correlations between age stages in multi-trait analyses. The full data were also analysed by random regression models to study how heritability and genetic correlations varied with age. Heritability estimates from univariate analyses were 0.20 ± 0.05, 0.15 ± 0.02, 0.36 ± 0.09, 0.22 ± 0.06 for W, P, Y and H age stages respectively. A similar trend of heritability over ages was found from random regression analyses, which decreased from 0.16 at 90 days to 0.09 at 120 days, following a steady increase to 0.32 at ~410 days, and then decreased afterwards to 0.24 at 520 days. Strong genetic correlations (>0.8) were found between W and P age stages, along with Y and H age stages. Sire by flock interaction effects were significant, and accounted for the reduced estimates of heritability and increased genetic correlations between age stages. The results indicated that a multiple-trait approach is required for genetic evaluation of worm egg count when measurements are at different ages, and the accuracy of evaluations would benefit from recording at least two separate age stages. Faecal worm egg count (WEC) is an important trait for breeding for host resistance to parasites in sheep. The aim of the present study was to investigate whether genetic parameters differed for WEC measured at weaning, post-weaning, yearling and hogget age stages. The results showed lower variation and heritability at younger ages, and genetic correlations across ages significantly lower than unity, indicating that breeders would benefit by recording WEC at two or more different ages. [ABSTRACT FROM AUTHOR]

This study explores the interaction between genetic potential for growth in Merino lambs and their birth type (BT) or rearing type (RT). Data on birthweight (BWT), weaning weight (WWT), post-weaning weight (PWWT), scan fat (PFAT) and eye muscle depth (PEMD) were used from 3920 single and 4492 twin-born lambs from 285 sires and 5279 dams. Univariate analysis showed a significant sire × BT interaction accounting for 1.59% and 2.49% of the phenotypic variation for BWT and WWT, respectively, and no significant effect for PWWT, PFAT and PEMD. Sire × RT interaction effects were much smaller and only significant for PEMD. Bivariate analysis indicated that the genetic correlation (rg) between trait expression in lambs born and reared as singles versus those born and reared as twins were high for BWT, WWT, PWWT (0.91 ± 0.02 – 0.96 ± 0.01), whereas rg for PFAT and PEMD were lower (0.81 ± 0.03 and 0.86 ± 0.02). The rg between traits expressed in lambs born and reared as singles versus those born as twins but reared as singles were lower: 0.77 ± 0.08, 0.88 ± 0.03, 0.66 ± 0.06 and 0.61 ± 0.08 for WWT, PWWT, PFAT and PEMD, respectively. A different RT only affected the expression of breeding values for PFAT and PEMD (rg 0.62 ± 0.04 and 0.47 ± 0.03, respectively). This study showed genotype × environment interaction for BWT and WWT (sire × BT interaction) and for PEMD (sire by RT interaction). However, sires' breeding value of a model that accounts for sire × BT interaction provides a very similar ranking of sires compared with a model that ignores it, implying that there is no need to correct for the effect in models for genetic evaluation. This study explored whether breeding values for bodyweight are equally expressed in lambs with different birth or rearing type. The correlation between breeding values for early growth of lamb when expressed in single or twin birth types was less than one whereas different rearing type influenced expression of breeding value at late growth. However, this interaction between genotype and birth or rearing type did not affect ranking of sire's breeding value in these two different environments, implying that there is no need to account for the effect of genetic evaluation. [ABSTRACT FROM AUTHOR]

Shoal margin collapses of several million cubic meters have occurred in the Western Scheldt estuary, the Netherlands, on average five times a year over the last decades. While these collapses involve significant volumes of material, their effect on the channel‐shoal morphology is unknown. We hypothesize that collapses dynamicize the channel‐shoal interactions, which could impact the ecological functioning, flood safety, and navigation in the estuary. The objective is to investigate how locations, probability, type, and volume of shoal margin collapse affect the channel‐shoal dynamics. We implemented an empirically validated parameterization for shoal margin collapses and tested its effect on simulated estuary morphological development in a Delft3D schematization of the Western Scheldt. Three sets of scenarios were analyzed for near‐field and far‐field effects on flow pattern and channel‐shoal morphology: (1) an observed shoal margin collapse of 2014, (2) initial large collapses on 10 locations, and (3) continuous collapses predicted by our novel probabilistic model over a time span of decades. Results show that a single shoal margin collapse only affects the local dynamics in the longitudinal flow direction and dampen out within a year for typical volumes, whereas larger disturbances that reach the seaward or landward sill at tidal channel junctions grow. The direction of the strongest tidally averaged flow determined the redistribution of the collapsed sediment. We conclude that adding the process of shoal margin collapses increases the channel‐shoal interactions and that in intensively dredged estuaries shoal margins oversteepen, amplifying the number of collapses, but because of dredging the natural morphological response is interrupted. Key Points: Shoal margin collapses perturb the channel‐shoal network of sandy estuariesDisturbances cause long‐term morphological changesDisturbances amplify asymmetry and instability at channel junctions [ABSTRACT FROM AUTHOR]

Estuarine intertidal areas are shaped by combined astronomical and meteorological forces. This paper reveals the relative importance of tide, surge, wind, and waves for the flow and sediment transport on large intertidal shoals. Results of an intensive field campaign have been used to validate a numerical model of the Roggenplaat intertidal shoal in the Eastern Scheldt Estuary, the Netherlands, in order to identify and quantify the importance of each of the processes over time and space. We show that its main tidal creeks are not the cause for the dominant direction of the net flow on the shoal. The tidal flow over the shoal is steered by the water level differences between the surrounding channels. Also during wind events, the tidal flow (enhanced by surge) is dominant in the creeks. In contrast, wind speeds of order 40 times the typical tidal flow velocity are sufficient to completely alter the flow direction and magnitude on an intertidal shoal. This has significant consequences for the sediment transport patterns. Apart from this wind‐driven flow dominance during these events, the wind also increases the bed shear stress by waves. For the largest intertidal part of the Roggenplaat, only ∼1–10% of the yearly transport results from the 50% least windy tides, even if the shoal is artificially lowered half the tidal range. This dominance of energetic meteorological conditions in the transports matches with field observations, in which the migration of the creeks and high parts of the shoal are in line with the predominant wind direction. Key Points: The geometry of the surrounding channels drive the flow on intertidal shoals; their local morphology only affects the detailed flow patternsWind‐driven flow is important on intertidal shoals if the wind speed exceeds about 40 times the tidal flow velocitiesWind and waves control the sediment transport on these shoals; the water level rising and falling rates control the transport in the creeks [ABSTRACT FROM AUTHOR]

Summary: With the new opportunities from DNA technology, multitier breeding schemes have the potential to become more effective and more integrated. Integrated breeding schemes can also be better adapted to account for potential genotype by environment interactions (G × E) between tiers. In this case, phenotypic and genotype information from lower tiers becomes more valuable as it involves measurement of traits that directly represent the breeding objective. The objective of this study was to compare scenarios that represented different selection strategies and their economic effectiveness in fine‐wool commercial sheep operations that exploit multitier breeding structures. Genomic selection (GS) applied in the multiplier and the commercial tier presented the largest additional revenue among all scenarios, as it resulted in the largest amount of genetic progress. The largest benefits from GS were outweighed by the genotyping costs, which made DNA parentage the most feasible strategy for the multiplier tier, resulting in the highest cumulative net present value (CNPV). The benefits of phenotypes and genotype information from the commercial environment were larger in the presence of G × E between the nucleus and the commercial tier. The CNPV was larger with a 50% reduction in genotyping costs, which increased the returns of GS scenarios by 2.7‐fold on average. Higher selection intensity when selecting multiplier rams also resulted in larger benefits. In this case, returns for the breeding scheme were 3.5‐fold higher when 33% of multiplier males were selected based on commercial information, compared to scenarios selecting 50% of the available multiplier rams. The benefits of collecting commercial phenotypes and genotypes were long term, which means that return on investment often took more than 10 years to be achieved, and were largely dependent on two‐stage selection to reduce cost while maintaining selection efficiency and on the cost of a genotype test. [ABSTRACT FROM AUTHOR]

Genetic correlations between 29 wool production and quality traits and 25 meat quality and nutritional value traits were estimated for Merino sheep from an Information Nucleus (IN). Genetic correlations among the meat quality and nutritional value traits are also reported. The IN comprised 8 flocks linked genetically and managed across a range of sheep production environments in Australia. The wool traits included over 5,000 yearling and 3,700 adult records for fleece weight, fiber diameter, staple length, staple strength, fiber diameter variation, scoured wool color, and visual scores for breech and body wrinkle. The meat quality traits were measured on samples from the M. longissimus thoracis et lumborum and included over 1,200 records from progeny of over 170 sires for intramuscular fat (IMF), shear force of meat aged for 5 d (SF5), 24 h postmortem pH (pH24LL; also measured in the semitendinosus muscle, pH24ST), fresh and retail meat color and meat nutritional value traits such as iron and zinc levels, and long-chain omega-3 and omega-6 polyunsaturated fatty acid levels. Estimated heritabilities for IMF, SF5, pH24LL, pH24ST, retail meat color lightness (L*), myoglobin, iron, zinc and across the range of long-chain fatty acids were 0.58 ± 0.11, 0.10 ± 0.09, 0.15 ± 0.07, 0.20 ± 0.10, 0.59 ± 0.15, 0.31 ± 0.09, 0.20 ± 0.09, 0.11 ± 0.09, and range of 0.00 (eicosapentaenoic, docosapentaenoic, and arachidonic acids) to 0.14 ± 0.07 (linoleic acid), respectively. The genetic correlations between the wool production and meat quality traits were low to negligible and indicate that wool breeding programs will have little or no effect on meat quality. There were moderately favorable genetic correlations between important yearling wool production traits and the omega-3 fatty acids that were reduced for corresponding adult wool production traits, but these correlations are unlikely to be important in wool/ meat breeding programs because they have high SE, and the omega-3 traits have little or no genetic variance. Significant genetic correlations among the meat quality traits included IMF with SF5 (-0.76 ± 0.24), fresh meat color L* (0.50 ± 0.18), and zinc (0.41 ± 0.19). Selection to increase IMF will improve meat tenderness and color which may address some of the issues with Merino meat quality. These estimated parameters allow Merino breeders to combine wool and meat objectives without compromising meat quality. [ABSTRACT FROM AUTHOR]

Female reproductive technologies such as multiple ovulation and embryo transfer (MOET) and juvenile in vitro fertilisation and embryo transfer (JIVET) can produce multiple offspring per mating in sheep and cattle. In breeding programs this allows for higher female selection intensity and, in the case of JIVET, a reduction in generation interval, resulting in higher rates of genetic gain. Low selection accuracy of young females entering JIVET has often dissuaded producers from using this technology. However, genomic selection (GS) could increase selection accuracy of candidates at a younger age to help increase rates of genetic gain. This increase might vary for different traits in multiple trait breeding programs depending on genetic parameters and the practicality of recording, particularly for hard to measure traits. This study used both stochastic (animals) and deterministic (GS) simulation to evaluate the effect of reproductive technologies on the genetic gain for various traits in sheep breeding programs, both with and without GS. Optimal contribution selection was used to manage inbreeding and to optimally assign reproductive technologies to individual selection candidates. Two Australian sheep industry indexes were used - a terminal sire index that focussed on growth and carcass traits (the 'Lamb 2020' index) and a Merino index that focuses on wool traits, bodyweight, and reproduction (MP+). We observed that breeding programs using artificial insemination or natural mating (AI/N) + MOET, compared with AI/N alone, yielded an extra 39% and 27% genetic gain for terminal and Merino indexes without GS, respectively. However, the addition of JIVET to AI/N + MOET without GS only yielded an extra 1% genetic gain for terminal index and no extra gain in the Merino index. When GS was used in breeding programs, we observed AI/N + MOET + JIVET outperformed AI/N + MOET by 21% and 33% for terminal and Merino indexes, respectively. The implementation of GS increased genetic gain where reproductive technologies were used by 9-34% in Lamb 2020 and 37-98% in MP+. Individual trait response to selection varied in each breeding program. The combination of GS and reproductive technologies allowed for greater genetic gain in both indexes especially for hard to measure traits, but had limited effect on the traits that already had a large amount of early age records. [ABSTRACT FROM AUTHOR]

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 < 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 < 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. [ABSTRACT FROM AUTHOR]

Genetic correlations between 29 wool production and quality traits and 14 whole carcass measures and carcass component traits were estimated from the Information Nucleus of 8 flocks managed across a range of Australian sheep production environments and genetically linked. Wool data were from over 5,000 Merino progeny born over 5 yr, whereas carcass data were from over 1,200 wether progeny of over 176 sires, slaughtered at about 21 kg carcass weight, on average. Wool traits included yearling and adult records for wool weight, fiber diameter, fiber diameter variation, staple strength, scoured color, and visual scores for breech and body wrinkle. Whole carcass measures included HCW, dressing percentage (DP), and various measures of fat depth and eye muscle dimensions. Carcass components were obtained by dissection, and lean meat yield (LMY) was predicted. Heritability estimates for whole carcass measures ranged from 0.12 ± 0.08 to 0.35 ± 0.10 and ranged from 0.17 ± 0.10 to 0.46 ± 0.10 for carcass dissection traits, with no evidence of important genotype × environment interactions. Genetic correlations indicated that selection for increased clean wool weight will result in reduced carcass fat (−0.17 to −0.34) and DP (−0.48 ± 0.15), with little effect on carcass muscle. Selection for lower fiber diameter will reduce HCW (−0.48 ± 0.15) as well as carcass fat (0.14 to 0.27) and muscle (0.21 to 0.50). There were high genetic correlations between live animal measures of fat and muscle depth and the carcass traits (generally greater than 0.5 in size). Selection to increase HCW (and DP) will result in sheep with fewer wrinkles on the body (−0.57 ± 0.10) and barer breeches (−0.74 ± 0.12, favorable), with minor deterioration in scoured wool color (reduced brightness and increased yellowness). Selection for reduced fat will also result in sheep with fewer body wrinkles (−0.42 to −0.79). Increasing LMY in Merinos through selection would result in a large reduction in carcass fat and DP (−0.66 to −0.84), with a smaller increase in carcass muscle and some increase in wool weight and wrinkles. Although no major antagonisms are apparent between the wool and carcass traits, developing selection indexes for dualpurpose wool and meat breeding objectives will require accurate estimates of genetic parameters to ensure that unfavorable relationships are suitably considered. The findings will aid development of dual-purpose wool and meat breeding objectives. [ABSTRACT FROM AUTHOR]

Economically important reproduction traits in sheep, such as number of lambs weaned and litter size, are expressed only in females and later in life after most selection decisions are made, which makes them ideal candidates for genomic selection. Accurate genomic predictions would lead to greater genetic gain for these traits by enabling accurate selection of young rams with high genetic merit. The aim of this study was to design and evaluate the accuracy of a genomic prediction method for female reproduction in sheep using daughter trait deviations ( DTD) for sires and ewe phenotypes (when individual ewes were genotyped) for three reproduction traits: number of lambs born ( NLB), litter size ( LSIZE) and number of lambs weaned. Genomic best linear unbiased prediction ( GBLUP), BayesR and pedigree BLUP analyses of the three reproduction traits measured on 5340 sheep (4503 ewes and 837 sires) with real and imputed genotypes for 510 174 SNPs were performed. The prediction of breeding values using both sire and ewe trait records was validated in Merino sheep. Prediction accuracy was evaluated by across sire family and random cross-validations. Accuracies of genomic estimated breeding values ( GEBVs) were assessed as the mean Pearson correlation adjusted by the accuracy of the input phenotypes. The addition of sire DTD into the prediction analysis resulted in higher accuracies compared with using only ewe records in genomic predictions or pedigree BLUP. Using GBLUP, the average accuracy based on the combined records (ewes and sire DTD) was 0.43 across traits, but the accuracies varied by trait and type of cross-validations. The accuracies of GEBVs from random cross-validations (range 0.17-0.61) were higher than were those from sire family cross-validations (range 0.00-0.51). The GEBV accuracies of 0.41-0.54 for NLB and LSIZE based on the combined records were amongst the highest in the study. Although BayesR was not significantly different from GBLUP in prediction accuracy, it identified several candidate genes which are known to be associated with NLB and LSIZE. The approach provides a way to make use of all data available in genomic prediction for traits that have limited recording. [ABSTRACT FROM AUTHOR]

Genetic correlations between 29 wool production and quality traits and live weight and ultrasound fat depth (FAT) and eye muscle depth (EMD) traits were estimated from the Information Nucleus (IN). The IN comprised 8 genetically linked flocks managed across a range of Australian sheep production environments. The data were from a maximum of 9,135 progeny born over 5 yr from 184 Merino sires and 4,614 Merino dams. The wool traits included records for yearling and adult fleece weight, fiber diameter (FD), staple length (SL), fiber diameter CV (FDCV), scoured color, and visual scores for breech and body wrinkle. We found high heritability for the major yearling wool production traits and some wool quality traits, whereas other wool quality traits, wool color, and visual traits were moderately heritable. The estimates of heritability for live weight generally increased with age as maternal effects declined. Estimates of heritability for the ultrasound traits were also higher when measured at yearling age rather than at postweaning age. The genetic correlations for fleece weight with live weights were positive (favorable) and moderate (approximately 0.5 ± 0.1), whereas those with FD were approximately 0.3 (unfavorable). The other wool traits had lower genetic correlations with the live weights. The genetic correlations for FAT and EMD with FD and SL were positive and low, with FDCV low to moderate negative, but variable with wool weight and negligible for the other wool traits. The genetic correlations for FAT and EMD with postweaning weight were positive and high (0.61 ± 0.18 to 0.75 ± 0.14) but were generally moderate with weights at other ages. Selection for increased live weight will result in a moderate correlated increase in wool weight as well as favorable reductions in breech cover and wrinkle, along with some unfavorable increases in FD and wool yellowness but little impact on other wool traits. The ultrasound meat traits, FAT and EMD, were highly positively genetically correlated (0.8), and selection to increase them would result in a small unfavorable correlated increase in FD, moderately favorable reductions in breech cover and wrinkle, but equivocal or negligible changes in other wool traits. The estimated parameters provide the basis for calculation of more accurate Australian Sheep Breeding Values and selection indexes that combine wool and meat objectives in Merino breeding programs. [ABSTRACT FROM AUTHOR]

Reducing daily methane production (DMP) via selection for lower estimated daily (pasture) feed intake (DFI) has the potential to be more cost effective than direct selection for DMP. Daily feed intake has a high heritability and high genetic correlation to DMP and has a potential lower cost of measurement. This study's main aim was to determine for a breeding nucleus the optimal proportion of randomly selected young male and female cattle in which to estimate DFI. This optimum proportion was determined by modeling the measurement costs and response to selection of Angus cattle on a (standard industry) Angus breeding index (ABI) augmented with DFI and DMP in a combined breeding objective (BO), but without DMP being measured. For the assumed herd structure and considering a 20 yr planning horizon, the highest net present value (NPV) occurred when 64% of males and no females were measured for DFI. The highest breakeven DFI test cost (A$41.51/head) and highest returns on investment (ROI) occurred when 36% of males and no females had DFI estimates. Higher ROI were achieved when all males had DFI estimates before any females had DFI estimates. There was a diminishing increase in rate of genetic gain when moving from 36% to 64% of males with DFI estimates, thus ROI decreased from 29.7% to 23.1%. When 36% of males had DFI estimates (and no females), herd DMP genetic gain was slightly positive as the DMP reduction per generation from male selection (-0.086) was more than offset by the DMP increase per generation from female selection (+0.110). The selection response for DMP only became negative when at least 40% of males had DFI estimates. Having 64% of males with DFI estimates resulted in a predicted genetic decrease in DMP (-0.018 kgCO2e/head per yr), compared to an increase of 0.052 kgCO2e/head per yr when no animals had DFI estimates. The optimum proportion of males with DFI estimates (36 to 64%) depends on the breeders attitude toward ROI and the value of genetic change for DMP. Sensitivity analysis showed that the economic value (EV), heritability and genetic variance of DFI had a higher impact on the NPV and ROI outcomes than parameters related to ABI and DMP, so future work should focus on obtaining robust estimates for DFI parameters. Higher EV for feed intake and DMP would result in higher percentages of animals being profitably measured for DFI, leading to larger reductions in DMP. [ABSTRACT FROM AUTHOR]

Breeding programmes for livestock require economic weights for traits that reflect the most profitable animal in a given production system, which affect the response in each trait after selection. The profitability of sheep production systems is affected by changes in pasture growth as well as grain, meat and wool prices between seasons and across years. Annual pasture growth varies between regions within Australia’s Mediterranean climate zone from low growth with long periods of drought to high growth with shorter periods of drought. Therefore, the objective of this study was to assess whether breeding objectives need to be adapted for regions, depending on how reliable the pasture growth is across years. We modelled farms with Merino sheep bred for wool and meat in 10 regions in Western Australia. Across these 10 regions, mean annual pasture growth decreased, and the CV of annual pasture growth increased as pasture growth for regions became less reliable. We calculated economic values for nine traits, optimising management across 11 years, including variation for pasture growth and wool, meat and grain prices between and within years from 2002 to 2012. These economic values were used to calculate responses to selection for each trait for the 10 regions. We identified two potential breeding objectives, one for regions with low or high reliability and the other for regions with medium reliability of pasture growth. Breeding objectives for high or low pasture growth reliability had more emphasis on live weight traits and number of lambs weaned. Breeding objectives for medium reliability of pasture growth had more emphasis on decreasing fibre diameter. Relative economic weights for fleece weight did not change across the regions. Regions with low or high pasture reliability had similar breeding objectives and response to selection, because the relationship between the economic values and CV of pasture growth were not linear for live weight traits and the number of lambs weaned. This non-linearity was caused by differences in distribution of pasture growth between regions, particularly during summer and autumn, when ewes were pregnant, with increases in energy requirements affecting the value of lambs weaned. In addition, increasing live weight increased the intake capacity of sheep, which meant that more poor quality pasture could be consumed during summer and autumn, which had more value in regions with low and high pasture reliability. We concluded that breeding values for sheep production systems should be customised depending on the reliability of pasture growth between years. [ABSTRACT FROM PUBLISHER]

A model of the sheep breeding industry with nucleus flocks, multiplier flocks and commercial sheep flocks was used to examine the value of genomic selection. The model reflected a dual-purpose Merino breeding objective, with genomic information improving selection accuracy by 39% for rams at 6 months of age and by 17% at 18 months. The current level of net dollar benefit to the sheep industry from selection, but without genomic testing, can be improved by 10-14% for a closed three-tiered breeding structure with rams used at 18 months. If the rams are first used at 6-7 months then the dollar gains can be improved by 15-17%, since genomic information can provide proportionately greater gains for young animals that have limited phenotypic information. In a two-tiered breeding system, with nucleus flocks selling rams direct to commercial producers, rather than through multiplier flocks, the dollar gains to industry from genomic testing increased to ~12-13% for rams bred at 18 months, and 20-22% if nucleus rams are used at 6-7 months. The optimal structure requires two-stage selection, with an initial selection based on information available without genomic testing, to limit the cost of testing to only the superior rams. However, the optimum proportion of rams tested depends on the system and the cost of testing. In order to recover the cost of genomic testing, the nucleus flocks must recover up to 5% of the extra genetic gain as extra profit from sale of rams to commercial sheep producers. A model of the sheep breeding industry examined the value of genomic information in sheep breeding programs. Benefits can be obtained by both the traditional three-tiered wool industry structure and studs using genomic information and selling directly to commercial producers, with most of the benefits retained by the commercial producers. The proportion of nucleus rams that use genetic tests must be optimised to achieve the maximum economic benefit. [ABSTRACT FROM AUTHOR]