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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]

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]

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]

The objectives of this study were to estimate the additive and dominance variance component of several weight and ultrasound scanned body composition traits in purebred and combined cross-bred sheep populations based on single nucleotide polymorphism ( SNP) marker genotypes and then to investigate the effect of fitting additive and dominance effects on accuracy of genomic evaluation. Additive and dominance variance components were estimated in a mixed model equation based on 'average information restricted maximum likelihood' using additive and dominance (co)variances between animals calculated from 48,599 SNP marker genotypes. Genomic prediction was based on genomic best linear unbiased prediction ( GBLUP), and the accuracy of prediction was assessed based on a random 10-fold cross-validation. Across different weight and scanned body composition traits, dominance variance ranged from 0.0% to 7.3% of the phenotypic variance in the purebred population and from 7.1% to 19.2% in the combined cross-bred population. In the combined cross-bred population, the range of dominance variance decreased to 3.1% and 9.9% after accounting for heterosis effects. Accounting for dominance effects significantly improved the likelihood of the fitting model in the combined cross-bred population. This study showed a substantial dominance genetic variance for weight and ultrasound scanned body composition traits particularly in cross-bred population; however, improvement in the accuracy of genomic breeding values was small and statistically not significant. Dominance variance estimates in combined cross-bred population could be overestimated if heterosis is not fitted in the model. [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]

Genotyping sheep for genome-wide SNPs at lower density and imputing to a higher density would enable cost-effective implementation of genomic selection, provided imputation was accurate enough. Here, we describe the design of a low-density (12k) SNP chip and evaluate the accuracy of imputation from the 12k SNP genotypes to 50k SNP genotypes in the major Australian sheep breeds. In addition, the impact of imperfect imputation on genomic predictions was evaluated by comparing the accuracy of genomic predictions for 15 novel meat traits including carcass and meat quality and omega fatty acid traits in sheep, from 12k SNP genotypes, imputed 50k SNP genotypes and real 50k SNP genotypes. The 12k chip design included 12 223 SNPs with a high minor allele frequency that were selected with intermarker spacing of 50-475 kb. SNPs for parentage and horned or polled tests also were represented. Chromosome ends were enriched with SNPs to reduce edge effects on imputation. The imputation performance of the 12k SNP chip was evaluated using 50k SNP genotypes of 4642 animals from six breeds in three different scenarios: (1) within breed, (2) single breed from multibreed reference and (3) multibreed from a single-breed reference. The highest imputation accuracies were found with scenario 2, whereas scenario 3 was the worst, as expected. Using scenario 2, the average imputation accuracy in Border Leicester, Polled Dorset, Merino, White Suffolk and crosses was 0.95, 0.95, 0.92, 0.91 and 0.93 respectively. Imputation scenario 2 was used to impute 50k genotypes for 10 396 animals with novel meat trait phenotypes to compare genomic prediction accuracy using genomic best linear unbiased prediction ( GBLUP) with real and imputed 50k genotypes. The weighted mean imputation accuracy achieved was 0.92. The average accuracy of genomic estimated breeding values ( GEBVs) based on only 12k data was 0.08 across traits and breeds, but accuracies varied widely. The mean GBLUP accuracies with imputed 50k data more than doubled to 0.21. Accuracies of genomic prediction were very similar for imputed and real 50k genotypes. There was no apparent impact on accuracy of GEBVs as a result of using imputed rather than real 50k genotypes, provided imputation accuracy was >90%. [ABSTRACT FROM AUTHOR]

Heritabilities and genetic correlations for milk production traits were estimated from first-parity test day records on 1022 Philippine dairy buffalo cows. Traits analysed included milk (MY), fat (FY) and protein (PY) yields, and fat (Fat%) and protein (Prot%) concentrations. Varying orders of Legendre polynomials (Legm) as well as the Wilmink function (Wil) were used in random regression models. These various models were compared based on log likelihood, Akaike's information criterion, Bayesian information criterion and genetic variance estimates. Six residual variance classes were sufficient for MY, FY, PY and Fat%, while seven residual classes for Prot%. Multivariate analysis gave higher estimates of genetic variance and heritability compared with univariate analysis for all traits. Heritability estimates ranged from 0.25 to 0.44, 0.13 to 0.31 and 0.21 to 0.36 for MY, FY and PY, respectively. Wilmink's function was the better fitting function for additive genetic effects for all traits. It was also the preferred function for permanent environment effects for Fat% and Prot%, but for MY, FY and PY, the Legm was the appropriate function. Genetic correlations of MY with FY and PY were high and they were moderately negative with Fat% and Prot%. To prevent deterioration in Fat% and Prot% and improve milk quality, more weight should be applied to milk component traits. [ABSTRACT FROM AUTHOR]

Summary Although genomic selection offers the prospect of improving the rate of genetic gain in meat, wool and dairy sheep breeding programs, the key constraint is likely to be the cost of genotyping. Potentially, this constraint can be overcome by genotyping selection candidates for a low density (low cost) panel of SNPs with sparse genotype coverage, imputing a much higher density of SNP genotypes using a densely genotyped reference population. These imputed genotypes would then be used with a prediction equation to produce genomic estimated breeding values. In the future, it may also be desirable to impute very dense marker genotypes or even whole genome re-sequence data from moderate density SNP panels. Such a strategy could lead to an accurate prediction of genomic estimated breeding values across breeds, for example. We used genotypes from 48 640 (50K) SNPs genotyped in four sheep breeds to investigate both the accuracy of imputation of the 50K SNPs from low density SNP panels, as well as prospects for imputing very dense or whole genome re-sequence data from the 50K SNPs (by leaving out a small number of the 50K SNPs at random). Accuracy of imputation was low if the sparse panel had less than 5000 (5K) markers. Across breeds, it was clear that the accuracy of imputing from sparse marker panels to 50K was higher if the genetic diversity within a breed was lower, such that relationships among animals in that breed were higher. The accuracy of imputation from sparse genotypes to 50K genotypes was higher when the imputation was performed within breed rather than when pooling all the data, despite the fact that the pooled reference set was much larger. For Border Leicesters, Poll Dorsets and White Suffolks, 5K sparse genotypes were sufficient to impute 50K with 80% accuracy. For Merinos, the accuracy of imputing 50K from 5K was lower at 71%, despite a large number of animals with full genotypes (2215) being used as a reference. For all breeds, the relationship of individuals to the reference explained up to 64% of the variation in accuracy of imputation, demonstrating that accuracy of imputation can be increased if sires and other ancestors of the individuals to be imputed are included in the reference population. The accuracy of imputation could also be increased if pedigree information was available and was used in tracking inheritance of large chromosome segments within families. In our study, we only considered methods of imputation based on population-wide linkage disequilibrium (largely because the pedigree for some of the populations was incomplete). Finally, in the scenarios designed to mimic imputation of high density or whole genome re-sequence data from the 50K panel, the accuracy of imputation was much higher (86-96%). This is promising, suggesting that in silico genome re-sequencing is possible in sheep if a suitable pool of key ancestors is sequenced for each breed. [ABSTRACT FROM AUTHOR]

Genetic correlations for body measurements and subjectively scored traits between foals and studbook horses were estimated using bivariate linear mixed models. Observations for nine foal and eleven studbook traits in Finnhorses on 6529 foals and 6596 studbook horses and in Standardbred trotters on 3069 foals and 2112 studbook horses were available from the Finnish horse breeding shows. The number of sires with progeny in both foal and studbook data was 203 in Finnhorse and 145 in Standardbred trotters. Estimates of heritability for body measurements in foals and studbook horses using univariate models were high in both breeds (0.41-0.84). Heritability estimates for subjectively scored traits using univariate models were generally higher for foals (0.08-0.46) than for studbook horses (0.06-0.21) in both breeds. Genetic correlations between foals and studbook horses for body measurements were highly positive ranging from 0.74 to 0.96 in Finnhorses and from 0.79 to 0.99 in Standardbred trotters. Low to highly positive genetic correlations between foals and studbook horses for subjectively scored traits were obtained in Finnhorse trotters, whereas in Standardbred trotters genetic correlations for subjectively scored traits varied from moderately negative to highly positive. Higher estimates of heritability for foal traits and generally high genetic correlations between the foal and studbook traits indicate that an early selection for conformation traits would be efficient in the breeding programmes. [ABSTRACT FROM AUTHOR]

Three microsatellite markers on goat chromosome 23 adjacent to the MHC were used to test for quantitative trait loci (QTL) affecting faecal worm egg count (WEC) and leukocyte traits in ten Australian Angora and twelve Australian Cashmere half-sib families (n = 16–57 per family). Data were collected from 280 Angora and 347 Cashmere kids over a 3- and 4-year period. A putative QTL affecting trichostrongyle WEC was found in two small families at the 5% chromosome-wise threshold level. The biggest QTL effect for WEC of 1.65 standard deviations (σp) was found within the region of OarCP73- BM1258. A significant QTL affecting blood eosinophil counts at the 1% chromosome–wise threshold level was detected at marker BM1258 (at 26 cM) in two Angora and Cashmere families. The magnitude of the putative QTL was 0.69 and 0.85 σp in Angora and Cashmere families, respectively. Due to the comparatively low power of the study these findings should be viewed as indicative rather than definitive. [ABSTRACT FROM AUTHOR]

Background Modification of allergens by glutaraldehyde in extracts used for immunotherapy reduces the risk for side-effects, but the therapeutic efficacy of such extracts still requires further evaluation. The aim of this study was to show the efficacy and safety of immunotherapy with a single-strength glutaraldehyde-modified aluminium hydroxide-adsorbed extract of birch pollen. Methods In a multi-centre, randomized, placebo-controlled double-blind setting, starting in 2001 between 1 August and 15 December, birch pollen-allergic subjects ( n=62) were injected subcutaneously with increasing doses of the allergen extract or placebo at weekly intervals over a 6-week period (or longer if adverse reactions occurred). Maintenance dose was given monthly for at least 18 months till June 2003. Efficacy was evaluated on the basis of the clinical index score (CIS), a combined symptom and medication score. Results Fifty-eight patients could be evaluated for clinical efficacy. Treatment with the birch pollen extract resulted in a lower CIS for the eye and nose during the peak birch pollen season of 2003, compared with placebo (reductions of 42% and 31%, respectively) ( P=0.017 and 0.039). Active treatment induced IgG and IgG4 antibodies reacting with Bet v 1 ( P<0.001). Sera from treated patients had a blocking effect on Bet v 1-induced basophil activation ( P<0.04). No major adverse reactions occurred, and local reactions, if occurring, were mild. Conclusion Immunotherapy with a modified slow-release birch pollen extract, administered in a single-strength preparation with a rapid dose increase, is safe and efficacious. IgG and IgG4 antibodies against native Bet v 1 are induced, which block basophil activation. [ABSTRACT FROM AUTHOR]

A multi-trait (MT) random regression (RR) test day (TD) model has been developed for genetic evaluation of somatic cell scores for Australian dairy cattle, where first, second and third lactations were considered as three different but correlated traits. The model includes herd-test-day, year-season, age at calving, heterosis and lactation curves modelled with Legendre polynomials as fixed effects, and random genetic and permanent environmental effects modelled with Legendre polynomials. Residual variance varied across the lactation trajectory. The genetic parameters were estimated usingasreml. The heritability estimates ranged from 0.05 to 0.16. The genetic correlations between lactations and between test days within lactations were consistent with most of the published results. Preconditioned conjugate gradient algorithm with iteration on data was implemented for solving the system of equations. For reliability approximation, the method of Tier and Meyer was used. The genetic evaluation system was validated with Interbull validation method III by comparing proofs from a complete evaluation with those from an evaluation based on a data set excluding the most recent 4 years. The genetic trend estimate was in the allowed range and correlations between the two sets of proofs were very high. Additionally, the RR model was compared to the previous test day model. The correlations of proofs between both models were high (0.97) for bulls with high reliabilities. The correlations of bulls decreased with increasing incompleteness of daughter performance information. The correlations between the breeding values from two consecutive runs were high ranging from 0.97 to 0.99. The MT RR TD model was able to make effective use of available information on young bulls and cows, and could offer an opportunity to breeders to utilize estimated breeding values for first and later lactations. [ABSTRACT FROM AUTHOR]

This paper presents results from a mapping experiment to detect quantitative trait loci (QTL) for resistance to Haemonchus contortus infestation in merino sheep. The primary trait analysed was faecal worm egg count in response to artificial challenge at 6 months of age. In the first stage of the experiment, whole genome linkage analysis was used for broad-scale mapping. The animal resource used was a designed flock comprising 571 individuals from four half-sib families. The average marker spacing was about 20 cM. For the primary trait, 11 QTL (as chromosomal/family combinations) were significant at the 5% chromosome-wide level, with allelic substitution effects of between 0.19 and 0.38 phenotypic standard deviation units. In general, these QTL did not have a significant effect on faecal worm egg count recorded at 13 months of age. In the second stage of the experiment, three promising regions (located on chromosomes 1, 3 and 4) were fine-mapped. This involved typing more closely spaced markers on individuals from the designed flock as well as an additional 495 individuals selected from a related population with a deeper pedigree. Analysis was performed using a linkage disequilibrium–linkage approach, under additive, dominant and multiple QTL models. Of these, the multiple QTL model resulted in the most refined QTL positions, with resolutions of <10 cM achieved for two regions. Because of the moderate size of effect of the QTL, and the apparent age and/or immune status specificity of the QTL, it is suggested that a panel of QTL will be required for significant genetic gains to be achieved within industry via marker-assisted selection. [ABSTRACT FROM AUTHOR]

Optimal selection on a single identified quantitative trait locus (QTL) with four modes of inheritance: normal autosomal, sex-limited, imprinting and X-linked, was evaluated in four breeding structures: single line selection (SLS), two-way crossing (2WC), three-way crossing (3WC) and reciprocal crossing (RC) by comparing extra benefit from mate selection over index selection to demonstrate effectiveness of mate selection in exploiting non-additive QTL. The results showed that the superiority varied at different QTL inheritance modes, initial favourable allele frequencies and breeding structures. The superiority tended to decrease with the increase of the favourable allele frequency except for over-dominant QTL and imprinted QTL in all breeding structures. Less superiority (below 9%) was observed for a recessive and a fully dominant QTL than for an over-dominant QTL (up to 27.11%). Normal autosomal and sex-linked QTL led to a similar trend of superiority from mate selection but the magnitude of the superiority with the latter was slightly higher than with the former for most combinations of the parameters. A high superiority (6.41–41.54%) was observed from mate selection over index selection for an imprinted QTL. A maternally imprinted QTL tended to lead to higher superiority from mate selection than a paternally imprinted QTL. X-linked QTL led to less superiority from mate selection than the other modes of QTL. A larger superiority from mate selection was observed for a recessive and a fully dominant QTL in structures 3WC and 2WC than structures RC and SLS. The superiority from autosomal QTL and X-linked QTL was lower in the structure RC than in other structures examined. [ABSTRACT FROM AUTHOR]

Genetic parameters for carcass and meat quality traits of about 18-month-old Merino rams (n = 5870), the progeny of 543 sires from three research resource flocks, were estimated. The estimates of heritability for hot carcass weight (HCW) and the various fat and muscle dimension measurements were moderate and ranged from 0.20 to 0.37. The brightness of meat (colour L*, 0.18 ± 0.03 standard error) and meat pH (0.22 ± 0.03) also had moderate estimates of heritability, although meat relative redness (colour a*, 0.10 ± 0.03) and relative yellowness (colour b*, 0.10 ± 0.03) were lower. Heritability estimates for live weights were moderate and ranged from 0.29 to 0.41 with significant permanent maternal environmental effects (0.13 to 0.10). The heritability estimates for the hogget wool traits were moderate to high and ranged from 0.27 to 0.60. The ultrasound measurements of fat depth (FATUS) and eye muscle depth (EMDUS) on live animals were highly genetically correlated with the corresponding carcass measurements (0.69 ± 0.09 FATC and 0.77 ± 0.07 EMD). Carcass tissue depth (FATGR) had moderate to low genetic correlations with carcass muscle measurements [0.18 ± 0.10 EMD and 0.05 ± 0.10 eye muscle area (EMA)], while those with FATC were negative. The genetic correlation between EMD and eye muscle width (EMW) was 0.41 ± 0.08, while EMA was highly correlated with EMD (0.89 ± 0.0) and EMW (0.78 ± 0.04). The genetic correlations for muscle colour with muscle measurements were moderately negative, while those with fat measurements were close to zero. Meat pH was positively correlated with muscle measurements (0.14 to 0.17) and negatively correlated with fat measurements (−0.06 to −0.18). EMDUS also showed a similar pattern of correlations to EMD with meat quality indicator traits, although FATUS had positive correlations with these traits which were generally smaller than their standard error. The genetic correlations among the meat colour traits were high and positive while those with meat pH were high and negative, which were all in the favourable direction. Generally, phenotypic correlations were similar or slightly lower than the corresponding genetic correlations. There were generally small to moderate negative genetic correlations between clean fleece weight (CFW) and carcass fat traits while those with muscle traits were close to zero. As the Merino is already a relatively lean breed, this implies that particular attention should be given to this relationship in Merino breeding programmes to prevent the reduction of fat reserves as a correlated response to selection for increased fleece weight. The ultrasound scan traits generally showed a similar pattern to the corresponding carcass fat and muscle traits. There was a small unfavourable genetic correlation between CFW and meat pH (0.19 ± 0.07). [ABSTRACT FROM AUTHOR]

Data from seven research resource flocks across Australia were combined to provide accurate estimates of genetic correlations among production traits in Merino sheep. The flocks represented contemporary Australian Merino fine, medium and broad wool strains over the past 30 years. Over 110 000 records were available for analysis for each of the major wool traits, and 50 000 records for reproduction and growth traits with over 2700 sires and 25 000 dams. Individual models developed from the single trait analyses were extended to the various combinations of two-trait models to obtain genetic correlations among six wool traits [clean fleece weight (CFW), greasy fleece weight, fibre diameter (FD), yield, coefficient of variation of fibre diameter and standard deviation of fibre diameter], four growth traits [birth weight, weaning weight, yearling weight (YWT), and hogget weight] and four reproduction traits [fertility, litter size, lambs born per ewe joined, lambs weaned per ewe joined (LW/EJ)]. This study has provided for the first time a comprehensive matrix of genetic correlations among these 14 wool, growth and reproduction traits. The large size of the data set has also provided estimates with very low standard errors. A moderate positive genetic correlation was observed between CFW and FD (0.29 ± 0.02). YWT was positively correlated with CFW (0.23 ± 0.04), FD (0.17 ± 0.04) and LWEJ (0.58 ± 0.06), while LW/EJ was negatively correlated with CFW (−0.26 ± 0.05) and positively correlated with FD (0.06 ± 0.04) and LS (0.68 ± 0.04). These genetic correlations, together with the estimates of heritability and other parameters provide the basis for more accurate prediction of outcomes in complex sheep-breeding programmes designed to improve several traits. [ABSTRACT FROM AUTHOR]

The objective of this study was to investigate an association between polymorphisms in the FABP4 gene and phenotypic variation for marbling and carcass weight (CWT) in a population of Hanwoo steers. We re-sequenced 4.3 kb of the FABP4 gene region in 24 Hanwoo bulls and identified 16 SNPs and 1 microsatellite polymorphism. Of these 16 SNPs, three SNPs [g.2774G>C (intron I), g.3473A>T (intron II) and g.3631G>A (exon III, creating a p.Met >Val amino acid substitution)] were genotyped in 583 steers to assess their association with carcass traits. The g.3473A allele showed a significant increasing effect on CWT ( P = 0.01) and the g.3631G allele was associated with higher marbling score ( P = 0.006). One haplotype of these three SNPs (CAG) was significantly associated with CWT ( P = 0.02) and marbling score ( P = 0.05) and could potentially be of value for marker assisted selection in Hanwoo cattle. The CAG haplotype effect for CWT was larger (11.14 ± 5.03 kg) than the largest single locus effect of g.3473A>T (5.01 ± 2.2 kg). [ABSTRACT FROM AUTHOR]

The author reflects on the developments in effective aimal breeding programmes in Australia, focusing on the adoption of technology and programmes by breeders from the science of animal breeding. Topics include the trends in the animal production systems in the country, the breeding programmes for sheep and cattle, and the challenges facing the animal breeding structure in its effort to achieve remarkable genetic gain.

Background Both genetic and nongenetic factors can predispose individuals to cardiovascular risk. Finding ways to alter these predispositions is important for cardiovascular disease prevention. Methods and Results We used a novel whole-genome approach to estimate the genetic and nongenetic effects on-and hence their predispositions to-cardiovascular risk and determined whether they vary with respect to lifestyle factors such as physical activity, smoking, alcohol consumption, and dietary intake. We performed analyses on the ARIC (Atherosclerosis Risk in Communities) Study (N=6896-7180) and validated findings using the UKBB (UK Biobank, N=14 076-34 538). Lifestyle modulation was evident for many cardiovascular traits such as body mass index and resting heart rate. For example, alcohol consumption modulated both genetic and nongenetic effects on body mass index, whereas smoking modulated nongenetic effects on heart rate, pulse pressure, and white blood cell count. We also stratified individuals according to estimated genetic and nongenetic effects that are modulated by lifestyle factors and showed distinct phenotype-lifestyle relationships across the stratified groups. Finally, we showed that neglecting lifestyle modulations of cardiovascular traits would on average reduce single nucleotide polymorphism heritability estimates of these traits by a small yet significant amount, primarily owing to the overestimation of residual variance. Conclusions Lifestyle changes are relevant to cardiovascular disease prevention. Individual differences in the genetic and nongenetic effects that are modulated by lifestyle factors, as shown by the stratified group analyses, implies a need for personalized lifestyle interventions. In addition, single nucleotide polymorphism-based heritability of cardiovascular traits without accounting for lifestyle modulations could be underestimated.

Parietal and frontal cortical areas play important roles in the control of goal-oriented behaviour. This review examines how signal processing in the parietal and frontal eye fields is involved in coding and storing space, directing attention and processing the sensorimotor transformation for saccades. After a survey of the functional specialization of these areas in monkeys, we discuss homologous regions in the human brain in terms of topographic organization, storage capacity, target selection, spatial remapping, reference frame transformations and effector specificity. The overall picture suggests that bottom-up sensory, top-down cognitive signals and efferent motor signals are integrated in dynamic sensorimotor maps as part of a functionally flexible parietofrontal network. Neuronal synchronization in these maps may be instrumental in amplifying behaviourally relevant representations and setting up a functional pathway to route information in this parietofrontal circuit., (© 2011 The Authors. European Journal of Neuroscience © 2011 Federation of European Neuroscience Societies and Blackwell Publishing Ltd.)