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Data on performance of animals are, in several situations, collected at the group rather than individual level. Genetic evaluations in farm animals, however, are based on phenotypic information collected at the individual level. Therefore, it would be very attractive to extend genetic evaluations by incorporating information collected at the group level. In this paper we show the use of data collected at the group level for the estimation of variance components and the prediction of breeding values. We outline a general procedure that can be applied in different farm animal species. In the present work this procedure was applied to BW, for which pooled, as well as individual, observations were available, thus allowing for a comparison of the estimates, and to egg production, for which only pooled data were available. For BW at 19 and 27 wk the estimated heritabilities based on individual observations were very similar to those based on pooled observations. For BW at 43 and 51 wk, heritability estimates based on individual and pooled data were different, which can be caused by the emergence of competition effects. The accuracy of EBV predicted from pooled observations was about 70 to 80% of the accuracy of EBV predicted from individual observations. This result quantifies the loss deriving from the use of pooled instead of individual observations. Results show that estimation of variance components and breeding values from pooled data instead of individual observations is theoretically and practically feasible.

Ease of measurement of linear size traits is of particular significance in livestock breeding, particularly under village breeding programs where measuring live weight is difficult. In this study, we estimated genetic parameters and realized responses for live weight (LW) and linear size traits using data from an ongoing Menz sheep nucleus selection program. Using the estimated genetic parameters and simulating a nucleus breeding program and a village-based breeding program for Menz sheep, we compared predicted responses from indirect selection on linear size traits and direct selection on LW. Heritability estimates were 0.46, 0.36, 0.27, 0.31, 0.08, 0.48 and 0.23 for LW, wither height, body length, chest girth, pelvic width, tail length and tail circumference, respectively. Genetic correlations of LW with linear size traits ranged from 0.40 for tail length to 0.98 for chest girth. Realized responses in LW resulting from selection for LW and fleece weight in the ongoing Menz sheep selection program ranged from 0.27 to 0.86 kg per generation. Based on estimated genetic parameters, we chose chest girth, wither height and body length for the simulation study. Predicted responses in LW from indirect selection on chest girth, wither height and body length were 94.8% (nucleus program) and 92.6% (village program) of the responses to direct selection. Our results strongly indicate that genetic improvement in LW through indirect selection on linear size traits is possible both under nucleus and village-based breeding programs. Implications of results of simulated selection programs on the ongoing Menz sheep improvement program are discussed.

In this study, maternal effects were described as age of dam at first and second calving, first-lactation body condition score (BCS) of the dam during gestation, and milk yield of the dam. The impact of these effects on first-lactation daughter BCS, fertility, and test-day milk yield was assessed. The effect of milk yield of dam on daughter 305-d yield in the latter's first 3 lactations was also investigated. The proportion of total phenotypic variance in daughter traits accounted for by maternal effects was calculated. Dams calving early for the first time (18 to 23 mo of age) had daughters that produced 4.5% more first-lactation daily milk, had 7% higher BCS, and had their first service 3 d earlier than cows whose dams calved late (30 to 36 mo). However, daughters of dams that calved early had difficulties conceiving as they needed 7% more inseminations and had a 7.5% higher return rate. Cows from second calvings of relatively young (36 to 41 mo) dams produced 6% more first-lactation daily milk, had 2% higher BCS, and showed a significantly better fertility profile than cows whose dams calved at a late age (47 to 55 mo) High maternal BCS during gestation had a favorable effect on daughter BCS, nonreturn rate, and number of inseminations per conception. However, it was also associated with a small decrease in daughter daily milk yield. Changes in dam BCS during gestation did not affect daughter performance significantly. Maternal effects of milk yield of the dam, expressed as her permanent environment during lactation, adversely affected daughter 305-d milk, fat, and protein yield. However, although the effect was significant, it was practically negligible (

Increases in genetic merit for milk yield are associated with increases in mobilization of body reserves. This study assessed the effects of genotype by environment (GxE) interactions on milk yield and energy and protein balances. Heifers (n = 100) with high or low genetic merit for milk yield were milked 2 or 3 times a day and received rations of low or high caloric density. The management factors were selected to induce substantial differences in milk production levels and model different management strategies. The 2 x 2 x 2 factorial arrangement enables the assessment of the effects of genotype, environment, and GxE interactions. Mean daily energy-corrected milk production in the first 100 d in milk varied between 21.8 and 35.2 kg among the groups. The experimental factors affected milk production in the presumed direction. Ration was the most determinant factor on milk production. Effects of milking frequency and genetic merit were significant only in the groups that were fed rations with high caloric density. Signs for severe negative energy balances, protein balances, and low body condition scores, all of which may be indicative of health risks, were not concentrated in the highest producing cows. Feed caloric density and milking frequency had stronger effects on energy balances and protein balances, with unfavorable effects of low caloric density feed and an extra milking. This emphasizes the possible effect of mismanagement on animal health risks. High genetic merit cows had significantly lower postpartum body condition scores. Genotype x environment interactions existed, but more information is needed to determine if cows of different genetic merit for milk yield are differently at risk for disease under specific conditions. High milk production levels per se will increase allostatic load, but need not compromise the health status of relatively young cows. Ongoing one-sided selection for high yield may be combined with good animal health, but because high genetic merit for milk yield seems intrinsically connected to the allocation of resources from maintenance toward milk, this puts increasing demands on farmers¿ time and management skills.

Estimates of genetic parameters for organic dairy farming have not been published previously, and neither is information available on the magnitude of genotype by environment interaction (GxE) between organic and conventional farming. However, organic farming is growing worldwide and basic information about genetic parameters is needed for future breeding strategies for organic dairy farming. The goal of this study was to estimate heritabilities of milk production traits under organic farming conditions and to estimate the magnitude of GxE between organic and conventional dairy farming. For this purpose, production records of first-parity Holstein heifers were used. Heritabilities of milk, fat and protein yield, and somatic cell score (SCS) were higher under organic farming conditions. For percentages of fat and protein, heritabilities of organic and conventional production were very similar. Genetic correlations between preorganic and organic, and organic and conventional milk production were 0.79 and 0.80, respectively. For fat yield, these correlations were 0.86 and 0.88, and for protein yield, these were 0.78 and 0.71, respectively. Our findings indicate that moderate GxE was present for yield traits. For percentage of fat and protein and SCS, genetic correlations between organic and conventional and preorganic production were close to unity, indicating that there was no GxE for these traits.

The objective of the present study was to use bivariate mixture models to study the relationships between body weight (BW) and ascites indicator traits. Existing data were used from an experiment in which birds were housed in 2 groups under different climate conditions. In the first group, BW, the ratio of right ventricular weight to total ventricular weight (RV:TV), and hematocrit value (HCT) were measured in 4,202 broilers under cold conditions; in the second group, the same traits were measured in 795 birds under normal temperature conditions. Cold-stress conditions were applied to identify individuals that were susceptible to ascites. The RV:TV and HCT were approximately normally distributed under normal temperature conditions, whereas the distributions of these traits were skewed under cold temperature conditions, suggesting different underlying distributions. Fitting a bivariate mixture model to the observations showed that there was only one homogeneous population for ascites traits under normal temperature conditions, whereas there was a mixture of (2) distributions under cold conditions. One distribution contained nonascitic birds and the other distribution contained ascitic birds. In the distribution of nonascitic birds, the inferred phenotypic correlations (phenotypic correlations with 2 distinguishing underlying distributions) of BW with RV:TV and HCT were close to zero (0.10 and ¿0.07, respectively), whereas in the distribution of ascitic birds, the inferred phenotypic correlations of BW with RV:TV and HCT were negative (¿0.39 and ¿0.4, respectively). The negative inferred correlations of BW with RV:TV and HCT in the distribution of ascitic birds resulted in negative overall correlations (correlations without 2 distinguishing distributions) of BW with RV:TV (¿0.30) and HCT (¿0.37) under cold conditions. The present results indicate that the overall correlations between BW and ascites traits are dependent on the relative frequency of ascitic and nonascitic birds in the population.

Longevity is an increasingly important trait in beef cattle. Increased longevity decreases costs for the farmer and increases revenue. The objective of this research was to investigate the phenotypic relationship between type traits and longevity in Chianina beef cattle, and the relationship between production and longevity, to analyze the effect of voluntary culling. Data included records on reproductive, productive, and type traits provided by the National Association of Italian Beef Cattle Breeders from 6,395 Chianina cows. The average length of productive life was 1,829 d. The herd-year had a strong effect on the risk of culling. The effects of 22 type traits were analyzed. All the muscularity traits analyzed were highly significant (P

International audience; The research with respect to displacement of the abomasum (DA) in dairy cattle is reviewed. Evaluated articles describe epidemiological and experimental studies. The occurrence is elevated with regard to breed, gender, age, concurrent diseases, environmental aspects and production levels as contributing factors and emphasis is placed on the effects of nutrition and metabolism. Reviewing the experimental work, distinction is made between the research into gas production in the abomasum and hypomotility of the abomasum, since both represent presumed pathways in the development of DA. Although the different fields of research have positive contributions to the understanding of the pathogenesis of DA, contradictions in the different studies are present. This is partly due to extrapolation of results from sheep to cows, or because of a low number of cows in the experiments. Finally, general suggestions are made for further research in the field of the pathogenesis of DA.

In the double-muscled (DM) Belgian Blue beef (BBB) breed, caesarean section (CS) is being applied systematically as a management tool to prevent dystocia. As a matter of fact, CS is the only possible way of calving in the breed. High birth weight and a relatively small pelvic area are the main causes of dystocia and, in the DM-BBB breed, the reasons for the systematically applied CS. Selection for lower birth weight and larger pelvic sizes might reduce dystocia and routine CS. Few data on inner pelvic sizes of pedigree animals are available. Using external measurements to estimate the inner pelvic sizes might be an option to resolve this problem. In this study, animals of the DM-BBB breed were measured and weighed on farms and in abattoirs. External and internal pelvic sizes increased with live weight and age of the animals. Gender had a significant influence on inner pelvic traits. Increased muscular conformation was associated with decreased inner pelvic dimensions. Models with weight, gender, age, withers height and outer pelvic width (TcTc) can be used to estimate inner pelvic sizes (R-2 between 0.35 and 0.77). The estimated inner pelvic sizes can then be used to genetically evaluate pelvic traits in the DM-BBB breed. Improving weight, withers height and TcTc width in combination with lowering muscular conformation may help to decrease the high rate of caesarean section in the DM-BBB.

Background In developing dairy sectors, genetic improvement programs have limited resources and recording of herds is minimal. This study evaluated different methods to estimate lactation yield and sampling schedules with fewer test-day records per lactation to determine recording regimes that (1) estimate lactation yield with a minimal impact on the accuracy of selection and (2) optimise the available resources. Methods Using Sahiwal cattle as a tropical dairy breed example, weekly milk records from 464 cows were used in a simulation study to generate different shaped lactation curves. The daily milk yields from these simulated lactation curves were subset to equally spaced (weekly, monthly and quarterly) and unequally spaced (with four, five or six records per lactation) test-day intervals. Lactation yield estimates were calculated from these subsets using two methods: the test-interval method and Wood’s (Nature 216:164-165, 1967) lactation curve model. Using the resulting lactation yields, breeding values were predicted and comparisons were made between the sampling regimes and estimation methods. Results The results show that, based on the mean square error of prediction, use of Wood’s lactation curve model to estimate total yield was more accurate than use of the test-interval method. However, the differences in the ranking of animals were small, i.e. a 1 to 5% difference in accuracy. Comparisons between the different test-day sampling regimes showed that, with the same number of records per lactation (for example, quarterly and four test-days), strategically timed test-days can result in more accurate estimates of lactation yield than test-days at equal intervals. Conclusions An important outcome of these results is that combining Wood’s model for lactation yield estimation and as few as four, five or six strategically placed test-day records can produce estimates of lactation yield that are comparable with estimates based on monthly test-day records using the test-interval method. Furthermore, calculations show that although using fewer test-days results in a decrease in the accuracy of selection, it does provide an opportunity to progeny-test more sires. Thus, using strategically timed test-days and Wood’s model to estimate lactation yield, can lead to a more efficient use of the allocated resources. Electronic supplementary material The online version of this article (doi:10.1186/s12711-014-0078-0) contains supplementary material, which is available to authorized users.

The aim of this study was to estimate the heritability for some growth traits of Japanese quail through the estimation of variance components by Bayesian methodology. For this purpose, 340 progenies of 34 sires were used. Live weight (LW42) and absolute and relative growth rates at 42 days of age (AGR42 and RGR42, respectively) were submitted to single-trait analysis under a sire model. A software (package MCMCglmm) was used for the estimations, and a single chain with 65,000 rounds was run for each trait with a thinning interval of 50. Burn-in was set at 15,000 and inferences were built on posterior samples of 1,000 draws for each trait. All marginal posterior densities were unimodal and marginal posterior distributions of sire variance are slightly skewed to the right. The results of the analyses showed high, moderate, and low heritability of LW42, AGR42, and RGR42, respectively. Akdeniz University Scientific Research Projects ManagementAkdeniz University [2011.03.0121.005] This research study, under project number 2011.03.0121.005, was funded by the Akdeniz University Scientific Research Projects Management.

Osteochondrosis (OC) is a degenerative joint condition developing in a short time frame in young growing gilts that may cause lameness at an older age, affecting welfare and leading to premature culling of breeding sows. Causes of OC are multifactorial including both genetic and environmental factors. Floor type has been suggested to affect OC prevalence and effects might be age dependent during the rearing period. The aim of this study was to investigate possible age-dependent effects of floor type, conventional concrete partially slatted versus wood shavings as deep bedding, on OC prevalence in gilts (Dutch Large White × Dutch Landrace) at slaughter (24 wk of age; 106.5 [14.7 SD] kg of BW). At weaning (4 wk of age; 6.9 [1.3 SD] kg of BW), 212 gilts were subjected to 1 of 4 flooring regimens. Gilts were either subjected to a conventional floor from weaning until slaughter (CC), wood shavings as bedding from weaning until slaughter (WW), a conventional floor from weaning until 10 wk of age after which gilts were switched to wood shavings as bedding (CW), or wood shavings as bedding from weaning until 10 wk of age after which gilts were switched to a conventional floor (WC). After slaughter the elbow, hock, and knee joints were macroscopically examined for OC and scored on a 5 point scale where 0 indicates no OC and 4 indicates the severest form of OC. There was no significant difference (P > 0.4) between treatments on the overall OC prevalence for any joint assessed or at the animal level (all joints combined). At the animal level, however, gilts had greater odds to have OC scores 3 and 4 in the CW treatment (odds ratios [OR] = 2.3; P = 0.05), WC treatment (OR = 2.6; P = 0.02), and WW treatment (OR = 3.7; P < 0.001) compared with gilts in the CC treatment. The results indicate that there are no age-dependent effects of floor types on overall OC prevalence. However, wood shavings as bedding seems to increase the odds for severe OC and might affect animal welfare in the long term.

Because of a ban on the use of beak trimming in some European countries, feather pecking is becoming a substantial problem in the layer industry, both from animal welfare and economic points of view. The feather condition score (FCS) as a measure of feather damage has been shown to be closely related to feather pecking behavior in laying hens housed in groups. To obtain a better understanding of genetic and other biological mechanisms underlying feather pecking behavior, data on FCS of a population of 2,724 female offspring from crossing 50 male W1 and 907 female WB purebred lines were used. The offspring of 25 sires were beak-trimmed, and the offspring of another 25 sires were non-beak-trimmed. Titers of plasma natural antibody (NAb) isotypes IgM and IgG binding keyhole limpet hemocyanin at 24 wk of age were measured. Feather condition was scored at 53 wk of age. In the first part of the present study, we estimated genetic parameters for FCS with 2 variance components models: a traditional linear animal model and a model combining direct and associative genetic effects. In the second part of the present study, a trait-based analysis for FCS was conducted to investigate whether NAb isotype titers can explain variation in FCS among individuals, by fitting a linear mixed model. Though the estimated associative genetic variance was substantial, associative effects for FCS were not statistically significant in both populations (P = 0.09 in beak-trimmed birds, and P = 0.08 in non-beak-trimmed birds). This suggests an insufficient number of records on FCS. Individual's NAb isotypes titers did not show direct effect for FCS of itself, but individual's IgG titers showed a suggestive effect on the FCS of cage mates (associative effect) in beak-trimmed laying hens, which need further confirmation.

International audience; Background Identifying the relevant environmental variables that cause GxE interaction is often difficult when they cannot be experimentally manipulated. Two statistical approaches can be applied to address this question. When data on candidate environmental variables are available, GxE interaction can be quantified as a function of specific environmental variables using a reaction norm model. Alternatively, a factor analytic model can be used to identify the latent common factor that explains GxE interaction. This factor can be correlated with known environmental variables to identify those that are relevant. Previously, we reported a significant GxE interaction for body weight at harvest in rainbow trout reared on three continents. Here we explore their possible causes.MethodsReaction norm and factor analytic models were used to identify which environmental variables (age at harvest, water temperature, oxygen, and photoperiod) may have caused the observed GxE interaction. Data on body weight at harvest was recorded on 8976 offspring reared in various locations: (1) a breeding environment in the USA (nucleus), (2) a recirculating aquaculture system in the Freshwater Institute in West Virginia, USA, (3) a high-altitude farm in Peru, and (4) a low-water temperature farm in Germany. Akaike and Bayesian information criteria were used to compare models.ResultsThe combination of days to harvest multiplied with daily temperature (Day*Degree) and photoperiod were identified by the reaction norm model as the environmental variables responsible for the GxE interaction. The latent common factor that was identified by the factor analytic model showed the highest correlation with Day*Degree. Day*Degree and photoperiod were the environmental variables that differed most between Peru and other environments. Akaike and Bayesian information criteria indicated that the factor analytical model was more parsimonious than the reaction norm model.ConclusionsDay*Degree and photoperiod were identified as environmental variables responsible for the strong GxE interaction for body weight at harvest in rainbow trout across four environments. Both the reaction norm and the factor analytic models can help identify the environmental variables responsible for GxE interaction. A factor analytic model is preferred over a reaction norm model when limited information on differences in environmental variables between farms is available.

In the era of genome-wide selection (GWS), genotype-by-environment (G×E) interactions can be studied using genomic information, thus enabling the estimation of SNP marker effects and the prediction of genomic estimated breeding values (GEBVs) for young candidates for selection in different environments. Although G×E studies in pigs are scarce, the use of artificial insemination has enabled the distribution of genetic material from sires across multiple environments. Given the relevance of reproductive traits such as the total number born (TNB) and the variation in environmental conditions encountered by commercial dams, understanding G×E interactions can be essential to choose the best sires for different environments. The present work proposes a two-step reaction norm approach for G×E analysis using genomic information. The first step provided estimates of environmental effects (herd-year-season - HYS), and the second step provided estimates of the intercept and slope for the TNB across different HYS levels, obtained from the first step, using a random regression model. In both steps, pedigree (A) and genomic (G) relationship matrices were considered. The genetic parameters (variance components, h2 and genetic correlations) were very similar when estimated using the A and G relationship matrices. The reaction norm graphs showed considerable differences in environmental sensitivity between sires, indicating a reranking of sires in terms of genetic merit across the HYS levels. Based on the G matrix analysis, SNP by environment interactions were observed. For some SNPs, the effects increased at increasing HYS levels, while for others, the effects decreased at increasing HYS levels or showed no changes between HYS levels. Cross-validation analysis demonstrated better performance of the genomic approach with respect to traditional pedigrees for both the G×E and standard models. The genomic reaction norm model resulted in an accuracy of GEBVs for “juvenile” boars varying from 0.14 to 0.44 across different HYS levels, while the accuracy of the standard genomic prediction model, without reaction norms, varied from 0.09 to 0.28. These results show that it is important and feasible to consider G×E interactions in evaluations of sires using genomic prediction models and that genomic information can increase the accuracy of selection across environments.

The objective of this review was to describe, compare and evaluate agreement, reliability, and validity of manual and automatic locomotion scoring systems (MLSSs and ALSSs, respectively) used in dairy cattle lameness research. There are many different types of MLSSs and ALSSs. Twenty-five MLSSs were found in 244 articles. MLSSs use different types of scale (ordinal or continuous) and different gait and posture traits need to be observed. The most used MLSS (used in 28% of the references) is based on asymmetric gait, reluctance to bear weight, and arched back, and is scored on a five-level scale. Fifteen ALSSs were found that could be categorized according to three approaches: (a) the kinetic approach measures forces involved in locomotion, (b) the kinematic approach measures time and distance of variables associated to limb movement and some specific posture variables, and (c) the indirect approach uses behavioural variables or production variables as indicators for impaired locomotion. Agreement and reliability estimates were scarcely reported in articles related to MLSSs. When reported, inappropriate statistical methods such as PABAK and Pearson and Spearman correlation coefficients were commonly used. Some of the most frequently used MLSSs were poorly evaluated for agreement and reliability. Agreement and reliability estimates for the original four-, five- or nine-level MLSS, expressed in percentage of agreement, kappa and weighted kappa, showed large ranges among and sometimes also within articles. After the transformation into a two-level scale, agreement and reliability estimates showed acceptable estimates (percentage of agreement = 75%; kappa and weighted kappa = 0.6), but still estimates showed a large variation between articles. Agreement and reliability estimates for ALSSs were not reported in any article. Several ALSSs use MLSSs as a reference for model calibration and validation. However, varying agreement and reliability estimates of MLSSs make a clear definition of a lameness case difficult, and thus affect the validity of ALSSs. MLSSs and ALSSs showed limited validity for hoof lesion detection and pain assessment. The utilization of MLSSs and ALSSs should aim to the prevention and efficient management of conditions that induce impaired locomotion. Long-term studies comparing MLSSs and ALSSs while applying various strategies to detect and control unfavourable conditions leading to impaired locomotion are required to determine the usefulness of MLSSs and ALSSs for securing optimal production and animal welfare in practice.

Feed is a major component of variable costs associated with dairy systems and is therefore an important consideration for breeding objectives. As a result, measures of feed efficiency are becoming popular traits for genetic analyses. Already, several countries account for feed efficiency in their breeding objectives by approximating the amount of energy required for milk production, maintenance, etc. However, variation in actual feed intake is currently not captured in dairy selection objectives, although this could be possible by evaluating traits such as residual feed intake (RFI), defined as the difference between actual and predicted feed (or energy) intake. As feed intake is expensive to accurately measure on large numbers of cows, phenotypes derived from it are obvious candidates for genomic selection provided that: (1) the trait is heritable; (2) the reliability of genomic predictions are acceptable to those using the breeding values; and (3) if breeding values are estimated for heifers, rather than cows then the heifer and cow traits need to be correlated. The accuracy of genomic prediction of dry matter intake (DMI) and RFI has been estimated to be around 0.4 in beef and dairy cattle studies. There are opportunities to increase the accuracy of prediction, for example, pooling data from three research herds (in Australia and Europe) has been shown to increase the accuracy of genomic prediction of DMI from 0.33 within country to 0.35 using a three-country reference population. Before including RFI as a selection objective, genetic correlations with other traits need to be estimated. Weak unfavourable genetic correlations between RFI and fertility have been published. This could be because RFI is mathematically similar to the calculation of energy balance and failure to account for mobilisation of body reserves correctly may result in selection for a trait that is similar to selecting for reduced (or negative) energy balance. So, if RFI is to become a selection objective, then including it in an overall multi-trait selection index where the breeding objective is net profit is sensible, as this would allow genetic correlations with other traits to be properly accounted for. If genetic parameters are accurately estimated then RFI is a logical breeding objective. If there is uncertainty in these, then DMI may be preferable.

Background Digital Dermatitis (DD) is a common disease of dairy cows, the pathogenesis of which is still not clear. This study examined some host responses associated with the typical lesions, in an attempt to further elucidate the pathogenesis of the disease. Twenty four samples representing the 5 different clinical stages of DD (M0-M4) were collected from slaughtered cattle for histopathological and immunological analyses. Results Significant increases in total epidermal thickness were found in M2, M3, and M4 when compared with M0 and M1. M3 samples, when compared with M0 and M1, were characterized by a significant increase in the thickness of the keratin layer. Counts of both eosinophils and neutrophils were at a maximum in the M2 stage and decreased in the M3 and M4 stage. A significant increase in IL8 expression was observed in the M2-M3 stages of the disease and immunohistochemical staining showed the source as keratinocytes, suggesting an important role for keratinocyte-derived IL8 in the pathogenesis of DD. Conclusion Results of the present study point to a strong stimulation of the innate immune response at the level of the keratinocytes throughout most of the clinical stages, and a delayed response of the adaptive immune reaction.

Increasing litter size has long been a goal of pig breeders and producers, and may have implications for pig (Sus scrofa domesticus) welfare. This paper reviews the scientific evidence on biological factors affecting sow and piglet welfare in relation to large litter size. It is concluded that, in a number of ways, large litter size is a risk factor for decreased animal welfare in pig production. Increased litter size is associated with increased piglet mortality, which is likely to be associated with significant negative animal welfare impacts. In surviving piglets, many of the causes of mortality can also occur in non-lethal forms that cause suffering. Intense teat competition may increase the likelihood that some piglets do not gain adequate access to milk, causing starvation in the short term and possibly long-term detriments to health. Also, increased litter size leads to more piglets with low birth weight which is associated with a variety of negative long-term effects. Finally, increased production pressure placed on sows bearing large litters may produce health and welfare concerns for the sow. However, possible biological approaches to mitigating health and welfare issues associated with large litters are being implemented. An important mitigation strategy is genetic selection encompassing traits that promote piglet survival, vitality and growth. Sow nutrition and the minimisation of stress during gestation could also contribute to improving outcomes in terms of piglet welfare. Awareness of the possible negative welfare consequences of large litter size in pigs should lead to further active measures being taken to mitigate the mentioned effects.

Random regression models were used to estimate the types and orders of random effects of (co)variance functions in the description of the growth trajectory of the Simbrasil cattle breed. Records for 7049 animals totaling 18,677 individual weighings were submitted to 15 models from the third to the fifth order including as fixed effects sex, contemporary group, feeding regimen, and type of reproduction and as random effects additive direct genetic effect, animal permanent environment, maternal additive genetic effect, and maternal permanent environment. The best-fit model presented order five to additive direct genetic effect, animal permanent environment, and maternal additive effect, with 6 classes of residual variances, and the maternal permanent environment effect was not significant, likely owing to the low average number of calves per cow. However, the model chosen for the growth curve presents three classes of residual variances, because even not showing the best fit it is more parsimonious, in addition to promoting a more realistic estimate of heritability.

The protein and fat content of Dutch bulk milk has been monitored since the 1950s and has increased considerably, by 11 and 20%, respectively, whereas milk yield has more than doubled. The change in protein and fat content of milk is advantageous for the dairy industry, as these are the 2 most economically valuable constituents of milk. Increases in protein and fat content of milk have allowed increases in the yield of various products such as cheese and butter. However, for cheese and other applications where casein micelles play a crucial role in structure and stability, it is not only casein content, but also the properties of the casein micelles that determine processability. Of particular importance herein is the salt partition in milk, but it is unknown whether increased protein content has affected the milk salts and their distribution between casein micelles and milk serum. It was, therefore, the objective of this research to determine the salt composition and protein content for individual cow milk and bulk milk over a period of 1 yr and to compare these data to results obtained during the 1930s, 1950s, and 1960s in the last century. Calcium, magnesium, sodium, potassium, and phosphorus content were determined by inductively coupled plasma atomic emission spectrometry and inorganic phosphate, citrate, chloride, and sulfate content by anion-exchange chromatography in bulk milk and milk ultracentrifugate. In addition, ionic calcium and ionic magnesium concentration were determined by the Donnan membrane technique. We concluded that historical increase in milk yield and protein content in milk have resulted in correlated changes in casein content and the micellar salt fraction of milk. In addition, the essential nutrients, calcium, magnesium, and phosphorus in milk have increased the past 75 yr; therefore, the nutritional value of milk has improved. Key words: milk protein , casein , calcium phosphate , magnesium

Piglet birth weight and litter uniformity were studied in sows of different parities and crossbred lines in relation to 1) the weaning-to-pregnancy interval (WPI); and 2) sow body condition changes (in BW and backfat thickness) during lactation and gestation in sows with a short WPI (= 7d). At the IPG research farm, individual piglet birth weights and sow body condition (BW and backfat thickness at farrowing and weaning) were measured of 949 TOPIGS20 and 889 TOPIGS40 sows with > 4 total born piglets, inseminated between 2003 and 2011. In all analyses, mean piglet birth weight and birth weight SD and CV were corrected for total number born. Total number born was higher in sows with a WPI of 8 to 21d (+ 1.2 piglets; n = 72) and >21d (+ 0.7 piglets; n = 182) compared with sows with a WPI = 7d (P 21d compared with sows with a WPI = 7d (P

Background Improvement of feed efficiency in pigs is of great economical and environmental interest and contributes to use limited resources efficiently to feed the world population. Genome scans for feed efficiency traits are of importance to reveal the underlying biological causes and increase the rate of genetic gain. The aim of this study was to determine the genomic architecture of feed efficiency measured by residual energy intake (REI), in association with production, feed conversion ratio (FCR) and nitrogen excretion traits through the identification of quantitative trait loci (QTL) at different stages of growth using a three generation full-sib design population which originated from a cross between Pietrain and a commercial dam line. Results Six novel QTL for REI were detected explaining 2.7-6.1% of the phenotypic variance in REI. At growth from 60–90 kg body weight (BW), a QTL with a significant dominance effect was identified for REI on SSC14, at a similar location to the QTL for feed intake and nitrogen excretion traits. At growth from 90–120 kg BW, three QTL for REI were detected on SSC2, SSC4 and SSC7 with significant additive, imprinting and additive effects, respectively. These QTL (except for the imprinted QTL) were positionally overlapping with QTL for FCR and nitrogen excretion traits. During final growth (120–140 kg BW), a further QTL for REI was identified on SSC8 with significant additive effect, which overlapped with QTL for nitrogen excretion. During entire analysed growth (60–140 kg BW), a novel additive QTL for REI on SSC4 was observed, with no overlapping with QTL for any other traits considered. Conclusions The occurrence of only one overlapping QTL of REI with feed intake suggests that only a small proportion of the variance in REI was explained by change in feed intake, whereas four overlapping QTL of REI with those of nitrogen excretion traits suggests that mostly underlying factors of feed utilisation such as metabolism and protein turnover were the reason for change in REI. Different QTL for REI were identified at different growth stages, indicating that different genes are responsible for efficiency in feed utilisation at different stages of growth.

Pigs housed together in a group influence each other’s growth. Part of this effect is genetic and can be represented in a social breeding value. It is unknown, however, which traits are associated with social breeding values. The aim of this study was, therefore, to investigate whether personality and response to novelty could be associated with social breeding values for growth in piglets. Female and castrated male piglets from 80 litters, with either an estimated relative positive or negative social breeding value (+SBV or –SBV) for growth, were individually tested in a backtest and novel environment test, and group-wise in a novel object (i.e., a feeder with feed) test and human approach test. All tests were performed during the suckling period. No differences between +SBV and –SBV piglets were found for the frequency and latency of struggling and vocalizing in the backtest (at least, P > 0.30). In the novel object test, piglets with a +SBV for growth touched the feeder faster than piglets with –SBV for growth (P = 0.01) and were more frequently present near the person in the human approach test (P 0.40), but piglets that struggled more in the backtest walked more in this test (P = 0.02). Behavior was affected by gender in each test. Female piglets were faster than castrated male piglets to start struggling in the backtest (P = 0.047). In the novel object test, females were faster than males to touch the feeder and sample the feed. In the human approach test, they were also faster than male piglets to touch a person (all, P

Background: Through social interactions, individuals affect one another’s phenotype. In such cases, an individual’s phenotype is affected by the direct (genetic) effect of the individual itself and the indirect (genetic) effects of the group mates. Using data on individual phenotypes, direct and indirect genetic (co)variances can be estimated. Together, they compose the total genetic variance that determines a population’s potential to respond to selection. However, it can be difficult or expensive to obtain individual phenotypes. Phenotypes on traits such as egg production and feed intake are, therefore, often collected on group level. In this study, we investigated whether direct, indirect and total genetic variances, and breeding values can be estimated from pooled data (pooled by group). In addition, we determined the optimal group composition, i.e. the optimal number of families represented in a group to minimise the standard error of the estimates. Methods: This study was performed in three steps. First, all research questions were answered by theoretical derivations. Second, a simulation study was conducted to investigate the estimation of variance components and optimal group composition. Third, individual and pooled survival records on 12 944 purebred laying hens were analysed to investigate the estimation of breeding values and response to selection. Results: Through theoretical derivations and simulations, we showed that the total genetic variance can be estimated from pooled data, but the underlying direct and indirect genetic (co)variances cannot. Moreover, we showed that the most accurate estimates are obtained when group members belong to the same family. Additional theoretical derivations and data analyses on survival records showed that the total genetic variance and breeding values can be estimated from pooled data. Moreover, the correlation between the estimated total breeding values obtained from individual and pooled data was surprisingly close to one. This indicates that, for survival in purebred laying hens, loss in response to selection will be small when using pooled instead of individual data. Conclusions: Using pooled data, the total genetic variance and breeding values can be estimated, but the underlying genetic components cannot. The most accurate estimates are obtained when group members belong to the same family.

Harvest weight has been the main selected trait for the GIFT strain of Nile tilapia (Oreochromis niloticus). However, growth rate and body shape are traits of increasing interest. In the Mekong Delta of Vietnam, intensive river-cage culture and low-input ponds are the most important production environments, whereas the breeding program is conducted in an intensive nucleus pond. The first objective was to estimate heritability and phenotypic and genetic correlations for harvest weight (HW), growth rate expressed as daily growth coefficient (DGC), condition factor (K), and shape expressed as ellipticity: mid-sagittal plane (EL-H), transverse plane (EL–T), and frontal plane (EH–T). The second objective was to estimate genotype by environment interactions (G × E), expressed as the genetic correlation (rg) between the nucleus and two production environments, cage and VAC (Vietnamese acronym for garden, pond and livestock pen), for these traits. Data were obtained from the 13th generation of selection of GIFT. Within the breeding nucleus, heritability was high for HW, DGC, but low for K, EL–H, EL–T, and EH–T. DGC was positively correlated with condition factor K (rg = 0.59), while the rg of HW with K was non-significant. This suggests that selection for harvest weight alone will not result in fish with higher condition factor. Genetic correlations between HW and body dimensions (L, H, T) were 0.89–0.98, but genetic correlations of DGC with ellipticity showed that fish selected for high growth rate will become more rotund rather than simply larger. GxE was minor for harvest weight and for growth, but substantial for shape traits. For DGC, genetic correlation was 0.77 between cage and VAC, but higher between the breeding nucleus and cage or VAC. For EL-H, substantial GxE (rg 0.54) was found between cage and nucleus pond. GxE was also found for EL–T between cage–VAC (rg 0.51), and for EH–T across all three environments, although with high standard errors of estimates. We conclude that selection in nucleus ponds will produce desired correlated responses in Nile tilapia grown in river-cages as they are expected to develop a more rotund and thicker body shape at the same length compared to fish grown in ponds.

The main focus of this study was to identify sow gestation features that affect growth rate (GR) and feed intake (FI) of their offspring during grower–finishing stage. Because the sow provides a specific environment to her offspring during gestation, certain features (e.g., BW of the sow), feed refusals or gestation group, may affect her ability to deliver and feed a healthy litter. Data on 17,743 grower–finishing pigs, coming from 604 sires and 681 crossbred sows, were obtained from the Institute for Pigs Genetics. Sow gestation features were collected during multiple gestations and divided into 3 clusters describing i) sow body condition (i.e., BW, backfat, and gestation length), ii) sow feed refusals (FR), the difference between offered and eaten feed during 3 periods of gestation: 1 to 28, 25 to 50, 45 to 80 d, and iii) sow group features (i.e., number of sows, and average parity). Sow gestation features were added to the base model 1 at a time to study their effect on GR and FI. Significant gestation features (P

Enhancing selection using two-stage selection is normally implemented by pre-selection for tagging weight (BWT) and by final selection for ungutted harvest weight (BWH) and thermal growth coefficient from tagging to harvest (TGC TH ). However, selection on harvest traits, i.e., gutted weight (GBWH), visceral percentage (VISW%), condition factor (CFH), and overall survival (SURV), can be enhanced by exploiting correlated traits. It can be hypothesized that the efficiency of two-stage selection on genetic response in BWH and TGC TH is dependent on their genetic ( r g ) and phenotypic ( r p ) correlations with BWT and therefore dependent on the time point of pre-selection. The aims of this study were, first, to estimate genetic parameters (heritability: h 2 , r p , and r g ) for BWT (7 months), BWS (weight at sorting, 9 months), BWH (14 months), TGC TH , GBWH, VISW%, CFH, and SURV. Second, these genetic parameters were used in two deterministic simulation studies; i) one- and two-stage selections to compare genetic responses in BWH and TGC TH , and ii) alternative selection indices using correlated traits to compare corresponding accuracy of selection ( r IH ) for slaughter traits, CFH, and SURV. Genetic parameters were estimated using an animal mixed model in ASReml on 2,041 fish records. The main results showed that, first, r g of BWT was 0.35 with BWH but − 0.25 with TGC TH , whereas the r g of BWS was 0.72 with BWH but 0.39 with TGC TH . Pre-selection for BWS led to genetic response of 54.15 g in BWH which was higher than the genetic response from pre-selection for BWT (51.90 g). Similarly, pre-selection on BWS enhanced correlated genetic response in TGC TH to 0.30 g (1/3) /°C*day. In contrast, pre-selection for BWT resulted in lower correlated genetic response in TGC TH of 0.20 g (1/3) /°C*day. It can be concluded that genetic improvement of BWH and TGC TH can be enhanced by postponing pre-selection to a later age. However, an optimal time point for tagging and pre-selection should be found to minimize common environmental effects and rearing costs during communal rearing of full-sibs. Second, including GBWH in a selection index can reduce unfavourable selection responses in VISW%. The GBWH is highly genetically correlated with BWH and can be easily indirectly selected. TGC TH is a good predictor for selection for lower VISW%, and higher SURV, but not for higher CFH. To control genetic changes in the condition factor, it should be included to the selection index.

Rainbow trout is a globally important fish species for aquaculture. However, fish for most farms worldwide are produced by only a few breeding companies. Selection based solely on fish performance recorded at a nucleus may lead to lower-than-expected genetic gains in other production environments when genotype-by-environment (G × E) interaction exists. The aim was to quantify the magnitude of G × E interaction of growth traits (tagging weight; BWT, harvest weight; BWH, and growth rate; TGC) measured across 4 environments, located in 3 different continents, by estimating genetic correlations between environments. A total of 100 families, of at least 25 in size, were produced from the mating 58 sires and 100 dams. In total, 13,806 offspring were reared at the nucleus (selection environment) in Washington State (NUC) and in 3 other environments: a recirculating aquaculture system in Freshwater Institute (FI), West Virginia; a high-altitude farm in Peru (PE), and a cold-water farm in Germany (GER). To account for selection bias due to selective mortality, a multitrait multienvironment animal mixed model was applied to analyze the performance data in different environments as different traits. Genetic correlation (rg) of a trait measured in different environments and rg of different traits measured in different environments were estimated. The results show that heterogeneity of additive genetic variances was mainly found for BWH measured in FI and PE. Additive genetic coefficient of variation for BWH in NUC, FI, PE, and GER were 7.63, 8.36, 8.64, and 9.75, respectively. Genetic correlations between the same trait in different environments were low, indicating strong reranking (BWT: rg = 0.15 to 0.37, BWH: rg = 0.19 to 0.48, TGC: rg = 0.31 to 0.36) across environments. The rg between BWT in NUC and BWH in both FI (0.31) and GER (0.36) were positive, which was also found between BWT in NUC and TGC in both FI (0.10) and GER (0.20). However, rg were negative between BWT in NUC and both BWH (–0.06) and TGC (–0.20) in PE. Correction for selection bias resulted in higher additive genetic variances. In conclusion, strong G × E interaction was found for BWT, BWH, and TGC. Accounting for G × E interaction in the breeding program, either by using sib information from testing stations or environment-specific breeding programs, would increase genetic gains for environments that differ significantly from NUC.

Osteochondrosis (OC) is one of the main causes of leg weakness causing premature culling in breeding sows and develops in a short time frame in young growing gilts. Dietary restriction may have different effects on OC prevalence depending on the age of the gilts. The aim of this study is to investigate age dependent effects of dietary restriction, ad libitum versus restricted (80% of ad libitum), on the occurrence of OC in gilts at slaughter (26 wk of age). At weaning (4 wk of age), 211 gilts were subjected to one of 4 treatments of feeding regime. Gilts were administered either ad libitum feeding from weaning until slaughter (AA); restricted feeding from weaning until slaughter (RR); ad libitum feeding from weaning until 10 wk of age, after which gilts were switched to restricted feeding (AR); or restricted feeding from weaning until 10 wk of age, after which gilts were switched to ad libitum feeding (RA). At slaughter, the elbow, hock, and knee joints were harvested. Joints were scored macroscopically for articular surface deformations indicative of OC. Gilts in the RA treatment had significantly higher odds to be affected with OC than gilts in the RR and AR treatments in the hock joint (OR = 3.3, P = 0.04 and OR = 8.5, P = 0.002, respectively), and at animal level (OR = 2.5, P = 0.001 and OR = 1.9, P = 0.01, respectively). Gilts in the AA treatment had higher odds to be affected with OC than gilts in the AR treatment in the hock joint (OR = 5.3, P = 0.01). The results indicate a possible pathway to reduce the prevalence of OC in breeding gilts which will have to last several parities. Switching from restricted feeding to ad libitum feeding after 10 wk of age increases OC prevalence as opposed to restricted feeding after 10 wk of age.

The Creole goat is a local breed used for meat production in Guadeloupe (French West Indies). As in other tropical countries, improvement of parasite resistance is needed. In this study, we compared predicted selection responses for alternative breeding programs with or without parasite resistance and resilience traits. The overall breeding goal included traits for production, reproduction, and parasite resilience and resistance to ensure a balanced selection outcome. The production traits were BW and dressing percentage (DP). The reproduction trait was fertility (FER), which was the number of doe kiddings per mating. The resistance trait was worm fecal egg count (FEC), which is a measurement of the number of gastro-intestinal parasite eggs found in the feces. The resilience trait was the packed cell volume (PCV), which is a measurement of the volume of red blood cells in the blood. Dressing percentage, BW, and FEC were measured at 11 mo of age, which is the mating or selling age. Fertility and PCV were measured on females at each kidding period. The breeding program accounting for the overall breeding goal and a selection index including all traits gave annual selection responses of 800 g for BW, 3.75% for FER, 0.08% for DP, −0.005 ln(eggs/g) for FEC, and 0.28% for PCV. The expected selection responses for BW and DP in this breeding program were reduced by 2% and 6%, respectively, compared with a breeding program not accounting for FEC and PCV. The overall breeding program, proposed for the Creole breed, offers the best breeding strategy in terms of expected selection responses, making it possible to improve all traits together. It offers a good balance between production and adaptation traits and may present some interest for the selection of other goat breeds in the tropics.

Conformation and locomotive characteristics (CLC), i.e., leg conformation and gait movement patterns, may be associated with osteochondrosis (OC) in pigs. Osteochondrosis and CLC increase the risk of premature culling. This study investigated whether CLC have an explanatory value, over the previously modelled effects of sex, feeding, and housing conditions, on the occurrence and severity of OC in several joints and at the animal level. At 154 to 156 d of age, 267 pigs were subjectively scored on 9 conformation and 2 locomotive characteristics. Scoring was performed on a 9-point linear grading scale. For conformation characteristics, score 5 indicated normal conformation and scores 1 and 9 indicated severe deviations from normal. For the locomotive characteristics, score 1 indicated normal locomotion and score 9 indicated severe deviation from normal. At 161 to 176 d of age, pigs were slaughtered and joints were dissected for macroscopic evaluation of OC status. Results showed that swaying hindquarters and a stiffer gait were associated with higher scores for OC in, respectively, the femoropatellar (P = 0.018) and tarsocrural joint (P = 0.005); smaller inner claws as compared to the outer claws of the front legs was associated with lower scores for OC than equally sized claws in the femoropatellar joint (P = 0.021) and on animal level (P = 0.010); steep and weak pasterns of the front legs were associated with higher scores for OC in the elbow joint (P = 0.004) and on animal level (P = 0.018); X-shaped hind legs was associated with higher scores for OC on animal level (P = 0.037); and steep and weak pasterns of the hind legs were associated with lower scores for OC than normal conformation in the tarsocrural joint (P = 0.05). This study found several CLC that were associated with OC in several joints and at an animal level. This study showed that certain CLC might be used as indicators of OC and included in the criteria for selection of replacement animals for the breeding herd.

This genome-wide association study aimed to identify loci associated with lactation-average somatic cell score (LASCS) and the standard deviation of test-day somatic cell score (SCS-SD). It is one of the first studies to combine detailed phenotypic and genotypic cow data from research dairy herds located in different countries. The combined data set contained up to 52 individual test-days per lactation and thereby aimed to capture temporary increases in somatic cell score associated with infection. Phenotypic data for analysis consisted of 46,882 test-day records on 1,484 cows, and genotypic data consisted of 37,590 single nucleotide polymorphisms (SNP). Using an animal model, the associations between each individual SNP and the phenotypic data were estimated. To account for the risk of false positives, a false discovery rate threshold of 0.20 was set. The analyses showed that LASCS was significantly associated with a SNP on Bos taurus autosome (BTA) 4 and a SNP on BTA18. Likewise, SCS-SD was associated with this SNP on BTA18. In addition, SCS-SD significantly associated with a SNP on BTA6. Relatively few associations were found, suggesting that LASCS and SCS-SD are controlled by multiple loci distributed across the genome, each with a relatively small effect. Increased knowledge on genetic regulation of LASCS and SCS-SD may aid in identification of genes that play a role in mastitis resistance. Such knowledge helps us understand the genetic mechanisms leading to mastitis and in discovery of targets for mastitis therapeutics.

Three discrete generations of GIFT fish (Nile tilapia strain, Oreochromis niloticus; a total of 10,065 fish with pedigree and phenotypic information) were tested in pond and cage culture environments to determine genotype by production environment interaction between both environments in Malaysia. Live weight (selected trait), standard length, body depth and width were recorded. A bivariate animal model was used to estimate variance and covariance components, whereby the homologous body traits in pond and cage environments were treated as genetically distinct traits. The heritabilities estimated for these body traits ranged from 0.19 to 0.40 in the pond environment, and from 0.23 to 0.34 in the cage environment. Across all traits the maternal common environmental effects ranged from 0.14 to 0.26 and were greater for the pond than for the cage environment. The genetic correlations between the pond and cage environments were 0.73 ± 0.09 for live weight, 0.81 ± 0.09 for standard length, 0.78 ± 0.10 for body depth, and 0.85 ± 0.13 for body width. Coupled with the total selection responses for live weight after two generations of selection, being 35% for the pond environment and 45% for the cage environment, we concluded that genotype by environment interaction for GIFT strain between pond and cage environments was not important. Hence, it would not be necessary to have two separate selective breeding programs for the GIFT strain in Malaysia.

The objectives of this study were to derive phenotypic and genetic prediction equations of liveweight from linear conformation traits, and estimate genetic and phenotypic parameters for these traits. Data pertained to 2,728 conformation and liveweight records of 613 cows in 1,529 lactations. Cows were raised at the Scottish Agricultural College research station and had calved between 2002 and 2010. Fifteen linear conformation traits were considered as predictors. To validate phenotypic predictions, the data set was randomly split into independent reference and validation subsets. Reference subsets were used to derive prediction equations with the use of a mixed model. Comparisons between predicted and actual liveweight in the validation subsets indicated that stature, chest width, body depth, and angularity could be used to derive phenotypic predictions of liveweight. Accuracy of these predictions was better for first-lactation than for all-lactation liveweight data. Significant genetic correlations between liveweight and the 4 predictor traits ranged from 0.49 to 0.76, and phenotypic correlations were 0.33 to 0.56. Estimated genetic (co)variances were used to develop prediction equations of animal genetic merit for liveweight from routinely calculated genetic evaluations for conformation traits.

Background Identifying genomic regions, and preferably individual genes, responsible for genetic variation in milk fat composition of bovine milk will enhance the understanding of biological pathways involved in fatty acid synthesis and may point to opportunities for changing milk fat composition via selective breeding. An association study of 50,000 single nucleotide polymorphisms (SNPs) was performed for even-chain saturated fatty acids (C4:0-C18:0), even-chain monounsaturated fatty acids (C10:1-C18:1), and the polyunsaturated C18:2cis9,trans11 (CLA) to identify genomic regions associated with individual fatty acids in bovine milk. Results The two-step single SNP association analysis found a total of 54 regions on 29 chromosomes that were significantly associated with one or more fatty acids. Bos taurus autosomes (BTA) 14, 19, and 26 showed highly significant associations with seven to ten traits, explaining a relatively large percentage of the total additive genetic variation. Many additional regions were significantly associated with the fatty acids. Some of the regions harbor genes that are known to be involved in fat synthesis or were previously identified as underlying quantitative trait loci for fat yield or content, such as ABCG2 and PPARGC1A on BTA 6; ACSS2 on BTA 13; DGAT1 on BTA 14; ACLY, SREBF1, STAT5A, GH, and FASN on BTA 19; SCD1 on BTA26; and AGPAT6 on BTA 27. Conclusions Medium chain and unsaturated fatty acids are strongly influenced by polymorphisms in DGAT1 and SCD1. Other regions also showed significant associations with the fatty acids studied. These additional regions explain a relatively small percentage of the total additive genetic variance, but they are relevant to the total genetic merit of an individual and in unraveling the genetic background of milk fat composition. Regions identified in this study can be fine mapped to find causal mutations. The results also create opportunities for changing milk fat composition through breeding by selecting individuals based on their genetic merit for milk fat composition.

This study was conducted to define the udder morphology and subjectively assessed by the use of linear scores in 156 ewes of Tahirova, Kivircik and Karacabey Merino breeds. Udder morphology was evaluated with respect to data in mid-lactation (90 days). Udder morphology was assessed for: the traits measured were teat length, teat angle, rear udder depth, udder circumference, udder length, udder width and udder volume. Linear scores were assessed for: teat placement, udder depth, degree of separation and degree of suspension of the udder. Analysis of variance was calculated by using of SAS statistical package. Correlations between udder measurements and linear scores were computed for individual examined breeds separately. Subjectively assessed udder measurements for udder circumference, udder length, teat angle and udder volume determined high correlations with actual measurements of the respective traits on udder in all examined breeds (rp = 0.477-0.729). Linear scores for udder depth and degree of suspension of the udder were highly correlated (rp = 0.714; 0.357; 0.343 for Tahirova; Kivircik and Karacabey Merino ewes). In conclusion, significant different were determined in udder characteristies linear udder traits and phenotypic correlations in Tahirova, Kivircik and Karacabey Merino ewes.

Milk fatty acid (FA) composition was compared among 4 cattle breeds in the Netherlands: Dutch Friesian (DF; 47 animals/3 farms), Meuse-Rhine-Yssel (MRY; 52/3), Groningen White Headed (GWH; 45/3), and Jersey (JER; 46/3). Each cow was sampled once between December 2008 and March 2009 during the indoor housing season, and samples were analyzed using gas chromatography. Significant breed differences were found for all traits including fat and protein contents, 13 major individual FA, 9 groups of FA, and 5 indices. The saturated fatty acid proportion, which is supposed to be unfavorable for human health, was smaller for GWH (68.9%) compared with DF (74.1%), MRY (72.3%), and JER (74.3%) breeds. The proportion of conjugated linoleic acid and the unsaturation index, which are associated positively with human health, were both highest for GWH. Differences in milk fat composition can be used in strategies to breed for milk with a FA profile more favorable for human health. Our results support the relevance of safeguarding the local Dutch breeds.

The objective of this study was to determine relations between reproductive performance, i.e. being a repeat breeder and litter size, in 2nd parity and reproductive performance in later parities. In addition, relations between the 1st and 2nd parity litter size and litter size in later parities were determined. First, 184,135 records from 46,571 sows were used to analyze the effect of being a repeat breeder in 2nd parity on subsequent farrowing rate, litter size and parity number at culling. Second, 161,521 records of 39,654 sows were used to analyze the effect of litter size from 1st insemination in 2nd parity, being either low (= 10 piglets total born), medium (11–13) or high (= 14), on subsequent litter size, farrowing rate and parity number at culling, with litter size in 1st parity included in the model as well. In total 15.7% of the sows inseminated in 2nd parity were a repeat breeder in 2nd parity. Being a repeat breeder in 2nd parity did not affect litter size in subsequent parities, however it decreased farrowing rate in parity 3 (4.1%) and 4 (3.4%), but not in later parities (P

The aim of this study was to detect new polymorphisms in the bovine ß-casein (ß-CN) gene and to evaluate association of (new) ß-CN protein variants with milk production traits and milk protein composition. Screening of the ß-CN gene in genomic DNA from 72 Holstein Friesian (HF) bulls resulted in detection of 19 polymorphisms and revealed the presence of ß-CN protein variant I in the Dutch HF population. Studies of association of ß-CN protein variants with milk composition usually do not discriminate protein variant I from variant A2. Association of ß-CN protein variants with milk composition was studied in 1857 first-lactation HF cows and showed that associations of protein variants A2 and I were quite different for several traits. ß-CN protein variant I was significantly associated with protein percentage and protein yield, and with as1-casein (as1-CN), as2-casein (as2-CN), ¿-casein (¿-CN), a-lactalbumin (a-LA), ß-lactoglobulin (ß-LG), casein index and casein yield. Inferring ß-¿-CN haplotypes showed that ß-CN protein variant I occurred only with ¿-CN variant B. Consequently, associations of ß-¿-CN haplotype IB with protein percentage, ¿-CN, a-LA, ß-LG and casein index are likely resulting from associations of ¿-CN protein variant B, while associations of ß-¿-CN haplotype IB with as1-CN and as2-CN seem to be resulting from associations of ß-CN variant I.

The gilthead seabream ( Sparus aurata ) is an important aquaculture species that has only been subject to an incipient selective breeding programme. This study, which examined the genetic architecture of seabream morphology and stress response to confinement, takes a step toward the use of marker assisted selection in this species. Major loci affecting these traits were mapped, using data from 460 offspring derived from seven paternal and 73 maternal half-sib families. Fish were killed following a four-hour confinement experiment to induce stress, after which 15 morphometric measurements were collected and blood was sampled for DNA extraction and plasma cortisol level determination. Heritabilities for the morphometric traits were moderate to high (0.24–0.58), with genetic and phenotypic correlations between the traits generally very high. However, the heritability of plasma cortisol level was not significantly different from zero. A population-specific genetic linkage map was built for 56 microsatellite markers, comprising 16 linkage groups (LG) and ten unlinked markers. Half-sib and variance components QTL analyses detected a single genome-wide significant QTL (SaimbcF7b), a single unlinked marker explaining 13–23% of the phenotypic variance in the majority of the morphometric traits. Several other putative QTL were identified for morphometric traits (on LG 4a, 7, 9, 18, A, C, F and I), along with two other QTL (LG10 and B) that were suggestive for stress response. Fitting body weight as a covariate for the morphometric traits resulted in three genome-wide significant QTL affecting aspects of body shape independent of overall body size. For stress response we only identified suggestive evidence for QTL. These findings contribute to understanding the genetic regulation of important economic traits in seabream.

L’organisation des schémas de sélection découle des particularités biologiques (prolificité, intervalle de générations…) propres à chaque espèce ou groupe d’espèces, ainsi que de la nature des caractères d’intérêt (précoces, tardifs…). Dans les filières porcine et avicole, où la diffusion des reproducteurs est largement mondialisée, la concurrence entre opérateurs induit une course au progrès génétique impliquant de maximiser l’efficacité de la sélection dans les races ou lignées pures, ainsi que de profiter des différents avantages du croisement (hétérosis, complémentarité entre populations, utilisation de gènes majeurs) dans les limites permises par le taux de reproduction élevé de ces espèces. La mise en oeuvre de ces principes conduit à des modalités d’organisation des schémas de sélection et de croisement de type pyramidal, caractéristique de ces filières. Elles exercent en retour un effet structurant sur les opérateurs génétiques eux-mêmes, conduisant à une typologie caractéristique, modulée par certaines particularités biologiques des animaux (format...),par la segmentation du marché des produits commerciaux dans la filière avicole (espèces, marchés de niche…), et par l’importance relative du secteur privé (partielle en filière porcine, totale en filière avicole). L’arrivée de la sélection génomique ne devrait pas bouleverser cette typologie, mais pose des problèmes de faisabilité économique., The organization of selection schemes results from biological specificities (prolificacy, generation intervals...) of each species along with the nature of the traits (early, late...). In porcine and poultry production where the distribution of breeding animals is global, the competition between operators has induced a race towards genetic progress implicating maximizing selection efficiency in pure breeds or lines, as well as taking advantage of crosses (heterosis, complementarity between populations, use of major genes) within the limits allowed by the high reproduction rate of these species. The use of these principles has led to the typical organization of selection schemes and pyramidal crossing, both characteristics of these productions. This organization structures the genetic operators themselves, leading to a characterized typology, modulated by biological specificities of the animals (size...), by the segmentation of commercial poultry product markets (species, niche markets...), and by the relative importance of private property of breeding animals (partial in pigs, total in poultry). The occurrence of genomic selection should not upset this typology, but creates problems of economic feasibility.