Abstract: Improved performance of crossbred animals is partly due to heterosis. One of the major genetic bases of heterosis is dominance, but it is seldom used in pedigree-based genetic evaluation of livestock. Recently, a trivariate genomic best linear unbiased prediction (GBLUP) model including dominance was developed, which can distinguish purebreds from crossbred animals explicitly. The objectives of this study were: (1) methodological, to show that inclusion of marker-based inbreeding accounts for directional dominance and inbreeding depression in purebred and crossbred animals, to revisit variance components of additive and dominance genetic effects using this model, and to develop marker-based estimators of genetic correlations between purebred and crossbred animals and of correlations of allele substitution effects between breeds; (2) to evaluate the impact of accounting for dominance effects and inbreeding depression on predictive ability for total number of piglets born (TNB) in a pig dataset composed of two purebred populations and their crossbreds. We also developed an equivalent model that makes the estimation of variance components tractable. For TNB in Danish Landrace and Yorkshire populations and their reciprocal crosses, the estimated proportions of dominance genetic variance to additive genetic variance ranged from 5 to 11%. Genetic correlations between breeding values for purebred and crossbred performances for TNB ranged from 0.79 to 0.95 for Landrace and from 0.43 to 0.54 for Yorkshire across models. The estimated correlation of allele substitution effects between Landrace and Yorkshire was low for purebred performances, but high for crossbred performances. Predictive ability for crossbred animals was similar with or without dominance. The inbreeding depression effect increased predictive ability and the estimated inbreeding depression parameter was more negative for Landrace than for Yorkshire animals and was in between for crossbred animals. Methodological developments led to closed-form estimators of inbreeding depression, variance components and correlations that can be easily interpreted in a quantitative genetics context. Our results confirm that genetic correlations of breeding values between purebred and crossbred performances within breed are positive and moderate. Inclusion of dominance in the GBLUP model does not improve predictive ability for crossbred animals, whereas inclusion of inbreeding depression does.

Abstract: We used genotype data from the caprine 50k Illumina BeadChip for the assessment of genetic diversity within and between 10 local Swiss goat breeds. Three different cluster methods allowed the goat samples to be assigned to the respective breed groups, whilst the samples of Nera Verzasca and Tessin Grey goats could not be differentiated from each other. The results of the different genetic diversity measures show that Appenzell, Toggenburg, Valais and Booted goats should be prioritized in future conservation activities. Furthermore, we examined runs of homozygosity (ROH) and compared genomic inbreeding coefficients based on ROH (FROH ) with pedigree-based inbreeding coefficients (FPED ). The linear relationship between FROH and FPED was confirmed for goats by including samples from the three main breeds (Saanen, Chamois and Toggenburg goats). FROH appears to be a suitable measure for describing levels of inbreeding in goat breeds with missing pedigree information. Finally, we derived selection signatures between the breeds. We report a total of 384 putative selection signals. The 25 most significant windows contained genes known for traits such as: coat color variation (MITF, KIT, ASIP), growth (IGF2, IGF2R, HRAS, FGFR3) and milk composition (PITX2). Several other putative genes involved in the formation of populations, which might have been selected for adaptation to the alpine environment, are highlighted. The results provide a contemporary background for the management of genetic diversity in local Swiss goat breeds.

Abstract: Genetic improvement in livestock populations can be achieved without significantly affecting genetic diversity if mating systems and selection decisions take genetic relationships among individuals into consideration. The objective of this study was to examine the genetic diversity of two commercial breeds of pigs. Genotypes from 1168 Landrace (LA) and 1094 Large White (LW) animals from a commercial breeding program in Brazil were obtained using the Illumina PorcineSNP60 Beadchip. Inbreeding estimates based on pedigree (F x) and genomic information using runs of homozygosity (F ROH) and the single nucleotide polymorphisms (SNP) by SNP inbreeding coefficient (F SNP) were obtained. Linkage disequilibrium (LD), correlation of linkage phase (r) and effective population size (N e ) were also estimated. Estimates of inbreeding obtained with pedigree information were lower than those obtained with genomic data in both breeds. We observed that the extent of LD was slightly larger at shorter distances between SNPs in the LW population than in the LA population, which indicates that the LW population was derived from a smaller N e . Estimates of N e based on genomic data were equal to 53 and 40 for the current populations of LA and LW, respectively. The correlation of linkage phase between the two breeds was equal to 0.77 at distances up to 50 kb, which suggests that genome-wide association and selection should be performed within breed. Although selection intensities have been stronger in the LA breed than in the LW breed, levels of genomic and pedigree inbreeding were lower for the LA than for the LW breed. The use of genomic data to evaluate population diversity in livestock animals can provide new and more precise insights about the effects of intense selection for production traits. Resulting information and knowledge can be used to effectively increase response to selection by appropriately managing the rate of inbreeding, minimizing negative effects of inbreeding depression and therefore maintaining desirable levels of genetic diversity.

Abstract: Previous research has indicated that certain breeds of dogs stay longer in shelters than others. However, exactly how breed perception and identification influences potential adopters' decisions remains unclear. Current dog breed identification practices in animal shelters are often based upon information supplied by the relinquishing owner, or staff determination based on the dog's phenotype. However, discrepancies have been found between breed identification as typically assessed by welfare agencies and the outcome of DNA analysis. In Study 1, the perceived behavioral and adoptability characteristics of a pit-bull-type dog were compared with those of a Labrador Retriever and Border Collie. How the addition of a human handler influenced those perceptions was also assessed. In Study 2, lengths of stay and perceived attractiveness of dogs that were labeled as pit bull breeds were compared to dogs that were phenotypically similar but were labeled as another breed at an animal shelter. The latter dogs were called "lookalikes." In Study 3, we compared perceived attractiveness in video recordings of pit-bull-type dogs and lookalikes with and without breed labels. Lastly, data from an animal shelter that ceased applying breed labeling on kennels were analyzed, and lengths of stay and outcomes for all dog breeds, including pit bulls, before and after the change in labeling practice were compared. In total, these findings suggest that breed labeling influences potential adopters' perceptions and decision-making. Given the inherent complexity of breed assignment based on morphology coupled with negative breed perceptions, removing breed labels is a relatively low-cost strategy that will likely improve outcomes for dogs in animal shelters.

Abstract: In this study, behavioral characteristics in purebred cats were hypothesized to associate with breed, eye color, coat color, and coat pattern. Owners of 574 single-breed, registered cats completed the Feline Behavioral Assessment and Research Questionnaire, which generates a standardized behavioral profile incorporating 20 factors. Subjects were also screened for evidence of fear-related aggression, territorial aggression and inappropriate social skills, fear of noises, redirected aggression, separation anxiety, and inappropriate elimination. Subject breeds included Abyssinians, Bengals, Birmans, Burmese, Devon rexes, Maine coons, Norwegian Forest cats, Orientals, Persians, Ragdolls, Siamese, and Tonkinese. Coat colors included agouti, black, brown, cinnamon, blue, lilac, fawn, caramel, taupe, red, cream, blue cream, apricot, and white. Phenotypic variants associated with albinism, tabby and tortoiseshell patterning, inhibition of melanin, production of pheomelanin, and white spotting were represented. Statistical analysis revealed significant differences in the Feline Behavioral Assessment and Research Questionnaire scores and frequency of behavior problems in cats of multiple coat colors, coat patterns, and breeds (P < 0.05). Interestingly, nearly all associations between behavior and coat type could be attributed to breed-based behavior differences. Associations independent of breed included increased cat aggression in agouti cats and prey interest in red cats, decreased stranger-directed aggression in piebald cats, and increased likelihood of separation anxiety in Siamese and Tonkinese patterned cats.

Abstract: Domestic dogs (Canis familiaris) have developed a close relationship with humans through the process of domestication. In human-dog interactions, eye contact is a key element of relationship initiation and maintenance. Previous studies have suggested that canine ability to produce human-directed communicative signals is influenced by domestication history, from wolves to dogs, as well as by recent breed selection for particular working purposes. To test the genetic basis for such abilities in purebred dogs, we examined gazing behavior towards humans using two types of behavioral experiments: the 'visual contact task' and the 'unsolvable task'. A total of 125 dogs participated in the study. Based on the genetic relatedness among breeds subjects were classified into five breed groups: Ancient, Herding, Hunting, Retriever-Mastiff and Working). We found that it took longer time for Ancient breeds to make an eye-contact with humans, and that they gazed at humans for shorter periods of time than any other breed group in the unsolvable situation. Our findings suggest that spontaneous gaze behavior towards humans is associated with genetic similarity to wolves rather than with recent selective pressure to create particular working breeds.

Abstract: Sheep are a valuable resource for meat and wool production. During the dry summer, pastures are scarce and animals face Seasonal Weight Loss (SWL), which decreases production yields. The study of breeds tolerant to SWL is important to understand the physiological mechanisms of tolerance to nutritional scarcity, and define breeding strategies. Merino, Damara and Dorper sheep breeds have been described as having different levels of tolerance to SWL. In this work, we assess their liver and muscle metabolomes, and compare the responses to feed restriction. Ram lambs from each breed were divided into growth and feed restricted groups, over 42 days. Tissue metabolomes were assessed by 1H-NMR. The Dorper restricted group showed few changes in both tissues, suggesting higher tolerance to nutritional scarcity. The Merinos exhibited more differences between treatment groups. Major differences were related to fat and protein mobilization, and antioxidant activity. Between the Damara groups, the main differences were observed in amino acid composition in muscle and in energy-related pathways in the liver. Integration of present results and previous data on the same animals support the hypothesis that, Dorper and Damara breeds are more tolerant to SWL conditions and thus, more suitable breeds for harsh environmental conditions.

Abstract: Although several studies indicate that meningoencephalitis of unknown aetiology (MUA) might affect every dog breed at every age, little is known about clinical presentation, diagnostic findings and long-term survival in large breed dogs. The aim of this study was therefore to compare the clinical presentation, diagnostic findings and long-term survival between large and small/medium breed dogs diagnosed with MUA. One hundred and eleven dogs met the inclusion criteria. 28 (25 per cent) dogs were considered large breed dogs compared with 83 (75 per cent) small/medium breed dogs. Large breed dogs presented significantly more often with a decreased mentation. Age, gender, duration of clinical signs prior to diagnosis, presence of seizures or cluster seizures, variables on complete blood count and cerebrospinal fluid analysis, and all variables on MRI were not significantly different between small/medium and large breed dogs. Median survival time was 281 and 106 days for the large and small/medium breed dogs, respectively, with no significant difference in survival curves for both groups. Although considered not typically affected by MUA, 25 per cent of dogs included in this study were considered large breed dogs. Therefore, MUA should be included in the differential diagnosis for large breed dogs presenting with intracranial neurological signs. If diagnosed with MUA, large breed dogs also carried a guarded prognosis.

Abstract: OBJECTIVE The aim of this study was to evaluate heat tolerance using heat tolerance indices, physiological, physical, thermographic, and hematological parameters in Santa Ines and Morada Nova sheep breeds in the Federal District, Brazil. METHODS Twenty-six adult hair sheep, one and a half years old, from two genetic groups (Santa Ines: 12 males and 4 females; Morada Nova: 7 males and 3 females) were used and data (rectal temperature, respiratory rate, heart rate, skin temperatures; hematological parameters) were collected during three consecutive days, twice a day (morning and afternoon), with a total of six repetitions. Also physical parameters (biometric measurements, skin and hair traits) and heat tolerance indices (temperature-humidity index, Iberia and Benezra) were evaluated. The analyses included analyses of variance, correlation, and principal components with a significance level of 5%. RESULTS The environmental indices, in general, indicate a situation of thermal discomfort for the animals during the afternoon. Breed significantly influenced (p<0.001) physiological and physical characteristics of skin, hair, biometric measurements and Iberia and Benezra heat tolerance indices. Santa Ines animals were bigger and had longer, greater number and darker hair, thicker skin, greater respiratory rate and Benezra index and lower Iberia index compared with Morada Nova breed. CONCLUSION Although both breeds can be considered adapted to the environmental conditions of the region, Morada Nova breed is most suitable for farming in the Midwest region. The positive correlation found between the thermographic temperatures and physiological parameters indicates that this technique can be used to evaluate thermal comfort. Also, it has the advantage that animals do not have to be handled, which favors animal welfare.

Abstract: Delivering beef of consistent quality to the consumer is vital for consumer satisfaction and will help to ensure demand and therefore profitability within the beef industry. In Australia, this is being tackled with Meat Standards Australia (MSA), which uses carcass traits and processing factors to deliver an individual eating quality guarantee to the consumer for 135 different 'cut by cooking methods' from each carcass. The carcass traits used in the MSA model, such as ossification score, carcass weight and marbling explain the majority of the differences between breeds and sexes. Therefore, it was expected that the model would predict with eating quality of bulls and dairy breeds with good accuracy. In total, 8128 muscle samples from 482 carcasses from France, Poland, Ireland and Northern Ireland were MSA graded at slaughter then evaluated for tenderness, juiciness, flavour liking and overall liking by untrained consumers, according to MSA protocols. The scores were weighted (0.3, 0.1, 0.3, 0.3) and combined to form a global eating quality (meat quality (MQ4)) score. The carcasses were grouped into one of the three breed categories: beef breeds, dairy breeds and crosses. The difference between the actual and the MSA-predicted MQ4 scores were analysed using a linear mixed effects model including fixed effects for carcass hang method, cook type, muscle type, sex, country, breed category and postmortem ageing period, and random terms for animal identification, consumer country and kill group. Bulls had lower MQ4 scores than steers and females and were predicted less accurately by the MSA model. Beef breeds had lower eating quality scores than dairy breeds and crosses for five out of the 16 muscles tested. Beef breeds were also over predicted in comparison with the cross and dairy breeds for six out of the 16 muscles tested. Therefore, even after accounting for differences in carcass traits, bulls still differ in eating quality when compared with females and steers. Breed also influenced eating quality beyond differences in carcass traits. However, in this case, it was only for certain muscles. This should be taken into account when estimating the eating quality of meat. In addition, the coefficients used by the Australian MSA model for some muscles, marbling score and ultimate pH do not exactly reflect the influence of these factors on eating quality in this data set, and if this system was to be applied to Europe then the coefficients for these muscles and covariates would need further investigation.

Abstract: Summary The genetic diversity in 23 dog breeds raised in Belgium was investigated using both genealogical analysis and microsatellite markers. Some of these breeds are native breeds, with only small populations maintained. Pedigree and molecular data, obtained from the Belgian kennel club, were used to calculate the inbreeding coefficients, realised effective population size as well as probabilities of gene origin and average observed heterozygosity. Inbreeding coefficients ranged from 0.8 to 44.7% and realised effective population size varied between 3.2 and 829.1, according to the used method and breed. Mean observed heterozygosity ranged from 0.47 to 0.73. Both pedigree and molecular methods reveal low genetic diversity and presence of bottlenecks, especially in native Belgian breeds with small population sizes. Furthermore, principal component analysis on the set of investigated diversity parameters revealed no groups of breeds that could be identified in which similar breeding strategies could be applied to maintain genetic diversity.

Abstract: Gastrointestinal parasites are the main cause of losses of cattle farms including feed conversion-failure and even death of heavily infected animals. We have conducted a random examination of 455 cows in the Special Region of Yogyakarta-Central Java from March to June 2016. The examined animals were Ongole and Local Cattle (PO) cross breed, Simmental breed, Limousin breed, Simmental and PO cross breed, PO and Limousin cross breed, Friesian Holstein breed (FH), Brahman breed, Angus breed, Angus and Brahman cross breed and Bali breed. McMaster technique, saturated NaCl flotation technique and Parfitt and Banks technique were used simultaneously in this study in order to identify the parasitic stages present in the coprological samples. The test results showed that approximately 65.93% of the cattle population was infected by parasitic stages, such as: Strongylidae (54.00%), Fasciola sp. (17.00%), Eimeria spp. (15.33%), Strongyloides sp. (4.67%), Paramphistomum sp. (4.00%), Trichuris sp. (3.67%) and Moniezia sp. (1.33%). Six different Eimeria species were identified: E. bovis, E. auburnensis, E. bukidnonensis, E. canadaensis, E. zurnii and E. cylindrica. Most of the animals presented monoinfections (79.33%), but concomitant infections were also observed (2 different parasites: 17.67%; 3 different parasites: 2.33%; more than 3 different parasites: 0.67%). With this work we proved the high level of parasitism in cattle of Central Java and we intensively highlight the need to find adequate control measures against parasitic diseases in order to reduce the detrimental impact of parasitosis in cattle.

Abstract: This paper aimed at testing the differences of adaptability of bovine dairy, dual purpose and local breeds during the summer transhumance to highland pastures (summer farms), evaluating temporal variations of body condition and of milk yield and quality. Data were from 799 dairy cows of specialised (Holstein Friesian and Brown Swiss), dual purpose (Simmental) and local (mostly Rendena and Alpine Grey) breeds, and were collected before and after the transhumance in 109 permanent dairy farms, and during transhumance in 15 summer farms of the Autonomous Province of Trento, north-eastern Italy. Body Condition Score (BCS), milk production and quality (fat, protein, casein, lactose, urea, SCS) were analysed for the fixed effects of breed, parity, days in milk, month, supplementary concentrate level, and for the random effects of summer farm and individual cow. Body condition score was influenced by transhumance to summer farms, with low values in July and a recovery at the end of the period. This patter...

Abstract: The reproduction of many species is determined by seasonally-driven resource supply. But it is difficult to quantify whether the fecundity is sensitive to short- or long-term exposure to environmental conditions such as rainfall that drive resource supply. Using 25 years of data on individual fecundity of European female rabbits, Oryctolagus cuniculus, from semiarid Australia, we investigate the role of individual body condition, rainfall and temperature as drivers of seasonal and long-term and population-level changes in fecundity (breeding probability, ovulation rate, embryo survival). We built distributed lag models in a hierarchical Bayesian framework to account for both immediate and time-lagged effects of climate and other environmental drivers, and possible shifts in reproduction over consecutive seasons. We show that rainfall during summer, when rabbits typically breed only rarely, increased breeding probability immediately and with time lags of up to 10 weeks. However, an earlier onset of the yearly breeding period did not result in more overall reproductive output. Better body condition was associated with an earlier onset of breeding and higher embryo survival. Breeding probability in the main breeding season declined with increased breeding activity in the preceding season and only individuals in good body condition were able to breed late in the season. Higher temperatures reduce breeding success across seasons. We conclude that a better understanding of seasonal dynamics and plasticity (and their interplay) in reproduction will provide crucial insights into how lagomorphs are likely to respond and potentially adapt to the influence of future climate and other environmental change.

Abstract: Seasonal Weight Loss (SWL) is an important constraint, limiting animal production in the Tropics and the Mediterranean. As a result, the study of physiological and biochemical mechanisms by which domestic animal breeds respond to SWL is important to those interested in animal breeding and the improvement thereof. To that end, the study of the proteome has been instrumental in gathering important information on physiological mechanisms, including those underlying SWL. In spite of that, little information is available concerning physiological mechanisms of SWL in production animals. The objective of this study was to determine differential protein expression in the muscle of three different breeds of sheep, the Australian Merino, the Dorper and the Damara, each showing different levels of tolerance to weight loss (low, medium and high, respectively). Per breed, two experimental groups were established, one labeled “Growth” and the other labeled “Restricted.” After forty-two days of dietary treatment, all animals were euthanized. Muscle samples were then taken. Total protein was extracted from the muscle, then quantified and two-dimensional gel electrophoresis were conducted using 24 cm pH 3–10 immobiline dry strips and colloidal coomassie staining. Gels were analyzed using Samespots® software and spots of interest were in-gel digested with trypsin. The isolated proteins were identified using MALDI-TOF/TOF. Results indicated relevant differences between breeds; several proteins are suggested as putative biomarkers of tolerance to weight loss: Desmin, Troponin T, Phosphoglucomutase and the Histidine Triad nucleotide-binding protein 1. This information is of relevance to and of possible use in selection programs aiming towards ruminant animal production in regions prone to droughts and weight loss.

Abstract: Goats are of special importance in the Mediterranean and tropical regions for producing a variety of dairy products. The scarcity of pastures during the dry season leads to seasonal weight loss (SWL), which affects milk production. In this work, we studied the effect of feed-restriction on two dairy goat breeds, with different tolerance levels to SWL: the Majorera breed (tolerant) and the Palmera breed (susceptible). Nuclear magnetic resonance (NMR) was used to compare the metabolome of an aqueous fraction of the mammary gland and milk serum from both breeds. Goats in mid-lactation were divided by breed, and each in two feed-regime groups: the control group and the restricted-fed group (to achieve 15-20% reduction of body weight at the end of the experiment). Milk and mammary gland samples were collected at the end of the experimental period (23rd day). (1)H NMR spectra were collected from the aqueous extract of the mammary gland biopsies and the milk serum. Profiling analysis has led to the identification of 46 metabolites in the aqueous extract of the mammary gland. Lactose, glutamate, glycine and lactate were found to be the most abundant. Analysis of milk serum allowed the identification of 50 metabolites, the most abundant being lactose, citrate and creatine. Significant differences were observed, in mammary gland biopsies and milk serum, between control and restricted-fed groups in both breeds, albeit with no differences between the breeds. Variations seem to be related to metabolism adaptation to the low-energy diet and are indicative of breed-specific microflora. Milk serum showed more metabolites varying between control and restricted groups, than the mammary gland. The Majorera breed also showed more variations than the Palmera breed in milk samples, which could be an indication of a prompt adaptation to SWL by the Majorera breed.

Abstract: Summary Factors to adjust the expected progeny differences (EPD) of each of 18 breeds to the base of Ang us EPD are reported in the column labeled 6 of Tables 1-7 for birth weight, weaning weight, y earling weight, maternal milk, marbling score, ribeye area, and fat thickness, respectively. An EPD is adjusted to the Angus base by adding the corresponding across-breed adjustment factor in column 6 to the EPD. It is critical that this adjustment be applied only to Spring 2012 EPD. Olde r or newer EPD may be computed on different bases and, therefore, could produce misleading results. When the base of a breed changes from year to year, its adjustment factor (Column 6) changes in the opposite direction and by about the same amount. Breed differences are changing over time as breeds put emphasis on different traits and their genetic trends differ accordingly. Therefore, it is necessary to qualify the point in time at which breed differences are represented. Column 5 of Tables 1-7 contains estimates of the differences be tween the averages of calves of each breed born in year 2010. Any differences (relative to their br eed means) in the samples of sires representing those breeds at the U.S. Meat Animal Research Center (USMARC) are adjusted out of these breed difference estimates and the across-breed adjustment factors. The breed difference estimates are reported as progeny differences, e.g., they represent the expected difference in progeny performance of calves sired by average bulls (born in 2010) of two different breeds and out of dams of a third, unrelated breed. In other words, they represent half the differences that would be expected between purebreds of the two breeds.

Abstract: The objective of this study was to determine the intra- and intergenetic diversities of eight different goat populations in Turkey including Hair, Angora, Kilis, Yayladag, Shami, Honamli, Saanen, and Alpine. A total of 244 DNA samples were genotyped using 11 microsatellites loci. The genetic differentiation between breeds was considerable as a result of the statistically significant (P 0.05). Heterozygosity values ranged between 0.62 and 0.73. According to the structure and assignment test, Angora and Yayladag goats were assigned to the breed they belong to, while other breeds were assigned to two or more different groups. Because this study for the first time presented genetic data on the Yayladag goat, results of structure analysis and assigned test suggest that further analyses are needed using additional and different molecular markers.