Abstract: A rose may be a rose by any other name, but when you call a dog a poodle it becomes a very different animal than if you call it a bulldog. Both the poodle and the bulldog are examples of dog breeds of which there are >400 recognized worldwide. Breed creation has played a significant role in shaping the modern dog from the length of his leg to the cadence of his bark. The selection and line-breeding required to maintain a breed has also reshaped the genome of the dog, resulting in a unique genetic pattern for each breed. The breed-based population structure combined with extensive morphologic variation and shared human environments have made the dog a popular model for mapping both simple and complex traits and diseases. In order to obtain the most benefit from the dog as a genetic system, it is necessary to understand the effect structured breeding has had on the genome of the species. That is best achieved by looking at genomic analyses of the breeds, their histories, and their relationships to each other.

Abstract: Identifying genomics regions that are affected by selection is important to understand the domestication and selection history of the domesticated chicken, as well as understanding molecular pathways underlying phenotypic traits and breeding goals. While whole-genome approaches, either high-density SNP chips or massively parallel sequencing, have been successfully applied to identify evidence for selective sweeps in chicken, it has been difficult to distinguish patterns of selection and stochastic and breed specific effects. Here we present a study to identify selective sweeps in a large number of chicken breeds (67 in total) using a high-density (58 K) SNP chip. We analyzed commercial chickens representing all major breeding goals. In addition, we analyzed non-commercial chicken diversity for almost all recognized traditional Dutch breeds and a selection of representative breeds from China. Based on their shared history or breeding goal we in silico grouped the breeds into 14 breed groups. We identified 396 chromosomal regions that show suggestive evidence of selection in at least one breed group with 26 of these regions showing strong evidence of selection. Of these 26 regions, 13 were previously described and 13 yield new candidate genes for performance traits in chicken. Our approach demonstrates the strength of including many different populations with similar, and breed groups with different selection histories to reduce stochastic effects based on single populations.

Abstract: Background: In national evaluations, direct genomic breeding values can be considered as correlated traits to those for which phenotypes are available for traditional estimation of breeding values. For this purpose, estimates of the accuracy of direct genomic breeding values expressed as genetic correlations between traits and their respective direct genomic breeding values are required. Methods: We derived direct genomic breeding values for 2239 registered Limousin and 2703 registered Simmental beef cattle genotyped with either the Illumina BovineSNP50 BeadChip or the Illumina BovineHD BeadChip. For the 264 Simmental animals that were genotyped with the BovineHD BeadChip, genotypes for markers present on the BovineSNP50 BeadChip were extracted. Deregressed estimated breeding values were used as observations in weighted analyses that estimated marker effects to derive direct genomic breeding values for each breed. For each breed, genotyped individuals were clustered into five groups using K-means clustering, with the aim of increasing within-group and decreasing between-group pedigree relationships. Cross-validation was performed five times for each breed, using four groups for training and the fifth group for validation. For each trait, we then applied a weighted bivariate analysis of the direct genomic breeding values of genotyped animals from all five validation sets and their corresponding deregressed estimated breeding values to estimate variance and covariance components. Results: After minimizing relationships between training and validation groups, estimated genetic correlations between each trait and its direct genomic breeding values ranged from 0.39 to 0.76 in Limousin and from 0.29 to 0.65 in Simmental. The efficiency of selection based on direct genomic breeding values relative to selection based on parent average information ranged from 0.68 to 1.28 in genotyped Limousin and from 0.51 to 1.44 in genotyped Simmental animals. The efficiencies were higher for 323 non-genotyped young Simmental animals, born after January 2012, and ranged from 0.60 to 2.04. Conclusions: Direct genomic breeding values show promise for routine use by Limousin and Simmental breeders to improve the accuracy of predicted genetic merit of their animals at a young age and increase response to selection. Benefits from selecting on direct genomic breeding values are greater for breeders who use natural mating sires in their herds than for those who use artificial insemination sires. Producers with unregistered commercial Limousin and Simmental cattle could also benefit from being able to identify genetically superior animals in their herds, an opportunity that has in the past been limited to seed stock animals.

Abstract: Background The Senepol cattle breed (SEN) was created in the early XXth century from a presumed cross between a European (EUT) breed (Red Poll) and a West African taurine (AFT) breed (N’Dama). Well adapted to tropical conditions, it is also believed trypanotolerant according to its putative AFT ancestry. However, such origins needed to be verified to define relevant husbandry practices and the genetic background underlying such adaptation needed to be characterized.

Abstract: The objective of the present study was to determine the prevalence and variation of natural gastrointestinal nematode (GIN) infections in lambs according to birth type, gender and breed based on individual faecal egg counts (FEC) from various regions in Germany. A total of 3,924 lambs (3 to 15 months old) with different genetic backgrounds (Merinoland, German Blackhead Mutton, Rhoen, Texel and Merino long-wool) were individually sampled during the grazing period between 2006 and 2008. Furthermore, pooled faecal samples from each of the farms were cultured in order to differentiate the third-stage larvae of the nematode spp. Sixty-three percent of the lambs were infected with GIN. The infections were mostly low to moderate and involved several nematode species. The Trichostrongylus spp. was the predominant species based on the percentage of larvae in faecal cultures. Only 11.4% of the lambs were free of Eimeria oocysts. Tapeworm eggs were encountered in 13.2% of all samples. The prevalence of GIN infections varied significantly (P 0.05) were observed between breeds regarding FEC. Inter-individual variations were higher than inter-breed differences, which may indicate the possibility of selection within these breeds for parasites resistance as described in earlier studies.

Abstract: Sub-clinical mastitis limits milk production and represents an important barrier to profitable livestock economics worldwide. Milk production from cows in Nigeria is not at optimum levels in view of many factors including sub-clinical mastitis. The overall herd-level prevalence rate for SCM was 85.33% (256/300 heads of cows) while the quarter-level prevalence rate of SCM was 43.25% (519/1,200 quarters). The prevalence of SCM was 50.67%, 43.67%, 39.67% and 39.13% for the left fore-quarter, right hind-quarter, left hind-quarter and right fore-quarter, respectively. The Rahaji breed had the highest prevalence of SCM with 65.91% (29/44), while the White Fulani breed had the least with 32.39% (57/176). A total of 32.33% (97/300) had only one mammary quarter affected, 30.33% (91/300) had two quarters affected, 16.00% (48/300) had three quarters affected while 6.67% (20/300) had all the four quarters affected. A total of 53.00% had SCM in multiple quarters (159/300). The risk of SCM decreased significantly among young lactating cows compared to older animals (OR = 0.283; P < 0.001; 95%CI = 0.155; 0.516). The Rahaji breed had significantly higher risk compared with the White Fulani breed (OR = 8.205; P = 0.013; 95% CI = 1.557; 43.226). Improved sanitation (washing hands before milking) will decrease the risk of SCM (OR = 0.173; P = 0.003; 95% CI = 0.054; 0.554). SCM is prevalent among lactating cows in the Nigerian Savannah; and this is associated with both animal characteristics (age, breed and individual milk quarters) and milking practices (hand washing).Good knowledge of the environment and careful management of the identified risk factors with improved sanitation should assist farm managers and veterinarians in implementing preventative programmes to reduce the incidence of SCM.

Abstract: The objective was to compare meat quality, muscle fiber characteristics, lipid oxidation and fatty acids of Limousin (LIM), Simmtental (SIM), Luxi (LX), Qinchuan (QC) and Jinnan (JN) offered the same diet in China. After finishing, eight bulls from each breed were randomly selected for slaughter at 18.5 months old. Longissimus dorsi (ld) muscle was taken from the carcass for meat quality evaluations. Breed had little effect on most of meat and fat color parameters except for Hue and b* in which QC had lower values. LIM showed higher pH (24 h) and better water holding capacity than other breeds. LIM showed the lowest dry matter content but the highest crude protein. LX and LIM had higher percentage and density of red muscle fiber than other breeds. Lipid oxidations were significantly lower in LIM than in QC, with the LX, SIM and JN having the intermediate values. Compared to other four breeds, QC provided the highest values of polyunsaturated fatty acids (PUFA), n-6 fatty acids and n-3 fatty acids. In conclusion, LIM scored better on most of meat quality characteristics; however, local breeds such as LX and QC also had better muscle fiber characteristics and better fatty acids composition.

Abstract: The study of population structure by pedigree analysis is useful to identify important circum- stances that affect the genetic history of populations. The intensive use of a small number of superior in- dividuals may reduce the genetic diversity of popula- tions. This situation is very common for the beef cattle breeds. Therefore, the objectives of the present study were to analyze the pedigree and possible inbreeding depression on traits of economic interest in the Marchi- giana and Bonsmara breeds and to test the inclusion of the individual inbreeding coefficient (F i) or individual increases in inbreeding coefficient (ΔFi) in the genetic evaluation model for the quantification of inbreeding depression. The complete pedigree file of the Marchi- giana breed included 29,411 animals born between 1950 and 2003. For the Bonsmara breed, the pedigree file included 18,695 animals born between 1988 and 2006. Only animals with at least 2 equivalent generations of known pedigree were kept in the analyses of inbreed- ing effect on birth weight, weaning weight measured at about 205 d, and BW at 14 mo in the Marchigiana breed, and on birth weight, weaning weight, and scro- tal circumference measured at 12 mo in the Bonsmara breed. The degree of pedigree knowledge was greater for Marchigiana than for Bonsmara animals. The average generation interval was 7.02 and 3.19 for the Marchi- giana and Bonsmara breed, respectively. The average inbreeding coefficient was 1.33% for Marchigiana and 0.26% for Bonsmara. The number of ancestors explain- ing 50% of the gene pool and effective population size computed via individual increase in coancestry were 13 and 97.79 for Marchigiana and 41 and 54.57 for Bons- mara, respectively. These estimates indicate reduction in genetic variability in both breeds. Inbreeding depres- sion was observed for most of the growth traits. The model including ΔF i can be considered more adequate to quantify inbreeding depression. The inclusion of F i or ΔFi in the genetic evaluation model may not result in better fit to the data. A genetic evaluation with si- multaneous estimation of inbreeding depression can be performed in Marchigiana and Bonsmara breeds, pro- viding additional information to producers and breed- ers.

Abstract: Extreme weather events, such as droughts and heat waves, are expected to become more severe and more frequent in the coming years, and understanding their impacts on demographic rates is of increasing interest to both evolutionary ecologists and conservation practitioners. An individual's breeding probability can be a sensitive indicator of the decision to initiate reproductive behavior under varying environmental conditions, has strong fitness consequences, and can be considered the first step in a life history trade-off between allocating resources for breeding activities or self-survival. Using a 14-year time series spanning large variation in climatic conditions and the entirety of a population's breeding range, we estimated the effects of extreme weather conditions (drought) on the state-specific probabilities of breeding and survival of an endangered bird, the Florida Snail Kite (Rostrhamus sociabilis plumbeus). Our analysis accounted for uncertainty in breeding status assignment, a common source of uncertainty that is often ignored when states are based on field observations. Breeding probabilities in adult kites (> 1 year of age) decreased during droughts, whereas the probability of breeding in young kites (1 year of age) tended to increase. Individuals attempting to breed showed no evidence of reduced future survival. Although population viability analyses of this species and other species often implicitly assume that all adults will attempt to breed, we find that breeding probabilities were significantly < 1 for all 13 estimable years considered. Our results suggest that experience is an important factor determining whether or not individuals attempt to breed during harsh environmental conditions and that reproductive effort may be constrained by an individual's quality and/or despotic behavior among individuals attempting to breed.

Abstract: A total of 2001 un-sexed day-old chicks of each Desi, Fayoumi and Rhode Island Red (RIR) breeds were obtained from hatchery of Poultry Research Institute, Rawalpindi. The birds were maintained on deep litter system for a period of 72 weeks. In floor pens, each breed was reared separately in a single pen until seven weeks of age when 2001 birds were randomly distributed between pens, with 21 to 24 birds of the same breed per pen (2.00 to 2.50 ft2/bird). The results revealed that the average day-old weight was highest in RIR, intermediate in Desi and lowest in Fayoumi. The RIR breed consumed more feed and gained maximum (p 0.05) amongst three breeds. The age of sexual maturity was lowest in Fayoumi followed by RIR and Desi....

Abstract: The study was conducted in the central rift valley of Ethiopia to define Arsi-Bale goat keepers’ breeding objectives and breeding practices and to describe flock management practices and rate of inbreeding in Arsi-Bale goat population. Two-stage sampling techniques were employed to select study sites and 202 respondents. Semistructured questionnaire and group discussion were used to collect the required information. Data were analyzed using statistical package for social science. Rate of inbreeding in the population and indices were also calculated. On average, each respondent holds around 12 goats in which 30.7, 66.6 and 2.7% were males, females and castrates, respectively. The most important purpose of goat production in the study area was for milk utilization. Farmers have multiple breeding objectives and they considered both subjective and objective selection criteria with slightly more emphasis on morphological characteristics for buck selection than replacement doe selection. Only 39.1% (n = 79) of respondents have their own breeding bucks. None of the respondents practiced controlled mating. Average rate of inbreeding in the population was around 0.20. Arsi-Bale goats are found to be adaptive to the prevailing condition. Therefore, any breed improvement strategy to be designed or implemented in the study area and other similar areas should consider important traditional breeding practices.

Abstract: The objective of the experiment was to study the performance, carcass traits and meat quality of purebred Aberdeen Angus (Ab) and Limousin (Li) bulls and Ab×Li crossbred bulls offered grass silage-grain-based rations and raised to heavy carcass weights. The experiment included eight bulls in all breed groups. The average slaughter age for all breeds was 540 days and the mean carcass weights for the Ab, Ab×Li and Li bulls were 391, 399 and 439 kg, respectively. Significant breed differences in carcass traits and meat quality were observed. The Limousin bulls tended to achieve a higher conformation score, produced less fat and had a higher percentage of valuable cuts compared with the Aberdeen Angus bulls. The crossbred Ab×Li bulls produced better conformed carcasses and a higher share of the rounds compared to the pure Ab bulls which indicate that this type of crossbreeding can enhance beef production under the studied conditions.

Abstract: Meat from very young, milk-fed, small ruminants is an appreciated product in Mediterranean countries where milk is the main product derived from the herds. Nevertheless, many aspects of the quality of the products are virtually unknown for many goat breeds, especially among those that are reared for their meat. In this study, the quality from 50 animals from 5 local goat breeds (one dairy purpose and 4 meat purpose) and 19 lambs (from Churra, a dairy breed) was compared at commercial cold carcass weights of 4.4-6.6 kg. Carcass quality, ultimate pH and meat colour were assessed following standard procedures. Statistical differences (p < 0.05) were found in all of the variables analysed. Some of these differences might have been due to the influence of the genotype, the dam’s production potential, or differences in carcass weight and age, but most were species dependent. Lambs differed from the kids, especially from those of meat purpose breeds, due to their high proportion of bone (25.0 vs. 21.3 to 23.7%), and a more intense meat colour (higher hue: 29.2 vs. 23.4 to 28.7, and chroma: 14.6 vs. 12.1 to 14.6). Among the goat breeds, Murciano Granadina (dairy breed) and Blanca Celtiberica (meat breed) were the most different in terms of carcass morphology, fatness, and meat colour. The other three local meat-purpose goat breeds (Moncaina, Negra Serrana, and Pirenaica) differed little. To obtain a better understanding of goat species, the differences among breeds, in kids or in their most common products, require further studies. Additional key words: carcass morphology; colour; goat; pH; sheep; tissue composition.

Abstract: Purpose and methods In situ conservation of pig genetic resources requires understanding of the farming systems under which the pigs are kept. The objective of the study was to characterise smallholder pig production systems where indigenous pigs are kept in order to assess opportunities for in situ conservation of these pigs. Factors influencing pig herd sizes, ranking of pigs in smallholder production systems, breeds and breed preferences, pig ownership patterns, traits preferred by farmers and constraints to production were investigated in a survey involving 199 farmers from Chirimhanzu District of Zimbabwe, Vhembe, Alfred Nzo and O. R. Tambo Districts of South Africa.

Abstract: This experiment was conducted to compare meat quality and carcass composition of a diverse sampling of sheep breeds. Finnsheep, Romanov, Dorper, White Dorper, Katahdin, Rambouillet, Suffolk, Texel, Dorset, and Composite (½ Columbia rams to ¼ Hampshire × ¼ Suffolk) rams were mated to mature Composite ewes. Lambs (n = 804) were reared intensively, grain fi nished, and serially harvested over a 63-d period. Average harvest age was 216 d and average HCW was 30.7 kg. At a common harvest age, progeny of Suffolk sires were heavier than progeny of all other breeds (P < 0.05) and their carcasses were heavier (P < 0.05) than progeny of all other breeds, except White Dorper and Dorper. Progeny of Finnsheep and Romanov sires had lighter (P < 0.05) carcasses than progeny of all other breeds. Progeny of Texel, Suffolk, White Dorper, and Dorper sires had larger (P < 0.05) LM area than all other breeds. Progeny of Finnsheep and Romanov sires had smaller (P < 0.05) LM area than all other breeds. Fat thickness at the 12th rib was greater (P < 0.05) for progeny of Dorper sires than those of all other breeds, except White Dorper and Katahdin. Fat thickness at the 4th sacral vertebrae was greater (P < 0.05) for progeny of White Dorper and Dorper sires than those of all other breeds. On a carcass weight-constant basis, progeny of Suffolk sires had a lesser (P < 0.05) percentage of ether-extractable carcass fat than progeny of all other breeds, except Texel. Regardless of harvest endpoint (age-constant or HCW-constant), LM of progeny of Finnsheep and Romanov sires contained a greater (P < 0.05) percentage of intramuscular fat and received greater (P < 0.05) marbling scores than Rambouillet, Suffolk, Texel, Dorset, or Composite. Regardless of harvest endpoint, progeny of Finnsheep, Romanov, and Katahdin sires had smaller LM slice shear force values and greater trained sensory panel tenderness ratings at 7 d postmortem than did progeny of Composite, Suffolk, and Dorset sires (P < 0.05). At an age-constant basis, small differences (P < 0.05) were observed among breeds for lamb fl avor intensity scores; however, when means were adjusted to a carcass weight-constant basis, breed of sire did not affect fl avor intensity or off-fl avor scores. These results document that each breed has relative strengths and weaknesses across traits, and that no single breed excels for all growth, carcass, and sensory traits.

Abstract: A cross sectional study was carried out from October 2010 to March 2011 at Andassa Livestock Research Center, North-West Ethiopia. The objective was to determine the prevalence of cattle flukes infection. Faecal samples were collected from a total of 384 cattle, cross breed (n= 39) and Fogera breed (n=345) of all age groups and sex. Sedimentation technique was employed for the recovery of fluke eggs from freshly collected fecal sample. The results indicated that the overall prevalence of bovine flukes infection was 60.42%. In this study, the highest prevalence was recorded from Paramphistomosis (45.83%) followed by Fasciolosis (23.96%), and Schistosomosis (9.89%). The prevalence of flukes infection was higher in age group 1- 2 years old. There was significant difference in case of Paramphistomosis among age groups. No significant association was found between crossed breeds and sex groups for fluke’s infection. The prevalence of Paramphistomosis was high in cross breed (58.97%) than Fogera breed (44.35%). However, in both cases, there was no significant difference. The result of the present study revealed that the prevalence of major bovine fluke infection in the study area was relatively low and is the definite proof of active infection.

Abstract: Five Argentine Pampinta (dairy breed) and six Corriedale (dual-purpose breed) adult rams were used to study the effect of season on sexual behavior, plasma testosterone (T) and semen characteristics for a period of 1 year. Scrotal circumference (SC) and T concentrations were determined at 2-week intervals. Each ram was exposed monthly to three ovariectomized ewes in one 20-min test and the total number of mounts and successful matings were recorded. Semen collection was attempted from each ram twice weekly for six co nsecutive weeks during each season. In both breeds, SC varied seasonally showing the lowest mean values during winter and spring and in the Corriedale rams (32.8 ± 0.3 cm) was smaller ( p 0.05) was recorded in T concentration between breeds and both breeds reached a peak in summer and autumn. Number of matings showed the maximal values in autumn in both breeds. Season had no significant effect on mass motility, sperm concentration and percentage of live sperm. Semen volume, percentage of progressive motility and total sperm per ejaculate were higher during summer and autumn than in other seasons of the year. Pampinta rams had thehighest values ( p< 0.05) of sperm concentration, total sperm per ejaculate and percentage of abnormal sperm. Results of this study show that sexual behavior, SC and T concentrations exhibit seasonal variation in Pampinta and Corriedale rams and that semen of superior quantity and quality is especially collected in both breeds during the summer and autumn.

Abstract: The use of animals that are resilient to challenging environments is becoming of increasing importance in animal production systems. Interest in breeds of sheep such as the Damara for sheep meat production is increasing in Australia. Anecdotally this breed outperforms the traditionally grazed Merino in the harsh rangeland environments encountered in the Pastoral Zone of Australia, but little evidence is available to support this claim. A trial was conducted to quantify differences in the efficiency of feed utilisation and growth performance of Damara and Merino sheep under two contrasting dietary regimes. Eighteen castrate males of each breed were offered a ‘low-quality’ diet (L) (7 MJ/kg ME; 8% crude protein, as per manufacturer’s analysis) followed by a ‘high-quality’ diet (H) (11 MJ/kg dry matter and 16% crude protein, as per manufacturer’s analysis). On the L diet, Damaras had similar ad libitum feed intake as Merinos, but the digestibility of feed dry matter and energy was ~10% higher in Damaras than Merinos. Damaras also gained weight (38 g/day) on the L diet, while Merinos lost weight (28 g/day) (P < 0.002). On the H diet the Damaras consumed 14% more feed (P < 0.053) and grew 30% faster than Merinos (P < 0.002), but there was no difference in the apparent dry matter or energy digestibility of the feed. At the conclusion of the trial the Damara carcasses were 22% heavier (28.1 versus 23.1 kg), and had higher dressing percentages (53.2 versus 41.5%) than Merinos, but the proportions of carcass components did not differ. The Damaras achieved higher total digestible energy intakes than the Merinos on both diets. On the low-quality feed this was achieved through higher feed digestibility and on the high-quality feed through greater voluntary feed intake. We speculate that this arises from variation between the breeds in rumen volume, particle flow and the site of digestion, but further studies are required to confirm this contention. The ability of Damara sheep to obtain more nutrients from widely differing feed bases makes them an attractive alternative sheep breed for sheep meat production. Furthermore, the presence of such variation between genotypes offers potential for selective breeding and development of commercial lines of sheep.

Abstract: Summary The Friesian horse breed is a beautiful breed for showing, riding and driving. However, some clinical problems seem to have a higher incidence in the Friesian breed compared to other breeds and this raises suspicions that these clinical entities may have a genetic basis.

Abstract: Santa Ines is the most common hair sheep breed in Brazil and probably has the highest genetic diversity among sheep breeds in this country. Successful breeding programs for Brazilian sheep breeds are not common for various reasons, including a lack of control of parentage in the flocks. We developed an allele frequency database for 23 STR loci for the Santa Ines breed based on 285 animals sampled from five populations distributed across the central-western and north-eastern regions of Brazil. The marker set included seven microsatellites used in the 2011 International Society for Animal Genetics sheep genotyping comparison tests and all eight microsatellites currently approved by the Brazilian Agricultural Ministry laboratory accreditation guidelines for sheep identification. The microsatellites had an average of 10 alleles and a mean expected heterozygosity of 0.745. Combined paternity exclusion probabilities when no parent or one parent was known were >99.99%. A small proportion (5.8%) of the existing genetic variation was found to be among the Santa Ines populations, possibly derived from genetic drift and selection. We found that the marker panel proposed by the Agricultural Ministry, although generally useful, should be enhanced by including more markers for improved exclusionary power in parentage testing. This database provides a useful tool for parentage testing of this major Brazilian breed, contributing to improved management and breeding of existing herds.