Majority Of Breeds Research Articles

The genomic structure of isolation across breed, country and strain for important South African and Australian sheep populations

BackgroundSouth Africa and Australia shares multiple important sheep breeds. For some of these breeds, genomic breeding values are provided to breeders in Australia, but not yet in South Africa. Combining genomic resources could facilitate development for across country selection, but the influence of population structures could be important to the compatability of genomic data from varying origins. The genetic structure within and across breeds, countries and strains was evaluated in this study by population genomic parameters derived from SNP-marker data. Populations were first analysed by breed and country of origin and then by subpopulations of South African and Australian Merinos.ResultsMean estimated relatedness according to the genomic relationship matrix varied by breed (-0.11 to 0.16) and bloodline (-0.08 to 0.06) groups and depended on co-ancestry as well as recent genetic links. Measures of divergence across bloodlines (FST: 0.04–0.12) were sometimes more distant than across some breeds (FST: 0.05–0.24), but the divergence of common breeds from their across-country equivalents was weak (FST: 0.01–0.04). According to mean relatedness, FST, PCA and Admixture, the Australian Ultrafine line was better connected to the SA Cradock Fine Wool flock than with other AUS bloodlines. Levels of linkage disequilibrium (LD) between adjacent markers was generally low, but also varied across breeds (r2: 0.14–0.22) as well as bloodlines (r2: 0.15–0.19). Patterns of LD decay was also unique to breeds, but bloodlines differed only at the absolute level. Estimates of effective population size (Ne) showed genetic diversity to be high for the majority of breeds (Ne: 128–418) but also for bloodlines (Ne: 137–369).ConclusionsThis study reinforced the genetic complexity and diversity of important sheep breeds, especially the Merino breed. The results also showed that implications of isolation can be highly variable and extended beyond breed structures. However, knowledge of useful links across these population substructures allows for a fine-tuned approach in the combination of genomic resources. Isolation across country rarely proved restricting compared to other structures considered. Consequently, research into the accuracy of across-country genomic prediction is recommended.

Association of periodontal disease with breed size, breed, weight, and age in pure-bred client-owned dogs in the United States

Despite periodontal disease (PD) being amongst the most common diagnoses in primary-care practice, the disease is generally underdiagnosed. However, the millions of clinical records generated by pet hospitals each year provide unique opportunities to generate insights about disease risk across large numbers of dogs. The objective of this study was to undertake a retrospective analysis of medical records to ascertain which sizes and breeds of dog are most frequently diagnosed with PD. Although data collection regarding PD was not consistent, it was assumed that the same inconsistencies in recording periodontal abnormalities were present across the range of bodyweight, breed categories and breeds.Over 3 million medical records across 60 breeds of dogs visiting a chain of veterinary hospitals in the United States collected over a 5-year period were analysed. Statistical analysis of a subset of these records found that extra-small (<6.5 kg) breeds of dog were up to five times more likely to be diagnosed with PD than giant breeds (>25 kg) (P <0.0001). The majority of breeds most frequently diagnosed with PD were in the extra-small, small (6.5−9 kg) and medium-small (9−15 kg) breed size categories. Additional risk factors for PD diagnosis included age, being overweight and time since last scale and polish. Veterinarians should consider targeting client education about dental health, and diagnostic efforts, towards canine patients of the small-breed size categories and those with a higher risk of developing PD (e.g. overweight).

Heritability of Unilateral Elbow Dysplasia in the Dog: A Retrospective Study of Sire and Dam Influence.

Canine elbow dysplasia is a significant health issue affecting many breeds. Unfortunately, treatments remain relatively limited, so control of this disease often falls to selectively breeding for dogs with normal elbows. The objectives of this study were to evaluate the heritability of left-sided vs. right-sided elbow dysplasia, and to assess potential differential sire and the dam influence on offspring elbow status. In a retrospective study, elbow data from 130,117 dogs over 2 years old representing 17 breeds were obtained from the database of the Orthopedic Foundation for Animals and included in the study. Heritability estimates for unilateral elbow dysplasia varied between breeds (ranging from 0.01 to 0.36) and were similar between the left and right elbows. The estimated genetic correlation between disease in the left and right elbow ~1 in the majority of breeds, with the exception of the hybrids, Australian Shepherds, and the Australian Cattle Dogs, likely due to low numbers of affected individuals. The sire and dam had equal impact on the offspring's elbow status. Furthermore, there was no increased risk for the sire or dam to pass on the same unilaterality of their elbow dysplasia to their offspring. However, the overall risk of elbow dysplasia in the offspring did increase when one or both parents were affected, though this also varied based on breed. Understanding of the impact that the sire and dam have on the offspring and of the overall heritability of both bilateral and unilateral elbow dysplasia is important in guiding breeding decisions to reduce the incidence in future generations of dogs.

Evidence of a genomic insertion in intron 2 of SOD1 causing allelic drop-out during routine diagnostic testing for canine degenerative myelopathy.

Degenerative myelopathy is a severe and progressive neurodegenerative disease and, in the majority of breeds, is associated with the c.118G>A substitution in exon 2 of the canine superoxide dismutase 1 (SOD1) gene. Our laboratories have been engaged in determining the cause of many discordant findings between the parental and the offspring genotypes found by different laboratories. In both cases, the discordant findings refer to actual heterozygous dogs that had been typed as homozygous for the variant allele. To that aim, the genomic context of the causative variant was investigated in two Hovawart dogs. An insertion of 54 nucleotides composed of a poly-T stretch and 15 nucleotides containing the duplication of the exon 2-intron 2 junction was found. The insertion was responsible for the partial mismatch of the reverse primer used for a direct sequencing assay. The mismatch hampered the amplification of the corresponding allele and caused an evident drop-out effect. The insertion is in complete linkage disequilibrium with the c.118G allele. The allele containing the insertion was highly prevalent in Hovawart dogs, accounting for the 26.6% of allele frequency. The insertion was also found in other unrelated breeds such as Rough Collies and Standard Poodles. In conclusion, the study illustrates the importance of correctly designing the primers to avoid inaccurate genotyping of the degenerative myelopathy causative variant in exon 2 of the SOD1 gene.

Characterization of the genetic diversity, structure and admixture of British chicken breeds

The characterization of livestock genetic diversity can inform breed conservation initiatives. The genetic diversity and genetic structure were assessed in 685 individual genotypes sampled from 24 British chicken breeds. A total of 239 alleles were found across 30 microsatellite loci with a mean number of 7.97 alleles per locus. The breeds were highly differentiated, with an average F(ST) of 0.25, similar to that of European chicken breeds. The genetic diversity in British chicken breeds was comparable to that found in European chicken breeds, with an average number of alleles per locus of 3.59, ranging from 2.00 in Spanish to 4.40 in Maran, and an average expected heterozygosity of 0.49, ranging from 0.20 in Spanish to 0.62 in Araucana. However, the majority of breeds were not in Hardy-Weinberg Equilibrium, as indicated by heterozygote deficiency in the majority of breeds (average F(IS) of 0.20), with an average observed heterozygote frequency of 0.39, ranging from 0.15 in Spanish to 0.49 in Cochin. Individual-based clustering analyses revealed that most individuals clustered to breed origin. However, genetic subdivisions occurred in several breeds, and this was predominantly associated with flock supplier and occasionally by morphological type. The deficit of heterozygotes was likely owing to a Wahlund effect caused by sampling from different flocks, implying structure within breeds. It is proposed that gene flow amongst flocks within breeds should be enhanced to maintain the current levels of genetic diversity. Additionally, certain breeds had low levels of both genetic diversity and uniqueness. Consideration is required for the conservation and preservation of these potentially vulnerable breeds.

Study of polymorphism of satellite DNA of improved and local horse breeds

Interbreed differentiation of 12 improved and local horse breeds is studied based on 17 DNA microsatellites. Genetic differences between breeds are established; private alleles are noted in the majority of breeds. Genetic distances between breeds are calculated, an analysis of which shows considerable genetic differences between local and improved breeds.

Characterization of Casein Gene Complex and Genetic Diversity Analysis in Indian Goats

Milk protein polymorphism plays an important role in genetic diversity analysis, phylogenetic studies, establishing geographical diversity, conservation decision, and improving breeding goals. Milk protein polymorphism in Indian goat breeds has not been well studied; therefore, an investigation was carried out to analyze the genetic structure of the casein gene and milk protein diversity at six milk protein loci in nine Indian goat breeds/genetic groups from varied agro-climatic zones. Milk protein genotyping was carried out in 1098 individual milk samples by SDS-PAGE at αS1-CN (CSN1S1), β-CN (CSN2), αS2-CN (CSN1S2), κ-CN (CSN3), β-LG, and α-LA loci. Indian goats exhibited αS1-casein A allele in higher frequency in the majority of breeds except Ganjam and local goats. The αS1-casein A allele frequencies varied from 0.45 to 0.77. A total of 16 casein haplotypes were observed in seven breeds and breed specific haplotypes were observed with respect to geographic region. The average number of alleles was lowest in Ganjam (1.66 ± 0.81) and highest in Sirohi goats (2.50 ± 1.05). Expected heterozygosity at six different loci demonstrated genetic diversity and breed fragmentation. Neighbor-Joining tree was built basing on Nei's distance. There was about 16.95% variability due to differences between breeds, indicating a strong subdivision. Principal component analysis was carried out to highlight the relationship among breeds. The variability among goat breeds was contributed by αS2-CN, β-LG and αS1-CN. The Indian goats exhibited αS1-CN (CSN1S1) A allele in higher frequency in all the breeds indicating the higher casein yield in their milk.

Late Summer and Fall Nesting in the Acorn Woodpecker and Other North American Terrestrial Birds

AbstractAcorn Woodpeckers (Melanerpes formicivorus) at Hastings Reservation in central coastal California exhibit a bimodal peak in annual breeding activity. One peak occurs in spring during which the majority of breeding takes place, while a second is centered in late August as the new acorn crop matures. These latter nests are mostly initiated in late summer but often do not fledge until at least late September and are thus referred to here as ‘fall’ nests. Fall nests occur in about one-third of all years, taking place when the acorn crop is large and summer temperatures are relatively high. Fledglings from fall nests constitute 4.3% of the population's total productivity and survive and recruit to the population at levels comparable to spring fledglings. Fall nesting is less likely in groups in which either the male or female breeding adults have undergone a change from the prior year, but groups are otherwise indistinguishable. Ecologically, fall nesting is closely tied to the acorn crop and thus to breeding success in the following, rather than the prior, spring. Among North American terrestrial birds in general, fall breeding has been reported in 16% of all species and is significantly more common among residents and colonially nesting species, in which the frequency exceeds 25%. Furthermore, fall nesting is likely to have been underreported in the literature. Thus, this phenomenon is at least an irregular part of the breeding biology of a substantial fraction of North American birds and should be considered a possibility in population studies of temperate-zone species. This is especially true given that fall nesting is likely to increase as global warming takes place.

LATE SUMMER AND FALL NESTING IN THE ACORN WOODPECKER AND OTHER NORTH AMERICAN TERRESTRIAL BIRDS

Acorn Woodpeckers (Melanerpes formicivorus) at Hastings Reservation in central coastal California exhibit a bimodal peak in annual breeding activity. One peak occurs in spring during which the majority of breeding takes place, while a second is centered in late August as the new acorn crop matures. These latter nests are mostly initiated in late summer but often do not fledge until at least late September and are thus referred to here as ‘fall’ nests. Fall nests occur in about one-third of all years, taking place when the acorn crop is large and summer temperatures are relatively high. Fledglings from fall nests constitute 4.3% of the population's total productivity and survive and recruit to the population at levels comparable to spring fledglings. Fall nesting is less likely in groups in which either the male or female breeding adults have undergone a change from the prior year, but groups are otherwise indistinguishable. Ecologically, fall nesting is closely tied to the acorn crop and thus to breeding success in the following, rather than the prior, spring. Among North American terrestrial birds in general, fall breeding has been reported in 16% of all species and is significantly more common among residents and colonially nesting species, in which the frequency exceeds 25%. Furthermore, fall nesting is likely to have been underreported in the literature. Thus, this phenomenon is at least an irregular part of the breeding biology of a substantial fraction of North American birds and should be considered a possibility in population studies of temperate-zone species. This is especially true given that fall nesting is likely to increase as global warming takes place.

Characterization and Genotyping of the Caprine κ-Casein Variants

κ-Casein (κ-CN) is the milk protein that determines the size and specific function of milk micelles, and its cleavage by chymosin is responsible for milk coagulation. We have previously detected and characterized four variants of the goat κ-CN in Spanish, French, and Italian breeds by screening the major part of the coding region in exon 4. Here we have sequenced and analyzed the full coding region of the κ-CN gene which includes exons 3 and 4. No additional mutations were found, with exception of a single nucleotide substitution in exon 3, which had no amino acid change. However, the analysis of the association between the different mutations resulted in two new variants designated κ-CN F and G. The novel variants are present in the Italian breeds Teramana, Girgentana, and Sarda (variant F). A protocol for rapid simultaneous genotyping of all known κ-CN variants using the primer extension method was described, and a total of 210 animals from nine European breeds were genotyped. Alleles A and B are the most frequent variants occuring in the majority of breeds with highest prevalence of the B variant, except for the Canaria breed where the A allele is more frequent. Sequence data suggest that the F variant is the original type of caprine κ-CN, other alleles being derived from this type following two different trunks by successive mutations.

Reproductive Responses to Nutritional Stress in Adult Female Collared Peccaries

The influence of nutrition on adult female collared peccary (Tayassu tajacu) breeding activity during the peak breeding season in Texas was studied under controlled conditions. Thirteen captive adults were fed either a high quality (15.2% crude protein and 3,300 kcal digestible energy/kg) or low quality (6.3% crude protein and 1,921 kcal digestible energy/kg) diet beginning 25 October 1983. The low quality diet simulated the energy and protein intake of an adult female during drought range conditions. During the peak breeding season (Jan-Feb) in 1985, a daily breeding program was implemented to monitor estrous behavior and fertility. All females were sacrificed after approximately 15 weeks. Three of 6 receiving the low quality diet showed no behavioral signs of estrus, whereas all females fed the high quality diet were bred. Duration of estrus averaged 1.3 and 3.5 days for cycling females on low and high quality diets, respectively. Only 1 of the 3 cycling females on the low quality diet became pregnant, whereas 6 out of 7 cycling females on the high quality diet became pregnant. Ovarian examination revealed <50% of the females receiving the low quality diet for 10 weeks entered the peak breeding season in an anestrous condition. This study suggests that prior nutritional stress among wild females will greatly influence the incidence of pregnancy and, hence, recruitment of young into the herd. J. WILDL. MANAGE. 50(2):295-300 Although the adult female collared peccary is a polyestrous breeder (Sowls 1966), the majority of breeding occurs during DecemberMarch in the southwestern United States. Field studies have shown substantial decreases in herd recruitment during periods of below average rainfall (Low 1970, Bissonette 1982, Sowls and Maurer 1985), presumably as a result of decreased quality or quantity of nutritionally adequate foods. Currently it is not known where in the peccary reproductive cycle potential recruits are lost or which physiological states are ost affected by nutritional stress mediated by rainfall. Recent observations support the hypothesis that nursling postnatal survival and ovarian activity are susceptible to periods of nutritional stress. Bissonette (1982) indicated postnatal mortality of nurslings contributed to low recruitment in southwestern Texas peccary populations. Few conceptions occur during summer, and seasonal delays in onset of peak breeding have been observed when range con'Present address: Department of Zoology, Oklahoma State University, Stillwater, OK 74078. This content downloaded from 157.55.39.102 on Mon, 03 Oct 2016 06:14:36 UTC All use subject to http://about.jstor.org/terms 296 PECCARY REPRODUCTIVE RESPONSES * Lochmiller et al. J. Wildl. Manage. 50(2):1986 Table 1. Ingredient and chemical composition of pelleted, experimental diets fed ad libitum to pregnant collared peccaries in southern Texas, October 1983-February 1984.