Genetic diversity in Polish hounds estimated by pedigree analysis

Data from 247 litters of Polish hounds born at 105 kennels between 1960 and 2004 was analysed in order to evaluate the genetic variability of the breed. The breed originated from 19 founders and the founder genome equivalent ranged from 2.043 to 1.287 over the span of forty-four years of breeding. The high imbalance of founder contributions to the gene pool was noted, with the dominant contribution of four founders. The low number of the founders and the high disproportion of particular dogs in breeding use resulted in the increasing value of inbreeding coefficient which ranged from 0.0771 to 0.370. The poor gene pool seems to be strictly connected to the deteriorating health of the population which draws into question the future of the breed.     

Inheritance of racing performance of Thoroughbred horses

Horse racing is a contest between horses, usually held for the purpose of betting. Thoroughbred horse racing is the most diffused form of horse racing throughout the world. Thoroughbred is one of the most versatile of horse breeds and has influenced the development of many other breeds. Thoroughbred horses served as a foundation stock for the development of the light horse breeds. The two types of horse racing are flat racing and jumping races/steeplechases. The measures of racing performance are broadly classified into three categories. They are time and its several variations, handicap or similar performance ratings and earnings. One common measure of the performance of racehorses evaluated genetically is racing time or final time. The heritability estimates differed according to method of estimation, age, sex, track and distance. Time measure generally had a heritability in the range of 0.1 to 0.2 with the higher values for shorter races. For handicap and earning measures the heritabilities reported were generally higher in the range of 0.3 to 0.4; hence these may be considered in genetic evaluation of racing performance of Thoroughbred horses. The average generation interval of Thoroughbred horses was 11.2 ± 4.5 and 9.7 ± 3.8 years for males and females respectively, which limits the genetic progress in racing horses. However, the major advantage is that the racing performance may be evaluated in both males and females and repeated observations can be obtained on the same animal in relatively short periods. These factors coupled with the reasonable heritability of some measures of racing performance, suggest that mass selection based on performance tests would be the selection procedure of choice to improve the racing performance of Thoroughbred horses. In general, the inbreeding at the rate that is usually practised in Thoroughbred population does not enable much gene fixing. However, practice of close inbreeding may be avoided, even though it still fascinates breeders at subconscious level.     

中国荷斯坦种公牛BLAD遗传缺陷的分子检测及系谱分析

本试验运用限制性片段长度多态性聚合酶链式反应（RFLP-PCR）方法,检测我国荷斯坦种公牛白细胞粘附缺陷（bovine leukocyte adhesion deficiency,BLAD）基因的携带频率。共检测了来自全国14个公牛站的587头种公牛,发现BLAD携带者8头,携带率为1.36%。对现有公牛系谱信息分析显示,携带者公牛来自美国、加拿大和中国,其中6头携带者公牛可以追溯到共同祖先Osborndale Ivanhoe。此外,本研究还对我国荷斯坦牛遗传缺陷的控制和携带者公牛的利用提出建议。     

Variation of gene frequencies in ASIP, MC1R and GREY loci in Thoroughbred horses

The objective of the study has been to verify the hypothesis that the coat colour is regarded in the selection of Polish Thoroughbred horse population. Formally, the colour is not a selection criterion in this breed selected mainly for speed. The material consisted of twelve groups of foals registered in successive volumes of the Stud Book (11,688 foals, in total) and their parents selected to the breeding stud. The frequency of alleles in ASIP, MC1R and GREY loci controlling the coat colours was estimated from the recessive phenotype frequency square in the groups of foals. The inflow of foreign genes was limited and the population great, hence the migration effect was very low. The drift and Wahlund effect hardly influenced the genetic structure in the groups which enabled to analyze the population not divided. The total offspring frequency of recessive a, e and g alleles amounted to 0.1552, 0.4877 and 0.9773, respectively. Accuracy of the assessment of the a and e frequency was confirmed on the basis of test matings. The a, e and g alleles were more frequent in dams than in sires and the a alleles occurred more often in fillies than in colts. The frequency of a and e alleles was higher in the offspring than in the parents. The genotype distribution in the offspring differed from the expected one, assessed from the gamete frequency in sires and in dams. Fewer bay foals were born than anticipated. All the results show that the coat colour is not entirely disregarded in the breeding of Thoroughbred horses. The dominant A and E alleles producing the colour are preferred in the selection, particularly in the sires. This leads to some alterations in the phenotypic structure of the population. On the other hand, the horses are mated randomly, irrespective of the coat colour.     

Relationship between genealogical and microsatellite information characterizing losses of genetic variability: Empirical evidence from the rare Xalda sheep breed

Preservation of rare genetic stocks requires continual monitoring of populations to avoid losses of genetic variability. Genetic variability can be described using genealogical and molecular parameters characterizing variation in allelic frequencies over time and providing interesting information on differentiation that occurred after the foundation of a conservation program. Here we analyze the pedigree of the rare Xalda sheep breed (1851 individuals) and the polymorphism of 14 microsatellites in 239 Xalda individuals. Individuals were assigned to a base population (BP) or 4 different cohorts (from C1 to C4) according to their pedigree information. Genetic parameters were computed at a genealogical and molecular level, namely inbreeding (F), observed (H_o) and expected (H_e) heterozygosity, individual coancestry coefficients (f and f_m), average relatedness (AR), mean molecular kinship (Mk), average number of allele per locus (A), effective number of ancestors (f_a), effective population size (N_e and N_e(m)) and founder genome equivalents (N_g and N_g(m)). In general, the computed parameters increased with pedigree depth from BP to C4, especially for the genealogical information and molecular coancestry-based parameters (f_m, Mk and N_g(m)). However, H_o and H_e showed the highest values for C1 and the molecular heterozygote deficiency within population (F_IS(m)) showed the lowest value for C1, thus indicating that loss of genetic variability occurs very soon after the implementation of conservation strategies. Although no genealogical or molecular parameters are sufficient by themselves for monitoring populations at the beginning of a conservation program, our data suggests that coancestry-based parameters may be better criteria than those of inbreeding or homozygosity because of the rapid and strong correlation established between f and f_(m). However, the obtaining of molecular information in well-established conservation programs could not be justified, at least in economic terms.     

Gene Dropping Analysis of Ancestral Contributions and Allele Survival in Japanese Thoroughbred Population

Genetic contributions of nine historically important ancestors and allelic diversity in the Japanese Thoroughbred population were examined by applying the gene dropping simulation to the foals produced from 1978 to 2005. Full pedigree records traced to ancestors (base animals) born around 1890 were used for the simulation. Alleles originated from some of the historically important ancestors were found to be at risk of future extinction, although their genetic contributions to the foal population have increased during the last three decades. The proportion of surviving alleles to the total alleles assigned to the base animals was 8.0% in the foal population in 2005, suggesting that a large part of genetic variability contained in the base animals is extinct in the current population.     

Harnessing the genetic toolbox for the benefit of the racing Thoroughbred

The understanding and application of genetics have grown extremely quickly since it has become possible to sequence the whole genome of an organism. The human genome sequence was completed in 2001 and that of the horse in 2007. The significance of this is that it makes it more feasible to explain how both genetically simple and complex traits are transmitted from one generation to the next and, therefore, to make informed breeding decisions, modify how horses are managed and trained to minimise the risk of disease and injury, and improve methods of prevention, diagnosis and treatment of many conditions. The science of genetics/genomics will continue to grow internationally, limited only by the funds available. The application of the science to man, horses and other species raises very complex moral and commercial issues. Thoroughbred breeders are perceived by some as resistant to change, but their apparent intransigence is often based on a genuine concern for the integrity of the breed. By taking control of the application of the advances in genetics, the Thoroughbred industry potentially has the opportunity to improve both the health and performance of Thoroughbreds. If, however, the science is applied in an uncoordinated manner, driven by commercial interests with no underlying concern for the horses themselves, there is a very real risk that breeders, the Thoroughbred breed and individual horses will all suffer as a consequence.     

Optimal genetic contribution selection in Danish Holstein depends on pedigree quality

The aim of this study was to assess the importance of pedigree depth when performing optimal contribution selection as implemented in the software program EVA. This was done by applying optimal genetic contribution in the breeding program of the major Danish Dairy breed Danish Holstein. In the analyses earlier breeding decisions were considered by including all AI waiting- and young bulls and contract matings. Twenty potential sires, 2169 potential dams, 1421 AI-bulls and 754 contract matings plus pedigree animals were included. Results showed that the outcome was very dependent on quality of pedigree, also for information going more than 25 years (5–7 generations) back. The analyses showed that EVA works satisfactorily as a management tool for planning of breeding schemes with respect to contributions of sires of sons at population level in maximising the genetic gain, while controlling the increase in future inbreeding. The more weight put on the average additive genetic relationship in next generation relative to genetic merit, the lower the average merit of the matings, and the lower average additive genetic relationship among the chosen matings and the present breeding animals. Furthermore more weight on average additive genetic relationship gives a more diverse use of sires of sons. Given the potential sires and dams the average additive genetic relationship among the selected matings and the present breeding animals can be reduced from 0.1621 to 0.1495 at the cost of 0.7 genetic S.D. units at the total merit index. This reduction was obtained when selection was only on reduction of average relationship compared to selection only on genetic merit. Optimal genetic contribution selection is a promising tool for managing breeding schemes for populations facing inbreeding problems, such as Danish Holstein and other dairy breeds. However sufficient pedigree information is a necessity.     

The role of reproductive technologies in breeding schemes for livestock populations in developing countries

The world is faced with the challenge to meet the increasing demand for livestock products while conserving animal genetic resource diversity and maintaining environmental integrity. Genetic improvement of local breeds can help to improve the livelihood of the livestock keepers, to increase the production of animal products and to conserve genetic diversity. Implementing breeding schemes in developing countries has proven to be very difficult. The objective of this paper is to discuss the role of reproductive technologies for the creation and dissemination of genetic improvement in livestock populations in developing countries. In the paper opportunities are discussed for implementing breeding schemes which minimize the need for extensive pedigree and performance recording. It is shown that genetic progress can be generated in a small population. Community-based breeding schemes offer a good starting point for involving farmers in improving local breeds. Artificial insemination to exchange genetic material between communities offers an opportunity to increase the rate of genetic improvement while restricting the rate of inbreeding. Furthermore, artificial insemination is a promising technique for dissemination of genetic gain to producers at a relatively low cost. Opportunities to use semen sexing in a crossbreeding scheme are presented. It is concluded that tailor-made solutions and long-term commitment are needed in order to meet the needs of farmers to increase their livelihoods and to meet the needs of the growing population of consumers.     

Pedigree analysis of genetic subdivision in a population of Japanese Black cattle

Twenty‐five subpopulations (i.e. populations of prefectures) of more than 2000 Japanese Black cows younger than or equal to 10 years of age were analyzed to evaluate the genetic relationships in the current population. The total number of cows analyzed was 392 346 and their pedigrees were traced back to 1944 or before. Using the pedigree records, the genetic relationships among the subpopulations were estimated by the two different measurements: (i) the average additive relationship coefficients and (ii) Nei's standard genetic distances. Principal component analysis (PCA) was performed to the matrix of the average additive relationship coefficients, and the factor loadings of subpopulations were plotted on the plane to visualize the genetic configuration of subpopulations. To understand the grouping process of the subpopulations, cluster analysis was applied to the matrix of the Nei's genetic distances, and a dendrogram was constructed. There was a high consistency between the results from PCA and cluster analysis. Eight subpopulations with relatively low migration rates showed their unique genetic compositions, and the other 17 subpopulations with high migration rates formed a single cluster. The major cause of the genetic similarity among the 17 subpopulations was inferred to be the strong genetic influence from one subpopulation (Hyogo prefecture) with prominent characteristics for meat quality.     

Flight Distance and Avoidance Score in Thoroughbred Foals and Yearlings and the Relationship with Handling Frequency in the Young Ages

Flight and avoidance reactions from human were examined using 168 postweaning Thoroughbred foals in 22 breeding farms. Further 114 yearlings of 168 foals were tested in the following summer. The foal handlings by the stabler were asked in questionnaire. The relationship between the behavioural reactions and the foal handling frequencies was analyzed. The flight reaction was estimated as the distance from the animal to a stranger when the animal began to flight away from his approach. The avoidance scores were set up from (1) (not resistant) to (5) (touch rejection) from human touching. In the stabler questionnaire, handling frequencies of “body brushing”, “rectal temperature measurement”, “hoof cleaning”, and “stall cleaning” in the early nursing period were asked. The handling frequencies were scored from (1) (not done) to (5) (every day). In the preliminary test, a measurement reliability of the flight distance and the avoidance score was confirmed. The mean flight distances were 0.56 m and 0.27 m in the postweaning foals and the yearlings, respectively. Touch-avoidance scores of the highest frequency were (3) and (2) in the postweaning foals and the yearlings, respectively. As the results of Spearman’s rank-correlation analysis, “body brushing” showed highly negative relationships with “flight distance” (ρ=–0.31, P<0.001) and “avoidance score” (ρ=–0.37, P<0.001) in the postweaning foals. In the yearlings, “hoof cleaning” also showed significantly negative relationships with these behavioural indices (ρ=–0.24, P<0.01; ρ=–0.22, P<0.01, respectively).     

Whole-genome sequence analysis reveals candidate genomic footprints and genes associated with reproductive traits in Thoroughbred horse

The primary objective of most horse breeding operations was to maximize reproductive efficiency and minimize the cost of producing live foals. Here, we compared individual horses from the Thoroughbred population (n = 17), known as a horse breed with poor reproductive performance, with other six horse populations (n = 28), to detect genomic signatures of positive selection underlying of reproductive traits. A number of protein-coding genes with significant (p-value <.01) higher F_ST values (616 genes) and a lower value for nucleotide diversity (π) (310 genes) were identified. The results of our study revealed some candidate genes such as IGFBP2, IGFBP5, GDF9, BRINP3 and GRID1 are possibly associated with functions influencing reproductive traits. These genes may have been under selection due to their essential roles in reproduction performance in horses. The candidate selected genes identified in this work should be of great interest for future research into genetic architecture of traits relevant to horse breeding programmes.     

The Effect of Age on Thoroughbred Racing Performance

Using a dataset of 274 male Thoroughbred racehorses in the United States, we study the effect of age on racing performance. Beyer speed figures, which are uniform measures of racing performance across distance and racing surface, are utilized in this study. A system of equations is estimated to determine quadratic improvement and decline in racing performance. We find that a typical horse’s peak racing age is 4.45 years. The rate of improvement from age 2 to 4 1/2 is greater than the rate of decline after age 4 1/2. A typical horse will improve by 10 (horse) lengths in sprints (less than 1 mile) and 15 lengths in routes (one mile or greater) from age 2 to 4 1/2. Over the next five years the typical decline is 6 lengths for sprints and 9 1/2 lengths for routes.     

Comparison of Thoroughbred Growth Data to Body Weights Predicted by the NRC

The National Research Council (NRC) recently published a method for calculating expected body weight (BW) in growing horses. The objective of this study was to compare foal BW data obtained from commercial Thoroughbred (TB) farms with BW estimates obtained using the 2007 NRC equation. A total of 9,589 observations on 885 growing TB horses were obtained. Data were sorted by age, and a subset was used for statistical analysis. Comparisons between actual BW and 2007 NRC-predicted BW at each month (0–18 months of age) were made using paired t-tests. The 2007 NRC closely predicted BW of growing TB horses at birth and between 6 and 9 months of age (within 3 kg). However, the equation underestimated BW between 1 and 5 months of age (by as much as 10 kg) and overestimated BW between 10 and 13 months of age (by as much as 9 kg). The 2007 NRC also underestimated BW by as much as 9 kg between 15 and 16 months of age. In the current study, the 2007 NRC equation did not precisely predict BW of horses at all ages. The 2007 NRC equation predicts that daily gain will decrease over time, whereas foals in the current study had an increase in daily gain between 12 and 14 months of age. Foals in the current study were raised in pasture-based management systems in which variations in forage availability and quality could have resulted in fluctuations in growth rate.