L. Vostrý

Contribution of domestic production records, Interbull estimated breeding values, and single nucleotide polymorphism genetic markers to the single-step genomic evaluation of milk production

Estimated breeding values (EBV) for first-lactation milk production of Holstein cattle in the Czech Republic were calculated using a conventional animal model and by single-step prediction of the genomic enhanced breeding value. Two overlapping data sets of milk production data were evaluated: (1) calving years 1991 to 2006, with 861,429 lactations and 1,918,901 animals in the pedigree and (2) calving years 1991 to 2010, with 1,097,319 lactations and 1,906,576 animals in the pedigree. Global Interbull (Uppsala, Sweden) deregressed proofs of 114,189 bulls were used in the analyses. Reliabilities of Interbull values were equivalent to an average of 8.53 effective records, which were used in a weighted analysis. A total of 1,341 bulls were genotyped using the Illumina BovineSNP50 BeadChip V2 (Illumina Inc., San Diego, CA). Among the genotyped bulls were 332 young bulls with no daughters in the first data set but more than 50 daughters (88.41, on average) with performance records in the second data set. For young bulls, correlations of EBV and genomic enhanced breeding value before and after progeny testing, corresponding average expected reliabilities, and effective daughter contributions (EDC) were calculated. The reliability of prediction pedigree EBV of young bulls was 0.41, corresponding to EDC=10.6. Including Interbull deregressed proofs improved the reliability of prediction by EDC=13.4 and including genotyping improved prediction reliability by EDC=6.2. Total average expected reliability of prediction reached 0.67, corresponding to EDC=30.2. The combination of domestic and Interbull sources for both genotyped and nongenotyped animals is valuable for improving the accuracy of genetic prediction in small populations of dairy cattle.

Short communication: Reliability of single-step genomic BLUP breeding values by multi-trait test-day model analysis

The purpose of our study was to develop an approximation procedure to estimate reliabilities of single-step genomic BLUP breeding values in a test-day model for routine evaluation of milk yield in a dairy cattle population. Input data consisted of 20,220,047 first-, second-, and third-lactation test-day milk yield records of 1,126,102 Czech Holstein cows (each lactation being considered a separate trait), with 1,844,679 animals in the pedigree file and with genomic data from 2,236 bulls. Evaluation was according to a multi-lactation model. The procedure was based on the effective number of records per animal from milk recording as well as from genomic and pedigree relationships. Traits were analyzed individually, and genetic covariances among traits were subsequently taken into account. The use of genomic information increased average reliability in young bulls from 0.276 to 0.505, but increased reliability in proven bulls only from 0.828 to 0.855. The reliabilities of genomic breeding values in multi-trait evaluation for first, second and third lactations, respectively, averaged 0.652, 0.673, and 0.633 for young bulls and 0.907, 0.894, and 0.852 for proven bulls. For an index combining all 3 lactations, the average reliability of a single-step genomic BLUP prediction was 0.712 and 0.925 for younger and proven bulls, respectively. Increased reliability due to genotyping in the population of all genotyped and nongenotyped animals was very small (<0.01) because of the small proportion of genotyped animals in the population.

Genetic diversity within and gene flow between three draught horse breeds using genealogical information

Three draught horse breeds are maintained in the Czech Republic: the Silesian Noriker (SN), the Noriker (N), and the Czech-Moravian Belgian (CMB). Because the SN and CMB populations are currently closed to outside breeding and are endangered (Genetic Resources), the loss of the genetic variation these horses represent is concerning. Genetic diversity within and between these three breeds and their population structures was analyzed based on pedigree information. Our goal was to identify and quantify factors that affected their genetic variability. The effective population size was analyzed in each breed. The numbers of generations were 22, 32, and 32 for the SN, N, and CMB breeds, respectively, with average equivalent known generations of 9.81, 8.45, and 8.91, respectively. The effective numbers of founders and ancestors contributing to the current genetic pool were, respectively, 69.42 and 22.32 for the SN breed, 98.48 and 42.20 for the N breed, and 43.33 and 23.32 for the CMB breed. The average inbreeding coefficients were 4.6%, 2%, and 4% for the SN, N, and CMB breeds, respectively, and the average inbreeding rate was 0.5% for the SN and CMB breeds and 0.2% for the N breed. The corresponding estimates of effective population size were 95, 195, and 101 for the SN, N, and CMB breeds, respectively. These statistics suggest that the genetic variability has decreased, and without changes in breeding strategy the genetic variability might continue to decline. Using genealogical F-statistics, small genetic differences were identified between the analyzed populations (FST = 0.02).

Characterization of greying, melanoma, and vitiligo quantitative inheritance in Old Kladruber horses

The paper deals with the greying process, melanoma, and vitiligo depigmentation occurrence in Old Kladruber horses (OKH). The study includes 376 animals of both sexes at the age of 1-25 years. The evaluation was performed repeatedly during 4 consecutive years. The greying status was measured spectro - photometrically on four body parts using L*a*b* colour system. Melanoma and vitiligo were detected visu - ally and by palpation in all the animals and classified using 5 (3) grade scale. The GLM procedure of SAS package was used to examine the influence of the effects of line, age, sex, stud, and year of evaluation. The GLM analysis confirmed a significant impact of age on greying. Parameter L* showed progressive increase until 10 years of age when all horses reached final grey level. Subsequent analyses suggested the influence of sex, i.e. a notably higher level of greying in mares. The incidence of melanoma was confirmed. Melanoma in OKH most frequently occurs on the bottom of the tail or at the anal and perineal area. Probably only benign forms of melanoma have been detected. The global occurrence of melanoma in OKH (ca. 13%) is substantially lower than in Lipizzan and Camargue horses. Overall incidence of melanoma in horses at the age of 15 and older reached 68%. Genetic parameters were estimated for melanoma grade, grey level, and vitiligo. Greying is strictly influenced by age ( h 2 = 0.52 ± 0.07). Prevalence of melanoma progresses with age ( h 2 = 0.07 ± 0.04). Vitiligos of both facial and anal parts are influenced by the effects studied ( h 2 = 0.20 ± 0.05 and 0.34 ± 0.06 for vitiligo A and vitiligo F, respectively).

Genetic parameters of longevity for improving profitability of beef cattle

The objective of this study was to estimate genetic parameters for longevity and assess the suitability of using these selection criteria to improve the genetic merit of the beef cattle population of the Czech Republic. The performance record database, which contains records of 363,000 beef cattle animals of 19 breeds and their crosses, was used. The populations of Charolais and Aberdeen Angus were large enough that the genetic parameter estimations and all analyses were done for these breeds separately. Two similar approaches of longevity definition based on probabilities were considered as follows: productive longevity (PL), which is the number of calvings at target ages of 78, 90, 150, and 160 mo, and longevity (L), which is based on the probabilities of cow reappearance in the next parity. A multibreed single-trait animal model for L and a multitrait animal model for combinations of 78/150 and 90/160 mo for PL were used. Specific combinations of months were established based on the analysis and represented the critical culling rates in the studied population. The high genetic correlations (0.88-0.95) of the combination 90/160 suggested that the PL at 160 mo of age can be predicted on the basis of the value at 90 mo, which will make earlier selection possible. Combination 78/150 is less efficient in the Czech population of beef cattle due to the lower correlations (0.79-0.93) between traits. The estimated heritabilities were low for both traits (below 0.14), but the additive genetic variance was sufficient for identifying animals with high genetic merit.

Factors affecting reproductive efficiency in German Shepherd bitches producing litters for Police of the Czech Republic

The present study on German Shepherd bitches bred in the same environment of a private kennel and producing offspring for working purposes aimed to ascertain if any of the parameters: litter size, number of live puppies, stillbirth and mortality of puppies is determined by the month of whelping, parity, number of whelpings for one bitch over the course of one year, pregnancy length or bitch age at the time of whelping. Reproductive records of 73 bitches of German Shepherd breed (GSB) documented since 2001 till 2013 were processed. A total of 298 whelpings resulted in 2075 puppies; mortality of puppies was evaluated within the first 3 weeks of life. A significant seasonal influence on litter size and number of live born puppies, but not on stillbirth or mortality, was found. The parity of GSB significantly influenced litter size, live born puppies, and the incidence of stillbirths. The number of whelpings in one bitch over the course of one year significantly influenced litter size, while puppy losses were the same when bitches were bred once or twice a year. Litter size and number of live born puppies had a significant negative effect on pregnancy length. Furthermore, the number of stillbirths significantly increased when pregnancy was prolonged. Bitch age did not influence litter size, number of live born puppies and stillbirths, however it significantly affected mortality.

Contribution of domestic and Interbull records to reliabilities of single-step genomic breeding values in dairy cattle

The method of approximating reliabilities of genomic breeding values in the single-step genomic BLUP evaluation procedure of Misztal et al. (2013) was used to evaluate the increase in reliability of breeding values for milk production in dairy cattle brought about by the inclusion of genomic data. Three strategies for approximation of reliabilities were compared: using only domestic records from performance testing of cows in the Czech Holstein dairy cattle population, using the same records in combination with Interbull breeding values of sires expressed as deregressed proofs, and using only the Interbull breeding values of sires expressed as deregressed proofs. The highest average reliability of genomic breeding values was achieved by the strategy using both domestic and Interbull data, for which the approximated reliabilities of genotyped bulls increased by 0.063. This general increase in reliability of genomic breeding values was small due to the small number of reference bulls available for the study. The overall increase in reliabilities for the entire population of dairy cattle was low but detectable. That modest increase was partially dependent on the unfavourable ratio of the number of genotyped bulls to the size of the analyzed population. Inclusion of Interbull data dramatically increased the benefits of genotyping in our test case - a relatively small population with substantial genetic contributions of foreign genes.

Preliminary analysis of utilization of genomic relationship in mating plan of Old Kladruber horse

The study analyzed 48 Old Kladruber horses genotyped by Illumina Equine SNP70 BeadChip for usefulness of genomic data in determining of mating plan. Totally 12 variants of data filtering and their impact on calculations in dependence of different parameters of GenCall Score, Minor Allele Frequency and assumed average values of loci of ancestors (l) was investigated. For possibility of comparison between genomic and commonly evaluated relationships, pedigree based relationship matrix was constructed and subsequently subtraction of pedigree from genomic matrix was performed. All matrices were thoroughly inspected and most suitable setting of parameters was chosen. Evaluation of genomic relationships can be successfully implemented in more precise method of mating plan design of Old Kladruber horses. Further genotyping and development of method for rescaling of differences between genomic and pedigree relationship matrices´ elements is advised for a purpose of better interpretation of results by breeders.

Detailed insight into genetic diversity of the Old Kladruber horse substructure in comparison to the Lipizzan breed

ABSTRACT The aim of the present study was to analyse the genetic subdivision of the Old Kladruber horse population compared to the historically close Lipizzan breed and to estimate genetic relatedness between them. A set of 13 microsatellites was used for genotyping a total of 270 Old Kladruber horses representing grey and black colour varieties and 418 Lipizzan horses from Slovak and Slovenian studs. The proportion of obtained heterozygosity indicates no major loss of genetic diversity within them. At the individual level across analysed populations, the formation of clusters in respect to breed’s origin and particular studs was observed. The Wright’s FST and genetic distances indicated genetic segregation of both colour varieties at the intraspecific level of the Kladruber breed. Moreover, the membership probability outputs showed that the frequencies of alleles varied across the three main regions represented by both Old Kladruber varieties and Lipizzan, depending on breeding history and strategy of studs.

Methods for calculating the breeding values of missing traits and their comparison

The objective of this study was to calculate the breeding values (BVs) of traits missing in a selection index. Different traits can be evaluated within the breeding programs of given countries. The BV of a trait can be calculated based on genetic correlations with other traits. Similarly, the BV of a missing trait can be calculated for imported bulls. Two methods of calculation were used. Method A was based on a regression of BVs. Method B was based on performing a de-regression of BVs and their retroactive calculation. Both of these methods were tested using a Czech and a Canadian database of BVs for Holstein bulls. The Czech database of Holstein bulls contained 766 bulls and the Canadian database 851. Two calculations were performed for bulls with low reliability of estimated BVs, the first calculation with their genetic correlation matrix and the second with a genetic correlation matrix created from a set of bulls with high reliability of BVs. These newly calculated BVs (CBVs) were then compared with the national BVs (NBVs) using correlation coefficients. The highest correlations were achieved with high reliability bulls when all traits were included into the calculation (34 evaluated traits). The correlations of these bulls averaged 0.82, with an average standard deviation of 0.19. The lowest correlations were found when low reliability bulls were included and the genetic correlation matrix from the high reliability bulls was applied. That average correlation was 0.74 and standard deviation 0.25. When only 15 traits were evaluated in the model, the average correlation for all sets was 0.68 with standard deviation of 0.28. These results show that calculating the BV of a missing trait is possible using both methods. Method B was slightly more accurate in its prediction.