Factors affecting daughters distribution among progeny testing Holstein bulls

The aim of this study was to investigate factors influencing the number of daughters of Holstein bulls during the progeny testing using data provided by the Italian Holstein Friesian Cattle Breeders Association. The hypothesis is that there are no differences among artificial insemination studs (AIS) on the daughters distribution among progeny testing bulls. For each bull and beginning from 21 months of age, the distribution of daughters over the progeny testing period was calculated. Data were available on 1973 bulls born between 1986 and 2004, progeny tested in Italy and with at least 4 paternal half-sibs. On average, bulls exited the genetic centre at 11.3±1.1 months and reached their first official genetic proof at 58.0±3.1 months of age. An analysis of variance was performed on the cumulative frequency of daughters at 24, 36, 48, and 60 months. The generalized linear model included the fixed effects of year of birth of the bull (18 levels), artificial insemination stud (4 levels) and sire of bull (137 levels). All effects significantly affected the variability of studied traits. Artificial insemination stud was the most important source of variation, followed by year of birth and sire of bull. Significant differences among AI studs exist, probably reflecting different strategies adopted during progeny testing

PARAMETRI GENETICI DEI CARATTERI PRODUTTIVI E DELLE CELLULE SOMATICHE IN VACCHE DI RAZZA BURLINA

The Burlina is a local dual-purpose cattle breed reared in North-East Italy, particularly in Treviso province which accounts for approximately80 % of the total number of cows. The objective of this thesis was to estimate genetic parameters for daily milk yield, fat and protein contents, and somatic cell score (SCS) in Burlina breed, and explore the level of genetic variability in the population for these traits of economic relevance. Monthly test-days and pedigree datasets were provided by the Breeders Association (APA) of Treviso province. After editing procedure, 13,228 records collected on 665 cows in 10 herds from 1999 to 2009 were available. An analysis of variance (ANOVA) was carried out to identify the most important sources of variation influencing production traits and SCS. The linear model included the fixed effects of herd-test day, lactation stage, and age at calving within parity, and the random effect of error. The (co)variance components were estimated using a multivariate animal model with the same effects considered in the previous model and two new random effects: the permanent environmental and the animal. The pedigree file (988 animals) included all individuals with phenotypic records and their ancestors. (Co)variance components were then used to estimate breeding values (EBV) of animals for the traits. On average, Burlina cows produced 16.5 kg/d of milk with 3.67% of fat and 3.33% of protein, and a SCS of 3.73. Heritability estimates were 0.188 for milk yield, 0.275 for fat content, 0.358 for protein content and 0.067 for SCS. Genetic correlations between SCS and production traits were negative and low: -0.115 between SCS and milk, -0.219 between SCS and fat and -0.298 between SCS and protein. Also, very low values were estimated between milk and protein (-0.089) and milk and fat (-0.001), while a positive medium-high value was found between fat and protein (0.629). Heritability estimates along with distributions of EBVs showed the existence of genetic variability for milk yield traits and SCS in the Burlina breed. The variability could be used to improve the population, but only if additive genetic relationships among animals are considered; this is necessary to monitor and control inbreeding levels of next generations.openSCA-15

National and international genetic evaluations for body condition score and related traits in Italian Holstein Friesian breed

Body condition score (BCS) has gained notable interest in the last decades as an important management tool in the dairy herd because it can be used as an indicator of overall energy status and of adipose stores mobilization during lactation. Moreover, BCS can be used as a predictor of fertility, health, and welfare status of cows. The Italian Holstein Breeder Association (ANAFI) started to collect data for BCS in 2007, but a national genetic evaluation for this trait is still not available. The increasing trade of dairy bull semen in the last thirty years has led to the increase of genetic links among countries. Nonetheless, using the genetic evaluations made by one country to evaluate bulls from another country without appropriate conversion is not a good way to compare animals. In 1983 the International Bull Evaluation Service (Interbull, Sweden) was established in response to the need for universal comparison criteria of dairy bulls across countries. The first international genetic evaluation for BCS was carried out in 2009 and involved 11 countries. Until now, Italian Holstein participated in the Interbull evaluation using angularity as the best predictor of BCS. When similar traits evaluated in 2 or more countries have different definitions, across-country genetic correlations are expected to be low and the ranking of bulls could be affected. Based on these considerations, it is important for the Italian Holstein Breeder Association to have a national evaluation for BCS and to participate in the Interbull evaluation with BCS as a direct trait. The aims of the thesis were to study the status of international genetic evaluation of BCS and overall type traits, to estimate genetic variance of BCS, to estimate the genetic correlations of BCS with production and type traits (in particular angularity and locomotion), and finally to analyse the results of the first international genetic evaluation with BCS as a direct trait in Italian Holstein bulls. The investigation performed among countries that participated in the Interbull evaluation showed that differences for overall traits were mostly due to the heterogeneity in trait definitions. For BCS, the differences were due to the use of best predictors. Overall traits are important in selection indices to improve functional traits, and their definition depends on the specific breeding goals in each country. Across-country genetic correlations were useful in evaluating differences among countries. The cluster analysis over the years showed that changes in the Interbull evaluation procedure and trait definition influenced the genetic correlations across countries. National genomic evaluation for type traits has been adopted by some countries, while at the international level, Interbull is developing the methodology required to provide international comparisons of genomically enhanced breeding values to member organizations. The additive genetic variances of BCS estimated in the Italian Holstein population were low but in agreement with estimates reported in literature. The genetic relationships of BCS with milk yield were moderate and indicated that high producing cows tend to be thinner. The correlations of BCS with fat and protein content and fat to protein ratio were almost negligible. BCS seemed to be genetically independent with most of type traits, except for chest width, rear leg set side view and rear udder height. BCS showed a strong genetic correlation with its predictor (angularity), although this correlation decreased over the years, due to the change in angularity definition that occurred in 2009. Locomotion showed low genetic variance, and favourable genetic correlations with production and type traits. Using BCS as a direct trait improved the Italian Holstein across-country genetic correlations, increasing the number of Italian bulls in the top positions of other countries’ ranks. At the same time, in the Italian rank, the number of bulls of countries using BCS increased as well. Clear unfavourable genetic trend was found in the Holstein Friesian breed from all countries that participated in the Interbull evaluation of BCS. The Italian bulls had an unfavourable genetic trend as well, which was negative for most of the years considered, even though it was in line with bulls from other countries

Direct and indirect genetic indices for milk coagulation properties in Italian Holstein Friesian sires

Aim of this study was to define direct and indirect indices for milk coagulation properties (MCP) in Italian Holstein Friesian sires. A total of 315,700 individual milk samples from 49,183 cows were collected in 479 dairy farms from September 2011 to February 2014. Rennet coagulation time (RCT) and curd firmness (a30) were predicted using mid-infrared spectroscopy. Sire breeding values (EBV) for RCT and a30 were estimated using a repeatability single-trait animal model, which included herd-test-day, days in milk, age at parities and season of parity as fixed effects, and cow permanent environment and animal as random effects. The direct genetic index for milk coagulation ability (IAC) was defined as the combination of EBV for RCT and a30 with equal weight, and then expressed on a scale with mean 100 and standard deviation of 5. A stepwise method was chosen to combine official EBVs for traits published by the Italian Holstein Friesian Cattle Breeders Association in a genetic index able to predict the direct IAC. Only sires with at least 10 daughters (scored for MCP) in 5 different herds were considered. The official EBVs retained by the regression analysis were those of protein and fat content, somatic cell score and the genetic variants for k-casein. Results of direct and indirect selection for MCP are presented.Aim of this study was to define direct and indirect indices for milk coagulation properties (MCP) in Italian Holstein Friesian sires. A total of 315,700 individual milk samples from 49,183 cows were collected in 479 dairy farms from September 2011 to February 2014. Rennet coagulation time (RCT) and curd firmness (a30) were predicted using mid-infrared spectroscopy. Sire breeding values (EBV) for RCT and a30 were estimated using a repeatability single-trait animal model, which included herd-test-day, days in milk, age at parities and season of parity as fixed effects, and cow permanent environment and animal as random effects. The direct genetic index for milk coagulation ability (IAC) was defined as the combination of EBV for RCT and a30 with equal weight, and then expressed on a scale with mean 100 and standard deviation of 5. A stepwise method was chosen to combine official EBVs for traits published by the Italian Holstein Friesian Cattle Breeders Association in a genetic index able to predict the direct IAC. Only sires with at least 10 daughters (scored for MCP) in 5 different herds were considered. The official EBVs retained by the regression analysis were those of protein and fat content, somatic cell score and the genetic variants for k-casein. Results of direct and indirect selection for MCP are presented

Short communication: Genetic relationships of milk coagulation properties with body condition score and linear type traits in Holstein-Friesian cows

Milk coagulation properties (MCP) are gaining popularity among dairy cattle producers and the improvement of traits associated with MCP is expected to result in a benefit for the dairy industry, especially in countries with a long tradition in cheese production. The objectives of this study were to estimate genetic correlations of MCP with body condition score (BCS) and type traits using data from first-parity Italian Holstein-Friesian cattle. The data analyzed consisted of 18,460 MCP records from 4,036 cows with information on both BCS and conformation traits. The cows were daughters of 246 sires and the pedigree file included a total of 37,559 animals. Genetic relationships of MCP with BCS and type traits were estimated using bivariate animal models. The model for MCP included fixed effects of stage of lactation, and random effects of herd-test-date, cow permanent environment, additive genetic animal, and residual. Fixed factors considered in the model for BCS and type traits were herd-date of evaluation and interaction between age at scoring and stage of lactation of the cow, and random terms were additive genetic animal, cow permanent environment, and residual. Genetic relationships between MCP and BCS, and MCP and type traits were generally low and significant only in a few cases, suggesting that MCP can be selected for without detrimental effects on BCS and linear type traits

Cluster Analysis on Across Country Genetic Correlations for Conformation Traits in Holstein Cattle Breed

The aim of this paper is to investigate across country genetic correlations of conformation traits of 21 Holstein bull populations, using cluster analysis. Data consisted of across country genetic correlations of 18 conformation traits estimated by Interbull for the April 2011 routine genetic evaluation. For cluster analysis, the distance measure (dij) between countries i and j was calculated as dij=1-rG2ij, where rGij is the genetic correlation between countries i and j. Traits showed different mean distances with the lowest value for udder depth (0.062) and the highest for locomotion (0.441). For traits with similar definition further investigation is needed to understand differences within cluster. Also, more attention needs to be paid to countries that define or record traits differently from what is suggested by World Holstein Friesian Federation

Effect of manipulating recombination rates on response to selection in livestock breeding programs

International audienceBackgroundIn this work, we performed simulations to explore the potential of manipulating recombination rates to increase response to selection in livestock breeding programs.MethodsWe carried out ten replicates of several scenarios that followed a common overall structure but differed in the average rate of recombination along the genome (expressed as the length of a chromosome in Morgan), the genetic architecture of the trait under selection, and the selection intensity under truncation selection (expressed as the proportion of males selected). Recombination rates were defined by simulating nine different chromosome lengths: 0.10, 0.25, 0.50, 1, 2, 5, 10, 15 and 20 Morgan, respectively. One Morgan was considered to be the typical chromosome length for current livestock species. The genetic architecture was defined by the number of quantitative trait variants (QTV) that affected the trait under selection. Either a large (10,000) or a small (1000 or 500) number of QTV was simulated. Finally, the proportions of males selected under truncation selection as sires for the next generation were equal to 1.2, 2.4, 5, or 10 %.ResultsIncreasing recombination rate increased the overall response to selection and decreased the loss of genetic variance. The difference in cumulative response between low and high recombination rates increased over generations. At low recombination rates, cumulative response to selection tended to asymptote sooner and the genetic variance was completely eroded. If the trait under selection was affected by few QTV, differences between low and high recombination rates still existed, but the selection limit was reached at all rates of recombination.ConclusionsHigher recombination rates can enhance the efficiency of breeding programs to turn genetic variation into response to selection. However, to increase response to selection significantly, the recombination rate would need to be increased 10- or 20-fold. The biological feasibility and consequences of such large increases in recombination rates are unknown

Трансформация производства радиоформатов в российском радиовещании в конце 2000-х годов

Additional file 4: Table S1. Standardised cumulative proportion of times that haplotypes of the top 50 focal individuals selected by AlphaSeqOpt, the key ancestors approach (PEDIG) or the two haplotype-based approaches of Bickhart et al. [15] and Gusev et al. [16] appear in the rest of the population. Table S2. Standardised cumulative proportion of times that haplotypes of the top 200 focal individuals selected by AlphaSeqOpt, the key ancestors approach (PEDIG) or the two haplotype-based approaches of Bickhart et al. [15] and Gusev et al. [16] appear in the rest of the population. Table S3. The cumulative sum of the pedigree-inferred expected marginal contributions of the top 50 and 200 focal individuals selected by the key ancestors approach (implemented in the PEDIG software) for pedigrees of 5, 10, 15, 30 and 50 generations

The potential of shifting recombination hotspots to increase genetic gain in livestock breeding

Abstract Background This study uses simulation to explore and quantify the potential effect of shifting recombination hotspots on genetic gain in livestock breeding programs. Methods We simulated three scenarios that differed in the locations of quantitative trait nucleotides (QTN) and recombination hotspots in the genome. In scenario 1, QTN were randomly distributed along the chromosomes and recombination was restricted to occur within specific genomic regions (i.e. recombination hotspots). In the other two scenarios, both QTN and recombination hotspots were located in specific regions, but differed in whether the QTN occurred outside of (scenario 2) or inside (scenario 3) recombination hotspots. We split each chromosome into 250, 500 or 1000 regions per chromosome of which 10% were recombination hotspots and/or contained QTN. The breeding program was run for 21 generations of selection, after which recombination hotspot regions were kept the same or were shifted to adjacent regions for a further 80 generations of selection. We evaluated the effect of shifting recombination hotspots on genetic gain, genetic variance and genic variance. Results Our results show that shifting recombination hotspots reduced the decline of genetic and genic variance by releasing standing allelic variation in the form of new allele combinations. This in turn resulted in larger increases in genetic gain. However, the benefit of shifting recombination hotspots for increased genetic gain was only observed when QTN were initially outside recombination hotspots. If QTN were initially inside recombination hotspots then shifting them decreased genetic gain. Discussion Shifting recombination hotspots to regions of the genome where recombination had not occurred for 21 generations of selection (i.e. recombination deserts) released more of the standing allelic variation available in each generation and thus increased genetic gain. However, whether and how much increase in genetic gain was achieved by shifting recombination hotspots depended on the distribution of QTN in the genome, the number of recombination hotspots and whether QTN were initially inside or outside recombination hotspots. Conclusions Our findings show future scope for targeted modification of recombination hotspots e.g. through changes in zinc-finger motifs of the PRDM9 protein to increase genetic gain in production species