Recent publications indicate that single‐step models are suitable to estimate breeding values, dominance deviations and total genetic values with acceptable quality. Additive single‐step methods ...implicitly extend known number of allele information from genotyped to non‐genotyped animals. This theory is well derived in an additive setting. It was recently shown, at least empirically, that this basic strategy can be extended to dominance with reasonable prediction quality. Our study addressed two additional issues. It illustrated the theoretical basis for extension and validated genomic predictions to dominance based on single‐step genomic best linear unbiased prediction theory. This development was then extended to include inbreeding into dominance relationships, which is a currently not yet solved issue. Different parametrizations of dominance relationship matrices were proposed. Five dominance single‐step inverse matrices were tested and described as C1, C2, C3, C4 and C5. Genotypes were simulated for a real pig population (n = 11,943 animals). In order to avoid any confounding issues with additive effects, pseudo‐records including only dominance deviations and residuals were simulated. SNP effects of heterozygous genotypes were summed up to generate true dominance deviations. We added random noise to those values and used them as phenotypes. Accuracy was defined as correlation between true and predicted dominance deviations. We conducted five replicates and estimated accuracies in three sets: between all (S1), non‐genotyped (S2) and inbred non‐genotyped (S3) animals. Potential bias was assessed by regressing true dominance deviations on predicted values. Matrices accounting for inbreeding (C3, C4 and C5) best fit. Accuracies were on average 0.77, 0.40 and 0.46 in S1, S2 and S3, respectively. In addition, C3, C4 and C5 scenarios have shown better accuracies than C1 and C2, and dominance deviations were less biased. Better matrix compatibility (accuracy and bias) was observed by re‐scaling diagonal elements to 1 minus the inbreeding coefficient (C5).
To assist cattle producers transition from microsatellite (MS) to single nucleotide polymorphism (SNP) genotyping for parental verification we previously devised an effective and inexpensive method ...to impute MS alleles from SNP haplotypes. While the reported method was verified with only a limited data set (N = 479) from Brown Swiss, Guernsey, Holstein, and Jersey cattle, some of the MS-SNP haplotype associations were concordant across these phylogenetically diverse breeds. This implied that some haplotypes predate modern breed formation and remain in strong linkage disequilibrium. To expand the utility of MS allele imputation across breeds, MS and SNP data from more than 8000 animals representing 39 breeds (Bos taurus and B. indicus) were used to predict 9410 SNP haplotypes, incorporating an average of 73 SNPs per haplotype, for which alleles from 12 MS markers could be accurately be imputed. Approximately 25% of the MS-SNP haplotypes were present in multiple breeds (N = 2 to 36 breeds). These shared haplotypes allowed for MS imputation in breeds that were not represented in the reference population with only a small increase in Mendelian inheritance inconsistancies. Our reported reference haplotypes can be used for any cattle breed and the reported methods can be applied to any species to aid the transition from MS to SNP genetic markers. While ~91% of the animals with imputed alleles for 12 MS markers had ≤1 Mendelian inheritance conflicts with their parents' reported MS genotypes, this figure was 96% for our reference animals, indicating potential errors in the reported MS genotypes. The workflow we suggest autocorrects for genotyping errors and rare haplotypes, by MS genotyping animals whose imputed MS alleles fail parentage verification, and then incorporating those animals into the reference dataset.
Meiotic recombination is an essential biological process that generates genetic diversity and ensures proper segregation of chromosomes during meiosis. From a large USDA dairy cattle pedigree with ...over half a million genotyped animals, we extracted 186,927 three-generation families, identified over 8.5 million maternal and paternal recombination events, and constructed sex-specific recombination maps for 59,309 autosomal SNPs. The recombination map spans for 25.5 Morgans in males and 23.2 Morgans in females, for a total studied region of 2,516 Mb (986 kb/cM in males and 1,085 kb/cM in females). The male map is 10% longer than the female map and the sex difference is most pronounced in the subtelomeric regions. We identified 1,792 male and 1,885 female putative recombination hotspots, with 720 hotspots shared between sexes. These hotspots encompass 3% of the genome but account for 25% of the genome-wide recombination events in both sexes. During the past forty years, males showed a decreasing trend in recombination rate that coincided with the artificial selection for milk production. Sex-specific GWAS analyses identified PRDM9 and CPLX1 to have significant effects on genome-wide recombination rate in both sexes. Two novel loci, NEK9 and REC114, were associated with recombination rate in both sexes, whereas three loci, MSH4, SMC3 and CEP55, affected recombination rate in females only. Among the multiple PRDM9 paralogues on the bovine genome, our GWAS of recombination hotspot usage together with linkage analysis identified the PRDM9 paralogue on chromosome 1 to be associated in the U.S. Holstein data. Given the largest sample size ever reported for such studies, our results reveal new insights into the understanding of cattle and mammalian recombination.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The intensive selection programs for milk made possible by mass artificial insemination increased the similarity among the genomes of North American (NA) Holsteins tremendously since the 1960s. This ...migration of elite alleles has caused certain regions of the genome to have runs of homozygosity (ROH) occasionally spanning millions of continuous base pairs at a specific locus. In this study, genome signatures of artificial selection in NA Holsteins born between 1953 and 2008 were identified by comparing changes in ROH between three distinct groups under different selective pressure for milk production. The ROH regions were also used to estimate the inbreeding coefficients. The comparisons of genomic autozygosity between groups selected or unselected since 1964 for milk production revealed significant differences with respect to overall ROH frequency and distribution. These results indicate selection has increased overall autozygosity across the genome, whereas the autozygosity in an unselected line has not changed significantly across most of the chromosomes. In addition, ROH distribution was more variable across the genomes of selected animals in comparison to a more even ROH distribution for unselected animals. Further analysis of genome-wide autozygosity changes and the association between traits and haplotypes identified more than 40 genomic regions under selection on several chromosomes (Chr) including Chr 2, 7, 16 and 20. Many of these selection signatures corresponded to quantitative trait loci for milk, fat, and protein yield previously found in contemporary Holsteins.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
First-lactation test-day milk, fat, and protein yields from New York, Wisconsin, and California herds from 1990 through 2000 were adjusted additively for age and lactation stage. A random regression ...model with third-order Legendre polynomials for permanent environmental and genetic effects was used. The model included a random effect with the same polynomial regressions for 2 yr of calvings within herd (herd-time effect) to provide herd-specific lactation curves that can change every 2 yr. (Co)variance components were estimated using expectation-maximization REML simultaneously with phenotypic variances that were modeled using a structural variance model. Maximum heritability for test-day milk yield was estimated to be ∼20% around 200 to 250 d in milk; heritabilities were slightly lower for test-day fat and protein yields. Herd-time effects explained 12 to 20% of phenotypic variance and had the greatest impact at start of lactation. Variances of test-day yields increased with time, subclass size, and milking frequency. Test month had limited influence on variance. Variance increased for cows in herds with low and high milk yields and for early and late lactation stages. Repeatabilities of variances observed for a given class of herd, test-day, and milking frequency were 14 to 17% across nested variance subclasses based on lactation stage.
A method of accounting for differences in covariance components of test-day milk records was developed based on transformation of regressions for random effects. Preliminary analysis indicated that ...genetic and nongenetic covariance structures differed by herd milk yield. Differences were found for phenotypic covariances and also for genetic, permanent environmental, and herd-time covariances. Heritabilities for test-day milk yield tended to be lower at the end and especially at the start of lactation; they also were higher (maximum of ∼25%) for high-yield herds and lower (maximum of 15%) for low-yield herds. Permanent environmental variances were on average 10% lower in high-yield herds. Relative herd-time variances were ∼10% at start of lactation and then began to decrease regardless of herd yield; high-yield herds increased in midlactation followed by another decrease, and medium-yield herds increased at the end of lactation. Regressors for random regression effects were transformed to adjust for heterogeneity of test-day yield covariances. Some animal reranking occurred because of this transformation of genetic and permanent environmental effects. When genetic correlations between environments were allowed to differ from 1, some additional animal re-ranking occurred. Correlations of variances of genetic and permanent-environmental regression solutions within herd, test-day, and milking frequency class with class mean milk yields were reduced with adjustment for heterogeneous covariance. The method suggests a number of innovative solutions to issues related to heterogeneous covariance structures, such as adjusted estimates in multibreed evaluation.
This paper presents an equilibrium explanation for the persistence of naive bidding. Specifically, we consider a common value auction in which a "naive" bidder (who ignores the winner's curse) ...competes against a fully rational bidder. We show that the naive bidder earns higher equilibrium profits than the rational bidder when the signal distribution is symmetric and unimodal. We then consider a sequence of such auctions with randomly selected participants from a population of naive and rational bidders, with the proportion of bidder types in the population evolving in response to their relative payoffs in the auctions. We show that the evolutionary equilibrium contains a strictly positive proportion of naive bidders. Finally, we consider more general examples in which a naive bidder matched against a rational bidder does (i) worse than his rational opponent, but (ii) better than a rational bidder matched against another rational bidder. Again, the evolutionary equilibrium contains a strictly positive proportion of naive bidders. The results suggest that overconfident recent entrants in Internet and other low transaction-cost auctions of items that appeal to a mass audience may earn higher payoffs than their experienced competitors and, thus, will not eventually be driven from the market.
BackgroundEstablishing whether patients are exposed to a ‘known cause’ is a key element in both the diagnostic assessment and the subsequent management of hypersensitivity pneumonitis ...(HP).ObjectiveThis study surveyed British interstitial lung disease (ILD) specialists to document current practice and opinion in relation to establishing causation in HP.MethodsBritish ILD consultants (pulmonologists) were invited by email to take part in a structured questionnaire survey, to provide estimates of demographic data relating to their service and to rate their level of agreement with a series of statements. A priori ‘consensus agreement’ was defined as at least 70% of participants replying that they ‘Strongly agree’ or ‘Tend to agree’.Results54 consultants took part in the survey from 27 ILD multidisciplinary teams. Participants estimated that 20% of the patients in their ILD service have HP, and of these, a cause is identifiable in 32% of cases. For patients with confirmed HP, an estimated 40% have had a bronchoalveolar lavage for differential cell counts, and 10% a surgical biopsy. Consensus agreement was reached for 25 of 33 statements relating to causation and either the assessment of unexplained ILD or management of confirmed HP.ConclusionsThis survey has demonstrated that although there is a degree of variation in the diagnostic approach for patients with suspected HP in Britain, there is consensus opinion for some key areas of practice. There are several factors in clinical practice that currently act as potential barriers to identifying the cause for British HP patients.
Days open was studied from information in lactation records collected through the National Cooperative Dairy Herd Improvement Program. Information on days open was available for 83% of United States ...records. Only 33% of records from the Wisconsin dairy records processing center included information on days open because 46% of herds had no reporting of this information, and a computation error caused information on days open for some cows in other herds not to be reported. When records from Wisconsin were excluded, information on days open was available for 90% of lactation records. Four percent of herds had no reporting of information on days open for any cows; 85% had above 80% reporting. Gestations computed from these data matched those from previous studies except for data from the Pennsylvania and Michigan dairy records processing centers, which had longer intervals. Errors in preparing records explained these longer intervals. When records from Michigan and Pennsylvania dairy records processing centers were excluded, gestations were 282 days for Ayrshires, 288 days for Brown Swiss, 286 days for Guernseys, 280 days for Holsteins, 279 days for Jerseys, 282 days for Milking Shorthorns, and 282 days for Red and White. With correction of computing problems and selection of appropriate procedures for missing information, data on days open available through the National Cooperative Dairy Herd Improvement Program appear to provide an adequate basis for adjusting lactation records.
Auctions with an inexpert bidder Deltas, George; Engelbrecht-Wiggans, Richard
Economics letters,
10/2001, Letnik:
73, Številka:
1
Journal Article
Recenzirano
We consider an auction in which the behavior of one potential bidder departs mildly from full rationality. We show that the presence of such an inexpert bidder can be enough to discourage all of an ...infinitely large population of fully rational potential bidders from entering an auction. Furthermore, this departure from full rationality does not reduce the inexpert bidder’s payoff.
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