We studied four formulae used to predict the accuracy of genomic selection prior to genotyping. The objectives of our study were to investigate the impact of the parameters of each formula on the values of accuracy calculated using these formulae, and to check whether the accuracies reported in the literature are in agreement with the formulae. First, we computed the marginal distribution of accuracy (by integration) for each parameter of all four formulae: heritability h2, reference population size T, number of markers M and number of effective segments in the genome Me. Then, we collected 145 accuracies and corresponding parameters reported in 13 publications on genomic selection (mainly in dairy cattle), and performed analysis of variance to test the differences between observed and predicted accuracy with effects of formulae and parameters. The variation of accuracy for different values of each parameter indicated that two parameters, T and Me, had a significant impact and that considerable differences existed between the formulae (mean accuracies differed by up to 0.20 point). The results of our meta‐analysis showed a big formula effect on the accuracies predicted using each formula, and also a significant effect of the value obtained for Me calculated from Ne (effective population size). Each formula can therefore be demonstrated to be optimal depending on the assumption used for Me. In conclusion, no rules can be applied to predict the reliability of genomic selection using these formulae. 相似文献
Despite the fact that the northern bobwhite (Colinus virginianus Linnaeus; hereafter, bobwhite) is one of the most well-studied and widely distributed wildlife species in North America, we know little about how bobwhite respond to oil and gas infrastructure. We investigated the impacts of oil and gas development on space use of bobwhite using a multiseason approach. We captured and monitored bobwhite in the breeding season (1 April–30 September, n = 135 individuals) and nonbreeding season (1 October–31 March, n = 30 coveys) and modeled their habitat selection in a resource-utilization function (third order, within home range selection) and resource-selection function (second order, home range selection) format. Generally, energy infrastructure effects on bobwhite were neutral, but breeding season bobwhite did select for areas near low-traffic roads (β = ? 0.31 ± 0.15 SE). In the nonbreeding season, coveys selected for areas within their home range with a limited viewshed (i.e., areas with limited visibility of anthropogenic structures; β = ? 0.03 ± 0.02 SE). Selection differed between sexes for well pads (t = ? 2.12, P = 0.04) but was otherwise similar. At the level of home range selection, bobwhite exhibited a preference for areas with a low density of oil and gas wells and a high density of low-traffic roads during both the breeding and nonbreeding seasons (breeding: βwell = ? 0.14 ± 0.02, βroad = 0.26 ± 0.27; nonbreeding: βwell = ? 0.08 ± 0.03, βroad = 0.16 ± 0.03). As a generalist species, bobwhite appear to be largely tolerant of energy infrastructure and associated disturbances at moderate levels of development but may be sensitive to high densities of oil and gas pads. 相似文献
1. In commercial layer breeding, extensive gene pools are tested and selected for market requirements which must be anticipated at least 5 years ahead. Field results confirm a continuous positive genetic trend in egg output and better feed efficiency which can be converted into land savings.
2. Animal welfare and cage-free housing dominate future needs of the market. Nesting behaviour and minimal tendency to develop feather-pecking or cannibalism without beak treatment are key trait complexes. Stronger shells for longer production cycles without moulting have to be combined with better bones.
3. No single big gene effect can be expected to control the multifactorial problem of feather-pecking. Adjusting the shape of the beak, with a heritability of .10–.25, can contribute to reducing the risk of severe cannibalism.
4. For better skeletal integrity, the assessment of bone quality in pedigree birds housed in enriched cages is done by keel bone palpation or ultrasound measurement of the humerus. Both traits show similar heritabilities in the range of .15–.30 and can be included in a balanced selection approach for performance, quality and welfare traits.
5. The combination of performance testing and genome-wide DNA marker analysis is a promising tool to generate more progress for a balanced performance and behaviour profile. 相似文献
The objective of this study was to evaluate, using three different genotype density panels, the accuracy of imputation from lower‐ to higher‐density genotypes in dairy and beef cattle. High‐density genotypes consisting of 777 962 single‐nucleotide polymorphisms (SNP) were available on 3122 animals comprised of 269, 196, 710, 234, 719, 730 and 264 Angus, Belgian Blue, Charolais, Hereford, Holstein‐Friesian, Limousin and Simmental bulls, respectively. Three different genotype densities were generated: low density (LD; 6501 autosomal SNPs), medium density (50K; 47 770 autosomal SNPs) and high density (HD; 735 151 autosomal SNPs). Imputation from lower‐ to higher‐density genotype platforms was undertaken within and across breeds exploiting population‐wide linkage disequilibrium. The mean allele concordance rate per breed from LD to HD when undertaken using a single breed or multiple breed reference population varied from 0.956 to 0.974 and from 0.947 to 0.967, respectively. The mean allele concordance rate per breed from 50K to HD when undertaken using a single breed or multiple breed reference population varied from 0.987 to 0.994 and from 0.987 to 0.993, respectively. The accuracy of imputation was generally greater when the reference population was solely comprised of the breed to be imputed compared to when the reference population comprised of multiple breeds, although the impact was less when imputing from 50K to HD compared to imputing from LD. 相似文献
Selection index methods can be used for deterministic assessment of the potential benefit of including marker information in genetic improvement programmes using marker-assisted selection (MAS). By specifying estimates of breeding values derived from marker information (M-EBV) as a correlated trait with heritability equal to 1, it was demonstrated that marker information can be incorporated in standard software for selection index predictions of response and rates of inbreeding, which requires specifying phenotypic traits and their genetic parameters. Path coefficient methods were used to derive genetic and phenotypic correlations between M-EBV and the phenotypic data. Methods were extended to multi-trait selection and to the case when M-EBV are based on high-density marker genotype data, as in genomic selection. Methods were applied to several example scenarios, which confirmed previous results that MAS substantially increases response to selection but also demonstrated that MAS can result in substantial reductions in the rates of inbreeding. Although further validation by stochastic simulation is required, the developed methodology provides an easy means of deterministically evaluating the potential benefits of MAS and to optimize selection strategies with availability of marker data. 相似文献