BackgroundA complete approach for genome-wide selection (GWS) involves reliable statistical genetics models and methods. Reports on this topic are common for additive genetic models but not for additive-dominance models. The objective of this paper was (i) to compare the performance of 10 additive-dominance predictive models (including current models and proposed modifications), fitted using Bayesian, Lasso and Ridge regression approaches; and (ii) to decompose genomic heritability and accuracy in terms of three quantitative genetic information sources, namely, linkage disequilibrium (LD), co-segregation (CS) and pedigree relationships or family structure (PR). The simulation study considered two broad sense heritability levels (0.30 and 0.50, associated with narrow sense heritabilities of 0.20 and 0.35, respectively) and two genetic architectures for traits (the first consisting of small gene effects and the second consisting of a mixed inheritance model with five major genes).ResultsG-REML/G-BLUP and a modified Bayesian/Lasso (called BayesA*B* or t-BLASSO) method performed best in the prediction of genomic breeding as well as the total genotypic values of individuals in all four scenarios (two heritabilities x two genetic architectures). The BayesA*B*-type method showed a better ability to recover the dominance variance/additive variance ratio. Decomposition of genomic heritability and accuracy revealed the following descending importance order of information: LD, CS and PR not captured by markers, the last two being very close.ConclusionsAmongst the 10 models/methods evaluated, the G-BLUP, BAYESA*B* (−2,8) and BAYESA*B* (4,6) methods presented the best results and were found to be adequate for accurately predicting genomic breeding and total genotypic values as well as for estimating additive and dominance in additive-dominance genomic models.

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Keywords:Masonry Church of the Nativity Narthex FE model Non-linear dynamic analysis Vault a b s t r a c tThe Church of the Nativity in Bethlehem has a narthex in the front that is as long as the façade of the Church and about six meters wide. Currently, the narthex is covered by five cross vaults, three of which in a dangerous state of decay, and it is internally divided by three walls perpendicular to the façade, which appears to be strongly rotated outwards with a maximum horizontal top displacement of about 40 cm. Inside the central cross vault, the narthex has been heavily damaged and propped since the thirties of the last century. Numerous attempts have been made over the time to identify the causes of such damage. Some archival researches, in-situ inspections of the subsoil and detailed laser scanner surveys, which were carried out during the recent restoration works in the Church and in the narthex, allowed for gaining a deeper insight into the construction features of the cross vaults and for putting forward some hypotheses about the possible causes of damage. This paper provides a scientific validation of these hypotheses by means of finite element numerical simulations, which try to reproduce the seismic response of the Church and the deformation process of a three-dimensional simplified model of the narthex from an assumed initial configuration up to an ultimate state of damage, comparable with the current one. Such models are discretized by means of tetrahedron elements obeying a damage plasticity law that exhibits a softening behavior in both tension and compression. The numerical simulations carried out provide some results that fit reasonably with the actual deformed configuration of the narthex and can be considered as a useful tool for further insights.

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The objective was to assess by simulation the efficacy of population structure analysis in plant breeding. Twelve populations and 300 inbred lines were simulated and genotyped using 100 microsatellite loci. The experimental material included populations with and without admixture, ancestry relationship and linkage disequilibrium, and with distinct levels of genetic differentiation and effective sizes. The analyses were performed using Structure software and employed all available models. For all the group number (K) tested, for both populations and inbred lines, the admixture model with correlated allelic frequencies provided the highest value for the logarithm of the marginal likelihood. Fitting appropriate model and using adequate sample size for individuals and markers, Structure was effective in identifying the correct population structure, migrants and individuals with genome from distinct populations. The linkage model did not result in an improvement in clustering relative to the admixture model with correlated allelic frequencies. The inclusion of prior information did not change the results; for some K values the analyses showed slight higher values of the marginal likelihood. The reduction in the number of individuals and markers negatively affected the results. There was a high variation in the most probable K value between the evaluated methods.

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