Metafounders are related to F fixation indices and reduce bias in single-step genomic evaluations.

Background: Metafounders are pseudo-individuals that encapsulate genetic heterozygosity and relationships within and across base pedigree populations, i.e. ancestral populations.

Genomic prediction with epistasis models: on the marker-coding-dependent performance of the extended GBLUP and properties of the categorical epistasis model (CE).

Background: Epistasis marker effect models incorporating products of marker values as predictor variables in a linear regression approach (extended GBLUP, EGBLUP) have been assessed as potentially beneficial for genomic prediction, but their performance depends on marker coding. Although this fact has been recognized in literature, the nature of the problem has not been thoroughly investigated so far.

Results: We illustrate how the choice of marker coding implicitly specifies the model of how effects of certain allele combinations at different loci contribute to the phenotype, and investigate coding-dependent properties of EGBLUP.

Quality control of genotypes using heritability estimates of gene content at the marker.

Quality control filtering of single-nucleotide polymorphisms (SNPs) is a key step when analyzing genomic data. Here we present a practical method to identify low-quality SNPs, meaning markers whose genotypes are wrongly assigned for a large proportion of individuals, by estimating the heritability of gene content at each marker, where gene content is the number of copies of a particular reference allele in a genotype of an animal (0, 1, or 2). If there is no mutation at the marker, gene content has an additive heritability of 1 by construction.

Rapid screening for phenotype-genotype associations by linear transformations of genomic evaluations.

Background: Currently, association studies are analysed using statistical mixed models, with marker effects estimated by a linear transformation of genomic breeding values. The variances of marker effects are needed when performing the tests of association. However, approaches used to estimate the parameters rely on a prior variance or on a constant estimate of the additive variance.

Genotype imputation accuracy in a F2 pig population using high density and low density SNP panels.

Background: F(2) resource populations have been used extensively to map QTL segregating between pig breeds. A limitation associated with the use of these resource populations for fine mapping of QTL is the reduced number of founding individuals and recombinations of founding haplotypes occurring in the population. These limitations, however, become advantageous when attempting to impute unobserved genotypes using within family segregation information.

Reduced faecal shedding of Escherichia coli O157:H7 in cattle following systemic vaccination with γ-intimin C₂₈₀ and EspB proteins.

Enterohaemorrhagic Escherichia coli (EHEC) O157:H7 is the most prevalent EHEC serotype that has been recovered from patients with haemolytic uremic syndrome (HUS) worldwide. Vaccination of cattle, the main reservoir of EHEC O157:H7, could be a logical strategy to fight infection in humans. This study evaluated a vaccine based on the carboxyl-terminal fragment of 280 amino acids of γ-intimin (γ-intimin C₂₈₀) and EspB, two key colonization factors of E.

Equivalence of multibreed animal models and hierarchical Bayes analysis for maternally influenced traits.

Background: It has been argued that multibreed animal models should include a heterogeneous covariance structure. However, the estimation of the (co)variance components is not an easy task, because these parameters can not be factored out from the inverse of the additive genetic covariance matrix. An alternative model, based on the decomposition of the genetic covariance matrix by source of variability, provides a much simpler formulation.

Improving 2D-DIGE protein expression analysis by two-stage linear mixed models: assessing experimental effects in a melanoma cell study.

Motivation: Difference in-gel electrophoresis (DIGE)-based protein expression analysis allows assessing the relative expression of proteins in two biological samples differently labeled (Cy5, Cy3 CyDyes). In the same gel, a reference sample is also used (Cy2 CyDye) for spot matching during image analysis and volume normalization. The standard statistical techniques to identify differentially expressed (DE) proteins are the calculation of fold-changes and the comparison of treatment means by the t-test.

Full conjugate analysis of normal multiple traits with missing records using a generalized inverted Wishart distribution.

A Markov chain Monte Carlo (MCMC) algorithm to sample an exchangeable covariance matrix, such as the one of the error terms (R0) in a multiple trait animal model with missing records under normal-inverted Wishart priors is presented. The algorithm (FCG) is based on a conjugate form of the inverted Wishart density that avoids sampling the missing error terms. Normal prior densities are assumed for the 'fixed' effects and breeding values, whereas the covariance matrices are assumed to follow inverted Wishart distributions.

Use of nootkatone as a senescence indicator for Rouge La Toma Cv. grapefruit (Citrus paradisi Macf.).

The objective of this research was to study the usefulness of nootkatone as a senescence indicator for Rouge La Toma cv. grapefruit (Citrus paradisi Macf.), simulating different treatments that included the normal postharvest handling of citrus fruits: temperature conditioning, cold storage, shipment periods to overseas markets such as Japan and the U.