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Keel bone damage, include deviations and fractures, is common in both white and brown laying hens, regardless of the housing system. Radiography for assessing birds' keel bones is was proposed by previous studies. However, radiographs show only 2 out of 3 dimensions of the dissected keel bones. The current study aimed to (1) investigate the association of radiographic optical density (keel and tibiotarsal) and geometry (keel) with dissected keel bone pathology. Previous studies suggested that keel bone fractures may result from internal pressure exerted by pelvic cavity contents. The current study also aimed to (2) investigate the potential associations between pelvic dimensions and measures of keel bone damage. A sample of 200 laying hens on a commercial farm were radiographed at 16, 29, 42, 55, and 68 weeks, and culled at the end of the laying period (week 74). The birds were examined post-mortem for pelvic dimensions and underwent whole-body radiography, followed by keel and tibiotarsal bone dissection and radiography, and keel bone scoring. The radiographs were used to estimate radiographic optical density (keel and tibiotarsal bone) and keel bone geometry (ratio of keel bone length to mid-depth). The method for on-farm radiography of laying hens, including live bird restraint, positioning for live keel imaging, and post-imaging measurements, was developed, tested, and found to be reproducible. The radiographs (1,116 images of 168 birds) and the respective measurements and post-mortem scores of keel bones are also provided for further development of radiographic metrics relevant to keel bone damage. Some longitudinal radiographic measurements of keel geometry (ratio of length to mid-depth) and optical density (keel and tibiotarsal) showed associations with the damage (deviations/fractures) observed on the dissected keel bones. The associations of keel damage were clearer with the radiographic keel geometry than with keel and tibiotarsal optical density, also clearer for the keel deviations than for keel fractures. The higher radiography ratio of keel length to middepth at weeks 42, 55 and 68 of age, the larger deviations size observed on the dissected keels at age of 74 weeks. The higher the tibiotarsal radiographic optical density at week 55 of age, the lower deviations size and fractures count observed on the dissected keels at age of 74 weeks. Pelvic dimensions showed a positive correlation with body weight, but a larger pelvic cavity was associated with increased keel bone damage. These findings lay the foundations for future use of on-farm radiography in identifying appropriate phenotypes for genetic selection for keel bone health. [ABSTRACT FROM AUTHOR]

Rainbow trout is one of the most popular aquaculture species worldwide, with a long history of domestication. However, limited information exists about the genetic diversity of farmed rainbow trout populations globally, with most available reports relying on low‐throughput genotyping technologies. Notably, no information exists about the genetic diversity status of farmed rainbow trout in Sweden. Double‐digest restriction‐site‐associated DNA sequencing was performed on more than 500 broodfish from two leading producers in Sweden and from the country's national breeding program. Following the detection of single nucleotide polymorphisms (SNPs), genetic diversity was studied by using either individual SNPs (n = 8680; one SNP retained per 300 bp sequence reads) or through SNP haplotypes (n = 20 558; all SNPs retained in 300 bp sequence reads). Similar amounts of genetic diversity were found amongst the three populations when individual SNPs were used. Furthermore, principal component analysis and discriminant analysis of principal components suggested two genetic clusters with the two industry populations grouped together. Genetic differentiation based on the FST fixation index was ~0.01 between the industry populations and ~0.05 when those were compared with the breeding program. Preliminary estimates of effective population size (Ne) and inbreeding (based on runs of homozygosity; FROH) were similar amongst the three populations (Ne ≈ 50–80; median FROH ≈ 0.11). Finally, the haplotype‐based analysis suggested that animals from the breeding program had higher shared coancestry levels than those from the other two populations. Overall, our study provides novel insights into the genetic diversity and structure of Sweden's three main farmed rainbow trout populations, which could guide their future management. [ABSTRACT FROM AUTHOR]

Abstract The aim of this paper was to describe, and when possible compare, the multivariate methods used by the participants in the EADGENE WP1.4 workshop. The first approach was for class discovery and class prediction using evidence from the data at hand. Several teams used hierarchical clustering (HC) or principal component analysis (PCA) to identify groups of differentially expressed genes with a similar expression pattern over time points and infective agent (E. coli or S. aureus). The main result from these analyses was that HC and PCA were able to separate tissue samples taken at 24 h following E. coli infection from the other samples. The second approach identified groups of differentially co-expressed genes, by identifying clusters of genes highly correlated when animals were infected with E. coli but not correlated more than expected by chance when the infective pathogen was S. aureus. The third approach looked at differential expression of predefined gene sets. Gene sets were defined based on information retrieved from biological databases such as Gene Ontology. Based on these annotation sources the teams used either the GlobalTest or the Fisher exact test to identify differentially expressed gene sets. The main result from these analyses was that gene sets involved in immune defence responses were differentially expressed.

Abstract Microarrays allow researchers to measure the expression of thousands of genes in a single experiment. Before statistical comparisons can be made, the data must be assessed for quality and normalisation procedures must be applied, of which many have been proposed. Methods of comparing the normalised data are also abundant, and no clear consensus has yet been reached. The purpose of this paper was to compare those methods used by the EADGENE network on a very noisy simulated data set. With the a priori knowledge of which genes are differentially expressed, it is possible to compare the success of each approach quantitatively. Use of an intensity-dependent normalisation procedure was common, as was correction for multiple testing. Most variety in performance resulted from differing approaches to data quality and the use of different statistical tests. Very few of the methods used any kind of background correction. A number of approaches achieved a success rate of 95% or above, with relatively small numbers of false positives and negatives. Applying stringent spot selection criteria and elimination of data did not improve the false positive rate and greatly increased the false negative rate. However, most approaches performed well, and it is encouraging that widely available techniques can achieve such good results on a very noisy data set.

Abstract A large variety of methods has been proposed in the literature for microarray data analysis. The aim of this paper was to present techniques used by the EADGENE (European Animal Disease Genomics Network of Excellence) WP1.4 participants for data quality control, normalisation and statistical methods for the detection of differentially expressed genes in order to provide some more general data analysis guidelines. All the workshop participants were given a real data set obtained in an EADGENE funded microarray study looking at the gene expression changes following artificial infection with two different mastitis causing bacteria: Escherichia coli and Staphylococcus aureus. It was reassuring to see that most of the teams found the same main biological results. In fact, most of the differentially expressed genes were found for infection by E. coli between uninfected and 24 h challenged udder quarters. Very little transcriptional variation was observed for the bacteria S. aureus. Lists of differentially expressed genes found by the different research teams were, however, quite dependent on the method used, especially concerning the data quality control step. These analyses also emphasised a biological problem of cross-talk between infected and uninfected quarters which will have to be dealt with for further microarray studies.

Abstract Microarray analyses have become an important tool in animal genomics. While their use is becoming widespread, there is still a lot of ongoing research regarding the analysis of microarray data. In the context of a European Network of Excellence, 31 researchers representing 14 research groups from 10 countries performed and discussed the statistical analyses of real and simulated 2-colour microarray data that were distributed among participants. The real data consisted of 48 microarrays from a disease challenge experiment in dairy cattle, while the simulated data consisted of 10 microarrays from a direct comparison of two treatments (dye-balanced). While there was broader agreement with regards to methods of microarray normalisation and significance testing, there were major differences with regards to quality control. The quality control approaches varied from none, through using statistical weights, to omitting a large number of spots or omitting entire slides. Surprisingly, these very different approaches gave quite similar results when applied to the simulated data, although not all participating groups analysed both real and simulated data. The workshop was very successful in facilitating interaction between scientists with a diverse background but a common interest in microarray analyses.

Abstract We describe the results from genetic dissection of a QTL region on chicken chromosome 2, shown to affect egg weight and quality in an earlier genome scan of an F2 intercross between two divergent egg layer lines. As the 90% confidence intervals for the detected QTL covered tens of centiMorgans, new analyses were needed. The datasets were reanalysed with denser marker intervals to characterise the QTL region. Analysis of a candidate gene from the original QTL region, vimentin, did not support its role in controlling egg white thinning. Even after reanalysis with additional seven markers in the QTL area, the 90% confidence intervals remained large or even increased, suggesting the presence of multiple linked QTL for the traits. A grid search fitting two QTL on chromosome 2 for each trait suggested that there are two distinct QTL areas affecting egg white thinning in both production periods and egg weight in the late production period. The results indicate possible pleiotropic effects of some of the QTL on egg quality and egg weight. However, it was not possible to make a distinction between close linkage versus pleiotropic effects.