Comparing the intestinal transcriptome of Meishan and Large White piglets during late fetal development reveals genes involved in glucose and lipid metabolism and immunity as valuable clues of intestinal maturity.

Background: Maturity of intestinal functions is critical for neonatal health and survival, but comprehensive description of mechanisms underlying intestinal maturation that occur during late gestation still remain poorly characterized. The aim of this study was to investigate biological processes specifically involved in intestinal maturation by comparing fetal jejunal transcriptomes of two representative porcine breeds (Large White, LW; Meishan, MS) with contrasting neonatal vitality and maturity, at two key time points during late gestation (gestational days 90 and 110). MS and LW sows inseminated with mixed semen (from breed LW and MS) gave birth to both purebred and crossbred fetuses.

Accounting for linkage disequilibrium in genome scans for selection without individual genotypes: The local score approach.

Detecting genomic footprints of selection is an important step in the understanding of evolution. Accounting for linkage disequilibrium in genome scans increases detection power, but haplotype-based methods require individual genotypes and are not applicable on pool-sequenced samples. We propose to take advantage of the local score approach to account for linkage disequilibrium in genome scans for selection, cumulating (possibly small) signals from single markers over a genomic segment, to clearly pinpoint a selection signal.

Differentially expressed genes and gene networks involved in pig ovarian follicular atresia.

Ovarian folliculogenesis corresponds to the development of follicles leading to either ovulation or degeneration, this latter process being called atresia. Even if atresia involves apoptosis, its mechanism is not well understood. The objective of this study was to analyze global gene expression in pig granulosa cells of ovarian follicles during atresia.

Exploring transcriptomic diversity in muscle revealed that cellular signaling pathways mainly differentiate five Western porcine breeds.

Background: Among transcriptomic studies, those comparing species or populations can increase our understanding of the impact of the evolutionary forces on the differentiation of populations. A particular situation is the one of short evolution time with breeds of a domesticated species that underwent strong selective pressures. In this study, the gene expression diversity across five pig breeds has been explored in muscle.

How do introgression events shape the partitioning of diversity among breeds: a case study in sheep.

Background: From domestication to the current pattern of differentiation, domestic species have been influenced by reticulate evolution with multiple events of migration, introgression, and isolation; this has resulted in a very large number of breeds. In order to manage these breeds and their genetic diversity, one must know the current genetic structure of the populations and the relationships among these. This paper presents the results of a genetic diversity analysis on an almost exhaustive sample of the sheep breeds reared in France.

Muscle transcriptomic investigation of late fetal development identifies candidate genes for piglet maturity.

Background: In pigs, the perinatal period is the most critical time for survival. Piglet maturation, which occurs at the end of gestation, leads to a state of full development after birth. Therefore, maturity is an important determinant of early survival.

Transcriptional reprogramming and phenotypical changes associated with growth of Xanthomonas campestris pv. campestris in cabbage xylem sap.

Xylem sap (XS) is the first environment that xylem phytopathogens meet in planta during the early infection steps. Xanthomonas campestris pv. campestris (Xcc), the causative agent of Brassicaceae black rot, colonizes the plant xylem vessels to ensure its multiplication and dissemination.

The structure of a gene co-expression network reveals biological functions underlying eQTLs.

What are the commonalities between genes, whose expression level is partially controlled by eQTL, especially with regard to biological functions? Moreover, how are these genes related to a phenotype of interest? These issues are particularly difficult to address when the genome annotation is incomplete, as is the case for mammalian species. Moreover, the direct link between gene expression and a phenotype of interest may be weak, and thus difficult to handle. In this framework, the use of a co-expression network has proven useful: it is a robust approach for modeling a complex system of genetic regulations, and to infer knowledge for yet unknown genes.

Detecting signatures of selection through haplotype differentiation among hierarchically structured populations.

The detection of molecular signatures of selection is one of the major concerns of modern population genetics. A widely used strategy in this context is to compare samples from several populations and to look for genomic regions with outstanding genetic differentiation between these populations. Genetic differentiation is generally based on allele frequency differences between populations, which are measured by FST or related statistics.

Genetic variability of transcript abundance in pig peri-mortem skeletal muscle: eQTL localized genes involved in stress response, cell death, muscle disorders and metabolism.

Background: The genetics of transcript-level variation is an exciting field that has recently given rise to many studies. Genetical genomics studies have mainly focused on cell lines, blood cells or adipose tissues, from human clinical samples or mice inbred lines. Few eQTL studies have focused on animal tissues sampled from outbred populations to reflect natural genetic variation of gene expression levels in animals.

Transcriptome profiling of sheep granulosa cells and oocytes during early follicular development obtained by laser capture microdissection.

Background: Successful achievement of early folliculogenesis is crucial for female reproductive function. The process is finely regulated by cell-cell interactions and by the coordinated expression of genes in both the oocyte and in granulosa cells. Despite many studies, little is known about the cell-specific gene expression driving early folliculogenesis.

Genetic characterization of the Blonde d'Aquitaine cattle breed using microsatellite markers and relationship with three other French cattle populations.

This study was conducted to evaluate the genetic diversity of Blonde d'Aquitaine, a well-muscled native French beef breed, and to understand the relationships between Blonde d'Aquitaine, Limousin and Salers. We also compared these three beef breeds to the Holstein dairy breed. For this purpose, a set of 16 microsatellite markers were investigated.

Detecting selection in population trees: the Lewontin and Krakauer test extended.

Detecting genetic signatures of selection is of great interest for many research issues. Common approaches to separate selective from neutral processes focus on the variance of F(ST) across loci, as does the original Lewontin and Krakauer (LK) test. Modern developments aim to minimize the false positive rate and to increase the power, by accounting for complex demographic structures.

Genetic variability, structure and assignment of Spanish and French pig populations based on a large sampling.

The Spanish and French pig populations share the common practice of quasi systematic paternity control of pure breed and composite line males. Ten microsatellite markers are in common between Spain and France controls, among the 17 markers used in France and the 13 used in Spain. After the adjustment of allele sizes, it is possible to merge the two datasets and to obtain a set of 5791 animals, including the vast majority of the males in the Duroc, Landrace, Large White and Piétrain French and Spanish breeds.

Methods for interpreting lists of affected genes obtained in a DNA microarray experiment.

Background: The aim of this paper was to describe and compare the methods used and the results obtained by the participants in a joint EADGENE (European Animal Disease Genomic Network of Excellence) and SABRE (Cutting Edge Genomics for Sustainable Animal Breeding) workshop focusing on post analysis of microarray data. The participating groups were provided with identical lists of microarray probes, including test statistics for three different contrasts, and the normalised log-ratios for each array, to be used as the starting point for interpreting the affected probes. The data originated from a microarray experiment conducted to study the host reactions in broilers occurring shortly after a secondary challenge with either a homologous or heterologous species of Eimeria.

Using microarrays to identify positional candidate genes for QTL: the case study of ACTH response in pigs.

Background: Microarray studies can supplement QTL studies by suggesting potential candidate genes in the QTL regions, which by themselves are too large to provide a limited selection of candidate genes. Here we provide a case study where we explore ways to integrate QTL data and microarray data for the pig, which has only a partial genome sequence. We outline various procedures to localize differentially expressed genes on the pig genome and link this with information on published QTL.

Predicting qualitative phenotypes from microarray data - the Eadgene pig data set.

Background: The aim of this work was to study the performances of 2 predictive statistical tools on a data set that was given to all participants of the Eadgene-SABRE Post Analyses Working Group, namely the Pig data set of Hazard et al. (2008). The data consisted of 3686 gene expressions measured on 24 animals partitioned in 2 genotypes and 2 treatments.

Pathway results from the chicken data set using GOTM, Pathway Studio and Ingenuity softwares.

Background: As presented in the introduction paper, three sets of differentially regulated genes were found after the analysis of the chicken infection data set from EADGENE. Different methods were used to interpret these results.

Results: GOTM, Pathway Studio and Ingenuity softwares were used to investigate the three lists of genes.

What do artificial neural networks tell us about the genetic structure of populations? The example of European pig populations.

General and genetic statistical methods are commonly used to deal with microsatellite data (highly variable neutral genetic markers). In this paper, the self-organizing map (SOM) that belongs to the unsupervised artificial neural networks (ANNs) was applied to analyse the structure of 58 European and two Chinese pig populations (Sus scrofa) including commercial lines, local breeds and cosmopolitan breeds. Results were compared with other unsupervised classification or ordination methods such as factorial correspondence analysis, hierarchical clustering from an allele sharing distance and the Bayesian genetic model and with principal components analysis and neighbour joining from allelic frequencies and genetic distances between populations.

A pilot study on transcriptome data analysis of folliculogenesis in pigs.

Three different stages of pig antral follicles have been studied in a granulosa-cell transcriptome analysis on nylon microarrays (1152 clones). The data have been generated from seven RNA follicle pools and several technical replicates were made. The objective of this paper was to state the feasibility of a transcriptomic protocol for the study of folliculogenesis in the pig.

Changes induced by dietary energy intake and divergent selection for muscle fat content in rainbow trout (Oncorhynchus mykiss), assessed by transcriptome and proteome analysis of the liver.

Background: Growing interest is turned to fat storage levels and allocation within body compartments, due to their impact on human health and quality properties of farm animals. Energy intake and genetic background are major determinants of fattening in most animals, including humans. Previous studies have evidenced that fat deposition depends upon balance between various metabolic pathways.

In vivo gene expression in granulosa cells during pig terminal follicular development.

Ovarian antral follicular development is clearly dependent on pituitary gonadotrophins FSH and LH. Although the endocrine mechanism that controls ovarian folliculogenesis leading to ovulation is quite well understood, the detailed mechanisms and molecular determinants in the different follicular compartments remain to be clarified. The aim of this study was to identify the genes differentially expressed in pig granulosa cells along the terminal ovarian follicle growth, to gain a comprehensive view of these molecular mechanisms.

A muscle transcriptome analysis identifies positional candidate genes for a complex trait in pig.

Muscle tenderness is an important complex trait for meat quality and thus for genetic improvement through animal breeding. However, the physiological or genetic control of tenderness development in muscle is still poorly understood. In this work, using transcriptome analysis, we found a relationship between gene expression variability and tenderness.