Systems-wide chicken DNA microarrays, gene expression profiling, and discovery of functional genes

Abstract

The goal of our current consortium project is to launch a new era--functional genomics of poultry--by providing genomic resources [expressed sequence tags (EST) and DNA microarrays] and by examining global gene expression in target tissues of chickens. DNA microarray analysis has been a fruitful strategy for the identification of functional genes in several model organisms (i.e., human, rodents, fruit fly, etc.). We have constructed and normalized five tissue-specific or multiple-tissue chicken cDNA libraries [liver, fat, breast, and leg muscle/epiphyseal growth plate, pituitary/hypothalamus/pineal, and reproductive tract (oviduct/ovary/testes)] for high-throughput DNA sequencing of EST. DNA sequence clustering was used to build contigs of overlapping sequence and to identify unique, non-redundant EST clones (unigenes), which permitted printing of systems-wide chicken DNA microarrays. One of the most promising genetic resources for gene exploration and functional gene mapping is provided by two sets of experimental lines of broiler-type chickens developed at INRA, France, by divergent selection for extremes in growth traits (fast-growing versus slow-growing; fatness versus leanness at a similar growth rate). We are using DNA microarrays for global gene expression profiling to identify candidate genes and to map growth, metabolic, and regulatory pathways that control important production traits. Candidate genes will be used for functional gene mapping and QTL analysis of F2 progeny from intercrosses made between divergent genetic lines (fat x lean lines; fast-growing x slow-growing lines). Using our first chicken liver microarray, we have already identified several interesting differentially expressed genes in commercial broilers and in divergently selected broiler lines. Many of these candidate genes are involved in the lipogenic pathway and are controlled in part by the thyrotropic axis. Thus, genome-wide transcriptional profiling is a powerful tool used to visualize the cascade of genetic circuits that govern complex biological responses. Global gene expression profiling and QTL scans should enable us to functionally map the genetic pathways that control growth, development, and metabolism of chickens. This emerging technology will have broad applications for poultry breeding programs (i.e., use of molecular markers) and for future production systems (i.e., the health and welfare of birds and the quality of poultry products).

Genetic effect of the prolactin receptor gene on egg production traits in chickens

“…Probing balanced selection and breeding for growth, reproduction, immunity, and metabolism in chickens for optimum performance has become a hot topic in research (Ou et al, 2009). The candidate gene approach is becoming increasingly economical and effective for finding candidate genes and quantitative trait nucleotides with significant effects on economically important traits (Kanehisa et al, 2002;Cogburn et al, 2003;Zhu and Zhao, 2007;Kuhn et al, 2008). According to the integration strategies described above, the PRLR gene was effectively selected and used to study genetic associations with egg production traits.…”

Lack of leptin activity in blood samples of Adélie penguin and bar-tailed godwit

“…In addition, adipose tissue gene expression arrays have failed to detect leptin in lean or fat strains of broilers . Similarly, extensive microarray analysis of chicken fat, liver, and other tissues has failed to identify leptin (Cogburn et al 2004, as has extensive EST screening of fat and other tissues (Cogburn et al 2003, Carre et al 2006 and proteomic analysis of abdominal adipose tissues of fat and lean broilers .…”

“…However, the CLEPR ligand has not yet been found (Friedman-Einat et al 1999, Dunn et al 2001, Amills et al 2003, Sharp et al 2008, Pitel et al 2009). In addition, despite the nearly complete sequencing of the chicken genome (Burt 2006) and extensive sequencing of chicken fat expressed sequence tags (ESTs) (Cogburn et al 2003), no sequence similarity to leptin has been identified, nor has any similarity been found at the protein level (Sharp et al 2008).…”

Identification of genes involved in regulatory mechanism of pigments in broiler chickens

“…Furthermore, these studies have provided information on global gene expression in chickens. Microarray analysis has proven useful as a flourishing approach for the classification of functional genes in several model organisms (e.g., humans, rodents, and fruit flies) (Cogburn et al, 2003) and is considered as a powerful tool for visualizing the molecular mechanism that governs complex biological responses; it is also used in gene expression analysis (van Hal et al, 2000). The technology is primarily used to assess the expression of different genes, search for new genes, the molecular diagnosis of disease, gene mutation and polymorphism analyses, and drug development in order to analyze and ascertain the specificity of these comprehensive gene expressions on large scale (Nakachi et al, 2008).…”