Candidate genes and bioinformatic analysisof biological pathways for epistatic regulationof growth in chicken

Selective breeding programmes for desired phenotypes in animals provide a good resource for researchers to understand the genetic basis underlying those phenotypes. Most traits of economic importance in animals are quantitative traits, which are controlled by genetic as well as environmental factors. Previous studies have shown that the mapping of the genomic regions containing genetic factors, which control the diverse phenotypes in complex traits of interest, resulted in the successful identification of causative mutations. The same forward genetics approach, which endeavours to identify the genetic basis of phenotypic diversity, was followed in this study. To identify and functionally evaluate the mutations controlling diverse phenotypic differences between the High-weight and Low-weight chicken lines, the previously fine mapped interacting quantitative trait loci (QTL) for growth in chicken were scanned for the presence of genes. Gene databases (Ensembl, RefSeq) and gene prediction tools (Genscan and N-Scan) were used to reveal as many genes as possible. To identify candidate genes for growth, the conservation pattern of those genes was studied using the phastCons programme in the PHAST package. The genes most conserved in evolution were identified and selected for further analysis. The evidence based, well-supported and annotated Ensemble conserved genes were identified as candidate genes for growth in general. Gene ontology terms for the candidate genes were obtained from the Gene Ontology (GO) database to study the molecular and biological functions of those candidate genes. KEGG biological pathways were mapped for the presence of identified candidate genes. The candidate genes were found having roles in many biological pathways. The biological pathways that contained candidate genes from multiple interacting QTL were identified as candidate pathways. Major candidate pathways include the Mitogen Activated Protein Kinase (MAPK) signalling pathway, which affects growth in general, and Adipocytokine signalling pathway, which imparts its anorectic effect through the leptin hormone. Further studies are required to analyse the functional effects of those candidate genes and pathways and eventually to identify the mutations affecting growth.