W586 Utilization of Advanced Genomic Technologies to Identify Causative Elements of Inherited Developmental Defects in the Chicken

Date: Saturday, January 14, 2012
Time: 5:00 PM
Room: Sunset
Elizabeth Robb , University of California, Davis, CA
Mary Delany , University Of California, Davis, CA
Advanced genomic technologies coupled with unique animal phenotypes can generate knowledge of biological pathways and processes. The chicken is a premier research model in developmental biology due to the advantages of access and ease of manipulation. The power of the chicken model was further improved by creation of tools and reagents (genome sequence, ESTs, gene expression and cDNA databases, microarrays, SNP arrays). UC Davis maintains congenic lines harboring single-gene, recessive mutations which result in abnormal developmental phenotypes. Three genetic lines, coloboma, diplopodia-1, and wingless-2, were studied to identify the causative element responsible for each developmental syndrome. Previously, 3K and 60K SNP array studies paired with fine-mapping led to the discovery of a specific chromosomal region associated with each syndrome. Recently, we designed a targeted-capture array and employed deep-sequencing to investigate the regions linked to each mutation. Bioinformatic analyses inclusive of reference-assisted de novo assembly and comparisons among the lines and to the reference genome identified unique genetic features (SNPs, short/long INDELs, large deletions) within each mutation region. These elements were assessed for linkage and coupled with a validation analysis to evaluate the contribution of the polymorphisms to the mutant phenotypes. To our knowledge this is the first successful employment of targeted capture array technology in chicken. The unique genetic resources under study are valuable models for discovering sequences and pathways important in amniote development; in particular these specific chicken genetic resources offer a valuable means of studying craniofacial morphogenesis as well as limb and organ development.