Defining the Sequence Elements and Candidate Genes for the Mutation.

Abstract

The chicken mutation exhibits features similar to human congenital developmental malformations such as ocular coloboma, cleft-palate, dwarfism, and polydactyly. The -associated region and encoded genes were investigated using advanced genomic, genetic, and gene expression technologies. Initially, the mutation was linked to a 990 kb region encoding 11 genes; the application of the genetic and genomic tools led to a reduction of the linked region to 176 kb and the elimination of 7 genes. Furthermore, bioinformatics analyses of capture array-next generation sequence data identified genetic elements including SNPs, insertions, deletions, gaps, chromosomal rearrangements, and miRNA binding sites within the introgressed causative region relative to the reference genome sequence. -specific variants within exons, UTRs, and splice sites were studied for their contribution to the mutant phenotype. Our compiled results suggest three genes for future studies. The three candidate genes, (a zinc transporter), (a centromere protein), and (a cyclin-dependent kinase), are differentially expressed (compared to normal embryos) at stages and in tissues affected by the mutation. Of these genes, two ( and ) are considered high-priority candidate based upon studies in other vertebrate model systems.