Genomics-assisted dissection of barley morphology and development

Abstract

We will use Illumina Oligo Pool Assay (OPA) technology to genotype 480 Bowman backcross derived nearly isogenic mutant lines at 3072 mapped genetic loci (6144 alleles). We will use simple pair-wise comparison with Bowman, their recurrent parent, to define the boundaries of the segments containing mutated alleles and compile a detailed comparative putative gene content map for each locus based on the barley, rice and emerging Brachypodium and maize genome sequences. While OPA genotyping will narrow the location of each mutant locus to a small genetic interval, identifying the mutated gene from all potential candidates will likely still require a forward genetics approach. To facilitate this, and all similar studies in the future, we propose to contribute to an established international strategy for the staged development of a genetically anchored physical map of the barley genome by end sequencing BACs that are currently undergoing High Information Content Fingerprint analysis and Overgo hybridisation to >12,000 unigenes. This will provide up to 400 Mbp of barley genomic DNA sequence information and will assist in anchoring the physical map to the barley gene map (~5-6000 mapped genes) and rice genome sequence. To demonstrate the utility of the developed information, resources and approach, each partner lab will identify a minimum BAC tiling path spanning a morphological /developmental mutant locus, identify candidate genes and initiate their functional characterisation by a combination of comparative allele sequencing (WT vs. Mutant) and the use of functional genomics tools available to the group (TILLING, transgenics, VIGS). All information will be made publicly available to the community for broader exploitation through existing web-based informatics resources.