Genomics-assisted dissection of barley morphology and development (ERA-PG 046)

我们将使用Illumina Oligo Pool Assay （OPA）技术对480个鲍曼回交衍生的近等基因突变系的3072个已定位的遗传位点（6144个等位基因）进行基因分型。我们将使用简单的与Bowman（他们的复发亲本）的成对比较来定义包含突变等位基因的片段的边界，并基于大麦、水稻和新兴的短柄草和玉米的基因组序列，为每个位点编制详细的比较推定基因含量图。虽然OPA基因分型将每个突变位点的位置缩小到一个小的遗传间隔，但从所有潜在的候选基因中识别突变基因可能仍然需要向前遗传学方法。为了促进这一研究，以及未来所有类似的研究，我们建议通过对目前正在进行高信息含量指纹分析和超过12,000个单基因杂交的bac进行末端测序，为分阶段开发大麦基因组遗传锚定物理图谱的既定国际战略做出贡献。这将提供高达400mbp的大麦基因组DNA序列信息，并将有助于将物理图谱锚定到大麦基因图谱（约5-6000个已绘制的基因）和水稻基因组序列。为了展示已开发的信息、资源和方法的效用，每个合作实验室将确定跨越形态/发育突变位点的最小BAC平铺路径，确定候选基因并通过比较等位基因测序（WT与突变）的组合和使用小组可用的功能基因组学工具（TILLING、转基因、VIGS）启动其功能特征。所有信息都将通过现有的基于网络的信息学资源向社会公开，以便更广泛地利用。

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.