Mining the allohexaploid wheat genome for useful sequence polymorphisms

Lead Research Organisation: John Innes Centre
Department Name: Contracts Office


The large size and polyploid nature of the bread wheat genome is a major barrier to genome sequencing. Because wheat yield increases achieved in the past have been primarily due to genetic improvements, and because there is major potential for further increases in sustainable yield and quality within existing and exotic germplasm, the challenge is to develop genomics resources for wheat improvement. In this project we are using next generation sequencing technology, gene enrichment methods and a novel sequence alignment and assembly approach to identify and validate sequence polymorphisms in key UK germplasm. This information will be provided directly to breeders and academics through genome databases to facilitate the genetic improvement of UK wheat varieties.The specific aims of the project are to generate a 5-fold sequence coverage of the reference Chinese Spring genome, generate a 5-fold sequence coverage of enriched genomes of the key UK research and breeding lines Avalon, Cadenza, Rialto and Savannah, and generate ~ 4 million cDNA sequences from normalised Chinese Spring cDNA. The sequences will be aligned to the closely related Brachypodium distachyon genome sequence to identify further genes and poorly expressed homoeologs and paralogs and 5’, 3’ and intron-exon splice junctions. The information generated will be used to identify and discriminate between intra and inter varietal sequence polymorphisms, a subset of which will be validated and used to screen a core-collection of UK-based germplasm. All sequences and related information will be deposited in public databases and displayed in genome browsers.


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