A draft sequence of the barley genome

Lead Research Organisation: Earlham Institute
Department Name: UNLISTED

Abstract

This project will make a major contribution towards improving the barley reference sequence and generating information about diverse cultivars that will facilitate genomics-assisted breeding of improved varieties. A new assembly and annotation will be generated by incorporating additional sequence resources and providing tools to access and visualise these integrated data sets via an Ensembl web browser. The estimated barley genome size is 5.3Gb, yet the first whole genome shotgun assembly from the IBSC contains only 1.8Gb of sequence assembled from Illumina whole genome shotgun reads and a small set of sequenced BACs and BAC-ends. This project will improve the barley genome by sequencing BAC clones (each approx. 100,000bp in size) using a strategy that combines cost effective short sequence reads of highly-multiplexed BAC clones on Illumina second generation technology with long reads (up to 10,000bp) from third generation sequencing technologies (e.g. Pacific Biosciences) to resolve larger problematic regions. In addition RNAseq data generated from a variety of tissues, at different developmental stages and under stress conditions, will contribute to our understanding of gene expression and alternative splicing, particularly in response to stress, whilst contributing to accurate gene model predictions and barley genome annotation. Exome capture using Nimblegen capture probes will be employed to detect variation within genic regions of up to 1000 barley cultivars from the James Hutton Institute's UK spring barley association mapping panel. This will allow cost-effective targeted resequencing of the transcribed regions of these widely-used lines. These resources will not only benefit barley researchers and breeders, but the knowledge gained from improved annotation of this diploid cereal will contribute to research in other triticeae species with more complex genetics such as hexaploid bread wheat.

Publications

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