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Next Generation Crop Genomics
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Assembling a prokaryote genome de novo is now a routine bioinformatics analysis with different technologies, algorithms and strategies currently in use and being developed. In a large extend this is also resolved for more complex animal species. The genomes for some plants, however, remain a challenge. Genomic features such as polyploidy, whole-genome duplications and high repeat content are examples of the complex architecture found in crop species. The advances in sequencing technologies have open up new opportunities to work with complex genomes. Reliable and relatively contiguous assemblies are still required but there is scope for the application of novel approaches that offer access to genetic variants. A fragmented draft assembly still offers a very valuable source of information that could be used for a variety of strategies. We have, for instance, designed exome capture platforms for both barley and wheat. Another example is the identification of trait-linked genes for disease resistance using bulk segregant analysis. I will report on a case study for hexaploid bread wheat in which we have developed tools to analyse RNA-Seq libraries generated from parental wheat lines and six bulks obtained from the backcrossed progeny made of susceptible and resistance plants.

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