Reflections and Opportunities: Gene Discovery in the Complex Wheat Genome

Abstract

Despite more than 80 years of wheat genetic studies, only several hundred genes out of the probable 120,000 coding sequences that are presumed present in the wheat genome have been mapped to chromosomes. Many fewer have been associated with traits, and very many fewer have been cloned and their mechanisms and mode of action elucidated. This past failure has been due to the complexity of the hexaploid wheat genome of more that 16,000 million base pairs, but also the paucity of molecular tools and investment relative to other agricultural species such as rice or maize. Fortunately, in recent years, the pace of gene discovery has greatly accelerated in wheat because of the development of molecular tools, including molecular marker based genetic maps, libraries of sequence, particularly ESTs, and microarrays. Most recently a BAC library covering the whole wheat genome in the model variety Chinese Spring has been constructed QTL and major gene discovery by forward genetics is now routine and a catalogue of mapped genes for both simple and complex traits is being accumulated. This is leading to plant breeding applications through marker-assisted selection and detailed genetical understanding in terms of trait architecture and genetic diversity. However, the knowledge of mechanisms by which mapped genes work is rare since cloning genes in the complex wheat genome is still a major undertaking both in terms of time and resources. Gene isolation by chromosome walking is the most direct, but also the most difficult route. But the feasibility of this has now been demonstrated for key genes, such as the Ph1 locus controlling homoeologous chromosome pairing. However, the resource implications indicate that only a few key genes are important enough for the investment, and short cuts through other approaches are generally necessary. Most commonly this involves isolating orthologues from model species, usually Arabidopsis and rice. This is possible, but examples show that it does not always work or is meaningful to do. Because of this, there is increasing interest in sequencing the whole genome, although a daunting undertaking in terms of cost and effort. However, sequencing other model species, such as the small grass, Brachypodium, can provide a useful substitute for wheat gene content, as well as providing closely linked markers for chromosome walking. Moreover, a comparison of the corresponding regions between rice and Brachypodium will enable wheat genes to be clearly identified and annotated