Theme 2 - Unlocking Genetic Variation (Lead Partner: JIC)
The genome variation theme is developing high throughput re-sequencing methods to access the wealth of natural genetic variation that exists in the genes of wild wheat relatives and ancestral species. This theme is closely linked to the BBSRC-funded Wheat Pre-Breeding programme (WISP). WISP's aim is to access the genetic variation in key germplasm that is relevant to wheat pre-breeding applications such as resistance to pathogens, environmental stresses such as drought and grain nutritional content. We also aim to identify induced genetic variation in TILLING populations of tetraploid and hexaploid wheat to enable a wider range and depth of research in wheat.
Accessing natural sequence variation by genome capture and resequencing
Sequence variation within genes is an important component of the expected genetic variation in wheat. The availability of an accurate non-redundant gene set within the first year of the project (see Theme 1) provides an opportunity to access sequence variation in wheat genes at a whole genome scale:
- using this gene data set, we will apply the technique of gene exon capture followed by Illumina sequencing of specific wheat lines. At the present time, this technique is the most cost effective high throughput method to access trait-related sequence variation for use in marker-assisted breeding and gene characterization.
The wheat lines to be sequenced will include single seed descent Watkins landraces that have useful traits (defined in year 2 of the WISP project), Paragon (the elite parent to which Watkins landraces are being crossed) and the wheat wild relatives, Aegilops tauschii, Triticum turgidum and Triticum dicoccoides.
- the sequence reads will be aligned to a reference set of wheat genes (from line Chinese Spring 42) then polymorphisms will be identified and annotated.
- A polymorphism database will be developed and made publicly available so users can design markers for selecting lines of interest in breeding programmes.
Identification of induced sequence variation in wheat
Mutagenised populations (for example TILLING populations) are another key source of genetic variation needed for characterizing gene function in wheat because these have been shown to have mutation rates almost two orders of magnitude higher than the levels of natural variation in cultivated wheat. In order to produce a catalog of sequence variation in mutated genes for functional genomics studies, we will:
- use existing tetraploid and hexaploid wheat populations that have been mutagenised with EMS and sequence the gene space using the genome capture technique described above.
- in total, 1,500 individuals for both the tetraploid and hexaploid populations will be examined. This number will provide a probability of >90% of identifying a knockout in any homoeologue in wheat.
- develop bioinformatic tools to visualize the identified mutations at both the DNA and protein level. Each mutation will be traced to the original mutant plant whose seeds will be available for order through the JIC Germplasm Resources Unit.