Large scale mapping of wheat transcripts and simultaneously defining the A B and D genome contribution to the hexaploid transcriptome

Bread wheat is the dominant UK arable crop. Current and increasing grain prices, the use of wheat as a convenient source of bioethanol and possible future food security issues, suggest that the trend to grow increased amounts of wheat in the UK might continue for the foreseeable future. However, the generation of new higher yielding or more disease resistant wheat varieties is a long term business, requiring considerable investment in (and retention of) trained personnel and resources. The use of molecular markers in wheat breeding is increasing; however the hexaploid nature of bread wheat (it contains DNA from three separate species) has limited the development of markers linked to agronomic traits. Work by various groups including my group at Bristol is slowly resulting in an increase in the number of useful markers such that there are now a few hundred microsatellites or Single Nucleotide Polymorphisms (SNPs) available for routine use. However, when one compares the situation in hexaploid wheat with that in diploid barley, where several thousand SNP-based markers are available, one immediately sees the considerable disadvantages of working with a polyploid crop (i.e. crops with the DNA from more than one species). Using funds provided by a 12 month BBSRC Tools & Resources Development Fund award my group has generated a new type of wheat microarray containing 244,000 features which is capable of discriminating between the genes from the three different species within the bread wheat genome (244K wheat array). Hence this array is capable of analysing wheat as though it were a diploid. As described our original T&R proposal my group has now validated this array and generated preliminary data which shows that this unique resource is capable of discriminating between the three genomes of hexaploid wheat and simultaneously generating information on large numbers of individual transcripts. In this application we propose to use the 244K wheat array to map several thousand wheat transcripts (and achieve an important and strategic goal for plant breeders and geneticists) and address hypotheses based research on the interaction between the three genomes that make up allohexaploid wheat.

The currently held view of most wheat geneticists is that genomic rearrangements probably do occur in the newly formed allohexaploid wheat and that these, together with epigenetic gene silencing, result in a genome and transcriptome which is less than the sum of its progenitors. However, due to the limited number of mapped markers used in all of the previous studies and the inability of all of the studies to discriminate between sequences derived from the different homoeologous chromosomes, definitive proof for this view remains elusive. In this proposal we aim to use recently technology, developed at Bristol, to simultaneously map several thousand wheat transcripts and identify progenitor specific transcripts in both the diploid and tetaploid progenitors and the resulting synthetic wheat to provide definitive proof to confirm or refute that genomic rearrangement and epigenetic silencing do occur during the generation of allohexaploid wheat. We will also use the transcript-related information obtained from synthetic wheat and compare this to the situation in current and established hexaploid wheat varieties to determine whether these rearrangements are predetermined or random in nature.