Can Cyclin Dependent Kinase Activity be manipulated to control chromosome pairing and recombination in plants?

This project will address an important problem, which has hampered the efficient exploitation of the genetic diversity held within wild relatives of wheat. Domestication resulted in a significant genetic bottleneck with the result that breadwheat is much less diverse than its wild relatives. Being able to work with wild relatives so that beneficial characteristics can be introduced into commercial wheat will be a major scientific achievement and dramatically improve the way breeders can generate new varieties of wheat with increased performance.

Some wild relatives are adapted to thrive under different climatic conditions to that of domestic wheat, or they carry natural resistance to important diseases and/or carry other important characteristics, which could influence yield. What we want to do is to develop approaches that will enable us to exploit this diversity effectively so as to introduce these favourable characteristics into wheat. In doing so we will be enable wheat breeders, amongst others, to improve wheat performance in a sustainable way, increase yield, and introduce disease resistance and drought tolerance.

What stops these wild relatives being used efficiently? Ideally, the wild relative and the wheat chromosomes should align and efficiently exchange (recombine) during meiosis but this does not occur effectively. Without recombination, there isn't the opportunity to introduce the genetic diversity of wild relatives into wheat. A genetic element called Ph1 controls this process. Ph1 has a positive effect in wheat itself, by stabilizing wheat as a polyploid during meiosis, but Ph1 does this by substantially reducing recombination between wild relative and wheat chromosomes or between segments of these chromosomes. Ph1 even reduces recombination between chromosomes derived from wheat landraces where they are significantly diverged. This makes gene transfer by recombination during meiosis difficult in the case of wild relatives, or inefficient in the case of landraces. Deletion of Ph1 enhances recombination but is very deleterious because it perturbs stability of the polyploid genome.

So how can we overcome this problem? In wheat and its hybrids, Ph1 regulates recombination. Understanding this regulation provides an insight into this process. It will provide us with an understanding of how the recombination process can be altered and tailored for specific needs, thus enabling us manipulate it for plant breeding. In understanding how to enhance recombination, the project will also identify approaches which prevent homoeologous recombination between chromosomes in wheat itself, and so stabilize it as a polyploid.

Our research focuses on the role of particular kinase-like genes found within the Ph1 locus. Kinases regulate or control the function of other proteins by means of transferring a phosphate group from ATP to particular amino acids within the target protein. They are highly sensitive to a range of compounds, including ATP analogues, that have been developed for biomedical purposes particularly in cancer biology and medicine. Therefore, there is a tremendous resource available for testing and identifying compounds that would be efficacious in the modulation of these related plant kinases. Moreover, we have recently identified Ph1 related kinases in the experimentally amenable model plant, Arabidopsis, that are phylogenetically conserved across all species, from plants to animals including humans.

In this project, we aim to investigate the role of kinase activity in chromosome pairing and recombination with the view to developing chemically mediated methods to modulate the activity of these in meiosis,. Such chemical tools would be tremendously useful in not only wheat breeding but potentially for other species as well.

Most related chromosomes of wild relatives of wheat exhibit extensive gene synteny along their chromosome length. The genes on these related chromosomes exhibit more than 95% homology at the sequence level. Despite this level of similarity, there is little recombination between wild relative and wheat chromosomes at meiosis due the presence of the Ph1 locus. Ph1 even reduces (homologous) recombination between chromosomes derived from wheat landraces where they are significantly diverged. Deletion of the Ph1 locus allows the chromosomes to behave more like homologous chromosomes and recombine. Recombination involves the initiation of double strand breaks within genic regions and then repair of these breaks. Recent data indicates that whether Ph1 is present or absent, homoeologues pair and the recombinational machinery is loaded. The final marker for crossing over MLH1 is even loaded, but the process then stalls unless Cdk activity is increased or Ph1 is deleted.

Recently a Ph1 like kinase, CDKG, has been identified in Arabidopsis, and it also affects pairing and recombination. This opens up the possibility of exploiting this system for dissecting the regulation of kinase activity during meiosis, including the development of methodology for modulating its function.

To understand the function of these kinases, we will first produce tools such as specific antibodies that will allow their isolation and manipulation. Using these tools, we will assess the behaviour of these kinases and their molecular function, and their interaction with selected classes of small molecules. Finally, we will develop a reliable and robust system for delivering these compounds into wheat and wheat-wild relative spikes at various stages of meiosis, either in the presence of Ph1 or not, and assessing the promotion of either homologous chromosome pairing in wheat itself or homoeologous pairing in the wheat-wild relative hybrid.

During the next 30 years, as much wheat grain will be required as has been produced since the beginning of agriculture. This will require a step change in breeding strategies. Breeders will need a combination of strategies including exploiting wild relatives of wheat carrying useful traits. One of the limiting factors highlighted by a number of high-level reviews (including by BBSRC) of such strategies is the ability to regulate chromosome exchange or recombination in wheat. The issue is further complicated by constraints placed on chromosome exchange resulting from the presence of related chromosomes. There are examples where wild relatives have been successfully exploited as a novel source of genetic variation for traits in wheat breeding programmes, e.g., the transfer by Sears of leaf rust resistance of Aegilops umbellulata to common wheat saved the US economy billions of dollars.

However, the introgression of genes from wild relatives into wheat is very time consuming and inefficient and therefore fell out of favour. Recently, international breeding centres have again started to exploit wild relatives to generate synthetic hexaploid Triticum aestivum, creating a "synthetic wheat" breeding programme. Some 25% of elite lines of wheat generated by CIMMYT are derived from crosses to these synthetic wheat genotypes. Having exploited this approach successfully, many argued that to increase yield production in wheat it is imperative to revisit the exploitation of genetic variation available in the wild relatives in breeding programmes. As a result of this, a number of private sector breeders encouraged the reestablishment of wheat alien introgression in the UK public sector, as part of BBSRC's wheat pre-breeding programme.

To facilitate the transfer of genetic variation via wheat/alien introgression, research is required to increase the speed and enhance the efficiency of the process. In brief, wheat/alien introgression involves hybridisation with a wild relative followed by repeated backcrossing to generate lines of wheat carrying an alien chromosome on which a target gene is located. A series of further crosses to specific genotypes/mutant lines are then required before the chromosome of the alien species can recombine with those of wheat, allowing the transfer of the target gene to wheat without linked deleterious effects.

The expected outcome of this project will be the creation of tools to allow breeders to better exploit the genetic potential of wild wheat relatives as well as enhancing "homologous" recombination between more divergent wheat chromosomes. It will provide an indication of how the level and distribution of recombination may be altered in wheat. The immediate beneficiaries will be those involved directly in wheat pre-breeding. The programme will also allow the development of a skills base, particularly in cytogenetics, a dying art in the UK which can be utilised by the next generation of scientists involved in wheat breeding and the larger wheat breeding community.

This research will make a contribution to food security and sustainable agriculture, key objectives of BBSRC's strategic plan. Wheat has been identified as a key crop by BBSRC and it has financially supported a new pre-breeding programme. Ultimately, the farming industry will benefit by having high-yielding, durable wheat cultivars tailored made to suit particular abiotic and biotic conditions. This in turn will have major societal benefits through the production of reasonably priced food produced in an environmentally sustainable manner.