A proof of concept that RECQ 7 can be used as a tool to increase recombination

Significant advances are being made in our understanding of complex crop traits through powerful phenotyping and genetic approaches, resulting in large numbers of traits associated with markers, genes or alleles (alternate forms of a gene). The potential of stacking these traits to drive improvements in crops, such as rapid yield increases or durable disease resistance, are enormous. The critical bottleneck in taking advantage of our increased understanding of complex crop traits is our ability to combine these traits effectively. Introducing a gene or allele associated with a specific trait into a crop often introduces additional unwanted genetic material, including alleles which can negatively affect the performance of the crop; a process called linkage drag. Our ability to rapidly stack multiple traits in elite cultivars, generating new combinations of alleles whilst breaking down the linkage drag of non-advantageous alleles is a major challenge. This is primarily due to low rates of recombination and that recombination tends to occur in the distal ends of chromosomes in many of our important crops. A key goal for scientists is to increase both the distribution and rate of recombination which will aid the targeted introduction of specific alleles, without unwanted deleterious genetic material.

This year we published a study demonstrating an untapped source of recombination by identifying large, high frequency gene conversions that occur across the wheat chromosomes. Moreover, using existing datasets we were able to identify that the RECQ7 gene regulates either or both the size and/or frequency of these events.

This grant proposal aims to build on these initial discoveries and the techniques developed. We propose to demonstrate the proof-of-concept that manipulation of RECQ7 offers a potential mechanism of increasing recombination thus driving novel allelic combinations. Generating this prototype tool is the first step to releasing the impact of this research in breeding programmes.

In many important crops recombination rates are low and tend to occur in the distal portion of chromosomes. This lack of recombination limits breeding efforts, leading to a high rate of linkage drag, making it difficult to generate new genetic combinations of alleles. It also hinders the ability to identify genes underlying traits. In our recent publication (Gardiner et al. 2019), we demonstrated that non-reciprocal exchanges of DNA, the result of either gene conversions (GC) or non-interfering double crossovers, are far larger and more frequent in wheat than other species characterised to date. We identified a QTL controlling GC frequency and a candidate gene RECQ7; a helicase found in a subset of plant species. We validated the role of RECQ7 in GC, using multiple knockouts in the Cadenza TILLING population.

The paper describes a set of methods that can now be used to investigate GC further. Moreover, the manipulation of RECQ7, offers a potential method for breaking up haplotype blocks and generating new allelic combinations.

In this proposal, we plan to test the hypothesis that by manipulating RECQ7 we can increase either the length or frequency of GC to drive increased recombination across the genome.

Wheat is the most widely grown crop in the world, globally accounting for 20% of our daily calories. This year, for the first time, global wheat demand has outstripped wheat production. In the UK wheat is also an important crop: in 2017 the wheat harvest for the UK was 14.8 million tonnes, with a value of £2bn; year-on-year yield gains are supported by a private breeding industry.

Access to improved crop varieties, delivered to market by the commercial plant breeding and seeds sector, is the foundation for successful, productive agriculture. Over the past 30 years more than 90% of the yield gains in our major crops are due to plant breeding innovation. Faced with the global challenges of food security, climate change and pressure on the world's finite natural resources, reports from the UK Government Office for Science (Foresight: The Future of Food and Farming, 2011) and Royal Society (Reaping the Benefits: Science and the sustainable intensification of global agriculture, 2009) have highlighted the need for continued progress in plant breeding as the single most important factor in meeting the food, feed and fuel needs of a world population set to reach 9.6 billion by 2050 (Source: Plant Breeding Matters, The business and science of crop improvement, British Society of Plant Breeding, 2014).

Improvements in the introgression of new traits can be achieved through better understanding of the recombination process and GC. GC are found throughout nature and are critical in shaping genome diversity and evolution. Advances in genome sequencing technology are allowing us to start to understand the size, frequency of GC events and the mechanisms controlling them. GCs provide breeders with an untapped source of recombination based on distribution, size and frequency which play an important role in generating novel allelic combinations in wheat.

The realisation of this impact will come from identifying genes that can be manipulated to increase the frequency and size of GC events. From our published work RECQ7 is a strong candidate and the overexpressing lines will demonstrate a proof-of-concept for industry. However, a transgenic approach does not have to be the only route and it may be possible to develop other strategies for manipulating the function of RECQ7.

This work will be carried out in response to the needs of several plant breeding companies who have provided letters of support. We will share the outcomes of our research more widely via publications in open access peer reviewed journals, and at relevant conferences (ie. PAG, Monogram, International Wheat Congress), via British Society of Plant Breeders publications, and via presentations at networking events such as Agri-Tech East or Agriculture and Horticulture Development Board meetings.

Furthermore, this work has economic, environmental and social impacts. The development of improved crop varieties with improved yields, end-use quality and environmental performance provides the essential foundation for sustainable, efficient agriculture, and the starting point for the UK's £90bn food supply chain.