A genomics-assisted synthetic hexaploid wheat gene isolation and pre-breeding platform for improved heat tolerance and sustainable production

Background: Wheat is the most important cereal for direct human consumption, and is crucial to populations most exposed to current and anticipated future failures in global food security. India is the world's second largest producer of wheat, while the UK is currently one of the world's highest yielding environments. However, a relatively narrow genetic base currently hampers wheat improvement by reducing our ability to breed new varieties adapted to changing environmental and disease pressures. In India, heat stress is having an increasingly negative impact on wheat yields, while in the UK losses due to drought loss cost >£60 million per year. The detrimental of heat stress in both countries is set to worsen, given current climate change scenarios for India and NW Europe. This will have serious impacts on India's wheat farming community (the majority of which grow wheat for their own consumption), as well as on UK production and global food security.

Increasing global demand for wheat, coupled with factors such as the effects of climate change and the necessity for sustainable wheat production, means that investment in breeding approaches that incorporate information on wheat genetic variation ('genome-assisted' approaches) are now widely accepted as critical. However, to fully exploit such approaches, novel wheat lines which possess desirable traits not normally found in currently used varieties must first be identified and utilised. The wild relatives of wheat possess immense genetic diversity, but most of this is underutilized. Useful genetic variation can be transferred into elite wheat backgrounds from progenitor species by recreating the original natural hybridisation process that occurred 10,000 years between two wheat progenitors to create modern bread wheat. These novel wheats (called 'synthetic hexaploid wheat', SHW) inject novel genetic variation into breeding programmes aimed at developing new varieties with increased tolerance to environmental stress and other sub-optimal environmental conditions.

Project aims and outcomes: This project aims to create novel SHW lines (using progenitor lines specifically selected to harbour heat stress tolerance), and use these to cross into modern Indian and UK varieties to create a large population of 1,500 progeny. This population will form the basis of a unique wheat biological resource upon which genomic-assisted approaches can be applied to investigate the novel genetic determinants of heat tolerance introduced via SHW. This will be achieved by:

(1) Identifying and typing the genetic variants present in the population.
(2) Using novel approaches to undertake detailed assessment of how each of the 1,500 progeny lines performs under heat stress.
(3) Assessing how different genes and gene variants are expressed when exposed to heat stress.

These datasets will be analysed to identify the genetic regions originating from the SHW parental lines that confer tolerance to heat stress. In this way, the project will simultaneously identify genetic markers that tag increased heat tolerance, as well as provide Indian- and UK-adapted wheat lines that express the beneficial traits.

The unique position of the project partners at the interface between wheat research and breeding will be leveraged to promote rapid translation of project outcomes into national wheat breeding programmes. This project provides biological and genetic resources/tools alongside a programme of knowledge exchange and capacity building, which will aid the progress of wheat R&D and breeding in India and the UK.

To deliver novel genetic variation for improved heat tolerance and sustainable production into the wheat genepool, this project leverages:

1 Novel synthetic hexaploid wheat (SHW)
2 Emerging sequencing and genomics technologies
3 Novel approaches for heat stress tolerance screening

to generate an integrated genetics, genomics & biological resource platform for quantitative trait analysis, fine mapping and pre-breeding for near-future translation to the Indian & UK wheat breeding sectors. This will be achieved by

1 Re-synthesis of SHW lines, using progenitor parental lines (Indian Triticum turgidum and Aegilops Tauschii) specifically selected for their heat tolerance
2 Deploying the SHW within a structured multi-parent population of 1,500 progeny, created by crossing 5x SHW lines to 3x Indian/UK varieties, generating a doubled haploid BC1F1-derived population
3 Utilise exome-capture and next generation sequencing (NGS) to identify inter-parental genetic polymorphisms, to enrich for D-genome SHW-derived SNPs
4 Genotype progeny lines using dense wheat SNP chips (>90,000 SNPs) supplemented by 500 D-genome SNPs
5 Deploy novel phenotypic screens to characterise the 1,500 progeny lines for heat tolerance parameters
6 NGS of parental and F1 hybrid mRNA for genome-wide assessment of allele- and homoeologue-specific expression imbalance, and its relevance to heat tolerance phenotype
7 Perform QTL analysis using joint linkage disequilibrium and linkage analysis for increased QTL precision

The project will deliver
1 A SHW-derived biological, genomic and genetic resource for the genetic dissection of traits controlling sustainable wheat production
2 Pre-breeding germplasm and selectable markers to improve heat tolerance in genetic backgrounds relevant to India and UK
3 Establish a medium-high throughput doubled haploid laboratory at PAU to service the Indian wheat breeding and R&D communities
4 Knowledge transfer and training between Indian & UK partners.

Impact summary
The core focus of this project is to utilise genomics-assisted approaches and SHW-derived germplasm to transfer and genetically characterise novel genetic variation for heat stress into Indian and UK genetic backgrounds. India is the world's second largest producer of wheat (~80mt per year, worth $12 billion). Wheat is the UK's major crop species, with an annual grain yield of 13 million tonnes and a pre-processed value of ~£2 billion. As a principle crop in booth countries, wheat production impacts on many sectors, as well as being a critical component of global food security.

Academics
The SHW-derived biological resource of 1,500 lines, and associated datasets, will provide a unique community resource for the genetic dissection of heat stress and other abiotic/biotic traits segregating within the population. The genomic and expression sequence datasets will provide resources to prime further investigations utilising the population. Identification of gene-based sequence variation via exome-capture/NGS of parental lines provides academics with data for future fine mapping and marker saturation studies. mRNA-seq data from parental lines and F1 hybrids +/- heat stress allows the basis of allelic expression differences to be characterised as cis- or trans-acting, providing information upon which the basis of genetic/epigenetic transcriptional control under heat stress can be further dissected in the population. Based around a structured programme of training courses, dissemination events, PhD secondments, and infrastructural upgrades, opportunities for bi-lateral knowledge exchange and training will develop impact by strengthening the knowledge base, skills and collaborative links of personnel in both countries. It will provide skills and expertise in disciplines of particular relevance to modern biosciences. Furthermore, the doubled haploid laboratory infrastructural upgrades at PAU will provide Indian academics with the facilities and capability to rapidly develop novel germplasm resources for genetic analysis of beneficial traits in wheat.

Breeders
In India, PAU will be able to translate project outcomes directly into their public wheat breeding programme. The availability of SHW-derived pre-breeding germplasm in genetic backgrounds relevant to India and the UK also provides private breeding companies active in both countries with for incorporation of targeted breeding for heat tolerance into their breeding programmes. Provision of molecular markers associated with loci conferring heat tolerance over multiple genetic backgrounds will facilitate transfer and tracking of potentially novel genes for heat tolerance within their programmes.

Farmers
In India, where production is almost exclusively for the internal market, increased yields via the development of varieties with improved heat stress tolerance will have direct beneficial impact on the rural-poor and small-medium scale farmers, achieved via increased production, yield stability and profitability. In the UK, the provision of improved varieties will help mitigate current and future yield losses due to heat stress, increasing the productivity and profitability of the UK arable industry.

Policy makers & wider public
Utilisation of varieties with increased tolerance to abiotic stress will improve yield and input costs, helping to increase sustainable wheat production and food security to the benefit of the wider public and environment. The alignment of Indian and UK research towards common goals in sustainable food production will increase the international impact and competitiveness of the bioscience and farming sectors in both countries. By demonstrating the ability of scientific R&D to provide solutions to national and international policy and goals on sustainable food production, project outcomes will help inform current and future government decision making processes on food security and bioscience research priorities.