Genomics-assisted selection of Solanum chilense introgression lines for enhancing drought resistance in tomatoes

Tomato, the biggest food crop after cereals and potato, is a vital source of nutrients, vitamins and other health promoting metabolites in the human diet: production must increase, and breeding for sustainable production is a high priority. Breeding for improved water use efficiency and ability to give high yields where water availability is poor are important traits for tomato, and other Solanaceous crops, including potato and Brinjal. Solanum pennellii, Solanum chilense and Solanum sitiens are the three tomato wild relatives that are found in arid areas and have the greatest adaptation to water-limited environments, and each has a distinct morphology, classification and ecotype. However, good genetic and genomic resources only exist for S. pennellii, where well-established and highly successful strategies have been employed to exploit allelic variation.
In this project we will develop novel genetic and genomic resources for the remaining drought-adapted species, S. chilense and S. sitiens. We will generate >400 x depth genomic sequence data and perform de novo genome assembly for these two genomes to provide an excellent reference sequence complete with structural variants at different scales; this will be done in close collaboration with European bioinformatics experts working with other Solanum genomes (Wageningen UR, RWTH Aachen University and Max Planck Institute of Molecular Plant Physiology), and will provide strong capacity building in bioinformatic skills and computing power.
Genome sequences will be used for SNP marker design and a genetic map constructed for an S. chilense x S. lycopersicum population. Genome sequences will become extremely valuable resources as QTL studies progress to the gene level.
We will rapidly create, using a high-throughput SNP genotyping platform, a population of introgression lines for S. chilense starting with a unique hybrid obtained by IIVR, now in the BC1F1 generation. The completed library will be screened for water use efficiency, root traits and resistance to wilting to discover new QTL. A rapid backcross program in MicroTom will be used to phenotypically select introgressions arising from a complex hybrid containing alleles from two S. chilense and one S. peruvianum accession. Introgressions present at the end of the selection process will be precisely defined by genome re-sequenced in preparation for fine mapping.

There are three wild relatives of cultivated tomato (Solanum lycopersicum) that are well known to be adapted to the very arid regions of South America: S. pennellii, S. chilense and S. sitiens. Much progress has been made in exploiting the germplasm of S. pennellii, which easily forms hybrids with S. lycopersicum. However, S. chilense and S. sitiens are more problematic as they fall outside the "esculentum group" for cross compatibility, but they remain a rich source of valuable alleles. In this project, we will develop the genomic resources for both S. chilense and S. sitiens by performing de novo genome assembly, and will develop introgressed line (IL) and inbred backcross line (IBL) populations to capture the S. chilense genome for QTL mapping and exploitation in breeding programs. This will utilise a rare hybrid between S. chilense and S. lycopersicum which has now been progressed to BC1F1. We will use the ILs to discover novel alleles for root traits and for water use efficiency, key target traits to improve sustainable water use in tomato production. Genomes will be sequenced to a depth of >400X using mate pair and paired end libraries with a range of insert sizes up to 40 kbp and assembled de novo with assistance from experienced project partners. OpGen Argus will be used for optical mapping to join scaffolds and improve the quality of the draft genomes. Genome re-sequencing of parental lines will be used to develop a set of 384 SNPs which will be used to select IL and IBL populations. A complex bridging line containing DNA from S. chilense and S. peruvianum which hybridises with cultivated tomato will be re-sequenced, and used to capture introgressions that confer wilting resistance by backcrossing five times to model tomato cultivar MicroTom with recurrent phenotypic selection. Re-sequencing will delimit captured introgressions.
Physiological mechanisms will be investigated in detail for introgression lines that show improved WUE or wilt resistance.

The genome sequences and genetic resources developed in this project and the QTLs identified will lead directly to the development of novel tomato varieties that have a reduced requirement for irrigation. Populations will be created using a current Indian cultivar as genetic background; therefore beneficial introgressions could potentially be delivered very rapidly by the Indian partners without extensive further breeding and selections.
Reduction in irrigation is beneficial to the environment as it will contribute to a more sustainable use of water resources which are currently often used in an unsustainable manner resulting in depletion of ground waters and reduced river flows, particularly in regions such as South East Asia, Southern Europe and California. Since the UK relies heavily upon imports of both fresh market and processing tomatoes, the sustainability of production overseas is important for UK food security. Improved water use efficiency can also increase yields and farmer incomes where availability of water is limiting to production: cultivars with higher water use efficiency will produce a higher yield for the same water inputs.
In the longer term, the same genetic and genomic resources can be used to breed tomato cultivars with resistance to a range of pest and diseases which will in turn increase profits and reduce the use of chemical pesticides. Higher yields and lower prices resulting form crop improvement in tomato will increase consumption and contribute to a healthier diet. A range of other cultivar improvements are possible when S. chilense and S. sitiens introgression lines become available to tomato breeders. The genome sequences will facilitate rapid marker assisted selection by providing hundreds of thousands of polymorphisms for molecular breeders to use.
The results of this project will allow UK and India-based breeding companies to develop novel cultivars which will increase sales of profitable hybrid seeds, and improve global market share. QTL discovered in tomato can potential by used in other Solanum crops through allele surveys in parallel germplasm collections, e.g. in potato, pepper and brinjal.
The project will increase UK and India's capability in advanced bioinformatics for researchers working with horticultural crops who will develop the skills and computing facilities for analysing very large data sets arising from next generation sequencing platforms; linking this capability to existing graduate teaching programs at Cranfield will cascade this skill to up to 20 MSc students each year who go on to work in a wide range of bioscience contexts.