Understanding the Genetic Basis of Traits for Rootstock Improvement in Vegetable Crops

Root traits are an important target for improving sustainable crop production as they control capture of water and nutrients from the soil, and have many other influences on the performance of the above ground part of the crop. In horticulture, many annual crops for the fresh market (e.g. tomato, pepper, cucumber and melon) are produced predominantly as grafts between a rootstock cultivar and a scion (shoot) cultivar. These rootstock cultivars are currently used to manage crop vigour and resistance to root diseases, and the sale of vegetable rootstock seed and grafted transplants is a large and profitable business because of the substantial beneficial effects of employing rootstocks. The global market for tomato rootstock seed alone is approximately £100 M. Increased consumption of fresh fruits and vegetables is known to reduce the incidence of debilitating chronic diseases which are a major burden on the health system; improving our ability to grow and therefore deliver high quality fresh produce at competitive prices is important to stimulate increased consumption.
Current research indicates that rootstocks can also confer resistance to stresses such as salinity, cold and nutrient limitation by providing improved root functions or by sending signals to the scion, but the genetic basis for these resistances, and of vigour, is poorly understood making breeding for these traits difficult and slow. This contrasts to the breeding of resistance to soil-borne diseases where many resistance genes are known and they are routinely and easily combined into new cultivars to provide multiple resistances. Improving our ability to breed for vigour and cold tolerance are the priorities for the rootstock seed industry because crop growth is limited in the cool early season and because sustaining the correct balance between vegetative and reproductive growth throughout the season can greatly increase crop yield.
The aims of this proposal are to fully characterise, with respect to gene identity and mechanism of action, current and novel loci that impact on rootstock performance including root system architecture, vigour and cold tolerance in tomato, our target crop. We have already identified loci for tomato root system architecture from the wild tomato species Solanum pennellii and obtained several monogenic mutants with altered root traits; in this project we will fully explore their genetic basis and mode of action. To further harness wild species genetic variation, we will generate a novel large recombinant inbred line (RIL) population from two S. habrochaites parental lines because this is the wild species most commonly used in commercial rootstocks and it is adapted to grow in the cool slopes of the Andes.
We will use the tomato reference genome, published in 2012, and the most recent high-throughput sequencing and genotyping technologies to map loci and to measure gene expression; this will allow candidate genes to be identified. These candidates will be tested to see if they are responsible for the observed phenotypes by altering their expression using genetic modification and by the selection of plants with mutations in these genes (TILLING). We will use state-of-the-art methods to measure how rootstock genotypes influence the growth and physiology of the shoot and to search for hormonal signals that control scion phenotypes.
The project team is made up of experts in root biology and tomato genetics who will work closely with a commercial seed company to deliver genetic markers and mechanistic understanding that will improve the ability to breed rootstocks with improved vigour in the short term, and to improve our understanding of the genetic control of root traits in all dicotyledonous crops for the benefit of crop improvement in the medium to long term.

Many annual fruit crops for the fresh market from the Solanaceae and Cucurbitaceae are produced predominantly as grafts between rootstock and scion cultivars and the rootstock genotype is chosen to manage crop vigour and resistance to root diseases. Current research indicates that rootstocks can also confer resistance to stresses such as salinity, cold and nutrient limitation by providing improved root functions or by sending signals to the scion, but the genetic basis for these resistances, and of vigour, is poorly understood making breeding for these traits difficult and slow. Improving our ability to breed for vigour and cold tolerance are the priorities for the rootstock seed industry, and root system architecture is a key component of vigour.
In this project we will fine-map QTL for RSA previously identified in S. pennellii and map-base-clone monogenic tomato mutant genes that affect root traits. We will make use of the tomato reference genome, published in 2012, and the most recent high-throughput sequencing and genotyping technologies. We will identify candidate genes in the mapping intervals using the extensive knowledge built up in Arabidopsis root research, and then validate them as causative genes using transgenic and TILILING approaches. To further harness wild species genetic variation, we will generate a novel recombinant inbred line (RIL) population of 350 lines which will be genotyped-by-sequencing and used for QTL analysis. The parental lines will be two S. habrochaites breeding lines with contrasting vigour and cold tolerance derived from the conventional breeding program of the industrial partner, and are chosen so that QTL can be readily delivered into hybrids though the male parental lines which are based on S. habrochaites in existing breeding strategies. We will use state-of-the-art methods to measure how rootstock genotypes influence the growth and physiology of the shoot and to search for hormonal signals that control scion phenotypes.

Societal benefits:
This project aims to increase the marketable yield of annual vegetable fruit crops through the development of improved rootstock cultivars that confer increased vigour and cold tolerance to the crop. Higher yield potential and higher productivity at the cooler shoulder periods in the early and late season will build resilience in fresh produce supply chains. There is good evidence that health, wellbeing and quality of life, especially the avoidance of chronic disease states in later life, are closely linked to a healthy diet high in fruits and vegetables. Fruits are expensive commodities and increasing availability and quality will help to reduce prices and to increase consumption. Encouraging consumers to eat more fruit and vegetables will improve the nation's health, e.g. reduce obesity and type-2 diabetes thus reducing welfare expenditure in concert with enhancing the general quality of life. This is especially important as the proportion of elderly people in the population is projected to increase dramatically with improved life expectancy. Improving yields in UK and in international production systems via rootstock cultivars rather than by increased inputs of agrochemicals, water and fertilizers is an excellent example of sustainable intensification. Reducing environmental impact of production is of significance to Environment Agency, Defra, Horticulture Development Company and glasshouse technology companies.

Economic benefits:
The identification of molecular markers and causative genes for improved vigour, cold tolerance and altered root system architecture will allow these traits to be combined rapidly with multiple disease resistance loci, thus accelerating the development of novel hybrid rootstock cultivars. This will improve the status of early-adopters of the technologies and enable them to compete more effectively in global markets. Vegetable rootstock seeds are an increasing and lucrative market (~US$100 million/year for tomato alone) with opportunities for market diversification. The proposal will provide excellent opportunities for UK-based breeding companies such as Syngenta to increase their market share by introducing improved and novel rootstock varieties. Furthermore science discoveries in tomato can later be implemented for other vegetable rootstock markets (other Solanaceous crops and Cucurbits). Fundamental understanding of the genetic regulation of root traits can also be applied to breeding strategies for broad-acre, non-grafted crops once the principles are established.
Growers will receive higher profits from the introduction of varieties which grow vigorously under relatively low air temperatures, especially in the early and late season in the UK. Reduced air temperatures will also lower transpiration and lead to a reduced heat loss from venting which is used to control humidity and fungal disease, giving further energy savings. Significant cost savings could be realised by growers in heated glasshouse production if average daily temperatures can be reduced by only 1 degree Celsius. Maintenance of productivity with reduced production costs will improve the UK's trade balance by reducing our reliance on imports; several UK-operating retailers are committed to doubling the sale of UK-grown produce by 2020. Fresh and processed fruit and vegetable products have significant added value for retailers with direct benefits on business growth, employment and UK Government tax receipts.

The proposal addresses the BBSRC delivery plan's "Grand Challenge 1" to "boost crop yields", "reduce greenhouse gas emissions" and "increase leverage from the private sector". It also addresses Grand Challenge 3 which seeks to "improve wellbeing" via healthier diets. The project addressed the top priorities of the UK Tomato Growers Association's R&D strategy to improve yields while controlling inputs and to reduce energy use.