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

根系性状是提高作物可持续生产的重要目标，因为它们控制着土壤对水分和养分的捕获，并对作物地上部分的性能有许多其他影响。在园艺中，许多新鲜市场的一年生作物（如番茄、辣椒、黄瓜和甜瓜）主要是作为砧木品种和接穗（芽）品种之间的嫁接而生产的。这些砧木品种目前被用于管理作物的活力和对根病的抗性，蔬菜砧木种子和嫁接移栽的销售是一项庞大而有利可图的业务，因为使用砧木具有实质性的有益效果。仅番茄砧木种子的全球市场就约为1亿英镑。众所周知，增加新鲜水果和蔬菜的消费可以减少慢性疾病的发病率，而慢性疾病是卫生系统的主要负担；提高我们的种植能力，从而以具有竞争力的价格提供高质量的新鲜农产品，对于刺激消费增长至关重要。目前的研究表明，砧木还可以通过提供改良的根系功能或通过向接穗发送信号来抵抗诸如盐、冷和营养限制等胁迫，但是对这些抗性和活力的遗传基础知之甚少，使得这些性状的育种困难和缓慢。这与土壤传播疾病的抗性育种形成对比，在土壤传播疾病中，许多抗性基因是已知的，它们通常很容易组合成新品种，以提供多种抗性。提高我们培育活力和耐寒性的能力是砧木种业的首要任务，因为作物生长在凉爽的早期季节受到限制，因为在整个季节保持营养生长和生殖生长之间的正确平衡可以大大提高作物产量。本提案的目的是充分表征，在基因身份和作用机制方面，影响砧木性能的现有和新的位点，包括根系结构，活力和耐寒性，我们的目标作物番茄。我们已经从野生番茄品种秋葵（Solanum pennellii）中鉴定出番茄根系结构的基因位点，并获得了几个根性状发生改变的单基因突变体；在这个项目中，我们将充分探索它们的遗传基础和作用方式。为了进一步利用野生物种的遗传变异，我们将从两个habrochaites亲本系中产生一个新的大型重组自交系（RIL）群体，因为这是商业砧木中最常用的野生物种，并且它适应在安第斯山脉凉爽的斜坡上生长。我们将使用2012年发表的番茄参考基因组，以及最新的高通量测序和基因分型技术来绘制位点和测量基因表达；这将使候选基因得以识别。将对这些候选植物进行测试，以确定它们是否对观察到的表型负责，方法是利用基因修饰改变它们的表达，并通过选择具有这些基因突变的植物（TILLING）。我们将使用最先进的方法来测量砧木基因型如何影响茎的生长和生理，并寻找控制接穗表型的激素信号。该项目团队由根系生物学和番茄遗传学专家组成，他们将与一家商业种子公司密切合作，提供遗传标记和机制理解，从而在短期内提高培育砧木的能力，并提高我们对所有双子叶作物根系性状遗传控制的理解，从而在中长期内促进作物改良。

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.