Integrating genetics and high throughput genomics to identify genes underlying tomato QTL for metabolites that influence fruit quality (TOMQML)

Fruits are an immensely important part of the human diet. Low fruit and vegetable intake is recognised as a major factor for increased risk of heart disease and certain cancers. Encouraging people to consume more fruit in their diet is not necessarily straight forward and depends on factors including cost and product quality. Some of the most important changes in fruit quality related to ripening involve the accumulation of primary metabolites such as sugars and acids which influence taste. Also alterations in the levels of secondary metabolites such as carotenoids and phenylpropanoids can have a significant impact on nutritional quality. The challenge is to understand how these individual ripening changes are controlled /modulated and develop commercially viable strategies for breeding novel and better fruit products. This project focuses on tomato as it is the most widely consumed fleshy fruit in the human diet, with a global value in excess of $10 bn. It has become the model for studying the development and ripening of fleshy fruits and a wealth of genetic and genomic resources are available. We will use a range of well characterised publicly available tomato lines and novel tomato genetic resources combined with a range of genetic and molecular approaches to identify the genes controlling tomato taste and the accumulation of health enhancing phytochemicals. In concert with these approaches, we will identify the links between major regulators of ripening and their associated metabolite changes. The project will make an important contribution to fundamental knowledge about the molecular basis of fruit ripening. The consortium consists of internationally recognized groups from universities and research institutes in Europe and the USA as well as a global supplier of vegetable seeds, collectively ensuring a framework for innovative excellence.

Fruits are an immensely important part of the human diet. Low fruit and vegetable intake is recognised as a major factor for increased risk of heart disease and certain cancers. This project focuses on identifying genes in tomato that are involved in the accumulation of primary metabolites such as sugars and acids which influence taste and alterations in the levels of secondary metabolites such as carotenoids and phenylpropanoids that can have a significant impact on nutritional quality. We will combine state of the art high throughput genomics technologies with quantitative genetic approaches for rapid identification of genes underlying tomato metabolite QTL. In concert with these approaches, we will identify the links between major regulators of ripening, e.g. RIN, CNR and their associated metabolite changes. We will achieve our objectives by using the 76 S. pennellii ILs, around 500 publicly available sub-ILs and new fixed recombinant lines (QTL-NILs) from these ILs. Additional populations will be used to capture allelic diversity. QTL for around 20 key primary and secondary metabolites already identified on the 76 S. pennellii ILs will be resolved to specific sub-lines or QTL-NILs. A new screen for ILs bearing QTL that can influence the retention of metabolites after harvest will also be undertaken. Candidate genes will then be nominated based on metabolomics and expression information from the ILs and sub-ILs. This process will be aided by the development of co-expression networks. Concurrently, we will proceed with positional cloning of 8 preselected QTL using a high-throughput marker platform. The project will make an important contribution to fundamental knowledge about the molecular basis of fruit ripening. The consortium consists of 7 internationally recognized groups from universities and research institutes in Europe and the USA as well as a global supplier of vegetable seeds, collectively ensuring a framework for innovative excellence.