YEARS

2012-2016

AUTHORS

Paul David Fraser

TITLE

The validation, characterisation and translation of outputs derived from network analysis and QTL mapping of tomato fruit quality traits (TomNET)

ABSTRACT

Tomato (Solanum lycopersicum) is the most important fruit crop in the world by volume consumed, with annual production of 150 million metric tons. Tomatoes are high value products with an annual value in 2009 of around 32 billion US dollars covering both processed and fresh products. They are a major component of healthy diets and provide ready sources of vitamins A, C, E and K, minerals including K and Fe and the lipophilic antioxidant lycopene (the pigment responsible for the characteristic red colour of ripe tomato fruit). There is a wealth of scientific evidence that now exists to corroborate that the consumption of fruits and vegetables is beneficial to human health. These benefits have been attributed to the presence of health promoting phytochemicals or "bioactives" in the food matrix. The challenge, particularly, in Western societies, is to deliver to the consumer better tasting, more nutritious tomatoes and other fruit which have a prolonged shelf-life at a cost affordable to the majority of consumers. The most important quality traits in tomato are colour, texture, flavour and nutritional content. Texture can also impact on taste, the release of nutrients and perhaps most importantly shelf-life. In the UK it is estimated that 40% of the food waste is uneaten fruits and vegetables. In addition to its economic and societal role, tomato has become a well established scientific model for understanding the development and ripening of fleshy fruit bearing crops, with strong evidence that many of the gene networks controlling ripening have been conserved across different taxa. In fruit crops, the key controller of quality traits is the process of ripening. The aim of TomNET project is to deliver better quality tomato fruit. Our approach will integrate systems analysis and quantitative genetic studies to identify and modulate regulatory genes that allow precise control of fruit development and the ripening process. By harnessing tomato wild-species variation, we can deliver these scientific discoveries into commercial practice in collaboration with Syngenta; our industrial partner in this LINK project. The project will build on several important resources and findings. Firstly a regulatory network holistically describing the interaction of gene transcripts during fruit development and ripening. Using computational approaches putative regulators of the ripening process have been identified. We have shown that one of these regulators can improve tomato fruit colour. Simultaneously, flavour related compounds responsible for good tasting fruit products are increased. In this project we will use the gene networks to identify additional regulators of ripening that display the potential to alter key fruit quality traits. For the transcriptional activator termed high pigment-4 (HP4), which we have validated as an important modulator of ripening related traits, detail characterisation at multiple levels of regulation will be carried out to ascertain the underlying mechanisms by which the gene product can exert its effects and influence the ripening process. The other key foundation of this project is the identification of genes underlying a complex QTL for texture. Within the target region several interacting components have been identified. In the project the function and interaction between these components will be elucidated by using stable transgenic lines. Combining the enhanced colour and texture traits will also be attempted. Finally natural variation will be exploited to deliver these traits into commercial elite backgrounds thus translating science discovery through to commercial practice. Technical Summary Building on outputs derived from transcriptional networks constructed for tomato fruit development and ripening and from quantitative genetics studies. We will now validate, characterise and translate the molecular tools identified into commercial backgrounds using the following technical approach. 1. Exploitation of the ripening regulatory network. Following our successful identification of a network derived transcription activator (HP4), involved in fruit pigmentation. Further functional testing of candidate genes regulating ripening and especially colour, texture and flavour will be carried out using Virus Induced Gene Silencing (VIGS) and through the generation of stable transgenic lines. 2. Characterisation of the HP4 transcriptional activator. In order to elucidate the underlying mechanisms associated with the action of HP4 in conferring ripening associated quality traits, we will perform an integrative multi-level approach to characterisation of the phenotype including detailed metabolomics. 3. Testing the involvement of QTL derived candidates in altering fruit texture. Candidate genes underlying texture QTL on tomato chromosomes 2 and 3 will be tested in transgenic plants. Detailed phenotypic assessment including texture, determinations, transcript and metabolite profiling and cell wall analysis will elucidate the biochemical and molecular mechanisms responsible for the enhancement of texture and shelf-life in our target QTL regions. 4. Combining enhanced colour and texture phenotypes. Crosses will be performed to ascertain how mutant alleles and QTLs responsible for colour and texture-based traits will function in combination and if they act in a synergistic manner. 5. Delivery of the traits into commercial practice. Using the unique resources of our industrial partner we will demonstrate the translational potential of candidate genes or QTL regions by marker assisted introgression into the parent of an elite hybrid.

FUNDED PUBLICATIONS

  • A genome-wide metabolomic resource for tomato fruit from Solanum pennellii.
  • Network inference analysis identifies an APRR2-like gene linked to pigment accumulation in tomato and pepper fruits.
  • articles:bb7270a4ae46b95f62621cb6ec6f8805
  • A genome-wide metabolomic resource for tomato fruit from Solanum pennellii
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    22 TRIPLES      17 PREDICATES      23 URIs      10 LITERALS

    Subject Predicate Object
    1 grants:eaa1aef2624ac70c5d86336d986a6268 sg:abstract Tomato (Solanum lycopersicum) is the most important fruit crop in the world by volume consumed, with annual production of 150 million metric tons. Tomatoes are high value products with an annual value in 2009 of around 32 billion US dollars covering both processed and fresh products. They are a major component of healthy diets and provide ready sources of vitamins A, C, E and K, minerals including K and Fe and the lipophilic antioxidant lycopene (the pigment responsible for the characteristic red colour of ripe tomato fruit). There is a wealth of scientific evidence that now exists to corroborate that the consumption of fruits and vegetables is beneficial to human health. These benefits have been attributed to the presence of health promoting phytochemicals or "bioactives" in the food matrix. The challenge, particularly, in Western societies, is to deliver to the consumer better tasting, more nutritious tomatoes and other fruit which have a prolonged shelf-life at a cost affordable to the majority of consumers. The most important quality traits in tomato are colour, texture, flavour and nutritional content. Texture can also impact on taste, the release of nutrients and perhaps most importantly shelf-life. In the UK it is estimated that 40% of the food waste is uneaten fruits and vegetables. In addition to its economic and societal role, tomato has become a well established scientific model for understanding the development and ripening of fleshy fruit bearing crops, with strong evidence that many of the gene networks controlling ripening have been conserved across different taxa. In fruit crops, the key controller of quality traits is the process of ripening. The aim of TomNET project is to deliver better quality tomato fruit. Our approach will integrate systems analysis and quantitative genetic studies to identify and modulate regulatory genes that allow precise control of fruit development and the ripening process. By harnessing tomato wild-species variation, we can deliver these scientific discoveries into commercial practice in collaboration with Syngenta; our industrial partner in this LINK project. The project will build on several important resources and findings. Firstly a regulatory network holistically describing the interaction of gene transcripts during fruit development and ripening. Using computational approaches putative regulators of the ripening process have been identified. We have shown that one of these regulators can improve tomato fruit colour. Simultaneously, flavour related compounds responsible for good tasting fruit products are increased. In this project we will use the gene networks to identify additional regulators of ripening that display the potential to alter key fruit quality traits. For the transcriptional activator termed high pigment-4 (HP4), which we have validated as an important modulator of ripening related traits, detail characterisation at multiple levels of regulation will be carried out to ascertain the underlying mechanisms by which the gene product can exert its effects and influence the ripening process. The other key foundation of this project is the identification of genes underlying a complex QTL for texture. Within the target region several interacting components have been identified. In the project the function and interaction between these components will be elucidated by using stable transgenic lines. Combining the enhanced colour and texture traits will also be attempted. Finally natural variation will be exploited to deliver these traits into commercial elite backgrounds thus translating science discovery through to commercial practice. Technical Summary Building on outputs derived from transcriptional networks constructed for tomato fruit development and ripening and from quantitative genetics studies. We will now validate, characterise and translate the molecular tools identified into commercial backgrounds using the following technical approach. 1. Exploitation of the ripening regulatory network. Following our successful identification of a network derived transcription activator (HP4), involved in fruit pigmentation. Further functional testing of candidate genes regulating ripening and especially colour, texture and flavour will be carried out using Virus Induced Gene Silencing (VIGS) and through the generation of stable transgenic lines. 2. Characterisation of the HP4 transcriptional activator. In order to elucidate the underlying mechanisms associated with the action of HP4 in conferring ripening associated quality traits, we will perform an integrative multi-level approach to characterisation of the phenotype including detailed metabolomics. 3. Testing the involvement of QTL derived candidates in altering fruit texture. Candidate genes underlying texture QTL on tomato chromosomes 2 and 3 will be tested in transgenic plants. Detailed phenotypic assessment including texture, determinations, transcript and metabolite profiling and cell wall analysis will elucidate the biochemical and molecular mechanisms responsible for the enhancement of texture and shelf-life in our target QTL regions. 4. Combining enhanced colour and texture phenotypes. Crosses will be performed to ascertain how mutant alleles and QTLs responsible for colour and texture-based traits will function in combination and if they act in a synergistic manner. 5. Delivery of the traits into commercial practice. Using the unique resources of our industrial partner we will demonstrate the translational potential of candidate genes or QTL regions by marker assisted introgression into the parent of an elite hybrid.
    2 sg:endYear 2016
    3 sg:fundingAmount 271641.0
    4 sg:fundingCurrency GBP
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    10 articles:bb7270a4ae46b95f62621cb6ec6f8805
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    16 Contains UK public sector information licensed under the Open Government Licence v2.0 (http://www.nationalarchives.gov.uk/doc/open-government-licence/version/2/).
    17 sg:scigraphId eaa1aef2624ac70c5d86336d986a6268
    18 sg:startYear 2012
    19 sg:title The validation, characterisation and translation of outputs derived from network analysis and QTL mapping of tomato fruit quality traits (TomNET)
    20 sg:webpage http://gtr.rcuk.ac.uk/project/25718D06-15C5-4DE9-9269-95B36269BC28
    21 rdf:type sg:Grant
    22 rdfs:label Grant: The validation, characterisation and translation of outputs derived from network analysis and QTL mapping of tomato fruit quality traits (TomNET)
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