Integrating genetics and high throughput genomics to indentify genes underlying tomato quantitative trait loci (QTL) for metabolites that influence fruit quality (TomQML)
Final Report Abstract
Fruits are an 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. Quality and health attributes are linked to molecular and biochemical changes in fruits during development and ripening. Some of the most important changes in fruit quality involve the accumulation of primary and secondary such as sugars and acids which influence taste and carotenoids and phenylpropanoids that can have a significant impact on nutritional quality. Tomato is the most widely consumed fleshy fruit in the human diet, with a global value in excess of around $30 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. The aim of the project was to understand the molecular mechanisms controlling the formation of primary and secondary metabolites responsible for tomato fruit quality traits and harness natural variation for the benefit of the European consumer. The multinational consortium included a global biotechnology company and involved screening for Quantitative Trait Loci (QTL) controlling primary and secondary metabolite accumulation. QTL mapping experiments involved generating more than one hundred new micro introgression lines (µ-ILs) from existing wild tomato species genetic resources and a range of TILLING and transgenic lines. Genes controlling tomato sugar metabolism and especially the relationship between levels of glucose and fructose in the fruit were major targets. A candidate sugar transporter gene underlying an S. pennellii QTL controlling fruit fructose / glucose ratios on Chr 4 was identified. Also a fructose / glucose ratio QTL on Chr 6 and a sucrose accumulator on Chr 12 were fine mapped. Malate was shown to play a crucial role in tomato starch metabolism and be important in postharvest properties of fruits. A tomato malate QTL on Chr 3 was resolved and metabolite analysis continues for candidate gene nomination. Another focus was the accumulation of branched chain amino acids (BCAA) in tomato that are essential components of the human diet and involved in volatile flavour generation. This involved characterisation of the BCAA transferase gene family and identification and functional testing of an isopropylmalate dehydrogenase underlying a BCAA QTL. Tomato fruit contain a wealth of secondary metabolites that are important in a healthy diet and protect against cardiovascular disease and certain cancers. A novel lycopene QTL on Chr 2 was resolved and candidate gene identified by expression analysis. Additional candidate genes under new QTLs for β-carotene and α-tocopherol, which is the form of vitamin E absorbed by humans, have also been identified. The project allowed initial investigation of substantially enhanced pigment composition of transgenic fruits over expressing regulatory gene linked to S. pennellii QTL on Chr 8. A pepper ortholog was identified by the industrial partner. Furthermore a comprehensive metabolite database for the S.pennellii ILs has been generated. The project provided insights into the links between metabolite changes and the higher regulatory network controlling ripening in fruits. The role of the AP2 transcription factor in ripening and its effect on metabolism was established and gene regulatory networks constructed by the partners are now being used to link AP2 to other major ripening control genes. The validation of candidate genes underlying metabolite QTL is still in progress in follow-up projects. TomQML facilitated development of Micro-Tom mutant collection part of which is being seed bulked for public distribution. It also facilitated the development of the TILLING platform at INRA Bordeaux. Several of the metabolite QTL regions are being introgressed into commercial lines by the industrial partner and translation to other fleshy fruit has identified alleles in pepper (sweet and hot) for colour intensity and retention.
Publications
- (2010). hi2-1, a QTL which improves harvest index, earliness and alters metabolite accumulation of processing tomatoes.Theor Appl Genet. 2010 Nov;121(8):1587-99
Gur A, Osorio S, Fridman E, Fernie AR, Zamir D
- (2010). The influence of fruit load on the tomato pericarp metabolome in a Solanum chmielewskii introgression line population. Plant Physiol. 2010 Nov; 154(3):1128-42
Do PT, Prudent M, Sulpice R, Causse M, Fernie AR
- (2011) Malate plays a crucial role in starch metabolism, ripening, and soluble solid content of tomato fruit and affects postharvest softening. Plant Cell. 23(1):162-84
Centeno DC, Osorio S, Nunes-Nesi A, Bertolo AL, Carneiro RT, Araújo WL, Steinhauser MC, Michalska J, Rohrmann J, Geigenberger P, Oliver SN, Stitt M, Carrari F, Rose JK, Fernie AR
- (2011) The genetic architecture of branched-chain amino acid accumulation in tomato fruits. J Exp Bot. 2011 Jul;62(11):3895-906
Kochevenko A, Fernie AR
- (2011) Transcriptome and metabolite profiling show that APETALA2a is a major regulator of tomato fruit ripening. Plant Cell. 23(3):923-41
Karlova R, Rosin FM, Busscher-Lange J, Parapunova V, Do PT, Fernie AR, Fraser PD, Baxter C, Angenent GC, de Maagd RA
- (2011) Yield quantitative trait loci from wild tomato are predominately expressed by the shoot.Theor Appl Genet. 2011 Feb;122(2):405-20
Gur A, Semel Y, Osorio S, Friedmann M, Seekh S, Ghareeb B, Mohammad A, Pleban T, Gera G, Fernie AR, Zamir D
- (2012) The tomato FRUITFULL homologs TDR4/FUL1 and MBP7/FUL2 regulate ethylene-independent aspects of fruit ripening. The Plant Cell 24 (11):4437-4451
Bemer M, Karlova R, Ballester AR, Tikunov YM, Bovy AG, Wolters-Arts M, Rossetto PdB, Angenent GC, de Maagd RA
- (2012). Catabolism of Branched Chain Amino Acids Supports Respiration but Not Volatile Synthesis in Tomato Fruits. Mol Plant. 5(2):366-75
Kochevenko A, Araújo WL, Maloney GS, Tieman DM, Do PT, Taylor MG, Klee HJ, Fernie AR
(See online at https://doi.org/10.1093/mp/ssr108) - (2012). Molecular identification of a further branched-chain aminotransferase 7 (BCAT7) in tomato plants. J Plant Physiol. 2012 169:437-43
Kochevenko A, Klee HJ, Fernie AR, Araújo WL
(See online at https://doi.org/10.1016/j.jplph.2011.12.002) - (2012). Vitamin Deficiencies in Humans: Can Plant Science Help? Plant Cell. 24:395-414
Fitzpatrick TB, Basset GJ, Borel P, Carrari F, Dellapenna D, Fraser PD, Hellmann H, Osorio S, Rothan C, Valpuesta V, Caris-Veyrat C, Fernie AR
(See online at https://doi.org/10.1105/tpc.111.093120) - (2013). A genome-wide metabolomic resource for tomato fruit from Solanum pennellii. Nature Scientific Reports 4: 3859
Perez-Fons L, Wells T, Corol DI, Ward JL, Gerrish C, Beale MH,Seymour GB, Bramley PM & Fraser PD
(See online at https://doi.org/10.1038/srep03859) - (2013). Network inference analysis identifies an APRR2-like gene linked to pigment accumulation in tomato and pepper fruits. Plant Physiol. 161(3):1476-85
Pan Y, Bradley G, Pyke K, Ball G, Lu C, Fray R, Marshall A, Jayasuta S, Baxter C, van Wijk R, Boyden L, Cade R, Chapman NH, Fraser PD, Hodgman C, Seymour GB
(See online at https://doi.org/10.1104/pp.112.212654)
