Identification and characterization of metabolite quantitative trait loci in tomato leaves and comparison with those reported for fruits and seeds

Adriano Nunes-Nesi, Saleh Alseekh, Franklin Magnum de Oliveira Silva, Nooshin Omranian, Gabriel Lichtenstein, Mohammad Mirnezhad, Roman R.R. González, Julia Sabio y Garcia, Mariana Conte, Kirsten A. Leiss, Peter G.L. Klinkhamer, Zoran Nikoloski, Fernando Carrari, Alisdair R. Fernie

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

Introduction: To date, most studies of natural variation and metabolite quantitative trait loci (mQTL) in tomato have focused on fruit metabolism, leaving aside the identification of genomic regions involved in the regulation of leaf metabolism. Objective: This study was conducted to identify leaf mQTL in tomato and to assess the association of leaf metabolites and physiological traits with the metabolite levels from other tissues. Methods: The analysis of components of leaf metabolism was performed by phenotypying 76 tomato ILs with chromosome segments of the wild species Solanum pennellii in the genetic background of a cultivated tomato (S. lycopersicum) variety M82. The plants were cultivated in two different environments in independent years and samples were harvested from mature leaves of non-flowering plants at the middle of the light period. The non-targeted metabolite profiling was obtained by gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). With the data set obtained in this study and already published metabolomics data from seed and fruit, we performed QTL mapping, heritability and correlation analyses. Results: Changes in metabolite contents were evident in the ILs that are potentially important with respect to stress responses and plant physiology. By analyzing the obtained data, we identified 42 positive and 76 negative mQTL involved in carbon and nitrogen metabolism. Conclusions: Overall, these findings allowed the identification of S. lycopersicum genome regions involved in the regulation of leaf primary carbon and nitrogen metabolism, as well as the association of leaf metabolites with metabolites from seeds and fruits.

LanguageEnglish
Article number46
JournalMetabolomics
Volume15
Issue number4
DOIs
Publication statusPublished - 1 Apr 2019

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Quantitative Trait Loci
Lycopersicon esculentum
Metabolites
Fruits
Seed
Fruit
Seeds
Metabolism
Nitrogen
Carbon
Plant Physiological Phenomena
Solanum
Metabolomics
Gas Chromatography
Mass Spectrometry
Association reactions
Chromosomes
Genome
Light
Physiology

Keywords

  • Leaf metabolism
  • Metabolite network
  • Metabolite QTL
  • Tomato

Cite this

Nunes-Nesi, A., Alseekh, S., de Oliveira Silva, F. M., Omranian, N., Lichtenstein, G., Mirnezhad, M., ... Fernie, A. R. (2019). Identification and characterization of metabolite quantitative trait loci in tomato leaves and comparison with those reported for fruits and seeds. Metabolomics, 15(4), [46]. https://doi.org/10.1007/s11306-019-1503-8
Nunes-Nesi, Adriano ; Alseekh, Saleh ; de Oliveira Silva, Franklin Magnum ; Omranian, Nooshin ; Lichtenstein, Gabriel ; Mirnezhad, Mohammad ; González, Roman R.R. ; y Garcia, Julia Sabio ; Conte, Mariana ; Leiss, Kirsten A. ; Klinkhamer, Peter G.L. ; Nikoloski, Zoran ; Carrari, Fernando ; Fernie, Alisdair R. / Identification and characterization of metabolite quantitative trait loci in tomato leaves and comparison with those reported for fruits and seeds. In: Metabolomics. 2019 ; Vol. 15, No. 4.
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abstract = "Introduction: To date, most studies of natural variation and metabolite quantitative trait loci (mQTL) in tomato have focused on fruit metabolism, leaving aside the identification of genomic regions involved in the regulation of leaf metabolism. Objective: This study was conducted to identify leaf mQTL in tomato and to assess the association of leaf metabolites and physiological traits with the metabolite levels from other tissues. Methods: The analysis of components of leaf metabolism was performed by phenotypying 76 tomato ILs with chromosome segments of the wild species Solanum pennellii in the genetic background of a cultivated tomato (S. lycopersicum) variety M82. The plants were cultivated in two different environments in independent years and samples were harvested from mature leaves of non-flowering plants at the middle of the light period. The non-targeted metabolite profiling was obtained by gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). With the data set obtained in this study and already published metabolomics data from seed and fruit, we performed QTL mapping, heritability and correlation analyses. Results: Changes in metabolite contents were evident in the ILs that are potentially important with respect to stress responses and plant physiology. By analyzing the obtained data, we identified 42 positive and 76 negative mQTL involved in carbon and nitrogen metabolism. Conclusions: Overall, these findings allowed the identification of S. lycopersicum genome regions involved in the regulation of leaf primary carbon and nitrogen metabolism, as well as the association of leaf metabolites with metabolites from seeds and fruits.",
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Nunes-Nesi, A, Alseekh, S, de Oliveira Silva, FM, Omranian, N, Lichtenstein, G, Mirnezhad, M, González, RRR, y Garcia, JS, Conte, M, Leiss, KA, Klinkhamer, PGL, Nikoloski, Z, Carrari, F & Fernie, AR 2019, 'Identification and characterization of metabolite quantitative trait loci in tomato leaves and comparison with those reported for fruits and seeds', Metabolomics, vol. 15, no. 4, 46. https://doi.org/10.1007/s11306-019-1503-8

Identification and characterization of metabolite quantitative trait loci in tomato leaves and comparison with those reported for fruits and seeds. / Nunes-Nesi, Adriano; Alseekh, Saleh; de Oliveira Silva, Franklin Magnum; Omranian, Nooshin; Lichtenstein, Gabriel; Mirnezhad, Mohammad; González, Roman R.R.; y Garcia, Julia Sabio; Conte, Mariana; Leiss, Kirsten A.; Klinkhamer, Peter G.L.; Nikoloski, Zoran; Carrari, Fernando; Fernie, Alisdair R.

In: Metabolomics, Vol. 15, No. 4, 46, 01.04.2019.

Research output: Contribution to journalArticleAcademicpeer-review

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T1 - Identification and characterization of metabolite quantitative trait loci in tomato leaves and comparison with those reported for fruits and seeds

AU - Nunes-Nesi, Adriano

AU - Alseekh, Saleh

AU - de Oliveira Silva, Franklin Magnum

AU - Omranian, Nooshin

AU - Lichtenstein, Gabriel

AU - Mirnezhad, Mohammad

AU - González, Roman R.R.

AU - y Garcia, Julia Sabio

AU - Conte, Mariana

AU - Leiss, Kirsten A.

AU - Klinkhamer, Peter G.L.

AU - Nikoloski, Zoran

AU - Carrari, Fernando

AU - Fernie, Alisdair R.

PY - 2019/4/1

Y1 - 2019/4/1

N2 - Introduction: To date, most studies of natural variation and metabolite quantitative trait loci (mQTL) in tomato have focused on fruit metabolism, leaving aside the identification of genomic regions involved in the regulation of leaf metabolism. Objective: This study was conducted to identify leaf mQTL in tomato and to assess the association of leaf metabolites and physiological traits with the metabolite levels from other tissues. Methods: The analysis of components of leaf metabolism was performed by phenotypying 76 tomato ILs with chromosome segments of the wild species Solanum pennellii in the genetic background of a cultivated tomato (S. lycopersicum) variety M82. The plants were cultivated in two different environments in independent years and samples were harvested from mature leaves of non-flowering plants at the middle of the light period. The non-targeted metabolite profiling was obtained by gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). With the data set obtained in this study and already published metabolomics data from seed and fruit, we performed QTL mapping, heritability and correlation analyses. Results: Changes in metabolite contents were evident in the ILs that are potentially important with respect to stress responses and plant physiology. By analyzing the obtained data, we identified 42 positive and 76 negative mQTL involved in carbon and nitrogen metabolism. Conclusions: Overall, these findings allowed the identification of S. lycopersicum genome regions involved in the regulation of leaf primary carbon and nitrogen metabolism, as well as the association of leaf metabolites with metabolites from seeds and fruits.

AB - Introduction: To date, most studies of natural variation and metabolite quantitative trait loci (mQTL) in tomato have focused on fruit metabolism, leaving aside the identification of genomic regions involved in the regulation of leaf metabolism. Objective: This study was conducted to identify leaf mQTL in tomato and to assess the association of leaf metabolites and physiological traits with the metabolite levels from other tissues. Methods: The analysis of components of leaf metabolism was performed by phenotypying 76 tomato ILs with chromosome segments of the wild species Solanum pennellii in the genetic background of a cultivated tomato (S. lycopersicum) variety M82. The plants were cultivated in two different environments in independent years and samples were harvested from mature leaves of non-flowering plants at the middle of the light period. The non-targeted metabolite profiling was obtained by gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). With the data set obtained in this study and already published metabolomics data from seed and fruit, we performed QTL mapping, heritability and correlation analyses. Results: Changes in metabolite contents were evident in the ILs that are potentially important with respect to stress responses and plant physiology. By analyzing the obtained data, we identified 42 positive and 76 negative mQTL involved in carbon and nitrogen metabolism. Conclusions: Overall, these findings allowed the identification of S. lycopersicum genome regions involved in the regulation of leaf primary carbon and nitrogen metabolism, as well as the association of leaf metabolites with metabolites from seeds and fruits.

KW - Leaf metabolism

KW - Metabolite network

KW - Metabolite QTL

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