A genetic map of candidate genes and QTLs involved in tomato fruit size and composition

Causse, Mathilde; Duffé, Philippe; Gómez, Marcela; Buret, Michel; Damidaux, R.; Zamir, Dani; Gur, Amit; Chevalier, Christian; Lemaire-Chamley, Martine; Rothan, Christophe

doi:10.1093/jxb/erh207

Cited by 174 publications

(130 citation statements)

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“…pennellii ILs and the S. lycopersicum 'M82' recurrent parent were grown under field conditions in France during 2000. Plant growth conditions were as described by Causse et al (2004).…”

Section: Plant Materials and Mapping Populationmentioning

confidence: 99%

High-Resolution Mapping of a Fruit Firmness-Related Quantitative Trait Locus in Tomato Reveals Epistatic Interactions Associated with a Complex Combinatorial Locus

Chapman

Bonnet²,

Grivet³

et al. 2012

Plant Physiology

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Fruit firmness in tomato (Solanum lycopersicum) is determined by a number of factors including cell wall structure, turgor, and cuticle properties. Firmness is a complex polygenic trait involving the coregulation of many genes and has proved especially challenging to unravel. In this study, a quantitative trait locus (QTL) for fruit firmness was mapped to tomato chromosome 2 using the Zamir Solanum pennellii interspecific introgression lines (ILs) and fine-mapped in a population consisting of 7,500 F2 and F3 lines from IL 2-3 and IL 2-4. This firmness QTL contained five distinct subpeaks, Fir s.p. QTL2.1 to Fir s.p. QTL2.5, and an effect on a distal region of IL 2-4 that was nonoverlapping with IL 2-3. All these effects were located within an 8.6-Mb region. Using genetic markers, each subpeak within this combinatorial locus was mapped to a physical location within the genome, and an ethylene response factor (ERF) underlying Fir s.p. QTL2.2 and a region containing three pectin methylesterase (PME) genes underlying Fir s.p. QTL2.5 were nominated as QTL candidate genes. Statistical models used to explain the observed variability between lines indicated that these candidates and the nonoverlapping portion of IL 2-4 were sufficient to account for the majority of the fruit firmness effects. Quantitative reverse transcription-polymerase chain reaction was used to quantify the expression of each candidate gene. ERF showed increased expression associated with soft fruit texture in the mapping population. In contrast, PME expression was tightly linked with firm fruit texture. Analysis of a range of recombinant lines revealed evidence for an epistatic interaction that was associated with this combinatorial locus.

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“…pennellii ILs and the S. lycopersicum 'M82' recurrent parent were grown under field conditions in France during 2000. Plant growth conditions were as described by Causse et al (2004).…”

Section: Plant Materials and Mapping Populationmentioning

confidence: 99%

High-Resolution Mapping of a Fruit Firmness-Related Quantitative Trait Locus in Tomato Reveals Epistatic Interactions Associated with a Complex Combinatorial Locus

Chapman

Bonnet²,

Grivet³

et al. 2012

Plant Physiology

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“…The microarrays were generated from (1) the nonredundant ESTs (923) from the three fruit cDNA libraries, (2) cDNAs (165) preferentially expressed in various phases of early fruit development and previously isolated in our laboratory (Lemaire-Chamley et al, 2000), and (3) cDNAs (303) selected from tomato EST databases according to their putative role in early fruit development and in fruit quality. These mainly included genes involved in sugar and organic acid transport and metabolism (Causse et al, 2004), in hormonal regulation, and in other developmental processes.…”

Section: Few Fruit-specific Genes Are Expressed During the Early Stagmentioning

confidence: 99%

Changes in Transcriptional Profiles Are Associated with Early Fruit Tissue Specialization in Tomato

et al. 2005

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The cell expansion phase contributes in determining the major characteristics of a fleshy fruit and represents two-thirds of the total fruit development in tomato (Solanum lycopersicum). So far, it has received very little attention. To evaluate the interest of a genomic scale approach, we performed an initial sequencing of approximately 1,200 cell expansion stage-related sequence tags from tomato fruit at 8, 12, and 15 d post anthesis. Interestingly, up to approximately 35% of the expressed sequence tags showed no homology with available tomato expressed sequence tags and up to approximately 21% with any known gene. Microarrays spotted with expansion phase-related cDNAs and other fruit cDNAs involved in various developmental processes were used (1) to profile gene expression in developing fruit and other plant organs and (2) to compare two growing fruit tissues engaged mostly in cell division (exocarp) or in cell expansion (locular tissue surrounding the seeds). Reverse transcription-polymerase chain reaction analysis was further used to confirm microarray results and to specify expression profiles of selected genes (24) in various tissues from expanding fruit. The wide range of genes expressed in the exocarp is consistent with a protective function and with a high metabolic activity of this tissue. In addition, our data show that the expansion of locular cells is concomitant with the expression of genes controlling water flow, organic acid synthesis, sugar storage, and photosynthesis and suggest that hormones (auxin and gibberellin) regulate this process. The data presented provide a basis for tissue-specific analyses of gene function in growing tomato fruit.After ovule fertilization, early tomato (Solanum lycopersicum) fruit development is characterized by a period of cell division followed by cell expansion, resulting in the formation of large vacuolated cells (Mohr and Stein, 1969). Cell expansion is the longest phase in fruit development and may contribute to 90% of the increase in fruit weight, depending on the cultivar. In addition, cell expansion contributes, along with ripening, to the major structural, biochemical, and physiological changes that characterize a fleshy fruit. The cell wall changes associated with cell enlargement and the continuous accumulation in the vacuole of water, sugars, organic acids, and other compounds are necessary to maintain the turgor pressure of the expanding cells. In addition, these physiological processes contribute significantly to the flavor, texture, and overall attractiveness of the ripe fruit. The succession of the different phases of tomato fruit development is not, however, as clear cut as described above. It varies greatly according to the fruit tissue considered (Joubès et al., 1999). Tomato fruit is a complex organ composed of two or more carpels separated by a radially orientated tissue called septum, which results from the fusion of two adjacent carpel walls (or pericarp). The pericarp encloses the locular cavity containing the seeds attached to a central pa...

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“…It has been used to study fruit shape and development (Causse et al, 2004;Brewer et al, 2007;Bertin et al, 2009), metabolite composition (Fridman et al, 2004;Tikunov et al, 2005;Schauer et al, 2006;Tieman et al, 2006;Bertin et al, 2009), flowering time (JimenezGomez et al, 2007), disease and fungus resistance (Chaerani et al, 2007;Finkers et al, 2007), tolerance to salinity (Cuartero et al, 2006;Villalta et al, 2007), and chilling (John Goodstal et al, 2005).…”

mentioning

confidence: 99%

“…In particular, a set of 76 near isogenic lines derived from an S. lycopersicum 'M82' 3 Solanum pennellii cross (Eshed and Zamir, 1994) has been subjected to extensive agronomic, physiological, and molecular phenotyping (Lippman et al, 2007). This has allowed quantitative trait loci (QTLs) to be detected that affect morphology and yield , fruit coloration (Liu et al, 2003), metabolite levels (Causse et al, 2004;Fridman et al, 2004;Baxter et al, 2005a;Schauer et al, 2006), volatile metabolites (Tieman et al, 2006), and antioxidants (Rousseaux et al, 2005). The cultivated tomato is one of the first examples of a crop plant that has benefited significantly from exotic germplasm introgression (Zamir, 2001;Lippman et al, 2007).…”

mentioning

confidence: 99%

“…An expanding range of molecular and genomics tools are available for tomato, including facile transformation (Klee et al, 1991), a large EST collection (Van der Hoeven et al, 2002), oligonucleotide-based arrays (Slocombe et al, 2008;Wang et al, 2009), emerging genome sequence information (Mueller et al, 2005a(Mueller et al, , 2005b, and a wide range of phenotyping (Causse et al, 2004) and metabolite profiling (Tikunov et al, 2005;Schauer et al, 2006;Fraser et al, 2007) technologies. Very recently, a prepublication tomato genome sequence was made available by the International Tomato Genome Sequencing Consortium (http:// solgenomics.net/).…”

mentioning

confidence: 99%

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Enzyme Activity Profiles during Fruit Development in Tomato Cultivars andSolanum pennellii

Steinhauser

Koehl

et al. 2010

Plant Physiology

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Enzymes interact to generate metabolic networks. The activities of more than 22 enzymes from central metabolism were profiled during the development of fruit of the modern tomato cultivar Solanum lycopersicum 'M82' and its wild relative Solanum pennellii (LA0716). In S. pennellii, the mature fruit remains green and contains lower sugar and higher organic acid levels. These genotypes are the parents of a widely used near introgression line population. Enzymes were also profiled in a second cultivar, S. lycopersicum 'Moneymaker', for which data sets for the developmental changes of metabolites and transcripts are available. Whereas most enzyme activities declined during fruit development in the modern S. lycopersicum cultivars, they remained high or even increased in S. pennellii, especially enzymes required for organic acid synthesis. The enzyme profiles were sufficiently characteristic to allow stages of development and cultivars and the wild species to be distinguished by principal component analysis and clustering. Many enzymes showed coordinated changes during fruit development of a given genotype. Comparison of the correlation matrices revealed a large overlap between the two modern cultivars and considerable overlap with S. pennellii, indicating that despite the very different development responses, some basic modules are retained. Comparison of enzyme activity, metabolite profiles, and transcript profiles in S. lycopersicum 'Moneymaker' revealed remarkably little connectivity between the developmental changes of transcripts and enzymes and even less between enzymes and metabolites. We discuss the concept that the metabolite profile is an emergent property that is generated by complex network interactions.

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A genetic map of candidate genes and QTLs involved in tomato fruit size and composition

Cited by 174 publications

References 48 publications

High-Resolution Mapping of a Fruit Firmness-Related Quantitative Trait Locus in Tomato Reveals Epistatic Interactions Associated with a Complex Combinatorial Locus

High-Resolution Mapping of a Fruit Firmness-Related Quantitative Trait Locus in Tomato Reveals Epistatic Interactions Associated with a Complex Combinatorial Locus

Changes in Transcriptional Profiles Are Associated with Early Fruit Tissue Specialization in Tomato

Enzyme Activity Profiles during Fruit Development in Tomato Cultivars andSolanum pennellii

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