The tomato genome: implications for plant breeding, genomics and evolution

Ranjan, Aashish; Ichihashi, Yasunori; Sinha, Neelima

doi:10.1186/gb-2012-13-8-167

Cited by 46 publications

(24 citation statements)

References 74 publications

(61 reference statements)

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“…1 Plant hormones participate in the growth and development of tomato organs, including fruits and seeds. 2–4 Gibberellins (GAs) are important hormones that control fruit set and growth, and seed development in tomato.…”

Section: Introductionmentioning

confidence: 99%

Identification and characterization of tomato gibberellin 2-oxidases (GA2oxs) and effects of fruit-specific SlGA2ox1 overexpression on fruit and seed growth and development

Shen¹,

Wang²,

Zhang³

et al. 2016

Hortic Res

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Gibberellins (GAs) play a crucial role in growth and development of the tomato fruit. Previously published studies focusing on the effect of GAs on tomato fruits used chemical treatments, constitutive overexpression or silencing of GA biosynthetic and catabolic genes globally throughout the plant. Fruit-specific overexpression of GA catabolic enzyme genes GA2-oxidases (GA2oxs), however, may provide an alternative method to study the role of endogenous GAs on the fruit development. In this study, we have identified 11 SlGA2ox proteins in tomato that are classified into three subgroups. Motif analysis and multiple sequence alignments have demonstrated that all SlGA2oxs, except SlGA2ox10, have similar motif compositions and high-sequence conservation. Quantitative reverse transcription-PCR analysis has showed that SlGA2oxs exhibit differential expression patterns in tomato fruits at different developmental stages. When the fruit-specific promoter TFM7 was used to control the expression of SlGA2ox1, we observed no changes in growth and development of vegetative organs. However, fruit weight, seed number and germination rate were significantly affected. We also treated tomato fruits with GA biosynthesis inhibitor and observed phenotypes similar to those of the transgenic fruits. Furthermore, we have demonstrated that expression of cell expansion and GA responsive genes were downregulated in transgenic tomato fruits, supporting that overexpression of the SlGA2ox1 leads to reduction in endogenous GAs. This study provides additional evidence that endogenous GAs and the SlGA2ox1 gene play an important role in controlling on fruit weight, seed development and germination in tomato plant.

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Section: Introductionmentioning

confidence: 99%

Identification and characterization of tomato gibberellin 2-oxidases (GA2oxs) and effects of fruit-specific SlGA2ox1 overexpression on fruit and seed growth and development

Shen¹,

Wang²,

Zhang³

et al. 2016

Hortic Res

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“…Cultivated tomatoes, along with their wild-relatives, harbor broad genetic diversity and large phenotypic variability (Moyle, 2008; Ranjan et al, 2012). Wide interspecific crosses bring together divergent genomes and hybridization of such diverse genotypes leads to extensive gene expression alterations compared to either parent.…”

Section: Introductionmentioning

confidence: 99%

eQTL regulating Transcript Levels Associated with Diverse Biological Processes in Tomato

Ranjan

Budke²,

Rowland³

et al. 2016

Preprint

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Variation in gene expression, in addition to sequence polymorphisms, is known to influence developmental, physiological and metabolic traits in plants. Genetic mapping populations have facilitated identification of expression Quantitative Trait Loci (eQTL), the genetic determinants of variation in gene expression patterns. We used an introgression population developed from the wild desert-adapted Solanum pennellii and domesticated tomato Solanum lycopersicum to identify the genetic basis of transcript level variation. We established the effect of each introgression on the transcriptome, and identified ~7,200 eQTL regulating the steady state transcript levels of 5,300 genes. Barnes-Hut t-distributed stochastic neighbor embedding clustering identified 42 modules revealing novel associations between transcript level patterns and biological processes. The results showed a complex genetic architecture of global transcript abundance pattern in tomato. Several genetic hotspots regulating a large number of transcript level patterns relating to diverse biological processes such as plant defense and photosynthesis were identified. Important eQTL regulating transcript level patterns were related to leaf number and complexity, and hypocotyl length. Genes associated with leaf development showed an inverse correlation with photosynthetic gene expression but eQTL regulating genes associated with leaf development and photosynthesis were dispersed across the genome. This comprehensive expression QTL analysis details the influence of these loci on plant phenotypes, and will be a valuable community resource for investigations on the genetic effects of eQTL on phenotypic traits in tomato.

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“…Integrating genome sequencing, transcriptomics, proteomics, metabolomics, ionomics, and phenomics allows large-scale gene function analysis with high-throughput technology and incorporates interaction of gene products at cellular and organism level. The complete genome sequence of rice and Arabidopsis and emerging sequence information for several other plant genomes, such as Populus , Medicago , lotus, tomato, pigeon pea, and maize, have enriched the genetic information to employ the tools for the determination of the function of many genes simultaneously (The Arabidopsis Genome Initiative 2000 ; International Rice Genome Sequencing Project 2005 ;Bell et al 2001 ;Nakamura et al 2002 ;Rensink and Buell 2005 ;Vij et al 2006 ;Ranjan et al 2012 ;Varshney et al 2012 ). The use of in silico gene discovery, high-throughput gene expression, altered gene expression by transgenesis, functional characterization of genes of interest via gene-inactivation techniques, and genetic and genomic approaches in understanding the basis of abiotic stress tolerance has been initiated in several plant species (Vij and Tyagi 2007 ;Sreenivasulu et al 2007 ;Sheldon and Roessner 2013 ).…”

Section: Functional Genomics Of Heavy Metal Tolerance In Plants: Apprmentioning

confidence: 99%

Elucidation of Abiotic Stress Signaling in Plants

2015

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The above image represents a depiction of activation of different signaling pathways by diverse stimuli that converge to activate intricate signaling and interaction networks to counter stress (top panel). Since environmental stresses infl uence most signifi cantly to the reduction in potential crop yield, progress is now largely anticipated through functional genomics studies in plants through the use of techniques such as large-scale analysis of gene expression pattern in response to stress and construction, analysis and use of plant protein interactome networks maps for effective engineering strategies to generate stress tolerant crops (top panel). The molecular aspects of these signaling pathways are extensively studied in model plant Arabidopsis thaliana and crop plant rice ( Oryza sativa ) (below).

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The tomato genome: implications for plant breeding, genomics and evolution

Abstract: The genome sequence of tomato (Solanum lycopersicum), one of the most important vegetable crops, has recently been decoded. We address implications of the tomato genome for plant breeding, genomics and evolutionary studies, and its potential to fuel future crop biology research.

Cited by 46 publications

References 74 publications

Identification and characterization of tomato gibberellin 2-oxidases (GA2oxs) and effects of fruit-specific SlGA2ox1 overexpression on fruit and seed growth and development

Identification and characterization of tomato gibberellin 2-oxidases (GA2oxs) and effects of fruit-specific SlGA2ox1 overexpression on fruit and seed growth and development

eQTL regulating Transcript Levels Associated with Diverse Biological Processes in Tomato

Elucidation of Abiotic Stress Signaling in Plants

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