Transcriptome Profiling of Tomato Fruit Development Reveals Transcription Factors Associated with Ascorbic Acid, Carotenoid and Flavonoid Biosynthesis

Fruits are unique to flowering plants and represent an important component of human and animal diets. Development and maturation of tomato fruit is a well-programmed process, and yet, only a limited number of factors involved in its regulation have been characterized. Micro-RNAs (miRNAs) are small, endogenous RNAs that regulate gene expression in animals and plants. Plant miRNAs have a vital role in the generation of plant forms through post-transcriptional regulation of the accumulation of developmental regulators, especially transcription factors. Recently, we and others have demonstrated that miRNAs and other type of small RNAs are expressed in tomato fruit, and target putative transcription factors during its development and maturation. The original objectives of the approved proposal were: 1. To identify fruit miRNA transcription factor target genes through a bioinformatic approach. 2. To identify fruit miRNA transcription factor target genes up-regulated in tomato Dicer-like 1 silenced fruit. 3. To establish the biological functions of selected transcription factors and examine their utility for improving fleshy fruit quality trait. This project was approved by BARD as a feasibility study to allow initial experiments to peruse objective 2 as described above in order to provide initial evidence that miRNAs do play a role in fruit development. The approach planned to achieve objective 2, namely to identify miRNA transcription factor targets was to clone and silence the expression of a tomato DCL1 homolog in different stages of fruit development and examine alterations to gene expression in such a fruit in order to identify pathways and target genes that are regulated by miRNA via DCL1. In parallel, we characterized two transcription factors that are regulated by miRNAs in the fruit. We report here on the cloning of tomato DCL1 homolog, characterization of its expression in fruit flesh and peel of wild type and ripening mutants and generation of transgenic plants that silence SlDCL1 specifically in the fruit. Our results suggest that the tomato homolog of DCL1, which is the major plant enzyme involved in miRNA biogenesis, is present in fruit flesh and peel and differentially expressed during various stages of fruit development. In addition, its expression is altered in ripening mutants. We also report on the cloning and expression analysis of Sl_SBP and Sl_ARF transcription factors, which serve as targets of miR157 and miR160, respectively. Our data suggest that Sl_SBP levels are highest during fruit ripening supporting a role for this gene in that process. On the other hand Sl_ARF is strongly expressed in green fruit up to breaker indicating a role for that gene at preripening stage which is consistent with preliminary in_situ analyses that suggest expression in ovules of immature green fruit. The results of this feasibility study together with our previous results that miRNAs are expressed in the fruit indeed provide initial evidence that these regulators and their targets play roles in fruit development and ripening. These genes are expected to provide novel means for genetic improvement of tomato fleshy fruit.

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Single and Double Mutations in Tomato Ripening Transcription Factors Have Distinct Effects on Fruit Development and Quality Traits

Frontiers in Plant Science ◽

10.3389/fpls.2021.647035 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jaclyn A. Adaskaveg ◽

Christian J. Silva ◽

Peng Huang ◽

Barbara Blanco-Ulate

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Fruit Development ◽

Tomato Fruit ◽

Genetic Interactions ◽

Developmental Defects ◽

Ripening Mutants ◽

Ripening Inhibitor ◽

High Concentrations ◽

First Time

Spontaneous mutations associated with the tomato transcription factors COLORLESS NON-RIPENING (SPL-CNR), NON-RIPENING (NAC-NOR), and RIPENING-INHIBITOR (MADS-RIN) result in fruit that do not undergo the normal hallmarks of ripening but are phenotypically distinguishable. Here, we expanded knowledge of the physiological, molecular, and genetic impacts of the ripening mutations on fruit development beyond ripening. We demonstrated through phenotypic and transcriptome analyses that Cnr fruit exhibit a broad range of developmental defects before the onset of fruit ripening, but fruit still undergo some ripening changes similar to wild type. Thus, Cnr should be considered as a fruit developmental mutant and not just a ripening mutant. Additionally, we showed that some ripening processes occur during senescence in the nor and rin mutant fruit, indicating that while some ripening processes are inhibited in these mutants, others are merely delayed. Through gene expression analysis and direct measurement of hormones, we found that Cnr, nor, and rin have alterations in the metabolism and signaling of plant hormones. Cnr mutants produce more than basal levels of ethylene, while nor and rin accumulate high concentrations of abscisic acid. To determine genetic interactions between the mutations, we created for the first time homozygous double mutants. Phenotypic analyses of the double ripening mutants revealed that Cnr has a strong influence on fruit traits and that combining nor and rin leads to an intermediate ripening mutant phenotype. However, we found that the genetic interactions between the mutations are more complex than anticipated, as the Cnr/nor double mutant fruit has a Cnr phenotype but displayed inhibition of ripening-related gene expression just like nor fruit. Our reevaluation of the Cnr, nor, and rin mutants provides new insights into the utilization of the mutants for studying fruit development and their implications in breeding for tomato fruit quality.

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Expression profiling of ascorbic acid-related genes during tomato fruit development and ripening and in response to stress conditions

Journal of Experimental Botany ◽

10.1093/jxb/ern322 ◽

2009 ◽

Vol 60 (2) ◽

pp. 663-678 ◽

Cited By ~ 153

Author(s):

Eugenia Ioannidi ◽

Mary S. Kalamaki ◽

Cawas Engineer ◽

Irene Pateraki ◽

Dimitris Alexandrou ◽

...

Keyword(s):

Ascorbic Acid ◽

Fruit Development ◽

Expression Profiling ◽

Tomato Fruit ◽

Stress Conditions ◽

Fruit Development And Ripening ◽

Response To Stress

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Qualitative and Quantitative Models Based on Handheld NIR Spectroscopy to Monitor the Tomato Fruit Development During Early and Full Season

Global Journal of Agricultural Innovation Research & Development ◽

10.15377/2409-9813.2014.01.01.4 ◽

2014 ◽

Vol 1 (1) ◽

pp. 27-38 ◽

Cited By ~ 2

Author(s):

C. Camps ◽

◽

L. Deltheil ◽

C. Gilli

Keyword(s):

Fruit Development ◽

Tomato Fruit ◽

Nir Spectroscopy ◽

Qualitative And Quantitative ◽

Quantitative Models

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[Delta]-Aminolevulinic acid dehydratase activity during tomato fruit development and ripening

10.31274/rtd-180813-8182 ◽

1994 ◽

Author(s):

Marios Costa Kyriacou

Keyword(s):

Fruit Development ◽

Aminolevulinic Acid ◽

Tomato Fruit ◽

Acid Dehydratase ◽

Fruit Development And Ripening ◽

Dehydratase Activity

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Discovery of DNA Binding Anticancer Drugs That Target Oncogenic Transcription Factors Associated With Human Breast Cancer

10.21236/ada403322 ◽

2001 ◽

Author(s):

Terry A. Beerman

Keyword(s):

Breast Cancer ◽

Transcription Factors ◽

Dna Binding ◽

Anticancer Drugs ◽

Human Breast Cancer ◽

Human Breast ◽

Factors Associated

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RNA-Seq Provides New Insights into the Molecular Events Involved in “Ball-Skin versus Bladder Effect” on Fruit Cracking in Litchi

International Journal of Molecular Sciences ◽

10.3390/ijms22010454 ◽

2021 ◽

Vol 22 (1) ◽

pp. 454

Author(s):

Jun Wang ◽

Xiao Fang Wu ◽

Yong Tang ◽

Jian Guo Li ◽

Ming Lei Zhao

Keyword(s):

Transcription Factors ◽

Plant Hormones ◽

Fruit Development ◽

Economic Value ◽

Lipid Synthesis ◽

Expression Level ◽

Agricultural Product ◽

Rna Seq ◽

Fruit Cracking ◽

Molecular Events

Fruit cracking is a disorder of fruit development in response to internal or external cues, which causes a loss in the economic value of fruit. Therefore, exploring the mechanism underlying fruit cracking is of great significance to increase the economic yield of fruit trees. However, the molecular mechanism underlying fruit cracking is still poorly understood. Litchi, as an important tropical and subtropical fruit crop, contributes significantly to the gross agricultural product in Southeast Asia. One important agricultural concern in the litchi industry is that some famous varieties with high economic value such as ‘Nuomici’ are susceptible to fruit cracking. Here, the cracking-susceptible cultivar ‘Nuomici’ and cracking-resistant cultivar ‘Huaizhi’ were selected, and the samples including pericarp and aril during fruit development and cracking were collected for RNA-Seq analysis. Based on weighted gene co-expression network analysis (WGCNA) and the “ball-skin versus bladder effect” theory (fruit cracking occurs upon the aril expanding pressure exceeds the pericarp strength), it was found that seven co-expression modules genes (1733 candidate genes) were closely associated with fruit cracking in ‘Nuomici’. Importantly, we propose that the low expression level of genes related to plant hormones (Auxin, Gibberellins, Ethylene), transcription factors, calcium transport and signaling, and lipid synthesis might decrease the mechanical strength of pericarp in ‘Nuomici’, while high expression level of genes associated with plant hormones (Auxin and abscisic acid), transcription factors, starch/sucrose metabolism, and sugar/water transport might increase the aril expanding pressure, thereby resulting in fruit cracking in ‘Nuomici’. In conclusion, our results provide comprehensive molecular events involved in the “ball-skin versus bladder effect” on fruit cracking in litchi.

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