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Kumar P, Irfan M. Green ripe fruit in tomato: unraveling the genetic tapestry from cultivated to wild varieties. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3203-3205. [PMID: 38845353 PMCID: PMC11156801 DOI: 10.1093/jxb/erae149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/10/2024]
Abstract
This article comments on:
Cui L, Zheng F, Li C, Li G, Ye J, Zhang Y, Wang T, Hong Z, Ye Z, Zhang J. 2024. Defective mutations in STAY-GREEN 1, PHYTOENE SYNTHASE 1, and MYB12 genes lead to formation of green ripe fruit in tomato. Journal of Experimental Botany 75, 3322–3336.
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Affiliation(s)
- Pankaj Kumar
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh 173230, India
| | - Mohammad Irfan
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
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Sharma D, Koul A, Bhushan S, Gupta S, Kaul S, Dhar MK. Insights into microRNA-mediated interaction and regulation of metabolites in tomato. PLANT BIOLOGY (STUTTGART, GERMANY) 2023; 25:1142-1153. [PMID: 37681459 DOI: 10.1111/plb.13572] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/23/2023] [Indexed: 09/09/2023]
Abstract
microRNAs direct regulation of various metabolic pathways in plants and animals. miRNAs may be useful in developing novel/elite genotypes, with enhanced metabolites and disease resistance. We examined miRNAs in tomato. In tomato, miRNAs in the carotenoid pathway have not been fully elucidated. We examined the potential role of miRNAs in biosynthesis of carotenoids, transcript profiling of miRNAs and their possible targets (genes and transcription factors) at different development stages of tomato using stem-loop PCR and RT-qPCR. We also identified miRNAs targeting key flavonoid genes, such as chalcone isomerase (CHI), and dihydroflavonol-4-reductase (DFR). Distinct expression profiles of miRNAs and their targets were found in fruits of three tomato accessions, suggesting carotenoid regulation by miRNAs at various stages of fruit development. This was also confirmed using HPLC of the carotenoids. The present study may help in understanding possible regulation of carotenoid biosynthesis. The identified miRNAs can be exploited to enhance biosynthesis of different carotenoids in plants.
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Affiliation(s)
- D Sharma
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, India
| | - A Koul
- Department of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - S Bhushan
- Department of Botany, Central University of Jammu, Bagla (Rahya Suchani), Samba, Jammu, India
| | - S Gupta
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, India
| | - S Kaul
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, India
| | - M K Dhar
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, India
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Naeem M, Zhao W, Ahmad N, Zhao L. Beyond green and red: unlocking the genetic orchestration of tomato fruit color and pigmentation. Funct Integr Genomics 2023; 23:243. [PMID: 37453947 DOI: 10.1007/s10142-023-01162-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023]
Abstract
Fruit color is a genetic trait and a key factor for consumer acceptability and is therefore receiving increasing importance in several breeding programs. Plant pigments offer plants with a variety of colored organs that attract animals for pollination, favoring seed dispersers and conservation of species. The pigments inside plant cells not only play a light-harvesting role but also provide protection against light damage and exhibit nutritional and ecological value for health and visual pleasure in humans. Tomato (Solanum lycopersicum) is a leading vegetable crop; its fruit color formation is associated with the accumulation of several natural pigments, which include carotenoids in the pericarp, flavonoids in the peel, as well as the breakdown of chlorophyll during fruit ripening. To improve tomato fruit quality, several techniques, such as genetic engineering and genome editing, have been used to alter fruit color and regulate the accumulation of secondary metabolites in related pathways. Recently, clustered regularly interspaced short palindromic repeat (CRISPR)-based systems have been extensively used for genome editing in many crops, including tomatoes, and promising results have been achieved using modified CRISPR systems, including CAS9 (CRISPR/CRISPR-associated-protein) and CRISPR/Cas12a systems. These advanced tools in biotechnology and whole genome sequencing of various tomato species will certainly advance the breeding of tomato fruit color with a high degree of precision. Here, we attempt to summarize the current advancement and effective application of genetic engineering techniques that provide further flexibility for fruit color formation. Furthermore, we have also discussed the challenges and opportunities of genetic engineering and genome editing to improve tomato fruit color.
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Affiliation(s)
- Muhammad Naeem
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Weihua Zhao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Naveed Ahmad
- Joint Center for Single Cell Biology, Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Lingxia Zhao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
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Ahmad I, Soni SK, M M, Pandey D. In-silico mining and characterization of MYB family genes in wilt-resistant hybrid guava (Psidium guajava × Psidium molle). J Genet Eng Biotechnol 2023; 21:74. [PMID: 37389653 DOI: 10.1186/s43141-023-00528-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 06/20/2023] [Indexed: 07/01/2023]
Abstract
BACKGROUND The MYB family is one of the most significant groups of transcription factors in plants. However, several MYBs have been linked to secondary metabolism and are important for determining the color of fruit's peel and pulp. Despite being a substantial fruit crop in tropical and subtropical areas of the world, wilt-resistant hybrid guava (Psidium guajava × Psidium molle; PGPM) has not yet been the subject of a thorough examination. This study's goal was to assess the expression of MYB in guava fruit pulp, roots, and seeds to predict its function by in silico analysis of the guava root transcriptome data. RESULTS In the current study, we have mined the MYBs family of MYB genes from the transcriptome of the PGPM guava root. We have mined 15 distinct MYB transcription factor genes/transcripts viz MYB3, MYB4, MYB23, MYB86, MYB90, MYB308, MYB5, MYB82, MYB114, MYB6, MYB305, MYB44, MYB51, MYB46, and MYB330. From the analyses, it was found that R2-MYB and R3-MYB domains are conserved in all known guava MYB proteins. The expression of six different MYB TFs was examined using semi-quantitative RT-PCR in "Shweta" pulp (white colour pulp), "Lalit" pulp (red color pulp), "Lalit" root, and "Lalit" seed. CONCLUSION There were 15 MYB family members observed in guava. They were unequally distributed across the chromosomes, most likely as a result of gene duplication. Additionally, the expression patterns of the particular MYBs showed that MYB may be involved in the control of wilt, fruit ripening, seed development, and root development. Our results allow for a more thorough functional characterization of the guava MYB family genes and open the door to additional research into one essential MYB transcription factor family of genes and its involvement in the growth and ripening of guava fruit.
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Affiliation(s)
- Israr Ahmad
- Division of Crop Improvement and Biotechnology, ICAR-Central Institute for Subtropical Horticulture, Rehmankhera, P.O. Kakori, Lucknow, Uttar Pradesh, 226101, India.
| | - Sumit K Soni
- Division of Crop Improvement and Biotechnology, ICAR-Central Institute for Subtropical Horticulture, Rehmankhera, P.O. Kakori, Lucknow, Uttar Pradesh, 226101, India.
| | - Muthukumar M
- Division of Crop Improvement and Biotechnology, ICAR-Central Institute for Subtropical Horticulture, Rehmankhera, P.O. Kakori, Lucknow, Uttar Pradesh, 226101, India
| | - Devendra Pandey
- Division of Crop Improvement and Biotechnology, ICAR-Central Institute for Subtropical Horticulture, Rehmankhera, P.O. Kakori, Lucknow, Uttar Pradesh, 226101, India
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Yang J, Li P, Li Y, Xiao Q. GelFAP v2.0: an improved platform for Gene functional analysis in Gastrodia elata. BMC Genomics 2023; 24:164. [PMID: 37016293 PMCID: PMC10074892 DOI: 10.1186/s12864-023-09260-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 03/20/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND Gastrodia elata (tianma), a well-known medicinal orchid, is widely used to treat various kinds of diseases with its dried tuber. In recent years, new chromosome-level genomes of G.elata have been released in succession, which offer an enormous resource pool for understanding gene function. Previously we have constructed GelFAP for gene functional analysis of G.elata. As genomes are updated and transcriptome data is accumulated, collection data in GelFAP cannot meet the need of researchers. RESULTS Based on new chromosome-level genome and transcriptome data, we constructed co-expression network of G. elata, and then we annotated genes by aligning with sequences from NR, TAIR, Uniprot and Swissprot database. GO (Gene Ontology) and KEGG (Kyoto Encylopaedia of Genes and Genomes) annotations were predicted by InterProScan and GhostKOALA software. Gene families were further predicted by iTAK (Plant Transcription factor and Protein kinase Identifier and Classifier), HMMER (hidden Markov models), InParanoid. Finally, we developed an improved platform for gene functional analysis in G. elata (GelFAP v2.0) by integrating new genome, transcriptome data and processed functional annotation. Several tools were also introduced to platform including BLAST (Basic Local Alignment Search Tool), GSEA (Gene Set Enrichment Analysis), Heatmap, JBrowse, Motif analysis and Sequence extraction. Based on this platform, we found that the flavonoid biosynthesis might be regulated by transcription factors (TFs) such as MYB, HB and NAC. We also took C4H and GAFP4 as examples to show the usage of our platform. CONCLUSION An improved platform for gene functional analysis in G. elata (GelFAP v2.0, www.gzybioinformatics.cn/Gelv2 ) was constructed, which provides better genome data, more transcriptome resources and more analysis tools. The updated platform might be preferably benefit researchers to carry out gene functional research for their project.
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Affiliation(s)
- Jiaotong Yang
- Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guizhou, 550025, China
| | - Pengfei Li
- Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guizhou, 550025, China
| | - Yuping Li
- Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guizhou, 550025, China
| | - Qiaoqiao Xiao
- Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guizhou, 550025, China.
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Sharma M, Bhushan S, Sharma D, Kaul S, Dhar MK. A Brief Review of Plant Cell Transfection, Gene Transcript Expression, and Genotypic Integration for Enhancing Compound Production. Methods Mol Biol 2023; 2575:153-179. [PMID: 36301475 DOI: 10.1007/978-1-0716-2716-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Plants possess a plethora of important secondary metabolites, which are unique sources of natural pigments, pharmaceutical compounds, food additives, natural pesticides, and other industrial components. The commercial significance of such metabolites/compounds has directed the research toward their production and exploration of methods for enhancement of production. Biotechnological tools are critical in selecting, integrating, multiplying, improving, and analyzing medicinal plants for secondary metabolite production. Out of many techniques that are being explored to enhance secondary metabolite production, "plant cell transfection" is the latest tool to achieve maximum output from the plant source. It is based upon the introduction of foreign DNA into the plant cell relying on physical treatment such as electroporation, cell squeezing, sonoporation, optical transfection nanoparticles, magnetofection, and chemical treatment or biological treatment that depends upon carrier. One of the promising tools that have been exploited is CRISPR-Cas9. Overall, the abovementioned tools focus on the stable transfection of desired gene transcripts. Since the integration and continuous expression of transfected gene of particular trait represents stable transfection of host cell genome, resulting from transfer of required trait to daughter cells ultimately leading to enhanced production of secondary metabolites of interest. This chapter will review a set of biotechnological tools that are candidates for achieving the enhanced bioactive compound production indicated here to be used for drug discovery.
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Affiliation(s)
- Munish Sharma
- Department of Plant Sciences, Central University of Himachal Pradesh, Shahpur, Kangra, Himachal Pradesh, India.
| | - Sakshi Bhushan
- Department of Botany, Central University of Jammu, Jammu, Jammu and Kashmir, India
| | - Deepak Sharma
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, Jammu and Kashmir, India
| | - Sanjana Kaul
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, Jammu and Kashmir, India
| | - Manoj K Dhar
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, Jammu and Kashmir, India
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Integrated Metabolomic and Transcriptomic Analyses Reveal the Basis for Carotenoid Biosynthesis in Sweet Potato (Ipomoea batatas (L.) Lam.) Storage Roots. Metabolites 2022; 12:metabo12111010. [DOI: 10.3390/metabo12111010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 11/07/2022] Open
Abstract
Carotenoids are important compounds of quality and coloration within sweet potato storage roots, but the mechanisms that govern the accumulation of these carotenoids remain poorly understood. In this study, metabolomic and transcriptomic analyses of carotenoids were performed using young storage roots (S2) and old storage roots (S4) from white-fleshed (variety S19) and yellow-fleshed (variety BS) sweet potato types. S19 storage roots exhibited significantly lower total carotenoid levels relative to BS storage roots, and different numbers of carotenoid types were detected in the BS-S2, BS-S4, S19-S2, and S19-S4 samples. β-cryptoxanthin was identified as a potential key driver of differences in root coloration between the S19 and BS types. Combined transcriptomic and metabolomic analyses revealed significant co-annotation of the carotenoid and abscisic acid (ABA) metabolic pathways, PSY (phytoene synthase), CHYB (β-carotene 3-hydroxylase), ZEP (zeaxanthin epoxidase), NCED3 (9-cis-epoxycarotenoid dioxygenase 3), ABA2 (xanthoxin dehydrogenase), and CYP707A (abscisic acid 8’-hydroxylase) genes were found to be closely associated with carotenoid and ABA content in these sweet potato storage roots. The expression patterns of the transcription factors OFP and FAR1 were associated with the ABA content in these two sweet potato types. Together, these results provide a valuable foundation for understanding the mechanisms governing carotenoid biosynthesis in storage roots, and offer a theoretical basis for sweet potato breeding and management.
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Byun J, Kim TG, Lee JH, Li N, Jung S, Kang BC. Identification of CaAN3 as a fruit-specific regulator of anthocyanin biosynthesis in pepper (Capsicum annuum). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2197-2211. [PMID: 35536305 DOI: 10.1007/s00122-022-04106-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/12/2022] [Indexed: 06/14/2023]
Abstract
The novel gene CaAN3 encodes an R2R3 MYB transcription factor that regulates fruit-specific anthocyanin accumulation. The key regulatory gene CaAN2 encodes an R2R3 MYB transcription factor that regulates anthocyanin biosynthesis in various tissues in pepper (Capsicum annuum). However, CaAN2 is not expressed in certain pepper accessions showing fruit-specific anthocyanin accumulation. In this study, we identified the novel locus CaAN3 as a regulator of fruit-specific anthocyanin biosynthesis, using an F2 population derived from a hybrid cultivar with purple immature fruits and segregating for CaAN3. We extracted total RNA, assembled two RNA pools according to fruit color, and carried out bulked segregant RNA sequencing. We aligned the raw reads to the pepper reference genome Dempsey and identified 6,672 significant single nucleotide polymorphisms (SNPs) by calculating the Δ(SNP-index) between the two pools. We then conducted molecular mapping to delimit the target region of CaAN3 to the interval 184.6-186.4 Mbp on chromosome 10. We focused on Dem.v1.00043895, encoding an R2R3 MYB transcription factor, as the strongest candidate gene. Sequence analysis revealed four insertion/deletion polymorphisms in the promoter region of the green CaAN3 allele. We employed virus-induced gene silencing and transient overexpression assays to characterize the function of the candidate gene. When Dem.v1.00043895 was silenced in pepper, anthocyanin accumulation decreased in the pericarp, while the transient overexpression of Dem.v1.00043895 in Nicotiana benthamiana leaves resulted in the accumulation of anthocyanins around the infiltration sites. These results showed that Dem.v1.00043895 is CaAN3, an activator of anthocyanin biosynthesis in pepper fruits.
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Affiliation(s)
- Jinyoung Byun
- Department of Agriculture, Forestry, and Bioresources, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Tae-Gun Kim
- Department of Agriculture, Forestry, and Bioresources, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Interdisciplinary Program in Agricultural GenomicsResearch Institute of Agriculture and Life SciencesSeoul National University, Seoul, South Korea
| | - Joung-Ho Lee
- Department of Agriculture, Forestry, and Bioresources, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Ning Li
- Cash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan City, 430064, Hubei Province, China
| | - Soyoung Jung
- Department of Agriculture, Forestry, and Bioresources, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Byoung-Cheorl Kang
- Department of Agriculture, Forestry, and Bioresources, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.
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Tang J, Li Y, Liu Z, Wei M, Shi Q, Yang F. Integrated Transcriptomics and Metabolomics Analyses Reveal the Molecular Mechanisms of Red-light on Carotenoids Biosynthesis in Tomato Fruit. FOOD QUALITY AND SAFETY 2022. [DOI: 10.1093/fqsafe/fyac009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
Carotenoids are the main pigments responsible of the coloration and account for the major antioxidant activity of tomato (Solanum lycopersicum L.) fruit. Significant increments in total carotenoids and lycopene levels were observed in tomato fruit illuminated by red-light relative to white light in previous studies, but the mechanism of carotenoids biosynthesis regulated by red-light is still unclear. In the present study, the influence of red-light on carotenoids biosynthesis in postharvest tomato fruit was conducted using targeted metabolomics and transcriptomic methods. A total of 25 differentially accumulated carotenoids and 1939 differentially expressed genes were isolated and identified. The results illustrated that the content of phytoene and lycopene were considerably higher in fruit treated with red-light than those with white light at 12 h. These differentially expressed genes are mainly enriched in plant hormone signal transduction, photosynthesis, secondary metabolite biosynthesis, and plant circadian. Moreover, from the results of co-expression network analysis, 15 transcription factors from red-light treated fruit were screened, of these, transcription factors of SlERF4, SlbHLH93 and SlIAA29, which involves in signal transduction of light and hormones, respectively, that may also play important roles in carotenoids biosynthesis regulated by red-light in tomato fruit. It is concluded that red-light enhanced carotenoids biosynthesis in postharvest tomato fruit and the mechanisms of enhanced carotenoids biosynthesis were not only associated with the direct regulation by red-light signaling, but also with the indirect regulation by hormonal signaling.
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Fruit Colour and Novel Mechanisms of Genetic Regulation of Pigment Production in Tomato Fruits. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7080259] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Fruit colour represents a genetic trait with ecological and nutritional value. Plants mainly use colour to attract animals and favour seed dispersion. Thus, in many species, fruit colour coevolved with frugivories and their preferences. Environmental factors, however, represented other adaptive forces and further diversification was driven by domestication. All these factors cooperated in the evolution of tomato fruit, one of the most important in human nutrition. Tomato phylogenetic history showed two main steps in colour evolution: the change from green-chlorophyll to red-carotenoid pericarp, and the loss of the anthocyanic pigmentation. These events likely occurred with the onset of domestication. Then spontaneous mutations repeatedly occurred in carotenoid and phenylpropanoid pathways, leading to colour variants which often were propagated. Introgression breeding further enriched the panel of pigmentation patterns. In recent decades, the genetic determinants underneath tomato colours were identified. Novel evidence indicates that key regulatory and biosynthetic genes undergo mechanisms of gene expression regulation that are much more complex than what was imagined before: post-transcriptional mechanisms, with RNA splicing among the most common, indeed play crucial roles to fine-tune the expression of this trait in fruits and offer new substrate for the rise of genetic variables, thus providing further evolutionary flexibility to the character.
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Mohd Yusof FF, Yaacob JS, Osman N, Ibrahim MH, Wan-Mohtar WAAQI, Berahim Z, Mohd Zain NA. Shading Effects on Leaf Gas Exchange, Leaf Pigments and Secondary Metabolites of Polygonum minus Huds., an Aromatic Medicinal Herb. PLANTS 2021; 10:plants10030608. [PMID: 33806923 PMCID: PMC8004659 DOI: 10.3390/plants10030608] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/08/2021] [Accepted: 03/10/2021] [Indexed: 11/28/2022]
Abstract
The growing demand for high value aromatic herb Polygonum minus-based products have increased in recent years, for its antioxidant, anticancer, antimicrobial, and anti-inflammatory potentials. Although few reports have indicated the chemical profiles and antioxidative effects of Polygonum minus, no study has been conducted to assess the benefits of micro-environmental manipulation (different shading levels) on the growth, leaf gas exchange and secondary metabolites in Polygonum minus. Therefore, two shading levels (50%:T2 and 70%:T3) and one absolute control (0%:T1) were studied under eight weeks and 16 weeks of exposures on Polygonum minus after two weeks. It was found that P. minus under T2 obtained the highest photosynthesis rate (14.892 µmol CO2 m−2 s−1), followed by T3 = T1. The increase in photosynthesis rate was contributed by the enhancement of the leaf pigments content (chlorophyll a and chlorophyll b). This was shown by the positive significant correlations observed between photosynthesis rate with chlorophyll a (r2 = 0.536; p ≤ 0.05) and chlorophyll b (r2 = 0.540; p ≤ 0.05). As the shading levels and time interval increased, the production of total anthocyanin content (TAC) and antioxidant properties of Ferric Reducing Antioxidant Power (FRAP) and 2,2-Diphenyl-1-picrylhydrazyl (DPPH) also increased. The total phenolic content (TPC) and total flavonoid content (TFC) were also significantly enhanced under T2 and T3. The current study suggested that P.minus induce the production of more leaf pigments and secondary metabolites as their special adaptation mechanism under low light condition. Although the biomass was affected under low light, the purpose of conducting the study to boost the bioactive properties in Polygonum minus has been fulfilled by 50% shading under 16 weeks’ exposure.
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Affiliation(s)
- Fairuz Fatini Mohd Yusof
- Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (F.F.M.Y.); (J.S.Y.); (N.O.)
| | - Jamilah Syafawati Yaacob
- Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (F.F.M.Y.); (J.S.Y.); (N.O.)
| | - Normaniza Osman
- Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (F.F.M.Y.); (J.S.Y.); (N.O.)
| | - Mohd Hafiz Ibrahim
- Department of Biology, Faculty of Science, Universiti Putra Malaysia, Serdang 43400, Malaysia;
| | - Wan Abd Al Qadr Imad Wan-Mohtar
- Functional Omics and Bioprocess Development Laboratory, Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
| | - Zulkarami Berahim
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang 43400, Malaysia;
| | - Nurul Amalina Mohd Zain
- Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (F.F.M.Y.); (J.S.Y.); (N.O.)
- Correspondence: ; Tel.: +60-379-674-355
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RNA-sequencing based gene expression landscape of guava cv. Allahabad Safeda and comparative analysis to colored cultivars. BMC Genomics 2020; 21:484. [PMID: 32669108 PMCID: PMC7364479 DOI: 10.1186/s12864-020-06883-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 07/06/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Guava (Psidium guajava L.) is an important fruit crop of tropical and subtropical areas of the world. Genomics resources in guava are scanty. RNA-Seq based tissue specific expressed genomic information, de novo transcriptome assembly, functional annotation and differential expression among contrasting genotypes has a potential to set the stage for the functional genomics for traits of commerce like colored flesh and apple color peel. RESULTS Development of fruit from flower involves orchestration of myriad molecular switches. We did comparative transcriptome sequencing on leaf, flower and fruit tissues of cv. Allahabad Safeda to understand important genes and pathways controlling fruit development. Tissue specific RNA sequencing and de novo transcriptome assembly using Trinity pipeline provided us the first reference transcriptome for guava consisting of 84,206 genes comprising 279,792 total transcripts with a N50 of 3603 bp. Blast2GO assigned annotation to 116,629 transcripts and PFam based HMM profile annotated 140,061 transcripts with protein domains. Differential expression with EdgeR identified 3033 genes in Allahabad Safeda tissues. Mapping the differentially expressed transcripts over molecular pathways indicate significant Ethylene and Abscisic acid hormonal changes and secondary metabolites, carbohydrate metabolism and fruit softening related gene transcripts during fruit development, maturation and ripening. Differential expression analysis among colored tissue comparisons in 3 cultivars Allahabad Safeda, Punjab Pink and Apple Color identified 68 candidate genes that might be controlling color development in guava fruit. Comparisons of red vs green peel in Apple Color, white pulp vs red pulp in Punjab Pink and fruit maturation vs ripening in non-colored Allahabad Safeda indicates up-regulation of ethylene biosynthesis accompanied to secondary metabolism like phenylpropanoid and monolignol pathways. CONCLUSIONS Benchmarking Universal Single-Copy Orthologs analysis of de novo transcriptome of guava with eudicots identified 93.7% complete BUSCO genes. In silico differential gene expression among tissue types of Allahabad Safeda and validation of candidate genes with qRT-PCR in contrasting color genotypes promises the utility of this first guava transcriptome for its potential of tapping the genetic elements from germplasm collections for enhancing fruit traits.
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Sharma D, Koul A, Kaul S, Dhar MK. Tissue-specific transcriptional regulation and metabolite accumulation in tomato (Solanum lycopersicum L.). PROTOPLASMA 2020; 257:1093-1108. [PMID: 32152722 DOI: 10.1007/s00709-020-01492-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/17/2020] [Indexed: 05/02/2023]
Abstract
Tomato is an excellent model for studying fruit development, ripening, and other secondary metabolic pathways such as carotenoid biosynthetic pathway, flavonoid pathway, and many more. Tomato fruit development and ripening occurs under tight genetic control and involves the expression of thousands of genes affecting fruit quality and accumulation of pigments and metabolites. Here, we have described the development of a microarray platform that has allowed establishment of a framework for quantification of the expression of large number of genes and transcription factors possibly regulating various secondary metabolic pathways in tomato. To unravel the molecular mechanisms of fruit development and ripening, a tomato 60-mer oligonucleotide 44 K microarray along with the custom array for many genes and transcription factors was designed and validated in the fruit and leaf tissues. Comparative profiling of gene expression studies has allowed us to identify a large number of differentially expressed genes and transcription factors. Gene ontology revealed the involvement of these genes in various biological, cellular, and molecular processes like isoprenoid, terpenoid, pigment, ethylene biosynthesis, phytohormone signaling, and fruit ripening. Further, correlation, as well as differential expression studies, has revealed that several transcription factors like RIN, AGAMOUS, TAGL1, MYB, MADS-box etc. could be the possible regulators of various secondary metabolic pathways. The present study has identified various metabolites, their biosynthetic pathways and genes which may possibly be controlled by different transcription factors. The present findings have laid a base for understanding the transcriptional and metabolic shifts which occur in parallel during programmed fruit ripening and developmental processes in tomato.
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Affiliation(s)
- Deepak Sharma
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006, India
| | - Archana Koul
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006, India
| | - Sanjana Kaul
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006, India
| | - Manoj K Dhar
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006, India.
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Koul A, Sharma D, Kaul S, Dhar MK. Identification and in silico characterization of cis-acting elements of genes involved in carotenoid biosynthesis in tomato. 3 Biotech 2019; 9:287. [PMID: 31297303 DOI: 10.1007/s13205-019-1798-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 06/06/2019] [Indexed: 02/06/2023] Open
Abstract
Carotenoids, the widespread and structurally diverse class of pigments, accumulate in the fruits of tomato plants in a tissue specific manner. The carotenoid biosynthetic pathway genes have been cloned and characterized in tomato and other plants, however, its regulation is still obscure. We collected and analyzed forty different accessions of tomato for the present study. HPLC analysis revealed differential accumulation of major carotenoids (lycopene and ß-carotene) in the ripe fruit tissue. In order to understand the underlying regulatory mechanisms in carotenoid biosynthesis and accumulation, we sequenced the cis-acting elements i.e. promoter, 5' and 3' untranslated regions of the carotenoid pathway genes, in all accessions, followed by their in silico validation. Major differences observed in the CAAT Box, Opaque-2 Box and L-box in the promoters of carotenoid isomerase and lycopene-beta cyclase genes, respectively, along with the variations in musashi binding element of 5' untranslated regions of the carotenoid isomerase gene, suggest their differential role in regulating the carotenogenesis process in tomato. The binding sites for various transcription factors namely RIN, AGAMOUS, CRY, RAP2.2 and PIF1 on the promoters of important carotenoid pathway genes were predicted in silico. We propose that expression of carotenoid genes and also the formation of protein product in ripe tomato fruits, is regulated efficiently by the binding of these transcription factors at selected sites in the promoter region. Finally, the differential expression of the above-mentioned genes in different developmental tissues supports the possible involvement of promoters and untranslated regions in carotenoid biosynthesis and accumulation process. The present study has generated significant information concerning regulatory players involved in the carotenoid biosynthesis in tomato.
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Identification and expression profiling of miRNAs in two color variants of carrot (Daucus carota L.) using deep sequencing. PLoS One 2019; 14:e0212746. [PMID: 30845212 PMCID: PMC6405255 DOI: 10.1371/journal.pone.0212746] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 02/08/2019] [Indexed: 12/31/2022] Open
Abstract
microRNAs represent small endogenous RNAs which are known to play a crucial role in various plant metabolic processes. Carrot being an important vegetable crop, represents one of the richest sources of carotenoids and anthocyanins. Most of the studies on microRNAs have been conducted in the aerial parts of the plants. However, carrot has the rare distinction of storing these compounds in roots. Therefore, carrot represents a good model system to unveil the regulatory roles of miRNAs in the underground edible part of the plant. For the first time, we report the genome wide identification and expression profiling of miRNAs in two contrasting color variants of carrot namely Orange Red and Purple Black using RNA-seq. Illumina sequencing resulted in the generation of 25.5M and 18.9M reads in Orange Red and Purple Black libraries, respectively. In total, 144 and 98 (read count >10), conserved microRNAs and 36 and 66 novel microRNAs were identified in Orange Red and Purple Black, respectively. Functional categorization and differential gene expression revealed the presence of several miRNA genes targeting various secondary metabolic pathways including carotenoid and anthocyanin biosynthetic pathways in the two libraries. 11 known and 2 novel microRNAs were further validated using Stem-Loop PCR and qRT-PCR. Also, target validation was performed for selected miRNA genes using RLM-RACE approach. The present work has laid a foundation towards understanding of various metabolic processes, particularly the color development in carrot. This information can be further employed in targeted gene expression for increasing the carotenoid and anthocyanin content in crop plants.
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Liu Y, Tikunov Y, Schouten RE, Marcelis LFM, Visser RGF, Bovy A. Anthocyanin Biosynthesis and Degradation Mechanisms in Solanaceous Vegetables: A Review. Front Chem 2018; 6:52. [PMID: 29594099 PMCID: PMC5855062 DOI: 10.3389/fchem.2018.00052] [Citation(s) in RCA: 311] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 02/22/2018] [Indexed: 12/26/2022] Open
Abstract
Anthocyanins are a group of polyphenolic pigments that are ubiquitously found in the plant kingdom. In plants, anthocyanins play a role not only in reproduction, by attracting pollinators and seed dispersers, but also in protection against various abiotic and biotic stresses. There is accumulating evidence that anthocyanins have health-promoting properties, which makes anthocyanin metabolism an interesting target for breeders and researchers. In this review, the state of the art knowledge concerning anthocyanins in the Solanaceous vegetables, i.e., pepper, tomato, eggplant, and potato, is discussed, including biochemistry and biological function of anthocyanins, as well as their genetic and environmental regulation. Anthocyanin accumulation is determined by the balance between biosynthesis and degradation. Although the anthocyanin biosynthetic pathway has been well-studied in Solanaceous vegetables, more research is needed on the inhibition of biosynthesis and, in particular, the anthocyanin degradation mechanisms if we want to control anthocyanin content of Solanaceous vegetables. In addition, anthocyanin metabolism is distinctly affected by environmental conditions, but the molecular regulation of these effects is poorly understood. Existing knowledge is summarized and current gaps in our understanding are highlighted and discussed, to create opportunities for the development of anthocyanin-rich crops through breeding and environmental management.
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Affiliation(s)
- Ying Liu
- Plant Breeding, Wageningen University and Research, Wageningen, Netherlands.,Horticulture and Product Physiology, Wageningen University and Research, Wageningen, Netherlands.,Graduate School Production Ecology & Resource Conservation, Wageningen University and Research, Wageningen, Netherlands
| | - Yury Tikunov
- Plant Breeding, Wageningen University and Research, Wageningen, Netherlands
| | - Rob E Schouten
- Horticulture and Product Physiology, Wageningen University and Research, Wageningen, Netherlands
| | - Leo F M Marcelis
- Horticulture and Product Physiology, Wageningen University and Research, Wageningen, Netherlands
| | - Richard G F Visser
- Plant Breeding, Wageningen University and Research, Wageningen, Netherlands
| | - Arnaud Bovy
- Plant Breeding, Wageningen University and Research, Wageningen, Netherlands
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Zhang J, Pan H, Gao Z, Shu B, Qi Y, Yi X, Qin G, Sheng Y, Chen H, Xu Y. Transcriptome analysis of colouration-related genes in two white-fleshed nectarine varieties and their yellow-fleshed mutants. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1438208] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Affiliation(s)
- Jinyun Zhang
- Horticulture Research Institute, Anhui Academy of Agricultural Science, Hefei, Anhui, PR China
| | - Haifa Pan
- Horticulture Research Institute, Anhui Academy of Agricultural Science, Hefei, Anhui, PR China
| | - Zhenghui Gao
- Horticulture Research Institute, Anhui Academy of Agricultural Science, Hefei, Anhui, PR China
| | - Bing Shu
- Horticulture Research Institute, Anhui Academy of Agricultural Science, Hefei, Anhui, PR China
| | - Yongjie Qi
- Horticulture Research Institute, Anhui Academy of Agricultural Science, Hefei, Anhui, PR China
| | - Xingkai Yi
- Horticulture Research Institute, Anhui Academy of Agricultural Science, Hefei, Anhui, PR China
| | - Gaihua Qin
- Horticulture Research Institute, Anhui Academy of Agricultural Science, Hefei, Anhui, PR China
| | - Yu Sheng
- Horticulture Research Institute, Anhui Academy of Agricultural Science, Hefei, Anhui, PR China
| | - Hongli Chen
- Horticulture Research Institute, Anhui Academy of Agricultural Science, Hefei, Anhui, PR China
| | - Yiliu Xu
- Anhui Academy of Agricultural Science, Hefei, Anhui, PR China
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Bonar N, Liney M, Zhang R, Austin C, Dessoly J, Davidson D, Stephens J, McDougall G, Taylor M, Bryan GJ, Hornyik C. Potato miR828 Is Associated With Purple Tuber Skin and Flesh Color. FRONTIERS IN PLANT SCIENCE 2018; 9:1742. [PMID: 30619382 PMCID: PMC6297172 DOI: 10.3389/fpls.2018.01742] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/08/2018] [Indexed: 05/10/2023]
Abstract
Anthocyanins are plant pigments responsible for the colors of many flowers, fruits and storage organs and have roles in abiotic and biotic stress resistance. Anthocyanins and polyphenols are bioactive compounds in plants including potato (Solanum tuberosum L.) which is the most important non-cereal crop in the world, cultivated for its tubers rich in starch and nutrients. The genetic regulation of the flavonoid biosynthetic pathway is relatively well known leading to the formation of anthocyanins. However, our knowledge of post-transcriptional regulation of anthocyanin biosynthesis is limited. There is increasing evidence that micro RNAs (miRNAs) and other small RNAs can regulate the expression level of key factors in anthocyanin production. In this study we have found strong associations between the high levels of miR828, TAS4 D4(-) and purple/red color of tuber skin and flesh. This was confirmed not only in different cultivars but in pigmented and non-pigmented sectors of the same tuber. Phytochemical analyses verified the levels of anthocyanins and polyphenols in different tissues. We showed that miR828 is able to direct cleavage of the RNA originating from Trans-acting siRNA gene 4 (TAS4) and initiate the production of phased small interfering RNAs (siRNAs) whose production depends on RNA-dependent RNA polymerase 6 (RDR6). MYB transcription factors were predicted as potential targets of miR828 and TAS4 D4(-) and their expression was characterized. MYB12 and R2R3-MYB genes showed decreased expression levels in purple skin and flesh in contrast with high levels of small RNAs in the same tissues. Moreover, we confirmed that R2R3-MYB and MYB-36284 are direct targets of the small RNAs. Overall, this study sheds light on the small RNA directed anthocyanin regulation in potato, which is an important member of the Solanaceae family.
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Affiliation(s)
- Nicola Bonar
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Michele Liney
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Runxuan Zhang
- Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Ceri Austin
- Environmental and Biochemical Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Jimmy Dessoly
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Diane Davidson
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Jennifer Stephens
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Gordon McDougall
- Environmental and Biochemical Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Mark Taylor
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Glenn J. Bryan
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Csaba Hornyik
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- *Correspondence: Csaba Hornyik,
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Kilambi HV, Manda K, Rai A, Charakana C, Bagri J, Sharma R, Sreelakshmi Y. Green-fruited Solanum habrochaites lacks fruit-specific carotenogenesis due to metabolic and structural blocks. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4803-4819. [PMID: 29048567 PMCID: PMC5853803 DOI: 10.1093/jxb/erx288] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 07/21/2017] [Indexed: 05/22/2023]
Abstract
Members of the tomato clade exhibit a wide diversity in fruit color, but the mechanisms governing inter-species diversity of coloration are largely unknown. The carotenoid profiles, carotenogenic gene expression and proteome profiles of green-fruited Solanum habrochaites (SH), orange-fruited S. galapagense, and red-fruited S. pimpinellifolium were compared with cultivated tomato [S. lycopersicum cv. Ailsa Craig (SL)] to decipher the molecular basis of coloration diversity. Green-fruited SH, though it showed normal expression of chromoplast-specific phytoene synthase1 and lycopene β-cyclase genes akin to orange/red-fruited species, failed to accumulate lycopene and β-carotene. The SH phytoene synthase1 cDNA encoded an enzymatically active protein, whereas the lycopene β-cyclase cDNA was barely active. Consistent with its green-fruited nature, SH's fruits retained chloroplast structure and PSII activity, and had impaired chlorophyll degradation with high pheophorbide a levels. Comparison of the fruit proteomes with SL revealed retention of the proteome complement related to photosynthesis in SH. Targeted peptide monitoring revealed a low abundance of key carotenogenic and sequestration proteins in SH compared with tomato. The green-fruitedness of SH appears to stem from blocks at several critical steps regulating fruit-specific carotenogenesis namely the absence of chloroplast to chromoplast transformation, block in carotenoid biosynthesis, and a dearth of carotenoid sequestering proteins.
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Affiliation(s)
- Himabindu Vasuki Kilambi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Kalyani Manda
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Avanish Rai
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Chaitanya Charakana
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Jayram Bagri
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Rameshwar Sharma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Yellamaraju Sreelakshmi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
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Koul A, Yogindran S, Sharma D, Kaul S, Rajam MV, Dhar MK. Carotenoid profiling, in silico analysis and transcript profiling of miRNAs targeting carotenoid biosynthetic pathway genes in different developmental tissues of tomato. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 108:412-421. [PMID: 27552179 DOI: 10.1016/j.plaphy.2016.08.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 08/01/2016] [Accepted: 08/01/2016] [Indexed: 06/06/2023]
Abstract
Carotenoid biosynthetic pathway is one of the highly significant and very well elucidated secondary metabolic pathways in plants. microRNAs are the potential regulators, widely known for playing a pivotal role in the regulation of various biological as well as metabolic processes. miRNAs may assist in the metabolic engineering of the secondary metabolites for the production of elite genotypes with increased biomass and content of various metabolites. miRNA mediated regulation of carotenoid biosynthetic genes has not been elucidated so far. To illustrate the potential regulatory role of miRNAs in carotenoid biosynthesis, transcript profiling of the known miRNAs and their possible target carotenoid genes was undertaken at eight different developmental stages of tomato, using stem-loop PCR approach combined with quantitative RT-PCR. The inter-relationship amongst carotenoid content, biosynthetic genes and miRNAs was studied in depth. Comparative expression profiles of miRNA and target genes showed variable expression in different tissues studied. The expression level of miRNAs and their target carotenoid genes displayed similar pattern in the vegetative tissues as compared to the reproductive ones, viz. fruit (different stages), indicating the possibility of regulation of carotenoid biosynthesis at various stages of fruit development. This was later confirmed by the HPLC analysis of the carotenoids. The present study has further enhanced the understanding of regulation of carotenoid biosynthetic pathway in plants. The identified miRNAs can be employed to manipulate the biosynthesis of different carotenoids, through metabolic engineering for the production of lycopene rich tomatoes.
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Affiliation(s)
- Archana Koul
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006, India
| | - Sneha Yogindran
- Department of Genetics, University of Delhi (South Campus), New Delhi, 110021, India
| | - Deepak Sharma
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006, India
| | - Sanjana Kaul
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006, India
| | | | - Manoj K Dhar
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, 180006, India.
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Ng J, Smith SD. How to make a red flower: the combinatorial effect of pigments. AOB PLANTS 2016; 8:plw013. [PMID: 26933150 PMCID: PMC4804202 DOI: 10.1093/aobpla/plw013] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 02/13/2016] [Indexed: 05/21/2023]
Abstract
Red flowers have evolved repeatedly across angiosperms and are frequently examined in an ecological context. However, less is known about the biochemical basis of red colouration in different taxa. In this study, we examine the spectral properties, anthocyanin composition and carotenoid expression of red flowers in the tomato family, Solanaceae, which have evolved independently multiple times across the group. Our study demonstrates that Solanaceae typically make red flowers either by the sole production of red anthocyanins or, more commonly, by the dual production of purple or blue anthocyanins and orange carotenoids. In using carotenoids to modify the effect of purple and/or blue anthocyanins, these Solanaceae species have converged on the same floral hue as those solely producing red anthocyanins, even when considering the visual system of pollinators. The use of blue anthocyanins in red flowers appears to differ from other groups, and suggests that the genetic changes underlying evolutionary shifts to red flowers may not be as predictable as previously suggested.
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Affiliation(s)
- Julienne Ng
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
| | - Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
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