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Panda M, Pradhan S, Mukherjee PK. Transcriptomics reveal useful resources for examining fruit development and variation in fruit size in Coccinia grandis. FRONTIERS IN PLANT SCIENCE 2024; 15:1386041. [PMID: 38863541 PMCID: PMC11165041 DOI: 10.3389/fpls.2024.1386041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 05/09/2024] [Indexed: 06/13/2024]
Abstract
Introduction The Cucurbitaceae family comprises many agronomically important members, that bear nutritious fruits and vegetables of great economic importance. Coccinia grandis, commonly known as Ivy gourd, belongs to this family and is widely consumed as a vegetable. Members of this family are known to display an impressive range of variation in fruit morphology. Although there have been studies on flower development in Ivy gourd, fruit development remains unexplored in this crop. Methods In this study, comparative transcriptomics of two Ivy gourd cultivars namely "Arka Neelachal Kunkhi" (larger fruit size) and "Arka Neelachal Sabuja" (smaller fruit size) differing in their average fruit size was performed. A de novo transcriptome assembly for Ivy gourd was developed by collecting fruits at different stages of development (5, 10, 15, and 20 days after anthesis i.e. DAA) from these two varieties. The transcriptome was analyzed to identify differentially expressed genes, transcription factors, and molecular markers. Results The transcriptome of Ivy gourd consisted of 155205 unigenes having an average contig size of 1472bp. Unigenes were annotated on publicly available databases to categorize them into different biological functions. Out of these, 7635 unigenes were classified into 38 transcription factor (TF) families, of which Trihelix TFs were most abundant. A total of 11,165 unigenes were found to be differentially expressed in both the varieties and the in silico expression results were validated through real-time PCR. Also, 98768 simple sequence repeats (SSRs) were identified in the transcriptome of Ivy gourd. Discussion This study has identified a number of genes, including transcription factors, that could play a crucial role in the determination of fruit shape and size in Ivy gourd. The presence of polymorphic SSRs indicated a possibility for marker-assisted selection for crop breeding in Ivy gourd. The information obtained can help select candidate genes that may be implicated in regulating fruit development and size in other fruit crops.
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Affiliation(s)
- Mitrabinda Panda
- Biotechnology Research Innovation Council-Institute of Life Sciences (BRIC-ILS), Bhubaneswar, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Seema Pradhan
- Biotechnology Research Innovation Council-Institute of Life Sciences (BRIC-ILS), Bhubaneswar, India
| | - Pulok K. Mukherjee
- Biotechnology Research Innovation Council-Institute of Bioresources and Sustainable Development (BRIC-IBSD), Imphal, India
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Jagram N, Dasgupta I. Principles and practice of virus induced gene silencing for functional genomics in plants. Virus Genes 2023; 59:173-187. [PMID: 36266497 DOI: 10.1007/s11262-022-01941-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 10/05/2022] [Indexed: 10/24/2022]
Abstract
Virus induced gene silencing (VIGS) has, of late, emerged as an important tool for transient silencing of genes in plants. This is now being increasingly used to determine functions of novel genes in a wide variety of plants, many of which are important crops yielding food and fiber or are sources of products having pharmaceutical uses. The technology for VIGS comprises the development of vectors derived from viruses, choosing the optimal orientation and size of the gene to be targeted and adopting the most suitable method of inoculation. This review gives a brief overview of the main aspects of VIGS technology as is being practiced. It also discusses the challenges the technology faces and the possible way ahead to improve its robustness, so that the technology finds wider applications.
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Affiliation(s)
- Neelam Jagram
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Indranil Dasgupta
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
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Zhang S, Tan FQ, Chung CH, Slavkovic F, Devani RS, Troadec C, Marcel F, Morin H, Camps C, Gomez Roldan MV, Benhamed M, Dogimont C, Boualem A, Bendahmane A. The control of carpel determinacy pathway leads to sex determination
in cucurbits. Science 2022; 378:543-549. [DOI: 10.1126/science.add4250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Male and female unisexual flowers evolved from hermaphroditic ancestors, and control of flower sex is useful for plant breeding. We isolated a female-to-male sex transition mutant in melon and identified the causal gene as the carpel identity gene
CRABS CLAW (CRC)
. We show that the master regulator of sex determination in cucurbits, the transcription factor
WIP1
whose expression orchestrates male flower development, recruits the corepressor TOPLESS to the
CRC
promoter to suppress its expression through histone deacetylation. Impairing TOPLESS-WIP1 physical interaction leads to
CRC
expression, carpel determination, and consequently the expression of the stamina inhibitor, the aminocyclopropane-1-carboxylic acid synthase 7 (
CmACS7
), leading to female flower development. Our findings suggest that sex genes evolved to interfere with flower meristematic function, leading to unisexual flower development.
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Affiliation(s)
- Siqi Zhang
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2); 91190 Gif sur Yvette, France
| | - Feng-Quan Tan
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2); 91190 Gif sur Yvette, France
| | - Ching-Hui Chung
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2); 91190 Gif sur Yvette, France
| | - Filip Slavkovic
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2); 91190 Gif sur Yvette, France
| | - Ravi Sureshbhai Devani
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2); 91190 Gif sur Yvette, France
| | - Christelle Troadec
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2); 91190 Gif sur Yvette, France
| | - Fabien Marcel
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2); 91190 Gif sur Yvette, France
| | - Halima Morin
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2); 91190 Gif sur Yvette, France
| | - Céline Camps
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2); 91190 Gif sur Yvette, France
| | - Maria Victoria Gomez Roldan
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2); 91190 Gif sur Yvette, France
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2); 91190 Gif sur Yvette, France
| | - Catherine Dogimont
- INRAE, Génétique et Amélioration des Fruits et Légumes (GAFL), 84143 Montfavet, France
| | - Adnane Boualem
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2); 91190 Gif sur Yvette, France
| | - Abdelhafid Bendahmane
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2); 91190 Gif sur Yvette, France
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