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Guan H, Yang X, Lin Y, Xie B, Zhang X, Ma C, Xia R, Chen R, Hao Y. The hormone regulatory mechanism underlying parthenocarpic fruit formation in tomato. FRONTIERS IN PLANT SCIENCE 2024; 15:1404980. [PMID: 39119498 PMCID: PMC11306060 DOI: 10.3389/fpls.2024.1404980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 07/05/2024] [Indexed: 08/10/2024]
Abstract
Parthenocarpic fruits, known for their superior taste and reliable yields in adverse conditions, develop without the need for fertilization or pollination. Exploring the physiological and molecular mechanisms behind parthenocarpic fruit development holds both theoretical and practical significance, making it a crucial area of study. This review examines how plant hormones and MADS-box transcription factors control parthenocarpic fruit formation. It delves into various aspects of plant hormones-including auxin, gibberellic acid, cytokinins, ethylene, and abscisic acid-ranging from external application to biosynthesis, metabolism, signaling pathways, and their interplay in influencing parthenocarpic fruit development. The review also explores the involvement of MADS family gene functions in these processes. Lastly, we highlight existing knowledge gaps and propose directions for future research on parthenocarpy.
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Affiliation(s)
- Hongling Guan
- College of Horticulture, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, School of Biology and Agriculture, Shaoguan University, Shaoguan, China
| | - Xiaolong Yang
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Yuxiang Lin
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Baoxing Xie
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xinyue Zhang
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Chongjian Ma
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, School of Biology and Agriculture, Shaoguan University, Shaoguan, China
| | - Rui Xia
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Riyuan Chen
- College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Yanwei Hao
- College of Horticulture, South China Agricultural University, Guangzhou, China
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2
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Gaccione L, Martina M, Barchi L, Portis E. A Compendium for Novel Marker-Based Breeding Strategies in Eggplant. PLANTS (BASEL, SWITZERLAND) 2023; 12:1016. [PMID: 36903876 PMCID: PMC10005326 DOI: 10.3390/plants12051016] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/06/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
The worldwide production of eggplant is estimated at about 58 Mt, with China, India and Egypt being the major producing countries. Breeding efforts in the species have mainly focused on increasing productivity, abiotic and biotic tolerance/resistance, shelf-life, the content of health-promoting metabolites in the fruit rather than decreasing the content of anti-nutritional compounds in the fruit. From the literature, we collected information on mapping quantitative trait loci (QTLs) affecting eggplant's traits following a biparental or multi-parent approach as well as genome-wide association (GWA) studies. The positions of QTLs were lifted according to the eggplant reference line (v4.1) and more than 700 QTLs were identified, here organized into 180 quantitative genomic regions (QGRs). Our findings thus provide a tool to: (i) determine the best donor genotypes for specific traits; (ii) narrow down QTL regions affecting a trait by combining information from different populations; (iii) pinpoint potential candidate genes.
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3
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Kaur H, Manchanda P, Kumar P, Dhall RK, Chhuneja P, Weng Y. Genome-wide identification and characterization of parthenocarpic fruit set-related gene homologs in cucumber (Cucumis sativus L.). Sci Rep 2023; 13:2403. [PMID: 36765113 PMCID: PMC9918540 DOI: 10.1038/s41598-023-29660-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Cucumber (Cucumis sativus L.), a major horticultural crop, in the family Cucurbitaceae is grown and consumed globally. Parthenocarpy is an ideal trait for many fruit and vegetables which produces seedless fruit desired by consumers. The seedlessness occurs when fruit develops without fertilization which can be either natural or induced. So far, a limited number of genes regulating parthenocarpic fruit set have been reported in several fruit or vegetable crops, most of which are involved in hormone biosynthesis or signalling. Although parthenocarpic cucumber has been widely used in commercial production for a long time; its genetic basis is not well understood. In this study, we retrieved thirty five parthenocarpy fruit-set related genes (PRGs) from bibliomic data in various plants. Thirty-five PRG homologs were identified in the cucumber genome via homology-based search. An in silico analysis was performed on phylogenetic tree, exon-intron structure, cis-regulatory elements in the promoter region, and conserved domains of their deduced proteins, which provided insights into the genetic make-up of parthenocarpy-related genes in cucumber. Simple sequence repeat (SSR) sequences were mined in these PRGs, and 31 SSR markers were designed. SSR genotyping identified three SSRs in two polymorphic genes. Quantitative real-time PCR of selected genes was conducted in five cucumber lines with varying degrees of parthenocarpic fruit set capacities, which revealed possible association of their expression with parthenocarpy. The results revealed that homologs CsWD40 and CsPIN-4 could be considered potential genes for determination of parthenocarpy as these genes showed parental polymorphism and differential gene expression in case of parthenocarpic and non-parthenocarpic parents.
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Affiliation(s)
- Harleen Kaur
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India
| | - Pooja Manchanda
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India.
| | - Pankaj Kumar
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India
| | - Rajinder Kumar Dhall
- Department of Vegetable Science, College of Horticulture and Forestry, Punjab Agricultural University, Ludhiana, 141004, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141004, India
| | - Yiqun Weng
- USDA-ARS Vegetable Crops Research Unit, Department of Horticulture, University of Wisconsin, Madison, WI, 53706, USA
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Montoya C, Mejia-Alvarado FS, Botero-Rozo D, Ayala-Diaz IM, Romero HM. Parthenocarpy-related genes induced by naphthalene acetic acid in oil palm interspecific O × G [ Elaeis oleifera (Kunth) Cortés × Elaeis guineensis Jacq.] hybrids. Front Genet 2023; 14:1099489. [PMID: 37021004 PMCID: PMC10067579 DOI: 10.3389/fgene.2023.1099489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 03/08/2023] [Indexed: 04/07/2023] Open
Abstract
Parthenocarpy is the development without fertilization of seedless fruits. In the oil palm industry, the development of parthenocarpic fruits is considered an attractive option to increase palm oil production. Previous studies have shown the application of synthetic auxins in Elaeis guineensis, and interspecific O×G hybrids (Elaeis oleifera (Kunth) Cortés × E. guineensis Jacq.) induces parthenocarpy. The aim of this study was to identify the molecular mechanism through transcriptomics and biology system approach to responding to how the application of NAA induces parthenocarpic fruits in oil palm O×G hybrids. The transcriptome changes were studied in three phenological stages (PS) of the inflorescences: i) PS 603, pre-anthesis III, ii) PS 607, anthesis, and iii) PS 700, fertilized female flower. Each PS was treated with NAA, Pollen, and control (any application). The expression profile was studied at three separate times: five minutes (T0), 24 hours (T1), and 48 h post-treatment (T2). The RNA sequencing (RNA seq) approach was used with 27 oil palm O×G hybrids for a total of 81 raw samples. RNA-Seq showed around 445,920 genes. Numerous differentially expressed genes (DEGs) were involved in pollination, flowering, seed development, hormone biosynthesis, and signal transduction. The expression of the most relevant transcription factors (TF) families was variable and dependent on the stage and time post-treatment. In general, NAA treatment expressed differentially more genes than Pollen. Indeed, the gene co-expression network of Pollen was built with fewer nodes than the NAA treatment. The transcriptional profiles of Auxin-responsive protein and Gibberellin-regulated genes involved in parthenocarpy phenomena agreed with those previously reported in other species. The expression of 13 DEGs was validated by RT-qPCR analysis. This detailed knowledge about the molecular mechanisms involved in parthenocarpy could be used to facilitate the future development of genome editing techniques that enable the production of parthenocarpic O×G hybrid cultivars without growth regulator application.
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Affiliation(s)
- Carmenza Montoya
- Oil Palm Biology and Breeding Research Program, Colombian Oil Palm Research Center—Cenipalma, Bogotá, Colombia
| | | | - David Botero-Rozo
- Oil Palm Biology and Breeding Research Program, Colombian Oil Palm Research Center—Cenipalma, Bogotá, Colombia
| | - Ivan Mauricio Ayala-Diaz
- Oil Palm Biology and Breeding Research Program, Colombian Oil Palm Research Center—Cenipalma, Bogotá, Colombia
| | - Hernan Mauricio Romero
- Oil Palm Biology and Breeding Research Program, Colombian Oil Palm Research Center—Cenipalma, Bogotá, Colombia
- Department of Biology, Universidad Nacional de Colombia, Bogotá, Colombia
- *Correspondence: Hernan Mauricio Romero,
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Vignati E, Lipska M, Dunwell JM, Caccamo M, Simkin AJ. Options for the generation of seedless cherry, the ultimate snacking product. PLANTA 2022; 256:90. [PMID: 36171415 PMCID: PMC9519733 DOI: 10.1007/s00425-022-04005-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/21/2022] [Indexed: 05/09/2023]
Abstract
This manuscript identifies cherry orthologues of genes implicated in the development of pericarpic fruit and pinpoints potential options and restrictions in the use of these targets for commercial exploitation of parthenocarpic cherry fruit. Cherry fruit contain a large stone and seed, making processing of the fruit laborious and consumption by the consumer challenging, inconvenient to eat 'on the move' and potentially dangerous for children. Availability of fruit lacking the stone and seed would be potentially transformative for the cherry industry, since such fruit would be easier to process and would increase consumer demand because of the potential reduction in costs. This review will explore the background of seedless fruit, in the context of the ambition to produce the first seedless cherry, carry out an in-depth analysis of the current literature around parthenocarpy in fruit, and discuss the available technology and potential for producing seedless cherry fruit as an 'ultimate snacking product' for the twenty-first century.
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Affiliation(s)
- Edoardo Vignati
- NIAB East Malling, Department of Genetics, Genomics and Breeding, New Road, West Malling, Kent, ME19 6BJ, UK
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading, Berkshire, RG6 6EU, UK
| | - Marzena Lipska
- NIAB East Malling, Department of Genetics, Genomics and Breeding, New Road, West Malling, Kent, ME19 6BJ, UK
| | - Jim M Dunwell
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading, Berkshire, RG6 6EU, UK
| | - Mario Caccamo
- NIAB, Cambridge Crop Research, Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Andrew J Simkin
- NIAB East Malling, Department of Genetics, Genomics and Breeding, New Road, West Malling, Kent, ME19 6BJ, UK.
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
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Htwe YM, Shi P, Zhang D, Li Z, Xiao Y, Yang Y, Lei X, Wang Y. Programmed Cell Death May Be Involved in the Seedless Phenotype Formation of Oil Palm. FRONTIERS IN PLANT SCIENCE 2022; 13:832017. [PMID: 35401608 PMCID: PMC8984474 DOI: 10.3389/fpls.2022.832017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Oil palm (Elaeis guineensis Jacq.) is a well-known vegetable oil-yielding crop. Seedlessness is one of the most prominent traits in oil palm due to its low processing costs and high oil content. Nevertheless, an extensive study on molecular mechanisms regulating seedless phenotype formation in oil palm is very limited so far. In this study, stigma, style, and ovary from seedless and seeded (Tenera and Pisifera) oil palm trees were used to investigate the possible mechanism. Results showed that non-pollination resulted in no fruits, and self- and cross-pollinations resulted in seedless fruits, while boron treatment had no effect on seedless phenotype formation, implying that seedless trees have incomplete self and outcrossing incompatibility. Furthermore, the transcriptome data analysis highlighted eight programmed cell death (PCD) genes and three groups of PCD-related genes: 4-coumarate-CoA ligase (4CL), S-RNase, and MADS-box. The majority of these genes were significantly up-regulated in the stigma and style of Seedless palm trees compared to Tenera and Pisifera. In addition, the co-expression network analysis confirmed the significant correlation among these genes. Moreover, two simple sequence repeats (SSR) markers (S41 and S44) were developed to identify the seedless phenotype. The up-regulation of 4CL and MADS-box TFs activated the expression of PCD genes; on the other hand, S-RNase resulted in pollen tube RNA degradation and triggered PCD. While the link between PCD and seedless phenotype formation in oil palm has not been extensively studied to date, these findings suggest a role of PCD in pollen tube lethality, leading to double fertilization failure and the seedless phenotype.
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Affiliation(s)
- Yin Min Htwe
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Peng Shi
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Dapeng Zhang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Zhiying Li
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Yong Xiao
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Yaodong Yang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Xintao Lei
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- Tropical Crops Genetic Resources Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Yong Wang
- Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
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Zhang S, Gu X, Shao J, Hu Z, Yang W, Wang L, Su H, Zhu L. Auxin Metabolism Is Involved in Fruit Set and Early Fruit Development in the Parthenocarpic Tomato "R35-P". FRONTIERS IN PLANT SCIENCE 2021; 12:671713. [PMID: 34408758 PMCID: PMC8365229 DOI: 10.3389/fpls.2021.671713] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Parthenocarpic tomato can set fruit and develop without pollination and exogenous hormone treatments under unfavorable environmental conditions, which is beneficial to tomato production from late fall to early spring in greenhouses. In this study, the endogenous hormones in the ovaries of the parthenocarpic tomato line "R35-P" (stigma removed or self-pollination) and the non-parthenocarpic tomato line "R35-N" (self-pollination) at four stages between preanthesis and postanthesis investigated, using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). A nearly twofold IAA (indoleacetic acid) content was found in "R35-P" rather than in "R35-N" at -2 and 0 days after anthesis (DAA). Except at -2 DAA, a lower ABA (abscisic acid) content was observed in Pe (stigma removed in "R35-P") compared to that in Ps (self-pollination in "R35-P") or CK (self-pollination in "R35-N"). After pollination, although the content of GA1 (gibberellins acid 1) in CK increased, the levels of GAs (gibberellins acids) were notably low. At all four stages, a lower SA (salicylic acid) content was found in Ps and CK than in Pe, while the content and the change trend were similar in Ps and CK. The variation tendencies of JA (jasmonic acid) varied among Pe, Ps, and CK at the studied periods. Furthermore, KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analyses of transcriptomic data identified 175 differentially expressed genes (DEGs) related to plant hormone signal transduction, including 63 auxin-related genes, 27 abscisic acid-related genes, 22 ethylene-related genes, 16 cytokinin-related genes, 16 salicylic acid-related genes, 14 brassinosteroid-related genes, 13 jasmonic acid-related genes, and 4 gibberellin-related genes at -2 DAA and 0 DAA. Our results suggest that the fate of a fruit set or degeneration occurred before anthesis in tomato. Auxins, whose levels were independent of pollination and fertilization, play prominent roles in controlling a fruit set in "R35-P," and other hormones are integrated in a synergistic or antagonistic way.
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Affiliation(s)
- Shaoli Zhang
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), College of Agriculture, Ludong University, Yantai, China
- Institute of Vegetable, Gansu Academy of Agricultural Science, Lanzhou, China
| | - Xin Gu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Jingcheng Shao
- Institute of Vegetable, Gansu Academy of Agricultural Science, Lanzhou, China
| | - Zhifeng Hu
- Institute of Vegetable, Gansu Academy of Agricultural Science, Lanzhou, China
| | - Wencai Yang
- College of Horticulture, China Agricultural University, Beijing, China
| | - Liping Wang
- Agricultural and Rural Bureau of Shouguang, Shouguang, China
| | - Hongyan Su
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), College of Agriculture, Ludong University, Yantai, China
| | - Luying Zhu
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong (Ludong University), College of Agriculture, Ludong University, Yantai, China
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Backiyarani S, Sasikala R, Sharmiladevi S, Uma S. Decoding the molecular mechanism of parthenocarpy in Musa spp. through protein-protein interaction network. Sci Rep 2021; 11:14592. [PMID: 34272422 PMCID: PMC8285514 DOI: 10.1038/s41598-021-93661-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/08/2021] [Indexed: 02/06/2023] Open
Abstract
Banana, one of the most important staple fruit among global consumers is highly sterile owing to natural parthenocarpy. Identification of genetic factors responsible for parthenocarpy would facilitate the conventional breeders to improve the seeded accessions. We have constructed Protein-protein interaction (PPI) network through mining differentially expressed genes and the genes used for transgenic studies with respect to parthenocarpy. Based on the topological and pathway enrichment analysis of proteins in PPI network, 12 candidate genes were shortlisted. By further validating these candidate genes in seeded and seedless accession of Musa spp. we put forward MaAGL8, MaMADS16, MaGH3.8, MaMADS29, MaRGA1, MaEXPA1, MaGID1C, MaHK2 and MaBAM1 as possible target genes in the study of natural parthenocarpy. In contrary, expression profile of MaACLB-2 and MaZEP is anticipated to highlight the difference in artificially induced and natural parthenocarpy. By exploring the PPI of validated genes from the network, we postulated a putative pathway that bring insights into the significance of cytokinin mediated CLAVATA(CLV)-WUSHEL(WUS) signaling pathway in addition to gibberellin mediated auxin signaling in parthenocarpy. Our analysis is the first attempt to identify candidate genes and to hypothesize a putative mechanism that bridges the gaps in understanding natural parthenocarpy through PPI network.
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Affiliation(s)
- Suthanthiram Backiyarani
- grid.465009.e0000 0004 1768 7371ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirapalli, Tamil Nadu 620 102 India
| | - Rajendran Sasikala
- grid.465009.e0000 0004 1768 7371ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirapalli, Tamil Nadu 620 102 India
| | - Simeon Sharmiladevi
- grid.465009.e0000 0004 1768 7371ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirapalli, Tamil Nadu 620 102 India
| | - Subbaraya Uma
- grid.465009.e0000 0004 1768 7371ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirapalli, Tamil Nadu 620 102 India
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Transcriptome Analysis of Eggplant Root in Response to Root-Knot Nematode Infection. Pathogens 2021; 10:pathogens10040470. [PMID: 33924485 PMCID: PMC8069755 DOI: 10.3390/pathogens10040470] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/31/2021] [Accepted: 04/09/2021] [Indexed: 12/22/2022] Open
Abstract
Eggplant (Solanum melongena L.), which belongs to the Solanaceae family, is an important vegetable crop. However, its production is severely threatened by root-knot nematodes (RKNs) in many countries. Solanum torvum, a wild relative of eggplant, is employed worldwide as rootstock for eggplant cultivation due to its resistance to soil-borne diseases such as RKNs. In this study, to identify the RKN defense mechanisms, the transcriptomic profiles of eggplant and Solanum torvum were compared. A total of 5360 differentially expressed genes (DEGs) were identified for the response to RKN infection. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that these DEGs are mainly involved in the processes of response to stimulus, protein phosphorylation, hormone signal transduction, and plant-pathogen interaction pathways. Many phytohormone-related genes and transcription factors (MYB, WRKY, and NAC) were differentially expressed at the four time points (ck, 7, 14, and 28 days post-infection). The abscisic acid signaling pathway might be involved in plant-nematode interactions. qRT-PCR validated the expression levels of some of the DEGs in eggplant. These findings demonstrate the nematode-induced expression profiles and provide some insights into the nematode resistance mechanism in eggplant.
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10
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Vidović M, Ćuković K. Isolation of high-quality RNA from recalcitrant leaves of variegated and resurrection plants. 3 Biotech 2020; 10:286. [PMID: 32550105 DOI: 10.1007/s13205-020-02279-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/25/2020] [Indexed: 01/16/2023] Open
Abstract
Resurrection plant Ramonda serbica is a suitable model to investigate mechanisms of desiccation tolerance, while variegated Pelargonium zonale has been proven to serve as an excellent model for the metabolite allocation between sink tissue and source tissue within the same organ. However, the genomes of these plants are still not sequenced, limiting their application in molecular studies. To investigate the transcript abundance by next-generation sequencing, high-quality RNA input is required. Leaves of both P. zonale and R. serbica are rich in polyphenols that interfere with high-quality RNA extraction by common protocols. Moreover, low water content and high amount of sugars and other osmoprotectants in desiccated R. serbica leaves present the additional challenge in total RNA extraction. Here, we evaluated and compared several already established TRIzol- and CTAB-based protocols aiming to develop the efficient, simple and low-cost methods for the extraction of the satisfactory yield RNA of great purity and integrity, required for the construction of high-quality cDNA libraries. Our results show that the CTAB-based protocol (i.e. CTAB 1b) enabled the extraction of high-quality RNA from photosynthetically active and non-photosynthetically active leaf sectors of P. zonale, with high RIN values. On the other hand, TRIzol-based protocol provided a high RNA yield with low contamination and high RNA integrity even in desiccated leaves of R. serbica. We envisage that the proposed protocol would be suitable for the RNA extractions from other desiccated organs (e.g. seeds, grains, pollen grains).
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Affiliation(s)
- Marija Vidović
- Department of Life Science, University of Belgrade, Institute for Multidisciplinary Research, Kneza Višeslava 1, Belgrade, 11030 Serbia
| | - Katarina Ćuković
- Department of Plant Physiology, Institute for Biological Research "Siniša Stanković"-National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
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11
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Koryznienė D, Jurkonienė S, Žalnierius T, Gavelienė V, Jankovska-Bortkevič E, Bareikienė N, Būda V. Heracleum sosnowskyi seed development under the effect of exogenous application of GA 3. PeerJ 2019; 7:e6906. [PMID: 31119089 PMCID: PMC6511387 DOI: 10.7717/peerj.6906] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/03/2019] [Indexed: 11/20/2022] Open
Abstract
Numerous studies have demonstrated the impact of exogenous gibberellin on fleshy fruit formation, but the effect on dry fruits is not yet well known. To test the role of gibberellin (GA3) in dry fruit formation, we analysed the impact of exogenous GA3 on the invasive plant Sosnowsky’s hogweed (H. sosnowskyi Manden.) seed development and germination. Treatment of GA3 concentrations of 0.07 mM, 0.14 mM, 0.28 mM, 0.43 mM was applied to flowers at the early stage of development. Seeds were collected from treated satellite umbels. It was observed that GA3treatment did not have a significant effect on the size of H. sosnowskyi seeds, but caused various changes in their shape. The data on semi-thin longitudinal sections of H. sosnowskyi mericarps and SEM micrographs of embryos showed that the embryos in GA3 (0.43 mM) treated variants were at torpedo stage, while in control variants—mature embryos. The germination of seeds of each variant was estimated by burying them in the soil. Our studies indicated that GA3 application reduced the germination of H. sosnowskyi seed from 98.0% (control) to 16.5% (GA3 concentration 0.43 mM). It was assumed that exogenous application of GA3 had influence on the development of dry Sosnowsky’s hogweed seeds and could be used to inhibit the spread of this invasive plant.
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Affiliation(s)
| | | | | | | | | | | | - Vincas Būda
- Institute of Ecology, Nature Research Centre, Vilnius, Lithuania
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Vergara-Pulgar C, Rothkegel K, González-Agüero M, Pedreschi R, Campos-Vargas R, Defilippi BG, Meneses C. De novo assembly of Persea americana cv. 'Hass' transcriptome during fruit development. BMC Genomics 2019; 20:108. [PMID: 30727956 PMCID: PMC6364401 DOI: 10.1186/s12864-019-5486-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 01/28/2019] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Avocado (Persea americana Mill.) is a basal angiosperm from the Lauraceae family. This species has a diploid genome with an approximated size of ~ 920 Mbp and produces a climacteric, fleshy and oily fruit. The flowering and fruit set are particularly prolonged processes, lasting between one to three months, generating important differences in physiological ages of the fruit within the same tree. So far there is no detailed genomic information regarding this species, being the cultivar 'Hass' especially important for avocado growers worldwide. With the aim to explore the fruit avocado transcriptome and to identify candidate biomarkers to monitore fruit development, we carried out an RNA-Seq approach during 4 stages of 'Hass' fruit development: 150 days after fruit set (DAFS), 240 DAFS, 300 DAFS (harvest) and 390 DAFS (late-harvest). RESULTS The 'Hass' de novo transcriptome contains 62,203 contigs (x̅=988 bp, N50 = 1050 bp). We found approximately an 85 and 99% of complete ultra-conserved genes in eukaryote and plantae database using BUSCO (Benchmarking Universal Single-Copy Orthologs) and CEGMA (Core Eukaryotic Gene Mapping Approach), respectively. Annotation was performed with BLASTx, resulting in a 58% of annotated contigs (90% of differentially expressed genes were annotated). Differentially expressed genes analysis (DEG; with False Discovery Rate ≤ 0.01) found 8672 genes considering all developmental stages. From this analysis, genes were clustered according to their expression pattern and 1209 genes show correlation with the four developmental stages. CONCLUSIONS Candidate genes are proposed as possible biomarkers for monitoring the development of the 'Hass' avocado fruit associated with lipid metabolism, ethylene signaling pathway, auxin signaling pathway, and components of the cell wall.
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Affiliation(s)
- Cristian Vergara-Pulgar
- Facultad de Ciencias de la Vida, Centro de Biotecnología Vegetal, Universidad Andres Bello, Avenida República 330, 8370035, Santiago, RM, Chile
| | - Karin Rothkegel
- Facultad de Ciencias de la Vida, Centro de Biotecnología Vegetal, Universidad Andres Bello, Avenida República 330, 8370035, Santiago, RM, Chile
| | - Mauricio González-Agüero
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11610, La Pintana, 831314, Santiago, RM, Chile
| | - Romina Pedreschi
- Escuela de Agronomía, Pontificia Universidad Católica de Valparaíso, Quillota, Chile
| | - Reinaldo Campos-Vargas
- Facultad de Ciencias de la Vida, Centro de Biotecnología Vegetal, Universidad Andres Bello, Avenida República 330, 8370035, Santiago, RM, Chile
| | - Bruno G Defilippi
- Instituto de Investigaciones Agropecuarias, INIA-La Platina, Santa Rosa 11610, La Pintana, 831314, Santiago, RM, Chile.
| | - Claudio Meneses
- Facultad de Ciencias de la Vida, Centro de Biotecnología Vegetal, Universidad Andres Bello, Avenida República 330, 8370035, Santiago, RM, Chile.
- FONDAP Center for Genome Regulation, Santiago, Chile.
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Somyong S, Walayaporn K, Jomchai N, Naktang C, Yodyingyong T, Phumichai C, Pootakham W, Tangphatsornruang S. Transcriptome analysis of oil palm inflorescences revealed candidate genes for an auxin signaling pathway involved in parthenocarpy. PeerJ 2018; 6:e5975. [PMID: 30588395 PMCID: PMC6301279 DOI: 10.7717/peerj.5975] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 10/19/2018] [Indexed: 12/15/2022] Open
Abstract
Oil palm parthenocarpic fruits, which are produced without fertilization, can be targeted to increase oil content because the majority of the fruit is occupied by mesocarp, the part in which palm oil is stored. Consequently, gaining an understanding of the parthenocarpic mechanism would be instrumental for producing parthenocarpic oil palm. This study aims to determine effects of auxin treatment and analyze differentially expressed genes in oil palm pistils at the pollination/anthesis stage, using an RNA sequencing (RNA seq) approach. The auxin treatment caused 100% parthenocarpy when auxin was sprayed before stigmas opened. The parthenocarpy decreased to 55%, 8% and 5% when the auxin was sprayed 1, 2 and 3 days after the opening of stigmas, respectively. Oil palm plants used for RNA seq were plants untreated with auxin as controls and auxin-treated plants on the day before pollination and 1 day after pollination. The number of raw reads ranged from 8,425,859 to 11,811,166 reads, with an average size ranging from 99 to 137 base pairs (bp). When compared with the oil palm transcriptome, the mapped reads ranged from 8,179,948 to 11,320,799 reads, representing 95.85–98.01% of the oil palm matching. Based on five comparisons between RNA seq of treatments and controls, and confirmation using reverse transcription polymerase chain reaction and quantitative real-time RT-PCR expression, five candidate genes, including probable indole-3-acetic acid (IAA)-amido synthetase GH3.8 (EgGH3.8), IAA-amido synthetase GH3.1 (EgGH3.1), IAA induced ARG7 like (EgARG7), tryptophan amino transferase-related protein 3-like (EgTAA3) and flavin-containing monooxygenase 1 (EgFMO1), were differentially expressed between auxin-treated and untreated samples. This evidence suggests a pathway of parthenocarpic fruit development at the beginning of fruit development. However, more research is needed to identify which genes are definitely involved in parthenocarpy.
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Affiliation(s)
- Suthasinee Somyong
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Kitti Walayaporn
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand.,Interdisciplinary Graduate Program in Genetic Engineering and Bioinformatics, Kasetsart University, Bangkok, Thailand
| | - Nukoon Jomchai
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Chaiwat Naktang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Tanapong Yodyingyong
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, Bangkok, Thailand
| | - Chalermpol Phumichai
- Department of Agronomy, Faculty of Agriculture, Kasetsart University, Bangkok, Thailand
| | - Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, Thailand
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Joldersma D, Liu Z. The making of virgin fruit: the molecular and genetic basis of parthenocarpy. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:955-962. [PMID: 29325151 PMCID: PMC6018997 DOI: 10.1093/jxb/erx446] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 11/25/2017] [Indexed: 05/16/2023]
Abstract
Fruit set-the commitment of an angiosperm plant to develop fruit-is a key developmental process that normally occurs following successful fertilization. Parthenocarpy arises when fruit automatically develop in the absence of fertilization. This review uses parthenocarpic fruit development as a focal device through which to recapitulate and understand the molecular effectors that mediate and regulate fruit set. The review demonstrates that studies of parthenocarpy are providing vital insight into plant development, signaling and, potentially, high-value agricultural products.
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Affiliation(s)
- Dirk Joldersma
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
- Correspondence:
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