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Qian M, Fan Y, Li Y, Liu M, Sun W, Duan H, Yu M, Chang W, Niu Y, Li X, Liang Y, Qu C, Li J, Lu K. Genome-wide association study and transcriptome comparison reveal novel QTL and candidate genes that control petal size in rapeseed. J Exp Bot 2021; 72:3597-3610. [PMID: 33712842 DOI: 10.1093/jxb/erab105] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Petal size determines the value of ornamental plants, and thus their economic value. However, the molecular mechanisms controlling petal size remain unclear in most non-model species. To identify quantitative trait loci and candidate genes controlling petal size in rapeseed (Brassica napus), we performed a genome-wide association study (GWAS) using data from 588 accessions over three consecutive years. We detected 16 significant single nucleotide polymorphisms (SNPs) associated with petal size, with the most significant SNPs located on chromosomes A05 and C06. A combination of GWAS and transcriptomic sequencing based on two accessions with contrasting differences in petal size identified 52 differentially expressed genes (DEGs) that may control petal size variation in rapeseed. In particular, the rapeseed gene BnaA05.RAP2.2, homologous to Arabidopsis RAP2.2, may be critical to the negative control of petal size through the ethylene signaling pathway. In addition, a comparison of petal epidermal cells indicated that petal size differences between the two contrasting accessions were determined mainly by differences in cell number. Finally, we propose a model for the control of petal size in rapeseed through ethylene and cytokinin signaling pathways. Our results provide insights into the genetic mechanisms regulating petal size in flowering plants.
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Affiliation(s)
- Mingchao Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Yonghai Fan
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Yanhua Li
- Institute of Characteristic Crop Research, Chongqing Academy of Agricultural Sciences, Chongqing 402160, China
| | - Miao Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Wei Sun
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Huichun Duan
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Mengna Yu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Wei Chang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Yue Niu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Xiaodong Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Ying Liang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Cunmin Qu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
| | - Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing 400715, China
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Dos Santos CP, Batista MC, da Cruz Saraiva KD, Roque ALM, de Souza Miranda R, Alexandre E Silva LM, Moura CFH, Alves Filho EG, Canuto KM, Costa JH. Transcriptome analysis of acerola fruit ripening: insights into ascorbate, ethylene, respiration, and softening metabolisms. Plant Mol Biol 2019; 101:269-296. [PMID: 31338671 DOI: 10.1007/s11103-019-00903-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 07/15/2019] [Indexed: 06/10/2023]
Abstract
The first transcriptome coupled to metabolite analyses reveals major trends during acerola fruit ripening and shed lights on ascorbate, ethylene signalling, cellular respiration, sugar accumulation, and softening key regulatory genes. Acerola is a fast growing and ripening fruit that exhibits high amounts of ascorbate. During ripening, the fruit experience high respiratory rates leading to ascorbate depletion and a quickly fragile and perishable state. Despite its growing economic importance, understanding of its developmental metabolism remains obscure due to the absence of genomic and transcriptomic data. We performed an acerola transcriptome sequencing that generated over 600 million reads, 40,830 contigs, and provided the annotation of 25,298 unique transcripts. Overall, this study revealed the main metabolic changes that occur in the acerola ripening. This transcriptional profile linked to metabolite measurements, allowed us to focus on ascorbate, ethylene, respiration, sugar, and firmness, the major metabolism indicators for acerola quality. Our results suggest a cooperative role of several genes involved in AsA biosynthesis (PMM, GMP1 and 3, GME1 and 2, GGP1 and 2), translocation (NAT3, 4, 6 and 6-like) and recycling (MDHAR2 and DHAR1) pathways for AsA accumulation in unripe fruits. Moreover, the association of metabolites with transcript profiles provided a comprehensive understanding of ethylene signalling, respiration, sugar accumulation and softening of acerola, shedding light on promising key regulatory genes. Overall, this study provides a foundation for further examination of the functional significance of these genes to improve fruit quality traits.
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Affiliation(s)
- Clesivan Pereira Dos Santos
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, 60451-970, Brazil
| | - Mathias Coelho Batista
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, 60451-970, Brazil
| | - Kátia Daniella da Cruz Saraiva
- Federal Institute of Education, Science and Technology of Paraíba, Campus Princesa Isabel, Princesa Isabel, Paraíba, Brazil
| | - André Luiz Maia Roque
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, 60451-970, Brazil
| | | | | | | | | | | | - José Hélio Costa
- Functional Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Ceará, 60451-970, Brazil.
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Singh P, Singh AP, Sane AP. Differential and reciprocal regulation of ethylene pathway genes regulates petal abscission in fragrant and non-fragrant roses. Plant Sci 2019; 280:330-339. [PMID: 30824012 DOI: 10.1016/j.plantsci.2018.12.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 12/12/2018] [Accepted: 12/14/2018] [Indexed: 06/09/2023]
Abstract
The fragrant rose, Rosa bourboniana, is highly sensitive to ethylene and shows rapid petal abscission (within 16-18 h) while the non-fragrant hybrid rose, R. hybrida, shows delayed abscission (50-52 h) due to reduced ethylene sensitivity. To understand the molecular basis governing these differences, all components of the ethylene pathway (biosynthesis/ receptor/signalling) were studied for expression during abscission. Transcript accumulation of most ethylene biosynthesis genes (ACS/ACO families) increased rapidly in petal abscission zones of R. bourboniana within 4-8 h of ethylene treatment. The expression of most receptor and signalling genes encoding CTRs, EIN2 and EIN3/EIL homologues also followed similar kinetics. Under natural field conditions where abscission takes longer, there was a temporal delay in transcript accumulation of most ethylene pathway genes while some biosynthesis genes (showing reduced ethylene sensitivity) were more strongly up-regulated by abscission cues. In contrast, in R. hybrida where even ethylene-induced abscission is considerably delayed, transcript accumulation of most ethylene biosynthesis and signalling genes was, surprisingly, reduced by ethylene and showed an opposite regulation compared to R. bourboniana. The results suggest that differential and reciprocal regulation of ethylene pathway is one of the major reasons for differences in petal abscission and vase-life between Rosa bourboniana and R. hybrida.
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Affiliation(s)
- Priya Singh
- Plant Gene Expression Lab, CSIR-National Botanical Research Institute (CSIR), Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Amar Pal Singh
- Plant Gene Expression Lab, CSIR-National Botanical Research Institute (CSIR), Lucknow, 226001, India
| | - Aniruddha P Sane
- Plant Gene Expression Lab, CSIR-National Botanical Research Institute (CSIR), Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Takács Z, Poór P, Borbély P, Czékus Z, Szalai G, Tari I. H 2O 2 homeostasis in wild-type and ethylene-insensitive Never ripe tomato in response to salicylic acid treatment in normal photoperiod and in prolonged darkness. Plant Physiol Biochem 2018; 126:74-85. [PMID: 29505970 DOI: 10.1016/j.plaphy.2018.02.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/22/2018] [Accepted: 02/23/2018] [Indexed: 06/08/2023]
Abstract
Ethylene proved to be an important modulator of salicylic acid (SA) signalling pathway. Since SA may regulate both the production and scavenging of hydrogen peroxide (H2O2), which show light-dependency, the aim of this study was to compare H2O2 metabolism in the leaves of SA-treated wild-type (WT) tomato (Solanum lycopersicum L. cv. Ailsa Craig) and in ethylene receptor Never-ripe (Nr) mutants grown in normal photoperiod or in prolonged darkness. H2O2 accumulation was higher in the WT than in the mutants in normal photoperiod after 1 mM SA treatment, while Nr leaves contained more H2O2 after light deprivation. The expression of certain superoxide dismutase (SOD) genes and activity of the enzyme followed the same tendency as H2O2, which was scavenged by different enzymes in the two genotypes. Catalase (CAT, EC 1.11.1.6) activity was inhibited by SA in WT, while the mutants maintained enhanced enzyme activity in the dark. Thus, in WT, CAT inhibition was the major component of the H2O2 accumulation elicited by 1 mM SA in a normal photoperiod, since the expression and/or activity of ascorbate (APX, EC 1.11.1.11) and guaiacol peroxidases (POD, EC 1.11.1.7) were induced in the leaves. The absence of APX and POD activation in mutant plants suggests that the regulation of these enzymes by SA needs functional ethylene signalling. While the block of ethylene perception in Nr mutants was overwritten in the transcription and activity of certain SOD and CAT isoenzymes during prolonged darkness, the low APX and POD activities led to H2O2 accumulation in these tissues.
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Affiliation(s)
- Zoltán Takács
- Department of Plant Biology, University of Szeged, H-6726 Szeged, Közép fasor 52., Hungary.
| | - Péter Poór
- Department of Plant Biology, University of Szeged, H-6726 Szeged, Közép fasor 52., Hungary.
| | - Péter Borbély
- Department of Plant Biology, University of Szeged, H-6726 Szeged, Közép fasor 52., Hungary.
| | - Zalán Czékus
- Department of Plant Biology, University of Szeged, H-6726 Szeged, Közép fasor 52., Hungary.
| | - Gabriella Szalai
- Department of Plant Physiology, Centre for Agricultural Research, Hungarian Academy of Sciences, H-2462 Martonvásár, Brunszvik u. 2., Hungary.
| | - Irma Tari
- Department of Plant Biology, University of Szeged, H-6726 Szeged, Közép fasor 52., Hungary.
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Schellingen K, Van Der Straeten D, Remans T, Vangronsveld J, Keunen E, Cuypers A. Ethylene signalling is mediating the early cadmium-induced oxidative challenge in Arabidopsis thaliana. Plant Sci 2015; 239:137-146. [PMID: 26398798 DOI: 10.1016/j.plantsci.2015.07.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 07/10/2015] [Accepted: 07/19/2015] [Indexed: 06/05/2023]
Abstract
Cadmium (Cd) induces the generation of reactive oxygen species (ROS) and stimulates ethylene biosynthesis. The phytohormone ethylene is a regulator of many developmental and physiological plant processes as well as stress responses. Previous research indicated various links between ethylene signalling and oxidative stress. Our results support a correlation between the Cd-induced oxidative challenge and ethylene signalling in Arabidopsis thaliana leaves. The effects of 24 or 72 h exposure to 5 μM Cd on plant growth and several oxidative stress-related parameters were compared between wild-type (WT) and ethylene insensitive mutants (etr1-1, ein2-1, ein3-1). Cadmium-induced responses observed in WT plants were mainly affected in etr1-1 and ein2-1 mutants, of which the growth was less inhibited by Cd exposure as compared to WT and ein3-1 mutants. Both etr1-1 and ein2-1 showed a delayed response in the glutathione (GSH) metabolism, including GSH levels and transcript levels of GSH synthesising and recycling enzymes. Furthermore, the expression of different oxidative stress marker genes was significantly lower in Cd-exposed ein2-1 mutants, evidencing that ethylene signalling is involved in early responses to Cd stress. A model for the cross-talk between ethylene signalling and oxidative stress is proposed.
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Affiliation(s)
- Kerim Schellingen
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium.
| | - Dominique Van Der Straeten
- Laboratory for Functional Plant Biology, Ghent University, Karel Lodewijk Ledeganckstraat 35, 9000 Ghent, Belgium.
| | - Tony Remans
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium.
| | - Jaco Vangronsveld
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium.
| | - Els Keunen
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium.
| | - Ann Cuypers
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium.
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