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Deng Q, Du P, Gangurde SS, Hong Y, Xiao Y, Hu D, Li H, Lu Q, Li S, Liu H, Wang R, Huang L, Wang W, Garg V, Liang X, Varshney RK, Chen X, Liu H. ScRNA-seq reveals dark- and light-induced differentially expressed gene atlases of seedling leaves in Arachis hypogaea L. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1848-1866. [PMID: 38391124 PMCID: PMC11182584 DOI: 10.1111/pbi.14306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024]
Abstract
Although the regulatory mechanisms of dark and light-induced plant morphogenesis have been broadly investigated, the biological process in peanuts has not been systematically explored on single-cell resolution. Herein, 10 cell clusters were characterized using scRNA-seq-identified marker genes, based on 13 409 and 11 296 single cells from 1-week-old peanut seedling leaves grown under dark and light conditions. 6104 genes and 50 transcription factors (TFs) displayed significant expression patterns in distinct cell clusters, which provided gene resources for profiling dark/light-induced candidate genes. Further pseudo-time trajectory and cell cycle evidence supported that dark repressed the cell division and perturbed normal cell cycle, especially the PORA abundances correlated with 11 TFs highly enriched in mesophyll to restrict the chlorophyllide synthesis. Additionally, light repressed the epidermis cell developmental trajectory extending by inhibiting the growth hormone pathway, and 21 TFs probably contributed to the different genes transcriptional dynamic. Eventually, peanut AHL17 was identified from the profile of differentially expressed TFs, which encoded protein located in the nucleus promoted leaf epidermal cell enlargement when ectopically overexpressed in Arabidopsis through the regulatory phytohormone pathway. Overall, our study presents the different gene atlases in peanut etiolated and green seedlings, providing novel biological insights to elucidate light-induced leaf cell development at the single-cell level.
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Affiliation(s)
- Quanqing Deng
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub‐Center of National Center of Oilseed Crops Improvement, Crops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Puxuan Du
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub‐Center of National Center of Oilseed Crops Improvement, Crops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Sunil S. Gangurde
- International Crops Research Institute for the Semi‐Arid TropicHyderabadIndia
| | - Yanbin Hong
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub‐Center of National Center of Oilseed Crops Improvement, Crops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Yuan Xiao
- School of Public HealthWannan Medical CollegeWuhuAnhui ProvinceChina
| | - Dongxiu Hu
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub‐Center of National Center of Oilseed Crops Improvement, Crops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Haifen Li
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub‐Center of National Center of Oilseed Crops Improvement, Crops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Qing Lu
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub‐Center of National Center of Oilseed Crops Improvement, Crops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Shaoxiong Li
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub‐Center of National Center of Oilseed Crops Improvement, Crops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Haiyan Liu
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub‐Center of National Center of Oilseed Crops Improvement, Crops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Runfeng Wang
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub‐Center of National Center of Oilseed Crops Improvement, Crops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Lu Huang
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub‐Center of National Center of Oilseed Crops Improvement, Crops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Wenyi Wang
- College of AgricultureSouth China Agricultural UniversityGuangzhouGuangdong ProvinceChina
| | - Vanika Garg
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
| | - Xuanqiang Liang
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub‐Center of National Center of Oilseed Crops Improvement, Crops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Rajeev K. Varshney
- College of AgricultureSouth China Agricultural UniversityGuangzhouGuangdong ProvinceChina
| | - Xiaoping Chen
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub‐Center of National Center of Oilseed Crops Improvement, Crops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
| | - Hao Liu
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub‐Center of National Center of Oilseed Crops Improvement, Crops Research InstituteGuangdong Academy of Agricultural SciencesGuangzhouGuangdong ProvinceChina
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Liu L, Gong Y, Yahaya BS, Chen Y, Shi D, Liu F, Gou J, Zhou Z, Lu Y, Wu F. Maize auxin response factor ZmARF1 confers multiple abiotic stresses resistances in transgenic Arabidopsis. PLANT MOLECULAR BIOLOGY 2024; 114:75. [PMID: 38878261 DOI: 10.1007/s11103-024-01470-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 05/12/2024] [Indexed: 06/29/2024]
Abstract
Prolonged exposure to abiotic stresses causes oxidative stress, which affects plant development and survival. In this research, the overexpression of ZmARF1 improved tolerance to low Pi, drought and salinity stresses. The transgenic plants manifested tolerance to low Pi by their superior root phenotypic traits: root length, root tips, root surface area, and root volume, compared to wide-type (WT) plants. Moreover, the transgenic plants exhibited higher root and leaf Pi content and upregulated the high affinity Pi transporters PHT1;2 and phosphorus starvation inducing (PSI) genes PHO2 and PHR1 under low Pi conditions. Transgenic Arabidopsis displayed tolerance to drought and salt stress by maintaining higher chlorophyll content and chlorophyll fluorescence, lower water loss rates, and ion leakage, which contributed to the survival of overexpression lines compared to the WT. Transcriptome profiling identified a peroxidase gene, POX, whose transcript was upregulated by these abiotic stresses. Furthermore, we confirmed that ZmARF1 bound to the auxin response element (AuxRE) in the promoter of POX and enhanced its transcription to mediate tolerance to oxidative stress imposed by low Pi, drought and salt stress in the transgenic seedlings. These results demonstrate that ZmARF1 has significant potential for improving the tolerance of crops to multiple abiotic stresses.
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Affiliation(s)
- Ling Liu
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, 644000, Sichuan, China
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
| | - Ying Gong
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Chengdu, Sichuan, China
| | - Baba Salifu Yahaya
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Chengdu, Sichuan, China
| | - Yushu Chen
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Chengdu, Sichuan, China
| | - Dengke Shi
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Chengdu, Sichuan, China
| | - Fangyuan Liu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Chengdu, Sichuan, China
| | - Junlin Gou
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Chengdu, Sichuan, China
| | - Zhanmei Zhou
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Chengdu, Sichuan, China
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China.
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Chengdu, Sichuan, China.
| | - Fengkai Wu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, 611130, Sichuan, China.
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Chengdu, Sichuan, China.
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Xiao S, Yang D, Li F, Tian X, Li Z. The EIN3/EIL-ERF9-HAK5 transcriptional cascade positively regulates high-affinity K + uptake in Gossypium hirsutum. THE NEW PHYTOLOGIST 2024; 241:2090-2107. [PMID: 38168024 DOI: 10.1111/nph.19500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/06/2023] [Indexed: 01/05/2024]
Abstract
High-affinity K+ (HAK) transporters play essential roles in facilitating root K+ uptake in higher plants. Our previous studies revealed that GhHAK5a, a member of the HAK family, is crucial for K+ uptake in upland cotton. Nevertheless, the precise regulatory mechanism governing the expression of GhHAK5a remains unclear. The yeast one-hybrid screening was performed to identify the transcription factors responsible for regulating GhHAK5a, and ethylene response factor 9 (GhERF9) was identified as a potential candidate. Subsequent dual-luciferase and electrophoretic mobility shift assays confirmed that GhERF9 binds directly to the GhHAK5a promoter, thereby activating its expression. Silencing of GhERF9 decreased the expression of GhHAK5a and exacerbated K+ deficiency symptoms in leaves, also decreased K+ uptake rate and K+ content in roots. Additionally, it was observed that the application of ethephon (an ethylene-releasing reagent) resulted in a significant upregulation of GhERF9 and GhHAK5a, accompanied by an increased rate of K+ uptake. Expectedly, GhEIN3b and GhEIL3c, the two key components involved in ethylene signaling, bind directly to the GhERF9 promoter. These findings provide valuable insights into the molecular mechanisms underlying the expression of GhHAK5a and ethylene-mediated K+ uptake and suggest a potential strategy to genetically enhance cotton K+ uptake by exploiting the EIN3/EILs-ERF9-HAK5 module.
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Affiliation(s)
- Shuang Xiao
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan Xilu, Haidian District, Beijing, 100193, China
| | - Doudou Yang
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan Xilu, Haidian District, Beijing, 100193, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Fangjun Li
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan Xilu, Haidian District, Beijing, 100193, China
| | - Xiaoli Tian
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan Xilu, Haidian District, Beijing, 100193, China
| | - Zhaohu Li
- State Key Laboratory of Plant Environmental Resilience, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan Xilu, Haidian District, Beijing, 100193, China
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Wu F, Yahaya BS, Gong Y, He B, Gou J, He Y, Li J, Kang Y, Xu J, Wang Q, Feng X, Tang Q, Liu Y, Lu Y. ZmARF1 positively regulates low phosphorus stress tolerance via modulating lateral root development in maize. PLoS Genet 2024; 20:e1011135. [PMID: 38315718 PMCID: PMC10868794 DOI: 10.1371/journal.pgen.1011135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 02/15/2024] [Accepted: 01/10/2024] [Indexed: 02/07/2024] Open
Abstract
Phosphorus (P) deficiency is one of the most critical factors for plant growth and productivity, including its inhibition of lateral root initiation. Auxin response factors (ARFs) play crucial roles in root development via auxin signaling mediated by genetic pathways. In this study, we found that the transcription factor ZmARF1 was associated with low inorganic phosphate (Pi) stress-related traits in maize. This superior root morphology and greater phosphate stress tolerance could be ascribed to the overexpression of ZmARF1. The knock out mutant zmarf1 had shorter primary roots, fewer root tip number, and lower root volume and surface area. Transcriptomic data indicate that ZmLBD1, a direct downstream target gene, is involved in lateral root development, which enhances phosphate starvation tolerance. A transcriptional activation assay revealed that ZmARF1 specifically binds to the GC-box motif in the promoter of ZmLBD1 and activates its expression. Moreover, ZmARF1 positively regulates the expression of ZmPHR1, ZmPHT1;2, and ZmPHO2, which are key transporters of Pi in maize. We propose that ZmARF1 promotes the transcription of ZmLBD1 to modulate lateral root development and Pi-starvation induced (PSI) genes to regulate phosphate mobilization and homeostasis under phosphorus starvation. In addition, ZmERF2 specifically binds to the ABRE motif of the promoter of ZmARF1 and represses its expression. Collectively, the findings of this study revealed that ZmARF1 is a pivotal factor that modulates root development and confers low-Pi stress tolerance through the transcriptional regulation of the biological function of ZmLBD1 and the expression of key Pi transport proteins.
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Affiliation(s)
- Fengkai Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, China
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
| | - Baba Salifu Yahaya
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, China
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
| | - Ying Gong
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, China
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
| | - Bing He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, China
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
| | - Junlin Gou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, China
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
| | - Yafeng He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, China
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
| | - Jing Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, China
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
| | - Yan Kang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, China
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
| | - Jie Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, China
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
| | - Qingjun Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, China
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
| | - Xuanjun Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, China
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
| | - Qi Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, China
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
| | - Yanli Lu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, China
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, China
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Liu F, Zhao P, Chen G, Wang Y, Yang Y. A comparative analysis of small RNA sequencing data in tubers of purple potato and its red mutant reveals small RNA regulation in anthocyanin biosynthesis. PeerJ 2023; 11:e15349. [PMID: 37223121 PMCID: PMC10202107 DOI: 10.7717/peerj.15349] [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: 04/15/2022] [Accepted: 04/13/2023] [Indexed: 05/25/2023] Open
Abstract
Anthocyanins are a group of natural pigments acting as stress protectants induced by biotic/abiotic stress in plants. Although the metabolic pathway of anthocyanin has been studied in potato, the roles of miRNAs on the metabolic pathway remain unclear. In this study, a purple tetraploid potato of SD92 and its red mutant of SD140 were selected to explore the regulation mechanism of miRNA in anthocyanin biosynthesis. A comparative analysis of small RNAs between SD92 and SD140 revealed that there were 179 differentially expressed miRNAs, including 65 up- and 114 down-regulated miRNAs. Furthermore, 31 differentially expressed miRNAs were predicted to potentially regulate 305 target genes. KEGG pathway enrichment analysis for these target genes showed that plant hormone signal transduction pathway and plant-pathogen interaction pathway were significantly enriched. The correlation analysis of miRNA sequencing data and transcriptome data showed that there were 140 negative regulatory miRNA-mRNA pairs. The miRNAs included miR171 family, miR172 family, miR530b_4 and novel_mir170. The mRNAs encoded transcription factors, hormone response factors and protein kinases. All these results indicated that miRNAs might regulate anthocyanin biosynthesis through transcription factors, hormone response factors and protein kinase.
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Affiliation(s)
- Fang Liu
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Peng Zhao
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Guangxia Chen
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yongqiang Wang
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yuanjun Yang
- Institute of Vegetables, Shandong Academy of Agricultural Sciences, Jinan, China
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Saputra TI, Maryanto SD, Tanjung ZA, Utomo C, Liwang T. Identification of microRNAs involved in the Phosphate starvation response in Oil Palm (Elaeis guineensis Jacq.). Mol Biol Rep 2023:10.1007/s11033-023-08484-4. [PMID: 37171552 DOI: 10.1007/s11033-023-08484-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 04/25/2023] [Indexed: 05/13/2023]
Abstract
BACKGROUND Plant microRNA, often known as miRNA, is a novel form of gene expression regulator that is known to play a significant role in phosphate starvation. The identification of microRNAs involved in the response to phosphate starvation in oil palms is beneficial for breeding programs. METHOD The main nursery stage seedlings of two oil palm progenies were treated with three different fertiliser namely: complete fertiliser with urea, P2O5, K2O, and MgO based on the standard procedure as a control (C); fertiliser with urea, K2O, MgO without P2O5 (P0); and no fertiliser (F0) for 24 weeks. A total of six oil palm roots were subjected to RNA isolation, followed by miRNA sequencing using the Illumina HiSeq 4000 platform, and all reads were computationally analysed. RESULTS In total, 119 potential miRNAs related to 5,891 genes were identified. The P-specific miRNAs were assumed based on the miRNAs that identified without P fertilizer treatment, resulted of twenty miRNA sequences in the treatment comparison of (C vs P0) vs (C vs F0). Those 20 miRNA sequences were grouped into 9 families, namely EgmiR319; EgmiR399; EgmiR396; EgmiR172; EgmiR156; EgmiR157; miR5648; miR5645; and EgmiRNA_unidentified. Two miRNAs were selected for RT-qPCR validation, namely EgMir399 and EgMir172. Their expression pattern was similar with the RNA sequencing results and shown opposite expression pattern with their target genes, UBC E2 24 and APETALA2, respectively. CONCLUSIONS The nine micro RNA families was identified in oil palm root tissue at phosphate starvation.
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Affiliation(s)
- Tengku Imam Saputra
- Genomic and Transcriptomic Section, Department of Biotechnology, PT SMART Tbk, Bogor, West Java, Indonesia.
| | - Sigit Dwi Maryanto
- Genomic and Transcriptomic Section, Department of Biotechnology, PT SMART Tbk, Bogor, West Java, Indonesia
| | - Zulfikar Achmad Tanjung
- Bioinformatics Section, Department of Biotechnology, PT SMART Tbk, Bogor, West Java, Indonesia
| | - Condro Utomo
- Department of Biotechnology, PT SMART Tbk, Bogor, West Java, Indonesia
| | - Tony Liwang
- Division of Plant Production and Biotechnology, PT SMART Tbk, Bogor, West Java, Indonesia
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Srivastava S, Ranjan M, Bano N, Asif MH, Srivastava S. Comparative transcriptome analysis reveals the phosphate starvation alleviation mechanism of phosphate accumulating Pseudomonas putida in Arabidopsis thaliana. Sci Rep 2023; 13:4918. [PMID: 36966146 PMCID: PMC10039930 DOI: 10.1038/s41598-023-31154-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/07/2023] [Indexed: 03/27/2023] Open
Abstract
Phosphate starvation is one of the major factors limiting plant productivity globally. Soil microflora with an inherent trait of phosphate accumulation directly influences soil phosphorus level by regulating its labile form in soil solution. However, the detailed mechanism involved during their interaction with plants under phosphate deficient conditions is still unexplored. Hence, to dissect these complex gene regulatory networks, transcriptome analysis of A. thaliana roots grown under phosphate starved conditions in presence of phosphate accumulating bacteria (Pseudomonas putida; RAR) was performed. Plants grown under phosphate starved conditions showed upregulation of phosphate starvation responsive genes associated with cell biogenesis, stress, photosynthesis, senescence, and cellular transport. Inoculation of RAR upregulated genes linked to defense, cell wall remodeling, and hormone metabolism in stressed plants. Gene ontology analysis indicated the induction of S-glycoside, glucosinolate, and glycosinolate metabolic processes in RAR inoculated plants under phosphate stressed conditions. Further, protein-protein interaction analysis revealed upregulation of root development, cation transport, anion transport, sulfur compound metabolic process, secondary metabolic process, cellular amino metabolic process, and response to salicylic acid in RAR inoculated plants under phosphate starved conditions. These results indicate the potential role of phosphate accumulating bacteria in alleviating phosphate starvation in plants by involving multiple pathways.
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Affiliation(s)
- Sonal Srivastava
- Division of Microbial Technology, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226 001, India
- Academy of Scientific and Innovative Research, AcSIR, Ghaziabad, 201002, India
| | - Manish Ranjan
- Division of Microbial Technology, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226 001, India
| | - Nasreen Bano
- Academy of Scientific and Innovative Research, AcSIR, Ghaziabad, 201002, India
- Computational Biology Laboratory, Genetics and Biotechnology Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226 001, India
| | - Mehar Hasan Asif
- Academy of Scientific and Innovative Research, AcSIR, Ghaziabad, 201002, India.
- Computational Biology Laboratory, Genetics and Biotechnology Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226 001, India.
| | - Suchi Srivastava
- Division of Microbial Technology, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226 001, India.
- Academy of Scientific and Innovative Research, AcSIR, Ghaziabad, 201002, India.
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Zhang X, Zhang L, Zhang D, Su D, Li W, Wang X, Chen Q, Cai W, Xu L, Cao F, Zhang D, Yu X, Li Y. Comprehensive analysis of metabolome and transcriptome reveals the mechanism of color formation in different leave of Loropetalum Chinense var. Rubrum. BMC PLANT BIOLOGY 2023; 23:133. [PMID: 36882694 PMCID: PMC9993627 DOI: 10.1186/s12870-023-04143-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 02/27/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND Loropetalum chinense var. rubrum (L. chinense var. rubrum) is a precious, coloured-leaf native ornamental plant in the Hunan Province. We found an L. chinense var. rubrum tree with three different leaf colours: GL (green leaf), ML (mosaic leaf), and PL (purple leaf). The mechanism of leaf coloration in this plant is still unclear. Therefore, this study aimed to identify the metabolites and genes involved in determining the colour composition of L. chinense var. rubrum leaves, using phenotypic/anatomic observations, pigment content detection, and comparative metabolomics and transcriptomics. RESULTS We observed that the mesophyll cells in PL were purple, while those in GL were green and those in ML were a mix of purple-green. The contents of chlorophyll a, b, carotenoids, and total chlorophyll in PL and ML were significantly lower than those in GL. While the anthocyanin content in PL and ML was significantly higher than that in GL. The metabolomics results showed the differences in the content of cyanidin 3-O-glucoside, delphinidin 3-O-glucoside, cyanidin 3,5-O-diglucoside, pelargonidin, and petunidin 3,5-diglucoside in ML, GL, and PL were significant. Considering that the change trend of anthocyanin content change was consistent with the leaf colour difference, we speculated that these compounds might influence the colour of L. chinense var. rubrum leaves. Using transcriptomics, we finally identified nine differentially expressed structural genes (one ANR (ANR1217); four CYP75As (CYP75A1815, CYP75A2846, CYP75A2909, and CYP75A1716); four UFGTs (UFGT1876, UFGT1649, UFGT1839, and UFGT3273) and nine transcription factors (two MYBs (MYB1057 and MYB1211), one MADS-box (MADS1235), two AP2-likes (AP2-like1779 and AP2-like2234), one bZIP (bZIP3720), two WD40s (WD2173 and WD1867) and one bHLH (bHLH1631) that might be related to flavonoid biosynthesis and then impacted the appearance of colour in L. chinense var. rubrum leaves. CONCLUSION This study revealed potential molecular mechanisms associated with leaf coloration in L. chinense var. rubrum by analyzing differential metabolites and genes related to the anthocyanin biosynthesis pathway. It also provided a reference for research on leaf colour variation in other ornamental plants.
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Affiliation(s)
- Xia Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
- College of Horticulture, Hunan Agricultural University, 410128, Changsha, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, 410128, Changsha, China
- Hunan Mid-subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, 410128, Changsha, China
| | - Li Zhang
- College of Horticulture, Hunan Agricultural University, 410128, Changsha, China
- Hunan Horticulture Research Institute, Hunan Academy of Agricultural Sciences, 410125, Changsha, China
| | - Damao Zhang
- College of Horticulture, Hunan Agricultural University, 410128, Changsha, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, 410128, Changsha, China
- Hunan Mid-subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, 410128, Changsha, China
| | - Dingding Su
- Institute of Advanced Agricultural Sciences, Peking University, 262041, Weifang, China
| | - Weidong Li
- Hunan Horticulture Research Institute, Hunan Academy of Agricultural Sciences, 410125, Changsha, China
- Hunan Key Laboratory of Innovation and Comprehensive Utilization, 410128, Changsha, China
| | - Xiangfei Wang
- College of Horticulture, Hunan Agricultural University, 410128, Changsha, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, 410128, Changsha, China
- Hunan Mid-subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, 410128, Changsha, China
| | - Qianru Chen
- College of Horticulture, Hunan Agricultural University, 410128, Changsha, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, 410128, Changsha, China
- Hunan Mid-subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, 410128, Changsha, China
| | - Wenqi Cai
- College of Horticulture, Hunan Agricultural University, 410128, Changsha, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, 410128, Changsha, China
- Hunan Mid-subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, 410128, Changsha, China
| | - Lu Xu
- College of Horticulture, Hunan Agricultural University, 410128, Changsha, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, 410128, Changsha, China
- Hunan Mid-subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, 410128, Changsha, China
| | - Fuxiang Cao
- College of Horticulture, Hunan Agricultural University, 410128, Changsha, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, 410128, Changsha, China
- Hunan Mid-subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, 410128, Changsha, China
| | - Dongling Zhang
- Department of Horticulture, University of Georgia, 30602, Athens, GA, USA.
| | - Xiaoying Yu
- College of Horticulture, Hunan Agricultural University, 410128, Changsha, China.
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, 410128, Changsha, China.
- Hunan Mid-subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, 410128, Changsha, China.
| | - Yanlin Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
- College of Horticulture, Hunan Agricultural University, 410128, Changsha, China.
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, 410128, Changsha, China.
- Hunan Mid-subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, 410128, Changsha, China.
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9
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Li X, Cheng Y, Wang Y, Yang X, Wei C, Guan J. Ethylene Signal Is Involved in the Regulation of Anthocyanin Accumulation in Flesh of Postharvest Plums ( Prunus salicina Lindl.). PLANTS (BASEL, SWITZERLAND) 2023; 12:893. [PMID: 36840243 PMCID: PMC9963230 DOI: 10.3390/plants12040893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/11/2023] [Accepted: 02/11/2023] [Indexed: 06/18/2023]
Abstract
Ethylene is positively correlated with the anthocyanin accumulation in postharvest plum fruit, but the regulation mechanism has not been fully clarified. In this work, the 'Friar' plum fruit under different storage temperatures (0, 10 and 25 °C) and treatments (100.0 μL L-1 ethylene and 1.0 μL L-1 1-MCP) were applied to study the relationship between anthocyanin accumulation and ethylene signal pathway. The fruits stored at 10 °C had higher ethylene production rate and more anthocyanin in flesh than those stored at 0 °C and 25 °C. Ten ethylene biosynthesis associated genes and forty-one ethylene signal transduction related genes were obtained from the previous transcriptome data. Among them, the expression levels of ethylene biosynthesis associated genes (PsACS1, PsACS4 and PsACO1), and ethylene signal transduction related genes (PsERS1s, PsETR2, PsERF1a, and PsERF12) were markedly higher in the fruits stored at 10 °C than those at 0 °C and 25 °C. Exogenous ethylene treatment enhanced while 1-MCP treatment inhibited the anthocyanin accumulation in the flesh under storage at 10 °C. In addition, exogenous ethylene treatment markedly increased the expression levels of PsACS1, PsACS4, PsACO1, PsETR2, PsERF1a, and PsERF12 in the flesh once it turning red, as well as the anthocyanin biosynthesis related genes (PsPAL, PsCHS, PsF3H, PsDRF, PsANS, PsUFGT and PsMYB10), whereas 1-MCP treatment manifested the contrary effects. Correlation analysis indicated that there was a significant positive correlation between genes expression related to ethylene signal pathway and anthocyanin biosynthesis, except for PsERF11. In conclusion, ethylene signal pathway is involved in the flesh reddening by up-regulating the anthocyanin biosynthesis related genes.
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Affiliation(s)
- Xueling Li
- Institute of Biotechnology and Food Sciences, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
- Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
| | - Yudou Cheng
- Institute of Biotechnology and Food Sciences, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
- Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
| | - Ying Wang
- Institute of Biotechnology and Food Sciences, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
- Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
| | - Xiaohe Yang
- Institute of Biotechnology and Food Sciences, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
- Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
| | - Chuangqi Wei
- Institute of Biotechnology and Food Sciences, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
- Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
| | - Junfeng Guan
- Institute of Biotechnology and Food Sciences, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050051, China
- Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
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10
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Wu Y, Li X, Zhang J, Zhao H, Tan S, Xu W, Pan J, Yang F, Pi E. ERF subfamily transcription factors and their function in plant responses to abiotic stresses. FRONTIERS IN PLANT SCIENCE 2022; 13:1042084. [PMID: 36531407 PMCID: PMC9748296 DOI: 10.3389/fpls.2022.1042084] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/09/2022] [Indexed: 06/09/2023]
Abstract
Ethylene Responsive Factor (ERF) subfamily comprise the largest number of proteins in the plant AP2/ERF superfamily, and have been most extensively studied on the biological functions. Members of this subfamily have been proven to regulate plant resistances to various abiotic stresses, such as drought, salinity, chilling and some other adversities. Under these stresses, ERFs are usually activated by mitogen-activated protein kinase induced phosphorylation or escape from ubiquitin-ligase enzymes, and then form complex with nucleic proteins before binding to cis-element in promoter regions of stress responsive genes. In this review, we will discuss the phylogenetic relationships among the ERF subfamily proteins, summarize molecular mechanism how the transcriptional activity of ERFs been regulated and how ERFs of different subgroup regulate the transcription of stress responsive genes, such as high-affinity K+ transporter gene PalHKT1;2, reactive oxygen species related genes LcLTP, LcPrx, and LcRP, flavonoids synthesis related genes FtF3H and LhMYBSPLATTER, etc. Though increasing researches demonstrate that ERFs are involved in various abiotic stresses, very few interact proteins and target genes of them have been comprehensively annotated. Hence, future research prospects are described on the mechanisms of how stress signals been transited to ERFs and how ERFs regulate the transcriptional expression of stress responsive genes.
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11
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Huang S, Zhang L, Cai T, Zhao Y, Liu J, Wu P, Ma X, Shuai P. Transcriptome Level Analysis of Genes of Exogenous Ethylene Applied under Phosphorus Stress in Chinese Fir. PLANTS (BASEL, SWITZERLAND) 2022; 11:2036. [PMID: 35956517 PMCID: PMC9370400 DOI: 10.3390/plants11152036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/23/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) is a widely grown gymnosperm in China. Phosphorus (P) is an indispensable nutrient for the growth of Chinese fir. Inorganic phosphate (Pi) deficiency exists in soils of many Chinese fir planting area regions, and the trees themselves have limited efficiency in utilizing P from the soil. Ethylene is important in regulation responses to nutrient deficiencies. However, little is known about how ethylene signals participate in Pi stress in Chinese fir. A total of six different treatments were performed to reveal the transcript levels of Chinese fir under Pi, ethephon (an ethylene-releasing compound), and CoCl2 (cobalt chloride, an ethylene biosynthesis inhibitor) treatments. We assembled a full-length reference transcriptome containing 22,243 unigenes as a reference for UMI RNA-seq (Digital RNA-seq). There were 586 Differentially Expressed Genes (DEGs) in the Pi starvation (NP) group, while DEGs from additional ethephon or CoCl2 in NP were 708 and 292, respectively. Among the DEGs in each treatment, there were 83 TFs in these treatment groups. MYB (v-myb avian myeloblastosis viral oncogene homolog) family was the most abundant transcription factors (TFs). Three ERF (Ethylene response factor) family genes were identified when only ethylene content was imposed as a variable. Enrichment analysis indicated that the ascorbate and aldarate metabolism pathway plays a key role in resistance to Pi deficiency. This study provides insights for further elucidating the regulatory mechanism of Pi deficiency in Chinese fir.
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Affiliation(s)
- Shuotian Huang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lixia Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Tingting Cai
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuxuan Zhao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiao Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Pengfei Wu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Chinese Fir Engineering Technology Research Center of the State Forestry and Grassland Administration, Fuzhou 350002, China
| | - Xiangqing Ma
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Chinese Fir Engineering Technology Research Center of the State Forestry and Grassland Administration, Fuzhou 350002, China
| | - Peng Shuai
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Chinese Fir Engineering Technology Research Center of the State Forestry and Grassland Administration, Fuzhou 350002, China
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12
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Integrative Analysis of miRNAs and Their Targets Involved in Ray Floret Growth in Gerbera hybrida. Int J Mol Sci 2022; 23:ijms23137296. [PMID: 35806310 PMCID: PMC9266715 DOI: 10.3390/ijms23137296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 11/30/2022] Open
Abstract
MicroRNAs (miRNAs) are involved in regulating many aspects of plant growth and development at the post-transcriptional level. Gerbera (Gerbera hybrida) is an important ornamental crop. However, the role of miRNAs in the growth and development of gerbera is still unclear. In this study, we used high-throughput sequencing to analyze the expression profiles of miRNAs in ray floret during inflorescence opening. A total of 164 miRNAs were obtained, comprising 24 conserved miRNAs and 140 novel miRNAs. Ten conserved and 15 novel miRNAs were differentially expressed during ray floret growth, and 607 differentially expressed target genes of these differentially expressed miRNAs were identified using psRNATarget. We performed a comprehensive analysis of the expression profiles of the miRNAs and their targets. The changes in expression of five miRNAs (ghy-miR156, ghy-miR164, ghy-miRn24, ghy-miRn75 and ghy-miRn133) were inversely correlated with the changes in expression of their eight target genes. The miRNA cleavage sites in candidate target gene mRNAs were determined using 5′-RLM-RACE. Several miRNA-mRNA pairs were predicted to regulate ray floret growth and anthocyanin biosynthesis. In conclusion, the results of small RNA sequencing provide valuable information to reveal the mechanisms of miRNA-mediated ray floret growth and anthocyanin accumulation in gerbera.
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13
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One AP2/ERF Transcription Factor Positively Regulates Pi Uptake and Drought Tolerance in Poplar. Int J Mol Sci 2022; 23:ijms23095241. [PMID: 35563632 PMCID: PMC9099566 DOI: 10.3390/ijms23095241] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 11/17/2022] Open
Abstract
Drought decreases the inorganic phosphate (Pi) supply of soil, resulting in Pi starvation of plants, but the molecular mechanism of how plants, especially the perennial trees, are tolerant to drought stress and Pi starvation, is still elusive. In this study, we identified an AP2/ERF transcription factor gene, PalERF2, from Populus alba var. pyramidalis, and it was induced by both mannitol treatment and Pi starvation. Overexpressing and knocking-down of PalERF2 both enhanced and attenuated tolerance to drought stress and Pi deficiency compared to WT, respectively. Moreover, the overexpression of PalERF2 up-regulated the expression levels of Pi starvation-induced (PSI) genes and increased Pi uptake under drought conditions; however, its RNAi poplar showed the opposite phenotypes. Subsequent analysis indicated that PalERF2 directly modulated expressions of drought-responsive genes PalRD20 and PalSAG113, as well as PSI genes PalPHL2 and PalPHT1;4, through binding to the DRE motifs on their promoters. These results clearly indicate that poplars can recruit PalERF2 to increase the tolerance to drought and also elevate Pi uptake under drought stress.
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14
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Pinit S, Ruengchaijatuporn N, Sriswasdi S, Buaboocha T, Chadchawan S, Chaiwanon J. Hyperspectral and genome-wide association analyses of leaf phosphorus status in local Thai indica rice. PLoS One 2022; 17:e0267304. [PMID: 35443012 PMCID: PMC9020724 DOI: 10.1371/journal.pone.0267304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 04/06/2022] [Indexed: 11/25/2022] Open
Abstract
Phosphorus (P) is an essential mineral nutrient and one of the key factors determining crop productivity. P-deficient plants exhibit visual leaf symptoms, including chlorosis, and alter spectral reflectance properties. In this study, we evaluated leaf inorganic phosphate (Pi) contents, plant growth and reflectance spectra (420–790 nm) of 172 Thai rice landrace varieties grown hydroponically under three different P supplies (overly sufficient, mildly deficient and severely deficient conditions). We reported correlations between Pi contents and reflectance ratios computed from two wavebands in the range of near infrared (720–790 nm) and visible energy (green-yellow and red edge) (r > 0.69) in Pi-deficient leaves. Artificial neural network models were also developed which could classify P deficiency levels with 85.60% accuracy and predict Pi content with R2 of 0.53, as well as highlight important waveband sections. Using 217 reflectance ratio indices to perform genome-wide association study (GWAS) with 113,114 SNPs, we identified 11 loci associated with the spectral reflectance traits, some of which were also associated with the leaf Pi content trait. Hyperspectral measurement offers a promising non-destructive approach to predict plant P status and screen large germplasm for varieties with high P use efficiency.
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Affiliation(s)
- Sompop Pinit
- Faculty of Science, Department of Botany, Center of Excellence in Environment and Plant Physiology, Chulalongkorn University, Bangkok, Thailand
- Faculty of Science, Program in Biotechnology, Chulalongkorn University, Bangkok, Thailand
| | | | - Sira Sriswasdi
- Faculty of Medicine, Computational Molecular Biology Group, Chulalongkorn University, Bangkok, Thailand
- Faculty of Medicine, Research Affairs, Chulalongkorn University, Bangkok, Thailand
| | - Teerapong Buaboocha
- Faculty of Science, Omics Sciences and Bioinformatics Center, Chulalongkorn University, Bangkok, Thailand
- Faculty of Science, Department of Biochemistry, Molecular Crop Research Unit, Chulalongkorn University, Bangkok, Thailand
| | - Supachitra Chadchawan
- Faculty of Science, Department of Botany, Center of Excellence in Environment and Plant Physiology, Chulalongkorn University, Bangkok, Thailand
| | - Juthamas Chaiwanon
- Faculty of Science, Department of Botany, Center of Excellence in Environment and Plant Physiology, Chulalongkorn University, Bangkok, Thailand
- * E-mail:
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15
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Zhang L, Chen L, Pang S, Zheng Q, Quan S, Liu Y, Xu T, Liu Y, Qi M. Function Analysis of the ERF and DREB Subfamilies in Tomato Fruit Development and Ripening. FRONTIERS IN PLANT SCIENCE 2022; 13:849048. [PMID: 35310671 PMCID: PMC8931701 DOI: 10.3389/fpls.2022.849048] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/02/2022] [Indexed: 05/26/2023]
Abstract
APETALA2/ethylene responsive factors (AP2/ERF) are unique regulators in the plant kingdom and are involved in the whole life activity processes such as development, ripening, and biotic and abiotic stresses. In tomato (Solanum lycopersicum), there are 140 AP2/ERF genes; however, their functionality remains poorly understood. In this work, the 14th and 19th amino acid differences in the AP2 domain were used to distinguish DREB and ERF subfamily members. Even when the AP2 domain of 68 ERF proteins from 20 plant species and motifs in tomato DREB and ERF proteins were compared, the binding ability of DREB and ERF proteins with DRE/CRT and/or GCC boxes remained unknown. During fruit development and ripening, the expressions of 13 DREB and 19 ERF subfamily genes showed some regular changes, and the promoters of most genes had ARF, DRE/CRT, and/or GCC boxes. This suggests that these genes directly or indirectly respond to IAA and/or ethylene (ET) signals during fruit development and ripening. Moreover, some of these may feedback regulate IAA or ET biosynthesis. In addition, 16 EAR motif-containing ERF genes in tomato were expressed in many organs and their total transcripts per million (TPM) values exceeded those of other ERF genes in most organs. To determine whether the EAR motif in EAR motif-containing ERF proteins has repression function, their EAR motifs were retained or deleted in a yeast one-hybrid (YIH) assay. The results indicate that most of EAR motif-containing ERF proteins lost repression activity after deleting the EAR motif. Moreover, some of these were expressed during ripening. Thus, these EAR motif-containing ERF proteins play vital roles in balancing the regulatory functions of other ERF proteins by completing the DRE/CRT and/or GCC box sites of target genes to ensure normal growth and development in tomato.
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Affiliation(s)
- Li Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, Shenyang Agricultural University, Shenyang, China
| | - LiJing Chen
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
- Key Laboratory of Agricultural Biotechnology of Liaoning Province, Shenyang Agricultural University, Shenyang, China
| | - ShengQun Pang
- College of Agriculture, Shihezi University, Shihezi, China
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization Xinjiang of Production and Construction Crops, Shihezi University, Shihezi, China
| | - Qun Zheng
- College of Agriculture, Shihezi University, Shihezi, China
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization Xinjiang of Production and Construction Crops, Shihezi University, Shihezi, China
| | - ShaoWen Quan
- College of Agriculture, Shihezi University, Shihezi, China
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization Xinjiang of Production and Construction Crops, Shihezi University, Shihezi, China
| | - YuFeng Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Tao Xu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - YuDong Liu
- College of Agriculture, Shihezi University, Shihezi, China
- Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization Xinjiang of Production and Construction Crops, Shihezi University, Shihezi, China
| | - MingFang Qi
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
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16
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Chen Y, Wu P, Zhang C, Guo Y, Liao B, Chen Y, Li M, Wu G, Wang Y, Jiang H. Ectopic Expression of JcCPL1, 2, and 4 Affects Epidermal Cell Differentiation, Anthocyanin Biosynthesis and Leaf Senescence in Arabidopsis thaliana. Int J Mol Sci 2022; 23:ijms23041924. [PMID: 35216041 PMCID: PMC8872631 DOI: 10.3390/ijms23041924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 02/01/2023] Open
Abstract
The CAPRICE (CPC)-like (CPL) genes belong to a single-repeat R3 MYB family, whose roles in physic nut (Jatropha curcas L.), an important energy plant, remain unclear. In this study, we identified a total of six CPL genes (JcCPL1–6) in physic nut. The JcCPL3, 4, and 6 proteins were localized mainly in the nucleus, while proteins JcCPL1, 2, and 5 were localized in both the nucleus and the cytoplasm. Ectopic overexpression of JcCPL1, 2, and 4 in Arabidopsis thaliana resulted in an increase in root hair number and decrease in trichome number. Consistent with the phenotype of reduced anthocyanin in shoots, the expression levels of anthocyanin biosynthesis genes were down-regulated in the shoots of these three transgenic A. thaliana lines. Moreover, we observed that OeJcCPL1, 2, 4 plants attained earlier leaf senescence, especially at the late developmental stage. Consistent with this, the expression levels of several senescence-associated and photosynthesis-related genes were, respectively, up-regulated and down-regulated in leaves. Taken together, our results indicate functional divergence of the six CPL proteins in physic nut. These findings also provide insight into the underlying roles of CPL transcription factors in leaf senescence.
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Affiliation(s)
- Yanbo Chen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China; (Y.C.); (B.L.)
| | - Pingzhi Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (P.W.); (Y.G.); (Y.C.); (M.L.); (G.W.)
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture/Key Laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Chao Zhang
- College of Agronomy, Northwest A&F University, Xianyang 712100, China;
| | - Yali Guo
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (P.W.); (Y.G.); (Y.C.); (M.L.); (G.W.)
| | - Bingbing Liao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China; (Y.C.); (B.L.)
| | - Yaping Chen
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (P.W.); (Y.G.); (Y.C.); (M.L.); (G.W.)
| | - Meiru Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (P.W.); (Y.G.); (Y.C.); (M.L.); (G.W.)
| | - Guojiang Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (P.W.); (Y.G.); (Y.C.); (M.L.); (G.W.)
| | - Yaqin Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China; (Y.C.); (B.L.)
- Correspondence: (Y.W.); (H.J.)
| | - Huawu Jiang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (P.W.); (Y.G.); (Y.C.); (M.L.); (G.W.)
- Correspondence: (Y.W.); (H.J.)
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17
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Bhadouria J, Giri J. Purple acid phosphatases: roles in phosphate utilization and new emerging functions. PLANT CELL REPORTS 2022; 41:33-51. [PMID: 34402946 DOI: 10.1007/s00299-021-02773-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 08/10/2021] [Indexed: 06/13/2023]
Abstract
Plants strive for phosphorus (P), which is an essential mineral for their life. Since P availability is limiting in most of the world's soils, plants have evolved with a complex network of genes and their regulatory mechanisms to cope with soil P deficiency. Among them, purple acid phosphatases (PAPs) are predominantly associated with P remobilization within the plant and acquisition from the soil by hydrolyzing organic P compounds. P in such compounds remains otherwise unavailable to plants for assimilation. PAPs are ubiquitous in plants, and similar enzymes exist in bacteria, fungi, mammals, and unicellular eukaryotes, but having some differences in their catalytic center. In the recent past, PAPs' roles have been extended to multiple plant processes like flowering, seed development, senescence, carbon metabolism, response to biotic and abiotic stresses, signaling, and root development. While new functions have been assigned to PAPs, the underlying mechanisms remained understood poorly. Here, we review the known functions of PAPs, the regulatory mechanisms, and their relevance in crop improvement for P-use-efficiency. We then discuss the mechanisms behind their functions and propose areas worthy of future research. Finally, we argue that PAPs could be a potential target for improving P utilization in crops. In turn, this is essential for sustainable agriculture.
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Affiliation(s)
- Jyoti Bhadouria
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Jitender Giri
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Zhu J, Guo X, Li X, Tang D. Composition of Flavonoids in the Petals of Freesia and Prediction of Four Novel Transcription Factors Involving in Freesia Flavonoid Pathway. FRONTIERS IN PLANT SCIENCE 2021; 12:756300. [PMID: 34868147 PMCID: PMC8634401 DOI: 10.3389/fpls.2021.756300] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
Freesia hybrida is rich in flower colors with beautiful flower shapes and pleasant aroma. Flavonoids are vital to the color formation of its flowers. In this study, five Freesia cultivars with different flower colors were used to study on the level of accumulation of their flavonoids and expression of flavonoid-related genes and further explore new novel transcription factor (TF). Ultra-high-performance liquid chromatography and VION ion mobility quadrupole time-of-flight mass spectrometer (UPLC-Q-TOF-MS) were used to determine the flavonoids. Combined with transcriptome sequencing technology, the molecular mechanism of the flavonoid metabolism difference in Freesia was revealed. A total of 10 anthoxanthin components and 12 anthocyanin components were detected using UPLC-Q-TOF-MS. All six common anthocyanin aglycones in high plants, including cyanidin, delphinidin, petunidin, peonidin, malvidin, and pelargonidin, were detected in Freesia at first time in this study. In orange, yellow, and white cultivars, anthoxanthins gradually decreased with the opening of the petals, while in red and purple cultivars, anthoxanthins first increased and then decreased. No anthocyanin was detected in yellow and white cultivars, while anthocyanins increased with the opening of the petals and reached their maximum at the flowering stage (S3) in other three cultivars. The correlation analysis revealed that the color of Freesia petals was closely related to the composition and content of anthoxanthins and anthocyanins. Petals of five cultivars at S3 were then selected for transcriptome sequencing by using the Illumina Hiseq 4000 platform, and a total of 100,539 unigenes were obtained. There were totally 5,162 differentially expressed genes (DEGs) when the four colored cultivars were compared with the white cultivar at S3. Comparing all DEGs with gene ontology (GO), KEGG, and Pfam databases, it was found that the genes involved in the flavonoid biosynthesis pathway were significantly different. In addition, AP2, WRKY, and bHLH TF families ranked the top three among all differently expressed TFs in all DEGs. Quantitative real-time PCR (qRT-PCR) technology was used to analyze the expression patterns of the structural genes of flavonoid biosynthesis pathway in Freesia. The results showed that metabolic process was affected significantly by structural genes in this pathway, such as CHS1, CHI2, DFR1, ANS1, 3GT1, and FLS1. Cluster analysis was performed by using all annotated WRKY and AP2 TFs and the above structural genes based on their relatively expression. Four novel candidate TFs of WRKY and AP2 family were screened. Their spatiotemporal expression patterns revealed that these four novel TFs may participate in the regulation of the flavonoid biosynthesis, thus controlling its color formation in Freesia petals.
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Affiliation(s)
- Jiayi Zhu
- School of Design, Shanghai Jiao Tong University, Shanghai, China
| | - Xueying Guo
- School of Design, Shanghai Jiao Tong University, Shanghai, China
| | - Xin Li
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai, China
| | - Dongqin Tang
- School of Design, Shanghai Jiao Tong University, Shanghai, China
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Li C, Li K, Liu X, Ruan H, Zheng M, Yu Z, Gai J, Yang S. Transcription Factor GmWRKY46 Enhanced Phosphate Starvation Tolerance and Root Development in Transgenic Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:700651. [PMID: 34594347 PMCID: PMC8477037 DOI: 10.3389/fpls.2021.700651] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/20/2021] [Indexed: 06/08/2023]
Abstract
Phosphorus (P) is one of the essential macronutrients, whose deficiency limits the growth and development of plants. In this study, we investigated the possible role of GmWRKY46 in the phosphate (Pi) starvation stress tolerance of soybean. GmWRKY46 belonged to the group III subfamily of the WRKY transcription factor family, which was localized in the nucleus and had transcriptional activator activity. GmWRKY46 could be strongly induced by Pi starvation, especially in soybean roots. Overexpression of GmWRKY46 significantly enhanced tolerance to Pi starvation and lateral root development in transgenic Arabidopsis. RNA-seq analysis showed that overexpression of GmWRKY46 led to change in many genes related to energy metabolisms, stress responses, and plant hormone signal transduction in transgenic Arabidopsis. Among these differential expression genes, we found that overexpression of AtAED1 alone could enhance the tolerance of transgenic Arabidopsis to Pi starvation. Y1H and ChIP-qPCR analyses showed that GmWRKY46 could directly bind to the W-box motif of the AtAED1 promoter in vitro and in vivo. Furthermore, results from intact soybean composite plants with GmWRKY46 overexpression showed that GmWRKY46 was involved in hairy roots development and subsequently affected plant growth and Pi uptake. These results provide a basis for the molecular genetic breeding of soybean tolerant to Pi starvation.
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Affiliation(s)
- Cheng Li
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Kangning Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, China
| | - Xinyi Liu
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Hui Ruan
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Mingming Zheng
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Zhijie Yu
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Junyi Gai
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Shouping Yang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
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Yang Z, Gao Z, Zhou H, He Y, Liu Y, Lai Y, Zheng J, Li X, Liao H. GmPTF1 modifies root architecture responses to phosphate starvation primarily through regulating GmEXPB2 expression in soybean. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:525-543. [PMID: 33960526 DOI: 10.1111/tpj.15307] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 04/28/2021] [Indexed: 06/12/2023]
Abstract
Though root architecture modifications may be critically important for improving phosphorus (P) efficiency in crops, the regulatory mechanisms triggering these changes remain unclear. In this study, we demonstrate that genotypic variation in GmEXPB2 expression is strongly correlated with root elongation and P acquisition efficiency, and enhancing its transcription significantly improves soybean yield in the field. Promoter deletion analysis was performed using 5' truncation fragments (P1-P6) of GmEXPB2 fused with the GUS gene in soybean transgenic hairy roots, which revealed that the P1 segment containing three E-box elements significantly enhances induction of gene expression in response to phosphate (Pi) starvation. Further experimentation demonstrated that GmPTF1, a basic-helix-loop-helix transcription factor, is the regulatory factor responsible for the induction of GmEXPB2 expression in response to Pi starvation. In short, Pi starvation induced expression of GmPTF1, with the GmPTF1 product directly binding to the E-box motif in the P1 region of the GmEXPB2 promoter. Plus, both GmPTF1 and GmEXPB2 highly expressed in lateral roots, and were significantly enhanced by P deficiency. Further work with soybean stable transgenic plants through RNA sequencing analysis showed that altering GmPTF1 expression significantly impacted the transcription of a series of cell wall genes, including GmEXPB2, and thereby affected root growth, biomass and P uptake. Taken together, this work identifies a novel regulatory factor, GmPTF1, involved in changing soybean root architecture partially through regulation of the expression of GmEXPB2 by binding the E-box motif in its promoter region.
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Affiliation(s)
- Zhaojun Yang
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhi Gao
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huiwen Zhou
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ying He
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yanxing Liu
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yelin Lai
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jiakun Zheng
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xinxin Li
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hong Liao
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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Barros VA, Chandnani R, de Sousa SM, Maciel LS, Tokizawa M, Guimaraes CT, Magalhaes JV, Kochian LV. Root Adaptation via Common Genetic Factors Conditioning Tolerance to Multiple Stresses for Crops Cultivated on Acidic Tropical Soils. FRONTIERS IN PLANT SCIENCE 2020; 11:565339. [PMID: 33281841 PMCID: PMC7688899 DOI: 10.3389/fpls.2020.565339] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 10/20/2020] [Indexed: 06/01/2023]
Abstract
Crop tolerance to multiple abiotic stresses has long been pursued as a Holy Grail in plant breeding efforts that target crop adaptation to tropical soils. On tropical, acidic soils, aluminum (Al) toxicity, low phosphorus (P) availability and drought stress are the major limitations to yield stability. Molecular breeding based on a small suite of pleiotropic genes, particularly those with moderate to major phenotypic effects, could help circumvent the need for complex breeding designs and large population sizes aimed at selecting transgressive progeny accumulating favorable alleles controlling polygenic traits. The underlying question is twofold: do common tolerance mechanisms to Al toxicity, P deficiency and drought exist? And if they do, will they be useful in a plant breeding program that targets stress-prone environments. The selective environments in tropical regions are such that multiple, co-existing regulatory networks may drive the fixation of either distinctly different or a smaller number of pleiotropic abiotic stress tolerance genes. Recent studies suggest that genes contributing to crop adaptation to acidic soils, such as the major Arabidopsis Al tolerance protein, AtALMT1, which encodes an aluminum-activated root malate transporter, may influence both Al tolerance and P acquisition via changes in root system morphology and architecture. However, trans-acting elements such as transcription factors (TFs) may be the best option for pleiotropic control of multiple abiotic stress genes, due to their small and often multiple binding sequences in the genome. One such example is the C2H2-type zinc finger, AtSTOP1, which is a transcriptional regulator of a number of Arabidopsis Al tolerance genes, including AtMATE and AtALMT1, and has been shown to activate AtALMT1, not only in response to Al but also low soil P. The large WRKY family of transcription factors are also known to affect a broad spectrum of phenotypes, some of which are related to acidic soil abiotic stress responses. Hence, we focus here on signaling proteins such as TFs and protein kinases to identify, from the literature, evidence for unifying regulatory networks controlling Al tolerance, P efficiency and, also possibly drought tolerance. Particular emphasis will be given to modification of root system morphology and architecture, which could be an important physiological "hub" leading to crop adaptation to multiple soil-based abiotic stress factors.
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Affiliation(s)
- Vanessa A. Barros
- Embrapa Maize and Sorghum, Sete Lagoas, Brazil
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rahul Chandnani
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Laiane S. Maciel
- Embrapa Maize and Sorghum, Sete Lagoas, Brazil
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | - Mutsutomo Tokizawa
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Jurandir V. Magalhaes
- Embrapa Maize and Sorghum, Sete Lagoas, Brazil
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Leon V. Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, Canada
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Tiziani R, Pii Y, Celletti S, Cesco S, Mimmo T. Phosphorus deficiency changes carbon isotope fractionation and triggers exudate reacquisition in tomato plants. Sci Rep 2020; 10:15970. [PMID: 32994443 PMCID: PMC7524771 DOI: 10.1038/s41598-020-72904-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 09/06/2020] [Indexed: 11/28/2022] Open
Abstract
Plant roots are able to exude vast amounts of metabolites into the rhizosphere in response to phosphorus (P) deficiency. Causing noteworthy costs in terms of energy and carbon (C) for the plants. Therefore, it is suggested that exudates reacquisition by roots could represent an energy saving strategy of plants. This study aimed at investigating the effect of P deficiency on the ability of hydroponically grown tomato plants to re-acquire specific compounds generally present in root exudates by using 13C-labelled molecules. Results showed that P deficient tomato plants were able to take up citrate (+ 37%) and malate (+ 37%), particularly when compared to controls. While glycine (+ 42%) and fructose (+ 49%) uptake was enhanced in P shortage, glucose acquisition was not affected by the nutritional status. Unexpectedly, results also showed that P deficiency leads to a 13C enrichment in both tomato roots and shoots over time (shoots-+ 2.66‰, roots-+ 2.64‰, compared to control plants), probably due to stomata closure triggered by P deficiency. These findings highlight that tomato plants are able to take up a wide range of metabolites belonging to root exudates, thus maximizing C trade off. This trait is particularly evident when plants grew in P deficiency.
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Affiliation(s)
- Raphael Tiziani
- Faculty of Science and Technology, Free University of Bolzano, 39100, Bolzano, Italy.
| | - Youry Pii
- Faculty of Science and Technology, Free University of Bolzano, 39100, Bolzano, Italy
| | - Silvia Celletti
- Faculty of Science and Technology, Free University of Bolzano, 39100, Bolzano, Italy
| | - Stefano Cesco
- Faculty of Science and Technology, Free University of Bolzano, 39100, Bolzano, Italy
| | - Tanja Mimmo
- Faculty of Science and Technology, Free University of Bolzano, 39100, Bolzano, Italy.
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24
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Peng Z, Tian J, Luo R, Kang Y, Lu Y, Hu Y, Liu N, Zhang J, Cheng H, Niu S, Zhang J, Yao Y. MiR399d and epigenetic modification comodulate anthocyanin accumulation in Malus leaves suffering from phosphorus deficiency. PLANT, CELL & ENVIRONMENT 2020; 43:1148-1159. [PMID: 31833568 DOI: 10.1111/pce.13697] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/17/2019] [Accepted: 12/03/2019] [Indexed: 05/14/2023]
Abstract
Inorganic phosphorus (Pi) deficiency induces anthocyanin accumulation in the leaves of some plant species; however, the molecular mechanisms underlying this phenomenon have not been well characterized. Here, we showed that microRNA399d (miR399d), high-affinity Pi transporter McPHT1;4, and McMYB10 are strongly induced in Malus leaves suffering from Pi deficiency. By culturing explants of transiently transformed plants in MS medium under conditions of Pi sufficiency and Pi deficiency, miR399d and McPHT1;4 were shown to play essential roles in the response to Pi deficiency and to play positive roles in the regulation of anthocyanin biosynthesis. Silencing of McHDA6 expression and treatment with the inhibitor trichostatin A suggested that the low expression of McHDA6 simultaneously reduced the transcription of McMET1 and decreased the methylation level of the McMYB10 promoter; however, the expression of McMYB10 and anthocyanin content were increased. Bimolecular fluorescence complementation and yeast two-hybrid assays revealed that McHDA6 binds directly to McMET1 through its BAH2 and DNMT1-RFD domains. Based on the results of our study, we propose a mechanism for the molecular regulation of anthocyanin biosynthesis, namely, the miR399d and epigenetic modification comodulation model, to explain the phenomenon in which leaves turn red under conditions of Pi deficiency.
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Affiliation(s)
- Zhen Peng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Ji Tian
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Rongli Luo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Yanhui Kang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Yanfen Lu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Yujing Hu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Na Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Jie Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Hao Cheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Shuqing Niu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Jie Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
| | - Yuncong Yao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing 102206, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, Beijing 102206, China
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Jasmonate and Ethylene-Regulated Ethylene Response Factor 22 Promotes Lanolin-Induced Anthocyanin Biosynthesis in 'Zaosu' Pear ( Pyrus bretschneideri Rehd.) Fruit. Biomolecules 2020; 10:biom10020278. [PMID: 32054132 PMCID: PMC7072184 DOI: 10.3390/biom10020278] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 02/07/2020] [Accepted: 02/08/2020] [Indexed: 12/02/2022] Open
Abstract
Anthocyanin contributes to the coloration of pear fruit and enhances plant defenses. Members of the ethylene response factor (ERF) family play vital roles in hormone and stress signaling and are involved in anthocyanin biosynthesis. Here, PbERF22 was identified from the lanolin-induced red fruit of ‘Zaosu’ pear (Pyrus bretschneideri Rehd.) using a comparative transcriptome analysis. Its expression level was up- and down-regulated by methyl jasmonate and 1-methylcyclopropene plus lanolin treatments, respectively, which indicated that PbERF22 responded to the jasmonate- and ethylene-signaling pathways. In addition, transiently overexpressed PbERF22 induced anthocyanin biosynthesis in ‘Zaosu’ fruit, and a quantitative PCR analysis further confirmed that PbERF22 facilitated the expression of anthocyanin biosynthetic structural and regulatory genes. Moreover, a dual luciferase assay showed that PbERF22 enhanced the activation effects of PbMYB10 and PbMYB10b on the PbUFGT promoter. Therefore, PbERF22 responses to jasmonate and ethylene signals and regulates anthocyanin biosynthesis. This provides a new perspective on the correlation between jasmonate–ethylene crosstalk and anthocyanin biosynthesis.
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He Y, Chen H, Zhou L, Liu Y, Chen H. Comparative transcription analysis of photosensitive and non-photosensitive eggplants to identify genes involved in dark regulated anthocyanin synthesis. BMC Genomics 2019; 20:678. [PMID: 31455222 PMCID: PMC6712802 DOI: 10.1186/s12864-019-6023-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/12/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Light is a key environmental factor in regulation of anthocyanin biosynthesis. Through a large number of bagging screenings, we obtained non-photosensitive eggplants that still have decent amount of anthocyanin synthesized after bagging. In the present study, transcriptome was made to explore the molecular mechanism of dark-regulated anthocyanin synthesis in non-photosensitive eggplant. RESULTS The transcriptome of the pericarp at 0 h, 0.5 h, 4 h, and 8 h after bag removal were sequenced and analyzed. Comparison of the sequencing data with those of photosensitive eggplant for the same time period showed that anthocyanin synthesis genes had different expression trends. Based on the expression trends of the structural genes, it was discovered that 22 transcription factors and 4 light signal transduction elements may be involved in the anthocyanin synthesis in two types of eggplants. Through transcription factor target gene prediction and yeast one-hybrid assay, SmBIM1, SmAP2, SmHD, SmMYB94, SmMYB19, SmTT8, SmYABBY, SmTTG2, and SmMYC2 were identified to be directly or indirectly bound to the promoter of the structural gene SmCHS. These results indicate that the identified 9 genes participated in the anthocyanin synthesis in eggplant peel and formed a network of interactions among themselves. CONCLUSIONS Based on the comparative transcription, the identified 22 transcription factors and 4 light signal transduction elements may act as the key factors in dark regulated anthocyanin synthesis in non-photosensitive eggplant. The results provided a step stone for further analysis of the molecular mechanism of dark-regulated anthocyanin synthesis in non-photosensitive eggplant.
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Affiliation(s)
- Yongjun He
- School of Agriculture and Biology, Shanghai JiaoTong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
| | - Hang Chen
- School of Agriculture and Biology, Shanghai JiaoTong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
| | - Lu Zhou
- School of Agriculture and Biology, Shanghai JiaoTong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
| | - Yang Liu
- School of Agriculture and Biology, Shanghai JiaoTong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
| | - Huoying Chen
- School of Agriculture and Biology, Shanghai JiaoTong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240 China
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