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Shang C, Hou Q, Qiao G, Tian T, Wen X. CpSPL10-CpELF4 module involves in the negative regulation of flower bud differentiation in Chinese cherry. Int J Biol Macromol 2024; 280:135964. [PMID: 39322142 DOI: 10.1016/j.ijbiomac.2024.135964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Revised: 09/19/2024] [Accepted: 09/21/2024] [Indexed: 09/27/2024]
Abstract
SQUAMOSA promoter-binding protein-like (SPL) genes play a crucial role in regulating floral induction. Despite such importance, a comprehensive study of SPLs in Chinese cherry flower bud development has been absent. In this study, 32 CpSPL genes were identified. According to expression profiling, CpSPLs exhibited tissue-specific expression and distinct trends throughout flower bud differentiation. Specifically, CpSPL10 was greatly expressed at the beginning of the differentiation, and its role was further investigated. Its overexpression extended the vegetative growth of transgenic tobacco plants, delayed flowering by about 20 days. Moreover, the accumulation of NbELF4 (Early flowering 4) transcripts was enhanced due to the up-regulated levels of CpSPL10 in tobacco plants. ELF4 functions as a major element of the circadian clock; its high expression typically delays the transition from vegetative-to-reproductive growth. Further experiments revealed that CpSPL10 interacts with CpSPL9 or a transposase-derived transcription factor CpFRS5 (FAR1-RELATED SEQUENCE 5) and activates the expression of the downstream gene CpELF4. Notably, the GUS fusing reporter assay detected the activation of CpSPL10 and CpELF4 promoters in shoot apical meristems of transgenic Arabidopsis. These findings revealed the negative regulation of the CpSPL10-CpELF4 module in flower bud differentiation, providing references for supplementing the specific relationships among SPL, FRS, and ELF4.
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Affiliation(s)
- Chunqiong Shang
- Institute for Forest Resources & Environment of Guizhou, College of Forestry, Guizhou University, Guiyang 550025, Guizhou Province, China; Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China
| | - Qiandong Hou
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China
| | - Guang Qiao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China
| | - Tian Tian
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China
| | - Xiaopeng Wen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, Guizhou University, Guiyang 550025, China.
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Mou SJ, Angon PB. Genome-wide characterization and expression profiling of FARL (FHY3/FAR1) family genes in Zea mays. J Genet Eng Biotechnol 2024; 22:100401. [PMID: 39179323 PMCID: PMC11342881 DOI: 10.1016/j.jgeb.2024.100401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 08/26/2024]
Abstract
A significant role of the plant is played by the transcription factor FARL, which is light signal transduction as well as plant growth and development. Despite being transposases, FARL has developed a variety of dominant biological actions in evolution and speciation. On the other hand, little is known about the Zea mays FARL protein family. This study identifies and characterizes fifteen ZmFARL genes genome-wide, and RNA sequencing data was used to profile their expression. 105 FARL proteins from five plant species were classified into five groups based on sequence alignment and phylogeny. The ZmFARL genes' exon-intron and motif distribution were conserved based on their evolutionary group. The fifteen ZmFARL genes were distributed over seven of the ten Z. mays chromosomes, although no duplication was discovered. Cis-element analysis reveals that ZmFARL genes play a variety of activities, including tissue-specific, stress- and hormone-responsive expressions. Furthermore, the results of the RNA sequencing used to profile expression showed that the genes ZmFARL2 and ZmFARL5 were much more expressed than other genes in various tissues, particularly in leaf characteristics. The identification of likely genes involved in cellular activity in Z. mays and related species will be aided by the characterization of the FARL genes.
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Affiliation(s)
- Sharah Jabeen Mou
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Prodipto Bishnu Angon
- Faculty of Agriculture, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh.
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3
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Kuo WH, Zhong L, Wright SJ, Goad DM, Olsen KM. Beyond cyanogenesis: Temperature gradients drive environmental adaptation in North American white clover (Trifolium repens L.). Mol Ecol 2024; 33:e17484. [PMID: 39072878 DOI: 10.1111/mec.17484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 07/15/2024] [Accepted: 07/18/2024] [Indexed: 07/30/2024]
Abstract
Species that repeatedly evolve phenotypic clines across environmental gradients have been highlighted as ideal systems for characterizing the genomic basis of local environmental adaptation. However, few studies have assessed the importance of observed phenotypic clines for local adaptation: conspicuous traits that vary clinally may not necessarily be the most critical in determining local fitness. The present study was designed to fill this gap, using a plant species characterized by repeatedly evolved adaptive phenotypic clines. White clover is naturally polymorphic for its chemical defence cyanogenesis (HCN release with tissue damage); climate-associated cyanogenesis clines have evolved throughout its native and introduced range worldwide. We performed landscape genomic analyses on 415 wild genotypes from 43 locations spanning much of the North American species range to assess the relative importance of cyanogenesis loci vs. other genomic factors in local climatic adaptation. We find clear evidence of local adaptation, with temperature-related climatic variables best describing genome-wide differentiation between sampling locations. The same climatic variables are also strongly correlated with cyanogenesis frequencies and gene copy number variations (CNVs) at cyanogenesis loci. However, landscape genomic analyses indicate no significant contribution of cyanogenesis loci to local adaptation. Instead, several genomic regions containing promising candidate genes for plant response to seasonal cues are identified - some of which are shared with previously identified QTLs for locally adaptive fitness traits in North American white clover. Our findings suggest that local adaptation in white clover is likely determined primarily by genes controlling the timing of growth and flowering in response to local seasonal cues. More generally, this work suggests that caution is warranted when considering the importance of conspicuous phenotypic clines as primary determinants of local adaptation.
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Affiliation(s)
- Wen-Hsi Kuo
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - Limei Zhong
- Jiangxi Key Laboratory of Molecular Biology and Gene Engineering, School of Life Sciences, Nanchang University, Nanchang, China
| | - Sara J Wright
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - David M Goad
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - Kenneth M Olsen
- Department of Biology, Washington University, St. Louis, Missouri, USA
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Zhao D, Guan P, Wei L, Gao J, Guo L, Tian D, Li Q, Guo Z, Cui H, Li Y, Guo J. Comprehensive identification and expression analysis of FAR1/FHY3 genes under drought stress in maize ( Zea mays L.). PeerJ 2024; 12:e17684. [PMID: 38952979 PMCID: PMC11216215 DOI: 10.7717/peerj.17684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 06/13/2024] [Indexed: 07/03/2024] Open
Abstract
Background FAR1/FHY3 transcription factors are derived from transposase, which play important roles in light signal transduction, growth and development, and response to stress by regulating downstream gene expression. Although many FAR1/FHY3 members have been identified in various species, the FAR1/FHY3 genes in maize are not well characterized and their function in drought are unknown. Method The FAR1/FHY3 family in the maize genome was identified using PlantTFDB, Pfam, Smart, and NCBI-CDD websites. In order to investigate the evolution and functions of FAR1 genes in maize, the information of protein sequences, chromosome localization, subcellular localization, conserved motifs, evolutionary relationships and tissue expression patterns were analyzed by bioinformatics, and the expression patterns under drought stress were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Results A total of 24 ZmFAR members in maize genome, which can be divided into five subfamilies, with large differences in protein and gene structures among subfamilies. The promoter regions of ZmFARs contain abundant abiotic stress-responsive and hormone-respovensive cis-elements. Among them, drought-responsive cis-elements are quite abundant. ZmFARs were expressed in all tissues detected, but the expression level varies widely. The expression of ZmFARs were mostly down-regulated in primary roots, seminal roots, lateral roots, and mesocotyls under water deficit. Most ZmFARs were down-regulated in root after PEG-simulated drought stress. Conclusions We performed a genome-wide and systematic identification of FAR1/FHY3 genes in maize. And most ZmFARs were down-regulated in root after drought stress. These results indicate that FAR1/FHY3 transcription factors have important roles in drought stress response, which can lay a foundation for further analysis of the functions of ZmFARs in response to drought stress.
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Affiliation(s)
- Dongbo Zhao
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Peiyan Guan
- College of Life Science, Dezhou University, Dezhou, Shandong, China
| | - Longxue Wei
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Jiansheng Gao
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Lianghai Guo
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Dianbin Tian
- Pingyuan County Rural Revitalization Service Center, Pingyuan, Shandong, China
| | - Qingfang Li
- Linyi County Agricultural and Rural Bureau, Linyi, Shandong, China
| | - Zhihui Guo
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Huini Cui
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Yongjun Li
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
| | - Jianjun Guo
- Dezhou Academy of Agricultural Science, Dezhou, Shandong, China
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Chen K, Hu Q, Ma X, Zhang X, Qian R, Zheng J. The effect of exogenous melatonin on waterlogging stress in Clematis. FRONTIERS IN PLANT SCIENCE 2024; 15:1385165. [PMID: 38957603 PMCID: PMC11217522 DOI: 10.3389/fpls.2024.1385165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/30/2024] [Indexed: 07/04/2024]
Abstract
Clematis is the queen of the vines, being an ornamental plant with high economic value. Waterlogging stress reduces the ornamental value of the plant and limits its application. Melatonin plays an important role in plant resistance to abiotic stresses. In this study, the physiological responses and gene expression levels of two wild species, namely, Clematis tientaiensis and Clematis lanuginosa, and two horticultural varieties, namely, 'Sen-No-Kaze' and 'Viva Polonia,' under waterlogging stress were analyzed to determine the effect of melatonin on waterlogging tolerance. The results showed that the waterlogging tolerances of C. lanuginosa and 'Sen-No-Kaze' were relatively poor, but were significantly improved by concentrations of 100 μmol·L-1 and 50 μmol·L-1 melatonin. C. tientaiensis and 'Viva Polonia' had relatively strong tolerance to waterlogging, and this was significantly improved by 200 μmol·L-1 melatonin. Under waterlogging stress, the relative conductivity and H2O2 content of Clematis increased significantly; the photosynthetic parameters and chlorophyll contents were significantly decreased; photosynthesis was inhibited; the contents of soluble protein and soluble sugars were decreased. Effective improvement of waterlogging tolerance after exogenous melatonin spraying, the relative conductivity was decreased by 4.05%-27.44%; the H2O2 content was decreased by 3.84%-23.28%; the chlorophyll content was increased by 35.59%-103.36%; the photosynthetic efficiency was increased by 25.42%-45.86%; the antioxidant enzyme activities of APX, POD, SOD, and CAT were increased by 28.03%-158.61%; the contents of proline, soluble protein, and soluble sugars were enhanced, and cell homeostasis was improved. Transcription sequencing was performed on wild Clematis with differences in waterlogging tolerance, and nine transcription factors were selected that were highly correlated with melatonin and that had the potential to improve waterlogging tolerance, among which LBD4, and MYB4 were significantly positively correlated with the antioxidant enzyme system, and bHLH36, DOF36, and WRKY4 were significantly negatively correlated. Photosynthetic capacity was positively correlated with DOF36 and WRKY4 while being significantly negatively correlated with MYB4, MOF1, DOF47, REV1 and ABR1. Melatonin could enhance the flooding tolerance of Clematis by improving photosynthetic efficiency and antioxidant enzyme activity. This study provides an important basis and reference for the application of melatonin in waterlogging-resistant breeding of Clematis.
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Affiliation(s)
- Kai Chen
- College of Landscape Architecture, Zhejiang A & F University, Hangzhou, China
- Wenzhou Key laboratory of Resource Plant Innovation and Utilization, Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Qingdi Hu
- Wenzhou Key laboratory of Resource Plant Innovation and Utilization, Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Xiaohua Ma
- Wenzhou Key laboratory of Resource Plant Innovation and Utilization, Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Xule Zhang
- Wenzhou Key laboratory of Resource Plant Innovation and Utilization, Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Renjuan Qian
- Wenzhou Key laboratory of Resource Plant Innovation and Utilization, Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
| | - Jian Zheng
- Wenzhou Key laboratory of Resource Plant Innovation and Utilization, Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, China
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Jiang Y, Zeng Z, He G, Liu M, Liu C, Liu M, Lv T, Wang A, Wang Y, Zhao M, Wang K, Zhang M. Genome-wide identification and integrated analysis of the FAR1/FHY3 gene family and genes expression analysis under methyl jasmonate treatment in Panax ginseng C. A. Mey. BMC PLANT BIOLOGY 2024; 24:549. [PMID: 38872078 DOI: 10.1186/s12870-024-05239-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 06/03/2024] [Indexed: 06/15/2024]
Abstract
Ginseng (Panax ginseng C. A. Mey.) is an important and valuable medicinal plant species used in traditional Chinese medicine, and its metabolite ginsenoside is the primary active ingredient. The FAR1/FHY3 gene family members play critical roles in plant growth and development as well as participate in a variety of physiological processes, including plant development and signaling of hormones. Studies have indicated that methyl jasmonate treatment of ginseng adventitious roots resulted in a significant increase in the content of protopanaxadiol ginsenosides. Therefore, it is highly significant to screen the FAR1/FHY3 gene family members in ginseng and preliminarily investigate their expression patterns in response to methyl jasmonic acid signaling. In this study, we screened and identified the FAR1/FHY3 family genes in the ginseng transcriptome databases. And then, we analyzed their gene structure and phylogeny, chromosomal localization and expression patterns, and promoter cis-acting elements, and made GO functional annotations on the members of this family. After that, we treated the ginseng adventitious roots with 200 mM methyl jasmonate and investigated the trend of the expression of four genes containing the largest number of methyl jasmonate cis-acting elements at different treatment times. All four genes were able to respond to methyl jasmonate, the most significant change was in the PgFAR40 gene. This study provides data support for subsequent studies of this family member in ginseng and provides experimental reference for subsequent validation of the function of this family member under methyl jasmonic acid signaling.
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Affiliation(s)
- Yang Jiang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Zixia Zeng
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Gaohui He
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Mengna Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Chang Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Mingming Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Tingting Lv
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Aimin Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Yi Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, Jilin, 130118, China
| | - Mingzhu Zhao
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China.
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, Jilin, 130118, China.
| | - Kangyu Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China.
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, Jilin, 130118, China.
| | - Meiping Zhang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, 130118, China.
- Jilin Engineering Research Center Ginseng Genetic Resources Development and Utilization, Jilin Agricultural University, Changchun, Jilin, 130118, China.
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Shi Q, Xia Y, Xue N, Wang Q, Tao Q, Li M, Xu D, Wang X, Kong F, Zhang H, Li G. Modulation of starch synthesis in Arabidopsis via phytochrome B-mediated light signal transduction. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:973-985. [PMID: 38391049 DOI: 10.1111/jipb.13630] [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: 07/17/2023] [Revised: 01/06/2024] [Accepted: 02/02/2024] [Indexed: 02/24/2024]
Abstract
Starch is a major storage carbohydrate in plants and is critical in crop yield and quality. Starch synthesis is intricately regulated by internal metabolic processes and external environmental cues; however, the precise molecular mechanisms governing this process remain largely unknown. In this study, we revealed that high red to far-red (high R:FR) light significantly induces the synthesis of leaf starch and the expression of synthesis-related genes, whereas low R:FR light suppress these processes. Arabidopsis phytochrome B (phyB), the primary R and FR photoreceptor, was identified as a critical positive regulator in this process. Downstream of phyB, basic leucine zipper transcription factor ELONGATED HYPOCOTYL5 (HY5) was found to enhance starch synthesis, whereas the basic helix-loop-helix transcription factors PHYTOCHROME INTERACTING FACTORs (PIF3, PIF4, and PIF5) inhibit starch synthesis in Arabidopsis leaves. Notably, HY5 and PIFs directly compete for binding to a shared G-box cis-element in the promoter region of genes encoding starch synthases GBSS, SS3, and SS4, which leads to antagonistic regulation of their expression and, consequently, starch synthesis. Our findings highlight the vital role of phyB in enhancing starch synthesis by stabilizing HY5 and facilitating PIFs degradation under high R:FR light conditions. Conversely, under low R:FR light, PIFs predominantly inhibit starch synthesis. This study provides insight into the physiological and molecular functions of phyB and its downstream transcription factors HY5 and PIFs in starch synthesis regulation, shedding light on the regulatory mechanism by which plants synchronize dynamic light signals with metabolic cues to module starch synthesis.
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Affiliation(s)
- Qingbiao Shi
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Ying Xia
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Na Xue
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Qibin Wang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Qing Tao
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Mingjing Li
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Di Xu
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
- National Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiaofei Wang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Fanying Kong
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Haisen Zhang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Gang Li
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
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Billah M, Renju L, Wei H, Qanmber G, Da Y, Lan Y, Qing-di Y, Fuguang L, Zhaoen Y. A cotton mitochondrial alternative electron transporter, GhD2HGDH, induces early flowering by modulating GA and photoperiodic pathways. PHYSIOLOGIA PLANTARUM 2024; 176:e14378. [PMID: 38887925 DOI: 10.1111/ppl.14378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/24/2024] [Accepted: 05/01/2024] [Indexed: 06/20/2024]
Abstract
D-2-hydroxyglutarate dehydrogenase (D2HGDH) is a mitochondrial enzyme containing flavin adenine dinucleotide FAD, existing as a dimer, and it facilitates the specific oxidation of D-2HG to 2-oxoglutarate (2-OG), which is a key intermediate in the tricarboxylic acid (TCA) cycle. A Genome-wide expression analysis (GWEA) has indicated an association between GhD2HGDH and flowering time. To further explore the role of GhD2HGDH, we performed a comprehensive investigation encompassing phenotyping, physiology, metabolomics, and transcriptomics in Arabidopsis thaliana plants overexpressing GhD2HGDH. Transcriptomic and qRT-PCR data exhibited heightened expression of GhD2HGDH in upland cotton flowers. Additionally, early-maturing cotton exhibited higher expression of GhD2HGDH across all tissues than delayed-maturing cotton. Subcellular localization confirmed its presence in the mitochondria. Overexpression of GhD2HGDH in Arabidopsis resulted in early flowering. Using virus-induced gene silencing (VIGS), we investigated the impact of GhD2HGDH on flowering in both early- and delayed-maturing cotton plants. Manipulation of GhD2HGDH expression levels led to changes in photosynthetic pigment and gas exchange attributes. GhD2HGDH responded to gibberellin (GA3) hormone treatment, influencing the expression of GA biosynthesis genes and repressing DELLA genes. Protein interaction studies, including yeast two-hybrid, luciferase complementation (LUC), and GST pull-down assays, confirmed the interaction between GhD2HGDH and GhSOX (Sulfite oxidase). The metabolomics analysis demonstrated GhD2HGDH's modulation of the TCA cycle through alterations in various metabolite levels. Transcriptome data revealed that GhD2HGDH overexpression triggers early flowering by modulating the GA3 and photoperiodic pathways of the flowering core factor genes. Taken together, GhD2HGDH positively regulates the network of genes associated with early flowering pathways.
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Affiliation(s)
- Masum Billah
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, China
| | - Liu Renju
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, China
| | - Hu Wei
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Ghulam Qanmber
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yan Da
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yang Lan
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, China
| | - Yan Qing-di
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, China
| | - Li Fuguang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yang Zhaoen
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
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Zhou SL, Zhang JX, Jiang S, Lu Y, Huang YS, Dong XM, Hu Q, Yao W, Zhang MQ, Xiao SH. Genome-wide identification of JAZ gene family in sugarcane and function analysis of ScJAZ1/2 in drought stress response and flowering regulation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108577. [PMID: 38579542 DOI: 10.1016/j.plaphy.2024.108577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/06/2024] [Accepted: 03/28/2024] [Indexed: 04/07/2024]
Abstract
The JASMONATE ZIM DOMAIN (JAZ) proteins are a key inhibitors of the jasmonic acid (JA) signaling pathway that play an important role in the regulation of plant growth and development and environmental stress responses. However, there is no systematic identification and functional analysis of JAZ gene family members in sugarcane. In this study, a total of 49 SsJAZ genes were identified from the wild sugarcane species Saccharum spontaneum genome that were unevenly distributed on 13 chromosomes. Phylogenetic analysis showed that all SsJAZ members can be divided into six groups, and most of the SsJAZ genes contained photoreactive and ABA-responsive elements. RNA-seq analysis revealed that SsJAZ1-1/2/3/4 and SsJAZ7-1 were significantly upregulated under drought stress. The transcript level of ScJAZ1 which is the homologous gene of SsJAZ1 in modern sugarcane cultivars was upregulated by JA, PEG, and abscisic acid (ABA). Moreover, ScJAZ1 can interact with three other JAZ proteins to form heterodimers. The spatial and temporal expression analysis showed that SsJAZ2-1/2/3/4 were highly expressed in different tissues and growth stages and during the day-night rhythm between 10:00 and 18:00. Overexpression of ScJAZ2 in Arabidopsis accelerated flowering through activating the expression of AtSOC1, AtFT, and AtLFY. Moreover, the transcription level of ScJAZ2 was about 30-fold in the early-flowering sugarcane variety than that of the non-flowering variety, indicating ScJAZ2 positively regulated flowering. This first systematic analysis of the JAZ gene family and function analysis of ScJAZ1/2 in sugarcane provide key candidate genes and lay the foundation for sugarcane breeding.
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Affiliation(s)
- Shao-Li Zhou
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Jin-Xu Zhang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Shuo Jiang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Yan Lu
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Yong-Shuang Huang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Xian-Man Dong
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Qin Hu
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Wei Yao
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Mu-Qing Zhang
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Sheng-Hua Xiao
- State Key Lab for Conservation and Utilization of Subtropical Agri-Biological Resources, Guangxi Key Lab for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China; Academy of Sugarcane and Sugar Industry, Guangxi University, Nanning, 530005, China.
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10
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Hughes CL, An Y, Maloof JN, Harmer SL. Light quality-dependent roles of REVEILLE proteins in the circadian system. PLANT DIRECT 2024; 8:e573. [PMID: 38481435 PMCID: PMC10936234 DOI: 10.1002/pld3.573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 01/25/2024] [Accepted: 02/10/2024] [Indexed: 03/17/2024]
Abstract
Several closely related Myb-like activator proteins are known to have partially redundant functions within the plant circadian clock, but their specific roles are not well understood. To clarify the function of the REVEILLE 4, REVEILLE 6, and REVEILLE 8 transcriptional activators, we characterized the growth and clock phenotypes of CRISPR-Cas9-generated single, double, and triple rve mutants. We found that these genes act synergistically to regulate flowering time, redundantly to regulate leaf growth, and antagonistically to regulate hypocotyl elongation. We previously reported that increasing intensities of monochromatic blue and red light have opposite effects on the period of triple rve468 mutants. Here, we further examined light quality-specific phenotypes of rve mutants and report that rve468 mutants lack the blue light-specific increase in expression of some circadian clock genes observed in wild type. To investigate the basis of these blue light-specific circadian phenotypes, we examined RVE protein abundances and degradation rates in blue and red light and found no significant differences between these conditions. We next examined genetic interactions between RVE genes and ZEITLUPE and ELONGATED HYPOCOTYL5, two factors with blue light-specific functions in the clock. We found that the RVEs interact additively with both ZEITLUPE and ELONGATED HYPOCOTYL5 to regulate circadian period, which suggests that neither of these factors are required for the blue light-specific differences that we observed. Overall, our results suggest that the RVEs have separable functions in plant growth and circadian regulation and that they are involved in blue light-specific circadian signaling via a novel mechanism.
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Affiliation(s)
- Cassandra L. Hughes
- Department of Plant BiologyUniversity of California, DavisDavisCaliforniaUSA
| | - Yuyan An
- College of Life SciencesShaanxi Normal UniversityXi'anChina
| | - Julin N. Maloof
- Department of Plant BiologyUniversity of California, DavisDavisCaliforniaUSA
| | - Stacey L. Harmer
- Department of Plant BiologyUniversity of California, DavisDavisCaliforniaUSA
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11
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Ren X, Chen L, Deng L, Zhao Q, Yao D, Li X, Cong W, Zang Z, Zhao D, Zhang M, Yang S, Zhang J. Comparative transcriptomic analysis reveals the molecular mechanism underlying seedling heterosis and its relationship with hybrid contemporary seeds DNA methylation in soybean. FRONTIERS IN PLANT SCIENCE 2024; 15:1364284. [PMID: 38444535 PMCID: PMC10913200 DOI: 10.3389/fpls.2024.1364284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 01/31/2024] [Indexed: 03/07/2024]
Abstract
Heterosis is widely used in crop production, but phenotypic dominance and its underlying causes in soybeans, a significant grain and oil crop, remain a crucial yet unexplored issue. Here, the phenotypes and transcriptome profiles of three inbred lines and their resulting F1 seedlings were analyzed. The results suggest that F1 seedlings with superior heterosis in leaf size and biomass exhibited a more extensive recompilation in their transcriptional network and activated a greater number of genes compared to the parental lines. Furthermore, the transcriptional reprogramming observed in the four hybrid combinations was primarily non-additive, with dominant effects being more prevalent. Enrichment analysis of sets of differentially expressed genes, coupled with a weighted gene co-expression network analysis, has shown that the emergence of heterosis in seedlings can be attributed to genes related to circadian rhythms, photosynthesis, and starch synthesis. In addition, we combined DNA methylation data from previous immature seeds and observed similar recompilation patterns between DNA methylation and gene expression. We also found significant correlations between methylation levels of gene region and gene expression levels, as well as the discovery of 12 hub genes that shared or conflicted with their remodeling patterns. This suggests that DNA methylation in contemporary hybrid seeds have an impact on both the F1 seedling phenotype and gene expression to some extent. In conclusion, our study provides valuable insights into the molecular mechanisms of heterosis in soybean seedlings and its practical implications for selecting superior soybean varieties.
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Affiliation(s)
- Xiaobo Ren
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Liangyu Chen
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
- Zhanjiang City Key Laboratory for Tropical Crops Genetic Improvement, South Subtropical Crops Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Lin Deng
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Qiuzhu Zhao
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Dan Yao
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Xueying Li
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Weixuan Cong
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Zhenyuan Zang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Dingyi Zhao
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Miao Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Songnan Yang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Jun Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
- National Crop Variety Approval and Characteristic Identification Station, Jilin Agricultural University, Changchun, China
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12
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He X, He Y, Dong Y, Gao Y, Sun X, Chen W, Xu X, Su C, Lv Y, Ren B, Yin H, Zeng J, Ma W, Mu P. Genome-wide analysis of FRF gene family and functional identification of HvFRF9 under drought stress in barley. FRONTIERS IN PLANT SCIENCE 2024; 15:1347842. [PMID: 38328701 PMCID: PMC10847358 DOI: 10.3389/fpls.2024.1347842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/09/2024] [Indexed: 02/09/2024]
Abstract
FHY3 and its homologous protein FAR1 are the founding members of FRS family. They exhibited diverse and powerful physiological functions during evolution, and participated in the response to multiple abiotic stresses. FRF genes are considered to be truncated FRS family proteins. They competed with FRS for DNA binding sites to regulate gene expression. However, only few studies are available on FRF genes in plants participating in the regulation of abiotic stress. With wide adaptability and high stress-resistance, barley is an excellent candidate for the identification of stress-resistance-related genes. In this study, 22 HvFRFs were detected in barley using bioinformatic analysis from whole genome. According to evolution and conserved motif analysis, the 22 HvFRFs could be divided into subfamilies I and II. Most promoters of subfamily I members contained abscisic acid and methyl jasmonate response elements; however, a large number promoters of subfamily II contained gibberellin and salicylic acid response elements. HvFRF9, one of the members of subfamily II, exhibited a expression advantage in different tissues, and it was most significantly upregulated under drought stress. In-situ PCR revealed that HvFRF9 is mainly expressed in the root epidermal cells, as well as xylem and phloem of roots and leaves, indicating that HvFRF9 may be related to absorption and transportation of water and nutrients. The results of subcellular localization indicated that HvFRF9 was mainly expressed in the nuclei of tobacco epidermal cells and protoplast of arabidopsis. Further, transgenic arabidopsis plants with HvFRF9 overexpression were generated to verify the role of HvFRF9 in drought resistance. Under drought stress, leaf chlorosis and wilting, MDA and O2 - contents were significantly lower, meanwhile, fresh weight, root length, PRO content, and SOD, CAT and POD activities were significantly higher in HvFRF9-overexpressing arabidopsis plants than in wild-type plants. Therefore, overexpression of HvFRF9 could significantly enhance the drought resistance in arabidopsis. These results suggested that HvFRF9 may play a key role in drought resistance in barley by increasing the absorption and transportation of water and the activity of antioxidant enzymes. This study provided a theoretical basis for drought resistance in barley and provided new genes for drought resistance breeding.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Ping Mu
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
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13
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Tang H, Jing D, Liu C, Xie X, Zhang L, Chen X, Li C. Genome-Wide Identification and Expression Analyses of the FAR1/FHY3 Gene Family Provide Insight into Inflorescence Development in Maize. Curr Issues Mol Biol 2024; 46:430-449. [PMID: 38248329 PMCID: PMC10814199 DOI: 10.3390/cimb46010027] [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: 12/04/2023] [Revised: 12/28/2023] [Accepted: 12/31/2023] [Indexed: 01/23/2024] Open
Abstract
As transcription factors derived from transposase, FAR-RED IMPAIRED RESPONSE1 (FAR1) and its homolog FHY3 play crucial roles in the regulation of light signaling and various stress responses by coordinating the expression of downstream target genes. Despite the extensive investigation of the FAR1/FHY3 family in Arabidopsis thaliana and other species, a comprehensive examination of these genes in maize has not been conducted thus far. In this study, we employed a genomic mining approach to identify 16 ZmFAR1 genes in the maize inbred line B73, which were further classified into five subgroups based on their phylogenetic relationships. The present study characterized the predicted polypeptide sequences, molecular weights, isoelectric points, chromosomal distribution, gene structure, conserved motifs, subcellular localizations, phylogenetic relationships, and cis-regulatory elements of all members belonging to the ZmFAR1 family. Furthermore, the tissue-specific expression of the 16 ZmFAR1 genes was analyzed using RNA-seq, and their expression patterns under far-red light conditions were validated in the ear and tassel through qRT-qPCR. The observed highly temporal and spatial expression patterns of these ZmFAR1 genes were likely associated with their specific functional capabilities under different light conditions. Further analysis revealed that six ZmFAR1 genes (ZmFAR1-1, ZmFAR1-10, ZmFAR1-11, ZmFAR1-12, ZmFAR1-14, and ZmFAR1-15) exhibited a response to simulated shading treatment and actively contributed to the development of maize ears. Through the integration of expression quantitative trait loci (eQTL) analyses and population genetics, we identified the presence of potential causal variations in ZmFAR1-14 and ZmFAR1-9, which play a crucial role in regulating the kernel row number and kernel volume weight, respectively. In summary, this study represents the initial identification and characterization of ZmFAR1 family members in maize, uncovering the functional variation in candidate regulatory genes associated with the improvement of significant agronomic traits during modern maize breeding.
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Affiliation(s)
- Huaijun Tang
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (H.T.); (C.L.); (X.X.); (L.Z.)
| | - De Jing
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
| | - Cheng Liu
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (H.T.); (C.L.); (X.X.); (L.Z.)
| | - Xiaoqing Xie
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (H.T.); (C.L.); (X.X.); (L.Z.)
| | - Lei Zhang
- Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (H.T.); (C.L.); (X.X.); (L.Z.)
| | - Xunji Chen
- Institute of Nuclear and Biotechnology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Changyu Li
- Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
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14
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Kim SC, Edgeworth KN, Nusinow DA, Wang X. Circadian clock factors regulate the first condensation reaction of fatty acid synthesis in Arabidopsis. Cell Rep 2023; 42:113483. [PMID: 37995186 PMCID: PMC10842715 DOI: 10.1016/j.celrep.2023.113483] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/16/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023] Open
Abstract
The circadian clock regulates temporal metabolic activities, but how it affects lipid metabolism is poorly understood. Here, we show that the central clock regulators LATE ELONGATED HYPOCOTYL (LHY) and CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) regulate the initial step of fatty acid (FA) biosynthesis in Arabidopsis. Triacylglycerol (TAG) accumulation in seeds was increased in LHY-overexpressing (LHY-OE) and decreased in lhycca1 plants. Metabolic tracking of lipids in developing seeds indicated that LHY enhanced FA synthesis. Transcript analysis revealed that the expression of genes involved in FA synthesis, including the one encoding β-ketoacyl-ACP synthase III (KASIII), was oppositely changed in developing seeds of LHY/CCA1-OEs and lhycca1. Chromatin immunoprecipitation, electrophoretic mobility shift, and transactivation assays indicated that LHY bound and activated the promoter of KASIII. Furthermore, phosphatidic acid, a metabolic precursor to TAG, inhibited LHY binding to KASIII promoter elements. Our data show a regulatory mechanism for plant lipid biosynthesis by the molecular clock.
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Affiliation(s)
- Sang-Chul Kim
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Kristen N Edgeworth
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA; Department of Biological and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO 63130, USA
| | | | - Xuemin Wang
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
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15
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Parmar S, Janila P, Gangurde SS, Variath MT, Sharma V, Bomireddy D, Manohar SS, Varshney RK, Singam P, Pandey MK. Genetic mapping identified major main-effect and three co-localized quantitative trait loci controlling high iron and zinc content in groundnut. THE PLANT GENOME 2023; 16:e20361. [PMID: 37408143 DOI: 10.1002/tpg2.20361] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 07/07/2023]
Abstract
Malnutrition is a major challenge globally, and groundnut is a highly nutritious self-pollinated legume crop blessed with ample genomic resources, including the routine deployment of genomic-assisted breeding. This study aimed to identify genomic regions and candidate genes for high iron (Fe) and zinc (Zn) content, utilizing a biparental mapping population (ICGV 00440 × ICGV 06040;). Genetic mapping and quantitative trait locus (QTL) analysis (474 mapped single-nucleotide polymorphism loci; 1536.33 cM) using 2 seasons of phenotypic data together with genotypic data identified 5 major main-effect QTLs for Fe content. These QTLs exhibited log-of-odds (LOD) scores ranging from 6.5 to 7.4, explaining phenotypic variation (PVE) ranging from 22% (qFe-Ah01) to 30.0% (qFe-Ah14). Likewise, four major main effect QTLs were identified for Zn content, with LOD score ranging from 4.4 to 6.8 and PVE ranging from 21.8% (qZn-Ah01) to 32.8% (qZn-Ah08). Interestingly, three co-localized major and main effect QTLs (qFe-Ah01, qZn-Ah03, and qFe-Ah11) were identified for both Fe and Zn contents. These genomic regions harbored key candidate genes, including zinc/iron permease transporter, bZIP transcription factor, and vacuolar iron transporter which likely play pivotal roles in the accumulation of Fe and Zn contents in seeds. The findings of this study hold potential for fine mapping and diagnostic marker development for high Fe and Zn contents in groundnut.
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Affiliation(s)
- Sejal Parmar
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - Pasupuleti Janila
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sunil S Gangurde
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Murali T Variath
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vinay Sharma
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Deekshitha Bomireddy
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Surendra S Manohar
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev K Varshney
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Prashant Singam
- Department of Genetics, Osmania University, Hyderabad, India
| | - Manish K Pandey
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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16
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Shanmugaraj N, Rajaraman J, Kale S, Kamal R, Huang Y, Thirulogachandar V, Garibay-Hernández A, Budhagatapalli N, Tandron Moya YA, Hajirezaei MR, Rutten T, Hensel G, Melzer M, Kumlehn J, von Wirén N, Mock HP, Schnurbusch T. Multilayered regulation of developmentally programmed pre-anthesis tip degeneration of the barley inflorescence. THE PLANT CELL 2023; 35:3973-4001. [PMID: 37282730 PMCID: PMC10615218 DOI: 10.1093/plcell/koad164] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/17/2023] [Accepted: 06/04/2023] [Indexed: 06/08/2023]
Abstract
Leaf and floral tissue degeneration is a common feature in plants. In cereal crops such as barley (Hordeum vulgare L.), pre-anthesis tip degeneration (PTD) starts with growth arrest of the inflorescence meristem dome, which is followed basipetally by the degeneration of floral primordia and the central axis. Due to its quantitative nature and environmental sensitivity, inflorescence PTD constitutes a complex, multilayered trait affecting final grain number. This trait appears to be highly predictable and heritable under standardized growth conditions, consistent with a developmentally programmed mechanism. To elucidate the molecular underpinnings of inflorescence PTD, we combined metabolomic, transcriptomic, and genetic approaches to show that barley inflorescence PTD is accompanied by sugar depletion, amino acid degradation, and abscisic acid responses involving transcriptional regulators of senescence, defense, and light signaling. Based on transcriptome analyses, we identified GRASSY TILLERS1 (HvGT1), encoding an HD-ZIP transcription factor, as an important modulator of inflorescence PTD. A gene-edited knockout mutant of HvGT1 delayed PTD and increased differentiated apical spikelets and final spikelet number, suggesting a possible strategy to increase grain number in cereals. We propose a molecular framework that leads to barley PTD, the manipulation of which may increase yield potential in barley and other related cereals.
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Affiliation(s)
- Nandhakumar Shanmugaraj
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Jeyaraman Rajaraman
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Sandip Kale
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Roop Kamal
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Yongyu Huang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Venkatasubbu Thirulogachandar
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Adriana Garibay-Hernández
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Nagaveni Budhagatapalli
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Yudelsy Antonia Tandron Moya
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Mohammed R Hajirezaei
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Götz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Michael Melzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Nicolaus von Wirén
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Hans-Peter Mock
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, Seeland 06466,Germany
- Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Halle 06120,Germany
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17
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Zheng Y, Sun Y, Liu Y. Emerging Roles of FHY3 and FAR1 as System Integrators in Plant Development. PLANT & CELL PHYSIOLOGY 2023; 64:1139-1145. [PMID: 37384577 DOI: 10.1093/pcp/pcad068] [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: 03/31/2023] [Revised: 06/07/2023] [Accepted: 06/27/2023] [Indexed: 07/01/2023]
Abstract
FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and its homolog FAR-RED-IMPAIRED RESPONSE1 (FAR1) are transcription factors derived from transposases essential for phytochrome A-mediated light signaling. In addition to their essential role in light signaling, FHY3 and FAR1 also play diverse regulatory roles in plant growth and development, including clock entrainment, seed dormancy and germination, senescence, chloroplast formation, branching, flowering and meristem development. Notably, accumulating evidence indicates that the emerging role of FHY3 and FAR1 in environmental stress signaling has begun to be revealed. In this review, we summarize these recent findings in the context of FHY3 and FAR1 as integrators of light and other developmental and stressful signals. We also discuss the antagonistic action of FHY3/FAR1 and Phytochrome Interating Factors (PIFs) in various cross-talks between light, hormone and environmental cues.
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Affiliation(s)
| | - Yanzhao Sun
- College of Horticulture, China Agricultural University, 2 Yuanmingyuan West Road, Haidian District, Beijing 100094, China
| | - Yang Liu
- College of Horticulture, China Agricultural University, 2 Yuanmingyuan West Road, Haidian District, Beijing 100094, China
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Kanojia A, Bhola D, Mudgil Y. Light signaling as cellular integrator of multiple environmental cues in plants. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1485-1503. [PMID: 38076763 PMCID: PMC10709290 DOI: 10.1007/s12298-023-01364-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/01/2023] [Accepted: 09/14/2023] [Indexed: 12/17/2023]
Abstract
Plants being sessile need to rapidly adapt to the constantly changing environment through modifications in their internal clock, metabolism, and gene expression. They have evolved an intricate system to perceive and transfer the signals from the primary environmental factors namely light, temperature and water to regulate their growth development and survival. Over past few decades rigorous research using molecular genetics approaches, especially in model plant Arabidopsis, has resulted in substantial progress in discovering various photoreceptor systems and light signaling components. In parallel several molecular pathways operating in response to other environmental cues have also been elucidated. Interestingly, the studies have shown that expression profiles of genes involved in photomorphogenesis can undergo modulation in response to other cues from the environment. Recently, the photoreceptor, PHYB, has been shown to function as a thermosensor. Downstream components of light signaling pathway like COP1 and PIF have also emerged as integrating hubs for various kinds of signals. All these findings indicate that light signaling components may act as central integrator of various environmental cues to regulate plant growth and development processes. In this review, we present a perspective on cross talk of signaling mechanisms induced in response to myriad array of signals and their integration with the light signaling components. By putting light signals on the central stage, we propose the possibilities of enhancing plant resilience to the changing environment by fine-tuning the genetic manipulation of its signaling components in the future.
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Affiliation(s)
- Abhishek Kanojia
- Department of Botany, University of Delhi, New Delhi, 110007 India
| | - Diksha Bhola
- Department of Botany, University of Delhi, New Delhi, 110007 India
| | - Yashwanti Mudgil
- Department of Botany, University of Delhi, New Delhi, 110007 India
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19
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Hughes CL, Harmer SL. Myb-like transcription factors have epistatic effects on circadian clock function but additive effects on plant growth. PLANT DIRECT 2023; 7:e533. [PMID: 37811362 PMCID: PMC10557472 DOI: 10.1002/pld3.533] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/23/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023]
Abstract
The functions of closely related Myb-like repressor and Myb-like activator proteins within the plant circadian oscillator have been well-studied as separate groups, but the genetic interactions between them are less clear. We hypothesized that these repressors and activators would interact additively to regulate both circadian and growth phenotypes. We used CRISPR-Cas9 to generate new mutant alleles and performed physiological and molecular characterization of plant mutants for five of these core Myb-like clock factors compared with a repressor mutant and an activator mutant. We first examined circadian clock function in plants likely null for both the repressor proteins, CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY), and the activator proteins, REVEILLE 4 (RVE4), REVEILLE (RVE6), and REVEILLE (RVE8). The rve468 triple mutant has a long period and flowers late, while cca1 lhy rve468 quintuple mutants, similarly to cca1 lhy mutants, have poor circadian rhythms and flower early. This suggests that CCA1 and LHY are epistatic to RVE4, RVE6, and RVE8 for circadian clock and flowering time function. We next examined hypocotyl elongation and rosette leaf size in these mutants. The cca1 lhy rve468 mutants have growth phenotypes intermediate between cca1 lhy and rve468 mutants, suggesting that CCA1, LHY, RVE4, RVE6, and RVE8 interact additively to regulate growth. Together, our data suggest that these five Myb-like factors interact differently in regulation of the circadian clock versus growth. More generally, the near-norm al seedling phenotypes observed in the largely arrhythmic quintuple mutant demonstrate that circadian-regulated output processes, like control of hypocotyl elongation, do not always depend upon rhythmic oscillator function.
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Affiliation(s)
| | - Stacey L. Harmer
- Department of Plant BiologyUniversity of CaliforniaDavisCaliforniaUSA
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20
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Singh V, Singh V. Characterizing the circadian connectome of Ocimum tenuiflorum using an integrated network theoretic framework. Sci Rep 2023; 13:13108. [PMID: 37567911 PMCID: PMC10421869 DOI: 10.1038/s41598-023-40212-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023] Open
Abstract
Across the three domains of life, circadian clock is known to regulate vital physiological processes, like, growth, development, defence etc. by anticipating environmental cues. In this work, we report an integrated network theoretic methodology comprising of random walk with restart and graphlet degree vectors to characterize genome wide core circadian clock and clock associated raw candidate proteins in a plant for which protein interaction information is available. As a case study, we have implemented this framework in Ocimum tenuiflorum (Tulsi); one of the most valuable medicinal plants that has been utilized since ancient times in the management of a large number of diseases. For that, 24 core clock (CC) proteins were mined in 56 template plant genomes to build their hidden Markov models (HMMs). These HMMs were then used to identify 24 core clock proteins in O. tenuiflorum. The local topology of the interologous Tulsi protein interaction network was explored to predict the CC associated raw candidate proteins. Statistical and biological significance of the raw candidates was determined using permutation and enrichment tests. A total of 66 putative CC associated proteins were identified and their functional annotation was performed.
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Affiliation(s)
- Vikram Singh
- Centre for Computational Biology and Bioinformatics, Central University of Himahcal Pradesh, Dharamshala, Himahcal Pradesh, 176206, India
| | - Vikram Singh
- Centre for Computational Biology and Bioinformatics, Central University of Himahcal Pradesh, Dharamshala, Himahcal Pradesh, 176206, India.
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21
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Chen Q, Song Y, Liu K, Su C, Yu R, Li Y, Yang Y, Zhou B, Wang J, Hu G. Genome-Wide Identification and Functional Characterization of FAR1-RELATED SEQUENCE ( FRS) Family Members in Potato ( Solanum tuberosum). PLANTS (BASEL, SWITZERLAND) 2023; 12:2575. [PMID: 37447143 DOI: 10.3390/plants12132575] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/01/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023]
Abstract
FAR1-RELATED SEQUENCE (FRS) transcription factors are generated by transposases and play vital roles in plant growth and development, light signaling transduction, phytohormone response, and stress resistance. FRSs have been described in various plant species. However, FRS family members and their functions remain poorly understood in vegetative crops such as potato (Solanum tuberosum, St). In the present study, 20 putative StFRS proteins were identified in potato via genome-wide analysis. They were non-randomly localized to eight chromosomes and phylogenetic analysis classified them into six subgroups along with FRS proteins from Arabidopsis and tomato. Conserved protein motif, protein domain, and gene structure analyses supported the evolutionary relationships among the FRS proteins. Analysis of the cis-acting elements in the promoters and the expression profiles of StFRSs in various plant tissues and under different stress treatments revealed the spatiotemporal expression patterns and the potential roles of StFRSs in phytohormonal and stress responses. StFRSs were differentially expressed in the cultivar "Xisen 6", which is exposed to a variety of stresses. Hence, these genes may be critical in regulating abiotic stress. Elucidating the StFRS functions will lay theoretical and empirical foundations for the molecular breeding of potato varieties with high light use efficiency and stress resistance.
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Affiliation(s)
- Qingshuai Chen
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Yang Song
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
- College of Life Science, Dezhou University, Dezhou 253023, China
| | - Kui Liu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Chen Su
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
- College of Life Science, Dezhou University, Dezhou 253023, China
| | - Ru Yu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Ying Li
- College of Life Science, Dezhou University, Dezhou 253023, China
| | - Yi Yang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Bailing Zhou
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Guodong Hu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
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22
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Zhang M, Zhang M, Wang J, Dai S, Zhang M, Meng Q, Ma N, Zhuang K. Salicylic acid regulates two photosystem II protection pathways in tomato under chilling stress mediated by ETHYLENE INSENSITIVE 3-like proteins. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:1385-1404. [PMID: 36948885 DOI: 10.1111/tpj.16199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/10/2023] [Indexed: 06/17/2023]
Abstract
Chilling stress seriously impairs photosynthesis and activates a series of molecular responses in plants. Previous studies have shown that ETHYLENE INSENSITIVE 3 (EIN3) and EIN3-like (SlEIL) proteins mediate ethylene signaling and reduce plant tolerance to freezing in tomato (Solanum lycopersicum). However, the specific molecular mechanisms underlying an EIN3/EILs-mediated photoprotection pathway under chilling stress are unclear. Here, we discovered that salicylic acid (SA) participates in photosystem II (PSII) protection via SlEIL2 and SlEIL7. Under chilling stress, the phenylalanine ammonia-lyase gene SlPAL5 plays an important role in the production of SA, which also induces WHIRLY1 (SlWHY1) transcription. The resulting accumulation of SlWHY1 activates SlEIL7 expression under chilling stress. SlEIL7 then binds to and blocks the repression domain of the heat shock factor SlHSFB-2B, releasing its inhibition of HEAT SHOCK PROTEIN 21 (HSP21) expression to maintain PSII stability. In addition, SlWHY1 indirectly represses SlEIL2 expression, allowing the expression of l-GALACTOSE-1-PHOSPHATE PHOSPHATASE3 (SlGPP3). The ensuing higher SlGPP3 abundance promotes the accumulation of ascorbic acid (AsA), which scavenges reactive oxygen species produced upon chilling stress and thus protects PSII. Our study demonstrates that SlEIL2 and SlEIL7 protect PSII under chilling stress via two different SA response mechanisms: one involving the antioxidant AsA and the other involving the photoprotective chaperone protein HSP21.
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Affiliation(s)
- Meng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Mingyue Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Jieyu Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Shanshan Dai
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Minghui Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Qingwei Meng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Nana Ma
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Kunyang Zhuang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, 271018, China
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23
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Huang T, Liu H, Tao JP, Zhang JQ, Zhao TM, Hou XL, Xiong AS, You X. Low light intensity elongates period and defers peak time of photosynthesis: a computational approach to circadian-clock-controlled photosynthesis in tomato. HORTICULTURE RESEARCH 2023; 10:uhad077. [PMID: 37323229 PMCID: PMC10261901 DOI: 10.1093/hr/uhad077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 04/09/2023] [Indexed: 06/17/2023]
Abstract
Photosynthesis is involved in the essential process of transforming light energy into chemical energy. Although the interaction between photosynthesis and the circadian clock has been confirmed, the mechanism of how light intensity affects photosynthesis through the circadian clock remains unclear. Here, we propose a first computational model for circadian-clock-controlled photosynthesis, which consists of the light-sensitive protein P, the core oscillator, photosynthetic genes, and parameters involved in the process of photosynthesis. The model parameters were determined by minimizing the cost function ( [Formula: see text]), which is defined by the errors of expression levels, periods, and phases of the clock genes (CCA1, PRR9, TOC1, ELF4, GI, and RVE8). The model recapitulates the expression pattern of the core oscillator under moderate light intensity (100 μmol m -2 s-1). Further simulation validated the dynamic behaviors of the circadian clock and photosynthetic outputs under low (62.5 μmol m-2 s-1) and normal (187.5 μmol m-2 s-1) intensities. When exposed to low light intensity, the peak times of clock and photosynthetic genes were shifted backward by 1-2 hours, the period was elongated by approximately the same length, and the photosynthetic parameters attained low values and showed delayed peak times, which confirmed our model predictions. Our study reveals a potential mechanism underlying the circadian regulation of photosynthesis by the clock under different light intensities in tomato.
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Affiliation(s)
- Ting Huang
- College of Horticulture, Nanjing Agricultural University/State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Horticultural Crop Biology and Germplasm Creation in East China of Ministry of Agriculture and Rural Affairs Nanjing 210095, Jiangsu, China
| | - Hui Liu
- College of Horticulture, Nanjing Agricultural University/State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Horticultural Crop Biology and Germplasm Creation in East China of Ministry of Agriculture and Rural Affairs Nanjing 210095, Jiangsu, China
| | - Jian-Ping Tao
- College of Horticulture, Nanjing Agricultural University/State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Horticultural Crop Biology and Germplasm Creation in East China of Ministry of Agriculture and Rural Affairs Nanjing 210095, Jiangsu, China
- The Institute of Agricultural Information, Jiangsu Province Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China
| | - Jia-Qi Zhang
- College of Horticulture, Nanjing Agricultural University/State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Horticultural Crop Biology and Germplasm Creation in East China of Ministry of Agriculture and Rural Affairs Nanjing 210095, Jiangsu, China
| | - Tong-Min Zhao
- Laboratory for Genetic Improvement of High Efficiency Horticultural Crops in Jiangsu Province, Institute of Vegetable Crop, Jiangsu Province Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China
| | - Xi-Lin Hou
- College of Horticulture, Nanjing Agricultural University/State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Horticultural Crop Biology and Germplasm Creation in East China of Ministry of Agriculture and Rural Affairs Nanjing 210095, Jiangsu, China
| | - Ai-Sheng Xiong
- College of Horticulture, Nanjing Agricultural University/State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Horticultural Crop Biology and Germplasm Creation in East China of Ministry of Agriculture and Rural Affairs Nanjing 210095, Jiangsu, China
| | - Xiong You
- College of Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu China
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24
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Wang Q, Liu M, Quan S, Shi Q, Tian T, Zhang H, Wang H, Li G. FAR-RED ELONGATED HYPOCOTYL3 increases leaf longevity by delaying senescence in arabidopsis. PLANT, CELL & ENVIRONMENT 2023; 46:1582-1595. [PMID: 36721872 DOI: 10.1111/pce.14554] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/04/2023] [Accepted: 01/15/2023] [Indexed: 06/18/2023]
Abstract
Senescence is the final stage of leaf development, limits and dictates the longevity of leaf. This stage is strictly controlled by internal developmental age signals and external environmental signals. However, the underlying mechanisms by which various signals integrating together to regulate leaf senescence remain largely unknown. Here, we show that the light signalling protein FAR-RED ELONGATED HYPOCOTYL3 (FHY3) directly represses the transcription of PHYTOCHROME-INTERACTING FACTOR4 (PIF4) and NON-YELLOWING1/STAY-GREEN1 (NYE1/SGR1), two key regulators of senescence, thus preventing chlorophyll degradation and extending the leaf longevity in Arabidopsis thaliana. Disrupting either PIF4 or NYE1 function completely rescued the early leaf senescence of fhy3-4 mutant. Interestingly, we found that FHY3 competes with PIF4 to bind to the G-box cis-element in NYE1 promoter, subsequently preventing the transcriptional activation of this gene by PIF4. Moreover, FHY3 transcript levels gradually increased in senescent leaves, which consist with disrupting FHY3 function accelerated chlorophyll degradation and shorted the leaf longevity. All these findings reveal that FHY3 is a master regulator that participates in multiple signalling pathways to increase leaf longevity. In addition, our study shed light on the dynamic regulatory mechanisms by which plants integrate light signalling and internal developmental cues to control leaf senescence and longevity.
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Affiliation(s)
- Qibin Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Meiling Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Shuxuan Quan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Qingbiao Shi
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Tian Tian
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Haisen Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Haiyang Wang
- State Key Laboratory for Conservation and Utilisation of Subtropical Agro-Bioresources, School of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Gang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
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25
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Li S, Mao X, He Z, Xu S, Guo Z, Shi S. Chromosomal-Scale Genome Assemblies of Two Coastal Plant Species, Scaevola taccada and S. hainanensis-Insight into Adaptation Outside of the Common Range. Int J Mol Sci 2023; 24:ijms24087355. [PMID: 37108516 PMCID: PMC10138301 DOI: 10.3390/ijms24087355] [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: 03/03/2023] [Revised: 04/07/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
While most of the species in Goodeniaceae family, excluding the Scaevola genus, are endemic to Australasia, S. taccada and S. hainanensis have expanded their distribution range to the tropical coastlines of the Atlantic and Indian Oceans. S. taccada appears to be highly adapted to coastal sandy lands and cliffs, and it has become invasive in places. S. hainanensis is found mainly in salt marshes near mangrove forests, and is at risk of extinction. These two species provide a good system to investigate adaptive evolution outside the common distribution range of this taxonomic group. Here, we report their chromosomal-scale genome assemblies with the objective of probing their genomic mechanisms related to divergent adaptation after leaving Australasia. The scaffolds were assembled into eight chromosome-scale pseudomolecules, which covered 90.12% and 89.46% of the whole genome assembly for S. taccada and S. hainanensis, respectively. Interestingly, unlike many mangroves, neither species has undergone whole-genome duplication. We show that private genes, specifically copy-number expanded genes are essential for stress response, photosynthesis, and carbon fixation. The gene families that are expanded in S. hainanensis and contracted in S. taccada might have facilitated adaptation to high salinity in S. hainanensis. Moreover, the genes under positive selection in S. hainanensis have contributed to its response to stress and its tolerance of flooding and anoxic environments. In contrast, compared with S. hainanensis, the more drastic copy number expansion of FAR1 genes in S. taccada might have facilitated its adaptation to the stronger light radiation present in sandy coastal lands. In conclusion, our study of the chromosomal-scale genomes of S. taccada and S. hainanensis provides novel insights into their genomic evolution after leaving Australasia.
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Affiliation(s)
- Sen Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Xiaomeng Mao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Department of Ecology and Genetics, Plant Ecology and Evolution, Uppsala University, Norbyvägen 18D, 75267 Uppsala, Sweden
| | - Ziwen He
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Shaohua Xu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- School of Ecology, Sun Yat-sen University, Guangzhou 510275, China
| | - Zixiao Guo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519082, China
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26
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Cai Z, Wang G, Li J, Kong L, Tang W, Chen X, Qu X, Lin C, Peng Y, Liu Y, Deng Z, Ye Y, Wu W, Duan Y. Thermo-Sensitive Spikelet Defects 1 acclimatizes rice spikelet initiation and development to high temperature. PLANT PHYSIOLOGY 2023; 191:1684-1701. [PMID: 36517254 PMCID: PMC10022635 DOI: 10.1093/plphys/kiac576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 10/20/2022] [Indexed: 06/17/2023]
Abstract
Crop reproductive development is vulnerable to heat stress, and the genetic modulation of thermotolerance during the reproductive phase, especially the early stage, remains poorly understood. We isolated a Poaceae-specific FAR-RED ELONGATED HYPOCOTYLS3 (FHY3)/FAR-RED IMPAIRED RESPONSE1 (FAR1)family transcription factor, Thermo-sensitive Spikelet Defects 1 (TSD1), derived from transposase in rice (Oryza sativa) TSD1 was highly expressed in spikelets, induced by heat, and specifically enhanced the thermotolerance of spikelet morphogenesis. Disrupting TSD1 did not affect vegetative growth but markedly retarded spikelet initiation and development, as well as caused varying degrees of spikelet degeneration, depending on the temperature. Most tsd1 spikelets were normal at low temperature but gradually degenerated as temperature increased, and all disappeared at high temperature, leading to naked branches. TSD1 directly promoted the transcription of YABBY1 and YABBY3 and could physically interact with YABBY1 and three TOB proteins, YABBY5, YABBY4, and YABBY3. These YABBY proteins can form either homodimers or heterodimers and play an important role in spikelet morphogenesis, similar to TSD1. Notably, the knockout mutant yab5-ko and double mutant tsd1 yab5-ko resembled tsd1 in spikelet appearance and response to temperature, indicating that these genes likely participate in spikelet development through the cooperative TSD1-YABBY module. These findings reveal a distinctive function of FHY3/FAR1 family genes and a unique TSD1-YABBY complex to acclimate spikelet development to high temperature in rice, providing insight into the regulating pathway of enhancing thermotolerance in plant reproductive development.
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Affiliation(s)
- Zhengzheng Cai
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops and Fujian Provincial Key Laboratory of Breeding by Design of Plant, Fujian Agriculture & Forestry University, Fuzhou 350002, China
| | - Gang Wang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops and Fujian Provincial Key Laboratory of Breeding by Design of Plant, Fujian Agriculture & Forestry University, Fuzhou 350002, China
| | - Jieqiong Li
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops and Fujian Provincial Key Laboratory of Breeding by Design of Plant, Fujian Agriculture & Forestry University, Fuzhou 350002, China
| | - Lan Kong
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops and Fujian Provincial Key Laboratory of Breeding by Design of Plant, Fujian Agriculture & Forestry University, Fuzhou 350002, China
| | - Weiqi Tang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops and Fujian Provincial Key Laboratory of Breeding by Design of Plant, Fujian Agriculture & Forestry University, Fuzhou 350002, China
| | - Xuequn Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops and Fujian Provincial Key Laboratory of Breeding by Design of Plant, Fujian Agriculture & Forestry University, Fuzhou 350002, China
| | - Xiaojie Qu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops and Fujian Provincial Key Laboratory of Breeding by Design of Plant, Fujian Agriculture & Forestry University, Fuzhou 350002, China
| | - Chenchen Lin
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops and Fujian Provincial Key Laboratory of Breeding by Design of Plant, Fujian Agriculture & Forestry University, Fuzhou 350002, China
| | - Yulin Peng
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops and Fujian Provincial Key Laboratory of Breeding by Design of Plant, Fujian Agriculture & Forestry University, Fuzhou 350002, China
| | - Yang Liu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops and Fujian Provincial Key Laboratory of Breeding by Design of Plant, Fujian Agriculture & Forestry University, Fuzhou 350002, China
| | - Zhanlin Deng
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops and Fujian Provincial Key Laboratory of Breeding by Design of Plant, Fujian Agriculture & Forestry University, Fuzhou 350002, China
| | - Yanfang Ye
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops and Fujian Provincial Key Laboratory of Breeding by Design of Plant, Fujian Agriculture & Forestry University, Fuzhou 350002, China
| | - Weiren Wu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops and Fujian Provincial Key Laboratory of Breeding by Design of Plant, Fujian Agriculture & Forestry University, Fuzhou 350002, China
| | - Yuanlin Duan
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops and Fujian Provincial Key Laboratory of Breeding by Design of Plant, Fujian Agriculture & Forestry University, Fuzhou 350002, China
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Qiu L, Zhou P, Wang H, Zhang C, Du C, Tian S, Wu Q, Wei L, Wang X, Zhou Y, Huang R, Huang X, Ouyang X. Photoperiod Genes Contribute to Daylength-Sensing and Breeding in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:899. [PMID: 36840246 PMCID: PMC9959395 DOI: 10.3390/plants12040899] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/04/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Rice (Oryza sativa L.), one of the most important food crops worldwide, is a facultative short-day (SD) plant in which flowering is modulated by seasonal and temperature cues. The photoperiodic molecular network is the core network for regulating flowering in rice, and is composed of photoreceptors, a circadian clock, a photoperiodic flowering core module, and florigen genes. The Hd1-DTH8-Ghd7-PRR37 module, a photoperiodic flowering core module, improves the latitude adaptation through mediating the multiple daylength-sensing processes in rice. However, how the other photoperiod-related genes regulate daylength-sensing and latitude adaptation remains largely unknown. Here, we determined that mutations in the photoreceptor and circadian clock genes can generate different daylength-sensing processes. Furthermore, we measured the yield-related traits in various mutants, including the main panicle length, grains per panicle, seed-setting rate, hundred-grain weight, and yield per panicle. Our results showed that the prr37, elf3-1 and ehd1 mutants can change the daylength-sensing processes and exhibit longer main panicle lengths and more grains per panicle. Hence, the PRR37, ELF3-1 and Ehd1 locus has excellent potential for latitude adaptation and production improvement in rice breeding. In summary, this study systematically explored how vital elements of the photoperiod network regulate daylength sensing and yield traits, providing critical information for their breeding applications.
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Affiliation(s)
- Leilei Qiu
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350002, China
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Peng Zhou
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350002, China
| | - Hao Wang
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Cheng Zhang
- Liaoning Rice Research Institute, Shenyang 110101, China
| | - Chengxing Du
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Shujun Tian
- Liaoning Rice Research Institute, Shenyang 110101, China
| | - Qinqin Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Litian Wei
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Xiaoying Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yiming Zhou
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Rongyu Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Xi Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Xinhao Ouyang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
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28
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Zhang P, Zhu W, He Y, Fan J, Shi J, Fu R, Hu J, Li L, Zhang D, Liang W. THERMOSENSITIVE BARREN PANICLE (TAP) is required for rice panicle and spikelet development at high ambient temperature. THE NEW PHYTOLOGIST 2023; 237:855-869. [PMID: 36263719 DOI: 10.1111/nph.18551] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
In cereal plants, the size of the panicle (inflorescence) is a critical factor for yield. Panicle size is determined by a complex interplay of genetic and environmental factors, but the mechanisms underlying adaptations to temperature stress during panicle development remain largely unknown. We identify the rice THERMOSENSITIVE BARREN PANICLE (TAP) gene, which encodes a transposase-derived FAR1-RELATED SEQUENCE (FRS) protein and is responsible for regulating panicle and spikelet development at high ambient temperature. The tap mutants display high temperature-dependent reproductive abnormalities, including compromised secondary branch and spikelet initiation and pleiotropic floral organ defects. Consistent with its thermosensitive phenotype, TAP expression is induced by high temperature. TAP directly promotes the expression of OsYABBY3 (OsYAB3), OsYAB4, and OsYAB5, which encode key transcriptional regulators in panicle and spikelet development. In addition, TAP physically interacts with OsYAB4 and OsYAB5 proteins; phenotypic analysis of osyab4 tap-1 and osyab5 tap-1 double mutants indicates that TAP-OsYAB4/OsYAB5 complexes act to maintain normal panicle and spikelet development. Taken together, our study reveals the novel role of a TE-derived transcription factor in controlling rice panicle development under high ambient temperatures, shedding light on the molecular mechanism underlying the adaptation of cereal crops to increasing environmental temperatures.
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Affiliation(s)
- Peng Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, China
| | - Wanwan Zhu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, China
| | - Yi He
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, China
| | - Junyi Fan
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, China
| | - Jin Shi
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, China
| | - Ruifeng Fu
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, China
| | - Jianping Hu
- Department of Energy Plant Research Laboratory and Plant Biology Department, Michigan State University, East Lansing, MI, 48824, USA
| | - Li Li
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, China
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 20040, China
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29
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BREVIPEDICELLUS Positively Regulates Salt-Stress Tolerance in Arabidopsis thaliana. Int J Mol Sci 2023; 24:ijms24021054. [PMID: 36674568 PMCID: PMC9866879 DOI: 10.3390/ijms24021054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/15/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023] Open
Abstract
Salt stress is one of the major environmental threats to plant growth and development. However, the mechanisms of plants responding to salt stress are not fully understood. Through genetic screening, we identified and characterized a salt-sensitive mutant, ses5 (sensitive to salt 5), in Arabidopsis thaliana. Positional cloning revealed that the decreased salt-tolerance of ses5 was caused by a mutation in the transcription factor BP (BREVIPEDICELLUS). BP regulates various developmental processes in plants. However, the biological function of BP in abiotic stress-signaling and tolerance are still not clear. Compared with wild-type plants, the bp mutant exhibited a much shorter primary-root and lower survival rate under salt treatment, while the BP overexpressors were more tolerant. Further analysis showed that BP could directly bind to the promoter of XTH7 (xyloglucan endotransglucosylase/hydrolase 7) and activate its expression. Resembling the bp mutant, the disruption of XTH7 gave rise to salt sensitivity. These results uncovered novel roles of BP in positively modulating salt-stress tolerance, and illustrated a putative working mechanism.
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30
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Li W, Tian YY, Li JY, Yuan L, Zhang LL, Wang ZY, Xu X, Davis SJ, Liu JX. A competition-attenuation mechanism modulates thermoresponsive growth at warm temperatures in plants. THE NEW PHYTOLOGIST 2023; 237:177-191. [PMID: 36028981 DOI: 10.1111/nph.18442] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Global warming has profound impact on growth and development, and plants constantly adjust their internal circadian clock to cope with external environment. However, how clock-associated genes fine-tune thermoresponsive growth in plants is little understood. We found that loss-of-function mutation of REVEILLE5 (RVE5) reduces the expression of circadian gene EARLY FLOWERING 4 (ELF4) in Arabidopsis, and confers accelerated hypocotyl growth under warm-temperature conditions. Both RVE5 and CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) accumulate at warm temperatures and bind to the same EE cis-element presented on ELF4 promoter, but the transcriptional repression activity of RVE5 is weaker than that of CCA1. The binding of CCA1 to ELF4 promoter is enhanced in the rve5-2 mutant at warm temperatures, and overexpression of ELF4 in the rve5-2 mutant background suppresses the rve5-2 mutant phenotype at warm temperatures. Therefore, the transcriptional repressor RVE5 finetunes ELF4 expression via competing at a cis-element with the stronger transcriptional repressor CCA1 at warm temperatures. Such a competition-attenuation mechanism provides a balancing system for modulating the level of ELF4 and thermoresponsive hypocotyl growth under warm-temperature conditions.
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Affiliation(s)
- Wei Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Ying-Ying Tian
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Jin-Yu Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Li Yuan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Lin-Lin Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Zhi-Ye Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Xiaodong Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Seth Jon Davis
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Jian-Xiang Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
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31
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ERF49 mediates brassinosteroid regulation of heat stress tolerance in Arabidopsis thaliana. BMC Biol 2022; 20:254. [DOI: 10.1186/s12915-022-01455-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 10/31/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Heat stress is a major abiotic stress affecting the growth and development of plants, including crop species. Plants have evolved various adaptive strategies to help them survive heat stress, including maintaining membrane stability, encoding heat shock proteins (HSPs) and ROS-scavenging enzymes, and inducing molecular chaperone signaling. Brassinosteroids (BRs) are phytohormones that regulate various aspects of plant development, which have been implicated also in plant responses to heat stress, and resistance to heat in Arabidopsis thaliana is enhanced by adding exogenous BR. Brassinazole resistant 1 (BZR1), a transcription factor and positive regulator of BR signal, controls plant growth and development by directly regulating downstream target genes. However, the molecular mechanism at the basis of BR-mediated heat stress response is poorly understood. Here, we report the identification of a new factor critical for BR-regulated heat stress tolerance.
Results
We identified ERF49 in a genetic screen for proteins required for BR-regulated gene expression. We found that ERF49 is the direct target gene of BZR1 and that overexpressing ERF49 enhanced sensitivity of transgenic plants to heat stress. The transcription levels of heat shock factor HSFA2, heat stress-inducible gene DREB2A, and three heat shock protein (HSP) were significantly reduced under heat stress in ERF49-overexpressed transgenic plants. Transcriptional activity analysis in protoplast revealed that BZR1 inhibits ERF49 expression by binding to the promoter of ERF49. Our genetic analysis showed that dominant gain-of-function brassinazole resistant 1-1D mutant (bzr1-1D) exhibited lower sensitivity to heat stress compared with wild-type. Expressing ERF49-SRDX (a dominant repressor reporter of ERF49) in bzr1-1D significantly decreased the sensitivity of ERF49-SRDX/bzr1-1D transgenic plants to heat stress compared to bzr1-1D.
Conclusions
Our data provide clear evidence that BR increases thermotolerance of plants by repressing the expression of ERF49 through BZR1, and this process is dependent on the expression of downstream heat stress-inducible genes. Taken together, our work reveals a novel molecular mechanism mediating plant response to high temperature stress.
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32
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Wang S, Steed G, Webb AAR. Circadian entrainment in Arabidopsis. PLANT PHYSIOLOGY 2022; 190:981-993. [PMID: 35512209 PMCID: PMC9516740 DOI: 10.1093/plphys/kiac204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Circadian clocks coordinate physiology and development as an adaption to the oscillating day/night cycle caused by the rotation of Earth on its axis and the changing length of day and night away from the equator caused by orbiting the sun. Circadian clocks confer advantages by entraining to rhythmic environmental cycles to ensure that internal events within the plant occur at the correct time with respect to the cyclic external environment. Advances in determining the structure of circadian oscillators and the pathways that allow them to respond to light, temperature, and metabolic signals have begun to provide a mechanistic insight to the process of entrainment in Arabidopsis (Arabidopsis thaliana). We describe the concepts of entrainment and how it occurs. It is likely that a thorough mechanistic understanding of the genetic and physiological basis of circadian entrainment will provide opportunities for crop improvement.
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Affiliation(s)
- Shouming Wang
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
- School of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China
| | - Gareth Steed
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
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33
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Cheng Y, Xiang N, Cheng X, Chen H, Guo X. Effect of photoperiod on polyphenol biosynthesis and cellular antioxidant capacity in mung bean (Vigna radiata) sprouts. Food Res Int 2022; 159:111626. [DOI: 10.1016/j.foodres.2022.111626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 06/29/2022] [Accepted: 07/05/2022] [Indexed: 11/04/2022]
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34
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A guiding role of the Arabidopsis circadian clock in cell differentiation revealed by time-series single-cell RNA sequencing. Cell Rep 2022; 40:111059. [PMID: 35830805 DOI: 10.1016/j.celrep.2022.111059] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 04/01/2022] [Accepted: 06/14/2022] [Indexed: 11/21/2022] Open
Abstract
Circadian rhythms and progression of cell differentiation are closely coupled in multicellular organisms. However, whether establishment of circadian rhythms regulates cell differentiation or vice versa has not been elucidated due to technical limitations. Here, we exploit high cell fate plasticity of plant cells to perform single-cell RNA sequencing during the entire process of cell differentiation. By analyzing reconstructed actual time series of the differentiation processes at single-cell resolution using a method we developed (PeakMatch), we find that the expression profile of clock genes is changed prior to cell differentiation, including induction of the clock gene LUX ARRYTHMO (LUX). ChIP sequencing analysis reveals that LUX induction in early differentiating cells directly targets genes involved in cell-cycle progression to regulate cell differentiation. Taken together, these results not only reveal a guiding role of the plant circadian clock in cell differentiation but also provide an approach for time-series analysis at single-cell resolution.
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35
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Cerca J, Petersen B, Lazaro-Guevara JM, Rivera-Colón A, Birkeland S, Vizueta J, Li S, Li Q, Loureiro J, Kosawang C, Díaz PJ, Rivas-Torres G, Fernández-Mazuecos M, Vargas P, McCauley RA, Petersen G, Santos-Bay L, Wales N, Catchen JM, Machado D, Nowak MD, Suh A, Sinha NR, Nielsen LR, Seberg O, Gilbert MTP, Leebens-Mack JH, Rieseberg LH, Martin MD. The genomic basis of the plant island syndrome in Darwin's giant daisies. Nat Commun 2022; 13:3729. [PMID: 35764640 PMCID: PMC9240058 DOI: 10.1038/s41467-022-31280-w] [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: 12/06/2021] [Accepted: 06/09/2022] [Indexed: 12/04/2022] Open
Abstract
The repeated, rapid and often pronounced patterns of evolutionary divergence observed in insular plants, or the ‘plant island syndrome’, include changes in leaf phenotypes, growth, as well as the acquisition of a perennial lifestyle. Here, we sequence and describe the genome of the critically endangered, Galápagos-endemic species Scalesia atractyloides Arnot., obtaining a chromosome-resolved, 3.2-Gbp assembly containing 43,093 candidate gene models. Using a combination of fossil transposable elements, k-mer spectra analyses and orthologue assignment, we identify the two ancestral genomes, and date their divergence and the polyploidization event, concluding that the ancestor of all extant Scalesia species was an allotetraploid. There are a comparable number of genes and transposable elements across the two subgenomes, and while their synteny has been mostly conserved, we find multiple inversions that may have facilitated adaptation. We identify clear signatures of selection across genes associated with vascular development, growth, adaptation to salinity and flowering time, thus finding compelling evidence for a genomic basis of the island syndrome in one of Darwin’s giant daisies. Many island plant species share a syndrome of characteristic phenotype and life history. Cerca et al. find the genomic basis of the plant island syndrome in one of Darwin’s giant daisies, while separating ancestral genomes in a chromosome-resolved polyploid assembly.
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Affiliation(s)
- José Cerca
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway.
| | - Bent Petersen
- Centre for Evolutionary Hologenomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen, Denmark.,Centre of Excellence for Omics-Driven Computational Biodiscovery, Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - José Miguel Lazaro-Guevara
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Angel Rivera-Colón
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Siri Birkeland
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.,Natural History Museum, University of Oslo, Oslo, Norway
| | - Joel Vizueta
- Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Siyu Li
- Department of Plant Biology, University of California, Davis, Davis, CA, 95616, USA
| | - Qionghou Li
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - João Loureiro
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-095, Coimbra, Portugal
| | - Chatchai Kosawang
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark
| | - Patricia Jaramillo Díaz
- Estación Científica Charles Darwin, Fundación Charles Darwin, Santa Cruz, Galápagos, Ecuador.,Department of Botany and Plant Physiology, University of Malaga, Malaga, Spain
| | - Gonzalo Rivas-Torres
- Colegio de Ciencias Biológicas y Ambientales COCIBA & Extensión Galápagos, Universidad San Francisco de Quito USFQ, Quito, 170901, Ecuador.,Galapagos Science Center, USFQ, UNC Chapel Hill, San Cristobal, Galapagos, Ecuador.,Estación de Biodiversidad Tiputini, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito USFQ, Quito, Ecuador.,Courtesy Faculty, Department of Wildlife Ecology and Conservation, University of Florida, 110 Newins-Ziegler Hall, Gainesville, FL, 32611, USA
| | | | - Pablo Vargas
- Departamento de Biodiversidad y Conservación, Real Jardín Botánico (RJB-CSIC), Plaza de Murillo 2, 28014, Madrid, Spain
| | - Ross A McCauley
- Department of Biology, Fort Lewis College, Durango, CO, 81301, USA
| | - Gitte Petersen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Luisa Santos-Bay
- Centre for Evolutionary Hologenomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen, Denmark
| | - Nathan Wales
- Department of Archaeology, University of York, York, UK
| | - Julian M Catchen
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - Daniel Machado
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, 7491, Norway
| | | | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich Research Park, NR4 7TU, Norwich, UK.,Department of Organismal Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, 75236, Uppsala, Sweden
| | - Neelima R Sinha
- Department of Plant Biology, University of California, Davis, Davis, CA, 95616, USA
| | - Lene R Nielsen
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Rolighedsvej 23, 1958, Frederiksberg C, Denmark
| | - Ole Seberg
- The Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway.,Centre for Evolutionary Hologenomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen, Denmark
| | | | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway.
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36
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Li S, Li Q, Tian X, Mu L, Ji M, Wang X, Li N, Liu F, Shu J, Crawford NM, Wang Y. PHB3 regulates lateral root primordia formation via NO-mediated degradation of AUXIN/INDOLE-3-ACETIC ACID proteins. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4034-4045. [PMID: 35303089 DOI: 10.1093/jxb/erac115] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/16/2022] [Indexed: 05/21/2023]
Abstract
We have previously shown that Arabidopsis thaliana Prohibitin 3 (PHB3) controls auxin-stimulated lateral root (LR) formation; however, the underlying molecular mechanism is unknown. Here, we demonstrate that PHB3 regulates lateral root (LR) development mainly through influencing lateral root primordia (LRP) initiation, via affecting nitric oxide (NO) accumulation. The reduced LRP in phb3 mutant was largely rescued by treatment with a NO donor. The decreased NO accumulation in phb3 caused a lower expression of GATA TRANSCRIPTION FACTOR 23 (GATA23) and LATERAL ORGAN BOUNDARIES DOMAIN 16 (LBD16) through inhibiting the degradation of INDOLE-3-ACETIC ACID INDUCIBLE 14/28 (IAA14/28). Overexpression of either GATA23 or LBD16 in phb3 mutant background recovered the reduced density of LRP. These results indicate that PHB3 regulates LRP initiation via NO-mediated auxin signalling, by modulating the degradation of IAA14/28.
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Affiliation(s)
- Shuna Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Qingqing Li
- College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, China
| | - Xiao Tian
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Lijun Mu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Meiling Ji
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Xiaoping Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Na Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Fei Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
| | - Jing Shu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
- College of Agriculture Science and Technology, Shandong Agriculture and Engineering University, Jinan Shandong, China
| | - Nigel M Crawford
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California, USA
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China
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37
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PIF-independent regulation of growth by an evening complex in the liverwort Marchantia polymorpha. PLoS One 2022; 17:e0269984. [PMID: 35709169 PMCID: PMC9202859 DOI: 10.1371/journal.pone.0269984] [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: 01/19/2022] [Accepted: 06/01/2022] [Indexed: 11/27/2022] Open
Abstract
Previous studies in the liverwort Marchantia polymorpha have shown that the putative evening complex (EC) genes LUX ARRHYTHMO (LUX) and ELF4-LIKE (EFL) have a function in the liverwort circadian clock. Here, we studied the growth phenotypes of MpLUX and MpEFL loss-of-function mutants, to establish if PHYTOCHROME-INTERACTING FACTOR (PIF) and auxin act downstream of the M. polymorpha EC in a growth-related pathway similar to the one described for the flowering plant Arabidopsis. We examined growth rates and cell properties of loss-of-function mutants, analyzed protein-protein interactions and performed gene expression studies using reporter genes. Obtained data indicate that an EC can form in M. polymorpha and that this EC regulates growth of the thallus. Altered auxin levels in Mplux mutants could explain some of the phenotypes related to an increased thallus surface area. However, because MpPIF is not regulated by the EC, and because Mppif mutants do not show reduced growth, the growth phenotype of EC-mutants is likely not mediated via MpPIF. In Arabidopsis, the circadian clock regulates elongation growth via PIF and auxin, but this is likely not an evolutionarily conserved growth mechanism in land plants. Previous inventories of orthologs to Arabidopsis clock genes in various plant lineages showed that there is high levels of structural differences between clocks of different plant lineages. Here, we conclude that there is also variation in the output pathways used by the different plant clocks to control growth and development.
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Rhodes BM, Siddiqui H, Khan S, Devlin PF. Dual Role for FHY3 in Light Input to the Clock. FRONTIERS IN PLANT SCIENCE 2022; 13:862387. [PMID: 35755710 PMCID: PMC9218818 DOI: 10.3389/fpls.2022.862387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
The red-light regulated transcription factors FHY3 and FAR1 form a key point of light input to the plant circadian clock in positively regulating expression of genes within the central clock. However, the fhy3 mutant shows an additional red light-specific disruption of rhythmicity which is inconsistent with this role. Here we demonstrate that only fhy3 and not far1 mutants show this red specific disruption of rhythmicity. We examined the differences in rhythmic transcriptome in red versus white light and reveal differences in patterns of rhythmicity among the central clock proteins suggestive of a change in emphasis within the central mechanism of the clock, changes which underlie the red specificity of the fhy3 mutant. In particular, changes in enrichment of promoter elements were consistent with a key role for the HY5 transcription factor, a known integrator of the ratio of red to blue light in regulation of the clock. Examination of differences in the rhythmic transcriptome in the fhy3 mutant in red light identified specific disruption of the CCA1-regulated ELF3 and LUX central clock genes, while the CCA1 target TBS element, TGGGCC, was enriched among genes that became arrhythmic. Coupled with the known interaction of FHY3 but not FAR1 with CCA1 we propose that the red-specific circadian phenotype of fhy3 may involve disruption of the previously demonstrated moderation of CCA1 activity by FHY3 rather than a disruption of its own transcriptional regulatory activity. Together, this evidence suggests a conditional redundancy between FHY3 and HY5 in the integration of red and blue light input to the clock in order to enable a plasticity in response to light and optimise plant adaptation. Furthermore, our evidence also suggests changes in CCA1 activity between red and white light transcriptomes. This, together with the documented interaction of HY5 with CCA1, leads us to propose a model whereby this integration of red and blue signals may at least partly occur via direct FHY3 and HY5 interaction with CCA1 leading to moderation of CCA1 activity.
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Affiliation(s)
| | | | | | - Paul F. Devlin
- Department of Biological Sciences, Royal Holloway, University of London, Egham, United Kingdom
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Phan KAT, Paeng SK, Chae HB, Park JH, Lee ES, Wi SD, Bae SB, Kim MG, Yun D, Kim W, Lee SY. Universal Stress Protein (
USP
) regulates the circadian rhythm of central oscillator genes in
Arabidopsis. FEBS Lett 2022; 596:1871-1880. [DOI: 10.1002/1873-3468.14410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 05/18/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Kieu Anh Thi Phan
- Division of Applied Life Science (BK21+) and PMBBRC, 2College of Pharmacy Gyeongsang National University Jinju, 52828 Korea
| | - Seol Ki Paeng
- Division of Applied Life Science (BK21+) and PMBBRC, 2College of Pharmacy Gyeongsang National University Jinju, 52828 Korea
| | - Ho Byoung Chae
- Division of Applied Life Science (BK21+) and PMBBRC, 2College of Pharmacy Gyeongsang National University Jinju, 52828 Korea
| | - Joung Hun Park
- Division of Applied Life Science (BK21+) and PMBBRC, 2College of Pharmacy Gyeongsang National University Jinju, 52828 Korea
| | - Eun Seon Lee
- Division of Applied Life Science (BK21+) and PMBBRC, 2College of Pharmacy Gyeongsang National University Jinju, 52828 Korea
| | - Seong Dong Wi
- Division of Applied Life Science (BK21+) and PMBBRC, 2College of Pharmacy Gyeongsang National University Jinju, 52828 Korea
| | - Su Bin Bae
- Division of Applied Life Science (BK21+) and PMBBRC, 2College of Pharmacy Gyeongsang National University Jinju, 52828 Korea
| | | | - Dae‐Jin Yun
- Department of Biomedical Science & Engineering Konkuk University Seoul, 05029 Korea
| | - Woe‐Yeon Kim
- Division of Applied Life Science (BK21+) and PMBBRC, 2College of Pharmacy Gyeongsang National University Jinju, 52828 Korea
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21+) and PMBBRC, 2College of Pharmacy Gyeongsang National University Jinju, 52828 Korea
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Li JY, Yang C, Tian YY, Liu JX. Regulation of Chloroplast Development and Function at Adverse Temperatures in Plants. PLANT & CELL PHYSIOLOGY 2022; 63:580-591. [PMID: 35141744 DOI: 10.1093/pcp/pcac022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
The chloroplast is essential for photosynthesis, plant growth and development. As semiautonomous organelles, the biogenesis and development of chloroplasts need to be well-regulated during plant growth and stress responses. Low or high ambient temperatures are adverse environmental stresses that affect crop growth and productivity. As sessile organisms, plants regulate the development and function of chloroplasts in a fluctuating temperature environment to maintain normal photosynthesis. This review focuses on the molecular mechanisms and regulatory factors required for chloroplast biogenesis and development under cold or heat stress conditions and highlights the importance of chloroplast gene transcription, RNA metabolism, ribosome function and protein homeostasis essential for chloroplast development under adverse temperature conditions.
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Affiliation(s)
- Jin-Yu Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, No. 866, Yuhangtang Road, Hangzhou, Zhejiang 310027, China
| | - Chuang Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, No. 866, Yuhangtang Road, Hangzhou, Zhejiang 310027, China
| | - Ying-Ying Tian
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, No. 866, Yuhangtang Road, Hangzhou, Zhejiang 310027, China
| | - Jian-Xiang Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, No. 866, Yuhangtang Road, Hangzhou, Zhejiang 310027, China
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Liu Y, Sun Y, Yao H, Zheng Y, Cao S, Wang H. Arabidopsis Circadian Clock Repress Phytochrome a Signaling. FRONTIERS IN PLANT SCIENCE 2022; 13:809563. [PMID: 35645991 PMCID: PMC9131076 DOI: 10.3389/fpls.2022.809563] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 04/04/2022] [Indexed: 06/15/2023]
Abstract
The plants' internal circadian clock can strongly influence phytochrome signaling in response to the changes in the external light environment. Phytochrome A (phyA) is the photoreceptor that mediates various far-red (FR) light responses. phyA signaling is modulated by FHY3 and FAR1, which directly activate the transcription of FHY1 and FHL, whose products are essential for light-induced phyA nuclear accumulation and subsequent light responses. However, the mechanisms by which the clock regulates phyA signaling are poorly understood. Here, we discovered that FHY1 expression is diurnally regulated, peaking in the middle of the day. Two Arabidopsis core clock components, CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and TIMING OF CAB EXPRESSION1 (TOC1), repress FHY3/FAR1-mediated FHY1/FHL activation. Consistently, the specific expression pattern of FHY1 under diurnal conditions is altered in cca1-1, toc1-101, CCA1, and TOC1 overexpression plants. Furthermore, far-red induced gene expression and particularly nuclear accumulation of phyA are compromised in TOC1 and CCA1 overexpression seedlings. Our results therefore revealed a previously unidentified FHY1 expression pattern in diurnal cycles, which is negatively regulated by CCA1 and TOC1.
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Affiliation(s)
- Yang Liu
- College of Horticulture, China Agricultural University, Beijing, China
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
| | - Yanzhao Sun
- College of Horticulture, China Agricultural University, Beijing, China
| | - Heng Yao
- College of Horticulture, China Agricultural University, Beijing, China
| | - Yanyan Zheng
- College of Horticulture, China Agricultural University, Beijing, China
| | - Shuyuan Cao
- College of Horticulture, China Agricultural University, Beijing, China
| | - Haiyang Wang
- College of Life Sciences, South China Agricultural University, Guangzhou, China
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Dai J, Sun J, Peng W, Liao W, Zhou Y, Zhou XR, Qin Y, Cheng Y, Cao S. FAR1/FHY3 Transcription Factors Positively Regulate the Salt and Temperature Stress Responses in Eucalyptus grandis. FRONTIERS IN PLANT SCIENCE 2022; 13:883654. [PMID: 35599891 PMCID: PMC9115564 DOI: 10.3389/fpls.2022.883654] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/05/2022] [Indexed: 06/15/2023]
Abstract
FAR-RED ELONGATED HYPOCOTYLS3 (FHY3) and its homolog FAR-RED IMPAIRED RESPONSE1 (FAR1), which play pivotal roles in plant growth and development, are essential for the photo-induced phyA nuclear accumulation and subsequent photoreaction. The FAR1/FHY3 family has been systematically characterized in some plants, but not in Eucalyptus grandis. In this study, genome-wide identification of FAR1/FHY3 genes in E. grandis was performed using bioinformatic methods. The gene structures, chromosomal locations, the encoded protein characteristics, 3D models, phylogenetic relationships, and promoter cis-elements were analyzed with this gene family. A total of 33 FAR1/FHY3 genes were identified in E. grandis, which were divided into three groups based on their phylogenetic relationships. A total of 21 pairs of duplicated repeats were identified by homology analysis. Gene expression analysis showed that most FAR1/FHY3 genes were differentially expressed in a spatial-specific manner. Gene expression analysis also showed that FAR1/FHY3 genes responded to salt and temperature stresses. These results and observation will enhance our understanding of the evolution and function of the FAR1/FHY3 genes in E. grandis and facilitate further studies on the molecular mechanism of the FAR1/FHY3 gene family in growth and development regulations, especially in response to salt and temperature.
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Affiliation(s)
- Jiahao Dai
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- University Key Laboratory of Forest Stress Physiology, Ecology and Molecular Biology of Fujian Province, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jin Sun
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenjing Peng
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenhai Liao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- University Key Laboratory of Forest Stress Physiology, Ecology and Molecular Biology of Fujian Province, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuhan Zhou
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xue-Rong Zhou
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, ACT, Australia
| | - Yuan Qin
- Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, College of Life Science, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Yan Cheng
- Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign School of Integrative Biology Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, College of Life Science, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shijiang Cao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- University Key Laboratory of Forest Stress Physiology, Ecology and Molecular Biology of Fujian Province, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
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Dash M, Somvanshi VS, Godwin J, Budhwar R, Sreevathsa R, Rao U. Exploring Genomic Variations in Nematode-Resistant Mutant Rice Lines. FRONTIERS IN PLANT SCIENCE 2022; 13:823372. [PMID: 35401589 PMCID: PMC8988285 DOI: 10.3389/fpls.2022.823372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Rice (Oryza sativa) production is seriously affected by the root-knot nematode Meloidogyne graminicola, which has emerged as a menace in upland and irrigated rice cultivation systems. Previously, activation tagging in rice was utilized to identify candidate gene(s) conferring resistance against M. graminicola. T-DNA insertional mutants were developed in a rice landrace (acc. JBT 36/14), and four mutant lines showed nematode resistance. Whole-genome sequencing of JBT 36/14 was done along with the four nematode resistance mutant lines to identify the structural genetic variations that might be contributing to M. graminicola resistance. Sequencing on Illumina NovaSeq 6000 platform identified 482,234 genetic variations in JBT 36/14 including 448,989 SNPs and 33,245 InDels compared to reference indica genome. In addition, 293,238-553,648 unique SNPs and 32,395-65,572 unique InDels were found in the four mutant lines compared to their JBT 36/14 background, of which 93,224 SNPs and 8,170 InDels were common between all the mutant lines. Functional annotation of genes containing these structural variations showed that the majority of them were involved in metabolism and growth. Trait analysis revealed that most of these genes were involved in morphological traits, physiological traits and stress resistance. Additionally, several families of transcription factors, such as FAR1, bHLH, and NAC, and putative susceptibility (S) genes, showed the presence of SNPs and InDels. Our results indicate that subject to further genetic validations, these structural genetic variations may be involved in conferring nematode resistance to the rice mutant lines.
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Affiliation(s)
- Manoranjan Dash
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | | | - Roli Budhwar
- Bionivid Technology Private Limited, Bangalore, India
| | | | - Uma Rao
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Thabet SG, Alomari DZ, Brinch-Pedersen H, Alqudah AM. Genetic analysis toward more nutritious barley grains for a food secure world. BOTANICAL STUDIES 2022; 63:6. [PMID: 35267113 PMCID: PMC8913823 DOI: 10.1186/s40529-022-00334-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Understanding the relationships between nutrition, human health and plant food source is among the highest priorities for public health. Therefore, enhancing the minerals content such as iron (Fe), zinc (Zn) and selenium (Se) in barley (Hordeum vulgare L.) grains is an urgent need to improve the nutritive value of barley grains in overcoming malnutrition and its potential consequencing. This study aimed to expedite biofortification of barley grains by elucidating the genetic basis of Zn, Fe, and Se accumulation in the grains, which will contribute to improved barley nutritional quality. RESULTS A genome-wide association study (GWAS) was conducted to detect the genetic architecture for grain Zn, Fe, and Se accumulations in 216 spring barley accessions across two years. All the accessions were genotyped by single nucleotide polymorphisms (SNPs) molecular markers. Mineral heritability values ranging from moderate to high were revealed in both environments. Remarkably, there was a high natural phenotypic variation for all micronutrient accumulation in the used population. High-LD SNP markers (222 SNPs) were detected to be associated with all micronutrients in barley grains across the two environments plus BLUEs. Three genomic regions were detected based on LD, which were identified for the most effective markers that had associations with more than one trait. The strongest SNP-trait associations were found to be physically located within genes that may be involved in grain Zn and Fe homeostasis. Two putative candidate genes were annotated as Basic helix loop helix (BHLH) family transcription factor and Squamosa promoter binding-like protein, respectively, and have been suggested as candidates for increased grain Zn, Fe, and Se accumulation. CONCLUSIONS These findings shed a light on the genetic basis of Zn, Fe, and Se accumulation in barley grains and have the potential to assist plant breeders in selecting accessions with high micronutrient concentrations to enhance grain quality and, ultimately human health.
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Affiliation(s)
- Samar G Thabet
- Department of Botany, Faculty of Science, Fayoum University, Fayoum, 63514, Egypt.
| | - Dalia Z Alomari
- Department of Agroecology, Aarhus University, 4200, Flakkebjerg, Slagelse, Denmark
| | | | - Ahmad M Alqudah
- Department of Agroecology, Aarhus University, 4200, Flakkebjerg, Slagelse, Denmark.
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Wang F, Wang X, Zhang Y, Yan J, Ahammed GJ, Bu X, Sun X, Liu Y, Xu T, Qi H, Qi M, Li T. SlFHY3 and SlHY5 act compliantly to enhance cold tolerance through the integration of myo-inositol and light signaling in tomato. THE NEW PHYTOLOGIST 2022; 233:2127-2143. [PMID: 34936108 DOI: 10.1111/nph.17934] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Plants have evolved sophisticated regulatory networks to cope with dynamically changing light and temperature environments during day-night and seasonal cycles. However, the integration mechanisms of light and low temperature remain largely unclear. Here, we show that low red : far-red ratio (LR : FR) induces FAR-RED ELONGATED HYPOCOTYL3 (SlFHY3) transcription under cold stress in tomato (Solanum lycopersicum). Reverse genetic approaches revealed that knocking out SlFHY3 decreases myo-inositol accumulation and increases cold susceptibility, whereas overexpressing SlFHY3 induces myo-inositol accumulation and enhances cold tolerance in tomato plants. SlFHY3 physically interacts with ELONGATED HYPOCOTYL5 (SlHY5) to promote the transcriptional activity of SlHY5 on MYO-INOSITOL-1-PHOSPHATE SYNTHASE 3 (SlMIPS3) and induce myo-inositol accumulation in tomato plants under cold stress. Disruption of SlHY5 and SlMIPS3 largely suppresses the cold tolerance of SlFHY3-overexpressing plants and myo-inositol accumulation in tomato. Furthermore, silencing of SlMIPS3 drastically reduces myo-inositol accumulation and compromises LR : FR-induced cold tolerance in tomato. Together, our results reveal a crucial role of SlFHY3 in LR : FR-induced cold tolerance in tomato and unravel a novel regulatory mechanism whereby plants integrate dynamic environmental light signals and internal cues (inositol biosynthesis) to induce and control cold tolerance in tomato plants.
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Affiliation(s)
- Feng Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang, 110866, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, 110866, China
| | - Xiujie Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Ying Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Jiarong Yan
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Golam Jalal Ahammed
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471000, China
| | - Xin Bu
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xin Sun
- College of Land and Environment, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yufeng Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang, 110866, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, 110866, China
| | - Tao Xu
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang, 110866, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, 110866, China
| | - Hongyan Qi
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang, 110866, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, 110866, China
| | - Mingfang Qi
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang, 110866, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, 110866, China
| | - Tianlai Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture, Ministry of Education, Shenyang, 110866, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, 110866, China
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Blanca J, Sanchez-Matarredona D, Ziarsolo P, Montero-Pau J, van der Knaap E, Díez MJ, Cañizares J. Haplotype analyses reveal novel insights into tomato history and domestication driven by long-distance migrations and latitudinal adaptations. HORTICULTURE RESEARCH 2022; 9:uhac030. [PMID: 35184177 PMCID: PMC8976693 DOI: 10.1093/hr/uhac030] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 01/14/2022] [Indexed: 05/22/2023]
Abstract
A novel haplotype-based approach that uses Procrustes analysis and automatic classification was used to provide further insights into tomato history and domestication. Agrarian societies domesticated species of interest by introducing complex genetic modifications. For tomatoes, two species, one of which had two botanical varieties, are thought to be involved in its domestication: the fully wild Solanum pimpinellifolium (SP), the wild and semi-domesticated Solanum lycopersicum var. cerasiforme (SLC) and the cultivated S. l. var. lycopersicum (SLL). The Procrustes approach showed that SP evolved into SLC during a gradual migration from the Peruvian deserts to the Mexican rainforests and that Peruvian and Ecuadorian SLC populations were the result of more recent hybridizations. Our model was supported by independent evidence, including ecological data from the accession collection site and morphological data. Furthermore, we showed that photosynthesis-, and flowering time-related genes were selected during the latitudinal migrations.
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Affiliation(s)
- Jose Blanca
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana, COMAV, Universitat Politècnica de València, Valencia 46022, Spain
| | - David Sanchez-Matarredona
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana, COMAV, Universitat Politècnica de València, Valencia 46022, Spain
| | - Peio Ziarsolo
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana, COMAV, Universitat Politècnica de València, Valencia 46022, Spain
| | - Javier Montero-Pau
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana, COMAV, Universitat Politècnica de València, Valencia 46022, Spain
| | - Esther van der Knaap
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA
- Department of Horticulture, University of Georgia, Athens, GA 30602, USA
| | - Ma José Díez
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana, COMAV, Universitat Politècnica de València, Valencia 46022, Spain
| | - Joaquín Cañizares
- Instituto Universitario de Conservación y Mejora de la Agrodiversidad Valenciana, COMAV, Universitat Politècnica de València, Valencia 46022, Spain
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Hosaka GK, Correr FH, da Silva CC, Sforça DA, Barreto FZ, Balsalobre TWA, Pasha A, de Souza AP, Provart NJ, Carneiro MS, Margarido GRA. Temporal Gene Expression in Apical Culms Shows Early Changes in Cell Wall Biosynthesis Genes in Sugarcane. FRONTIERS IN PLANT SCIENCE 2021; 12:736797. [PMID: 34966397 PMCID: PMC8710541 DOI: 10.3389/fpls.2021.736797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
Multiple genes in sugarcane control sucrose accumulation and the biosynthesis of cell wall components; however, it is unclear how these genes are expressed in its apical culms. To better understand this process, we sequenced mRNA from +1 stem internodes collected from four genotypes with different concentrations of soluble solids. Culms were collected at four different time points, ranging from six to 12-month-old plants. Here we show differentially expressed genes related to sucrose metabolism and cell wall biosynthesis, including genes encoding invertases, sucrose synthase and cellulose synthase. Our results showed increased expression of invertases in IN84-58, the genotype with lower sugar and higher fiber content, as well as delayed expression of secondary cell wall-related cellulose synthase for the other genotypes. Interestingly, genes involved with hormone metabolism were differentially expressed across time points in the three genotypes with higher soluble solids content. A similar result was observed for genes controlling maturation and transition to reproductive stages, possibly a result of selection against flowering in sugarcane breeding programs. These results indicate that carbon partitioning in apical culms of contrasting genotypes is mainly associated with differential cell wall biosynthesis, and may include early modifications for subsequent sucrose accumulation. Co-expression network analysis identified transcription factors related to growth and development, showing a probable time shift for carbon partitioning occurred in 10-month-old plants.
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Affiliation(s)
- Guilherme Kenichi Hosaka
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Fernando Henrique Correr
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Carla Cristina da Silva
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Danilo Augusto Sforça
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Fernanda Zatti Barreto
- Plant Biotechnology Laboratory, Centre for Agricultural Sciences, Federal University of São Carlos (CCA-UFSCar), Araras, Brazil
| | | | - Asher Pasha
- Department of Cell and Systems Biology, Centre for the Analysis of the Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Nicholas James Provart
- Department of Cell and Systems Biology, Centre for the Analysis of the Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| | - Monalisa Sampaio Carneiro
- Plant Biotechnology Laboratory, Centre for Agricultural Sciences, Federal University of São Carlos (CCA-UFSCar), Araras, Brazil
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Zhang LL, Luo A, Davis SJ, Liu JX. Timing to grow: roles of clock in thermomorphogenesis. TRENDS IN PLANT SCIENCE 2021; 26:1248-1257. [PMID: 34404586 DOI: 10.1016/j.tplants.2021.07.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 07/12/2021] [Accepted: 07/23/2021] [Indexed: 05/23/2023]
Abstract
Plants coordinate their growth and developmental programs with changes in temperature. This process is termed thermomorphogenesis. The underlying molecular mechanisms have begun to emerge in these nonstressful responses to adjustments in prevailing temperature. The circadian clock is an internal timekeeper that ensures growth, development, and fitness across a wide range of environmental conditions and it responds to thermal changes. Here, we highlight how the circadian clock gates thermoresponsive hypocotyl growth in plants, with an emphasis on different action mode of evening complex (EC) in thermomorphogenesis. We also discuss the biochemical and molecular mechanisms of EC in transducing temperature signals to the key integrator PIF4. This provides future perspectives on unanswered questions on EC-associated thermomorphogenesis.
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Affiliation(s)
- Lin-Lin Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Anni Luo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
| | - Seth Jon Davis
- Department of Biology, University of York, Heslington, York, YO105DD, UK; Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Jian-Xiang Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310027, China.
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Gao X, Wang L, Zhang H, Zhu B, Lv G, Xiao J. Transcriptome analysis and identification of genes associated with floral transition and fruit development in rabbiteye blueberry (Vaccinium ashei). PLoS One 2021; 16:e0259119. [PMID: 34710165 PMCID: PMC8553168 DOI: 10.1371/journal.pone.0259119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/12/2021] [Indexed: 11/30/2022] Open
Abstract
Flowering and fruit set are important traits affecting fruit quality and yield in rabbiteye blueberry (Vaccinium ashei). Intense efforts have been made to elucidate the influence of vernalization and phytohormones on flowering, but the molecular mechanisms of flowering and fruit set remain unclear. To unravel these mechanisms, we performed transcriptome analysis to explore blueberry transcripts from flowering to early fruit stage. We divided flowering and fruit set into flower bud (S2), initial flower (S3), bloom flower (S4), pad fruit (S5), and cup fruit (S6) based on phenotype and identified 1,344, 69, 658, and 189 unique differentially expressed genes (DEGs) in comparisons of S3/S2, S4/S3, S5/S4, and S6/S5, respectively. There were obviously more DEGs in S3/S2 and S5/S4 than in S4/S3, and S6/S5, suggesting that S3/S2 and S5/S4 represent major transitions from buds to fruit in blueberry. GO and KEGG enrichment analysis indicated these DEGs were mostly enriched in phytohormone biosynthesis and signaling, transporter proteins, photosynthesis, anthocyanins biosynthesis, disease resistance protein and transcription factor categories, in addition, transcript levels of phytohormones and transporters changed greatly throughout the flowering and fruit set process. Gibberellic acid and jasmonic acid mainly acted on the early stage of flowering development like expression of the florigen gene FT, while the expression of auxin response factor genes increased almost throughout the process from bud to fruit development. Transporter proteins were mainly associated with minerals during the early flowering development stage and sugars during the early fruit stage. At the early fruit stage, anthocyanins started to accumulate, and the fruit was susceptible to diseases such as fungal infection. Expression of the transcription factor MYB86 was up-regulated during initial fruit development, which may promote anthocyanin accumulation. These results will aid future studies exploring the molecular mechanism underlying flowering and fruit set of rabbiteye blueberry.
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Affiliation(s)
- Xuan Gao
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, Anhui, China
| | - Lida Wang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, Anhui, China
| | - Hong Zhang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, Anhui, China
- Anhui Microanaly Gene Limited Liability Company, Hefei, Anhui, China
| | - Bo Zhu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, Anhui, China
| | - Guosheng Lv
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, Anhui, China
| | - Jiaxin Xiao
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, Anhui Normal University, Wuhu, Anhui, China
- * E-mail:
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50
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Sharma S, Sanyal SK, Sushmita K, Chauhan M, Sharma A, Anirudhan G, Veetil SK, Kateriya S. Modulation of Phototropin Signalosome with Artificial Illumination Holds Great Potential in the Development of Climate-Smart Crops. Curr Genomics 2021; 22:181-213. [PMID: 34975290 PMCID: PMC8640849 DOI: 10.2174/1389202922666210412104817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/21/2021] [Accepted: 03/01/2021] [Indexed: 11/22/2022] Open
Abstract
Changes in environmental conditions like temperature and light critically influence crop production. To deal with these changes, plants possess various photoreceptors such as Phototropin (PHOT), Phytochrome (PHY), Cryptochrome (CRY), and UVR8 that work synergistically as sensor and stress sensing receptors to different external cues. PHOTs are capable of regulating several functions like growth and development, chloroplast relocation, thermomorphogenesis, metabolite accumulation, stomatal opening, and phototropism in plants. PHOT plays a pivotal role in overcoming the damage caused by excess light and other environmental stresses (heat, cold, and salinity) and biotic stress. The crosstalk between photoreceptors and phytohormones contributes to plant growth, seed germination, photo-protection, flowering, phototropism, and stomatal opening. Molecular genetic studies using gene targeting and synthetic biology approaches have revealed the potential role of different photoreceptor genes in the manipulation of various beneficial agronomic traits. Overexpression of PHOT2 in Fragaria ananassa leads to the increase in anthocyanin content in its leaves and fruits. Artificial illumination with blue light alone and in combination with red light influence the growth, yield, and secondary metabolite production in many plants, while in algal species, it affects growth, chlorophyll content, lipid production and also increases its bioremediation efficiency. Artificial illumination alters the morphological, developmental, and physiological characteristics of agronomic crops and algal species. This review focuses on PHOT modulated signalosome and artificial illumination-based photo-biotechnological approaches for the development of climate-smart crops.
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Affiliation(s)
- Sunita Sharma
- Lab of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sibaji K. Sanyal
- Lab of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Kumari Sushmita
- Lab of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Manisha Chauhan
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi-110025, India
| | - Amit Sharma
- Multidisciplinary Centre for Advanced Research and Studies, Jamia Millia Islamia, New Delhi-110025, India
| | - Gireesh Anirudhan
- Integrated Science Education and Research Centre (ISERC), Institute of Science (Siksha Bhavana), Visva Bharati (A Central University), Santiniketan (PO), West Bengal, 731235, India
| | - Sindhu K. Veetil
- Lab of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Suneel Kateriya
- Lab of Optobiology, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
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