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Yang Y, Li Y, Jin L, Li P, Zhou Q, Sheng M, Ma X, Shoji T, Hao X, Kai G. A transcription factor of SHI family AaSHI1 activates artemisinin biosynthesis genes in Artemisia annua. BMC Genomics 2024; 25:776. [PMID: 39123103 PMCID: PMC11312704 DOI: 10.1186/s12864-024-10683-7] [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: 02/22/2024] [Accepted: 08/01/2024] [Indexed: 08/12/2024] Open
Abstract
BACKGROUND Transcription factors (TFs) of plant-specific SHORT INTERNODES (SHI) family play a significant role in regulating development and metabolism in plants. In Artemisia annua, various TFs from different families have been discovered to regulate the accumulation of artemisinin. However, specific members of the SHI family in A. annua (AaSHIs) have not been identified to regulate the biosynthesis of artemisinin. RESULTS We found five AaSHI genes (AaSHI1 to AaSHI5) in the A. annua genome. The expression levels of AaSHI1, AaSHI2, AaSHI3 and AaSHI4 genes were higher in trichomes and young leaves, also induced by light and decreased when the plants were subjected to dark treatment. The expression pattern of these four AaSHI genes was consistent with the expression pattern of four structural genes of artemisinin biosynthesis and their specific regulatory factors. Dual-luciferase reporter assays, yeast one-hybrid assays, and transient transformation in A. annua provided the evidence that AaSHI1 could directly bind to the promoters of structural genes AaADS and AaCYP71AV1, and positively regulate their expressions. This study has presented candidate genes, with AaSHI1 in particular, that can be considered for the metabolic engineering of artemisinin biosynthesis in A. annua. CONCLUSIONS Overall, a genome-wide analysis of the AaSHI TF family of A. annua was conducted. Five AaSHIs were identified in A. annua genome. Among the identified AaSHIs, AaSHI1 was found to be localized to the nucleus and activate the expression of structural genes of artemisinin biosynthesis including AaADS and AaCYP71AV1. These results indicated that AaSHI1 had positive roles in modulating artemisinin biosynthesis, providing candidate genes for obtaining high-quality new A. annua germplasms.
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Affiliation(s)
- Yinkai Yang
- Zhejiang Provincial TCM Key Laboratory of Chinese Medicine Resource Innovation and Transformation, Zhejiang International Science and Technology Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Jinhua Academy, School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Yongpeng Li
- Zhejiang Provincial TCM Key Laboratory of Chinese Medicine Resource Innovation and Transformation, Zhejiang International Science and Technology Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Jinhua Academy, School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Li Jin
- Zhejiang Provincial TCM Key Laboratory of Chinese Medicine Resource Innovation and Transformation, Zhejiang International Science and Technology Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Jinhua Academy, School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Pengyang Li
- Zhejiang Provincial TCM Key Laboratory of Chinese Medicine Resource Innovation and Transformation, Zhejiang International Science and Technology Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Jinhua Academy, School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Qin Zhou
- Zhejiang Provincial TCM Key Laboratory of Chinese Medicine Resource Innovation and Transformation, Zhejiang International Science and Technology Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Jinhua Academy, School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Miaomiao Sheng
- Zhejiang Provincial TCM Key Laboratory of Chinese Medicine Resource Innovation and Transformation, Zhejiang International Science and Technology Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Jinhua Academy, School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Xiaojing Ma
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-Di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Tsubasa Shoji
- Institute of Natural Medicine, University of Toyama, Toyama, 930-0194, Japan
| | - Xiaolong Hao
- Zhejiang Provincial TCM Key Laboratory of Chinese Medicine Resource Innovation and Transformation, Zhejiang International Science and Technology Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Jinhua Academy, School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China.
| | - Guoyin Kai
- Zhejiang Provincial TCM Key Laboratory of Chinese Medicine Resource Innovation and Transformation, Zhejiang International Science and Technology Cooperation Base for Active Ingredients of Medicinal and Edible Plants and Health, Jinhua Academy, School of Pharmaceutical Sciences, Academy of Chinese Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China.
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Sun Y, Zhou K, Wang X, Li X, Zhang X, Han N, Zhang J, Chen S. Identification and characterization of CsERECTA, a major gene controlling stem elongation through regulating GA biosynthesis in cucumber. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:151. [PMID: 38849610 DOI: 10.1007/s00122-024-04660-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 05/25/2024] [Indexed: 06/09/2024]
Abstract
Dwarfing is an ideal agronomic trait in crop breeding, which can improve lodging resistance and increase crop productivity. In this study, we identified a dwarf mutant cp-3 from an EMS-mutagenized population, which had extremely short internodes, and the cell length and number of internodes were significantly reduced. Meanwhile, exogenous GA3 treatment partially rescued the plant height of the cp-3. Inheritance analysis showed that the cp-3 mutant was regulated via a recessive nuclear locus. A candidate gene, CsERECTA, encoding an LRR receptor-like serine/threonine-protein kinase, was cloned through a map-based cloning strategy. Sequence analysis showed that a nucleotide mutation (C ~ T) in exon 26 of CsERECTA led to premature termination of the protein. Subsequently, two transgenic lines were generated using the CRISPR/Cas9 system, and they showed plant dwarfing. Plant endogenous hormones quantitative and RNA-sequencing analysis revealed that GA3 content and the expression levels of genes related to GA biosynthesis were significantly reduced in Cser knockout mutants. Meanwhile, exogenous GA3 treatment partially rescued the dwarf phenotype of Cser knockout mutants. These findings revealed that CsERECTA controls stem elongation by regulating GA biosynthesis in cucumber.
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Affiliation(s)
- Yinhui Sun
- College of Horticulture, Northwest A&F University, Yangling, China
- Shaanxi Engineering Research Center for Vegetables, Yangling, 712100, China
| | - Keke Zhou
- College of Horticulture, Northwest A&F University, Yangling, China
- Shaanxi Engineering Research Center for Vegetables, Yangling, 712100, China
| | - Xin Wang
- College of Horticulture, Northwest A&F University, Yangling, China
- Shaanxi Engineering Research Center for Vegetables, Yangling, 712100, China
| | - Xuzhen Li
- College of Horticulture, Northwest A&F University, Yangling, China
- Shaanxi Engineering Research Center for Vegetables, Yangling, 712100, China
| | - Xiaojiang Zhang
- College of Horticulture, Northwest A&F University, Yangling, China
- Shaanxi Engineering Research Center for Vegetables, Yangling, 712100, China
| | - Ni Han
- College of Horticulture, Northwest A&F University, Yangling, China
- Shaanxi Engineering Research Center for Vegetables, Yangling, 712100, China
| | - Jie Zhang
- College of Horticulture, Northwest A&F University, Yangling, China
- Shaanxi Engineering Research Center for Vegetables, Yangling, 712100, China
| | - Shuxia Chen
- College of Horticulture, Northwest A&F University, Yangling, China.
- Shaanxi Engineering Research Center for Vegetables, Yangling, 712100, China.
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Chu LL, Zheng WX, Liu HQ, Sheng XX, Wang QY, Wang Y, Hu CG, Zhang JZ. ACC SYNTHASE4 inhibits gibberellin biosynthesis and FLOWERING LOCUS T expression during citrus flowering. PLANT PHYSIOLOGY 2024; 195:479-501. [PMID: 38227428 DOI: 10.1093/plphys/kiae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 01/17/2024]
Abstract
Flowering is an essential process in fruit trees. Flower number and timing have a substantial impact on the yield and maturity of fruit. Ethylene and gibberellin (GA) play vital roles in flowering, but the mechanism of coordinated regulation of flowering in woody plants by GA and ethylene is still unclear. In this study, a lemon (Citrus limon L. Burm) 1-aminocyclopropane-1-carboxylic acid synthase gene (CiACS4) was overexpressed in Nicotiana tabacum and resulted in late flowering and increased flower number. Further transformation of citrus revealed that ethylene and starch content increased, and soluble sugar content decreased in 35S:CiACS4 lemon. Inhibition of CiACS4 in lemon resulted in effects opposite to that of 35S:CiACS4 in transgenic plants. Overexpression of the CiACS4-interacting protein ETHYLENE RESPONSE FACTOR3 (CiERF3) in N. tabacum resulted in delayed flowering and more flowers. Further experiments revealed that the CiACS4-CiERF3 complex can bind the promoters of FLOWERING LOCUS T (CiFT) and GOLDEN2-LIKE (CiFE) and suppress their expression. Moreover, overexpression of CiFE in N. tabacum led to early flowering and decreased flowers, and ethylene, starch, and soluble sugar contents were opposite to those in 35S:CiACS4 transgenic plants. Interestingly, CiFE also bound the promoter of CiFT. Additionally, GA3 and 1-aminocyclopropanecarboxylic acid (ACC) treatments delayed flowering in adult citrus, and treatment with GA and ethylene inhibitors increased flower number. ACC treatment also inhibited the expression of CiFT and CiFE. This study provides a theoretical basis for the application of ethylene to regulate flower number and mitigate the impacts of extreme weather on citrus yield due to delayed flowering.
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Affiliation(s)
- Le-Le Chu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei-Xuan Zheng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Hai-Qiang Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Xing-Xing Sheng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Qing-Ye Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Yue Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Chun-Gen Hu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Jin-Zhi Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
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Fujii S, Yamamoto E, Ito S, Tangpranomkorn S, Kimura Y, Miura H, Yamaguchi N, Kato Y, Niidome M, Yoshida A, Shimosato-Asano H, Wada Y, Ito T, Takayama S. SHI family transcription factors regulate an interspecific barrier. NATURE PLANTS 2023; 9:1862-1873. [PMID: 37798337 DOI: 10.1038/s41477-023-01535-5] [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: 09/13/2022] [Accepted: 09/05/2023] [Indexed: 10/07/2023]
Abstract
Pre-zygotic interspecies incompatibility in angiosperms is an important mechanism to prevent unfavourable hybrids between species. Here we report our identification of STIGMATIC PRIVACY 2 (SPRI2), a transcription factor that has a zinc-finger domain and regulates interspecies barriers in Arabidopsis thaliana, via genome-wide association study. Knockout analysis of SPRI2/SRS7 and its paralogue SPRI2-like/SRS5 demonstrated their necessity in rejecting male pollen from other species within female pistils. Additionally, they govern mRNA transcription of xylan O-acetyltransferases (TBL45 and TBL40) related to cell wall modification, alongside SPRI1, a pivotal transmembrane protein for interspecific pollen rejection. SPRI2/SRS7 is localized as condensed structures in the nucleus formed via liquid-liquid phase separation (LLPS), and a prion-like sequence in its amino-terminal region was found to be responsible for the formation of the condensates. The LLPS-regulated SPRI2/SRS7 discovered in this study may contribute to the establishment of interspecific reproductive barriers through the transcriptional regulation of cell wall modification genes and SPRI1.
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Affiliation(s)
- Sota Fujii
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan.
- Suntory Rising Stars Encouragement Program in Life Sciences Fellow, Tokyo, Japan.
| | - Eri Yamamoto
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Seitaro Ito
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Surachat Tangpranomkorn
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
- GRA&GREEN Inc., Nagoya, Japan
| | - Yuka Kimura
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Hiroki Miura
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Nobutoshi Yamaguchi
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Yoshinobu Kato
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Saitama, Japan
| | - Maki Niidome
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Aya Yoshida
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Hiroko Shimosato-Asano
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Yuko Wada
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Toshiro Ito
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Seiji Takayama
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan.
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Lu W, Wang Y, Shi Y, Liang Q, Lu X, Su D, Xu X, Pirrello J, Gao Y, Huang B, Li Z. Identification of SRS transcription factor family in Solanum lycopersicum, and functional characterization of their responses to hormones and abiotic stresses. BMC PLANT BIOLOGY 2023; 23:495. [PMID: 37833639 PMCID: PMC10576376 DOI: 10.1186/s12870-023-04506-2] [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: 06/04/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023]
Abstract
The SHI RELATED SEQUENCE (SRS) family plays a vital role in the development of multiple plant organs such as floral meristem determinacy, organ morphogenesis, and signal transduction. Nevertheless, there is little understanding of the biological significance of tomato SRS family at this point. Our research identified eight SlSRS family members and classified them into three subfamilies based on phylogenetics, conserved motifs, and characteristic domain analysis. The intraspecies and interspecies collinearity analysis revealed clues of SRS family evolution. Many cis-elements related to hormones, stresses, and plant development can be found in the promoter region of SlSRS genes. All of eight SlSRS proteins were located in the nucleus and possessed transcriptional activity, half of which were transcriptional activators, and the other half were transcriptional repressors. Except for SlSRS1, which showed high transcript accumulation in vegetative organs, most SlSRS genes expressed ubiquitously in all flower organs. In addition, all SlSRS genes could significantly respond to at least four different plant hormones. Further, expression of SlSRS genes were regulated by various abiotic stress conditions. In summary, we systematically analyzed and characterized the SlSRS family, reviewed the expression patterns and preliminarily investigated the protein function, and provided essential information for further functional research of the tomato SRS genes in the determination of reproductive floral organs and the development of plants, and possibly other plants.
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Affiliation(s)
- Wang Lu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Yan Wang
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Yuan Shi
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Qin Liang
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Xiangyin Lu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Deding Su
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Xin Xu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Julien Pirrello
- Laboratory of Plant Science Research, Fruit Genomics and Biotechnology, UMR5546, University of Toulouse, CNRS, UPS, Toulouse-NP, Toulouse, France
| | - Ying Gao
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Baowen Huang
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China.
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China.
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China.
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China.
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6
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Duan E, Lin Q, Wang Y, Ren Y, Xu H, Zhang Y, Wang Y, Teng X, Dong H, Wang Y, Jiang X, Chen X, Lei J, Yang H, Chen R, Jiang L, Wang H, Wan J. The transcriptional hub SHORT INTERNODES1 integrates hormone signals to orchestrate rice growth and development. THE PLANT CELL 2023; 35:2871-2886. [PMID: 37195873 PMCID: PMC10396361 DOI: 10.1093/plcell/koad130] [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: 12/08/2022] [Revised: 03/20/2023] [Accepted: 04/26/2023] [Indexed: 05/19/2023]
Abstract
Plants have evolved sophisticated mechanisms to coordinate their growth and stress responses via integrating various phytohormone signaling pathways. However, the precise molecular mechanisms orchestrating integration of the phytohormone signaling pathways remain largely obscure. In this study, we found that the rice (Oryza sativa) short internodes1 (shi1) mutant exhibits typical auxin-deficient root development and gravitropic response, brassinosteroid (BR)-deficient plant architecture and grain size as well as enhanced abscisic acid (ABA)-mediated drought tolerance. Additionally, we found that the shi1 mutant is also hyposensitive to auxin and BR treatment but hypersensitive to ABA. Further, we showed that OsSHI1 promotes the biosynthesis of auxin and BR by activating the expression of OsYUCCAs and D11, meanwhile dampens ABA signaling by inducing the expression of OsNAC2, which encodes a repressor of ABA signaling. Furthermore, we demonstrated that 3 classes of transcription factors, AUXIN RESPONSE FACTOR 19 (OsARF19), LEAF AND TILLER ANGLE INCREASED CONTROLLER (LIC), and OsZIP26 and OsZIP86, directly bind to the promoter of OsSHI1 and regulate its expression in response to auxin, BR, and ABA, respectively. Collectively, our results unravel an OsSHI1-centered transcriptional regulatory hub that orchestrates the integration and self-feedback regulation of multiple phytohormone signaling pathways to coordinate plant growth and stress adaptation.
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Affiliation(s)
- Erchao Duan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Qibing Lin
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yihua Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Yulong Ren
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huan Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuanyan Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunlong Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuan Teng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Hui Dong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Yupeng Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaokang Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoli Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Jie Lei
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Hang Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Rongbo Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Ling Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Haiyang Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianmin Wan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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7
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Hu M, Xie M, Cui X, Huang J, Cheng X, Liu L, Yan S, Liu S, Tong C. Characterization and Potential Function Analysis of the SRS Gene Family in Brassica napus. Genes (Basel) 2023; 14:1421. [PMID: 37510325 PMCID: PMC10379590 DOI: 10.3390/genes14071421] [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: 06/15/2023] [Revised: 07/07/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
SRS (SHI-related sequence) transcription factors play a crucial role in plant growth, development, and abiotic stress response. Although Brassica napus (B. napus) is one of the most important oil crops in the world, the role of SRS genes in B. napus (BnSRS) has not been well investigated. Therefore, we employed a bioinformatics approach to identify BnSRS genes from genomic data and investigated their characteristics, functions, and expression patterns, to gain a better understanding of how this gene family is involved in plant development and growth. The results revealed that there were 34 BnSRS gene family members in the genomic sequence of B. napus, unevenly distributed throughout the sequence. Based on the phylogenetic analysis, these BnSRS genes could be divided into four subgroups, with each group sharing comparable conserved motifs and gene structure. Analysis of the upstream promoter region showed that BnSRS genes may regulate hormone responses, biotic and abiotic stress response, growth, and development in B. napus. The protein-protein interaction analysis revealed the involvement of BnSRS genes in various biological processes and metabolic pathways. Our analysis of BnSRS gene expression showed that 23 BnSRS genes in the callus tissue exhibited a dominant expression pattern, suggesting their critical involvement in cell dedifferentiation, cell division, and tissue development. In addition, association analysis between genotype and agronomic traits revealed that BnSRS genes may be linked to some important agronomic traits in B. napus, suggesting that BnSRS genes were widely involved in the regulation of important agronomic traits (including C16.0, C18.0, C18.1, C18.2 C18.3, C20.1, C22.1, GLU, protein, TSW, and FFT). In this study, we predicted the evolutionary relationships and potential functions of BnSRS gene family members, providing a basis for the development of BnSRS gene functions which could facilitate targeted functional studies and genetic improvement for elite breeding in B. napus.
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Affiliation(s)
- Ming Hu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Meili Xie
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Xiaobo Cui
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Junyan Huang
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Xiaohui Cheng
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Lijiang Liu
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Shunping Yan
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shengyi Liu
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Chaobo Tong
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
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8
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Lepri A, Longo C, Messore A, Kazmi H, Madia VN, Di Santo R, Costi R, Vittorioso P. Plants and Small Molecules: An Up-and-Coming Synergy. PLANTS (BASEL, SWITZERLAND) 2023; 12:1729. [PMID: 37111951 PMCID: PMC10145415 DOI: 10.3390/plants12081729] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/16/2023] [Accepted: 04/18/2023] [Indexed: 06/19/2023]
Abstract
The emergence of Arabidopsis thaliana as a model system has led to a rapid and wide improvement in molecular genetics techniques for studying gene function and regulation. However, there are still several drawbacks that cannot be easily solved with molecular genetic approaches, such as the study of unfriendly species, which are of increasing agronomic interest but are not easily transformed, thus are not prone to many molecular techniques. Chemical genetics represents a methodology able to fill this gap. Chemical genetics lies between chemistry and biology and relies on small molecules to phenocopy genetic mutations addressing specific targets. Advances in recent decades have greatly improved both target specificity and activity, expanding the application of this approach to any biological process. As for classical genetics, chemical genetics also proceeds with a forward or reverse approach depending on the nature of the study. In this review, we addressed this topic in the study of plant photomorphogenesis, stress responses and epigenetic processes. We have dealt with some cases of repurposing compounds whose activity has been previously proven in human cells and, conversely, studies where plants have been a tool for the characterization of small molecules. In addition, we delved into the chemical synthesis and improvement of some of the compounds described.
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Affiliation(s)
- A. Lepri
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (A.L.); (C.L.); (H.K.)
| | - C. Longo
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (A.L.); (C.L.); (H.K.)
| | - A. Messore
- Department of Chemistry and Technology of Drug, Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (V.N.M.); (R.D.S.); (R.C.)
| | - H. Kazmi
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (A.L.); (C.L.); (H.K.)
| | - V. N. Madia
- Department of Chemistry and Technology of Drug, Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (V.N.M.); (R.D.S.); (R.C.)
| | - R. Di Santo
- Department of Chemistry and Technology of Drug, Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (V.N.M.); (R.D.S.); (R.C.)
| | - R. Costi
- Department of Chemistry and Technology of Drug, Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (V.N.M.); (R.D.S.); (R.C.)
| | - P. Vittorioso
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (A.L.); (C.L.); (H.K.)
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9
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Huang H, Song J, Feng Y, Zheng L, Chen Y, Luo K. Genome-Wide Identification and Expression Analysis of the SHI-Related Sequence Family in Cassava. Genes (Basel) 2023; 14:genes14040870. [PMID: 37107628 PMCID: PMC10138042 DOI: 10.3390/genes14040870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
The SHORT INTERNODES (SHI)-related sequences (SRS) are plant-specific transcription factors that have been quantitatively characterized during plant growth, regeneration, and stress responses. However, the genome-wide discovery of SRS family genes and their involvement in abiotic stress-related activities in cassava have not been documented. A genome-wide search strategy was used to identify eight family members of the SRS gene family in cassava (Manihot esculenta Crantz). Based on their evolutionary linkages, all MeSRS genes featured homologous RING-like zinc finger and IXGH domains. Genetic architecture and conserved motif analysis validated the categorization of MeSRS genes into four groups. Eight pairs of segmental duplications were detected, resulting in an increase in the number of MeSRS genes. Orthologous studies of SRS genes among cassava and three different plant species (Arabidopsis thaliana, Oryza sativa, and Populus trichocarpa) provided important insights into the probable history of the MeSRS gene family. The functionality of MeSRS genes was elucidated through the prediction of protein–protein interaction networks and cis-acting domains. RNA-seq data demonstrated tissue/organ expression selectivity and preference of the MeSRS genes. Furthermore, qRT-PCR investigation of MeSRS gene expression after exposure to salicylic acid (SA) and methyl jasmonate (MeJA) hormone treatments, as well as salt (NaCl) and osmotic (polyethylene glycol, PEG) stresses, showed their stress-responsive patterns. This genome-wide characterization and identification of the evolutionary relationships and expression profiles of the cassava MeSRS family genes will be helpful for further research into this gene family and its function in stress response. It may also assist future agricultural efforts to increase the stress tolerance of cassava.
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Affiliation(s)
- Huling Huang
- Sanya Nanfan Research Institute, School of Tropical Crops, Hainan University, Haikou 572025, China
| | - Jiming Song
- Institute of Tropical and subtropical Economic Crops, Yunnan Provincial Academy of Agricultural Sciences, Baoshan 678000, China
| | - Yating Feng
- Sanya Nanfan Research Institute, School of Tropical Crops, Hainan University, Haikou 572025, China
| | - Linling Zheng
- Sanya Nanfan Research Institute, School of Tropical Crops, Hainan University, Haikou 572025, China
| | - Yinhua Chen
- Sanya Nanfan Research Institute, School of Tropical Crops, Hainan University, Haikou 572025, China
| | - Kai Luo
- Sanya Nanfan Research Institute, School of Tropical Crops, Hainan University, Haikou 572025, China
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10
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Sun C, Yu L, Zhang S, Gu Q, Wang M. Genome-wide characterization of the SHORT INTER-NODES/STYLISH and Shi-Related Sequence family in Gossypium hirsutum and functional identification of GhSRS21 under salt stress. FRONTIERS IN PLANT SCIENCE 2023; 13:1078083. [PMID: 36684735 PMCID: PMC9846857 DOI: 10.3389/fpls.2022.1078083] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Saline stress is a significant factor that caused crop growth inhibition and yield decline. SHORT INTERNODES/STYLISH (SHI/STY) and SHI-RELATED SEQUENCE (SRS) transcription factors are specific to plants and share a conserved RING-like zinc-finger domain (CX2CX7CX4CX2C2X6C). However, the functions of SHI/STY and SRS genes in cotton responses to salt stress remain unclear. In this study, 26 GhSRSs were identified in Gossypium hirsutum, which further divided into three subgroups. Phylogenetic analysis of 88 SRSs from8 plant species revealed independent evolutionary pattern in some of SRSs derived from monocots. Conserved domain and subcellular location predication of GhSRSs suggested all of them only contained the conserved RING-like zinc-finger domain (DUF702) domain and belonged to nucleus-localized transcription factors except for the GhSRS22. Furthermore, synteny analysis showed structural variation on chromosomes during the process of cotton polyploidization. Subsequently, expression patterns of GhSRS family members in response to salt and drought stress were analyzed in G. hirsutum and identified a salt stress-inducible gene GhSRS21. The GhSRS21 was proved to localize in the nuclear and silencing it in G. hirsutum increased the cotton resistance to salt using the virus-induced gene silencing (VIGS) system. Finally, our transcriptomic data revealed that GhSRS21 negatively controlled cotton salt tolerance by regulating the balance between ROS production and scavenging. These results will increase our understanding of the SRS gene family in cotton and provide the candidate resistant gene for cotton breeding.
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Affiliation(s)
- Chendong Sun
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Li Yu
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Shuojun Zhang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Qijuan Gu
- Key Laboratory of Microbiol Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, China
| | - Mei Wang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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11
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Fang D, Zhang W, Ye Z, Hu F, Cheng X, Cao J. The plant specific SHORT INTERNODES/STYLISH (SHI/STY) proteins: Structure and functions. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:685-695. [PMID: 36565613 DOI: 10.1016/j.plaphy.2022.12.018] [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: 05/24/2022] [Revised: 12/02/2022] [Accepted: 12/18/2022] [Indexed: 06/17/2023]
Abstract
Plant specific SHORT INTERNODES/STYLISH (SHI/STY) protein is a transcription factor involved in the formation and development of early lateral organs in plants. However, research on the SHI/STY protein family is not focused enough. In this article, we review recent studies on SHI/STY genes and explore the evolution and structure of SHI/STY. The biological functions of SHI/STYs are discussed in detail in this review, and the application of each biological function to modern agriculture is discussed. All SHI/STY proteins contain typical conserved RING-like zinc finger domain and IGGH domain. SHI/STYs are involved in the formation and development of lateral root, stem extension, leaf morphogenesis, and root nodule development. They are also involved in the regulation of pistil and stamen development and flowering time. At the same time, the regulation of some GA, JA, and auxin signals also involves these family proteins. For each aspect, unanswered or poorly understood questions were identified to help define future research areas. This review will provide a basis for further functional study of this gene family.
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Affiliation(s)
- Da Fang
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Weimeng Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Ziyi Ye
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Fei Hu
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Xiuzhu Cheng
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jun Cao
- School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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12
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Um TY, Hong SY, Han JS, Jung KH, Moon S, Choi BS, Basnet P, Chung YS, Lee SW, Yang WT, Kim DH. Gibberellic acid sensitive dwarf encodes an ARPC2 subunit that mediates gibberellic acid biosynthesis, effects to grain yield in rice. FRONTIERS IN PLANT SCIENCE 2022; 13:1027688. [PMID: 36618614 PMCID: PMC9813395 DOI: 10.3389/fpls.2022.1027688] [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: 08/25/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
The plant hormone gibberellic acid (GA) is important for plant growth and productivity. Actin-related proteins (ARPs) also play central roles in plant growth, including cell elongation and development. However, the relationships between ARPs and GA signaling and biosynthesis are not fully understood. Here, we isolated OsGASD, encoding an ARP subunit from rice (Oryza sativa), using the Ac/Ds knockout system. The osgasd knockout (Ko) mutation reduced GA3 content in shoots as well as plant growth and height. However, GA application restored the plant height of the osgasd Ko mutant to a height similar to that of the wild type (WT). Rice plants overexpressing OsGASD (Ox) showed increased plant height and grain yield compared to the WT. Transcriptome analysis of flag leaves of OsGASD Ox and osgasd Ko plants revealed that OsGASD regulates cell development and the expression of elongation-related genes. These observations suggest that OsGASD is involved in maintaining GA homeostasis to regulate plant development, thereby affecting rice growth and productivity.
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Affiliation(s)
- Tae Young Um
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, Republic of Korea
| | - So Yeon Hong
- College of Life Science and Natural Resources, Dong-A University, Busan, Republic of Korea
| | - Ji Sung Han
- College of Life Science and Natural Resources, Dong-A University, Busan, Republic of Korea
| | - Ki Hong Jung
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin, Republic of Korea
| | - Sunok Moon
- Graduate School of Green-Bio Science, Kyung Hee University, Yongin, Republic of Korea
| | - Beom-Soon Choi
- Research Institute, NBIT Co., Ltd., Chuncheon, Republic of Korea
| | - Prakash Basnet
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon, Republic of Korea
| | - Young Soo Chung
- College of Life Science and Natural Resources, Dong-A University, Busan, Republic of Korea
| | - Seon Woo Lee
- College of Life Science and Natural Resources, Dong-A University, Busan, Republic of Korea
| | - Won Tae Yang
- College of Life Science and Natural Resources, Dong-A University, Busan, Republic of Korea
| | - Doh Hoon Kim
- College of Life Science and Natural Resources, Dong-A University, Busan, Republic of Korea
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13
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Liu X, Wang J, Sabir IA, Sun W, Wang L, Xu Y, Zhang N, Liu H, Jiu S, Liu L, Zhang C. PavGA2ox-2L inhibits the plant growth and development interacting with PavDWARF in sweet cherry (Prunus avium L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 186:299-309. [PMID: 35932654 DOI: 10.1016/j.plaphy.2022.07.019] [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: 04/25/2022] [Revised: 06/27/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Dwarf dense planting is helpful to improve the yield and quality of sweet cherry, which has enormous market demand. GA2oxs (GA oxidases) affect plant height, dormancy release, flower development, and seed germination by participating in the metabolic regulation and signal transduction of GA (Gibberellin). However, the research on GA2ox in sweet cherry is little and worthy of further investigation. Therefore, we identified the PavGA2ox-2L gene from sweet cherry, close to PynGA2ox-2 from Prunus yedoensis var. Nudiflora. The phylogenetic analysis indicated conserved functions with these evolutionarily closer GA2ox subfamily genes. Subcellular localization forecast analysis indicated that PavGA2ox-2L was localized in the nucleus or cytoplasm. The expression levels of PavGA2ox-2L were higher in winter, indicating that PavGA2ox-2L promoted maintained flower bud dormancy. The expression levels of PavGA2ox-2L were significantly increased after GA4+7 treatment while decreased after GR24 (a synthetic analog of SLs (Strigolactones)) or TIS108 (a triazole-type SL-biosynthesis inhibitor) treatments. Over-expression of PavGA2ox-2L resulted in decreased plant height, delayed flowering time, and low seed germination rate in Arabidopsis thaliana. Furthermore, the interaction between PavGA2ox-2L and PavDWARF was verified by Y2H and BiFC assays. In the current investigation, PavGA2ox-2L functions as a GA metabolic gene that promotes dwarf dense planting, delays flowering time, and inhibits seed germination. In addition, it also participates in regulating plant growth and development through the interaction with the critical negative regulator PavDWARF of Gibberellin. These results will help us better explore the molecular mechanism of GA2ox-mediated dwarf and late-maturing varieties for fruit trees.
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Affiliation(s)
- Xunju Liu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Minhang, Shanghai, 200240, China.
| | - Jiyuan Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Minhang, Shanghai, 200240, China.
| | - Irfan Ali Sabir
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Minhang, Shanghai, 200240, China.
| | - Wanxia Sun
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Minhang, Shanghai, 200240, China.
| | - Li Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Minhang, Shanghai, 200240, China.
| | - Yan Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Minhang, Shanghai, 200240, China.
| | - Niangong Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Minhang, Shanghai, 200240, China.
| | - Haobo Liu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Minhang, Shanghai, 200240, China.
| | - Songtao Jiu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Minhang, Shanghai, 200240, China.
| | - Lu Liu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Minhang, Shanghai, 200240, China.
| | - Caixi Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Minhang, Shanghai, 200240, China.
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14
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Zhu X, Wang B, Wang X, Wei X. Genome-wide identification, structural analysis and expression profiles of short internodes related sequence gene family in quinoa. Front Genet 2022; 13:961925. [PMID: 36072673 PMCID: PMC9443693 DOI: 10.3389/fgene.2022.961925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 07/01/2022] [Indexed: 11/27/2022] Open
Abstract
Based on the whole genome data information of Chenopodium quinoa Willd, the CqSRS gene family members were systematically identified and analyzed by bioinformatics methods, and the responses of CqSRS genes to NaCl (100 mmol/L), salicylic acid (200 umol/L) and low temperature (4°C) were detected by qRT-PCR. The results showed that a total of 10 SHI related sequence genes were identified in quinoa, and they were distributed on 9 chromosomes, and there were four pairs of duplicated genes. The number of amino acids encoded ranged from 143 aa to 370 aa, and the isoelectric point ranged from 4.81 to 8.90. The secondary structure was mainly composed of random coil (Cc). Most of the SRS gene encoding proteins were located in the cytoplasm (5 CqSRS). Phylogenetic analysis showed that the CqSRS genes were divided into three groups, and the gene structure showed that the number of exons of CqSRS was between two-five. Promoter analysis revealed that there are a total of 44 elements related to plant hormone response elements, light response elements, stress response elements and tissue-specific expression in the upstream regin of the gene. Protein interaction showed that all 10 CqSRS proteins appeared in the known protein interaction network diagram in Arabidopsis. Expression profile analysis showed that CqSRS genes had different expression patterns, and some genes had tissue-specific expression. qRT-PCR showed that all SRS family genes responded to ABA、NaCl、drought and low-temperature treatments, but the expression levels of different CqSRS genes were significantly different under various stresses. This study lays a foundation for further analyzed the function of CqSRS genes.
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Affiliation(s)
- Xiaolin Zhu
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Baoqiang Wang
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xian Wang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaohong Wei
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
- *Correspondence: Xiaohong Wei,
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15
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Fang D, Zhang W, Cheng X, Hu F, Ye Z, Cao J. Molecular evolutionary analysis of the SHI/STY gene family in land plants: A focus on the Brassica species. FRONTIERS IN PLANT SCIENCE 2022; 13:958964. [PMID: 35991428 PMCID: PMC9386158 DOI: 10.3389/fpls.2022.958964] [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: 06/01/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
The plant-specific SHORT INTERNODES/STYLISH (SHI/STY) proteins belong to a family of transcription factors that are involved in the formation and development of early lateral roots. However, the molecular evolution of this family is rarely reported. Here, a total of 195 SHI/STY genes were identified in 21 terrestrial plants, and the Brassica species is the focus of our research. Their physicochemical properties, chromosome location and duplication, motif distribution, exon-intron structures, genetic evolution, and expression patterns were systematically analyzed. These genes are divided into four clades (Clade 1/2/3/4) based on phylogenetic analysis. Motif distribution and gene structure are similar in each clade. SHI/STY proteins are localized in the nucleus by the prediction of subcellular localization. Collinearity analysis indicates that the SHI/STYs are relatively conserved in evolution. Whole-genome duplication is the main factor for their expansion. SHI/STYs have undergone intense purifying selection, but several positive selection sites are also identified. Most promoters of SHI/STY genes contain different types of cis-elements, such as light, stress, and hormone-responsive elements, suggesting that they may be involved in many biological processes. Protein-protein interaction predicted some important SHI/STY interacting proteins, such as LPAT4, MBOATs, PPR, and UBQ3. In addition, the RNA-seq and qRT-PCR analysis were studied in detail in rape. As a result, SHI/STYs are highly expressed in root and bud, and can be affected by Sclerotinia sclerotiorum, drought, cold, and heat stresses. Moreover, quantitative real-time PCR (qRT-PCR) analyses indicates that expression levels of BnSHI/STYs are significantly altered in different treatments (cold, salt, drought, IAA, auxin; ABA, abscisic acid; 6-BA, cytokinin). It provides a new understanding of the evolution and expansion of the SHI/STY family in land plants and lays a foundation for further research on their functions.
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16
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Sukiran NA, Pollastri S, Steel PG, Knight MR. Plant growth promotion by the interaction of a novel synthetic small molecule with GA-DELLA function. PLANT DIRECT 2022; 6:e398. [PMID: 35492684 PMCID: PMC9039627 DOI: 10.1002/pld3.398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 01/23/2022] [Accepted: 03/16/2022] [Indexed: 05/14/2023]
Abstract
Synthesized small molecules are useful as tools to investigate hormonal signaling involved in plant growth and development. They are also important as agrochemicals to promote beneficial properties of crops in the field. We describe here the synthesis and mode of action of a novel growth-promoting chemical, A1. A1 stimulates enhanced growth in both shoot and root tissues of plants, acting by increasing both dry and fresh weight. This suggests that A1 not only promotes uptake of water but also increases production of cellular material. A1 treatment of Arabidopsisleads to the degradation of DELLA growth-inhibitory proteins suggesting that A1-mediated growth promotion is dependent upon this mechanism. We performed genetic analysis to confirm this and further dissect the mechanism of A1 action upon growth in Arabidopsis. A quintuple dellamutant was insensitive to A1, confirming that the mode of action was indeed via a DELLA-dependent mechanism. The ga1-5gibberellin synthesis mutant was similarly insensitive, suggesting that to promote growth in ArabidopsisA1 requires the presence of endogenous gibberellins. This was further suggested by the observation that double mutants of GID1 gibberellin receptor genes were insensitive to A1. Taken together, our data suggest that A1 acts to enhance sensitivity to endogenous gibberellins thus leading to observed enhanced growth via DELLA degradation. A1 and related compounds will be useful to identify novel signaling components involved in plant growth and development, and as agrochemicals suitable for a wide range of crop species.
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Affiliation(s)
- Nur Afiqah Sukiran
- Department of BiosciencesDurham UniversityDurhamUK
- Department of ChemistryDurham UniversityDurhamUK
| | - Susanna Pollastri
- Institute for Sustainable Plant ProtectionNational Research Council of ItalyFlorenceItaly
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17
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Yang Y, Qi L, Nian L, Zhu X, Yi X, Jiyu Z, Qiu J. Genome-Wide Identification and Expression Analysis of the SRS Gene Family in Medicago sativa. DNA Cell Biol 2021; 40:1539-1553. [PMID: 34931872 DOI: 10.1089/dna.2021.0462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
SHI-related sequence (SRS) transcription factors, specific to plants, act as crucial regulators of plant organ growth and development. Here, we examined the Medicago sativa (alfalfa) SRS gene family (MsSRSs) to analyze the structure and function of MsSRSs using bioinformatics methods, and verify their abiotic stress responses through growth experiments. Twenty-seven MsSRS genes were identified from the genome-wide data of nontransgenic alfalfa. MsSRSs were distributed on 16 chromosomes and classified into seven different subfamilies by phylogenetic analysis. Forty-five cis-regulatory elements related to stress and phytohormone responsiveness, and tissue-specific expression occurred in the promoter sequences of MsSRSs. Ks values and Ka/Ks ratios of duplicate gene pairs showed that purifying selection affected most duplicate genes during their evolutionary history, while rapid recent positive selection strongly influenced MsSRS25 and MsSRS01. Real-time fluorescence quantitative PCR results showed that MsSRS genes could be induced by cold and salt stress. Within 12 h of salt stress exposure, the expression levels of seven and nine MsSRSs showed significant upregulation and downregulation, respectively. Within 12 h of cold stress exposure, the expression levels of the 3 and 13 selected MsSRSs showed significant upregulation and downregulation, respectively. Thus, this study provides novel comprehensive information on the MsSRS gene family, helpful for the study of SRS-mediated tolerance in alfalfa and the functional characteristics of SRS genes in other plants.
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Affiliation(s)
- Yingbo Yang
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou, China.,Guangxi Institute of Animal Sciences, Nanning, China
| | - Lin Qi
- College of Agricultural, Henan Science and Technology University, Luoyang, China
| | - Lili Nian
- College of Forestry, Gansu Agricultural University, Lanzhou, China
| | - Xiaolin Zhu
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Xianfeng Yi
- Guangxi Institute of Animal Sciences, Nanning, China
| | - Zhang Jiyu
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Jinhua Qiu
- Guangxi Institute of Animal Sciences, Nanning, China
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18
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Zhang Y, Liu J, Yu J, Zhang H, Yang Z. Relationship between the Phenylpropanoid Pathway and Dwarfism of Paspalum seashore Based on RNA-Seq and iTRAQ. Int J Mol Sci 2021; 22:ijms22179568. [PMID: 34502485 PMCID: PMC8431245 DOI: 10.3390/ijms22179568] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/27/2021] [Accepted: 08/31/2021] [Indexed: 11/24/2022] Open
Abstract
Seashore paspalum is a major warm-season turfgrass requiring frequent mowing. The use of dwarf cultivars with slow growth is a promising method to decrease mowing frequency. The present study was conducted to provide an in-depth understanding of the molecular mechanism of T51 dwarfing in the phenylpropane pathway and to screen the key genes related to dwarfing. For this purpose, we obtained transcriptomic information based on RNA-Seq and proteomic information based on iTRAQ for the dwarf mutant T51 of seashore paspalum. The combined results of transcriptomic and proteomic analysis were used to identify the differential expression pattern of genes at the translational and transcriptional levels. A total of 8311 DEGs were detected at the transcription level, of which 2540 were upregulated and 5771 were downregulated. Based on the transcripts, 2910 proteins were identified using iTRAQ, of which 392 (155 upregulated and 237 downregulated) were DEPs. The phenylpropane pathway was found to be significantly enriched at both the transcriptional and translational levels. Combined with the decrease in lignin content and the increase in flavonoid content in T51, we found that the dwarf phenotype of T51 is closely related to the abnormal synthesis of lignin and flavonoids in the phenylpropane pathway. CCR and HCT may be the key genes for T51 dwarf. This study provides the basis for further study on the dwarfing mechanism of seashore paspalum. The screening of key genes lays a foundation for further studies on the molecular mechanism of seashore paspalum dwarfing.
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Büyük İ, Okay A, Aras S. Identification and Characterization of SRS Genes in Phaseolus vulgaris Genome and Their Responses Under Salt Stress. Biochem Genet 2021; 60:482-503. [PMID: 34282530 DOI: 10.1007/s10528-021-10108-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 07/06/2021] [Indexed: 11/29/2022]
Abstract
SHI-Related Sequence (SRS) transcription factors comprise a protein family with important roles in growth and development. However, the genome-wide study of the SRS protein family has not yet been carried out in the common bean. For this reason, the SRS family has been characterized in depth at both gene and protein levels and several bioinformatics methods have been used. As a result, 10 SRS genes have been identified and their proteins have been phylogenetically categorized into three major groups within the common bean. By investigating duplications that play a major role in the development of gene families, 19 duplication events have been identified in the SRS family (18 segmental and 1 tandem). In addition, using available RNAseq data, comparative expression analysis of Pvul-SRS genes was performed and expression changes in Pvul-SRS-1, 2, 4, 6, 7, and 10 genes were observed under both salt and drought stress. Five Pvul-SRS genes were selected based on RNAseq data (Pvul-SRS-1, 2, 4, 6, and 10) and screened with RT-qPCR in two common bean cultivars (Yakutiye 'salt-resistant' and Zulbiye 'salt-susceptible' cv.). These genes also showed different levels of expression between two common bean cultivars under salt stress conditions and this may explain the responses of Pvul-SRS genes against abiotic stress. In summary, this work is the first study in which in silico identification and characterization of Pvul-SRS genes have been examined at gene expression level. The results could therefore provide the basis for future studies of functional characterization of Pvul-SRS genes.
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Affiliation(s)
- İlker Büyük
- Department of Biology, Faculty of Science, Ankara University, Ankara, Turkey.
| | - Aybüke Okay
- Department of Biology, Faculty of Science, Ankara University, Ankara, Turkey
| | - Sümer Aras
- Department of Biology, Faculty of Science, Ankara University, Ankara, Turkey
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20
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Johnson A, Mcassey E, Diaz S, Reagin J, Redd PS, Parrilla DR, Nguyen H, Stec A, McDaniel LAL, Clemente TE, Stupar RM, Parrott WA, Hancock CN. Development of mPing-based activation tags for crop insertional mutagenesis. PLANT DIRECT 2021; 5:e00300. [PMID: 33506165 PMCID: PMC7814626 DOI: 10.1002/pld3.300] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 11/13/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
Modern plant breeding increasingly relies on genomic information to guide crop improvement. Although some genes are characterized, additional tools are needed to effectively identify and characterize genes associated with crop traits. To address this need, the mPing element from rice was modified to serve as an activation tag to induce expression of nearby genes. Embedding promoter sequences in mPing resulted in a decrease in overall transposition rate; however, this effect was negated by using a hyperactive version of mPing called mmPing20. Transgenic soybean events carrying mPing-based activation tags and the appropriate transposase expression cassettes showed evidence of transposition. Expression analysis of a line that contained a heritable insertion of the mmPing20F activation tag indicated that the activation tag induced overexpression of the nearby soybean genes. This represents a significant advance in gene discovery technology as activation tags have the potential to induce more phenotypes than the original mPing element, improving the overall effectiveness of the mutagenesis system.
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Affiliation(s)
- Alexander Johnson
- Institute of Plant Breeding, Genetics & Genomics/Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGAUSA
| | - Edward Mcassey
- Institute of Plant Breeding, Genetics & Genomics/Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGAUSA
- Present address:
School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHIUSA
| | - Stephanie Diaz
- Department of Biology and GeologyUniversity of South Carolina AikenAikenSCUSA
- Present address:
Department of BiochemistryPurdue UniversityWest LafayetteINUSA
| | - Jacob Reagin
- Department of Biology and GeologyUniversity of South Carolina AikenAikenSCUSA
| | - Priscilla S. Redd
- Department of Biology and GeologyUniversity of South Carolina AikenAikenSCUSA
| | - Daymond R. Parrilla
- Department of Biology and GeologyUniversity of South Carolina AikenAikenSCUSA
- Present address:
Department of Molecular and Comparative PathobiologyJohns Hopkins School of MedicineBaltimoreMDUSA
| | - Hanh Nguyen
- Department of Agronomy and Horticulture/Center for Plant Science InnovationUniversity of NebraskaLincolnNEUSA
| | - Adrian Stec
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
| | - Lauren A. L. McDaniel
- Institute of Plant Breeding, Genetics & Genomics/Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGAUSA
| | - Thomas E. Clemente
- Department of Agronomy and Horticulture/Center for Plant Science InnovationUniversity of NebraskaLincolnNEUSA
| | - Robert M. Stupar
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
| | - Wayne A. Parrott
- Institute of Plant Breeding, Genetics & Genomics/Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGAUSA
| | - C. Nathan Hancock
- Department of Biology and GeologyUniversity of South Carolina AikenAikenSCUSA
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21
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Mitros T, Session AM, James BT, Wu GA, Belaffif MB, Clark LV, Shu S, Dong H, Barling A, Holmes JR, Mattick JE, Bredeson JV, Liu S, Farrar K, Głowacka K, Jeżowski S, Barry K, Chae WB, Juvik JA, Gifford J, Oladeinde A, Yamada T, Grimwood J, Putnam NH, De Vega J, Barth S, Klaas M, Hodkinson T, Li L, Jin X, Peng J, Yu CY, Heo K, Yoo JH, Ghimire BK, Donnison IS, Schmutz J, Hudson ME, Sacks EJ, Moose SP, Swaminathan K, Rokhsar DS. Genome biology of the paleotetraploid perennial biomass crop Miscanthus. Nat Commun 2020; 11:5442. [PMID: 33116128 PMCID: PMC7595124 DOI: 10.1038/s41467-020-18923-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 08/19/2020] [Indexed: 02/05/2023] Open
Abstract
Miscanthus is a perennial wild grass that is of global importance for paper production, roofing, horticultural plantings, and an emerging highly productive temperate biomass crop. We report a chromosome-scale assembly of the paleotetraploid M. sinensis genome, providing a resource for Miscanthus that links its chromosomes to the related diploid Sorghum and complex polyploid sugarcanes. The asymmetric distribution of transposons across the two homoeologous subgenomes proves Miscanthus paleo-allotetraploidy and identifies several balanced reciprocal homoeologous exchanges. Analysis of M. sinensis and M. sacchariflorus populations demonstrates extensive interspecific admixture and hybridization, and documents the origin of the highly productive triploid bioenergy crop M. × giganteus. Transcriptional profiling of leaves, stem, and rhizomes over growing seasons provides insight into rhizome development and nutrient recycling, processes critical for sustainable biomass accumulation in a perennial temperate grass. The Miscanthus genome expands the power of comparative genomics to understand traits of importance to Andropogoneae grasses. The perennial grass Miscanthus is a promising biomass crop. Here, via genomics and transcriptomics, the authors reveal its allotetraploid origin, characterize gene expression associated with rhizome development and nutrient recycling, and describe the hybrid origin of the triploid M. x giganteus.
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Affiliation(s)
- Therese Mitros
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.,DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois, Urbana-Champaign, IL, 61801, USA
| | - Adam M Session
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.,U.S. Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Brandon T James
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois, Urbana-Champaign, IL, 61801, USA.,HudsonAlpha Biotechnology Institute, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Guohong Albert Wu
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Mohammad B Belaffif
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois, Urbana-Champaign, IL, 61801, USA.,HudsonAlpha Biotechnology Institute, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Lindsay V Clark
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA.,High Performance Biological Computing, Roy J. Carver Biotechnology Center, University of Illinois, 206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Shengqiang Shu
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Hongxu Dong
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA
| | - Adam Barling
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA
| | - Jessica R Holmes
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA.,High Performance Biological Computing, Roy J. Carver Biotechnology Center, University of Illinois, 206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Jessica E Mattick
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA.,Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Jessen V Bredeson
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Siyao Liu
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA.,Department of Genetics, Curriculum of Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Kerrie Farrar
- Institute of Biological, Environmental AND Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, UK
| | - Katarzyna Głowacka
- Institute of Plant Genetics, Polish Academy of Sciences, 60-479, Poznań, Poland.,Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Stanisław Jeżowski
- Institute of Plant Genetics, Polish Academy of Sciences, 60-479, Poznań, Poland
| | - Kerrie Barry
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Won Byoung Chae
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA.,Department of Environmental Horticulture, Dankook University, Cheonan, 31116, Republic of Korea
| | - John A Juvik
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA
| | - Justin Gifford
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA
| | - Adebosola Oladeinde
- Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA
| | - Toshihiko Yamada
- Field Science Center for Northern Biosphere, 10-chōme-3 Kita 11 Jōnishi, Kita-ku, Sapporo, Hokkaido, 060-0811, Japan
| | - Jane Grimwood
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA.,HudsonAlpha Biotechnology Institute, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Nicholas H Putnam
- Dovetail Genomics, 100 Enterprise Way, Scotts Valley, CA, 95066, USA
| | - Jose De Vega
- Earlham Institute, Norwich Research Park Innovation Centre, Norwich, NR4 7UZ, UK
| | - Susanne Barth
- Teagasc, Crops, Environment and Land Use Programme, Oak Park Research Centre, Carlow, R93XE12, Ireland
| | - Manfred Klaas
- Teagasc, Crops, Environment and Land Use Programme, Oak Park Research Centre, Carlow, R93XE12, Ireland
| | - Trevor Hodkinson
- Botany, School of Natural Sciences, Trinity College Dublin, The University of Dublin, D2, Dublin, Ireland
| | - Laigeng Li
- Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, Shanghai, 200032, China
| | - Xiaoli Jin
- Department of Agronomy, Zhejiang University, Hangzhou, 310058, China
| | - Junhua Peng
- HuaZhi Rice Biotech Company, Changsha, 410125, Hunan, China
| | - Chang Yeon Yu
- Department of Applied Plant Sciences, Kangwon National University, Chuncheon, Gangwon, 200-701, Republic of Korea
| | - Kweon Heo
- Department of Applied Plant Sciences, Kangwon National University, Chuncheon, Gangwon, 200-701, Republic of Korea
| | - Ji Hye Yoo
- Department of Applied Plant Sciences, Kangwon National University, Chuncheon, Gangwon, 200-701, Republic of Korea
| | - Bimal Kumar Ghimire
- Department of Applied Bioscience, Konkuk University, Seoul, 05029, Republic of Korea
| | - Iain S Donnison
- Institute of Biological, Environmental AND Rural Sciences (IBERS), Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, UK
| | - Jeremy Schmutz
- U.S. Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA.,HudsonAlpha Biotechnology Institute, 601 Genome Way Northwest, Huntsville, AL, 35806, USA
| | - Matthew E Hudson
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois, Urbana-Champaign, IL, 61801, USA.,Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Erik J Sacks
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois, Urbana-Champaign, IL, 61801, USA.,Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Stephen P Moose
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois, Urbana-Champaign, IL, 61801, USA.,Department of Crop Sciences, University of Illinois, 1102S Goodwin Ave, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Kankshita Swaminathan
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois, Urbana-Champaign, IL, 61801, USA. .,HudsonAlpha Biotechnology Institute, 601 Genome Way Northwest, Huntsville, AL, 35806, USA.
| | - Daniel S Rokhsar
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA. .,DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois, Urbana-Champaign, IL, 61801, USA. .,U.S. Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA. .,Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 9040495, Japan. .,Chan-Zuckerberg BioHub, 499 Illinois St, San Francisco, CA, 94158, USA.
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22
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Yang J, Xu P, Yu D. Genome-Wide Identification and Characterization of the SHI-Related Sequence Gene Family in Rice. Evol Bioinform Online 2020; 16:1176934320941495. [PMID: 32963469 PMCID: PMC7488920 DOI: 10.1177/1176934320941495] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 06/15/2020] [Indexed: 12/23/2022] Open
Abstract
Rice (Oryza sativa) yield is correlated to various factors. Transcription regulators are important factors, such as the typical SHORT INTERNODES-related sequences (SRSs), which encode proteins with single zinc finger motifs. Nevertheless, knowledge regarding the evolutionary and functional characteristics of the SRS gene family members in rice is insufficient. Therefore, we performed a genome-wide screening and characterization of the OsSRS gene family in Oryza sativa japonica rice. We also examined the SRS proteins from 11 rice sub-species, consisting of 3 cultivars, 6 wild varieties, and 2 other genome types. SRS members from maize, sorghum, Brachypodium distachyon, and Arabidopsis were also investigated. All these SRS proteins exhibited species-specific characteristics, as well as monocot- and dicot-specific characteristics, as assessed by phylogenetic analysis, which was further validated by gene structure and motif analyses. Genome comparisons revealed that segmental duplications may have played significant roles in the recombination of the OsSRS gene family and their expression levels. The family was mainly subjected to purifying selective pressure. In addition, the expression data demonstrated the distinct responses of OsSRS genes to various abiotic stresses and hormonal treatments, indicating their functional divergence. Our study provides a good reference for elucidating the functions of SRS genes in rice.
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Affiliation(s)
- Jun Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Peng Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, China
| | - Diqiu Yu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China.,CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Kunming, China.,Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, Yunnan, China
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23
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Development and Characterization of an Ethyl Methane Sulfonate (EMS) Induced Mutant Population in Capsicum annuum L. PLANTS 2020; 9:plants9030396. [PMID: 32210121 PMCID: PMC7154856 DOI: 10.3390/plants9030396] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 11/29/2022]
Abstract
Plant breeding explores genetic diversity in useful traits to develop new, high-yielding, and improved cultivars. Ethyl methane sulfonate (EMS) is a chemical widely used to induce mutations at loci that regulate economically essential traits. Additionally, it can knock out genes, facilitating efforts to elucidate gene functions through the analysis of mutant phenotypes. Here, we developed a mutant population using the small and pungent ornamental Capsicum annuum pepper “Micro-Pep”. This accession is particularly suitable for mutation studies and molecular research due to its compact growth habit and small size. We treated 9500 seeds with 1.3% EMS and harvested 3996 M2 lines. We then selected 1300 (32.5%) independent M2 families and evaluated their phenotypes over four years. The mutants displayed phenotypic variations in plant growth, habit, leaf color and shape, and flower and fruit morphology. An experiment to optimize Targeting Induced Local Lesions IN Genomes (TILLING) in pepper detected nine EMS-induced mutations in the eIF4E gene. The M2 families developed here exhibited broad phenotypic variation and should be valuable genetic resources for functional gene analysis in pepper molecular breeding programs using reverse genetics tools, including TILLING.
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24
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Zhao SP, Song XY, Guo LL, Zhang XZ, Zheng WJ. Genome-Wide Analysis of the Shi-Related Sequence Family and Functional Identification of GmSRS18 Involving in Drought and Salt Stresses in Soybean. Int J Mol Sci 2020; 21:E1810. [PMID: 32155727 PMCID: PMC7084930 DOI: 10.3390/ijms21051810] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 02/29/2020] [Accepted: 03/04/2020] [Indexed: 11/25/2022] Open
Abstract
The plant-special SHI-RELATED SEQUENCE (SRS) family plays vital roles in various biological processes. However, the genome-wide analysis and abiotic stress-related functions of this family were less reported in soybean. In this work, 21 members of soybean SRS family were identified, which were divided into three groups (Group I, II, and III). The chromosome location and gene structure were analyzed, which indicated that the members in the same group may have similar functions. The analysis of stress-related cis-elements showed that the SRS family may be involved in abiotic stress signaling pathway. The analysis of expression patterns in various tissues demonstrated that SRS family may play crucial roles in special tissue-dependent regulatory networks. The data based on soybean RNA sequencing (RNA-seq) and quantitative Real-Time PCR (qRT-PCR) proved that SRS genes were induced by drought, NaCl, and exogenous abscisic acid (ABA). GmSRS18 significantly induced by drought and NaCl was selected for further functional verification. GmSRS18, encoding a cell nuclear protein, could negatively regulate drought and salt resistance in transgenic Arabidopsis. It can affect stress-related physiological index, including chlorophyll, proline, and relative electrolyte leakage. Additionally, it inhibited the expression levels of stress-related marker genes. Taken together, these results provide valuable information for understanding the classification of soybean SRS transcription factors and indicates that SRS plays important roles in abiotic stress responses.
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Affiliation(s)
- Shu-Ping Zhao
- College of Agronomy, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling 712100, China; (S.-P.Z.); (X.-Z.Z.)
| | - Xin-Yuan Song
- Agro-biotechnology Research Institute, Jilin Academy of Agriculture Sciences, Changchun 130033, China;
| | - Lin-Lin Guo
- College of Agronomy, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling 712100, China; (S.-P.Z.); (X.-Z.Z.)
| | - Xiang-Zhan Zhang
- College of Agronomy, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling 712100, China; (S.-P.Z.); (X.-Z.Z.)
| | - Wei-Jun Zheng
- College of Agronomy, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling 712100, China; (S.-P.Z.); (X.-Z.Z.)
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25
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Guo F, Ma J, Hou L, Shi S, Sun J, Li G, Zhao C, Xia H, Zhao S, Wang X, Zhao Y. Transcriptome profiling provides insights into molecular mechanism in Peanut semi-dwarf mutant. BMC Genomics 2020; 21:211. [PMID: 32138648 PMCID: PMC7059693 DOI: 10.1186/s12864-020-6614-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 02/24/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plant height, mainly decided by main stem height, is the major agronomic trait and closely correlated to crop yield. A number of studies had been conducted on model plants and crops to understand the molecular and genetic basis of plant height. However, little is known on the molecular mechanisms of peanut main stem height. RESULTS In this study, a semi-dwarf peanut mutant was identified from 60Co γ-ray induced mutant population and designated as semi-dwarf mutant 2 (sdm2). The height of sdm2 was only 59.3% of its wild line Fenghua 1 (FH1) at the mature stage. The sdm2 has less internode number and short internode length to compare with FH1. Gene expression profiles of stem and leaf from both sdm2 and FH1 were analyzed using high throughput RNA sequencing. The differentially expressed genes (DEGs) were involved in hormone biosynthesis and signaling pathways, cell wall synthetic and metabolic pathways. BR, GA and IAA biosynthesis and signal transduction pathways were significantly enriched. The expression of several genes in BR biosynthesis and signaling were found to be significantly down-regulated in sdm2 as compared to FH1. Many transcription factors encoding genes were identified as DEGs. CONCLUSIONS A large number of genes were found differentially expressed between sdm2 and FH1. These results provide useful information for uncovering the molecular mechanism regulating peanut stem height. It could facilitate identification of causal genes for breeding peanut varieties with semi-dwarf phenotype.
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Affiliation(s)
- Fengdan Guo
- College of Life Science, Shandong Normal University, Jinan, People's Republic of China.,Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, People's Republic of China
| | - Junjie Ma
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, People's Republic of China.,Life Science College of Shandong University, Jinan, 250100, People's Republic of China
| | - Lei Hou
- College of Life Science, Shandong Normal University, Jinan, People's Republic of China.,Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, People's Republic of China
| | - Suhua Shi
- College of Life Science, Shandong Normal University, Jinan, People's Republic of China.,Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, People's Republic of China
| | - Jinbo Sun
- College of Life Science, Shandong Normal University, Jinan, People's Republic of China.,Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, People's Republic of China
| | - Guanghui Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, People's Republic of China
| | - Chuanzhi Zhao
- College of Life Science, Shandong Normal University, Jinan, People's Republic of China.,Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, People's Republic of China
| | - Han Xia
- College of Life Science, Shandong Normal University, Jinan, People's Republic of China.,Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, People's Republic of China
| | - Shuzhen Zhao
- College of Life Science, Shandong Normal University, Jinan, People's Republic of China.,Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, People's Republic of China
| | - Xingjun Wang
- College of Life Science, Shandong Normal University, Jinan, People's Republic of China. .,Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, People's Republic of China. .,Life Science College of Shandong University, Jinan, 250100, People's Republic of China.
| | - Yanxiu Zhao
- College of Life Science, Shandong Normal University, Jinan, People's Republic of China.
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26
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Yuan TT, Xu HH, Li J, Lu YT. Auxin abolishes SHI-RELATED SEQUENCE5-mediated inhibition of lateral root development in Arabidopsis. THE NEW PHYTOLOGIST 2020; 225:297-309. [PMID: 31403703 DOI: 10.1111/nph.16115] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/03/2019] [Indexed: 06/10/2023]
Abstract
Lateral roots (LRs), which form in the plant postembryonically, determine the architecture of the root system. While negative regulatory factors that inhibit LR formation and are counteracted by auxin exist in the pericycle, these factors have not been characterised. Here, we report that SHI-RELATED SEQUENCE5 (SRS5) is an intrinsic negative regulator of LR formation and that auxin signalling abolishes this inhibitory effect of SRS5. Whereas LR primordia (LRPs) and LRs were fewer and less dense in SRS5ox and Pro35S:SRS5-GFP plants than in the wild-type, they were more abundant and denser in the srs5-2 loss-of-function mutant. SRS5 inhibited LR formation by directly downregulating the expression of LATERAL ORGAN BOUNDARIES-DOMAIN 16 (LBD16) and LBD29. Auxin repressed SRS5 expression. Auxin-mediated repression of SRS5 expression was not observed in the arf7-1 arf19-1 double mutant, likely because ARF7 and ARF19 bind to the promoter of SRS5 and inhibit its expression in response to auxin. Taken together, our data reveal that SRS5 negatively regulates LR formation by repressing the expression of LBD16 and LBD29 and that auxin releases this inhibitory effect through ARF7 and ARF19.
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Affiliation(s)
- Ting-Ting Yuan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Heng-Hao Xu
- Laboratory of Marine Pharmaceutical Compound Screening, Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Huaihai Institute of Technology, Lianyungang, 222005, China
| | - Juan Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ying-Tang Lu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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27
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He B, Shi P, Lv Y, Gao Z, Chen G. Gene coexpression network analysis reveals the role of SRS genes in senescence leaf of maize ( Zea mays L.). J Genet 2020; 99:3. [PMID: 32089522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Shi-related sequence (SRS) proteins are plant-specific transcription factors that play important roles in developmental processes, including regulating hormone biosynthesis, response or signal transduction. However, systematical analysis of the SRS gene family in maize has not yet been conducted. In this study, 11 SRS genes with 13 transcripts were identified and characterized. The characteristics of the gene family were analysed in terms of phylogenetic relationships, chromosome distribution and gene structure. RNA-sequencing data analysis showed that the expression patterns of SRS genes were quite different from each other in maize, indicating their divergence in function. Interestingly, the GRMZM2G077752 gene is highly expressed in senescent leaves. Using further coexpression network analysis, we determined that the module containing GRMZM2G077752 were over-represented by genes related to abscisic acid (ABA) stimulus and carbohydrate metabolic process. This result indicated that GRMZM2G077752 might perceive ABA signal and cause the activation of carbohydrate remobilization during leaf ageing. This study provides valuable information for understanding the functions of the SRS genes in maize.
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Affiliation(s)
- Bing He
- School of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu, People's Republic of China.
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28
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He B, Shi P, Lv Y, Gao Z, Chen G. Gene coexpression network analysis reveals the role of SRS genes in senescence leaf of maize (Zea mays L.). J Genet 2019. [DOI: 10.1007/s12041-019-1162-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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29
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Duan E, Wang Y, Li X, Lin Q, Zhang T, Wang Y, Zhou C, Zhang H, Jiang L, Wang J, Lei C, Zhang X, Guo X, Wang H, Wan J. OsSHI1 Regulates Plant Architecture Through Modulating the Transcriptional Activity of IPA1 in Rice. THE PLANT CELL 2019; 31:1026-1042. [PMID: 30914468 PMCID: PMC6533028 DOI: 10.1105/tpc.19.00023] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/27/2019] [Accepted: 03/24/2019] [Indexed: 05/20/2023]
Abstract
Tillering and panicle branching are important determinants of plant architecture and yield potential in rice (Oryza sativa). IDEAL PLANT ARCHITECTURE1 (IPA1) encodesSQUAMOSA PROMOTER BINDING PROTEIN-LIKE14, which acts as a key transcription factor regulating tiller outgrowth and panicle branching by directly activating the expression of O. sativa TEOSINTE BRANCHED1 (OsTB1) and O. sativa DENSE AND ERECT PANICLE1 (OsDEP1), thereby influencing grain yield in rice. Here, we report the identification of a rice mutant named shi1 that is characterized by dramatically reduced tiller number, enhanced culm strength, and increased panicle branch number. Map-based cloning revealed that O. sativa SHORT INTERNODES1 (OsSHI1) encodes a plant-specific transcription factor of the SHI family with a characteristic family-specific IGGH domain and a conserved zinc-finger DNA binding domain. Consistent with the mutant phenotype, OsSHI1 is predominantly expressed in axillary buds and young panicle, and its encoded protein is exclusively targeted to the nucleus. We show that OsSHI1 physically interacts with IPA1 both in vitro and in vivo. Moreover, OsSHI1 could bind directly to the promoter regions of both OsTB1 and OsDEP1 through a previously unrecognized cis-element (T/GCTCTAC motif). OsSHI1 repressed the transcriptional activation activity of IPA1 by affecting its DNA binding activity toward the promoters of both OsTB1 and OsDEP1, resulting in increased tiller number and diminished panicle size. Taken together, our results demonstrate that OsSHI1 regulates plant architecture through modulating the transcriptional activity of IPA1 and provide insight into the establishment of plant architecture in rice.
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Affiliation(s)
- Erchao Duan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Yihua Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaohui Li
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Qibing Lin
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ting Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yupeng Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chunlei Zhou
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Huan Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Ling Jiang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiulin Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cailin Lei
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xin Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuping Guo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiyang Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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30
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Zúñiga-Mayo VM, Gómez-Felipe A, Herrera-Ubaldo H, de Folter S. Gynoecium development: networks in Arabidopsis and beyond. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1447-1460. [PMID: 30715461 DOI: 10.1093/jxb/erz026] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/14/2019] [Indexed: 05/27/2023]
Abstract
Life has always found a way to preserve itself. One strategy that has been developed for this purpose is sexual reproduction. In land plants, the gynoecium is considered to be at the top of evolutionary innovation, since it has been a key factor in the success of the angiosperms. The gynoecium is composed of carpels with different tissues that need to develop and differentiate in the correct way. In order to control and guide gynoecium development, plants have adapted elements of pre-existing gene regulatory networks (GRNs) but new ones have also evolved. The GRNs can interact with internal factors (e.g. hormones and other metabolites) and external factors (e.g. mechanical signals and temperature) at different levels, giving robustness and flexibility to gynoecium development. Here, we review recent findings regarding the role of cytokinin-auxin crosstalk and the genes that connect these hormonal pathways during early gynoecium development. We also discuss some examples of internal and external factors that can modify GRNs. Finally, we make a journey through the flowering plant lineage to determine how conserved are these GRNs that regulate gynoecium and fruit development.
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Affiliation(s)
- Victor M Zúñiga-Mayo
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Guanajuato, México
| | - Andrea Gómez-Felipe
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Guanajuato, México
| | - Humberto Herrera-Ubaldo
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Guanajuato, México
| | - Stefan de Folter
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Guanajuato, México
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31
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Yuan TT, Xu HH, Zhang Q, Zhang LY, Lu YT. The COP1 Target SHI-RELATED SEQUENCE5 Directly Activates Photomorphogenesis-Promoting Genes. THE PLANT CELL 2018; 30:2368-2382. [PMID: 30150309 PMCID: PMC6241259 DOI: 10.1105/tpc.18.00455] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/25/2018] [Accepted: 08/24/2018] [Indexed: 05/03/2023]
Abstract
Plant seedlings undergo distinct developmental processes in the dark and in the light. Several genes, including ELONGATED HYPOCOTYL5 (HY5), B-BOX PROTEIN21 (BBX21), and BBX22, have been identified as photomorphogenesis-promoting factors in Arabidopsis thaliana; however, the overexpression of these genes does not induce photomorphogenesis in the dark. Using an activation-tagging approach, we identified SRS5ox, which overexpresses SHI-RELATED SEQUENCE5 (SRS5) following induction with estradiol. SRS5 overexpression in SRS5ox and Pro35S:SRS5-GFP seedlings results in a constitutive photomorphogenesis phenotype in the dark, whereas SRS5 loss of function in the srs5-2 mutant results in long hypocotyls in the light. This indicates that SRS5 is a positive regulator of photomorphogenesis. Furthermore, SRS5 promotes photomorphogenesis by directly binding to the promoters of photomorphogenesis-promoting genes, such as HY5, BBX21, and BBX22, and activating their expression, thus affecting the expression of downstream light-signaling genes. These data indicate that SRS5 acts in the upregulation of photomorphogenesis-promoting genes. In addition, CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1), which plays a central repressive role in seedling photomorphogenesis, directly ubiquitinates SRS5, promoting its degradation in the dark. Taken together, our results demonstrate that SRS5 directly activates the expression of downstream genes HY5, BBX21, and BBX22 and is a target of COP1-mediated degradation in Arabidopsis.
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Affiliation(s)
- Ting-Ting Yuan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Heng-Hao Xu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Qing Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Lin-Yu Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ying-Tang Lu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
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32
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Moin M, Bakshi A, Saha A, Dutta M, Kirti PB. Gain-of-function mutagenesis approaches in rice for functional genomics and improvement of crop productivity. Brief Funct Genomics 2018; 16:238-247. [PMID: 28137760 DOI: 10.1093/bfgp/elw041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The epitome of any genome research is to identify all the existing genes in a genome and investigate their roles. Various techniques have been applied to unveil the functions either by silencing or over-expressing the genes by targeted expression or random mutagenesis. Rice is the most appropriate model crop for generating a mutant resource for functional genomic studies because of the availability of high-quality genome sequence and relatively smaller genome size. Rice has syntenic relationships with members of other cereals. Hence, characterization of functionally unknown genes in rice will possibly provide key genetic insights and can lead to comparative genomics involving other cereals. The current review attempts to discuss the available gain-of-function mutagenesis techniques for functional genomics, emphasizing the contemporary approach, activation tagging and alterations to this method for the enhancement of yield and productivity of rice.
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33
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Subrahmaniam HJ, Libourel C, Journet EP, Morel JB, Muños S, Niebel A, Raffaele S, Roux F. The genetics underlying natural variation of plant-plant interactions, a beloved but forgotten member of the family of biotic interactions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:747-770. [PMID: 29232012 DOI: 10.1111/tpj.13799] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/02/2017] [Accepted: 12/06/2017] [Indexed: 05/22/2023]
Abstract
Despite the importance of plant-plant interactions on crop yield and plant community dynamics, our understanding of the genetic and molecular bases underlying natural variation of plant-plant interactions is largely limited in comparison with other types of biotic interactions. By listing 63 quantitative trait loci (QTL) mapping and global gene expression studies based on plants directly challenged by other plants, we explored whether the genetic architecture and the function of the candidate genes underlying natural plant-plant interactions depend on the type of interactions between two plants (competition versus commensalism versus reciprocal helping versus asymmetry). The 16 transcriptomic studies are unevenly distributed between competitive interactions (n = 12) and asymmetric interactions (n = 4, all focusing on response to parasitic plants). By contrast, 17 and 30 QTL studies were identified for competitive interactions and asymmetric interactions (either weed suppressive ability or response to parasitic plants), respectively. Surprisingly, no studies have been carried out on the identification of genetic and molecular bases underlying natural variation in positive interactions. The candidate genes underlying natural plant-plant interactions can be classified into seven categories of plant function that have been identified in artificial environments simulating plant-plant interactions either frequently (photosynthesis, hormones), only recently (cell wall modification and degradation, defense pathways against pathogens) or rarely (ABC transporters, histone modification and meristem identity/life history traits). Finally, we introduce several avenues that need to be explored in the future to obtain a thorough understanding of the genetic and molecular bases underlying plant-plant interactions within the context of realistic community complexity.
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Affiliation(s)
| | - Cyril Libourel
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Etienne-Pascal Journet
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
- AGIR, Université de Toulouse, INRA, INPT, INP-EI PURPAN, Castanet-Tolosan, France
| | - Jean-Benoît Morel
- BGPI, INRA, CIRAD, SupAgro, Université de Montpellier, Montpellier, France
| | - Stéphane Muños
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Andreas Niebel
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Sylvain Raffaele
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Fabrice Roux
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
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34
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Estornell LH, Landberg K, Cierlik I, Sundberg E. SHI/ STY Genes Affect Pre- and Post-meiotic Anther Processes in Auxin Sensing Domains in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2018; 9:150. [PMID: 29491878 PMCID: PMC5817092 DOI: 10.3389/fpls.2018.00150] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/29/2018] [Indexed: 05/13/2023]
Abstract
In flowering plants, mature sperm cells are enclosed in pollen grains formed in structures called anthers. Several cell layers surrounding the central sporogenous cells of the anther are essential for directing the developmental processes that lead to meiosis, pollen formation, and the subsequent pollen release. The specification and function of these tissues are regulated by a large number of genetic factors. Additionally, the plant hormone auxin has previously been shown to play important roles in the later phases of anther development. Using the R2D2 auxin sensor system we here show that auxin is sensed also in the early phases of anther cell layer development, suggesting that spatiotemporal regulation of auxin levels is important for early anther morphogenesis. Members of the SHI/STY transcription factor family acting as direct regulators of YUC auxin biosynthesis genes have previously been demonstrated to affect early anther patterning. Using reporter constructs we show that SHI/STY genes are dynamically active throughout anther development and their expression overlaps with those of three additional downstream targets, PAO5, EOD3 and PGL1. Characterization of anthers carrying mutations in five SHI/STY genes clearly suggests that SHI/STY transcription factors affect anther organ identity. In addition, their activity is important to repress periclinal cell divisions as well as premature entrance into programmed cell death and cell wall lignification, which directly influences the timing of anther dehiscence and the pollen viability. The SHI/STY proteins also prevent premature pollen germination suggesting that they may play a role in the induction or maintenance of pollen dormancy.
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35
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Bull H, Casao MC, Zwirek M, Flavell AJ, Thomas WTB, Guo W, Zhang R, Rapazote-Flores P, Kyriakidis S, Russell J, Druka A, McKim SM, Waugh R. Barley SIX-ROWED SPIKE3 encodes a putative Jumonji C-type H3K9me2/me3 demethylase that represses lateral spikelet fertility. Nat Commun 2017; 8:936. [PMID: 29038434 PMCID: PMC5643332 DOI: 10.1038/s41467-017-00940-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/29/2017] [Indexed: 11/30/2022] Open
Abstract
The barley inflorescence (spike) comprises a multi-noded central stalk (rachis) with tri-partite clusters of uni-floretted spikelets attached alternately along its length. Relative fertility of lateral spikelets within each cluster leads to spikes with two or six rows of grain, or an intermediate morphology. Understanding the mechanisms controlling this key developmental step could provide novel solutions to enhanced grain yield. Classical genetic studies identified five major SIX-ROWED SPIKE (VRS) genes, with four now known to encode transcription factors. Here we identify and characterise the remaining major VRS gene, VRS3, as encoding a putative Jumonji C-type H3K9me2/me3 demethylase, a regulator of chromatin state. Exploring the expression network modulated by VRS3 reveals specific interactions, both with other VRS genes and genes involved in stress, hormone and sugar metabolism. We show that combining a vrs3 mutant allele with natural six-rowed alleles of VRS1 and VRS5 leads to increased lateral grain size and greater grain uniformity. The VRS genes of barley control the fertility of the lateral spikelets on the barley inflorescence. Here, Bull et al. show that VRS3 encodes a putative Jumonji C-type histone demethylase that regulates expression of other VRS genes, and genes involved in stress, hormone and sugar metabolism.
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Affiliation(s)
- Hazel Bull
- James Hutton Limited, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland.,Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland
| | - M Cristina Casao
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland
| | - Monika Zwirek
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland
| | - Andrew J Flavell
- Division of Plant Sciences, School of Life Sciences, The University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland
| | - William T B Thomas
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland
| | - Wenbin Guo
- Division of Plant Sciences, School of Life Sciences, The University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland.,Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland
| | - Runxuan Zhang
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland
| | - Paulo Rapazote-Flores
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland
| | - Stylianos Kyriakidis
- Division of Plant Sciences, School of Life Sciences, The University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland
| | - Joanne Russell
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland
| | - Arnis Druka
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland
| | - Sarah M McKim
- Division of Plant Sciences, School of Life Sciences, The University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland.
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland. .,Division of Plant Sciences, School of Life Sciences, The University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland.
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36
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Pfannebecker KC, Lange M, Rupp O, Becker A. An Evolutionary Framework for Carpel Developmental Control Genes. Mol Biol Evol 2017; 34:330-348. [PMID: 28049761 DOI: 10.1093/molbev/msw229] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Carpels are the female reproductive organs of flowering plants (angiosperms), enclose the ovules, and develop into fruits. The presence of carpels unites angiosperms, and they are suggested to be the most important autapomorphy of the angiosperms, e.g., they prevent inbreeding and allow efficient seed dispersal. Many transcriptional regulators and coregulators essential for carpel development are encoded by diverse gene families and well characterized in Arabidopsis thaliana. Among these regulators are AGAMOUS (AG), ETTIN (ETT), LEUNIG (LUG), SEUSS (SEU), SHORT INTERNODE/STYLISH (SHI/STY), and SEPALLATA1, 2, 3, 4 (SEP1, 2, 3, 4). However, the timing of the origin and their subsequent molecular evolution of these carpel developmental regulators are largely unknown. Here, we have sampled homologs of these carpel developmental regulators from the sequenced genomes of a wide taxonomic sampling of the land plants, such as Physcomitrella patens, Selaginella moellendorfii, Picea abies, and several angiosperms. Careful phylogenetic analyses were carried out that provide a phylogenetic background for the different gene families and provide minimal estimates for the ages of these developmental regulators. Our analyses and published work show that LUG-, SEU-, and SHI/STY-like genes were already present in the Most Recent Common Ancestor (MRCA) of all land plants, AG- and SEP-like genes were present in the MRCA of seed plants and their origin may coincide with the ξ Whole Genome Duplication. Our work shows that the carpel development regulatory network was, in part, recruited from preexisting network components that were present in the MRCA of angiosperms and modified to regulate gynoecium development.
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Affiliation(s)
- Kai C Pfannebecker
- Department of Biology and Chemistry, Institute of Botany, Justus-Liebig-University, Gießen, Germany
| | - Matthias Lange
- Department of Biology and Chemistry, Institute of Botany, Justus-Liebig-University, Gießen, Germany
| | - Oliver Rupp
- Department of Biology and Chemistry, Institute of Bioinformatics and Systems Biology, Justus-Liebig-University, Gießen, Germany
| | - Annette Becker
- Department of Biology and Chemistry, Institute of Botany, Justus-Liebig-University, Gießen, Germany
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37
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Gao X, Walworth AE, Mackie C, Song GQ. Overexpression of blueberry FLOWERING LOCUS T is associated with changes in the expression of phytohormone-related genes in blueberry plants. HORTICULTURE RESEARCH 2016; 3:16053. [PMID: 27818778 PMCID: PMC5080838 DOI: 10.1038/hortres.2016.53] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/25/2016] [Accepted: 09/26/2016] [Indexed: 05/08/2023]
Abstract
Flowering locus T (FT) is a primary integrator in the regulation of plant flowering. Overexpressing a blueberry (Vaccinium corymbosum L.) FT gene (VcFT) (herein VcFT-OX) resulted in early flowering and dwarfing in 'Aurora' plants (herein 'VcFT-Aurora'). In this study, we found that VcFT-OX reduced shoot regeneration from leaf explants. To investigate the potential roles of the phytohormone pathway genes associated with VcFT-OX, differentially expressed (DE) genes in leaf tissues of 'VcFT-Aurora' plants were annotated and analyzed using non-transgenic 'Aurora' plants as a control. Three DE floral genes, including the blueberry SUPPRESSOR of Overexpression of constans 1 (VcSOC1) (gibberellin related), Abscisic acid responsive elements-binding factor 2 (VcABF2) and protein related to ABI3/VP1 (VcABI3/VP1) (ethylene-related), are present under both the phytohormone-responsive and the dwarfing-related Gene Ontology terms. The gene networks of the DE genes overall showed the molecular basis of the multifunctional aspects of VcFT overexpression beyond flowering promotion and suggested that phytohormone changes could be signaling molecules with important roles in the phenotypic changes driven by VcFT-OX.
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Affiliation(s)
- Xuan Gao
- Department of Horticulture, Plant Biotechnology Resource and Outreach Center, Michigan State University, East Lansing, MI 48824, USA
- Key Laboratory for the Conservation and Utilization of Important Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Aaron E Walworth
- Department of Horticulture, Plant Biotechnology Resource and Outreach Center, Michigan State University, East Lansing, MI 48824, USA
| | - Charity Mackie
- Department of Horticulture, Plant Biotechnology Resource and Outreach Center, Michigan State University, East Lansing, MI 48824, USA
| | - Guo-qing Song
- Department of Horticulture, Plant Biotechnology Resource and Outreach Center, Michigan State University, East Lansing, MI 48824, USA
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Gan L, Di R, Chao Y, Han L, Chen X, Wu C, Yin S. De Novo Transcriptome Analysis for Kentucky Bluegrass Dwarf Mutants Induced by Space Mutation. PLoS One 2016; 11:e0151768. [PMID: 27010560 PMCID: PMC4807101 DOI: 10.1371/journal.pone.0151768] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 03/03/2016] [Indexed: 01/02/2023] Open
Abstract
Kentucky bluegrass (Poa pratensis L.) is a major cool-season turfgrass requiring frequent mowing. Utilization of cultivars with slow growth is a promising method to decrease mowing frequency. In this study, two dwarf mutant selections of Kentucky bluegrass (A12 and A16) induced by space mutation were analyzed for the differentially expressed genes compared with the wild type (WT) by the high-throughput RNA-Seq technology. 253,909 unigenes were obtained by de novo assembly. 24.20% of the unigenes had a significant level of amino acid sequence identity to Brachypodium distachyon proteins, followed by Hordeum vulgare with 18.72% among the non-redundant (NR) Blastx top hits. Assembled unigenes were associated with 32 pathways using KEGG orthology terms and their respective KEGG maps. Between WT and A16 libraries, 4,203 differentially expressed genes (DEGs) were identified, whereas there were 883 DEGs between WT and A12 libraries. Further investigation revealed that the DEG pathways were mainly involved in terpenoid biosynthesis and plant hormone metabolism, which might account for the differences of plant height and leaf blade color between dwarf mutant and WT plants. Our study presents the first comprehensive transcriptomic data and gene function analysis of Poa pratensis L., providing a valuable resource for future studies in plant dwarfing breeding and comparative genome analysis for Pooideae plants.
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Affiliation(s)
- Lu Gan
- Institute of Turfgrass Science, Beijing Forestry University, Beijing, 100083, China
| | - Rong Di
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, New Jersey, 08901, United States of America
| | - Yuehui Chao
- Institute of Turfgrass Science, Beijing Forestry University, Beijing, 100083, China
| | - Liebao Han
- Institute of Turfgrass Science, Beijing Forestry University, Beijing, 100083, China
| | - Xingwu Chen
- Institute of Turfgrass Science, Beijing Forestry University, Beijing, 100083, China
| | - Chao Wu
- Institute of Turfgrass Science, Beijing Forestry University, Beijing, 100083, China
| | - Shuxia Yin
- Institute of Turfgrass Science, Beijing Forestry University, Beijing, 100083, China
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Zhang Y, von Behrens I, Zimmermann R, Ludwig Y, Hey S, Hochholdinger F. LATERAL ROOT PRIMORDIA 1 of maize acts as a transcriptional activator in auxin signalling downstream of the Aux/IAA gene rootless with undetectable meristem 1. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:3855-63. [PMID: 25911745 PMCID: PMC4473986 DOI: 10.1093/jxb/erv187] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Only little is known about target genes of auxin signalling downstream of the Aux/IAA-ARF module. In the present study, it has been demonstrated that maize lateral root primordia 1 (lrp1) encodes a transcriptional activator that is directly regulated by the Aux/IAA protein ROOTLESS WITH UNDETECTABLE MERISTEM 1 (RUM1). Expression of lrp1 is confined to early root primordia and meristems and is auxin-inducible. Based on its primary protein structure, LRP1 is predicted to be a transcription factor. This notion is supported by exclusive LRP1 localization in the nucleus and its ability to activate downstream gene activity. Based on the observation that lrp1 transcription is completely repressed in the semi-dominant gain of function mutant rum1, it was demonstrated that the lrp1 promoter is a direct target of RUM1 proteins. Subsequently, promoter activation assays indicated that RUM1 represses the expression of a GFP reporter fused to the native promoter of lrp1. Constitutive repression of lrp1 in rum1 mutants is a consequence of the stability of mutated rum1 proteins which cannot be degraded by the proteasome and thus constitutively bind to the lrp1 promoter and repress transcription. Taken together, the repression of the transcriptional activator lrp1 by direct binding of RUM1 to its promoter, together with specific expression of lrp1 in root meristems, suggests a function in maize root development via the RUM1-dependent auxin signalling pathway.
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Affiliation(s)
- Yanxiang Zhang
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, Friedrich-Ebert-Allee 144, University of Bonn, D-53113 Bonn, Germany Center for Molecular Cell and Systems Biology, College of Life Science, Fujian Agriculture & Forestry University, 350002 Fuzhou, China
| | - Inga von Behrens
- ZMBP, Center for Plant Molecular Biology, Department of General Genetics, University of Tuebingen, D-72076 Tuebingen, Germany
| | - Roman Zimmermann
- ZMBP, Center for Plant Molecular Biology, Department of General Genetics, University of Tuebingen, D-72076 Tuebingen, Germany
| | - Yvonne Ludwig
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, Friedrich-Ebert-Allee 144, University of Bonn, D-53113 Bonn, Germany
| | - Stefan Hey
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, Friedrich-Ebert-Allee 144, University of Bonn, D-53113 Bonn, Germany
| | - Frank Hochholdinger
- INRES, Institute of Crop Science and Resource Conservation, Crop Functional Genomics, Friedrich-Ebert-Allee 144, University of Bonn, D-53113 Bonn, Germany
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Bianchi VJ, Rubio M, Trainotti L, Verde I, Bonghi C, Martínez-Gómez P. Prunus transcription factors: breeding perspectives. FRONTIERS IN PLANT SCIENCE 2015; 6:443. [PMID: 26124770 PMCID: PMC4464204 DOI: 10.3389/fpls.2015.00443] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 05/29/2015] [Indexed: 05/18/2023]
Abstract
Many plant processes depend on differential gene expression, which is generally controlled by complex proteins called transcription factors (TFs). In peach, 1533 TFs have been identified, accounting for about 5.5% of the 27,852 protein-coding genes. These TFs are the reference for the rest of the Prunus species. TF studies in Prunus have been performed on the gene expression analysis of different agronomic traits, including control of the flowering process, fruit quality, and biotic and abiotic stress resistance. These studies, using quantitative RT-PCR, have mainly been performed in peach, and to a lesser extent in other species, including almond, apricot, black cherry, Fuji cherry, Japanese apricot, plum, and sour and sweet cherry. Other tools have also been used in TF studies, including cDNA-AFLP, LC-ESI-MS, RNA, and DNA blotting or mapping. More recently, new tools assayed include microarray and high-throughput DNA sequencing (DNA-Seq) and RNA sequencing (RNA-Seq). New functional genomics opportunities include genome resequencing and the well-known synteny among Prunus genomes and transcriptomes. These new functional studies should be applied in breeding programs in the development of molecular markers. With the genome sequences available, some strategies that have been used in model systems (such as SNP genotyping assays and genotyping-by-sequencing) may be applicable in the functional analysis of Prunus TFs as well. In addition, the knowledge of the gene functions and position in the peach reference genome of the TFs represents an additional advantage. These facts could greatly facilitate the isolation of genes via QTL (quantitative trait loci) map-based cloning in the different Prunus species, following the association of these TFs with the identified QTLs using the peach reference genome.
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Affiliation(s)
- Valmor J. Bianchi
- Department of Plant Physiology, Instituto de Biologia, Universidade Federal de PelotasPelotas-RS, Brazil
| | - Manuel Rubio
- Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones CientíficasMurcia, Spain
| | | | - Ignazio Verde
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CRA) - Centro di ricerca per la frutticolturaRoma, Italy
| | - Claudio Bonghi
- Department of Agronomy, Food, Natural Resources, and Environment (DAFNAE). University of PaduaPadova, Italy
| | - Pedro Martínez-Gómez
- Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura, Consejo Superior de Investigaciones CientíficasMurcia, Spain
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Shared Genomic Regions Between Derivatives of a Large Segregating Population of Maize Identified Using Bulked Segregant Analysis Sequencing and Traditional Linkage Analysis. G3-GENES GENOMES GENETICS 2015; 5:1593-602. [PMID: 26038364 PMCID: PMC4528316 DOI: 10.1534/g3.115.017665] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Delayed transition from the vegetative stage to the reproductive stage of development and increased plant height have been shown to increase biomass productivity in grasses. The goal of this project was to detect quantitative trait loci using extremes from a large synthetic population, as well as a related recombinant inbred line mapping population for these two traits. Ten thousand individuals from a B73 × Mo17 noninbred population intermated for 14 generations (IBM Syn14) were grown at a density of approximately 16,500 plants ha(-1). Flowering time and plant height were measured within this population. DNA was pooled from the 46 most extreme individuals from each distributional tail for each of the traits measured and used in bulk segregant analysis (BSA) sequencing. Allelic divergence at each of the ∼1.1 million SNP loci was estimated as the difference in allele frequencies between the selected extremes. Additionally, 224 intermated B73 × Mo17 recombinant inbred lines were concomitantly grown at a similar density adjacent to the large synthetic population and were assessed for flowering time and plant height. Using the BSA sequencing method, 14 and 13 genomic regions were identified for flowering time and plant height, respectively. Linkage mapping with the RIL population identified eight and three regions for flowering time and plant height, respectively. Of the regions identified, three colocalized between the two populations for flowering time and two colocalized for plant height. This study demonstrates the utility of using BSA sequencing for the dissection of complex quantitative traits important for production of lignocellulosic ethanol.
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Baron E, Richirt J, Villoutreix R, Amsellem L, Roux F. The genetics of intra‐ and interspecific competitive response and effect in a local population of an annual plant species. Funct Ecol 2015. [DOI: 10.1111/1365-2435.12436] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Etienne Baron
- Laboratoire Génétique et Evolution des Populations Végétales UMR CNRS 8198 Université des Sciences et Technologies de Lille – Lille 1 F‐59655 Villeneuve d'Ascq Cedex France
- INRA Laboratoire des Interactions Plantes‐Microorganismes (LIPM) UMR441 F‐31326 Castanet‐Tolosan France
- CNRS Laboratoire des Interactions Plantes‐Microorganismes (LIPM) UMR2594 F‐31326 Castanet‐Tolosan France
| | - Julien Richirt
- Laboratoire Génétique et Evolution des Populations Végétales UMR CNRS 8198 Université des Sciences et Technologies de Lille – Lille 1 F‐59655 Villeneuve d'Ascq Cedex France
| | - Romain Villoutreix
- Laboratoire Génétique et Evolution des Populations Végétales UMR CNRS 8198 Université des Sciences et Technologies de Lille – Lille 1 F‐59655 Villeneuve d'Ascq Cedex France
| | - Laurent Amsellem
- Laboratoire Génétique et Evolution des Populations Végétales UMR CNRS 8198 Université des Sciences et Technologies de Lille – Lille 1 F‐59655 Villeneuve d'Ascq Cedex France
| | - Fabrice Roux
- Laboratoire Génétique et Evolution des Populations Végétales UMR CNRS 8198 Université des Sciences et Technologies de Lille – Lille 1 F‐59655 Villeneuve d'Ascq Cedex France
- INRA Laboratoire des Interactions Plantes‐Microorganismes (LIPM) UMR441 F‐31326 Castanet‐Tolosan France
- CNRS Laboratoire des Interactions Plantes‐Microorganismes (LIPM) UMR2594 F‐31326 Castanet‐Tolosan France
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Arisha MH, Shah SNM, Gong ZH, Jing H, Li C, Zhang HX. Ethyl methane sulfonate induced mutations in M2 generation and physiological variations in M1 generation of peppers (Capsicum annuum L.). FRONTIERS IN PLANT SCIENCE 2015; 6:399. [PMID: 26089827 PMCID: PMC4454883 DOI: 10.3389/fpls.2015.00399] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 05/18/2015] [Indexed: 05/10/2023]
Abstract
This study was conducted to enhance genetic variability in peppers (Capsicum annuum, cv B12) using ethyl methanesulphonate (EMS). Exposure to an EMS concentration of 0.6%, v/v for 12 h was used to mutagenize 2000 seeds for the first generation (M1). It was observed that the growth behaviors including plant height, flowering date, and number of seeds per first fruit were different in the M1 generation than in wild type (WT) plants. In addition one phenotypic mutation (leaf shape and plant architecture) was observed during the M1 generation. During the seedling stage in the M2 generation, the observed changes were in the form of slow growth or chlorophyll defect (e.g., albino, pale green, and yellow seedlings). At maturity, there were three kinds of phenotypic mutations observed in three different families of the mutant population. The first observed change was a plant with yellow leaf color, and the leaves of this mutant plant contained 62.19% less chlorophyll a and 64.06% less chlorophyll b as compared to the wild-type. The second mutation resulted in one dwarf plant with a very short stature (6 cm), compact internodes and the leaves and stem were rough and thick. The third type of mutation occurred in four plants and resulted in the leaves of these plants being very thick and longer than those of WT plants. Furthermore, anatomical observations of the leaf blade section of this mutant plant type contained more xylem and collenchyma tissue in the leaf midrib of the mutant plant than WT. In addition, its leaf blade contained thicker palisade and spongy tissue than the WT.
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Affiliation(s)
- Mohamed H. Arisha
- College of Horticulture, Northwest A&F University, YanglingChina
- State Key Laboratories for Stress Biology of Arid Region Crop, Northwest A&F University, YanglingChina
- Department of Horticulture, Faculty of Agriculture, Zagazig University, ZagazigEgypt
| | - Syed N. M. Shah
- College of Horticulture, Northwest A&F University, YanglingChina
- State Key Laboratories for Stress Biology of Arid Region Crop, Northwest A&F University, YanglingChina
- Department of Horticulture, Faculty of Agriculture, Gomal University, Dera Ismail KhanPakistan
| | - Zhen-Hui Gong
- College of Horticulture, Northwest A&F University, YanglingChina
- State Key Laboratories for Stress Biology of Arid Region Crop, Northwest A&F University, YanglingChina
- *Correspondence: Zhen-Hui Gong, College of Horticulture, Northwest A&F University, No.3 Taicheng Road, Yangling, Shaanxi Province 712100, China
| | - Hua Jing
- College of Horticulture, Northwest A&F University, YanglingChina
| | - Chao Li
- College of Horticulture, Northwest A&F University, YanglingChina
| | - Huai-Xia Zhang
- College of Horticulture, Northwest A&F University, YanglingChina
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Wang GL, Xiong F, Que F, Xu ZS, Wang F, Xiong AS. Morphological characteristics, anatomical structure, and gene expression: novel insights into gibberellin biosynthesis and perception during carrot growth and development. HORTICULTURE RESEARCH 2015; 2:15028. [PMID: 26504574 PMCID: PMC4595985 DOI: 10.1038/hortres.2015.28] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 05/23/2015] [Accepted: 05/24/2015] [Indexed: 05/08/2023]
Abstract
Gibberellins (GAs) are considered potentially important regulators of cell elongation and expansion in plants. Carrot undergoes significant alteration in organ size during its growth and development. However, the molecular mechanisms underlying gibberellin accumulation and perception during carrot growth and development remain unclear. In this study, five stages of carrot growth and development were investigated using morphological and anatomical structural techniques. Gibberellin levels in leaf, petiole, and taproot tissues were also investigated for all five stages. Gibberellin levels in the roots initially increased and then decreased, but these levels were lower than those in the petioles and leaves. Genes involved in gibberellin biosynthesis and signaling were identified from the carrotDB, and their expression was analyzed. All of the genes were evidently responsive to carrot growth and development, and some of them showed tissue-specific expression. The results suggested that gibberellin level may play a vital role in carrot elongation and expansion. The relative transcription levels of gibberellin pathway-related genes may be the main cause of the different bioactive GAs levels, thus exerting influences on gibberellin perception and signals. Carrot growth and development may be regulated by modification of the genes involved in gibberellin biosynthesis, catabolism, and perception.
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Affiliation(s)
- Guang-Long Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Fei Xiong
- Key Laboratories of Crop Genetics and Physiology of the Jiangsu Province and Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Feng Que
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhi-Sheng Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Feng Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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Huang Y, Tao Z, Liu Q, Wang X, Yu J, Liu G, Wang H. BnEPFL6, an EPIDERMAL PATTERNING FACTOR-LIKE (EPFL) secreted peptide gene, is required for filament elongation in Brassica napus. PLANT MOLECULAR BIOLOGY 2014; 85:505-517. [PMID: 24838654 DOI: 10.1007/s11103-014-0200-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Accepted: 05/11/2014] [Indexed: 06/03/2023]
Abstract
Inflorescence architecture, pedicel length and stomata patterning in Arabidopsis thaliana are specified by inter-tissue communication mediated by ERECTA and its signaling ligands in the EPIDERMAL PATTERNING FACTOR-LIKE (EPFL) family of secreted cysteine-rich peptides. Here, we identified and characterized BnEPFL6 from Brassica napus. Heterologous expression of this gene under the double enhanced CaMV promoter (D35S) in Arabidopsis resulted in shortened stamen filaments, filaments degradation, and reduced filament cell size that displayed down-regulated expression of AHK2, in which phenotypic variation of ahk2-1 mutant presented highly consistent with that of BnEPFL6 transgenic lines. Especially, the expression level of BnEPFL6 in the shortened filaments of four B. napus male sterile lines (98A, 86A, SA, and Z11A) was similar to that of BnEPFL6 in the transgenic Arabidopsis lines. The activity of pBnEPFL6.2::GUS was intensive in the filaments of transgenic lines. These observations reveal that BnEPFL6 plays an important role in filament elongation and may also affect organ morphology and floral organ specification via a BnEPFL6-mediated cascade.
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Affiliation(s)
- Yi Huang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, People's Republic of China,
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Ordonio RL, Ito Y, Hatakeyama A, Ohmae-Shinohara K, Kasuga S, Tokunaga T, Mizuno H, Kitano H, Matsuoka M, Sazuka T. Gibberellin deficiency pleiotropically induces culm bending in sorghum: an insight into sorghum semi-dwarf breeding. Sci Rep 2014; 4:5287. [PMID: 24924234 PMCID: PMC4055941 DOI: 10.1038/srep05287] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 05/23/2014] [Indexed: 11/09/2022] Open
Abstract
Regulation of symmetrical cell growth in the culm is important for proper culm development. So far, the involvement of gibberellin (GA) in this process has not yet been demonstrated in sorghum. Here, we show that GA deficiency resulting from any loss-of-function mutation in four genes (SbCPS1, SbKS1, SbKO1, SbKAO1) involved in the early steps of GA biosynthesis, not only results in severe dwarfism but also in abnormal culm bending. Histological analysis of the bent culm revealed that the intrinsic bending was due to an uneven cell proliferation between the lower and upper sides of culm internodes. GA treatment alleviated the bending and dwarfism in mutants, whereas the GA biosynthesis inhibitor, uniconazole, induced such phenotypes in wild-type plants--both in a concentration-dependent manner, indicating an important role of GA in controlling erectness of the sorghum culm. Finally, we propose that because of the tight relationship between GA deficiency-induced dwarfism and culm bending in sorghum, GA-related mutations have unlikely been selected in the history of sorghum breeding, as could be inferred from previous QTL and association studies on sorghum plant height that did not pinpoint GA-related genes.
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Affiliation(s)
- Reynante L Ordonio
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Nagoya, Aichi 464-8601, Japan
| | - Yusuke Ito
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Nagoya, Aichi 464-8601, Japan
| | - Asako Hatakeyama
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Nagoya, Aichi 464-8601, Japan
| | - Kozue Ohmae-Shinohara
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Nagoya, Aichi 464-8601, Japan
| | - Shigemitsu Kasuga
- Education and Research Center of Alpine Field Science, Faculty of Agriculture, Shinshu University, Minamiminowa, Nagano 399-4598, Japan
| | | | - Hiroshi Mizuno
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Hidemi Kitano
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Nagoya, Aichi 464-8601, Japan
| | - Makoto Matsuoka
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Nagoya, Aichi 464-8601, Japan
| | - Takashi Sazuka
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Nagoya, Aichi 464-8601, Japan
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Chen YA, Chi WC, Trinh NN, Huang LY, Chen YC, Cheng KT, Huang TL, Lin CY, Huang HJ. Transcriptome profiling and physiological studies reveal a major role for aromatic amino acids in mercury stress tolerance in rice seedlings. PLoS One 2014; 9:e95163. [PMID: 24840062 PMCID: PMC4026224 DOI: 10.1371/journal.pone.0095163] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 03/25/2014] [Indexed: 11/22/2022] Open
Abstract
Mercury (Hg) is a serious environmental pollution threat to the planet. The accumulation of Hg in plants disrupts many cellular-level functions and inhibits growth and development, but the mechanism is not fully understood. To gain more insight into the cellular response to Hg, we performed a large-scale analysis of the rice transcriptome during Hg stress. Genes induced with short-term exposure represented functional categories of cell-wall formation, chemical detoxification, secondary metabolism, signal transduction and abiotic stress response. Moreover, Hg stress upregulated several genes involved in aromatic amino acids (Phe and Trp) and increased the level of free Phe and Trp content. Exogenous application of Phe and Trp to rice roots enhanced tolerance to Hg and effectively reduced Hg-induced production of reactive oxygen species. Hg induced calcium accumulation and activated mitogen-activated protein kinase. Further characterization of the Hg-responsive genes we identified may be helpful for better understanding the mechanisms of Hg in plants.
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Affiliation(s)
- Yun-An Chen
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan, ROC
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan, ROC
| | - Wen-Chang Chi
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Ngoc Nam Trinh
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Li-Yao Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Ying-Chih Chen
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Kai-Teng Cheng
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Tsai-Lien Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Chung-Yi Lin
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Hao-Jen Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan, ROC
- * E-mail:
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Bateman RM, James KE, Rudall PJ. Contrast in levels of morphological versus molecular divergence between closely related Eurasian species ofPlatanthera(Orchidaceae) suggests recent evolution with a strong allometric component. ACTA ACUST UNITED AC 2013. [DOI: 10.1179/2042349712y.0000000013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Yamaguchi N, Komeda Y. The role of CORYMBOSA1/BIG and auxin in the growth of Arabidopsis pedicel and internode. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 209:64-74. [PMID: 23759104 DOI: 10.1016/j.plantsci.2013.04.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 04/09/2013] [Accepted: 04/28/2013] [Indexed: 05/09/2023]
Abstract
The developmental regulation of pedicel and internode ensures that plants of the same species have similar inflorescence architecture. In Arabidopsis, the elongation of pedicels and internodes must be temporally and spatially regulated. We previously isolated the corymbosa1 (crm1) mutant, which has a corymb-like inflorescence because of shortened pedicels and internodes. CRM1/BIG encodes a membrane-associated protein and is required for auxin transport. Although CRM1/BIG and auxin have important roles in the development of pedicels and internodes, the developmental changes in cell growth in pedicels and internodes have not been examined. Here, we investigated the role of auxin in the cell growth of pedicels and internodes. Wild-type plants had rapid pedicel and internodal elongation that resulted from the temporal control of cell division and elongation. The crm1 mutants had defects in cell division and elongation. Auxin signaling and cell cycle gene expression in crm1 inflorescences were lower than those in the wild type. Moreover, wild-type plants treated with an auxin transport inhibitor and mutants defective in auxin signaling had shorter pedicels and internodes, with fewer and smaller cells. Our results suggest that auxin transport and signaling have important roles in controlling the proliferation and elongation of pedicel and internodal cells.
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Affiliation(s)
- Nobutoshi Yamaguchi
- Laboratory of Plant Science, Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
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Overexpression of the AtSHI gene in poinsettia, Euphorbia pulcherrima, results in compact plants. PLoS One 2013; 8:e53377. [PMID: 23308204 PMCID: PMC3538768 DOI: 10.1371/journal.pone.0053377] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 11/27/2012] [Indexed: 01/14/2023] Open
Abstract
Euphorbia pulcherrima, poinsettia, is a non-food and non-feed vegetatively propagated ornamental plant. Appropriate plant height is one of the most important traits in poinsettia production and is commonly achieved by application of chemical growth retardants. To produce compact poinsettia plants with desirable height and reduce the utilization of growth retardants, the Arabidopsis SHORT INTERNODE (AtSHI) gene controlled by the cauliflower mosaic virus 35S promoter was introduced into poinsettia by Agrobacterium-mediated transformation. Three independent transgenic lines were produced and stable integration of transgene was verified by PCR and Southern blot analysis. Reduced plant height (21–52%) and internode lengths (31–49%) were obtained in the transgenic lines compared to control plants. This correlates positively with the AtSHI transcript levels, with the highest levels in the most dwarfed transgenic line (TL1). The indole-3-acetic acid (IAA) content appeared lower (11–31% reduction) in the transgenic lines compared to the wild type (WT) controls, with the lowest level (31% reduction) in TL1. Total internode numbers, bract numbers and bract area were significantly reduced in all transgenic lines in comparison with the WT controls. Only TL1 showed significantly lower plant diameter, total leaf area and total dry weight, whereas none of the AtSHI expressing lines showed altered timing of flower initiation, cyathia abscission or bract necrosis. This study demonstrated that introduction of the AtSHI gene into poinsettia by genetic engineering can be an effective approach in controlling plant height without negatively affecting flowering time. This can help to reduce or avoid the use of toxic growth retardants of environmental and human health concern. This is the first report that AtSHI gene was overexpressed in poinsettia and transgenic poinsettia plants with compact growth were produced.
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