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Liu L, Yahaya BS, Li J, Wu F. Enigmatic role of auxin response factors in plant growth and stress tolerance. FRONTIERS IN PLANT SCIENCE 2024; 15:1398818. [PMID: 38903418 PMCID: PMC11188990 DOI: 10.3389/fpls.2024.1398818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 05/23/2024] [Indexed: 06/22/2024]
Abstract
Abiotic and biotic stresses globally constrain plant growth and impede the optimization of crop productivity. The phytohormone auxin is involved in nearly every aspect of plant development. Auxin acts as a chemical messenger that influences gene expression through a short nuclear pathway, mediated by a family of specific DNA-binding transcription factors known as Auxin Response Factors (ARFs). ARFs thus act as effectors of auxin response and translate chemical signals into the regulation of auxin responsive genes. Since the initial discovery of the first ARF in Arabidopsis, advancements in genetics, biochemistry, genomics, and structural biology have facilitated the development of models elucidating ARF action and their contributions to generating specific auxin responses. Yet, significant gaps persist in our understanding of ARF transcription factors despite these endeavors. Unraveling the functional roles of ARFs in regulating stress response, alongside elucidating their genetic and molecular mechanisms, is still in its nascent phase. Here, we review recent research outcomes on ARFs, detailing their involvement in regulating leaf, flower, and root organogenesis and development, as well as stress responses and their corresponding regulatory mechanisms: including gene expression patterns, functional characterization, transcriptional, post-transcriptional and post- translational regulation across diverse stress conditions. Furthermore, we delineate unresolved questions and forthcoming challenges in ARF research.
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Affiliation(s)
- Ling Liu
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Baba Salifu Yahaya
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Sichuan, China
| | - Jing Li
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Sichuan, China
| | - Fengkai Wu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang, Sichuan, China
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Gao Z, Wu Y, Li M, Ding L, Li J, Liu Y, Cao Y, Hua Y, Jia Q, Wang D. The auxin response factor ( ARF) gene family in Cyclocarya paliurus: genome-wide identification and their expression profiling under heat and drought stresses. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:921-944. [PMID: 38974352 PMCID: PMC11222355 DOI: 10.1007/s12298-024-01474-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 05/20/2024] [Accepted: 06/18/2024] [Indexed: 07/09/2024]
Abstract
Auxin response factors (ARFs), as the main components of auxin signaling, play a crucial role in various processes of plant growth and development, as well as in stress response. So far, there have been no reports on the genome-wide identification of the ARF transcription factor family in Cyclocarya paliurus, a deciduous tree plant in the family Juglaceae. In this study, a total of 34 CpARF genes were identified based on whole genome sequence, and they were unevenly distributed on 16 chromosomes, with the highest distribution on chromosome 6. Domain analysis of CpARF proteins displayed that 31 out of 34 CpARF proteins contain a typical B3 domain (DBD domain), except CpARF12/ CpARF14/CpARF31, which all belong to Class VI. And 20 CpARFs (58.8%) contain an auxin_IAA binding domain, and are mainly distributed in classes I, and VI. Phylogenetic analysis showed that CpARF was divided into six classes (I-VI), each containing 4, 4, 1, 8, 4, and 13 members, respectively. Gene duplication analysis showed that there are 14 segmental duplications and zero tandem repeats were identified in the CpARF gene family of the C. paliurus genome. The Ka/Ks ratio of duplicate gene pairs indicates that CpARF genes are subjected to strong purification selection pressure. Synteny analysis showed that C. paliurus shared the highest homology in 74 ARF gene pairs with Juglans regia, followed by 73, 51, 25, and 11 homologous gene pairs with Populus trichocarpa, Juglans cathayensis, Arabidopsis, and rice, respectively. Promoter analysis revealed that 34 CpARF genes had cis-elements related to hormones, stress, light, and growth and development except for CpARF12. The expression profile analysis showed that almost all CpARF genes were differentially expressed in at least one tissue, and several CpARF genes displayed tissue-specific expression. Furthermore, 24 out of the 34 CpARF genes have significantly response to drought stress (P < 0.05), and most of them (16) being significantly down-regulated under moderate drought treatment. Meanwhile, the majority of CpARF genes (28) have significantly response to drought stress (P < 0.05), and most of them (26) are significantly down-regulated under severe drought treatment. Furthermore, 32 out of the 34 CpARF genes have significantly response to high, middle, and low salt stress under salt treatment (P < 0.05). Additionally, subcellular localization analysis confirmed that CpARF16 and CpARF32 were all localized to nucleus. Thus, our findings expand the understanding of the function of CpARF genes and provide a basis for further functional studies on CpARF genes in C. paliurus. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01474-1.
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Affiliation(s)
- Ziyong Gao
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 Zhejiang China
| | - Yazhu Wu
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 Zhejiang China
| | - Muzi Li
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 Zhejiang China
| | - Lan Ding
- Linan District Agriculture and Rural Bureau, Hangzhou, 311399 People’s Republic of China
| | - Junyi Li
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 Zhejiang China
| | - Ying Liu
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 Zhejiang China
| | - Yu Cao
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 Zhejiang China
| | - Yangguang Hua
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 Zhejiang China
| | - Qiaojun Jia
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 Zhejiang China
| | - Dekai Wang
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 Zhejiang China
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Zhang Y, Wu W, Shen H, Yang L. Genome-wide identification and expression analysis of ARF gene family in embryonic development of Korean pine (Pinus koraiensis). BMC PLANT BIOLOGY 2024; 24:267. [PMID: 38600459 PMCID: PMC11005186 DOI: 10.1186/s12870-024-04827-w] [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: 12/29/2023] [Accepted: 02/16/2024] [Indexed: 04/12/2024]
Abstract
BACKGROUND The Auxin Responsive Factor (ARF) family plays a crucial role in mediating auxin signal transduction and is vital for plant growth and development. However, the function of ARF genes in Korean pine (Pinus koraiensis), a conifer species of significant economic value, remains unclear. RESULTS This study utilized the whole genome of Korean pine to conduct bioinformatics analysis, resulting in the identification of 13 ARF genes. A phylogenetic analysis revealed that these 13 PkorARF genes can be classified into 4 subfamilies, indicating the presence of conserved structural characteristics within each subfamily. Protein interaction prediction indicated that Pkor01G00962.1 and Pkor07G00704.1 may have a significant role in regulating plant growth and development as core components of the PkorARFs family. Additionally, the analysis of RNA-seq and RT-qPCR expression patterns suggested that PkorARF genes play a crucial role in the development process of Korean pine. CONCLUSION Pkor01G00962.1 and Pkor07G00704.1, which are core genes of the PkorARFs family, play a potentially crucial role in regulating the fertilization and developmental process of Korean pine. This study provides a valuable reference for investigating the molecular mechanism of embryonic development in Korean pine and establishes a foundation for cultivating high-quality Korean pine.
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Affiliation(s)
- Yue Zhang
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Wei Wu
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Hailong Shen
- State Forestry and Grassland Administration Engineering Technology Research Center of Korean Pine, Harbin, 150040, China.
| | - Ling Yang
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, 150040, China.
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Dawane A, Deshpande S, Vijayaraghavreddy P, Vemanna RS. Polysome-bound mRNAs and translational mechanisms regulate drought tolerance in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108513. [PMID: 38513519 DOI: 10.1016/j.plaphy.2024.108513] [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: 10/06/2023] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 03/23/2024]
Abstract
Plants evolved several acquired tolerance traits for drought stress adaptation to maintain the cellular homeostasis. Drought stress at the anthesis stage in rice affects productivity due to the inefficiency of protein synthesis machinery. The effect of translational mechanisms on different pathways involved in cellular tolerance plays an important role. We report differential responses of translation-associated mechanisms in rice using polysome bound mRNA sequencing at anthesis stage drought stress in resistant Apo and sensitive IR64 genotypes. Apo maintained higher polysomes with 60 S-to-40 S and polysome-to-monosome ratios which directly correlate with protein levels under stress. IR64 has less protein levels under stress due to defective translation machinery and reduced water potential. Many polysome-bound long non-coding RNAs (lncRNA) were identified in both genotypes under drought, influencing translation. Apo had higher levels of N6-Methyladenosine (m6A) mRNA modifications that contributed for sustained translation. Translation machinery in Apo could maintain higher levels of photosynthetic machinery-associated proteins in drought stress, which maintain gas exchange, photosynthesis and yield under stress. The protein stability and ribosome biogenesis mechanisms favoured improved translation in Apo. The phytohormone signalling and transcriptional responses were severely affected in IR64. Our results demonstrate that, the higher translation ability of Apo favours maintenance of photosynthesis and physiological responses that are required for drought stress adaptation.
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Affiliation(s)
- Akashata Dawane
- Laboratory of Plant Functional Genomics, Regional Centre for Biotechnology, Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Haryana, 121 001, India
| | - Sanjay Deshpande
- Laboratory of Plant Functional Genomics, Regional Centre for Biotechnology, Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Haryana, 121 001, India
| | | | - Ramu S Vemanna
- Laboratory of Plant Functional Genomics, Regional Centre for Biotechnology, Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Haryana, 121 001, India.
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Zhang MJ, Xue YY, Xu S, Jin XR, Man XC. Identification of ARF genes in Cucurbita pepo L and analysis of expression patterns, and functional analysis of CpARF22 under drought, salt stress. BMC Genomics 2024; 25:112. [PMID: 38273235 PMCID: PMC10809590 DOI: 10.1186/s12864-024-09992-8] [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: 09/04/2023] [Accepted: 01/08/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Auxin transcription factor (ARF) is an important transcription factor that transmits auxin signals and is involved in plant growth and development as well as stress response. However, genome-wide identification and responses to abiotic and pathogen stresses of the ARF gene family in Cucurbita pepo L, especially pathogen stresses, have not been reported. RESULTS Finally, 33 ARF genes (CpARF01 to CpARF33) were identified in C.pepo from the Cucurbitaceae genome database using bioinformatics methods. The putative protein contains 438 to 1071 amino acids, the isoelectric point is 4.99 to 8.54, and the molecular weight is 47759.36 to 117813.27 Da, the instability index ranged from 40.74 to 68.94, and the liposoluble index ranged from 62.56 to 76.18. The 33 genes were mainly localized in the nucleus and cytoplasm, and distributed on 16 chromosomes unevenly. Phylogenetic analysis showed that 33 CpARF proteins were divided into 6 groups. According to the amino acid sequence of CpARF proteins, 10 motifs were identified, and 1,3,6,8,10 motifs were highly conserved in most of the CpARF proteins. At the same time, it was found that genes in the same subfamily have similar gene structures. Cis-elements and protein interaction networks predicted that CpARF may be involved in abiotic factors related to the stress response. QRT-PCR analysis showed that most of the CpARF genes were upregulated under NaCl, PEG, and pathogen treatment compared to the control. Subcellular localization showed that CpARF22 was localized in the nucleus. The transgenic Arabidopsis thaliana lines with the CpARF22 gene enhanced their tolerance to salt and drought stress. CONCLUSION In this study, we systematically analyzed the CpARF gene family and its expression patterns under drought, salt, and pathogen stress, which improved our understanding of the ARF protein of zucchini, and laid a solid foundation for functional analysis of the CpARF gene.
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Affiliation(s)
- Ming-Jun Zhang
- College of Plant Protection, Gansu Agricultural University, Lanzhou, 730070, China
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, Gansu Agricultural University, Lanzhou, 730070, China
| | - Ying-Yu Xue
- College of Plant Protection, Gansu Agricultural University, Lanzhou, 730070, China.
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Shuang Xu
- College of Plant Protection, Gansu Agricultural University, Lanzhou, 730070, China
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xuan-Ru Jin
- College of Plant Protection, Gansu Agricultural University, Lanzhou, 730070, China
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xing-Chu Man
- College of Plant Protection, Gansu Agricultural University, Lanzhou, 730070, China
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, Gansu Agricultural University, Lanzhou, 730070, China
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Arpita K, Sharma S, Srivastava H, Kumar K, Mushtaq M, Gupta P, Jain R, Gaikwad K. Genome-wide survey, molecular evolution and expression analysis of Auxin Response Factor (ARF) gene family indicating their key role in seed number per pod in pigeonpea (C. cajan L. Millsp.). Int J Biol Macromol 2023; 253:126833. [PMID: 37709218 DOI: 10.1016/j.ijbiomac.2023.126833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/26/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023]
Abstract
Auxin Response Factors (ARF) are a family of transcription factors that mediate auxin signalling and regulate multiple biological processes. Their crucial role in increasing plant biomass/yield influenced this study, where a systematic analysis of ARF gene family was carried out to identify the key proteins controlling embryo/seed developmental pathways in pigeonpea. A genome-wide scan revealed the presence of 12 ARF genes in pigeonpea, distributed across the chromosomes 1, 3, 4, 8 and 11. Domain analysis of ARF proteins showed the presence of B3 DNA binding, AUX response, and IAA domains. Majority of them are of nuclear origin, and do not exhibit the level of genomic expansion as observed in Glycine max (51 members). The duplication events seem to range from 31.6 to 42.3 million years ago (mya). Promoter analysis revealed the presence of multiple cis-acting elements related to stress responses, hormone signalling and other development processes. The expression atlas data highlighted the expression of CcARF8 in hypocotyl, bud and flower whereas, CcARF7 expression was significantly high in pod. The real-time expression of CcARF2, CcARF3 and CcARF18 was highest in genotypes with high seed number indicating their key role in regulating embryo development and determining seed set in pigeonpea.
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Affiliation(s)
- Kumari Arpita
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India.
| | - Harsha Srivastava
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Kuldeep Kumar
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India; ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh 208024, India
| | - Muntazir Mushtaq
- Shoolini Univeristy of Biotechnology and Management Sciences, Himachal Pradesh 173229, India
| | - Palak Gupta
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Rishu Jain
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India.
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Jing H, Wilkinson EG, Sageman-Furnas K, Strader LC. Auxin and abiotic stress responses. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:7000-7014. [PMID: 37591508 PMCID: PMC10690732 DOI: 10.1093/jxb/erad325] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/14/2023] [Indexed: 08/19/2023]
Abstract
Plants are exposed to a variety of abiotic stresses; these stresses have profound effects on plant growth, survival, and productivity. Tolerance and adaptation to stress require sophisticated stress sensing, signaling, and various regulatory mechanisms. The plant hormone auxin is a key regulator of plant growth and development, playing pivotal roles in the integration of abiotic stress signals and control of downstream stress responses. In this review, we summarize and discuss recent advances in understanding the intersection of auxin and abiotic stress in plants, with a focus on temperature, salt, and drought stresses. We also explore the roles of auxin in stress tolerance and opportunities arising for agricultural applications.
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Affiliation(s)
- Hongwei Jing
- Department of Biology, Duke University, Durham, NC 27008, USA
| | | | | | - Lucia C Strader
- Department of Biology, Duke University, Durham, NC 27008, USA
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Zhang P, Wang T, Cao L, Jiao Z, Ku L, Dou D, Liu Z, Fu J, Xie X, Zhu Y, Chong L, Wei L. Molecular mechanism analysis of ZmRL6 positively regulating drought stress tolerance in maize. STRESS BIOLOGY 2023; 3:47. [PMID: 37971599 PMCID: PMC10654321 DOI: 10.1007/s44154-023-00125-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 09/26/2023] [Indexed: 11/19/2023]
Abstract
MYB-related genes, a subclass of MYB transcription factor family, have been documented to play important roles in biological processes such as secondary metabolism and stress responses that affect plant growth and development. However, the regulatory roles of MYB-related genes in drought stress response remain unclear in maize. In this study, we discovered that a 1R-MYB gene, ZmRL6, encodes a 96-amino acid protein and is highly drought-inducible. We also found that it is conserved in both barley (Hordeum vulgare L.) and Aegilops tauschii. Furthermore, we observed that overexpression of ZmRL6 can enhance drought tolerance while knock-out of ZmRL6 by CRISPR-Cas9 results in drought hypersensitivity. DAP-seq analyses additionally revealed the ZmRL6 target genes mainly contain ACCGTT, TTACCAAAC and AGCCCGAG motifs in their promoters. By combining RNA-seq and DAP-seq results together, we subsequently identified eight novel target genes of ZmRL6 that are involved in maize's hormone signal transduction, sugar metabolism, lignin synthesis, and redox signaling/oxidative stress. Collectively, our data provided insights into the roles of ZmRL6 in maize's drought response.
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Affiliation(s)
- Pengyu Zhang
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, China
- Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Tongchao Wang
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, China
| | - Liru Cao
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, China
- Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Zhixin Jiao
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Lixia Ku
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, China
| | - Dandan Dou
- Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Zhixue Liu
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, China
| | - Jiaxu Fu
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xiaowen Xie
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yingfang Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Leelyn Chong
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Li Wei
- National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, China.
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Shaffique S, Hussain S, Kang SM, Imran M, Injamum-Ul-Hoque M, Khan MA, Lee IJ. Phytohormonal modulation of the drought stress in soybean: outlook, research progress, and cross-talk. FRONTIERS IN PLANT SCIENCE 2023; 14:1237295. [PMID: 37929163 PMCID: PMC10623132 DOI: 10.3389/fpls.2023.1237295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/07/2023] [Indexed: 11/07/2023]
Abstract
Phytohormones play vital roles in stress modulation and enhancing the growth of plants. They interact with one another to produce programmed signaling responses by regulating gene expression. Environmental stress, including drought stress, hampers food and energy security. Drought is abiotic stress that negatively affects the productivity of the crops. Abscisic acid (ABA) acts as a prime controller during an acute transient response that leads to stomatal closure. Under long-term stress conditions, ABA interacts with other hormones, such as jasmonic acid (JA), gibberellins (GAs), salicylic acid (SA), and brassinosteroids (BRs), to promote stomatal closure by regulating genetic expression. Regarding antagonistic approaches, cytokinins (CK) and auxins (IAA) regulate stomatal opening. Exogenous application of phytohormone enhances drought stress tolerance in soybean. Thus, phytohormone-producing microbes have received considerable attention from researchers owing to their ability to enhance drought-stress tolerance and regulate biological processes in plants. The present study was conducted to summarize the role of phytohormones (exogenous and endogenous) and their corresponding microbes in drought stress tolerance in model plant soybean. A total of n=137 relevant studies were collected and reviewed using different research databases.
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Affiliation(s)
- Shifa Shaffique
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Saddam Hussain
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
| | - Sang-Mo Kang
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Muhamad Imran
- Biosafety Division, National Institute of Agriculture Science, Rural Development Administration, Jeonju, Republic of Korea
| | - Md Injamum-Ul-Hoque
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Muhammad Aaqil Khan
- Department of Chemical and Life Science, Qurtaba University of Science and Information Technology, Peshawar, Pakistan
| | - In-Jung Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
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Zhai Y, Shen X, Sun Y, Liu Q, Ma N, Zhang X, Jia Q, Liang Z, Wang D. Genome-wide investigation of ARF transcription factor gene family and its responses to abiotic stress in Coix (Coix lacryma-jobi L.). PROTOPLASMA 2023; 260:1389-1405. [PMID: 37041371 DOI: 10.1007/s00709-023-01855-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 03/23/2023] [Indexed: 06/19/2023]
Abstract
Auxin response factor (ARF) is an important transcription factor that regulates the expression of auxin-responsive genes by direct binding to their promoters, which play a central role in plant growth, development, and response to abiotic stresses. The availability of the entire Coix (Coix lacryma-jobi L.) genome sequence provides an opportunity to investigate the characteristics and evolutionary history of the ARF gene family in this medicine and food homology plant for the first time. In this study, a total of 27 ClARF genes were identified based on the genome-wide sequence of Coix. Twenty-four of the 27 ClARF genes were unevenly distributed on 8 chromosomes except Chr 4 and 10, and the remaining three genes (ClARF25-27) were not assigned to any chromosome. Most of the ClARF proteins were predicted to be localized to the nucleus, except ClARF24, which was localized to both the plasma membrane and nucleus. Twenty-seven ClARFs were clustered into six subgroups based on the phylogenetic analysis. Duplication analysis showed that segmental duplication, rather than tandem duplications promoting the expansion of the ClARF gene family. Synteny analysis showed that purifying selection might have been a primary driving force in the development of the ARF gene family in Coix and other investigated cereal plants. The prediction of the cis element of the promoter showed that 27 ClARF genes contain several stress response elements, suggesting that ClARFs might be involved in the abiotic stress response. Expression profile analysis shows that 27 ClARF genes were all expressed in the root, shoot, leaf, kernel, glume, and male flower of Coix with varying expression levels. Furthermore, qRT-PCR analyses revealed that the majority of ClARFs members were upregulated or downregulated in response to hormone treatment and abiotic stress. The current study expands our understanding of the functional roles of ClARFs in stress responses and provides basic information for the ClARF genes.
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Affiliation(s)
- Yufeng Zhai
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China
| | - Xiaoxia Shen
- Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
- Songyang Institute of Zhejiang Chinese Medical University, Lishui, 323400, China
| | - Yimin Sun
- Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
| | - Qiao Liu
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China
| | - Nan Ma
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China
| | - Xiaodan Zhang
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China
- State Key Laboratory of Dao-Di Herbs, Beijng, 100700, China
| | - Qiaojun Jia
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China
| | - Zongsuo Liang
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China
- State Key Laboratory of Dao-Di Herbs, Beijng, 100700, China
| | - Dekai Wang
- Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China.
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Chen F, Zhang J, Ha X, Ma H. Genome-wide identification and expression analysis of the Auxin-Response factor (ARF) gene family in Medicago sativa under abiotic stress. BMC Genomics 2023; 24:498. [PMID: 37644390 PMCID: PMC10463752 DOI: 10.1186/s12864-023-09610-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/20/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Alfalfa (Medicago sativa) is the most widely planted legume forage and one of the most economically valuable crops in the world. The periodic changes in its growth and development and abiotic stress determine its yield and economic benefits. Auxin controls many aspects of alfalfa growth by regulating gene expression, including organ differentiation and stress response. Auxin response factors (ARF) are transcription factors that play an essential role in auxin signal transduction and regulate the expression of auxin-responsive genes. However, the function of ARF transcription factors is unclear in autotetraploid-cultivated alfalfa. RESULT A total of 81 ARF were identified in the alfalfa genome in this study. Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were analyzed, identifying that ARF genes are mainly involved in transcriptional regulation and plant hormone signal transduction pathways. Phylogenetic analysis showed that MsARF was divided into four clades: I, II, III, and IV, each containing 52, 13, 7, and 9 genes, respectively. The promoter region of the MsARF gene contained stress-related elements, such as ABRE, TC-rich repeats, MBS, LTR. Proteins encoded by 50 ARF genes were localized in the nucleus without guide peptides, signal peptides, or transmembrane structures, indicating that most MsARF genes are not secreted or transported but only function in the nucleus. Protein structure analysis revealed that the secondary and tertiary structures of the 81 MsARF genes varied. Chromosomal localization analysis showed 81 MsARF genes were unevenly distributed on 25 chromosomes, with the highest distribution on chromosome 5. Furthermore, 14 segmental duplications and two sets of tandem repeats were identified. Expression analysis indicated that the MsARF was differentially expressed in different tissues and under various abiotic stressors. The quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis showed that the expression profiles of 23 MsARF genes were specific to abiotic stresses such as drought, salt, high temperature, and low temperature, as well as tissue-specific and closely related to the duration of stress. CONCLUSION This study identified MsARF in the cultivated alfalfa genome based on the autotetraploid level, which GO, KEGG analysis, phylogenetic analysis, sequence characteristics, and expression pattern analysis further confirmed. Together, these findings provide clues for further investigation of MsARF functional verification and molecular breeding of alfalfa. This study provides a novel approach to systematically identify and characterize ARF transcription factors in autotetraploid cultivated alfalfa, revealing 23 MsARF genes significantly involved in response to various stresses.
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Affiliation(s)
- Fenqi Chen
- College of Pratacultural Science, Gansu Agricultural University, Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Sino-U.S. Center for Grazingland Ecosystem Sustainability, Yingmencun, Anning District, Gansu province, Lanzhou, Gansu, 730070, China
| | - Jinqing Zhang
- College of Pratacultural Science, Gansu Agricultural University, Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Sino-U.S. Center for Grazingland Ecosystem Sustainability, Yingmencun, Anning District, Gansu province, Lanzhou, Gansu, 730070, China
| | - Xue Ha
- College of Pratacultural Science, Gansu Agricultural University, Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Sino-U.S. Center for Grazingland Ecosystem Sustainability, Yingmencun, Anning District, Gansu province, Lanzhou, Gansu, 730070, China
| | - Huiling Ma
- College of Pratacultural Science, Gansu Agricultural University, Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Sino-U.S. Center for Grazingland Ecosystem Sustainability, Yingmencun, Anning District, Gansu province, Lanzhou, Gansu, 730070, China.
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El Mamoun I, Bouzroud S, Zouine M, Smouni A. The Knockdown of AUXIN RESPONSE FACTOR 2 Confers Enhanced Tolerance to Salt and Drought Stresses in Tomato ( Solanum lycopersicum L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:2804. [PMID: 37570958 PMCID: PMC10420960 DOI: 10.3390/plants12152804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/19/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023]
Abstract
Auxin response factors (ARFs) act as key elements of the auxin-signaling pathway and play important roles in the process of a plant's growth, development, and response to environmental conditions. We studied the implication of the SlARF2 gene in the tomato response to salt (150 mM of NaCl) and drought (15% PEG 20000) stresses. The functional characterization of SlARF2 knockdown tomato mutants revealed that the downregulation of this gene enhanced primary root length and root branching and reduced plant wilting. At the physiological level, the arf2 mutant line displayed higher chlorophyll, soluble sugars, proline, and relative water contents as well as lower stomatal conductance and a decreased malondialdehyde content. Moreover, SlARF2 knockdown tomato mutants demonstrated higher activities of the antioxidant enzymes superoxide dismutase (SOD) and catalase (CAT) under salt and drought stresses than the wild type. Indeed, the stress tolerance of the arf2 mutant was also reflected by the upregulation of stress-related genes involved in ROS scavenging and plant defense, including SOD, CAT, dehydration-responsive element-binding protein, and early responsive to dehydration, which can ultimately result in a better resistance to salt and drought stresses. Furthermore, the transcriptional levels of the Δ1-pyrroline-5-carboxylate synthase (P5CS) gene were upregulated in the arf2 mutant after stress, in correlation with the higher levels of proline. Taken together, our findings reveal that SlARF2 is implicated in salt and drought tolerance in tomato and provides some considerable elements for improving the abiotic stress tolerance and increasing the crop yields of tomato.
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Affiliation(s)
- Ibtihaj El Mamoun
- Laboratoire de Biotechnologie et de Physiologie Végétales, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University in Rabat, Rabat 10000, Morocco;
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Université Toulouse Paul Sabatier (UPS), Toulouse-INP, 31320 Auzeville-Tolosane, France
| | - Sarah Bouzroud
- Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University in Rabat, Rabat 10000, Morocco;
| | - Mohamed Zouine
- Laboratoire de Recherche en Sciences Végétales, UMR5546, Université de Toulouse, Centre National de la Recherche Scientifique (CNRS), Université Toulouse Paul Sabatier (UPS), Toulouse-INP, 31320 Auzeville-Tolosane, France
| | - Abdelaziz Smouni
- Laboratoire de Biotechnologie et de Physiologie Végétales, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University in Rabat, Rabat 10000, Morocco;
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Tao GY, Xie YH, Li WF, Li KP, Sun C, Wang HM, Sun XM. LkARF7 and LkARF19 overexpression promote adventitious root formation in a heterologous poplar model by positively regulating LkBBM1. Commun Biol 2023; 6:372. [PMID: 37020138 PMCID: PMC10076273 DOI: 10.1038/s42003-023-04731-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 03/17/2023] [Indexed: 04/07/2023] Open
Abstract
Cuttage propagation involves adventitious root formation induced by auxin. In our previous study, Larix kaempferi BABY BOOM 1 (LkBBM1), which is known to regulate adventitious root formation, was affected by auxin. However, the relationship between LkBBM1 and auxin remains unclear. Auxin response factors (ARFs) are a class of important transcription factors in the auxin signaling pathway and modulate the expression of early auxin-responsive genes by binding to auxin response elements. In the present study, we identified 14 L. kaempferi ARFs (LkARFs), and found LkARF7 and LkARF19 bound to LkBBM1 promoter and enhanced its transcription using yeast one-hybrid, ChIP-qPCR, and dual-luciferase assays. In addition, the treatment with naphthalene acetic acid promoted the expression of LkARF7 and LkARF19. We also found that overexpression of these two genes in poplar promoted adventitious root formation. Furthermore, LkARF19 interacted with the DEAD-box ATP-dependent RNA helicase 53-like protein to form a heterodimer to regulate adventitious root formation. Altogether, our results reveal an additional regulatory mechanism underlying the control of adventitious root formation by auxin.
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Affiliation(s)
- Gui-Yun Tao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yun-Hui Xie
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Wan-Feng Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Kui-Peng Li
- Guangxi Forestry Research Institute, Guangxi, 530009, China
| | - Chao Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Hong-Ming Wang
- College of Bioengineering and Biotechnology, Tianshui Normal University, Gansu, 741000, China
| | - Xiao-Mei Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China.
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14
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Phylogeny, gene structures, and expression patterns of the auxin response factor (GhARF2) in upland cotton (Gossypium hirsutum L.). Mol Biol Rep 2023; 50:1089-1099. [PMID: 36399242 DOI: 10.1007/s11033-022-07999-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 09/30/2022] [Indexed: 11/21/2022]
Abstract
BACKGROUND Auxin response factors (ARFs) are a class of transcription factors that regulate the expression of auxin-responsive genes and play important functions in plant growth and development. To understand the biological functions of the auxin response factor GhARF2 gene in upland cotton, the coding sequence (CDS) of GhARF2 gene was cloned, and its protein sequence, evolutionary relationship, subcellular localization and expression pattern were analysed. METHODS The CDS sequence of GhARF2 gene was cloned from upland cotton variety Baimian No.1, and its protein sequence was analyzed by bioinformatics method. The subcellular localization of GhARF2 protein was detected by tobacco epidermal transient transformation system, and the tissue expression and stress expression pattern of GhARF2 were analyzed by quantitative Real‑Time PCR (qRT-PCR). RESULTS The full-length CDS of GhARF2 gene was 2583 bp, encoded 860 amino acids, and had a molecular weight and an isoelectric point of 95.46 KDa and 6.02, respectively. The GhARF2 protein had multiple phosphorylation sites, no transmembrane domain, and secondary structures dominated by random coils and alpha helix. The GhARF2 protein had 3 conserved typical domains of ARF gene family members, including the B3 DNA binding domain, the Auxin_resp domain, and the Aux/IAA domain. Phylogenetic analysis revealed that ARF2 proteins in different species were clustered in the Group A subgroup, in which GhARF2 was closely related to TcARF2 of Theobroma cacao L. (Malvaceae). The subcellular localization results showed that the GhARF2 protein was localized in the nucleus. Analysis of tissue expression pattern showed that the GhARF2 gene was expressed in all tested tissues, with the highest expression levels in sepal, followed by leaf, and the lowest expression levels in fiber. Further stress expression analysis showed that the GhARF2 gene was induced by drought, high-temperature, low-temperature and salt stress, and had different expression patterns under different stress conditions. CONCLUSION These results established a foundation for understanding the functions of GhARF2 and breeding varieties with high-stress tolerance in cotton.
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Amin N, Ahmad N, Khalifa MAS, Du Y, Mandozai A, Khattak AN, Piwu W. Identification and Molecular Characterization of RWP-RK Transcription Factors in Soybean. Genes (Basel) 2023; 14:genes14020369. [PMID: 36833296 PMCID: PMC9956977 DOI: 10.3390/genes14020369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 02/04/2023] Open
Abstract
The RWP-RK is a small family of plant-specific transcription factors that are mainly involved in nitrate starvation responses, gametogenesis, and root nodulation. To date, the molecular mechanisms underpinning nitrate-regulated gene expression in many plant species have been extensively studied. However, the regulation of nodulation-specific NIN proteins during nodulation and rhizobial infection under nitrogen starvation in soybean still remain unclear. Here, we investigated the genome-wide identification of RWP-RK transcription factors and their essential role in nitrate-inducible and stress-responsive gene expression in soybean. In total, 28 RWP-RK genes were identified from the soybean genome, which were unevenly distributed on 20 chromosomes from 5 distinct groups during phylogeny classification. The conserved topology of RWP-RK protein motifs, cis-acting elements, and functional annotation has led to their potential as key regulators during plant growth, development, and diverse stress responses. The RNA-seq data revealed that the up-regulation of GmRWP-RK genes in the nodules indicated that these genes might play crucial roles during root nodulation in soybean. Furthermore, qRT-PCR analysis revealed that most GmRWP-RK genes under Phytophthora sojae infection and diverse environmental conditions (such as heat, nitrogen, and salt) were significantly induced, thus opening a new window of possibilities into their regulatory roles in adaptation mechanisms that allow soybean to tolerate biotic and abiotic stress. In addition, the dual luciferase assay indicated that GmRWP-RK1 and GmRWP-RK2 efficiently bind to the promoters of GmYUC2, GmSPL9, and GmNIN, highlighting their possible involvement in nodule formation. Together, our findings provide novel insights into the functional role of the RWP-RK family during defense responses and root nodulation in soybean.
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Affiliation(s)
- Nooral Amin
- Plant Biotechnology Centre, College of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Naveed Ahmad
- Joint Center for Single Cell Biology, Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mohamed A. S. Khalifa
- Plant Biotechnology Centre, College of Agronomy, Jilin Agricultural University, Changchun 130118, China
- Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | - Yeyao Du
- Plant Biotechnology Centre, College of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Ajmal Mandozai
- Plant Biotechnology Centre, College of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Aimal Nawaz Khattak
- Institute of Crop Science Chinese Academy of Agriculture Sciences, Beijing 100000, China
| | - Wang Piwu
- Plant Biotechnology Centre, College of Agronomy, Jilin Agricultural University, Changchun 130118, China
- Correspondence:
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Genome-Wide Identification and Characterization of Auxin Response Factor (ARF) Gene Family Involved in Wood Formation and Response to Exogenous Hormone Treatment in Populus trichocarpa. Int J Mol Sci 2023; 24:ijms24010740. [PMID: 36614182 PMCID: PMC9820880 DOI: 10.3390/ijms24010740] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/03/2023] Open
Abstract
Auxin is a key regulator that virtually controls almost every aspect of plant growth and development throughout its life cycle. As the major components of auxin signaling, auxin response factors (ARFs) play crucial roles in various processes of plant growth and development. In this study, a total of 35 PtrARF genes were identified, and their phylogenetic relationships, chromosomal locations, synteny relationships, exon/intron structures, cis-elements, conserved motifs, and protein characteristics were systemically investigated. We also analyzed the expression patterns of these PtrARF genes and revealed that 16 of them, including PtrARF1, 3, 7, 11, 13-17, 21, 23, 26, 27, 29, 31, and 33, were preferentially expressed in primary stems, while 15 of them, including PtrARF2, 4, 6, 9, 10, 12, 18-20, 22, 24, 25, 28, 32, and 35, participated in different phases of wood formation. In addition, some PtrARF genes, with at least one cis-element related to indole-3-acetic acid (IAA) or abscisic acid (ABA) response, responded differently to exogenous IAA and ABA treatment, respectively. Three PtrARF proteins, namely PtrARF18, PtrARF23, and PtrARF29, selected from three classes, were characterized, and only PtrARF18 was a transcriptional self-activator localized in the nucleus. Moreover, Y2H and bimolecular fluorescence complementation (BiFC) assay demonstrated that PtrARF23 interacted with PtrIAA10 and PtrIAA28 in the nucleus, while PtrARF29 interacted with PtrIAA28 in the nucleus. Our results provided comprehensive information regarding the PtrARF gene family, which will lay some foundation for future research about PtrARF genes in tree development and growth, especially the wood formation, in response to cellular signaling and environmental cues.
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Ruggiero A, Punzo P, Van Oosten MJ, Cirillo V, Esposito S, Costa A, Maggio A, Grillo S, Batelli G. Transcriptomic and splicing changes underlying tomato responses to combined water and nutrient stress. FRONTIERS IN PLANT SCIENCE 2022; 13:974048. [PMID: 36507383 PMCID: PMC9732681 DOI: 10.3389/fpls.2022.974048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/07/2022] [Indexed: 06/17/2023]
Abstract
Tomato is a horticultural crop of high economic and nutritional value. Suboptimal environmental conditions, such as limited water and nutrient availability, cause severe yield reductions. Thus, selection of genotypes requiring lower inputs is a goal for the tomato breeding sector. We screened 10 tomato varieties exposed to water deficit, low nitrate or a combination of both. Biometric, physiological and molecular analyses revealed different stress responses among genotypes, identifying T270 as severely affected, and T250 as tolerant to the stresses applied. Investigation of transcriptome changes caused by combined stress in roots and leaves of these two genotypes yielded a low number of differentially expressed genes (DEGs) in T250 compared to T270, suggesting that T250 tailors changes in gene expression to efficiently respond to combined stress. By contrast, the susceptible tomato activated approximately one thousand and two thousand genes in leaves and roots respectively, indicating a more generalized stress response in this genotype. In particular, developmental and stress-related genes were differentially expressed, such as hormone responsive factors and transcription factors. Analysis of differential alternative splicing (DAS) events showed that combined stress greatly affects the splicing landscape in both genotypes, highlighting the important role of AS in stress response mechanisms. In particular, several stress and growth-related genes as well as transcription and splicing factors were differentially spliced in both tissues. Taken together, these results reveal important insights into the transcriptional and post-transcriptional mechanisms regulating tomato adaptation to growth under reduced water and nitrogen inputs.
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Affiliation(s)
- Alessandra Ruggiero
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division, Portici, Italy
| | - Paola Punzo
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division, Portici, Italy
| | | | - Valerio Cirillo
- Department of Agricultural Sciences, University of Naples, Federico II, Portici, Italy
| | - Salvatore Esposito
- CREA-CI, Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, Foggia, Italy
| | - Antonello Costa
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division, Portici, Italy
| | - Albino Maggio
- Department of Agricultural Sciences, University of Naples, Federico II, Portici, Italy
| | - Stefania Grillo
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division, Portici, Italy
| | - Giorgia Batelli
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and Bioresources, Research Division, Portici, Italy
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Hu M, Qi Z, Ren Z, Tong J, Wang B, Wu Z, Hao J, Liu N. Genome-Wide Analysis of Auxin Response Factors in Lettuce ( Lactuca sativa L.) Reveals the Positive Roles of LsARF8a in Thermally Induced Bolting. Int J Mol Sci 2022; 23:13509. [PMID: 36362292 PMCID: PMC9653848 DOI: 10.3390/ijms232113509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/24/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
Warm temperatures induce plant bolting accompanied by flower initiation, where endogenous auxin is dynamically associated with accelerated growth. Auxin signaling is primarily regulated by a family of plant-specific transcription factors, AUXIN RESPONSE FACTORS (ARFs), which either activate or repress the expression of downstream genes in response to developmental and environmental cues. However, the relationship between ARFs and bolting has not been completely understood in lettuce yet. Here, we identified 24 LsARFs (Lactuca sativa ARFs) in the lettuce genome. The phylogenetic tree indicated that LsARFs could be classified into three clusters, which was well supported by the analysis of exon-intron structure, consensus motifs, and domain compositions. RNA-Seq analysis revealed that more than half of the LsARFs were ubiquitously expressed in all tissues examined, whereas a small number of LsARFs responded to UV or cadmium stresses. qRT-PCR analysis indicated that the expression of most LsARFs could be activated by more than one phytohormone, underling their key roles as integrative hubs of different phytohormone signaling pathways. Importantly, the majority of LsARFs displayed altered expression profiles under warm temperatures, implying that their functions were tightly associated with thermally accelerated bolting in lettuce. Importantly, we demonstrated that silencing of LsARF8a, expression of which was significantly increased by elevated temperatures, resulted in delayed bolting under warm temperatures, suggesting that LsARF8a might conduce to the thermally induced bolting. Together, our results provide molecular insights into the LsARF gene family in lettuce, which will facilitate the genetic improvement of the lettuce in an era of global warming.
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Affiliation(s)
- Manman Hu
- National Engineering Research Center for Vegetables, Key Laboratory of Urban Agriculture (North China), Institute of Vegetable Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Zhengyang Qi
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Zheng Ren
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Jing Tong
- National Engineering Research Center for Vegetables, Key Laboratory of Urban Agriculture (North China), Institute of Vegetable Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Baoju Wang
- National Engineering Research Center for Vegetables, Key Laboratory of Urban Agriculture (North China), Institute of Vegetable Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Zhanhui Wu
- National Engineering Research Center for Vegetables, Key Laboratory of Urban Agriculture (North China), Institute of Vegetable Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Jinghong Hao
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Ning Liu
- National Engineering Research Center for Vegetables, Key Laboratory of Urban Agriculture (North China), Institute of Vegetable Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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Wu Y, Sun Z, Qi F, Tian M, Wang J, Zhao R, Wang X, Wu X, Shi X, Liu H, Dong W, Huang B, Zheng Z, Zhang X. Comparative transcriptomics analysis of developing peanut ( Arachis hypogaea L.) pods reveals candidate genes affecting peanut seed size. FRONTIERS IN PLANT SCIENCE 2022; 13:958808. [PMID: 36172561 PMCID: PMC9511224 DOI: 10.3389/fpls.2022.958808] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/03/2022] [Indexed: 06/16/2023]
Abstract
Pod size is one of the most important agronomic features of peanuts, which directly affects peanut yield. Studies on the regulation mechanism underpinning pod size in cultivated peanuts remain hitherto limited compared to model plant systems. To better understand the molecular elements that underpin peanut pod development, we conducted a comprehensive analysis of chronological transcriptomics during pod development in four peanut accessions with similar genetic backgrounds, but varying pod sizes. Several plant transcription factors, phytohormones, and the mitogen-activated protein kinase (MAPK) signaling pathways were significantly enriched among differentially expressed genes (DEGs) at five consecutive developmental stages, revealing an eclectic range of candidate genes, including PNC, YUC, and IAA that regulate auxin synthesis and metabolism, CYCD and CYCU that regulate cell differentiation and proliferation, and GASA that regulates seed size and pod elongation via gibberellin pathway. It is plausible that MPK3 promotes integument cell division and regulates mitotic activity through phosphorylation, and the interactions between these genes form a network of molecular pathways that affect peanut pod size. Furthermore, two variant sites, GCP4 and RPPL1, were identified which are stable at the QTL interval for seed size attributes and function in plant cell tissue microtubule nucleation. These findings may facilitate the identification of candidate genes that regulate pod size and impart yield improvement in cultivated peanuts.
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Affiliation(s)
- Yue Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Ziqi Sun
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Feiyan Qi
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Mengdi Tian
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Juan Wang
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Ruifang Zhao
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Xiao Wang
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Xiaohui Wu
- College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xinlong Shi
- College of Agriculture, Henan University of Science and Technology, Luoyang, China
| | - Hongfei Liu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Wenzhao Dong
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Bingyan Huang
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Zheng Zheng
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
| | - Xinyou Zhang
- Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China
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20
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Chacon DS, Santos MDM, Bonilauri B, Vilasboa J, da Costa CT, da Silva IB, Torres TDM, de Araújo TF, Roque ADA, Pilon AC, Selegatto DM, Freire RT, Reginaldo FPS, Voigt EL, Zuanazzi JAS, Scortecci KC, Cavalheiro AJ, Lopes NP, Ferreira LDS, dos Santos LV, Fontes W, de Sousa MV, Carvalho PC, Fett-Neto AG, Giordani RB. Non-target molecular network and putative genes of flavonoid biosynthesis in Erythrina velutina Willd., a Brazilian semiarid native woody plant. FRONTIERS IN PLANT SCIENCE 2022; 13:947558. [PMID: 36161018 PMCID: PMC9493460 DOI: 10.3389/fpls.2022.947558] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/26/2022] [Indexed: 06/16/2023]
Abstract
Erythrina velutina is a Brazilian native tree of the Caatinga (a unique semiarid biome). It is widely used in traditional medicine showing anti-inflammatory and central nervous system modulating activities. The species is a rich source of specialized metabolites, mostly alkaloids and flavonoids. To date, genomic information, biosynthesis, and regulation of flavonoids remain unknown in this woody plant. As part of a larger ongoing research goal to better understand specialized metabolism in plants inhabiting the harsh conditions of the Caatinga, the present study focused on this important class of bioactive phenolics. Leaves and seeds of plants growing in their natural habitat had their metabolic and proteomic profiles analyzed and integrated with transcriptome data. As a result, 96 metabolites (including 43 flavonoids) were annotated. Transcripts of the flavonoid pathway totaled 27, of which EvCHI, EvCHR, EvCHS, EvCYP75A and EvCYP75B1 were identified as putative main targets for modulating the accumulation of these metabolites. The highest correspondence of mRNA vs. protein was observed in the differentially expressed transcripts. In addition, 394 candidate transcripts encoding for transcription factors distributed among the bHLH, ERF, and MYB families were annotated. Based on interaction network analyses, several putative genes of the flavonoid pathway and transcription factors were related, particularly TFs of the MYB family. Expression patterns of transcripts involved in flavonoid biosynthesis and those involved in responses to biotic and abiotic stresses were discussed in detail. Overall, these findings provide a base for the understanding of molecular and metabolic responses in this medicinally important species. Moreover, the identification of key regulatory targets for future studies aiming at bioactive metabolite production will be facilitated.
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Affiliation(s)
- Daisy Sotero Chacon
- Department of Pharmacy, Federal University of Rio Grande do Norte (UFRN), Natal, RN, Brazil
| | | | - Bernardo Bonilauri
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, United States
| | - Johnatan Vilasboa
- Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Cibele Tesser da Costa
- Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | - Taffarel de Melo Torres
- Bioinformatics, Biostatistics and Computer Biology Nucleus, Rural Federal University of the Semiarid, Mossoró, RN, Brazil
| | | | - Alan de Araújo Roque
- Institute for Sustainable Development and Environment, Dunas Park Herbarium, Natal, RN, Brazil
| | - Alan Cesar Pilon
- NPPNS, Department of Biomolecular Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (FCFRP-USP), Ribeirão Preto, SP, Brazil
| | - Denise Medeiros Selegatto
- Zimmermann Group, European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - Rafael Teixeira Freire
- Signal and Information Processing for Sensing Systems, Institute for Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Eduardo Luiz Voigt
- Department of Cell Biology and Genetics, Center for Biosciences, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | | | - Kátia Castanho Scortecci
- Department of Cell Biology and Genetics, Center for Biosciences, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | | | - Norberto Peporine Lopes
- NPPNS, Department of Biomolecular Sciences, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (FCFRP-USP), Ribeirão Preto, SP, Brazil
| | | | - Leandro Vieira dos Santos
- Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Wagner Fontes
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasilia, DF, Brazil
| | - Marcelo Valle de Sousa
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, University of Brasilia, Brasilia, DF, Brazil
| | - Paulo Costa Carvalho
- Computational and Structural Proteomics Laboratory, Carlos Chagas Institute, Fiocruz, PR, Brazil
| | - Arthur Germano Fett-Neto
- Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Raquel Brandt Giordani
- Department of Pharmacy, Federal University of Rio Grande do Norte (UFRN), Natal, RN, Brazil
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21
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Gao J, Qian Z, Zhang Y, Zhuang S. Exogenous spermidine regulates the anaerobic enzyme system through hormone concentrations and related-gene expression in Phyllostachys praecox roots under flooding stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 186:182-196. [PMID: 35868108 DOI: 10.1016/j.plaphy.2022.07.002] [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: 05/17/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
PURPOSE Acclimation to hypoxia and anoxia is important in various ecological systems, especially flooded soil. Phyllostachys pracecox is sensitive to flooding, and therefore, it is important to explore ways of alleviating hypoxia stress in the roots. In this study, we investigated the regulatory effect of spermidine (Spd) on flooded P. praecox seedlings. METHODS A batch experiment was carried out in roots treated with Spd under flooding for eight days. The following factors were subsequently measured: growth, survival rate, root respiratory activity, soluble protein and anaerobic respiration enzyme contents (pyruvate decarboxylase, PDC; alcohol dehydrogenase, ADH; lactate dehydrogenase, LDH; alanine aminotransferase, AlaAT), S-adenosylmethionine decarboxylase (SAMDC), nitrate reductase (NR), ACC oxidase (ACO) and ACC synthetase (ACS) activities, free Spd, spermine (Spm) and the diamine precursor putrescine (Put) content, indole-3-acetic acid (IAA) and abscisic acid (ABA) content, ethylene emissions and expression of hormone-related genes. RESULTS Application of Spd promoted root growth (root length, volume, surface and dry weight) and root respiratory inhibition, improved the soluble protein content, and reduced the O2·- production rate, H2O2 and MDA content to alleviate the damage of roots under flooding. A significant increase in SAMDC activity, and ABA and IAA contents were also observed, along with a reduction in ethylene emissions, NR, ACO and ACS activities (p < 0.05). Exogenous Spd increased the free Spd and Spm contents in the P. praecox roots, but decreased the free Put content. Taken together, these findings suggest that hypoxia stress was alleviated. Moreover, exogenous Spd up-regulated the expression of auxin-related genes ARF1, AUX1, AUX2, AUX3 and AUX4, and down-regulated the expression of ethylene-related ACO and ACS genes during flooding. In addition, correlation and RDA analysis showed that ARF1, ACO and ACS significantly promoted the expression of auxin, ACO and ACS enzyme activities, respectively (p < 0.05), while ADH, NR, AlaAT, ethylene emissions, Put, Spd, ACS and ACO were significantly correlated with ACS, ACO, and auxin-related gene expression (p < 0.05). Overall, ethylene emissions, ACS and ACO were identified as the main drivers of ethylene and auxin-related gene structure. CONCLUSIONS These results suggest that Spd regulated hormone concentrations, the content of Spd, Spm and Put, and related gene expression, in turn regulating physiological changes such as anaerobic enzyme activity, mitigating flooding stress in the roots and improving overall growth. Spd therefore has the potential to improve the adaptability of P. praecox to flooding stress.
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Affiliation(s)
- Jianshuang Gao
- State Key Lab of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhuangzhuang Qian
- College of Forestry, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China
| | - Yuhe Zhang
- State Key Lab of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shunyao Zhuang
- State Key Lab of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
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22
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Mandal S, Ghorai M, Anand U, Samanta D, Kant N, Mishra T, Rahman MH, Jha NK, Jha SK, Lal MK, Tiwari RK, Kumar M, Radha, Prasanth DA, Mane AB, Gopalakrishnan AV, Biswas P, Proćków J, Dey A. Cytokinin and abiotic stress tolerance -What has been accomplished and the way forward? Front Genet 2022; 13:943025. [PMID: 36017502 PMCID: PMC9395584 DOI: 10.3389/fgene.2022.943025] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/30/2022] [Indexed: 11/27/2022] Open
Abstract
More than a half-century has passed since it was discovered that phytohormone cytokinin (CK) is essential to drive cytokinesis and proliferation in plant tissue culture. Thereafter, cytokinin has emerged as the primary regulator of the plant cell cycle and numerous developmental processes. Lately, a growing body of evidence suggests that cytokinin has a role in mitigating both abiotic and biotic stress. Cytokinin is essential to defend plants against excessive light exposure and a unique kind of abiotic stress generated by an altered photoperiod. Secondly, cytokinin also exhibits multi-stress resilience under changing environments. Furthermore, cytokinin homeostasis is also affected by several forms of stress. Therefore, the diverse roles of cytokinin in reaction to stress, as well as its interactions with other hormones, are discussed in detail. When it comes to agriculture, understanding the functioning processes of cytokinins under changing environmental conditions can assist in utilizing the phytohormone, to increase productivity. Through this review, we briefly describe the biological role of cytokinin in enhancing the performance of plants growth under abiotic challenges as well as the probable mechanisms underpinning cytokinin-induced stress tolerance. In addition, the article lays forth a strategy for using biotechnological tools to modify genes in the cytokinin pathway to engineer abiotic stress tolerance in plants. The information presented here will assist in better understanding the function of cytokinin in plants and their effective investigation in the cropping system.
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Affiliation(s)
- Sayanti Mandal
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune, Maharashtra, India
| | - Mimosa Ghorai
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
| | - Uttpal Anand
- CytoGene Research & Development LLP, Barabanki, Uttar Pradesh, India
| | - Dipu Samanta
- Department of Botany, Dr. Kanailal Bhattacharyya College, Howrah, West Bengal, India
| | - Nishi Kant
- School of Health and Allied Science, ARKA Jain University, Jamshedpur, Jharkhand, India
| | - Tulika Mishra
- Department of Botany, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, Uttar Pradesh, India
| | - Md. Habibur Rahman
- Department of Global Medical Science, Wonju College of Medicine, Yonsei University, Wonju, Gangwon-do, South Korea
| | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
- Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali, India
- Department of Biotechnology, School of Applied and Life Sciences (SALS), Uttaranchal University, Dehradun, India
| | - Saurabh Kumar Jha
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
- Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali, India
- Department of Biotechnology, School of Applied and Life Sciences (SALS), Uttaranchal University, Dehradun, India
| | - Milan Kumar Lal
- Division of Crop Physiology, Biochemistry and Post Harvest Technology, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Rahul Kumar Tiwari
- Division of Crop Physiology, Biochemistry and Post Harvest Technology, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Manoj Kumar
- Chemical and Biochemical Processing Division, ICAR-Central Institute for Research on Cotton Technology, Mumbai, Maharashtra, India
| | - Radha
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh, India
| | | | - Abhijit Bhagwan Mane
- Department of Zoology, Dr. Patangrao Kadam Mahavidhyalaya (affiliated to Shivaji University Kolhapur), Ramanandnagar (Burli), Sangli, Maharashtra, India
| | - Abilash Valsala Gopalakrishnan
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Protha Biswas
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
| | - Jarosław Proćków
- Department of Plant Biology, Institute of Environmental Biology, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
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23
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Systematic Identification and Expression Analysis of the Auxin Response Factor (ARF) Gene Family in Ginkgo biloba L. Int J Mol Sci 2022; 23:ijms23126754. [PMID: 35743196 PMCID: PMC9223646 DOI: 10.3390/ijms23126754] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/04/2022] [Accepted: 06/14/2022] [Indexed: 12/10/2022] Open
Abstract
Auxin participates in various physiological and molecular response-related developmental processes and is a pivotal hormone that regulates phenotypic formation in plants. Auxin response factors (ARFs) are vital transcription factors that mediate downstream auxin signaling by explicitly binding to auxin-responsive genes' promoters. Here, to investigate the possible developmental regulatory functions of ARFs in Ginkgo biloba, through employing comprehensive bioinformatics, we recognized 15 putative GbARF members. Conserved domains and motifs, gene and protein structure, gene duplication, GO enrichment, transcriptome expression profiles, and qRT-PCR all showed that Group I and III members were highly conserved. Among them, GbARF10b and GbARF10a were revealed as transcriptional activators in the auxin response for the development of Ginkgo male flowers through sequences alignment, cis-elements analysis and GO annotation; the results were corroborated for the treatment of exogenous SA. Moreover, the GbARFs expansion occurred predominantly by segmental duplication, and most GbARFs have undergone purifying selection. The Ka/Ks ratio test identified the functional consistence of GbARF2a and GbARF2c, GbARF10b, and GbARF10a in tissue expression profiles and male flower development. In summary, our study established a new research basis for exploring Ginkgo GbARF members' roles in floral organ development and hormone response.
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24
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Bose R, Sengupta M, Basu D, Jha S. The rolB-transgenic Nicotiana tabacum plants exhibit upregulated ARF7 and ARF19 gene expression. PLANT DIRECT 2022; 6:e414. [PMID: 35774625 PMCID: PMC9219009 DOI: 10.1002/pld3.414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 05/08/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Agrobacterium rhizogenes root oncogenic locus B (rolB) is known to induce hairy roots along with triggering several physiological and morphological changes when present as a transgene. However, it is still unknown how this gene triggers these changes within the plant system. In this study, the effect of rolB in-planta, when present as a transgene, was assessed on the gene expression levels of auxin response factors (ARFs)-transcription factors which are key players in auxin-mediated responses. The goal was to uncover Auxin/ARF-driven transcriptional networks potentially active and working selectively, if any, in rolB transgenic background, which might potentially be associated with hairy root development. Hence, the approach involved establishing rolB-transgenic Nicotiana tabacum plants, selecting ARFs (NtARFs) for context-relevance using bioinformatics followed by gene expression profiling. It was observed that out of the chosen NtARFs, NtARF7 and NtARF19 exhibited a consistent pattern of gene upregulation across organ types. In order to understand the significance of these selective gene upregulation, ontology-based transcriptional network maps of the differentially and nondifferentially expressed ARFs were constructed, guided by co-expression databases. The network maps suggested that NtARF7-NtARF19 might have major deterministic, underappreciated roles to play in root development in a rolB-transgenic background-as observed by higher number of "root-related" biological processes present as nodes compared to network maps for similarly constructed other non-differentially expressed ARFs. Based on the inferences drawn, it is hypothesized that rolB, when present as a transgene, might drive hairy root development by selective induction of NtARF7 and NtARF19, suggesting a functional link between the two, leading to the specialized and characteristic rolB-associated traits.
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Affiliation(s)
- Rahul Bose
- Department of GeneticsUniversity of CalcuttaKolkataWest BengalIndia
| | - Mainak Sengupta
- Department of GeneticsUniversity of CalcuttaKolkataWest BengalIndia
| | - Debabrata Basu
- Division of Plant BiologyBose InstituteKolkataWest BengalIndia
| | - Sumita Jha
- Department of BotanyUniversity of CalcuttaKolkataWest BengalIndia
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25
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Verma S, Negi NP, Pareek S, Mudgal G, Kumar D. Auxin response factors in plant adaptation to drought and salinity stress. PHYSIOLOGIA PLANTARUM 2022; 174:e13714. [PMID: 35560231 DOI: 10.1111/ppl.13714] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 05/07/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
Salinity and drought stresses affect plant growth worldwide and limit crop production. Auxin is crucial in regulating plants' salinity and drought stress adaptative response. As a chemical messenger, auxin influences gene expression through a family of functionally distinct transcription factors, the DNA-binding AUXIN RESPONSE FACTORS (ARFs). Various studies have revealed the important roles of ARFs in regulating drought and salinity stress responses in plants. Different ARFs regulate soluble sugar content, promote root development, and maintain chlorophyll content under drought and saline stress conditions to help plants adapt to these stresses. The functional characterization of ARFs pertaining to the regulation of drought and salinity stress responses is still in its infancy. Interestingly, the small RNA-mediated post-transcriptional regulation of ARF expression has been shown to influence plant responses to both stresses. The current knowledge on the diverse roles of ARFs in conferring specificity to auxin-mediated drought and salinity stress responses has not been reviewed to date. In this review, we summarize the recent research concerning the role of ARFs in response to drought and salinity stresses: gene expression patterns, functional characterization, and post-transcriptional regulation under drought and salinity stresses. We have also reviewed the modulation of ARF expression by other molecular regulators in the context of drought and salt stress signaling.
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Affiliation(s)
- Swati Verma
- College of Horticulture and Forestry Thunag, Dr. Y. S. Parmar University of Horticulture and Forestry, Solan, India
| | - Neelam Prabha Negi
- University Institute of Biotechnology, Chandigarh University, Mohali, India
| | - Shalini Pareek
- School of Life Sciences, Jaipur National University, Jaipur, Rajasthan, India
| | - Gaurav Mudgal
- University Institute of Biotechnology, Chandigarh University, Mohali, India
| | - Deepak Kumar
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
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26
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Zhao Y, Wang Y, Zhao X, Yan M, Ren Y, Yuan Z. ARF6s Identification and Function Analysis Provide Insights Into Flower Development of Punica granatum L. FRONTIERS IN PLANT SCIENCE 2022; 13:833747. [PMID: 35321445 PMCID: PMC8937018 DOI: 10.3389/fpls.2022.833747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
Based on the genome and small-RNA sequencing of pomegranate, miRNA167 and three target genes PgARF6 were identified in "Taishanhong" genome. Three PgARF6 genes and their corresponding protein sequences, expression patterns in pomegranate flower development and under exogenous hormones treatments were systematically analyzed in this paper. We found that PgARF6s are nuclear proteins with conserved structures. However, PgARF6s had different protein structures and expression profiles in pomegranate flower development. At the critical stages of pomegranate ovule sterility (8.1-14.0 mm), the expression levels of PgARF6s in bisexual flowers were lower than those in functional male flowers. Interestingly, PgARF6c expression level was significantly higher than PgARF6a and PgARF6b. Under the treatment of exogenous IBA and 6-BA, PgARF6s were down-regulated, and the expression of PgARF6c was significantly inhibited. PgmiR167a and PgmiR167d had the binding site on PgARF6 genes sequences, and PgARF6a has the directly targeted regulatory relationship with PgmiR167a in pomegranate. At the critical stage of ovule development (8.1-12.0 mm), exogenous IBA and 6-BA promoted the content of GA and ZR accumulation, inhibited BR accumulation. There was a strong correlation between the expression of PgARF6a and PgARF6b. Under exogenous hormone treatment, the content of ZR, BR, GA, and ABA were negatively correlated with the expressions of PgARF6 genes. However, JA was positively correlated with PgARF6a and PgARF6c under IBA treatment. Thus, our results provide new evidence for PgARF6 genes involving in ovule sterility in pomegranate flowers.
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Affiliation(s)
- Yujie Zhao
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Yuying Wang
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Xueqing Zhao
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Ming Yan
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Yuan Ren
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Zhaohe Yuan
- Co-innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Forestry, Nanjing Forestry University, Nanjing, China
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27
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Brophy JAN. Toward synthetic plant development. PLANT PHYSIOLOGY 2022; 188:738-748. [PMID: 34904660 PMCID: PMC8825267 DOI: 10.1093/plphys/kiab568] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/01/2021] [Indexed: 06/14/2023]
Abstract
The ability to engineer plant form will enable the production of novel agricultural products designed to tolerate extreme stresses, boost yield, reduce waste, and improve manufacturing practices. While historically, plants were altered through breeding to change their size or shape, advances in our understanding of plant development and our ability to genetically engineer complex eukaryotes are leading to the direct engineering of plant structure. In this review, I highlight the central role of auxin in plant development and the synthetic biology approaches that could be used to turn auxin-response regulators into powerful tools for modifying plant form. I hypothesize that recoded, gain-of-function auxin response proteins combined with synthetic regulation could be used to override endogenous auxin signaling and control plant structure. I also argue that auxin-response regulators are key to engineering development in nonmodel plants and that single-cell -omics techniques will be essential for characterizing and modifying auxin response in these plants. Collectively, advances in synthetic biology, single-cell -omics, and our understanding of the molecular mechanisms underpinning development have set the stage for a new era in the engineering of plant structure.
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Affiliation(s)
- Jennifer A N Brophy
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
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28
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Liu B, Zhu J, Lin L, Yang Q, Hu B, Wang Q, Zou XX, Zou SQ. Genome-Wide Identification and Co-Expression Analysis of ARF and IAA Family Genes in Euscaphis konishii: Potential Regulators of Triterpenoids and Anthocyanin Biosynthesis. Front Genet 2022; 12:737293. [PMID: 35069676 PMCID: PMC8766721 DOI: 10.3389/fgene.2021.737293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 11/18/2021] [Indexed: 11/30/2022] Open
Abstract
Euscaphis konishii is an evergreen plant that is widely planted as an industrial crop in Southern China. It produces red fruits with abundant secondary metabolites, giving E. konishii high medicinal and ornamental value. Auxin signaling mediated by members of the AUXIN RESPONSE FACTOR (ARF) and auxin/indole-3-acetic acid (Aux/IAA) protein families plays important roles during plant growth and development. Aux/IAA and ARF genes have been described in many plants but have not yet been described in E. konishii. In this study, we identified 34 EkIAA and 29 EkARF proteins encoded by the E. konishii genome through database searching using HMMER. We also performed a bioinformatic characterization of EkIAA and EkARF genes, including their phylogenetic relationships, gene structures, chromosomal distribution, and cis-element analysis, as well as conserved motifs in the proteins. Our results suggest that EkIAA and EkARF genes have been relatively conserved over evolutionary history. Furthermore, we conducted expression and co-expression analyses of EkIAA and EkARF genes in leaves, branches, and fruits, which identified a subset of seven EkARF genes as potential regulators of triterpenoids and anthocyanin biosynthesis. RT-qPCR, yeast one-hybrid, and transient expression analyses showed that EkARF5.1 can directly interact with auxin response elements and regulate downstream gene expression. Our results may pave the way to elucidating the function of EkIAA and EkARF gene families in E. konishii, laying a foundation for further research on high-yielding industrial products and E. konishii breeding.
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Affiliation(s)
- Bobin Liu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, School of Wetlands, Yancheng Teachers University, Yancheng, China.,College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.,Fujian Colleges and Universities Engineering Research Institute for Conservation and Utilization of Natural Bioresources, Fuzhou, China
| | - Juanli Zhu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.,Fujian Colleges and Universities Engineering Research Institute for Conservation and Utilization of Natural Bioresources, Fuzhou, China
| | - Lina Lin
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.,Fujian Colleges and Universities Engineering Research Institute for Conservation and Utilization of Natural Bioresources, Fuzhou, China
| | - Qixin Yang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.,Fujian Colleges and Universities Engineering Research Institute for Conservation and Utilization of Natural Bioresources, Fuzhou, China
| | - Bangping Hu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.,Fujian Colleges and Universities Engineering Research Institute for Conservation and Utilization of Natural Bioresources, Fuzhou, China
| | - Qingying Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.,Fujian Colleges and Universities Engineering Research Institute for Conservation and Utilization of Natural Bioresources, Fuzhou, China
| | - Xiao-Xing Zou
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.,Fujian Colleges and Universities Engineering Research Institute for Conservation and Utilization of Natural Bioresources, Fuzhou, China
| | - Shuang-Quan Zou
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.,Fujian Colleges and Universities Engineering Research Institute for Conservation and Utilization of Natural Bioresources, Fuzhou, China
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Luo L, Yang X, Guo M, Lan T, Yu Y, Mo B, Chen X, Gao L, Liu L. TRANS-ACTING SIRNA3-derived short interfering RNAs confer cleavage of mRNAs in rice. PLANT PHYSIOLOGY 2022; 188:347-362. [PMID: 34599593 PMCID: PMC8774828 DOI: 10.1093/plphys/kiab452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/29/2021] [Indexed: 05/11/2023]
Abstract
Plant TRANS-ACTING SIRNA3 (TAS3)-derived short interfering RNAs (siRNAs) include tasiR-AUXIN RESPONSE FACTORs (ARFs), which are functionally conserved in targeting ARF genes, and a set of non-tasiR-ARF siRNAs, which have rarely been studied. In this study, TAS3 siRNAs were systematically characterized in rice (Oryza sativa). Small RNA sequencing results showed that an overwhelming majority of TAS3 siRNAs belong to the non-tasiR-ARF group, while tasiR-ARFs occupy a diminutive fraction. Phylogenetic analysis of TAS3 genes across dicot and monocot plants revealed that the siRNA-generating regions were highly conserved in grass species, especially in the Oryzoideae. Target genes were identified for not only tasiR-ARFs but also non-tasiR-ARF siRNAs by analyzing rice Parallel Analysis of RNA Ends datasets, and some of these siRNA-target interactions were experimentally confirmed using tas3 mutants generated by genome editing. Consistent with the de-repression of target genes, phenotypic alterations were observed for mutants in three TAS3 loci in comparison to wild-type rice. The regulatory role of ribosomes in the TAS3 siRNA-target interactions was further revealed by the fact that TAS3 siRNA-mediated target cleavage, in particular tasiR-ARFs targeting ARF2/3/14/15, occurred extensively in rice polysome samples. Altogether, our study sheds light into TAS3 genes in plants and expands our knowledge about rice TAS3 siRNA-target interactions.
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Affiliation(s)
- Linlin Luo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Guangdong Province, Shenzhen 518060, China
- College of Physics and Optoelectronic Engineering, Shenzhen University, Guangdong Province, Shenzhen 518060, China
| | - Xiaoyu Yang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Guangdong Province, Shenzhen 518060, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Mingxi Guo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Guangdong Province, Shenzhen 518060, China
| | - Ting Lan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Guangdong Province, Shenzhen 518060, China
| | - Yu Yu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Guangdong Province, Shenzhen 518060, China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Guangdong Province, Shenzhen 518060, China
| | - Xuemei Chen
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Guangdong Province, Shenzhen 518060, China
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, California 92521, USA
| | - Lei Gao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Guangdong Province, Shenzhen 518060, China
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Guangdong Province, Shenzhen 518060, China
- Author for communication:
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Jin L, Yarra R, Zhou L, Cao H. The auxin response factor (ARF) gene family in Oil palm (Elaeis guineensis Jacq.): Genome-wide identification and their expression profiling under abiotic stresses. PROTOPLASMA 2022; 259:47-60. [PMID: 33792785 DOI: 10.1007/s00709-021-01639-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
Auxin response factors (ARFs) play vital role in controlling growth and developmental processes of plants via regulating the auxin signaling pathways. However, the identification and functional roles of ARFs in oil palm plants remain elusive. Here, we identified a total of 23 ARF (EgARF) genes in oil palm through a genome-wide identification approach. The EgARF gene structure analysis revealed the presence of intron-rich ARF gene family in genome of oil palm. Further analysis demonstrated the uneven distribution of 23EgARFs on 16 chromosomes of oil palm. Phylogenetic analysis clustered all the EgARFs into four groups. Twenty-one EgARFs contained BDD, ARF, and CTD domains, whereas EgARF5 and EgARF7 lacked the CTD domain. The evolution of ARF genes in oil palm genome has been expanded by segmental duplication events. The cis-acting regulatory elements of EgARF gene family were predominantly associated with the stress and hormone responses. Expression profiling data demonstrated the constitutive and tissue-specific expression of EgARF genes in various tissues of oil palm. Real-time PCR analysis of 19 EgARF genes expression levels under cold, drought, and salt stress conditions proved their prominent role under abiotic stress responses. Altogether, our study provides a basis for studying the molecular and functional roles of ARF genes in oil palm.
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Affiliation(s)
- Longfei Jin
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, 571339, Hainan, People's Republic of China.
| | | | - Lixia Zhou
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, 571339, Hainan, People's Republic of China
| | - Hongxing Cao
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, 571339, Hainan, People's Republic of China
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Tang Y, Du G, Xiang J, Hu C, Li X, Wang W, Zhu H, Qiao L, Zhao C, Wang J, Yu S, Sui J. Genome-wide identification of auxin response factor (ARF) gene family and the miR160-ARF18-mediated response to salt stress in peanut (Arachis hypogaea L.). Genomics 2021; 114:171-184. [PMID: 34933069 DOI: 10.1016/j.ygeno.2021.12.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/08/2021] [Accepted: 12/15/2021] [Indexed: 11/30/2022]
Abstract
Auxin response factors (ARFs) are transcription factors that regulate the transcription of auxin-responsive genes during plant growth and development. In this study, 29 and 30 ARF members were identified from the two wild peanut species, A. duranensis and A. ipaensis, respectively. The ARFs, including their classifications, conserved domains and evolutionary relationships were characterized. RNA-seq analyses revealed that some of the ARF genes were responsive to abiotic stress, particularly high salinity. In addition to abiotic stress, the expression of 2 ARF members was also regulated by biotic stress, specifically Bradyrhizobium infection in A. duranensis. The ARF gene Arahy.7DXUOK was predicted to be a potential target of miR160. Overexpression of miR160 could cause degradation of the Arahy.7DXUOK target gene transcript and increased salt tolerance in miR160OX transgenic plants. Therefore, these molecular characterization and expression profile analyses provide comprehensive information on ARF family members and will help to elucidate their functions to facilitate further research on peanuts.
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Affiliation(s)
- Yanyan Tang
- College of Agronomy, Qingdao Agricultural University, Dry-land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao 266109, China
| | - Guoning Du
- College of Agronomy, Qingdao Agricultural University, Dry-land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao 266109, China
| | - Jie Xiang
- College of Agronomy, Qingdao Agricultural University, Dry-land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao 266109, China
| | - Changli Hu
- College of Agronomy, Qingdao Agricultural University, Dry-land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao 266109, China
| | - Xiaoting Li
- College of Agronomy, Qingdao Agricultural University, Dry-land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao 266109, China
| | - Weihua Wang
- College of Agronomy, Qingdao Agricultural University, Dry-land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao 266109, China
| | - Hong Zhu
- College of Agronomy, Qingdao Agricultural University, Dry-land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao 266109, China
| | - Lixian Qiao
- College of Agronomy, Qingdao Agricultural University, Dry-land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao 266109, China
| | - Chunmei Zhao
- College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Jingshan Wang
- College of Agronomy, Qingdao Agricultural University, Dry-land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao 266109, China
| | - Shanlin Yu
- College of Agronomy, Qingdao Agricultural University, Dry-land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao 266109, China
| | - Jiongming Sui
- College of Agronomy, Qingdao Agricultural University, Dry-land Farming Technology Laboratory of Shandong Province, Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao 266109, China..
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Werghi S, Herrero FA, Fakhfakh H, Gorsane F. Auxin drives tomato spotted wilt virus (TSWV) resistance through epigenetic regulation of auxin response factor ARF8 expression in tomato. Gene 2021; 804:145905. [PMID: 34411646 DOI: 10.1016/j.gene.2021.145905] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 11/26/2022]
Abstract
Tomato spotted wilt virus (TSWV) causes severe losses of tomato crops worldwide. To cope dynamically with such a threat, plants deploy strategies acting at the molecular and the epigenetic levels. We found that tomato symptoms progress in a specific-genotype-manner upon TSWV infection. Susceptible genotypes showed within the Auxin Response Factor (ARF8) promoter coupled to enhanced expression of miRNA167a, reduced ARF8 gene and decreased levels of the hormone auxin. This constitutes a deliberate attempt of TSWV to disrupt plant growth to promote spread in sensitive cultivars. Epigenetic regulation through the level of cytosine methylation and the miR167a-ARF8 module are part of a complex network modulating auxin-triggered synthesis and shaping tomato responses to TSWV. Furthermore, modulation of miR167a-ARF8 regulatory module could be applied in tomato-resistance breeding programs.
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Affiliation(s)
- Sirine Werghi
- Laboratory of Molecular Genetics, Immunology and Biotechnology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 2092, Tunisia
| | - Frederic Aparicio Herrero
- Institute of Molecular and Cellular Biology of Plants (UPV-CSIC), Valencia 46022, Spain; Dept of Biotechnology, ETSIAMN, Universidad Politécnica de Valencia, 46002, Spain
| | - Hatem Fakhfakh
- Laboratory of Molecular Genetics, Immunology and Biotechnology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 2092, Tunisia; Faculty of Sciences of Bizerte, Zarzouna 702, University of Carthage, Tunisia
| | - Faten Gorsane
- Laboratory of Molecular Genetics, Immunology and Biotechnology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 2092, Tunisia; Faculty of Sciences of Bizerte, Zarzouna 702, University of Carthage, Tunisia.
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Hosaka GK, Correr FH, da Silva CC, Sforça DA, Barreto FZ, Balsalobre TWA, Pasha A, de Souza AP, Provart NJ, Carneiro MS, Margarido GRA. Temporal Gene Expression in Apical Culms Shows Early Changes in Cell Wall Biosynthesis Genes in Sugarcane. FRONTIERS IN PLANT SCIENCE 2021; 12:736797. [PMID: 34966397 PMCID: PMC8710541 DOI: 10.3389/fpls.2021.736797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
Multiple genes in sugarcane control sucrose accumulation and the biosynthesis of cell wall components; however, it is unclear how these genes are expressed in its apical culms. To better understand this process, we sequenced mRNA from +1 stem internodes collected from four genotypes with different concentrations of soluble solids. Culms were collected at four different time points, ranging from six to 12-month-old plants. Here we show differentially expressed genes related to sucrose metabolism and cell wall biosynthesis, including genes encoding invertases, sucrose synthase and cellulose synthase. Our results showed increased expression of invertases in IN84-58, the genotype with lower sugar and higher fiber content, as well as delayed expression of secondary cell wall-related cellulose synthase for the other genotypes. Interestingly, genes involved with hormone metabolism were differentially expressed across time points in the three genotypes with higher soluble solids content. A similar result was observed for genes controlling maturation and transition to reproductive stages, possibly a result of selection against flowering in sugarcane breeding programs. These results indicate that carbon partitioning in apical culms of contrasting genotypes is mainly associated with differential cell wall biosynthesis, and may include early modifications for subsequent sucrose accumulation. Co-expression network analysis identified transcription factors related to growth and development, showing a probable time shift for carbon partitioning occurred in 10-month-old plants.
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Affiliation(s)
- Guilherme Kenichi Hosaka
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Fernando Henrique Correr
- Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Carla Cristina da Silva
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Danilo Augusto Sforça
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Fernanda Zatti Barreto
- Plant Biotechnology Laboratory, Centre for Agricultural Sciences, Federal University of São Carlos (CCA-UFSCar), Araras, Brazil
| | | | - Asher Pasha
- Department of Cell and Systems Biology, Centre for the Analysis of the Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Nicholas James Provart
- Department of Cell and Systems Biology, Centre for the Analysis of the Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| | - Monalisa Sampaio Carneiro
- Plant Biotechnology Laboratory, Centre for Agricultural Sciences, Federal University of São Carlos (CCA-UFSCar), Araras, Brazil
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Hou Q, Qiu Z, Wen Z, Zhang H, Li Z, Hong Y, Qiao G, Wen X. Genome-Wide Identification of ARF Gene Family Suggests a Functional Expression Pattern during Fruitlet Abscission in Prunus avium L. Int J Mol Sci 2021; 22:11968. [PMID: 34769398 PMCID: PMC8584427 DOI: 10.3390/ijms222111968] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/20/2021] [Accepted: 11/02/2021] [Indexed: 11/16/2022] Open
Abstract
Auxin response factors (ARFs) play a vital role in plant growth and development. In the current study, 16 ARF members have been identified in the sweet cherry (Prunus avium L.) genome. These genes are all located in the nucleus. Sequence analysis showed that genes in the same subgroup have similar exon-intron structures. A phylogenetic tree has been divided into five groups. The promoter sequence includes six kinds of plant hormone-related elements, as well as abiotic stress response elements such as low temperature or drought. The expression patterns of PavARF in different tissues, fruitlet abscission, cold and drought treatment were comprehensively analyzed. PavARF10/13 was up-regulated and PavARF4/7/11/12/15 was down-regulated in fruitlet abscising. These genes may be involved in the regulation of fruit drop in sweet cherry fruits. This study comprehensively analyzed the bioinformatics and expression pattern of PavARF, which can lay the foundation for further understanding the PavARF family in plant growth development and fruit abscission.
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Affiliation(s)
- Qiandong Hou
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-Bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Q.H.); (Z.Q.); (Z.W.); (Y.H.); (G.Q.)
| | - Zhilang Qiu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-Bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Q.H.); (Z.Q.); (Z.W.); (Y.H.); (G.Q.)
| | - Zhuang Wen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-Bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Q.H.); (Z.Q.); (Z.W.); (Y.H.); (G.Q.)
| | - Huimin Zhang
- College of Forestry, Guizhou University/Institute for Forest Resources & Environment of Guizhou, Guiyang 550025, China; (H.Z.); (Z.L.)
| | - Zhengchun Li
- College of Forestry, Guizhou University/Institute for Forest Resources & Environment of Guizhou, Guiyang 550025, China; (H.Z.); (Z.L.)
| | - Yi Hong
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-Bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Q.H.); (Z.Q.); (Z.W.); (Y.H.); (G.Q.)
| | - Guang Qiao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-Bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Q.H.); (Z.Q.); (Z.W.); (Y.H.); (G.Q.)
| | - Xiaopeng Wen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Collaborative Innovation Center for Mountain Ecology & Agro-Bioengineering (CICMEAB), Institute of Agro-Bioengineering/College of Life Sciences, Guizhou University, Guiyang 550025, China; (Q.H.); (Z.Q.); (Z.W.); (Y.H.); (G.Q.)
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Li P, Ma Q, Qu C, Zhu S, Zhao K, Ma X, Li Z, Zhang X, Gong F, Yin D. Genome-wide identification and expression analysis of auxin response factors in peanut ( Arachis hypogaea L.). PeerJ 2021; 9:e12319. [PMID: 34721990 PMCID: PMC8542371 DOI: 10.7717/peerj.12319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 09/25/2021] [Indexed: 12/14/2022] Open
Abstract
Auxin response factors (ARFs) are transcription factors that regulate the expression of auxin response genes, and have important functions in plant growth and development. In this study, available genome data for peanut (Arachis hypogaea L.) were used to identify AhARF genes. In total, 61 AhARFs and 23 AtARFs were divided into six groups (I-VI). Molecular structural analysis revealed that the protein members of AhARF contain at least two domains, the B3 domain and the Auxin-resp domain, and that some have a C-terminal dimerisation domain. Screening of the transcriptome data of 22 tissues of A. hypogaea cv. Tifrunner in a public database showed high expression levels of AhARF2 and AhARF6. AhARF6 was expressed more highly in the stem and branch than in the root and leaf of the wild species Arachis monticola (A. mon) and cultivated species H103. After treatment with exogenous auxin (NAA), the expression of AhARF6 was inhibited, and this inhibition was greater in A. mon than in H103. The transcriptome map revealed that the expression of AhARF6 was higher in the larger pods of H8107 and ZP06 than in the medium pods of H103 and small pods of A. mon. Moreover, AhARF6-5 was proven to be localised in the nucleus, consistent with the location of AtARF6. These results suggest that AhARF6 may play an important role in pod development in peanut.
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Affiliation(s)
- Peipei Li
- Henan Agricultural University, College of Agronomy & Center for Crop Genome Engineering, Henan Agricultural University, Henan, China, Zhengzhou, Henan Province, China
| | - Qian Ma
- Henan Agricultural University, College of Agronomy & Center for Crop Genome Engineering, Henan Agricultural University, Henan, China, Zhengzhou, Henan Province, China
| | - Chengxin Qu
- Henan Agricultural University, College of Agronomy & Center for Crop Genome Engineering, Henan Agricultural University, Henan, China, Zhengzhou, Henan Province, China
| | - Shuliang Zhu
- Henan Agricultural University, College of Agronomy & Center for Crop Genome Engineering, Henan Agricultural University, Henan, China, Zhengzhou, Henan Province, China
| | - Kunkun Zhao
- Henan Agricultural University, College of Agronomy & Center for Crop Genome Engineering, Henan Agricultural University, Henan, China, Zhengzhou, Henan Province, China
| | - Xingli Ma
- Henan Agricultural University, College of Agronomy & Center for Crop Genome Engineering, Henan Agricultural University, Henan, China, Zhengzhou, Henan Province, China
| | - Zhongfeng Li
- Henan Agricultural University, College of Agronomy & Center for Crop Genome Engineering, Henan Agricultural University, Henan, China, Zhengzhou, Henan Province, China
| | - Xingguo Zhang
- Henan Agricultural University, College of Agronomy & Center for Crop Genome Engineering, Henan Agricultural University, Henan, China, Zhengzhou, Henan Province, China
| | - Fangping Gong
- Henan Agricultural University, College of Agronomy & Center for Crop Genome Engineering, Henan Agricultural University, Henan, China, Zhengzhou, Henan Province, China
| | - Dongmei Yin
- Henan Agricultural University, College of Agronomy & Center for Crop Genome Engineering, Henan Agricultural University, Henan, China, Zhengzhou, Henan Province, China
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Yuan TT, Xiang ZX, Li W, Gao X, Lu YT. Osmotic stress represses root growth by modulating the transcriptional regulation of PIN-FORMED3. THE NEW PHYTOLOGIST 2021; 232:1661-1673. [PMID: 34420215 DOI: 10.1111/nph.17687] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/14/2021] [Indexed: 06/13/2023]
Abstract
Osmotic stress influences root system architecture, and polar auxin transport (PAT) is well established to regulate root growth and development. However, how PAT responds to osmotic stress at the molecular level remains poorly understood. In this study, we explored whether and how the auxin efflux carrier PIN-FORMED3 (PIN3) participates in osmotic stress-induced root growth inhibition in Arabidopsis (Arabidopsis thaliana). We observed that osmotic stress induces a HD-ZIP II transcription factor-encoding gene HOMEODOMAIN ARABIDOPSIS THALIANA2 (HAT2) expression in roots. The hat2 loss-of-function mutant is less sensitive to osmotic stress in terms of root meristem growth. Consistent with this phenotype, whereas the auxin response is downregulated in wild-type roots under osmotic stress, the inhibition of auxin response by osmotic stress was alleviated in hat2 roots. Conversely, transgenic lines overexpressing HAT2 (Pro35S::HAT2) had shorter roots and reduced auxin accumulation compared with wild-type plants. PIN3 expression was significantly reduced in the Pro35S::HAT2 lines. We determined that osmotic stress-mediated repression of PIN3 was alleviated in the hat2 mutant because HAT2 normally binds to the promoter of PIN3 and inhibits its expression. Taken together, our data revealed that osmotic stress inhibits root growth via HAT2, which regulates auxin activity by directly repressing PIN3 transcription.
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Affiliation(s)
- Ting-Ting Yuan
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China
| | - Zhi-Xin Xiang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China
| | - Wen Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China
| | - Xiang Gao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China
| | - Ying-Tang Lu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, 430072, China
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Genome-Wide Identification of ARF Transcription Factor Gene Family and Their Expression Analysis in Sweet Potato. Int J Mol Sci 2021; 22:ijms22179391. [PMID: 34502298 PMCID: PMC8431151 DOI: 10.3390/ijms22179391] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/08/2021] [Accepted: 08/24/2021] [Indexed: 12/25/2022] Open
Abstract
Auxin response factors (ARFs) are a family of transcription factors that play an important role of auxin regulation through their binding with auxin response elements. ARF genes are represented by a large multigene family in plants; however, to our knowledge, the ARF gene family has not been well studied and characterized in sweet potatoes. In this study, a total of 25 ARF genes were identified in Ipomea trifida. The identified ItrARF genes’ conserved motifs, chromosomal locations, phylogenetic relationships, and their protein characteristics were systemically investigated using different bioinformatics tools. The expression patterns of ItfARF genes were analyzed within the storage roots and normal roots at an early stage of development. ItfARF16b and ItfARF16c were both highly expressed in the storage root, with minimal to no expression in the normal root. ItfARF6a and ItfARF10a exhibited higher expression in the normal root but not in the storage root. Subsequently, ItfARF1a, ItfARF2b, ItfARF3a, ItfARF6b, ItfARF8a, ItfARF8b, and ItfARF10b were expressed in both root types with moderate to high expression for each. All ten of these ARF genes and their prominent expression signify their importance within the development of each respective root type. This study provides comprehensive information regarding the ARF family in sweet potatoes, which will be useful for future research to discover further functional verification of these ItfARF genes.
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Whole-Genome Duplication and Purifying Selection Contributes to the Functional Redundancy of Auxin Response Factor ( ARF) Genes in Foxtail Millet ( Setaria italica L.). Int J Genomics 2021; 2021:2590665. [PMID: 34414231 PMCID: PMC8369178 DOI: 10.1155/2021/2590665] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 07/19/2021] [Indexed: 11/20/2022] Open
Abstract
Auxin response factors (ARFs) play crucial roles in auxin-mediated response, whereas molecular genetics of ARF genes was seldom investigated in Setaria italica, an important crop and C4 model plant. In the present study, genome-wide evolutionary analysis of ARFs was performed in S. italica. Twenty-four SiARF genes were identified and unevenly distributed on eight of the nine chromosomes in S. italica. Duplication mode exploration implied that 13 SiARF proteins were originated from whole-genome duplication and suffered purifying selection. Phylogeny reconstruction of SiARFs by maximum likelihood and neighbor-joining trees revealed SiARFs could be divided into four clades. SiARFs clustered within the same clade shared similar gene structure and protein domain composition, implying functional redundancy. Moreover, amino acid composition of the middle regions was conserved in SiARFs belonged to the same clade. SiARFs were categorized into either activators or repressors according to the enrichment of specific amino acids. Intrinsic disorder was featured in the middle regions of ARF activators. Finally, expression profiles of SiARFs under hormone and abiotic stress treatment not only revealed their potential function in stress response but also indicate their functional redundancy. Overall, our results provide insights into evolutionary aspects of SiARFs and benefit for further functional characterization.
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Abbas F, Ke Y, Zhou Y, Yu Y, Waseem M, Ashraf U, Li X, Yu R, Fan Y. Genome-wide analysis of ARF transcription factors reveals HcARF5 expression profile associated with the biosynthesis of β-ocimene synthase in Hedychium coronarium. PLANT CELL REPORTS 2021. [PMID: 34052884 DOI: 10.1007/s00299021-02709-2701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Herein, 37 ARF genes were identified and analyzed in Hedychium coronarium and HcARF5 showed a potential role in the regulation of HcTPS3. Auxin is an important plant hormone, implicated in various aspects of plant growth and development processes especially in the biosynthesis of various secondary metabolites. Auxin response factors (ARF) belong to the transcription factors (TFs) gene family and play a crucial role in transcriptional activation/repression of auxin-responsive genes by directly binding to their promoter region. Nevertheless, whether ARF genes are involved in the regulatory mechanism of volatile compounds in flowering plants is largely unknown. β-ocimene is a key floral volatile compound synthesized by terpene synthase 3 (HcTPS3) in Hedychium coronarium. A comprehensive analysis of H. coronarium genome reveals 37 candidate ARF genes in the whole genome. Tissue-specific expression patterns of HcARFs family members were assessed using available transcriptome data. Among them, HcARF5 showed a higher expression level in flowers, and significantly correlated with the key structural β-ocimene synthesis gene (HcTPS3). Furthermore, transcript levels of both genes were associated with the flower development. Under hormone treatments, the response of HcARF5 and HcTPS3, and the emission level of β-ocimene contents were evaluated. Subcellular and transcriptional activity assay showed that HcARF5 localizes to the nucleus and possesses transcriptional activity. Yeast one-hybrid (Y1H) and dual-luciferase assays revealed that HcARF5 directly regulates the transcriptional activity of HcTPS3. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays showed that HcARF5 interacts with scent-related HcIAA4, HcIAA6, and HcMYB1 in vivo. Overall, these results indicate that HcARF5 is potentially involved in the regulation of β-ocimene synthesis in H. coronarium.
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Affiliation(s)
- Farhat Abbas
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Yanguo Ke
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
- College of Economics and Management, Kunming University, Kunming, 650214, China
| | - Yiwei Zhou
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Yunyi Yu
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Muhammad Waseem
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Umair Ashraf
- Department of Botany, Division of Science and Technology, University of Education, Lahore, 54770, Punjab, Pakistan
| | - Xinyue Li
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Rangcai Yu
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yanping Fan
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, 510642, China.
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Abbas F, Ke Y, Zhou Y, Yu Y, Waseem M, Ashraf U, Li X, Yu R, Fan Y. Genome-wide analysis of ARF transcription factors reveals HcARF5 expression profile associated with the biosynthesis of β-ocimene synthase in Hedychium coronarium. PLANT CELL REPORTS 2021; 40:1269-1284. [PMID: 34052884 DOI: 10.1007/s00299-021-02709-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/28/2021] [Indexed: 05/19/2023]
Abstract
Herein, 37 ARF genes were identified and analyzed in Hedychium coronarium and HcARF5 showed a potential role in the regulation of HcTPS3. Auxin is an important plant hormone, implicated in various aspects of plant growth and development processes especially in the biosynthesis of various secondary metabolites. Auxin response factors (ARF) belong to the transcription factors (TFs) gene family and play a crucial role in transcriptional activation/repression of auxin-responsive genes by directly binding to their promoter region. Nevertheless, whether ARF genes are involved in the regulatory mechanism of volatile compounds in flowering plants is largely unknown. β-ocimene is a key floral volatile compound synthesized by terpene synthase 3 (HcTPS3) in Hedychium coronarium. A comprehensive analysis of H. coronarium genome reveals 37 candidate ARF genes in the whole genome. Tissue-specific expression patterns of HcARFs family members were assessed using available transcriptome data. Among them, HcARF5 showed a higher expression level in flowers, and significantly correlated with the key structural β-ocimene synthesis gene (HcTPS3). Furthermore, transcript levels of both genes were associated with the flower development. Under hormone treatments, the response of HcARF5 and HcTPS3, and the emission level of β-ocimene contents were evaluated. Subcellular and transcriptional activity assay showed that HcARF5 localizes to the nucleus and possesses transcriptional activity. Yeast one-hybrid (Y1H) and dual-luciferase assays revealed that HcARF5 directly regulates the transcriptional activity of HcTPS3. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays showed that HcARF5 interacts with scent-related HcIAA4, HcIAA6, and HcMYB1 in vivo. Overall, these results indicate that HcARF5 is potentially involved in the regulation of β-ocimene synthesis in H. coronarium.
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Affiliation(s)
- Farhat Abbas
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Yanguo Ke
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
- College of Economics and Management, Kunming University, Kunming, 650214, China
| | - Yiwei Zhou
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Yunyi Yu
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Muhammad Waseem
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Umair Ashraf
- Department of Botany, Division of Science and Technology, University of Education, Lahore, 54770, Punjab, Pakistan
| | - Xinyue Li
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Rangcai Yu
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yanping Fan
- The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou, 510642, China.
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Li Y, Luo W, Sun Y, Chang H, Ma K, Zhao Z, Lu L. Identification and Expression Analysis of miR160 and Their Target Genes in Cucumber. Biochem Genet 2021; 60:127-152. [PMID: 34117971 DOI: 10.1007/s10528-021-10093-4] [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] [Received: 02/18/2021] [Accepted: 06/02/2021] [Indexed: 11/28/2022]
Abstract
miR160 plays a crucial role in various biological processes by regulating their target gene auxin response factor (ARF) in plants. However, little is known about miR160 and ARF in cucumber fruit expansion. Here, 4 Csa-MIR160 family members and 17 CsARFs were identified through a genome-wide search. Csa-miR160 showed a closer relationship with those in melon. Phylogenetic analysis revealed that CsARFs were divided into four classes and most of CsARFs presented a closer evolutionary relationship with those from tomato. Putative cis-elements analysis predicted that Csa-MIR160 and CsARFs were involved in light, phytohormone and stress response, which proved that they might take part in light, phytohormone and stress signaling pathway by the miR160-ARF module. In addition, CsARF5, CsARF11, CsARF13 and CsARF14 were predicted as the target genes of Csa-miR160. qRT-PCR revealed that Csa-miR160 and their target gene CsARFs were differentially expressed in differential cucumber tissues and developmental stages. Csa-miR160d was only expressed in the expanded cucumber fruit. CsARF5, CsARF11 and CsARF13 exhibited the lower expression in the expanded fruit than those in the ovary, while, CsARF14 showed the reverse trend. Our results suggested that Csa-miR160d might play a crucial role in cucumber fruit expansion by negatively targeting CsARF5, CsARF11 and CsARF13. This is the first genome-wide analysis of miR160 in cucumber. These findings provide useful information and resources for further studying the role of miR160 and ARF in cucumber fruit expansion.
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Affiliation(s)
- Yaoyao Li
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, 453003, China.,Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, 453003, China
| | - Weirong Luo
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, 453003, China.,Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, 453003, China
| | - Yongdong Sun
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, 453003, China. .,Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, 453003, China.
| | - Huaicheng Chang
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, 453003, China.,Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, 453003, China
| | - Kai Ma
- Institute of Horticulture, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Zhenxiang Zhao
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, 453003, China.,Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, 453003, China
| | - Lin Lu
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, 453003, China.,Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, 453003, China
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Wang L, Yang X, Gao Y, Yang S. Genome-Wide Identification and Characterization of TALE Superfamily Genes in Soybean ( Glycine max L.). Int J Mol Sci 2021; 22:4117. [PMID: 33923457 PMCID: PMC8073939 DOI: 10.3390/ijms22084117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 11/16/2022] Open
Abstract
The three-amino-acid-loop-extension (TALE) superfamily genes broadly existed in plants, which played important roles in plant growth, development and abiotic stress responses. In this study, we identified 68 Glycine max TALE (GmTALE) superfamily members. Phylogenetic analysis divided the GmTALE superfamily into the BEL1-like (BLH/BELL homeodomain) and the KNOX (KNOTTED-like homeodomain) subfamilies. Moreover, the KNOX subfamily could be further categorized into three clades (KNOX Class I, KNOX Class II and KNOX Class III). The GmTALE genes showed similarities in the gene structures in the same subfamily or clade, whose coding proteins exhibited analogous motif and conserved domain compositions. Besides, synteny analyses and evolutionary constraint evaluations of the TALE members among soybean and different species provided more clues for GmTALE superfamily evolution. The cis-element analyses in gene promoter regions and relevant gene expression profiling revealed different regulating roles of GmTALE genes during soybean plant development, saline and dehydration stresses. Genome-wide characterization, evolution, and expression profile analyses of GmTALE genes can pave the way for future gene functional research and facilitate their roles for applications in genetic improvement on soybean in saline and dehydration stresses.
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Affiliation(s)
| | | | | | - Shouping Yang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (L.W.); (X.Y.); (Y.G.)
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Yuan C, Li C, Lu X, Zhao X, Yan C, Wang J, Sun Q, Shan S. Comprehensive genomic characterization of NAC transcription factor family and their response to salt and drought stress in peanut. BMC PLANT BIOLOGY 2020; 20:454. [PMID: 33008287 PMCID: PMC7532626 DOI: 10.1186/s12870-020-02678-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 09/24/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Peanut is one of the most important oil crop species worldwide. NAC transcription factor (TF) genes play important roles in the salt and drought stress responses of plants by activating or repressing target gene expression. However, little is known about NAC genes in peanut. RESULTS We performed a genome-wide characterization of NAC genes from the diploid wild peanut species Arachis duranensis and Arachis ipaensis, which included analyses of chromosomal locations, gene structures, conserved motifs, expression patterns, and cis-acting elements within their promoter regions. In total, 81 and 79 NAC genes were identified from A. duranensis and A. ipaensis genomes. Phylogenetic analysis of peanut NACs along with their Arabidopsis and rice counterparts categorized these proteins into 18 distinct subgroups. Fifty-one orthologous gene pairs were identified, and 46 orthologues were found to be highly syntenic on the chromosomes of both A. duranensis and A. ipaensis. Comparative RNA sequencing (RNA-seq)-based analysis revealed that the expression of 43 NAC genes was up- or downregulated under salt stress and under drought stress. Among these genes, the expression of 17 genes in cultivated peanut (Arachis hypogaea) was up- or downregulated under both stresses. Moreover, quantitative reverse transcription PCR (RT-qPCR)-based analysis revealed that the expression of most of the randomly selected NAC genes tended to be consistent with the comparative RNA-seq results. CONCLUSION Our results facilitated the functional characterization of peanut NAC genes, and the genes involved in salt and drought stress responses identified in this study could be potential genes for peanut improvement.
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Affiliation(s)
- Cuiling Yuan
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Chunjuan Li
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Xiaodong Lu
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Xiaobo Zhao
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Caixia Yan
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Juan Wang
- Shandong Peanut Research Institute, Qingdao, 266100, China
| | - Quanxi Sun
- Shandong Peanut Research Institute, Qingdao, 266100, China.
| | - Shihua Shan
- Shandong Peanut Research Institute, Qingdao, 266100, China.
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Wang L, Ding X, Gao Y, Yang S. Genome-wide identification and characterization of GRAS genes in soybean (Glycine max). BMC PLANT BIOLOGY 2020; 20:415. [PMID: 32891114 PMCID: PMC7487615 DOI: 10.1186/s12870-020-02636-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/30/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND GRAS proteins are crucial transcription factors, which are plant-specific and participate in various plant biological processes. Thanks to the rapid progress of the whole genome sequencing technologies, the GRAS gene families in different plants have been broadly explored and studied. However, comprehensive research on the soybean (Glycine max) GRAS gene family is relatively lagging. RESULTS In this study, 117 Glycine max GRAS genes (GmGRAS) were identified. Further phylogenetic analyses showed that the GmGRAS genes could be categorized into nine gene subfamilies: DELLA, HAM, LAS, LISCL, PAT1, SCL3, SCL4/7, SCR and SHR. Gene structure analyses turned out that the GmGRAS genes lacked introns and were relatively conserved. Conserved domains and motif patterns of the GmGRAS members in the same subfamily or clade exhibited similarities. Notably, the expansion of the GmGRAS gene family was driven both by gene tandem and segmental duplication events. Whereas, segmental duplications took the major role in generating new GmGRAS genes. Moreover, the synteny and evolutionary constraints analyses of the GRAS proteins among soybean and distinct species (two monocots and four dicots) provided more detailed evidence for GmGRAS gene evolution. Cis-element analyses indicated that the GmGRAS genes may be responsive to diverse environmental stresses and regulate distinct biological processes. Besides, the expression patterns of the GmGRAS genes were varied in various tissues, during saline and dehydration stresses and during seed germination processes. CONCLUSIONS We conducted a systematic investigation of the GRAS genes in soybean, which may be valuable in paving the way for future GmGRAS gene studies and soybean breeding.
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Affiliation(s)
- Liang Wang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xianlong Ding
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yingqi Gao
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shouping Yang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
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Ma F, Huang J, Yang J, Zhou J, Sun Q, Sun J. Identification, expression and miRNA targeting of auxin response factor genes related to phyllody in the witches’ broom disease of jujube. Gene 2020; 746:144656. [DOI: 10.1016/j.gene.2020.144656] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 04/04/2020] [Accepted: 04/06/2020] [Indexed: 11/16/2022]
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Ribba T, Garrido-Vargas F, O'Brien JA. Auxin-mediated responses under salt stress: from developmental regulation to biotechnological applications. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3843-3853. [PMID: 32433743 DOI: 10.1093/jxb/eraa241] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 05/18/2020] [Indexed: 05/10/2023]
Abstract
As sessile organisms, plants are exposed to multiple abiotic stresses commonly found in nature. To survive, plants have developed complex responses that involve genetic, epigenetic, cellular, and morphological modifications. Among different environmental cues, salt stress has emerged as a critical problem contributing to yield losses and marked reductions in crop production. Moreover, as the climate changes, it is expected that salt stress will have a significant impact on crop production in the agroindustry. On a mechanistic level, salt stress is known to be regulated by the crosstalk of many signaling molecules such as phytohormones, with auxin having been described as a key mediator of the process. Auxin plays an important role in plant developmental responses and stress, modulating a complex balance of biosynthesis, transport, and signaling that among other things, finely tune physiological changes in plant architecture and Na+ accumulation. In this review, we describe current knowledge on auxin's role in modulating the salt stress response. We also discuss recent and potential biotechnological approaches to tackling salt stress.
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Affiliation(s)
- Tomas Ribba
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas and Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal. Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O'Higgins, Santiago, Chile
| | - Fernanda Garrido-Vargas
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas and Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal. Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O'Higgins, Santiago, Chile
| | - José Antonio O'Brien
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas and Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal. Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O'Higgins, Santiago, Chile
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Down Regulation and Loss of Auxin Response Factor 4 Function Using CRISPR/Cas9 Alters Plant Growth, Stomatal Function and Improves Tomato Tolerance to Salinity and Osmotic Stress. Genes (Basel) 2020; 11:genes11030272. [PMID: 32138192 PMCID: PMC7140898 DOI: 10.3390/genes11030272] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/23/2020] [Accepted: 02/28/2020] [Indexed: 12/25/2022] Open
Abstract
Auxin controls multiple aspects of plant growth and development. However, its role in stress responses remains poorly understood. Auxin acts on the transcriptional regulation of target genes, mainly through Auxin Response Factors (ARF). This study focuses on the involvement of SlARF4 in tomato tolerance to salinity and osmotic stress. Using a reverse genetic approach, we found that the antisense down-regulation of SlARF4 promotes root development and density, increases soluble sugars content and maintains chlorophyll content at high levels under stress conditions. Furthermore, ARF4-as displayed higher tolerance to salt and osmotic stress through reduced stomatal conductance coupled with increased leaf relative water content and Abscisic acid (ABA) content under normal and stressful conditions. This increase in ABA content was correlated with the activation of ABA biosynthesis genes and the repression of ABA catabolism genes. Cu/ZnSOD and mdhar genes were up-regulated in ARF4-as plants which can result in a better tolerance to salt and osmotic stress. A CRISPR/Cas9 induced SlARF4 mutant showed similar growth and stomatal responses as ARF4-as plants, which suggest that arf4-cr can tolerate salt and osmotic stresses. Our data support the involvement of ARF4 as a key factor in tomato tolerance to salt and osmotic stresses and confirm the use of CRISPR technology as an efficient tool for functional reverse genetics studies.
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Li H, Zhang X, Tong B, Wang Y, Yang C. Expression analysis of the BpARF genes in Betula platyphylla under drought stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 148:273-281. [PMID: 31986481 DOI: 10.1016/j.plaphy.2020.01.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/04/2020] [Accepted: 01/18/2020] [Indexed: 06/10/2023]
Abstract
Auxin response factors (ARFs) play an important role in modulating plant growth and development processes by regulating the expression of auxin-responsive genes. However, the modes of action of ARFs in birch (Betula platyphylla) remain largely unknown. In this study, fifteen ARF genes were identified in the birch (B. platyphylla) genome. Bioinformatics analysis revealed that the 15 BpARF genes were unevenly distributed on 7 chromosomes. The 15 BpARF proteins clustered into 6 groups, and all of them contained ARF and B3 motifs. The cis-acting elements present within the promoters of the BpARF genes were mostly related to stress resistance. Expression analysis revealed that most of the BpARF genes were significantly upregulated or downregulated in response to drought treatment in at least one organ. In particular, the expression of BpARF1 was significantly induced by drought stress. The function of BpARF1 was further studied via a transient transformation system. Under drought stress conditions, compared with vector control plants, BpARF1 RNA interference (RNAi)-inhibited plants presented reduced reactive oxygen species (ROS) accumulation, enhanced peroxide (POD) and superoxide dismutase (SOD) activities, increased ascorbic acid (AsA) and proline contents, and reduced electrolyte leakage and water loss rates. Conversely, BpARF1 overexpression plants displayed the opposite physiological changes. These results suggest that the silencing of BpARF1 can improve the drought tolerance of B. platyphylla.
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Affiliation(s)
- Hongyan Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China; Forestry Science Institute of Heilongjiang Province, 134 Haping Road, Harbin, 150081, China
| | - Xin Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Botong Tong
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China
| | - Yucheng Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
| | - Chuanping Yang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.
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Velada I, Cardoso H, Porfirio S, Peixe A. Expression Profile of PIN-Formed Auxin Efflux Carrier Genes during IBA-Induced In Vitro Adventitious Rooting in Olea europaea L. PLANTS 2020; 9:plants9020185. [PMID: 32028698 PMCID: PMC7076448 DOI: 10.3390/plants9020185] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 01/28/2020] [Accepted: 02/02/2020] [Indexed: 12/24/2022]
Abstract
Exogenous auxins supplementation plays a central role in the formation of adventitious roots (AR) for several plant species. However, the molecular mechanisms underlying the process of adventitious rooting are still not completely understood and many plants with economic value, including several olive cultivars, exhibit a recalcitrant behavior towards cutting propagation, which limits its availability in plant nurseries. PIN-formed proteins are auxin efflux transporters that have been widely characterized in several plant species due to their involvement in many developmental processes including root formation. The present study profiled the expression of the OePIN1a-c, OePIN2b, OePIN3a-c, OePIN5a-c, OePIN6, and OePIN8 gene members during indole-3-butyric acid (IBA)-induced in vitro adventitious rooting using the olive cultivar ‘Galega vulgar’. Gene expression analysis by quantitative real time PCR (RT-qPCR) showed drastic downregulation of most transcripts, just a few hours after explant inoculation, in both nontreated and IBA-treated microcuttings, albeit gene downregulation was less pronounced in IBA-treated stems. In contrast, OePIN2b showed a distinct expression pattern being upregulated in both conditions, and OePIN5b was highly upregulated in IBA-induced stems. All transcripts, except OePIN8, showed different expression profiles between nontreated and IBA-treated explants throughout the rooting experiment. Additionally, high levels of reactive oxygen species (ROS) were observed soon after explant preparation, decreasing a few hours after inoculation. Altogether, the results suggest that wounding-related ROS production, associated with explant preparation for rooting, may have an impact on auxin transport and distribution via changes in OePIN gene expression. Moreover, the application of exogenous auxin may modulate auxin homeostasis through regulation of those genes, leading to auxin redistribution throughout the stem-base tissue, which may ultimately play an important role in AR formation.
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Affiliation(s)
- Isabel Velada
- MED—Mediterranean Institute for Agriculture, Environment and Development, Instituto de Investigação e Formação Avançada, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
- Correspondence: (I.V.); (A.P.)
| | - Hélia Cardoso
- MED—Mediterranean Institute for Agriculture, Environment and Development, Instituto de Investigação e Formação Avançada, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
| | - Sara Porfirio
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Augusto Peixe
- MED—Mediterranean Institute for Agriculture, Environment and Development & Departamento de Fitotecnia, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
- Correspondence: (I.V.); (A.P.)
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Xu L, Wang D, Liu S, Fang Z, Su S, Guo C, Zhao C, Tang Y. Comprehensive Atlas of Wheat ( Triticum aestivum L.) AUXIN RESPONSE FACTOR Expression During Male Reproductive Development and Abiotic Stress. FRONTIERS IN PLANT SCIENCE 2020; 11:586144. [PMID: 33101350 PMCID: PMC7554351 DOI: 10.3389/fpls.2020.586144] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/14/2020] [Indexed: 05/13/2023]
Abstract
AUXIN RESPONSE FACTOR (ARF) proteins regulate a wide range of signaling pathways, from general plant growth to abiotic stress responses. Here, we performed a genome-wide survey in wheat (Triticum aestivum) and identified 69 TaARF members that formed 24 homoeologous groups. Phylogenetic analysis clustered TaARF genes into three clades, similar to ARF genes in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). Structural characterization suggested that ARF gene structure and domain composition are well conserved between plant species. Expression profiling revealed diverse patterns of TaARF transcript levels across a range of developmental stages, tissues, and abiotic stresses. A number of TaARF genes shared similar expression patterns and were preferentially expressed in anthers. Moreover, our systematic analysis identified three anther-specific TaARF genes (TaARF8, TaARF9, and TaARF21) whose expression was significantly altered by low temperature in thermosensitive genic male-sterile (TGMS) wheat; these TaARF genes are candidates to participate in the cold-induced male sterility pathway, and offer potential applications in TGMS wheat breeding and hybrid seed production. Moreover, we identified putative functions for a set of TaARFs involved in responses to abscisic acid and abiotic stress. Overall, this study characterized the wheat ARF gene family and generated several hypotheses for future investigation of ARF function during anther development and abiotic stress.
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Affiliation(s)
- Lei Xu
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Dezhou Wang
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Shan Liu
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Zhaofeng Fang
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Shichao Su
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Chunman Guo
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Changping Zhao
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- *Correspondence: Changping Zhao, ; Yimiao Tang,
| | - Yimiao Tang
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Beijing Engineering Research Center for Hybrid, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- *Correspondence: Changping Zhao, ; Yimiao Tang,
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