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Sunani SK, Koti PS, Sunitha NC, Choudhary M, Jeevan B, Anilkumar C, Raghu S, Gadratagi BG, Bag MK, Acharya LK, Ram D, Bashyal BM, Das Mohapatra S. Ustilaginoidea virens, an emerging pathogen of rice: the dynamic interplay between the pathogen virulence strategies and host defense. PLANTA 2024; 260:92. [PMID: 39261328 DOI: 10.1007/s00425-024-04523-x] [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: 06/09/2024] [Accepted: 08/30/2024] [Indexed: 09/13/2024]
Abstract
MAIN CONCLUSION The Ustilaginoidea virens -rice pathosystem has been used as a model for flower-infecting fungal pathogens. The molecular biology of the interactions between U. virens and rice, with an emphasis on the attempt to get a deeper comprehension of the false smut fungus's genomes, proteome, host range, and pathogen biology, has been investigated. Meta-QTL analysis was performed to identify potential QTL hotspots for use in marker-assisted breeding. The Rice False Smut (RFS) caused by the fungus Ustilaginoidea virens currently threatens rice cultivators across the globe. RFS infects rice panicles, causing a significant reduction in grain yield. U. virens can also parasitize other hosts though they play only a minor role in its life cycle. Furthermore, because it produces mycotoxins in edible rice grains, it puts both humans and animals at risk of health problems. Although fungicides are used to control the disease, some fungicides have enabled the pathogen to develop resistance, making its management challenging. Several QTLs have been reported but stable gene(s) that confer RFS resistance have not been discovered yet. This review offers a comprehensive overview of the pathogen, its virulence mechanisms, the genome and proteome of U. virens, and its molecular interactions with rice. In addition, information has been compiled on reported resistance QTLs, facilitating the development of a consensus genetic map using meta-QTL analysis for identifying potential QTL hotspots. Finally, this review highlights current developments and trends in U. virens-rice pathosystem research while identifying opportunities for future investigations.
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Affiliation(s)
- Sunil Kumar Sunani
- Department of Plant Pathology, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India
- ICAR-Indian Institute of Pulse Research (RS), Bhubaneswar, Odisha, India
| | - Prasanna S Koti
- University of Agricultural Sciences, GKVK, Bangalore, Karnataka, India
| | - N C Sunitha
- ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - Manoj Choudhary
- Plant Pathology Department, University of Florida, Gainesville, FL, USA
- ICAR-National Centre for Integrated Pest Management, New Delhi, India
| | - B Jeevan
- Department of Plant Pathology, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India.
- ICAR-National Rice Research Institute, Cuttack, Odisha, India.
| | - C Anilkumar
- ICAR-National Rice Research Institute, Cuttack, Odisha, India.
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, USA.
| | - S Raghu
- ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | | | - Manas Kumar Bag
- ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | | | - Dama Ram
- Department of Plant Pathology, Agriculture University, Jodhpur, Rajasthan, India
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Liao B, Liang P, Tong L, Lu L, Lu Y, Zheng R, Zheng X, Chen J, Hao Z. The Role of Liriodendron Dof Gene Family in Abiotic Stress Response. PLANTS (BASEL, SWITZERLAND) 2024; 13:2009. [PMID: 39065535 PMCID: PMC11281171 DOI: 10.3390/plants13142009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024]
Abstract
The DOF (DNA-binding with one finger) transcription factors are exclusive to plants and play crucial roles in plant growth, development, and environmental adaptation. Although extensive research has been conducted on the Dof gene family in Arabidopsis, maize, and Solanum, investigations concerning the role of this gene family in Liriodendron remain unreported, leaving its biological function largely unknown. In this study, we performed a comprehensive genome-wide identification of the Dof gene family based on the Liriodendron genome, resulting in the discovery of a total of 17 LcDof gene members. Based on the results of phylogenetic analysis, the 17 LcDof proteins were classified into eight subfamilies. The motif analysis revealed the diverse nature of motifs within the D1 subfamily, which includes a distinct type of Dof transcription factor known as CDF (Cycling Dof Factor). We further characterized the chromosomal distribution, gene structure, conserved protein motifs, and cis-elements in the promoter regions. Additionally, utilizing transcriptome data from Liriodendron hybrids and conducting RT-qPCR experiments, we investigated the expression patterns of LhDofs under various abiotic stresses such as drought, cold, and heat stress. Notably, we found that several LhDofs, particularly LhDof4 and LhDof6, were significantly upregulated in response to abiotic stress. Furthermore, we cloned LhDof4 and LhDof6 genes and found that its encoding protein was mainly located in the nucleus by transient transformation in Liriodendron hybrids protoplast. Subsequently, we used LhDof6-overexpressing Liriodendron hybrid seedlings. We found that overexpression of LhDof6 enhanced the cold tolerance of the plants, increasing their survival rate at -20 °C. This result was further validated by changes in physiological indicators.
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Affiliation(s)
- Bojun Liao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (B.L.); (P.L.); (L.T.); (L.L.); (Y.L.)
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Pengxiang Liang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (B.L.); (P.L.); (L.T.); (L.L.); (Y.L.)
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Lu Tong
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (B.L.); (P.L.); (L.T.); (L.L.); (Y.L.)
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Lu Lu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (B.L.); (P.L.); (L.T.); (L.L.); (Y.L.)
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Ye Lu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (B.L.); (P.L.); (L.T.); (L.L.); (Y.L.)
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Renhua Zheng
- Fujian Academy of Forestry, Fuzhou 350012, China; (R.Z.); (X.Z.)
- National Germplasm Bank of Chinese Fir at Fujian Yangkou Forest Farm, Shunchang, Nanping 353211, China
| | - Xueyan Zheng
- Fujian Academy of Forestry, Fuzhou 350012, China; (R.Z.); (X.Z.)
- National Germplasm Bank of Chinese Fir at Fujian Yangkou Forest Farm, Shunchang, Nanping 353211, China
| | - Jinhui Chen
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (B.L.); (P.L.); (L.T.); (L.L.); (Y.L.)
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
| | - Zhaodong Hao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (B.L.); (P.L.); (L.T.); (L.L.); (Y.L.)
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing 210037, China
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He X, Zhang MM, Huang Y, Yu J, Zhao X, Zheng Q, Liu ZJ, Lan S. Genome-Based Identification of the Dof Gene Family in Three Cymbidium Species and Their Responses to Heat Stress in Cymbidium goeringii. Int J Mol Sci 2024; 25:7662. [PMID: 39062906 PMCID: PMC11277557 DOI: 10.3390/ijms25147662] [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: 06/21/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
As an important genus in Orchidaceae, Cymbidium has rich ecological diversity and significant economic value. DNA binding with one zinc finger (Dof) proteins are pivotal plant-specific transcription factors that play crucial roles in the growth, development, and stress response of plants. Although the Dof genes have been identified and functionally analyzed in numerous plants, exploration in Orchidaceae remains limited. We conducted a thorough analysis of the Dof gene family in Cymbidium goeringii, C. ensifolium, and C. sinensis. In total, 91 Dof genes (27 CgDofs, 34 CeDofs, 30 CsDofs) were identified, and Dof genes were divided into five groups (I-V) based on phylogenetic analysis. All Dof proteins have motif 1 and motif 2 conserved domains and over half of the genes contained introns. Chromosomal localization and collinearity analysis of Dof genes revealed their evolutionary relationships and potential gene duplication events. Analysis of cis-elements in CgDofs, CeDofs, and CsDofs promoters showed that light-responsive cis-elements were the most common, followed by hormone-responsive elements, plant growth-related elements, and abiotic stress response elements. Dof proteins in three Cymbidium species primarily exhibit a random coil structure, while homology modeling exhibited significant similarity. In addition, RT-qPCR analysis showed that the expression levels of nine CgDofs changed greatly under heat stress. CgDof03, CgDof22, CgDof27, CgDof08, and CgDof23 showed varying degrees of upregulation. Most upregulated genes under heat stress belong to group I, indicating that the Dof genes in group I have great potential for high-temperature resistance. In conclusion, our study systematically demonstrated the molecular characteristics of Dof genes in different Cymbidium species, preliminarily revealed the patterns of heat stress, and provided a reference for further exploration of stress breeding in orchids.
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Affiliation(s)
- Xin He
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (M.-M.Z.); (J.Y.); (X.Z.)
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (Q.Z.)
| | - Meng-Meng Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (M.-M.Z.); (J.Y.); (X.Z.)
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (Q.Z.)
| | - Ye Huang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (Q.Z.)
| | - Jiali Yu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (M.-M.Z.); (J.Y.); (X.Z.)
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (Q.Z.)
| | - Xuewei Zhao
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (M.-M.Z.); (J.Y.); (X.Z.)
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (Q.Z.)
| | - Qinyao Zheng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (Q.Z.)
| | - Zhong-Jian Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (M.-M.Z.); (J.Y.); (X.Z.)
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (Q.Z.)
| | - Siren Lan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (M.-M.Z.); (J.Y.); (X.Z.)
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.H.); (Q.Z.)
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Song H, Ji X, Wang M, Li J, Wang X, Meng L, Wei P, Xu H, Niu T, Liu A. Genome-wide identification and expression analysis of the Dof gene family reveals their involvement in hormone response and abiotic stresses in sunflower (Helianthus annuus L.). Gene 2024; 910:148336. [PMID: 38447680 DOI: 10.1016/j.gene.2024.148336] [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: 11/27/2023] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/08/2024]
Abstract
DNA binding with one finger (Dof), plant-specific zinc finger transcription factors, can participate in various physiological and biochemical processes during the life of plants. As one of the most important oil crops in the world, sunflower (Helianthus annuus L.) has significant economic and ornamental value. However, a systematic analysis of H. annuus Dof (HaDof) members and their functions has not been extensively conducted. In this study, we identified 50 HaDof genes that are unevenly distributed on 17 chromosomes of sunflower. We present a comprehensive overview of the HaDof genes, including their chromosome locations, phylogenetic analysis, and expression profile characterization. Phylogenetic analysis classified the 366 Dof members identified from 11 species into four groups (further subdivided into nine subfamilies). Segmental duplications are predominantly contributed to the expansion of sunflower Dof genes, and all segmental duplicate gene pairs are under purifying selection due to strong evolutionary constraints. Furthermore, we observed differential expression patterns for HaDof genes in normal tissues as well as under hormone treatment or abiotic stress conditions by analyzing RNA-seq data from previous studies and RT-qPCR data in our current study. The expression of HaDof04 and HaDof43 were not detected in any samples, which implied that they may be gradually undergoing pseudogenization process. Some HaDof genes, such as HaDof25 and HaDof30, showed responsiveness to exogenous plant hormones, such as kinetin, brassinosteroid, auxin or strigolactone, while others like HaDof15 and HaDof35 may participate in abiotic stress resistance of sunflower seedling. Our study represents the initial step towards understanding the phylogeny and expression characterization of sunflower Dof family genes, which may provide valuable reference information for functional studies on hormone response, abiotic stress resistance, and molecular breeding in sunflower and other species.
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Affiliation(s)
- Huifang Song
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Xuchao Ji
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Mingyang Wang
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China
| | - Juan Li
- School of Life Science, Shanxi Normal University, Taiyuan 030031, China
| | - Xi Wang
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Liying Meng
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Peipei Wei
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Haiyan Xu
- Department of Life Sciences, Changzhi University, Changzhi 046011, China
| | - Tianzeng Niu
- Department of Life Sciences, Changzhi University, Changzhi 046011, China.
| | - Ake Liu
- Department of Life Sciences, Changzhi University, Changzhi 046011, China.
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Cao L, Ye F, Fahim AM, Ma C, Pang Y, Zhang X, Zhang Q, Lu X. Transcription factor ZmDof22 enhances drought tolerance by regulating stomatal movement and antioxidant enzymes activities in maize (Zea mays L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:132. [PMID: 38750241 DOI: 10.1007/s00122-024-04625-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 04/14/2024] [Indexed: 06/09/2024]
Abstract
KEY MESSAGE The Dof22 gene encoding a deoxyribonucleic acid binding with one finger in maize, which is associated with its drought tolerance. The identification of drought stress regulatory genes is essential for the genetic improvement of maize yield. Deoxyribonucleic acid binding with one finger (Dof), a plant-specific transcription factor family, is involved in signal transduction, morphogenesis, and environmental stress responses. In present study, by weighted correlation network analysis (WGCNA) and gene co-expression network analysis, 15 putative Dof genes were identified from maize that respond to drought and rewatering. A real-time fluorescence quantitative PCR showed that these 15 genes were strongly induced by drought and ABA treatment, and among them ZmDof22 was highly induced by drought and ABA treatment. Its expression level increased by nearly 200 times after drought stress and more than 50 times after ABA treatment. After the normal conditions were restored, the expression levels were nearly 100 times and 40 times of those before treatment, respectively. The Gal4-LexA/UAS system and transcriptional activation analysis indicate that ZmDof22 is a transcriptional activator regulating drought tolerance and recovery ability in maize. Further, overexpressed transgenic and mutant plants of ZmDof22 by CRISPR/Cas9, indicates that the ZmDof22, improves maize drought tolerance by promoting stomatal closure, reduces water loss, and enhances antioxidant enzyme activity by participating in the ABA pathways. Taken together, our findings laid a foundation for further functional studies of the ZmDof gene family and provided insights into the role of the ZmDof22 regulatory network in controlling drought tolerance and recovery ability of maize.
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Affiliation(s)
- Liru Cao
- Grain Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
- The Shennong Laboratory, Zhengzhou, 450002, Henan, China
| | - Feiyu Ye
- Grain Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Abbas Muhammad Fahim
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, Gansu, China
| | - Chenchen Ma
- Grain Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Yunyun Pang
- Grain Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Xin Zhang
- Grain Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Qianjin Zhang
- Grain Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China
| | - Xiaomin Lu
- Grain Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, Henan, China.
- The Shennong Laboratory, Zhengzhou, 450002, Henan, China.
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Li P, Fang T, Chong X, Chen J, Yue J, Wang Z. CmDOF18 positively regulates salinity tolerance in Chrysanthemum morifolium by activating the oxidoreductase system. BMC PLANT BIOLOGY 2024; 24:232. [PMID: 38561659 PMCID: PMC10985857 DOI: 10.1186/s12870-024-04914-y] [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: 12/26/2023] [Accepted: 03/15/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND Chrysanthemum, one of the four major cut flowers all over the world, is very sensitive to salinity during cultivation. DNA binding with one finger (DOF) transcription factors play important roles in biological processes in plants. The response mechanism of CmDOF18 from chrysanthemum to salt stress remains unclear. RESULTS In this study, CmDOF18 was cloned from Chrysanthemum morifolium, and its expression was induced by salinity stress. The gene encodes a 291-amino acid protein with a typical DOF domain. CmDOF18 was localized to the nucleus in onion epidermal cells and showed transcriptional activation in yeast. CmDOF18 transgenic plants were generated to identify the role of this gene in resistance to salinity treatment. Chrysanthemum plants overexpressing CmDOF18 were more resistant to salinity stress than wild-type plants. Under salinity stress, the malondialdehyde content and leaf electrolyte conductivity in CmDOF18-overexpressing transgenic plants were lower than those in wild-type plants, while the proline content, chlorophyll content, superoxide dismutase activity and peroxidase activity were higher than those in wild-type plants. The opposite findings were observed in gene-silenced plants compared with wild-type plants. The gene expression levels of oxidoreductase increased in CmDOF18-overexpressing transgenic plants but decreased in CmDOF18-SRDX gene-silenced transgenic plants. CONCLUSION In summary, we analyzed the function of CmDOF18 from chrysanthemum, which may regulate salinity stress in plants, possibly due to its role in the regulation of oxidoreductase.
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Affiliation(s)
- Peiling Li
- College of Horticulture, Xinyang Agriculture and Forestry University, Xinyang, 464000, China
| | - Tingting Fang
- College of Horticulture, Xinyang Agriculture and Forestry University, Xinyang, 464000, China
| | - Xinran Chong
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden Mem. Sun Yat-Sen, Nanjing, 210000, China
| | - Juanjuan Chen
- College of Horticulture, Xinyang Agriculture and Forestry University, Xinyang, 464000, China
| | - Jianhua Yue
- College of Horticulture, Xinyang Agriculture and Forestry University, Xinyang, 464000, China
| | - Zhiyong Wang
- College of Horticulture, Xinyang Agriculture and Forestry University, Xinyang, 464000, China.
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden Mem. Sun Yat-Sen, Nanjing, 210000, China.
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Kevei Z, Larriba E, Romero-Bosquet MD, Nicolás-Albujer M, Kurowski TJ, Mohareb F, Rickett D, Pérez-Pérez JM, Thompson AJ. Genes involved in auxin biosynthesis, transport and signalling underlie the extreme adventitious root phenotype of the tomato aer mutant. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:76. [PMID: 38459215 PMCID: PMC10923741 DOI: 10.1007/s00122-024-04570-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 01/30/2024] [Indexed: 03/10/2024]
Abstract
The use of tomato rootstocks has helped to alleviate the soaring abiotic stresses provoked by the adverse effects of climate change. Lateral and adventitious roots can improve topsoil exploration and nutrient uptake, shoot biomass and resulting overall yield. It is essential to understand the genetic basis of root structure development and how lateral and adventitious roots are produced. Existing mutant lines with specific root phenotypes are an excellent resource to analyse and comprehend the molecular basis of root developmental traits. The tomato aerial roots (aer) mutant exhibits an extreme adventitious rooting phenotype on the primary stem. It is known that this phenotype is associated with restricted polar auxin transport from the juvenile to the more mature stem, but prior to this study, the genetic loci responsible for the aer phenotype were unknown. We used genomic approaches to define the polygenic nature of the aer phenotype and provide evidence that increased expression of specific auxin biosynthesis, transport and signalling genes in different loci causes the initiation of adventitious root primordia in tomato stems. Our results allow the selection of different levels of adventitious rooting using molecular markers, potentially contributing to rootstock breeding strategies in grafted vegetable crops, especially in tomato. In crops vegetatively propagated as cuttings, such as fruit trees and cane fruits, orthologous genes may be useful for the selection of cultivars more amenable to propagation.
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Affiliation(s)
- Zoltan Kevei
- Centre for Soil, AgriFood and Biosciences, Cranfield University, College Road, Bedfordshire, MK43 0AL, UK.
| | - Eduardo Larriba
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202, Elche, Spain
| | | | | | - Tomasz J Kurowski
- Centre for Soil, AgriFood and Biosciences, Cranfield University, College Road, Bedfordshire, MK43 0AL, UK
| | - Fady Mohareb
- Centre for Soil, AgriFood and Biosciences, Cranfield University, College Road, Bedfordshire, MK43 0AL, UK
| | - Daniel Rickett
- Syngenta Crop Protection, Jealott's Hill International Research Centre, Bracknell Berkshire, RG42 6EY, UK
| | | | - Andrew J Thompson
- Centre for Soil, AgriFood and Biosciences, Cranfield University, College Road, Bedfordshire, MK43 0AL, UK
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Kaur H, Manchanda P, Sidhu GS, Chhuneja P. Genome-wide identification and characterization of flowering genes in Citrus sinensis (L.) Osbeck: a comparison among C. Medica L., C. Reticulata Blanco, C. Grandis (L.) Osbeck and C. Clementina. BMC Genom Data 2024; 25:20. [PMID: 38378481 PMCID: PMC10880302 DOI: 10.1186/s12863-024-01201-5] [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: 03/02/2023] [Accepted: 01/30/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Flowering plays an important role in completing the reproductive cycle of plants and obtaining next generation of plants. In case of citrus, it may take more than a year to achieve progeny. Therefore, in order to fasten the breeding processes, the juvenility period needs to be reduced. The juvenility in plants is regulated by set of various flowering genes. The citrus fruit and leaves possess various medicinal properties and are subjected to intensive breeding programs to produce hybrids with improved quality traits. In order to break juvenility in Citrus, it is important to study the role of flowering genes. The present study involved identification of genes regulating flowering in Citrus sinensis L. Osbeck via homology based approach. The structural and functional characterization of these genes would help in targeting genome editing techniques to induce mutations in these genes for producing desirable results. RESULTS A total of 43 genes were identified which were located on all the 9 chromosomes of citrus. The in-silico analysis was performed to determine the genetic structure, conserved motifs, cis-regulatory elements (CREs) and phylogenetic relationship of the genes. A total of 10 CREs responsible for flowering were detected in 33 genes and 8 conserved motifs were identified in all the genes. The protein structure, protein-protein interaction network and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was performed to study the functioning of these genes which revealed the involvement of flowering proteins in circadian rhythm pathways. The gene ontology (GO) and gene function analysis was performed to functionally annotate the genes. The structure of the genes and proteins were also compared among other Citrus species to study the evolutionary relationship among them. The expression study revealed the expression of flowering genes in floral buds and ovaries. The qRT-PCR analysis revealed that the flowering genes were highly expressed in bud stage, fully grown flower and early stage of fruit development. CONCLUSIONS The findings suggested that the flowering genes were highly conserved in citrus species. The qRT-PCR analysis revealed the tissue specific expression of flowering genes (CsFT, CsCO, CsSOC, CsAP, CsSEP and CsLFY) which would help in easy detection and targeting of genes through various forward and reverse genetic approaches.
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Affiliation(s)
- Harleen Kaur
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141001, Punjab, India
| | - Pooja Manchanda
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141001, Punjab, India.
| | - Gurupkar S Sidhu
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141001, Punjab, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, 141001, Punjab, India
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Yang Y, Li X, Li C, Zhang H, Tuerxun Z, Hui F, Li J, Liu Z, Chen G, Cai D, Chen X, Li B. Isolation and Functional Characterization of a Constitutive Promoter in Upland Cotton ( Gossypium hirsutum L.). Int J Mol Sci 2024; 25:1917. [PMID: 38339199 PMCID: PMC10855717 DOI: 10.3390/ijms25031917] [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: 12/05/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/12/2024] Open
Abstract
Multiple cis-acting elements are present in promoter sequences that play critical regulatory roles in gene transcription and expression. In this study, we isolated the cotton FDH (Fiddlehead) gene promoter (pGhFDH) using a real-time reverse transcription-PCR (qRT-PCR) expression analysis and performed a cis-acting elements prediction analysis. The plant expression vector pGhFDH::GUS was constructed using the Gateway approach and was used for the genetic transformation of Arabidopsis and upland cotton plants to obtain transgenic lines. Histochemical staining and a β-glucuronidase (GUS) activity assay showed that the GUS protein was detected in the roots, stems, leaves, inflorescences, and pods of transgenic Arabidopsis thaliana lines. Notably, high GUS activity was observed in different tissues. In the transgenic lines, high GUS activity was detected in different tissues such as leaves, stalks, buds, petals, androecium, endosperm, and fibers, where the pGhFDH-driven GUS expression levels were 3-10-fold higher compared to those under the CaMV 35S promoter at 10-30 days post-anthesis (DPA) during fiber development. The results indicate that pGhFDH can be used as an endogenous constitutive promoter to drive the expression of target genes in various cotton tissues to facilitate functional genomic studies and accelerate cotton molecular breeding.
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Affiliation(s)
- Yang Yang
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
| | - Xiaorong Li
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
| | - Chenyu Li
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
- College of Agronomy, Xinjiang Agricultural University, Urumqi 830052, China
| | - Hui Zhang
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
| | - Zumuremu Tuerxun
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
| | - Fengjiao Hui
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China;
| | - Juan Li
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
| | - Zhigang Liu
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
| | - Guo Chen
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
| | - Darun Cai
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
| | - Xunji Chen
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
| | - Bo Li
- Xinjiang Key Laboratory of Crop Biotechnology, The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Institute of Nuclear and Biological Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (Y.Y.); (X.L.); (C.L.); (H.Z.); (Z.T.); (J.L.); (Z.L.); (G.C.); (D.C.)
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Han S, Han X, Qi C, Guo F, Yin J, Liu Y, Zhu Y. Genome-Wide Identification of DUF668 Gene Family and Expression Analysis under F. solani, Chilling, and Waterlogging Stresses in Zingiber officinale. Int J Mol Sci 2024; 25:929. [PMID: 38256002 PMCID: PMC10815606 DOI: 10.3390/ijms25020929] [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: 12/10/2023] [Revised: 01/06/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
The domains of unknown function (DUF) superfamilies contain proteins with conserved amino acid sequences without known functions. Among them, DUF668 was indicated widely involving the stress response of plants. However, understanding ZoDUF668 is still lacking. Here, 12 ZoDUF668 genes were identified in ginger by the bioinformatics method and unevenly distributed on six chromosomes. Conserved domain analysis showed that members of the same subfamily had similar conserved motifs and gene structures. The promoter region of ZoDUF668s contained the light, plant hormone and stress-responsive elements. The prediction of miRNA targeting relationship showed that nine ginger miRNAs targeted four ZoDUF668 genes through cleavage. The expression patterns of 12 ZoDUF668 genes under biotic and abiotic stress were analyzed using RT-qPCR. The results showed that the expression of seven ZoDUF668 genes was significantly downregulated under Fusarium solani infection, six ZoDUF668 genes were upregulated under cold stress, and five ZoDUF668 genes were upregulated under waterlogging stress. These results indicate that the ZoDUF668 gene has different expression patterns under different stress conditions. This study provides excellent candidate genes and provides a reference for stress-resistance research in ginger.
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Affiliation(s)
- Shuo Han
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Key Laboratory of Vegetable Ecological Cultivation on Highland, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China; (S.H.); (X.H.); (C.Q.)
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Co-Construction by Ministry and Province, College of Agriculture, Yangtze University, Jingzhou 434025, China; (Y.L.); (Y.Z.)
| | - Xiaowen Han
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Key Laboratory of Vegetable Ecological Cultivation on Highland, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China; (S.H.); (X.H.); (C.Q.)
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Co-Construction by Ministry and Province, College of Agriculture, Yangtze University, Jingzhou 434025, China; (Y.L.); (Y.Z.)
| | - Chuandong Qi
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Key Laboratory of Vegetable Ecological Cultivation on Highland, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China; (S.H.); (X.H.); (C.Q.)
| | - Fengling Guo
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Key Laboratory of Vegetable Ecological Cultivation on Highland, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China; (S.H.); (X.H.); (C.Q.)
| | - Junliang Yin
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Key Laboratory of Vegetable Ecological Cultivation on Highland, Ministry of Agriculture and Rural Affairs, Wuhan 430064, China; (S.H.); (X.H.); (C.Q.)
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Co-Construction by Ministry and Province, College of Agriculture, Yangtze University, Jingzhou 434025, China; (Y.L.); (Y.Z.)
| | - Yiqing Liu
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Co-Construction by Ministry and Province, College of Agriculture, Yangtze University, Jingzhou 434025, China; (Y.L.); (Y.Z.)
| | - Yongxing Zhu
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River, Co-Construction by Ministry and Province, College of Agriculture, Yangtze University, Jingzhou 434025, China; (Y.L.); (Y.Z.)
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Blanc-Mathieu R, Dumas R, Turchi L, Lucas J, Parcy F. Plant-TFClass: a structural classification for plant transcription factors. TRENDS IN PLANT SCIENCE 2024; 29:40-51. [PMID: 37482504 DOI: 10.1016/j.tplants.2023.06.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/25/2023]
Abstract
Transcription factors (TFs) bind DNA at specific sequences to regulate gene expression. This universal process is achieved via their DNA-binding domain (DBD). In mammals, the vast diversity of DBD structural conformations and the way in which they contact DNA has been used to organize TFs in the TFClass hierarchical classification. However, the numerous DBD types present in plants but absent from mammalian genomes were missing from this classification. We reviewed DBD 3D structures and models available for plant TFs to classify most of the 56 recognized plant TF types within the TFClass framework. This extended classification adds eight new classes and 37 new families corresponding to DBD structures absent in mammals. Plant-TFClass provides a unique resource for TF comparison across families and organisms.
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Affiliation(s)
- Romain Blanc-Mathieu
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France
| | - Renaud Dumas
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France
| | - Laura Turchi
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France
| | - Jérémy Lucas
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France
| | - François Parcy
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 Avenue des Martyrs, F-38054, Grenoble, France.
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12
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Liu W, Ren W, Liu X, He L, Qin C, Wang P, Kong L, Li Y, Liu Y, Ma W. Identification and characterization of Dof genes in Cerasus humilis. FRONTIERS IN PLANT SCIENCE 2023; 14:1152685. [PMID: 37077646 PMCID: PMC10106723 DOI: 10.3389/fpls.2023.1152685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 03/21/2023] [Indexed: 05/03/2023]
Abstract
Introduction Dof genes encode plant-specific transcription factors, which regulate various biological processes such as growth, development, and secondary metabolite accumulation. Methods We conducted whole-genome analysis of Chinese dwarf cherry (Cerasus humilis) to identify ChDof genes and characterize the structure, motif composition, cis-acting elements, chromosomal distribution, and collinearity of these genes as well as the physical and chemical properties, amino acid sequences, and phylogenetic evolution of the encoded proteins. Results The results revealed the presence of 25 ChDof genes in C. humilis genome. All 25 ChDof genes could be divided into eight groups, and the members of the same group had similar motif arrangement and intron-exon structure. Promoter analysis showed that cis-acting elements responsive to abscisic acid, low temperature stress, and light were dominant. Transcriptome data revealed that most ChDof genes exhibited tissue-specific expression. Then, we performed by qRT-PCR to analyze the expression patterns of all 25 ChDof genes in fruit during storage. The results indicated that these genes exhibited different expression patterns, suggesting that they played an important role in fruit storage. Discussion The results of this study provide a basis for further investigation of the biological function of Dof genes in C. humilis fruit.
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Affiliation(s)
- Weili Liu
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
- Experimental Teaching and Training Center, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Weichao Ren
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Xiubo Liu
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
- School of Jiamusi, Heilongjiang University of Chinese Medicine, Jiamusi, China
| | - Lianqing He
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Chen Qin
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Panpan Wang
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Lingyang Kong
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Yang Li
- Berry Resource Research Center, Yichun Branch of Heilongjiang Academy of Forestry, Yichun, China
| | - Yunwei Liu
- Berry Resource Research Center, Yichun Branch of Heilongjiang Academy of Forestry, Yichun, China
| | - Wei Ma
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
- Experimental Teaching and Training Center, Heilongjiang University of Chinese Medicine, Harbin, China
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13
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Zhang Q, Zhong S, Dong Q, Yang H, Yang H, Tan F, Chen C, Ren T, Shen J, Cao G, Luo P. Identification of Photoperiod- and Phytohormone-Responsive DNA-Binding One Zinc Finger (Dof) Transcription Factors in Akebia trifoliata via Genome-Wide Expression Analysis. Int J Mol Sci 2023; 24:ijms24054973. [PMID: 36902404 PMCID: PMC10002981 DOI: 10.3390/ijms24054973] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 02/22/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
As a kind of plant-specific transcription factor (TF), DNA-Binding One Zinc Finger (Dof) is widely involved in the response to environmental change, and as an evolutionarily important perennial plant species, Akebia trifoliata is ideal for studying environmental adaptation. In this study, a total of 41 AktDofs were identified in the A. trifoliata genome. First, the characteristics, including the length, exon number, and chromosomal distribution of the AktDofs and the isoelectric point (PI), amino acid number, molecular weight (MW), and conserved motifs of their putative proteins, were reported. Second, we found that all AktDofs evolutionarily underwent strong purifying selection, and many (33, 80.5%) of them were generated by whole-genome duplication (WGD). Third, we outlined their expression profiles by the use of available transcriptomic data and RT-qPCR analysis. Finally, we identified four candidate genes (AktDof21, AktDof20, AktDof36, and AktDof17) and three other candidate genes (AktDof26, AktDof16, and AktDof12) that respond to long day (LD) and darkness, respectively, and that are closely associated with phytohormone-regulating pathways. Overall, this research is the first to identify and characterize the AktDofs family and is very helpful for further research on A. trifoliata adaptation to environmental factors, especially photoperiod changes.
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Affiliation(s)
- Qiuyi Zhang
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Shengfu Zhong
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Qing Dong
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Hao Yang
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Huai Yang
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Feiquan Tan
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Chen Chen
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Tianheng Ren
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Jinliang Shen
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Guoxing Cao
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Peigao Luo
- Key Laboratory of Plant Genetics and Breeding, Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
- Correspondence:
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Carrillo L, Baroja-Fernández E, Renau-Morata B, Muñoz FJ, Canales J, Ciordia S, Yang L, Sánchez-López ÁM, Nebauer SG, Ceballos MG, Vicente-Carbajosa J, Molina RV, Pozueta-Romero J, Medina J. Ectopic expression of the AtCDF1 transcription factor in potato enhances tuber starch and amino acid contents and yield under open field conditions. FRONTIERS IN PLANT SCIENCE 2023; 14:1010669. [PMID: 36937996 PMCID: PMC10014720 DOI: 10.3389/fpls.2023.1010669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Cycling Dof transcription factors (CDFs) have been involved in different aspects of plant growth and development. In Arabidopsis and tomato, one member of this family (CDF1) has recently been associated with the regulation of primary metabolism and abiotic stress responses, but their roles in crop production under open field conditions remain unknown. METHODS In this study, we compared the growth, and tuber yield and composition of plants ectopically expressing the CDF1 gene from Arabidopsis under the control of the 35S promoter with wild-type (WT) potato plants cultured in growth chamber and open field conditions. RESULTS In growth chambers, the 35S::AtCDF1 plants showed a greater tuber yield than the WT by increasing the biomass partition for tuber development. Under field conditions, the ectopic expression of CDF1 also promoted the sink strength of the tubers, since 35S::AtCDF1 plants exhibited significant increases in tuber size and weight resulting in higher tuber yield. A metabolomic analysis revealed that tubers of 35S::AtCDF1 plants cultured under open field conditions accumulated higher levels of glucose, starch and amino acids than WT tubers. A comparative proteomic analysis of tubers of 35S::AtCDF1 and WT plants cultured under open field conditions revealed that these changes can be accounted for changes in the expression of proteins involved in energy production and different aspects of C and N metabolism. DISCUSSION The results from this study advance our collective understanding of the role of CDFs and are of great interest for the purposes of improving the yield and breeding of crop plants.
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Affiliation(s)
- Laura Carrillo
- Centro de Biotecnología y Genómica de Plantas (CBGP) UPM-INIA/CSIC, Campus de Montegancedo, Madrid, Spain
| | - Edurne Baroja-Fernández
- Instituto de Agrobiotecnología (IdAB), CSIC-Gobierno de Navarra, Mutiloabeti, Nafarroa, Spain
| | - Begoña Renau-Morata
- Departamento de Biología Vegetal, Universitat de València. Vicent Andrés Estellés, Burjassot, Spain
| | - Francisco J. Muñoz
- Instituto de Agrobiotecnología (IdAB), CSIC-Gobierno de Navarra, Mutiloabeti, Nafarroa, Spain
| | - Javier Canales
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- ANID–Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Sergio Ciordia
- Unidad Proteomica (CNB), Centro Nacional de Biotecnología (CNB-CSIC), Cantoblanco, Madrid, Spain
| | - Lu Yang
- Centro de Biotecnología y Genómica de Plantas (CBGP) UPM-INIA/CSIC, Campus de Montegancedo, Madrid, Spain
| | | | - Sergio G. Nebauer
- Departamento de Producción Vegetal, Universitat Politècnica de València., València, Spain
| | - Mar G. Ceballos
- Centro de Biotecnología y Genómica de Plantas (CBGP) UPM-INIA/CSIC, Campus de Montegancedo, Madrid, Spain
| | - Jesús Vicente-Carbajosa
- Centro de Biotecnología y Genómica de Plantas (CBGP) UPM-INIA/CSIC, Campus de Montegancedo, Madrid, Spain
| | - Rosa V. Molina
- Departamento de Producción Vegetal, Universitat Politècnica de València., València, Spain
| | - Javier Pozueta-Romero
- Institute for Mediterranean and Subtropical Horticulture “La Mayora” (IHSM), CSIC-UMA, Málaga, Spain
| | - Joaquín Medina
- Centro de Biotecnología y Genómica de Plantas (CBGP) UPM-INIA/CSIC, Campus de Montegancedo, Madrid, Spain
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Wei JT, Zhao SP, Zhang HY, Jin LG, Yu TF, Zheng L, Ma J, Chen J, Zhou YB, Chen M, Fu JD, Ma YZ, Xu ZS. GmDof41 regulated by the DREB1-type protein improves drought and salt tolerance by regulating the DREB2-type protein in soybean. Int J Biol Macromol 2023; 230:123255. [PMID: 36639088 DOI: 10.1016/j.ijbiomac.2023.123255] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 01/09/2023] [Indexed: 01/12/2023]
Abstract
Despite their essential and multiple roles in biological processes, the molecular mechanism of Dof transcription factors (TFs) for responding to abiotic stresses is rarely reported in plants. We identified a soybean Dof gene GmDof41 which was involved in the responses to drought, salt, and exogenous ABA stresses. Overexpression of GmDof41 in soybean transgenic hairy roots attenuated H2O2 accumulation and regulated proline homeostasis, resulting in the drought and salt tolerance. Yeast one-hybrid and electrophoretic mobility shift assay (EMSA) illustrated that GmDof41 was regulated by the DREB1-type protein GmDREB1B;1 that could improve drought and salt tolerance in plants. Further studies illustrated GmDof41 can directly bind to the promoter of GmDREB2A which encodes a DREB2-type protein and affects abiotic stress tolerance in plants. Collectively, our results suggested that GmDof41 positively regulated drought and salt tolerance by correlating with GmDREB1B;1 and GmDREB2A. This study provides an important basis for further exploring the abiotic stress-tolerance mechanism of Dof TFs in soybean.
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Affiliation(s)
- Ji-Tong Wei
- National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops/Key Laboratory of Quality Evaluation and Nutrition Health of Agro-Products, Ministry of Agriculture and Rural Affairs, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Shu-Ping Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops/Key Laboratory of Quality Evaluation and Nutrition Health of Agro-Products, Ministry of Agriculture and Rural Affairs, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Hui-Yuan Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops/Key Laboratory of Quality Evaluation and Nutrition Health of Agro-Products, Ministry of Agriculture and Rural Affairs, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Long-Guo Jin
- National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops/Key Laboratory of Quality Evaluation and Nutrition Health of Agro-Products, Ministry of Agriculture and Rural Affairs, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Tai-Fei Yu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops/Key Laboratory of Quality Evaluation and Nutrition Health of Agro-Products, Ministry of Agriculture and Rural Affairs, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Lei Zheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops/Key Laboratory of Quality Evaluation and Nutrition Health of Agro-Products, Ministry of Agriculture and Rural Affairs, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Jian Ma
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Jun Chen
- National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops/Key Laboratory of Quality Evaluation and Nutrition Health of Agro-Products, Ministry of Agriculture and Rural Affairs, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Yong-Bin Zhou
- National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops/Key Laboratory of Quality Evaluation and Nutrition Health of Agro-Products, Ministry of Agriculture and Rural Affairs, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Ming Chen
- National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops/Key Laboratory of Quality Evaluation and Nutrition Health of Agro-Products, Ministry of Agriculture and Rural Affairs, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Jin-Dong Fu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops/Key Laboratory of Quality Evaluation and Nutrition Health of Agro-Products, Ministry of Agriculture and Rural Affairs, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - You-Zhi Ma
- National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops/Key Laboratory of Quality Evaluation and Nutrition Health of Agro-Products, Ministry of Agriculture and Rural Affairs, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences/Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China
| | - Zhao-Shi Xu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops/Key Laboratory of Quality Evaluation and Nutrition Health of Agro-Products, Ministry of Agriculture and Rural Affairs, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; College of Agronomy, Jilin Agricultural University, Changchun 130118, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences/Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China.
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16
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Singh A, Karjagi C, Kaur S, Jeet G, Bhamare D, Gupta S, Kumar S, Das A, Gupta M, Chaudhary DP, Bhushan B, Jat BS, Kumar R, Dagla MC, Kumar M. Characterization of phi112, a Molecular Marker Tightly Linked to the o2 Gene of Maize, and Its Utilization in Multiplex PCR for Differentiating Normal Maize from QPM. Genes (Basel) 2023; 14:531. [PMID: 36833458 PMCID: PMC9957476 DOI: 10.3390/genes14020531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 02/25/2023] Open
Abstract
Quality Protein Maize (QPM) contains higher amounts of essential amino acids lysine and tryptophan. The QPM phenotype is based on regulating zein protein synthesis by opaque2 transcription factor. Many gene modifiers act to optimize the amino acid content and agronomic performance. An SSR marker, phi112, is present upstream of the opaque2 DNA gene. Its analysis has shown the presence of transcription factor activity. The functional associations of opaque2 have been determined. The putative transcription factor binding at phi112 marked DNA was identified through computational analysis. The present study is a step towards understanding the intricate network of molecular interactions that fine-tune the QPM genotype to influence maize protein quality. In addition, a multiplex PCR assay for differentiation of QPM from normal maize is shown, which can be used for Quality Control at various stages of the QPM value chain.
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Affiliation(s)
- Alla Singh
- ICAR-Indian Institute of Maize Research, P.A.U. Campus, Ludhiana 141004, India
| | - Chikkappa Karjagi
- ICAR-Indian Institute of Maize Research, Pusa Campus, Delhi 110012, India
| | - Sehgeet Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141004, India
| | - Gagan Jeet
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141004, India
| | - Deepak Bhamare
- ICAR-Indian Institute of Maize Research, P.A.U. Campus, Ludhiana 141004, India
| | - Sonu Gupta
- ICAR-Indian Institute of Maize Research, P.A.U. Campus, Ludhiana 141004, India
| | - Sunil Kumar
- ICAR-Indian Institute of Maize Research, P.A.U. Campus, Ludhiana 141004, India
| | - Abhijit Das
- ICAR-Indian Institute of Maize Research, P.A.U. Campus, Ludhiana 141004, India
| | - Mamta Gupta
- ICAR-Indian Institute of Maize Research, P.A.U. Campus, Ludhiana 141004, India
| | - D. P. Chaudhary
- ICAR-Indian Institute of Maize Research, P.A.U. Campus, Ludhiana 141004, India
| | - Bharat Bhushan
- ICAR-Indian Institute of Maize Research, P.A.U. Campus, Ludhiana 141004, India
| | - B. S. Jat
- ICAR-Indian Institute of Maize Research, P.A.U. Campus, Ludhiana 141004, India
| | - Ramesh Kumar
- ICAR-Indian Institute of Maize Research, P.A.U. Campus, Ludhiana 141004, India
| | - M. C. Dagla
- ICAR-Indian Institute of Maize Research, P.A.U. Campus, Ludhiana 141004, India
| | - Manoj Kumar
- ICAR—Central Institute for Research on Cotton Technology, Mumbai 400019, India
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Shi B, Haq IU, Fiaz S, Alharthi B, Xu ML, Wang JL, Hou WH, Feng XB. Genome-wide identification and expression analysis of the ZF-HD gene family in pea ( Pisum sativum L.). Front Genet 2023; 13:1089375. [PMID: 36685917 PMCID: PMC9849798 DOI: 10.3389/fgene.2022.1089375] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023] Open
Abstract
Pea is a conventional grain-feed-grass crop in Tibet and the only high-protein legume in the region; therefore, it plays an important role in Tibetan food and grass security. Zinc finger-homeodomain (ZF-HD) belongs to a family of homozygous heterotypic cassette genes, which play an important role in plant growth, development, and response to adversity stress. Using a bioinformatics approach, 18 PsZF-HD family members were identified. These genes were distributed across seven chromosomes and two scaffold fragments, and evolutionary analysis classified them into two subgroups, MIF and ZHD. The MIF subgroup was subdivided into three subclasses (PsMIFⅠ-III), and the ZHD subgroup was subdivided into five subclasses (ZHDⅠ-V). The PsZF-HD members were named PsMIF1-PsMIF4 and PsZHD1-PsZHD14. Twelve conserved motifs and four conserved domains were identified from PsZF-HD family, of which MIF subgroup only contained one domain, while ZHD subgroup contained two types of domains. In addition, there were significant differences in the three-dimensional structures of the protein members of the two subgroups. Most PsZF-HD genes had no introns (13/18), and only five genes had one intron. Forty-five cis-acting elements were predicted and screened, involving four categories: light response, stress, hormone, and growth and development. Transcriptome analysis of different tissues during pea growth and development showed that PsZHD11, 8, 13, 14 and MIF4 were not expressed or were individually expressed in low amounts in the tissues, while the other 13 PsZF-HDs genes were differentially expressed and showed tissue preference, as seen in aboveground reproductive organs, where PsZHD6, 2, 10 and MIF1 (except immature seeds) were highly expressed. In the aerial vegetative organs, PsZHD6, 1, and 10 were significantly overexpressed, while in the underground root system, PsMIF3 was specifically overexpressed. The leaf transcriptome under a low-nitrogen environment showed that the expression levels of 17 PsZF-HDs members were upregulated in shoot organs. The leaf transcriptome analysis under a low-temperature environment showed stress-induced upregulation of PsZHD10 and one genes and down-regulation of PsZHD6 gene. These results laid the foundation for deeper exploration of the functions of the PsZF-HD genes and also improved the reference for molecular breeding for stress resistance in peas.
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Affiliation(s)
- Bowen Shi
- Plant Sciences College, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, China
| | - Inzamam Ul Haq
- College of Plant Protection, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Badr Alharthi
- Department of Biology, University College of Al Khurmah, Taif University, Saudi Arabia
| | - Ming-Long Xu
- Plant Sciences College, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, China
| | - Jian-Lin Wang
- Plant Sciences College, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, China
| | - Wei-Hai Hou
- Plant Sciences College, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, China,*Correspondence: Wei-Hai Hou, ; Xi-Bo Feng,
| | - Xi-Bo Feng
- Plant Sciences College, Tibet Agricultural and Animal Husbandry University, Linzhi, Tibet, China,*Correspondence: Wei-Hai Hou, ; Xi-Bo Feng,
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18
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Tabassum J, Raza Q, Riaz A, Ahmad S, Rashid MAR, Javed MA, Ali Z, Kang F, Khan IA, Atif RM, Luo J. Exploration of the genomic atlas of Dof transcription factor family across genus Oryza provides novel insights on rice breeding in changing climate. FRONTIERS IN PLANT SCIENCE 2022; 13:1004359. [PMID: 36407584 PMCID: PMC9671800 DOI: 10.3389/fpls.2022.1004359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Abstract
DNA-binding with one finger (Dof) transcription factors have been demonstrated to regulate various stresses and developmental processes in plants. Their identification and comparative evolutionary analyses in cultivated and wild species of genus oryza were yet to be explored. In this context, we report a comprehensive genomics atlas of DNA-binding with one finger (Dof) family genes in 13 diverse rice genomes (five cultivated and eight rice wild-relatives) through a genome-wide scanning approach. A galore of 238 Dof genes, identified across the genus Oryza, are categorized into seven distinct subgroups by comparative phylogenetic analysis with the model plant Arabidopsis. Conserved motifs and gene structure analyses unveiled the prevalence of species- and subgroups-specific structural and functional diversity that is expediating with the evolutionary period. Our results indicate that Dof genes might have undergone strong purifying selections and segmental duplications to expand their gene family members in corresponding Oryza genomes. We speculate that miR2927 potentially targets the Dof domain to regulate gene expression under different climatic conditions, which are supported by in-silico and wet-lab experiments-based expression profiles. In a nutshell, we report several superior haplotypes significantly associated with early flowering in a treasure trove of 3,010 sequenced rice accessions and have validated these haplotypes with two years of field evaluation-based flowering data of a representative subpanel. Finally, we have provided some insights on the resolution of Oryza species phylogeny discordance and divergence highlighting the mosaic evolutionary history of the genus Oryza. Overall, this study reports a complete genomic landscape of the Dof family in cultivated and wild Oryza species that could greatly facilitate in fast-track development of early maturing and climate-resilient rice cultivars through modern haplotype-led breeding.
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Affiliation(s)
- Javaria Tabassum
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Qasim Raza
- Precision Agriculture and Analytics Lab, National Centre in Big Data and Cloud Computing, Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture Faisalabad, Faisalabad, Pakistan
- Molecular Breeding Laboratory, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Pakistan
| | - Awais Riaz
- Molecular Breeding Laboratory, Rice Research Institute, Kala Shah Kaku, Sheikhupura, Pakistan
- Department of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Shakeel Ahmad
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- National Center for Genome Editing for Crop Improvement and Human Health, Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | | | - Muhammad Arshad Javed
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Zulfiqar Ali
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Fengyu Kang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Iqrar Ahmad Khan
- Precision Agriculture and Analytics Lab, National Centre in Big Data and Cloud Computing, Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture Faisalabad, Faisalabad, Pakistan
- Institute of Horticultural Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Rana Muhammad Atif
- Precision Agriculture and Analytics Lab, National Centre in Big Data and Cloud Computing, Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture Faisalabad, Faisalabad, Pakistan
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Ju Luo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
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19
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Zhang F, Fan R, Yan L, Hu L, Su F, Yang D, Li J. Genome-wide identification of black pepper (Piper nigrum L.) Dof gene family and the differential gene screening in resistance to Phytophthora capsici. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01232-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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20
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Li T, Wang X, Elango D, Zhang W, Li M, Zhang F, Pan Q, Wu Y. Genome-wide identification, phylogenetic and expression pattern analysis of Dof transcription factors in blueberry ( Vaccinium corymbosum L.). PeerJ 2022; 10:e14087. [PMID: 36213501 PMCID: PMC9536302 DOI: 10.7717/peerj.14087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/29/2022] [Indexed: 01/20/2023] Open
Abstract
Background DNA binding with one finger (Dof) proteins are plant-specific transcription factor (TF) that plays a significant role in various biological processes such as plant growth and development, hormone regulation, and resistance to abiotic stress. The Dof genes have been identified and reported in multiple plants, but so far, the whole genome identification and analysis of Dof transcription factors in blueberry (Vaccinium corymbosum L.) have not been reported yet. Methods Using the Vaccinium genome, we have identified 51 VcDof genes in blueberry. We have further analyzed their physicochemical properties, phylogenetic relationships, gene structure, collinear analysis, selective evolutionary pressure, cis-acting promoter elements, and tissue and abiotic stress expression patterns. Results Fifty-one VcDof genes were divided into eight subfamilies, and the genes in each subfamily contained similar gene structure and motif ordering. A total of 24 pairs of colinear genes were screened; VcDof genes expanded mainly due to whole-genome duplication, which was subjected to strong purifying selection pressure during the evolution. The promoter of VcDof genes contains three types of cis-acting elements for plant growth and development, phytohormone and stress defense responsiveness. Expression profiles of VcDof genes in different tissues and fruit developmental stages of blueberry indicated that VcDof2 and VcDof45 might play a specific role in anthesis and fruit growth and development. Expression profiles of VcDof genes in different stress indicated that VcDof1, VcDof11, and VcDof15 were highly sensitive to abiotic stress. This study provides a theoretical basis for further clarifying the biological function of Dof genes in blueberry.
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Affiliation(s)
- Tianjie Li
- Tianjin Agricultural University, Tianjin, China
| | - Xiaoyu Wang
- Inner Mongolia Minzu University, Mongolia, China
| | | | | | - Min Li
- Inner Mongolia Minzu University, Mongolia, China
| | - Fan Zhang
- Tianjin Agricultural University, Tianjin, China
| | - Qi Pan
- Tianjin Agricultural University, Tianjin, China
| | - Ying Wu
- Tianjin Agricultural University, Tianjin, China
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21
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Gao H, Song W, Severing E, Vayssières A, Huettel B, Franzen R, Richter R, Chai J, Coupland G. PIF4 enhances DNA binding of CDF2 to co-regulate target gene expression and promote Arabidopsis hypocotyl cell elongation. NATURE PLANTS 2022; 8:1082-1093. [PMID: 35970973 PMCID: PMC9477738 DOI: 10.1038/s41477-022-01213-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 07/04/2022] [Indexed: 05/19/2023]
Abstract
How specificity is conferred within gene regulatory networks is an important problem in biology. The basic helix-loop-helix PHYTOCHROME-INTERACTING FACTORs (PIFs) and single zinc-finger CYCLING DOF FACTORs (CDFs) mediate growth responses of Arabidopsis to light and temperature. We show that these two classes of transcription factor (TF) act cooperatively. CDF2 and PIF4 are temporally and spatially co-expressed, they interact to form a protein complex and act in the same genetic pathway to promote hypocotyl cell elongation. Furthermore, PIF4 substantially strengthens genome-wide occupancy of CDF2 at a subset of its target genes. One of these, YUCCA8, encodes an auxin biosynthesis enzyme whose transcription is increased by PIF4 and CDF2 to contribute to hypocotyl elongation. The binding sites of PIF4 and CDF2 in YUCCA8 are closely spaced, and in vitro PIF4 enhances binding of CDF2. We propose that this occurs by direct protein interaction and because PIF4 binding alters DNA conformation. Thus, we define mechanisms by which PIF and CDF TFs cooperate to achieve regulatory specificity and promote cell elongation in response to light.
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Affiliation(s)
- He Gao
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Wen Song
- Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Edouard Severing
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Alice Vayssières
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Bruno Huettel
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Rainer Franzen
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - René Richter
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jijie Chai
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - George Coupland
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
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22
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PIF4 and CDF2 co-operate to regulate cell elongation in Arabidopsis thaliana. NATURE PLANTS 2022; 8:990-991. [PMID: 35986216 DOI: 10.1038/s41477-022-01220-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
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23
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Gandass N, Salvi P. Intrinsically disordered protein, DNA binding with one finger transcription factor ( OsDOF27) implicates thermotolerance in yeast and rice. FRONTIERS IN PLANT SCIENCE 2022; 13:956299. [PMID: 35968137 PMCID: PMC9372624 DOI: 10.3389/fpls.2022.956299] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Intrinsically disorder regions or proteins (IDRs or IDPs) constitute a large subset of the eukaryotic proteome, which challenges the protein structure-function paradigm. These IDPs lack a stable tertiary structure, yet they play a crucial role in the diverse biological process of plants. This study represents the intrinsically disordered nature of a plant-specific DNA binding with one finger transcription factor (DOF-TF). Here, we have investigated the role of OsDOF27 and characterized it as an intrinsically disordered protein. Furthermore, the molecular role of OsDOF27 in thermal stress tolerance has been elucidated. The qRT-PCR analysis revealed that OsDOF27 was significantly upregulated under different abiotic stress treatments in rice, particularly under heat stress. The stress-responsive transcript induction of OsDOF27 was further correlated with enriched abiotic stress-related cis-regulatory elements present in its promoter region. The in vivo functional analysis of the potential role of OsDOF27 in thermotolerance was further studied in yeast and in planta. Ectopic expression of OsDOF27 in yeast implicates thermotolerance response. Furthermore, the rice transgenic lines with overexpressing OsDOF27 revealed a positive role in mitigating heat stress tolerance. Collectively, our results evidently show the intrinsically disorderedness in OsDOF27 and its role in thermal stress response in rice.
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24
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Wang Z, Wong DCJ, Chen Z, Bai W, Si H, Jin X. Emerging Roles of Plant DNA-Binding With One Finger Transcription Factors in Various Hormone and Stress Signaling Pathways. FRONTIERS IN PLANT SCIENCE 2022; 13:844201. [PMID: 35668792 PMCID: PMC9165642 DOI: 10.3389/fpls.2022.844201] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 03/25/2022] [Indexed: 05/24/2023]
Abstract
Coordinated transcriptional regulation of stress-responsive genes orchestrated by a complex network of transcription factors (TFs) and the reprogramming of metabolism ensure a plant's continued growth and survival under adverse environmental conditions (e.g., abiotic stress). DNA-binding with one finger (Dof) proteins, a group of plant-specific TF, were identified as one of several key components of the transcriptional regulatory network involved in abiotic stress responses. In many plant species, Dofs are often activated in response to a wide range of adverse environmental conditions. Dofs play central roles in stress tolerance by regulating the expression of stress-responsive genes via the DOFCORE element or by interacting with other regulatory proteins. Moreover, Dofs act as a key regulatory hub of several phytohormone pathways, integrating abscisic acid, jasmonate, SA and redox signaling in response to many abiotic stresses. Taken together, we highlight a unique role of Dofs in hormone and stress signaling that integrates plant response to adverse environmental conditions with different aspects of plant growth and development.
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Affiliation(s)
- Zemin Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Darren Chern Jan Wong
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - Zhengliang Chen
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Wei Bai
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Huaijun Si
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xin Jin
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
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25
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Sharma DL, Bhoite R, Reeves K, Forrest K, Smith R, Dowla MANNU. Genome-wide superior alleles, haplotypes and candidate genes associated with tolerance on sodic-dispersive soils in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1113-1128. [PMID: 34985536 PMCID: PMC8942925 DOI: 10.1007/s00122-021-04021-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
The pleiotropic SNPs/haplotypes, overlapping genes (metal ion binding, photosynthesis), and homozygous/biallelic SNPs and transcription factors (HTH myb-type and BHLH) hold great potential for improving wheat yield potential on sodic-dispersive soils. Sodic-dispersive soils have multiple subsoil constraints including poor soil structure, alkaline pH and subsoil toxic elemental ion concentration, affecting growth and development in wheat. Tolerance is required at all developmental stages to enhance wheat yield potential on such soils. An in-depth investigation of genome-wide associations was conducted using a field phenotypic data of 206 diverse Focused Identification of Germplasm Strategy (FIGS) wheat lines for two consecutive years from different sodic and non-sodic plots and the exome targeted genotyping by sequencing (tGBS) assay. A total of 39 quantitative trait SNPs (QTSs), including 18 haplotypes were identified on chromosome 1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 5A, 5D, 6B, 7A, 7B, 7D for yield and yield-components tolerance. Among these, three QTSs had common associations for multiple traits, indicating pleiotropism and four QTSs had close associations for multiple traits, within 32.38 Mb. The overlapping metal ion binding (Mn, Ca, Zn and Al) and photosynthesis genes and transcription factors (PHD-, Dof-, HTH myb-, BHLH-, PDZ_6-domain) identified are known to be highly regulated during germination, maximum stem elongation, anthesis, and grain development stages. The homozygous/biallelic SNPs having allele frequency above 30% were identified for yield and crop establishment/plants m-2. These SNPs correspond to HTH myb-type and BHLH transcription factors, brassinosteroid signalling pathway, kinase activity, ATP and chitin binding activity. These resources are valuable in haplotype-based breeding and genome editing to improve yield potential on sodic-dispersive soils.
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Affiliation(s)
- Darshan Lal Sharma
- Department of Primary Industries and Regional Development, 3 Baron-Hay Ct, South Perth, WA, 6151, Australia.
- College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia.
| | - Roopali Bhoite
- Department of Primary Industries and Regional Development, 3 Baron-Hay Ct, South Perth, WA, 6151, Australia.
- College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia.
| | - Karyn Reeves
- Department of Primary Industries and Regional Development, 3 Baron-Hay Ct, South Perth, WA, 6151, Australia
| | - Kerrie Forrest
- Centre for AgriBioscience, Agriculture Victoria, Bundoora, AgriBioVIC, Australia
| | - Rosemary Smith
- Department of Primary Industries and Regional Development, 3 Baron-Hay Ct, South Perth, WA, 6151, Australia
| | - Mirza A N N U Dowla
- Department of Primary Industries and Regional Development, 3 Baron-Hay Ct, South Perth, WA, 6151, Australia
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26
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Wang L, Dai W, Shi Y, Wang Y, Zhang C. Cloning and activity analysis of the highly expressed gene VviABCG20 promoter in seed and its activity is negatively regulated by the transcription factor VviDof14. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 315:111152. [PMID: 35067313 DOI: 10.1016/j.plantsci.2021.111152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 12/09/2021] [Accepted: 12/11/2021] [Indexed: 06/14/2023]
Abstract
Half-size ATP binding cassette G (ABCG) transporters participate in the growth and development of plants by transporting substrates. The VviABCG20 gene is highly expressed in seed and plays an important role in seed development/abortion. However, little is known about the function of the VviABCG20 promoter (pVviABCG20) and its regulatory factors. In our study, we obtained pVviABCG20s from 15 seeded and seedless grape varieties and there were two types of 'a' and 'b' with 41 bp non-deletion or deletion, respectively. The pVviABCG20 activity was higher in seeds, siliques, flowers and roots of pVviABCG20-GUS Arabidopsis. The GUS activity analysis revealed that the activities of P4 (-586 bp) to P7 (-155 bp) were becoming increasingly weaker, and the P7 activity almost disappears compared with the pVviABCG20 (P0, -1604). Yeast one-hybrid and GUS activity analysis indicated that VviDof14 binds to the AAAG element in the P7' (-586 bp) fragment of the pVviABCG20 and regulated the activity negatively. The quantitative real-time PCR analysis suggested that the expression of VviDof14 in Thompson seedless seeds was higher than that in Pinot noir. Our study laid the foundation for further analysis of the functions of the pVviABCG20 and its regulator VviDof14 in grape seed development/abortion.
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Affiliation(s)
- Ling Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, P.R. China, Yangling, Shaanxi, China
| | - Weina Dai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, P.R. China, Yangling, Shaanxi, China
| | - Yuanyuan Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, P.R. China, Yangling, Shaanxi, China
| | - Yuejin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, P.R. China, Yangling, Shaanxi, China
| | - Chaohong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, P.R. China, Yangling, Shaanxi, China.
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Aamir M, Karmakar P, Singh VK, Kashyap SP, Pandey S, Singh BK, Singh PM, Singh J. A novel insight into transcriptional and epigenetic regulation underlying sex expression and flower development in melon (Cucumis melo L.). PHYSIOLOGIA PLANTARUM 2021; 173:1729-1764. [PMID: 33547804 DOI: 10.1111/ppl.13357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
Melon (Cucumis melo L.) is an important cucurbit and has been considered as a model plant for studying sex determination. The four most common sexual morphotypes in melon are monoecious (A-G-M), gynoecious (--ggM-), andromonoecious (A-G-mm), and hermaphrodite (--ggmm). Sex expression in melons is complex, as the genes and associated networks that govern the sex expression are not fully explored. Recently, RNA-seq transcriptomic profiling, ChIP-qPCR analysis integrated with gene ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathways predicted the differentially expressed genes including sex-specific ACS and ACO genes, in regulating the sex-expression, phytohormonal cross-talk, signal transduction, and secondary metabolism in melons. Integration of transcriptional control through genetic interaction in between the ACS7, ACS11, and WIP1 in epistatic or hypostatic manner, along with the recruitment of H3K9ac and H3K27me3, epigenetically, overall determine sex expression. Alignment of protein sequences for establishing phylogenetic evolution, motif comparison, and protein-protein interaction supported the structural conservation while presence of the conserved hydrophilic and charged residues across the diverged evolutionary group predicted the functional conservation of the ACS protein. Presence of the putative cis-binding elements or DNA motifs, and its further comparison with DAP-seq-based cistrome and epicistrome of Arabidopsis, unraveled strong ancestry of melons with Arabidopsis. Motif comparison analysis also characterized putative genes and transcription factors involved in ethylene biosynthesis, signal transduction, and hormonal cross-talk related to sex expression. Overall, we have comprehensively reviewed research findings for a deeper insight into transcriptional and epigenetic regulation of sex expression and flower development in melons.
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Affiliation(s)
- Mohd Aamir
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Pradip Karmakar
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Vinay Kumar Singh
- Centre for Bioinformatics, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Sarvesh Pratap Kashyap
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Sudhakar Pandey
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Binod Kumar Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Prabhakar Mohan Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
| | - Jagdish Singh
- Division of Crop Improvement, ICAR-Indian Institute of Vegetable Research (ICAR-IIVR), Varanasi, India
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Yu L, Ma S, Zhang X, Tian D, Yang S, Jia X, Traw MB. Ancient rapid functional differentiation and fixation of the duplicated members in rice Dof genes after whole genome duplication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1365-1381. [PMID: 34585814 DOI: 10.1111/tpj.15516] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 09/03/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
Whole genome duplication (WGD) in plants is typically followed by genomic downsizing, where large portions of the new genome are lost. Whether this downsizing is accompanied by increased or decreased evolutionary rates of the remaining genes is poorly known, not least because homeolog pairings are often obscured by chromosomal rearrangement. Here, we use the newly published genome from a sedge, namely Kobresia littledalei, and CRISPR/Cas-9 editing to investigate how the Rho WGD event 70 million years ago (MYA) affected transcription factor evolutionary rates, fates, and function in rice (Oryza sativa) and sorghum (Sorghum bicolor). We focus on the 30-member DNA-binding with one zinc finger (Dof) transcription factor family in both crops due to their agronomic importance. Using the known speciation dates of rice from Kobresia (97 MYA) and sorghum (50 MYA), we find that rates of amino acid substitution in the critical Dof domain region were over twofold higher during the 20-million-year period following the WGD than before or afterward. Through comparison of synteny blocks, we report that at least 11% of Dof genes were purged from 70 to 50 MYA, while only 6% have been lost in the most recent 50-million-year interval. CRISPR/Cas9 editing revealed widespread fitness-related defects in flowering and lack of redundancy of paired members, as well as significant differences in expression between gene pairs. Together these findings demonstrate the strength of Dof genes as a model for deep evolutionary study and offer one of the most detailed portraits yet of the Rho WGD impact on a gene lineage.
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Affiliation(s)
- Luyao Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Shiying Ma
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xiaohui Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xianqing Jia
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
- Key Laboratory of Plant Nutrition and Fertilizers, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Milton Brian Traw
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
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Li R, Tan Y, Zhang H. Regulators of Starch Biosynthesis in Cereal Crops. Molecules 2021; 26:molecules26237092. [PMID: 34885674 PMCID: PMC8659000 DOI: 10.3390/molecules26237092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 11/19/2021] [Accepted: 11/21/2021] [Indexed: 01/07/2023] Open
Abstract
Starch is the main food source for human beings and livestock all over the world, and it is also the raw material for production of industrial alcohol and biofuel. A considerable part of the world’s annual starch production comes from crops and their seeds. With the increasing demand for starch from food and non-food industries and the growing loss of arable land due to urbanization, understanding starch biosynthesis and its regulators is essential to produce the desirable traits as well as more and better polymers via biotechnological approaches in cereal crops. Because of the complexity and flexibility of carbon allocation in the formation of endosperm starch, cereal crops require a broad range of enzymes and one matching network of regulators to control the providential functioning of these starch biosynthetic enzymes. Here, we comprehensively summarize the current knowledge about regulatory factors of starch biosynthesis in cereal crops, with an emphasis on the transcription factors that directly regulate starch biosynthesis. This review will provide new insights for the manipulation of bioengineering and starch biosynthesis to improve starch yields or qualities in our diets and in industry.
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Affiliation(s)
- Ruiqing Li
- State Key Laboratory of Rice Biology, Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310029, China;
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Yuanyuan Tan
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310029, China;
| | - Huali Zhang
- State Key Laboratory of Rice Biology, Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310029, China;
- Correspondence:
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Thakur T, Gandass N, Mittal K, Jamwal P, Muthamilarasan M, Salvi P. A rapid, efficient, and low-cost BiFC protocol and its application in studying in vivo interaction of seed-specific transcription factors, RISBZ and RPBF. Funct Integr Genomics 2021; 21:593-603. [PMID: 34436705 DOI: 10.1007/s10142-021-00801-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 07/26/2021] [Accepted: 08/01/2021] [Indexed: 10/20/2022]
Abstract
Proteins regulate cellular and biological processes in all living organisms. More than 80% of the proteins interact with one another to perform their respective functions; therefore, studying the protein-protein-interaction has gained attention in functional characterization studies. Bimolecular fluorescence complement (BiFC) assay is widely adopted to determine the physical interaction of two proteins in vivo. Here, we developed a simple, yet effective BiFC assay for protein-protein-interaction using transient Agrobacterium-mediated-transformation of onion epidermal cells by taking case study of Rice-P-box-Binding-Factor (RPBF) and rice-seed-specific-bZIP (RISBZ) in vivo interaction. Our result revealed that both the proteins, i.e., RISBZ and RPBF, interacted in the nucleus and cytosol. These two transcription factors are known for their coordinate/synergistic regulation of seed-protein content via concurrent binding to the promoter region of the seed storage protein (SSP) encoding genes. We further validated our results with BiFC assay in Nicotiana by agroinfiltration method, which exhibited similar results as Agrobacterium-mediated-transformation of onion epidermal cells. We also examined the subcellular localization of RISBZ and RPBF to assess the efficacy of the protocol. The subcellular localization and BiFC assay presented here is quite easy-to-follow, reliable, and reproducible, which can be completed within 2-3 days without using costly instruments and technologies that demand a high skill set.
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Affiliation(s)
- Tanika Thakur
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, 140308, India
| | - Nishu Gandass
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, 140308, India
| | - Kajal Mittal
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, 140308, India
| | - Pallavi Jamwal
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, 140308, India
| | - Mehanathan Muthamilarasan
- Repository of Tomato Genomics Resources, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, Telangana, India
| | - Prafull Salvi
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, Punjab, 140308, India.
- DST-INSPIRE Faculty, Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute, Mohali, India.
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Peng B, Zhao X, Wang Y, Li C, Li Y, Zhang D, Shi Y, Song Y, Wang L, Li Y, Wang T. Genome-wide association studies of leaf angle in maize. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:50. [PMID: 37309541 PMCID: PMC10236034 DOI: 10.1007/s11032-021-01241-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 07/04/2021] [Indexed: 06/14/2023]
Abstract
Compact plant-type with small leaf angle has increased canopy light interception, which is conducive to the photosynthesis of the population and higher population yield at high density planting in maize. In this study, a panel of 285 diverse maize inbred lines genotyped with 56,000 SNPs was used to investigate the genetic basis of leaf angle across 3 consecutive years using a genome-wide association study (GWAS). The leaf angle showed broad phenotypic variation and high heritability across different years. Population structure analysis subdivided the panel into four subgroups that correspond to the four major empirical germplasm origins in China, i.e., Tangsipingtou, Reid, Lancaster and P. When tested with the optimal GWAS model, we found that the Q + K model was the best in reducing false positive. In total, 96 SNPs accounting for 5.54-10.44% of phenotypic variation were significantly (P < 0.0001) associated with leaf angle across three years. According to the linkage disequilibrium decay distance, 96 SNPs were binned into 43 QTLs for leaf angle. Seven major QTLs with R2 > 8% stably detected in at least 2 years, and BLUP values were clustered in four genomic regions (bins 2.01, 2.07, 5.06, and 10.04). Seven important candidate genes, Zm00001d001961, Zm00001d006348, Zm00001d006463, Zm00001d017618, Zm00001d024919, Zm00001d025018, and Zm00001d025033 were predicted for the seven stable major QTLs, respectively. The markers identified in this study can be used for molecular breeding for leaf angle, and the candidate genes would contribute to further understanding of the genetic basis of leaf angle. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01241-0.
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Affiliation(s)
- Bo Peng
- Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences/Tianjin Key Laboratory of Crop Genetics and Breeding, 300384 Tianjin, China
| | - Xiaolei Zhao
- Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences/Tianjin Key Laboratory of Crop Genetics and Breeding, 300384 Tianjin, China
| | - Yi Wang
- Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences/Tianjin Key Laboratory of Crop Genetics and Breeding, 300384 Tianjin, China
| | - Chunhui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yongxiang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Dengfeng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yunsu Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yanchun Song
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Lei Wang
- Handan Academy of Agricultural Sciences, Handan, 056001 Hebei China
| | - Yu Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Tianyu Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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Genome-wide survey of sugar beet (Beta vulgaris subsp. vulgaris) Dof transcription factors reveals structural diversity, evolutionary expansion and involvement in taproot development and biotic stress response. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00777-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Wang P, Yan Z, Zong X, Yan Q, Zhang J. Genome-Wide Analysis and Expression Profiles of the Dof Family in Cleistogenes songorica under Temperature, Salt and ABA Treatment. PLANTS 2021; 10:plants10050850. [PMID: 33922432 PMCID: PMC8146245 DOI: 10.3390/plants10050850] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/05/2021] [Accepted: 04/19/2021] [Indexed: 12/05/2022]
Abstract
The DNA-binding with one zinc finger (Dof) family of plant-specific transcription factors has a variety of important functions in gene transcriptional regulation, development, and stress responses. However, the structure and expression patterns of Dof family have not been identified in Cleistogenes songorica, which is an important xerophytic and perennial gramineous grass in desert grassland. In this study, 50 Dof genes were identified in C. songorica and could be classified into four groups. According to genome-wide analysis, 46 of 50 Dof genes were located on 20 chromosomes, and the gene structure and conserved protein motif of these proteins were analyzed. In addition, phylogenetic analysis of Dof genes in C. songorica, Arabidopsis thaliana, Oryza sativa, and Brachypodium distachyon estimated the evolutionary relationships, and these genes were grouped into seven clusters. Moreover, the expression profiles of these Dof genes in C. songorica were analyzed in response to high/low temperature, salinity, and ABA treatments. These results will provide valuable information for future studies on gene classification, cloning, and functional characterization of this family in C. songorica.
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Affiliation(s)
| | | | | | | | - Jiyu Zhang
- Correspondence: ; Tel.: +86-138-9332-9958
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Genome-Wide In Silico Identification and Comparative Analysis of Dof Gene Family in Brassica napus. PLANTS 2021; 10:plants10040709. [PMID: 33916912 PMCID: PMC8067633 DOI: 10.3390/plants10040709] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/31/2021] [Accepted: 04/06/2021] [Indexed: 01/02/2023]
Abstract
DNA binding with one finger (DOF) proteins are plant-specific transcription factors that play roles in diverse plant functions. However, little is known about the DOF protein repertoire of the allopolyploid crop, Brassica napus. This in silico study identified 117 Brassica napus Dof genes (BnaDofs) and classified them into nine groups (A, B1, B2, C1, C2.1, C2.2, C3, D1, and D2), based on phylogenetic analysis. Most members belonging to a particular group displayed conserved gene structural organisation and protein motif distribution. Evolutionary analysis exemplified that the divergence of the Brassica genus from Arabidopsis, the whole-genome triplication event, and the hybridisation of Brassica oleracea and Brassica rapa to form B. napus, followed by gene loss and rearrangements, led to the expansion and divergence of the Dof transcription factor (TF) gene family in B. napus. So far, this is the largest number of Dof genes reported in a single eudicot species. Functional annotation of BnaDof proteins, cis-element analysis of their promoters, and transcriptomic analysis suggested potential roles in organ development, the transition from the vegetative to the reproductive stage, light responsiveness, phytohormone responsiveness, as well as potential regulatory roles in abiotic stress. Overall, our results provide a comprehensive understanding of the molecular structure, evolution, and possible functional roles of Dof genes in plant development and abiotic stress response.
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TaAP2-15, An AP2/ERF Transcription Factor, Is Positively Involved in Wheat Resistance to Puccinia striiformis f. sp. tritici. Int J Mol Sci 2021; 22:ijms22042080. [PMID: 33669850 PMCID: PMC7923241 DOI: 10.3390/ijms22042080] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 12/25/2022] Open
Abstract
AP2 transcription factors play a crucial role in plant development and reproductive growth, as well as response to biotic and abiotic stress. However, the role of TaAP2-15, in the interaction between wheat and the stripe fungus, Puccinia striiformis f. sp. tritici (Pst), remains elusive. In this study, we isolated TaAP2-15 and characterized its function during the interaction. TaAP2-15 was localized in the nucleus of wheat and N. benthamiana. Silencing of TaAP2-15 by barley stripe mosaic virus (BSMV)-mediated VIGS (virus-induced gene silencing) increased the susceptibility of wheat to Pst accompanied by enhanced growth of the pathogen (number of haustoria, haustorial mother cells and hyphal length). We confirmed by quantitative real-time PCR that the transcript levels of pathogenesis-related genes (TaPR1 and TaPR2) were down-regulated, while reactive oxygen species (ROS)-scavenging genes (TaCAT3 and TaFSOD3D) were induced accompanied by reduced accumulation of H2O2. Furthermore, we found that TaAP2-15 interacted with a zinc finger protein (TaRZFP34) that is a homolog of OsRZFP34 in rice. Together our findings demonstrate that TaAP2-15 is positively involved in resistance of wheat to the stripe rust fungus and provides new insights into the roles of AP2 in the host-pathogen interaction.
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Wang Z, Wang Y, Tong Q, Xu G, Xu M, Li H, Fan P, Li S, Liang Z. Transcriptomic analysis of grapevine Dof transcription factor gene family in response to cold stress and functional analyses of the VaDof17d gene. PLANTA 2021; 253:55. [PMID: 33523295 DOI: 10.1007/s00425-021-03574-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/16/2021] [Indexed: 05/11/2023]
Abstract
Dof genes enhance cold tolerance in grapevine and VaDof17d is tightly associated with the cold-responsive pathway and with the raffinose family oligosaccharides. DNA-binding with one finger (Dof) proteins comprise a large family that plays important roles in the regulation of abiotic stresses. No in-depth analysis of Dof genes has been performed in the grapevine. In this study, we analyzed a total of 25 putative Dof genes in grapevine at genomic and transcriptomic levels, compiled expression profiles of 11 selected VaDof genes under cold stress and studied the potential function of the VaDof17d gene in grapevine calli. The 25 Dof proteins can be classified into four phylogenetic groups. RNA-seq and qRT-PCR results demonstrated that a total of 11 VaDof genes responded to cold stress. Comparative mRNA sequencing of 35S::VaDof17d grape calli showed that VaDof17d was tightly associated with the cold-responsive pathway and with the raffinose family oligosaccharides (RFOs), as observed by the up-regulation of galactinol synthase (GolS) and raffinose synthase genes. We found that the Dof17d-ED (CRISPR/Cas9-mediated mutagenesis of Dof17d-ED) mutant had low cold tolerance with a decreased RFOs level during cold stress. These results formed the fundamental knowledge for further analysis of the biological roles of Dof genes in the grapevine's adaption to cold stresses.
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Affiliation(s)
- Zemin Wang
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Science, Beijing, 100093, People's Republic of China
- University of the Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yi Wang
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Science, Beijing, 100093, People's Republic of China
- University of the Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Qian Tong
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Science, Beijing, 100093, People's Republic of China
- University of the Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Guangzhao Xu
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Science, Beijing, 100093, People's Republic of China
- University of the Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Meilong Xu
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Science, Beijing, 100093, People's Republic of China
- University of the Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
- State Key Laboratory of the Seedling Bioengineering, Yinchuan, 750004, People's Republic of China
| | - Huayang Li
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Science, Beijing, 100093, People's Republic of China
- University of the Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Peige Fan
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Science, Beijing, 100093, People's Republic of China
- China Wine Industry Technology Institute, Yinchuan, 750021, People's Republic of China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Science, Beijing, 100093, People's Republic of China.
- University of the Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, Chinese Academy of Science, Beijing, 100093, People's Republic of China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, People's Republic of China.
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Wang J, Chen W, Wang H, Li Y, Wang B, Zhang L, Wan X, Li M. Transcription factor CsDOF regulates glutamine metabolism in tea plants (Camellia sinensis). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 302:110720. [PMID: 33288026 DOI: 10.1016/j.plantsci.2020.110720] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/09/2020] [Accepted: 10/12/2020] [Indexed: 06/12/2023]
Abstract
Glutamine plays a critical role in ammonium assimilation, and contributes substantially to the taste and nutritional quality of tea. To date, little research has been done on glutamine synthesis in tea plants. Here, a zinc finger protein CsDOF and a glutamine synthetase (GS)-encoding gene CsGS2 from tea plant (Camellia sinensis cv 'Shuchazao') were characterized, and their role in glutamine biosynthesis was determined using transient suppression assays in tea leaves and overexpression in Arabidopsis thaliana. The expression patterns of CsDOF and CsGS2, the GS activity and the glutamine content of photosynthetic tissues (leaf and bud) were significantly induced by shade. Suppressing the expression of CsDOF resulted in downregulated expression of CsGS2 and reduction of the leaf glutamine content. Moreover, in CsDOF-silenced plants, the expression of CsDOF and the glutamine content under shade treatment were higher than in natural light. The glutamine content and CsGS2 transcript level were also decreased in tea leaves when CsGS2 was suppressed, while they were higher under shade treatment than in natural light in CsGS2-silenced plants. In addition, the glutamine content and GS2 transcript level were increased when CsDOF and CsGS2 was overexpressed in Arabidopsis thaliana, respectively. In binding analyses, CsDOF directly bound to an AAAG motif in the promoter of CsGS2, and promotes its activity. The study shed new light on the molecular mechanism by which CsDOF activates CsGS2 gene expression and contributes to glutamine biosynthesis in tea plants.
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Affiliation(s)
- Jinhe Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Wenzhen Chen
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Hanyue Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Yuanda Li
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Biao Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Lixia Zhang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, 230036, China.
| | - Min Li
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, 271018, China.
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Shi Y, Chang YL, Wu HT, Shalmani A, Liu WT, Li WQ, Xu JW, Chen KM. OsRbohB-mediated ROS production plays a crucial role in drought stress tolerance of rice. PLANT CELL REPORTS 2020; 39:1767-1784. [PMID: 32980968 DOI: 10.1007/s00299-020-02603-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/17/2020] [Accepted: 09/13/2020] [Indexed: 06/11/2023]
Abstract
We found that a rice NADPH oxidase gene OsRbohB contributes drought tolerance and its functions are involved in the interaction of the OsRbohB-mediated ROS production and ABA signaling. The plasma membrane NADPH oxidases, also known as respiratory burst oxidase homologs, are the key producers of ROS under both normal and stress conditions in plants. However, their functions in rice development and stress tolerance are still under investigation. Here, we found that a rice NADPH oxidase gene OsRbohB, also named OsNOX1, is expressed in all tissues examined throughout the development stages with higher transcripts in leaves. The transcriptional expression of OsRbohB is also strongly stimulated by dehydration, salt and several phytohormonal treatments. Compared with wide-type and the OsRbohB-overexpressing transgenic plants, osrbohB, a Tos17 insertion knockout mutant of OsRbohB, shows lower ROS production, abscisic acid (ABA) content and transcripts of a series of stress-related genes. The osrbohB mutant also exhibits lower seed germination rate, organ size and thousand seed weight, but higher stomatal aperture and sensitivity to drought. Moreover, a number of genes involved in plant development, stress response, transcriptional regulation, and particularly ABA signaling are differentially expressed in osrbohB plants under both normal growth and drought conditions. All these results suggest the roles of OsRbohB in drought tolerance of rice, which probably performed through the interaction of the OsRbohB-mediated ROS production and ABA signaling.
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Affiliation(s)
- Yi Shi
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, 712100, Shanxi, China
| | - Yan-Li Chang
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, 712100, Shanxi, China
| | - Hai-Tao Wu
- College of Science, Northwest A&F University, Yangling, 712100, Shanxi, China
| | - Abdullah Shalmani
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, 712100, Shanxi, China
| | - Wen-Ting Liu
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, 712100, Shanxi, China
| | - Wen-Qiang Li
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, 712100, Shanxi, China
| | - Jian-Wei Xu
- College of Science, Northwest A&F University, Yangling, 712100, Shanxi, China
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, 712100, Shanxi, China.
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Domínguez-Figueroa J, Carrillo L, Renau-Morata B, Yang L, Molina RV, Marino D, Canales J, Weih M, Vicente-Carbajosa J, Nebauer SG, Medina J. The Arabidopsis Transcription Factor CDF3 Is Involved in Nitrogen Responses and Improves Nitrogen Use Efficiency in Tomato. FRONTIERS IN PLANT SCIENCE 2020; 11:601558. [PMID: 33329669 PMCID: PMC7732579 DOI: 10.3389/fpls.2020.601558] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/29/2020] [Indexed: 06/12/2023]
Abstract
Nitrate is an essential macronutrient and a signal molecule that regulates the expression of multiple genes involved in plant growth and development. Here, we describe the participation of Arabidopsis DNA binding with one finger (DOF) transcription factor CDF3 in nitrate responses and shows that CDF3 gene is induced under nitrate starvation. Moreover, knockout cdf3 mutant plants exhibit nitrate-dependent lateral and primary root modifications, whereas CDF3 overexpression plants show increased biomass and enhanced root development under both nitrogen poor and rich conditions. Expression analyses of 35S::CDF3 lines reveled that CDF3 regulates the expression of an important set of nitrate responsive genes including, glutamine synthetase-1, glutamate synthase-2, nitrate reductase-1, and nitrate transporters NRT2.1, NRT2.4, and NRT2.5 as well as carbon assimilation genes like PK1 and PEPC1 in response to N availability. Consistently, metabolite profiling disclosed that the total amount of key N metabolites like glutamate, glutamine, and asparagine were higher in CDF3-overexpressing plants, but lower in cdf3-1 in N limiting conditions. Moreover, overexpression of CDF3 in tomato increased N accumulation and yield efficiency under both optimum and limiting N supply. These results highlight CDF3 as an important regulatory factor for the nitrate response, and its potential for improving N use efficiency in crops.
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Affiliation(s)
- José Domínguez-Figueroa
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Laura Carrillo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Begoña Renau-Morata
- Departamento de Producción Vegetal, Universitat Politécnica de Valencia, Valencia, Spain
| | - Lu Yang
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Rosa-V Molina
- Departamento de Producción Vegetal, Universitat Politécnica de Valencia, Valencia, Spain
| | - Daniel Marino
- Department of Plant Biology and Ecology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Javier Canales
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
- ANID–Millennium Science Initiative Program-Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Martin Weih
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jesús Vicente-Carbajosa
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
| | - Sergio G. Nebauer
- Departamento de Producción Vegetal, Universitat Politécnica de Valencia, Valencia, Spain
| | - Joaquín Medina
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Madrid, Spain
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40
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Ganie AH, Pandey R, Kumar MN, Chinnusamy V, Iqbal M, Ahmad A. Metabolite Profiling and Network Analysis Reveal Coordinated Changes in Low-N Tolerant and Low-N Sensitive Maize Genotypes under Nitrogen Deficiency and Restoration Conditions. PLANTS 2020; 9:plants9111459. [PMID: 33137957 PMCID: PMC7716227 DOI: 10.3390/plants9111459] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/20/2020] [Accepted: 10/25/2020] [Indexed: 11/16/2022]
Abstract
Nitrogen (N), applied in the form of a nitrogenous fertilizer, is one of the main inputs for agricultural production. Food production is closely associated with the application of N. However, the application of nitrogenous fertilizers to agricultural fields is associated with heavy production of nitrous oxide because agricultural crops can only utilize 30-40% of applied N, leaving behind unused 60-70% N in the environment. The global warming effect of this greenhouse gas is approximately 300 times more than of carbon dioxide. Under the present scenario of climate change, it is critical to maintain the natural balance between food production and environmental sustainability by targeting traits responsible for improving nitrogen-use-efficiency (NUE). Understanding of the molecular mechanisms behind the metabolic alterations due to nitrogen status needs to be addressed. Additionally, mineral nutrient deficiencies and their associated metabolic networks have not yet been studied well. Given this, the alterations in core metabolic pathways of low-N tolerant (LNT) and low-N sensitive (LNS) genotypes of maize under N-deficiency and their efficiency of recovering the changes upon resupplying N were investigated by us, using the GC-MS and LC-MS based metabolomic approach. Significant genotype-specific changes were noted in response to low-N. The N limitation affected the whole plant metabolism, most significantly the precursors of primary metabolic pathways. These precursors may act as important targets for improving the NUE. Limited availability of N reduced the levels of N-containing metabolites, organic acids and amino acids, but soluble sugars increased. Major variations were encountered in LNS, as compared to LNT. This study has revealed potential metabolic targets in response to the N status, which are indeed the prospective targets for crop improvement.
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Affiliation(s)
| | - Renu Pandey
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi 110012, India; (R.P.); (M.N.K.); (V.C.)
| | - M. Nagaraj Kumar
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi 110012, India; (R.P.); (M.N.K.); (V.C.)
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi 110012, India; (R.P.); (M.N.K.); (V.C.)
| | - Muhammad Iqbal
- Department of Botany, Jamia Hamdard, New Delhi 110062, India; (A.H.G.); (M.I.)
| | - Altaf Ahmad
- Department of Botany, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
- Correspondence: ; Tel.: +00-91-9999886334
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41
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Comparative Study of Pine Reference Genomes Reveals Transposable Element Interconnected Gene Networks. Genes (Basel) 2020; 11:genes11101216. [PMID: 33081418 PMCID: PMC7602945 DOI: 10.3390/genes11101216] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/11/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
Sequencing the giga-genomes of several pine species has enabled comparative genomic analyses of these outcrossing tree species. Previous studies have revealed the wide distribution and extraordinary diversity of transposable elements (TEs) that occupy the large intergenic spaces in conifer genomes. In this study, we analyzed the distribution of TEs in gene regions of the assembled genomes of Pinus taeda and Pinus lambertiana using high-performance computing resources. The quality of draft genomes and the genome annotation have significant consequences for the investigation of TEs and these aspects are discussed. Several TE families frequently inserted into genes or their flanks were identified in both species’ genomes. Potentially important sequence motifs were identified in TEs that could bind additional regulatory factors, promoting gene network formation with faster or enhanced transcription initiation. Node genes that contain many TEs were observed in multiple potential transposable element-associated networks. This study demonstrated the increased accumulation of TEs in the introns of stress-responsive genes of pines and suggests the possibility of rewiring them into responsive networks and sub-networks interconnected with node genes containing multiple TEs. Many such regulatory influences could lead to the adaptive environmental response clines that are characteristic of naturally spread pine populations.
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42
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Cao B, Cui Y, Lou K, Luo D, Liu Z, Zhou Q. Genome-Wide Identification and Expression Analysis of the Dof Gene Family in Medicago sativa L. Under Various Abiotic Stresses. DNA Cell Biol 2020; 39:1976-1989. [PMID: 33001712 DOI: 10.1089/dna.2020.5652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Dof transcription factor is a plant-specific transcriptional regulator that plays important roles in plant development and acts as a mediator in plant external stress responses. However, Dofs have previously been identified in several plants but not in alfalfa (Medicago sativa L.), one of the most widely cultivated forage legumes. In the present study, a total of 40 MsDof genes were identified, and the phylogenetic reconstruction, classification, conserved motifs, and expression patterns under abscisic acid (ABA), cold, heat, drought and salt stresses of these Dof genes were comprehensively analyzed. The Dof genes family in alfalfa could be classified into eight classes. Gene ontology (GO) and tissue-specific analysis indicated that most MsDof genes may be involved in biological functions during plant growth. Moreover, the expression profiles and quantitative real-time PCR analysis indicated that eight candidate abiotic tolerance genes were induced in response to four abiotic stresses. This study identified the possibility of abiotic tolerance candidate genes playing various roles in stress resistance at the whole genome level, which would provide new information on the Dof family in alfalfa.
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Affiliation(s)
- Bo Cao
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yue Cui
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Keke Lou
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Dong Luo
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Zhipeng Liu
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Qiang Zhou
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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43
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Genome-wide identification of the maize 2OGD superfamily genes and their response to Fusarium verticillioides and Fusarium graminearum. Gene 2020; 764:145078. [PMID: 32858175 DOI: 10.1016/j.gene.2020.145078] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/15/2020] [Accepted: 08/19/2020] [Indexed: 01/05/2023]
Abstract
In maize, eat rot and stalk rot caused by Fusarium verticillioides and Fusarium graminearum lead to contamination of moldy grains to produce mycotoxins. Identification of resistance genes against these pathogens for maize breeding is an effective way for disease control. Several 2-oxoglutarate-dependent dioxygenase (2OGD) proteins have been found to confer resistance to different pathogens in diverse plant species. However, little is known about the 2OGD superfamily in maize. Here, we identified 103 putative 2OGD genes in maize from a genome-wide analysis, and divided them into three classes - DOXA, DOXB, and DOXC. We further comprehensively investigated their gene structure, chromosome distribution, phylogenetic tree, gene-function enrichment, and expression profiles among different tissues. The genes encoding three 2OGD proteins, ACO, F3H, and NCS involved in ethylene biosynthesis, flavonoids biosynthesis, and alkaloids biosynthesis pathways, respectively, were identified to be induced by F. verticillioides and F. graminearum. The promoters of the three genes contain the binding sites for the transcription factor ZmDOF and ZmHSF, which are also induced by the two pathogens. The results imply that the three 2OGDs and the two transcription factors might be involved in the resistance to the two pathogens. This study provided a comprehensive understanding of the 2OGD superfamily in maize and laid the foundation for the further functional analysis of their roles in maize resistance to eat rot and stalk rot.
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44
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Genome-wide identification and evolution of Dof transcription factor family in cultivated and ancestral cotton species. Genomics 2020; 112:4155-4170. [PMID: 32650093 DOI: 10.1016/j.ygeno.2020.07.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 06/03/2020] [Accepted: 07/02/2020] [Indexed: 11/24/2022]
Abstract
The DNA-binding with one finger (Dof) proteins are transcription factors involved in many biological processes in plants. To predict the evolutionary pattern, a genome-wide in-silico analysis of Dof TFs family in diploid (Gossypium arboreum and Gossypium raimondii) and allotetraploid (Gossypium hirsutum and Gossypium barbadense) cotton species were carried out. In G. arboreum, we have identified 58 non-redundant genes encoding Dof proteins renamed as GaDof (G. arboreum Dof), 55 Dof genes were identified in G. raimondii (GrDof), 89 were predicted ffrom G. hirsutum (GhDof) and the highest, 110 Dof genes were identified in G. barbadense (GbDof). The phylogenetic analysis, physical location, gene structure, conserved domain analyses were also investigated for G. arboreum, G. raimondii, and G. hirsutum. The gene expression pattern in G. hirsutum, at different growth stages, revealing the probable involvement of some GhDof genes in growth and development. These genes may improve seed germination and growth in cotton.
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45
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Ravindran P, Yong SY, Mohanty B, Kumar PP. An LRR-only protein regulates abscisic acid-mediated abiotic stress responses during Arabidopsis seed germination. PLANT CELL REPORTS 2020; 39:909-920. [PMID: 32277267 DOI: 10.1007/s00299-020-02538-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/30/2020] [Indexed: 05/22/2023]
Abstract
LRRop-1, induced by DOF6 transcription factor, negatively regulates abiotic stress responses during Arabidopsis seed germination. The lrrop-1 mutant has reduced ABA signaling, which is part of the underlying stress-remediation mechanism. The large family of leucine-rich repeat (LRR) proteins plays a role in plant immune responses. Most LRR proteins have multiple functional domains, but a subfamily is known to possess only the LRR domain. The roles of these LRR-only proteins in Arabidopsis remain largely uncharacterized. In the present study, we have identified 44 LRR-only proteins in Arabidopsis and phylogenetically classified them into nine sub-groups. We characterized the function of LRRop-1, belonging to sub-group V. LRRop-1 encodes a predominantly ER-localized LRR domain-containing protein that is highly expressed in seeds and rosette leaves. Promoter motif analysis revealed an enrichment in binding sites for several GA-responsive and stress-responsive transcription factors. The lrrop-1 mutant seeds showed enhanced seed germination on medium containing abscisic acid (ABA), paclobutrazol and NaCl compared to the wild type (WT), demonstrating higher abiotic stress tolerance. Also, the lrrop-1 mutant seeds have lower levels of endogenous ABA, but higher levels of gibberellic acid (GA) and jasmonic acid-Ile (JA-Ile) compared to the WT. Furthermore, lrrop-1 mutant seeds imbibed with ABA exhibited reduced expression of ABA-responsive genes compared to similarly treated WT seeds, suggesting suppressed ABA signaling events in the mutant. Furthermore, chromatin immunoprecipitation (ChIP) data showed that DNA BINDING1 ZINC FINGER6 (DOF6), a negative regulator of seed germination, could directly bind to the LRRop-1 promoter and up-regulate its expression. Thus, our results show that LRRop-1 regulates ABA-mediated abiotic stress responses during Arabidopsis seed germination.
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Affiliation(s)
- Pratibha Ravindran
- NUS Environmental Research Institute (NERI), National University of Singapore, T-Lab Building, 5A Engineering Drive 1, Singapore, 117411, Singapore
| | - Shi Yin Yong
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore
| | - Bijayalakshmi Mohanty
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117585, Singapore
| | - Prakash P Kumar
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, 117543, Singapore.
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Renau-Morata B, Carrillo L, Dominguez-Figueroa J, Vicente-Carbajosa J, Molina RV, Nebauer SG, Medina J. CDF transcription factors: plant regulators to deal with extreme environmental conditions. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3803-3815. [PMID: 32072179 DOI: 10.1093/jxb/eraa088] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 02/03/2020] [Indexed: 05/23/2023]
Abstract
In terrestrial environments, water and nutrient availabilities and temperature conditions are highly variable, and especially in extreme environments limit survival, growth, and reproduction of plants. To sustain growth and maintain cell integrity under unfavourable environmental conditions, plants have developed a variety of biochemical and physiological mechanisms, orchestrated by a large set of stress-responsive genes and a complex network of transcription factors. Recently, cycling DOF factors (CDFs), a group of plant-specific transcription factors (TFs), were identified as components of the transcriptional regulatory networks involved in the control of abiotic stress responses. The majority of the members of this TF family are activated in response to a wide range of adverse environmental conditions in different plant species. CDFs regulate different aspects of plant growth and development such as photoperiodic flowering-time control and root and shoot growth. While most of the functional characterization of CDFs has been reported in Arabidopsis, recent data suggest that their diverse roles extend to other plant species. In this review, we integrate information related to structure and functions of CDFs in plants, with special emphasis on their role in plant responses to adverse environmental conditions.
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Affiliation(s)
- Begoña Renau-Morata
- Departamento de Producción Vegetal, Universitat Politécnica de Valencia, Camino de Vera s/n, Valencia, Spain
| | - Laura Carrillo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Autopista M40 (km 38), Madrid, Spain
| | - Jose Dominguez-Figueroa
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Autopista M40 (km 38), Madrid, Spain
| | - Jesús Vicente-Carbajosa
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Autopista M40 (km 38), Madrid, Spain
| | - Rosa V Molina
- Departamento de Producción Vegetal, Universitat Politécnica de Valencia, Camino de Vera s/n, Valencia, Spain
| | - Sergio G Nebauer
- Departamento de Producción Vegetal, Universitat Politécnica de Valencia, Camino de Vera s/n, Valencia, Spain
| | - Joaquín Medina
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Autopista M40 (km 38), Madrid, Spain
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47
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Yu Q, Li C, Zhang J, Tian Y, Wang H, Zhang Y, Zhang Z, Xiang Q, Han X, Zhang L. Genome-wide identification and expression analysis of the Dof gene family under drought stress in tea ( Camellia sinensis). PeerJ 2020; 8:e9269. [PMID: 32566398 PMCID: PMC7293185 DOI: 10.7717/peerj.9269] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 05/10/2020] [Indexed: 12/17/2022] Open
Abstract
Background DNA-binding one zinc finger (Dof) proteins are plant-specific transcription factors important for seed development, hormone regulation, and defense against abiotic stress. Although drought stress is a key determinant of plant physiology and metabolic homeostasis, the role of Dof genes in different degrees of PEG6000-induced drought stress has received little attention. Methods Tea plants (Camellia sinensis) were exposed to mild, moderate and severe drought stress. The Tea Genome and Plant TFDB databases were used to identify Dof gene family members in the tea plant. Clustal W2.1, MEGA6.0, ScanProsite, SMART, ExPASy, GSDS, MEME and STRING were used to build a phylogenetic tree, predict the molecular masses and isoelectric points of the Dof proteins, and construct a predicted protein-protein interaction network between the CsDof TFs and proteins in the A. thaliana database. The expression patterns of Dof genes in different tissues were analyzed, and qRT-PCR was used to measure the expression of Dof genes under different degrees of drought stress in tea. Results We identified 16 Dof genes in tea (C. sinensis cv. Huangjinya) using whole-genome analysis. Through comparative analysis of tea and Arabidopsis thaliana, we divided the Dof genes into four families (A, B, C, and D). We identified 15 motifs in the amino acid sequences of the CsDof proteins. Gene sequences and motif structures were highly conserved among families, especially in the B1 and C2 subfamilies. The protein-protein interaction network indicated that multiple CsDof proteins may be involved in the response to drought stress. Real-time PCR was used to examine the tissue-specific expression patterns of the CsDof genes and to measure their responses to different levels of PEG6000-induced drought stress in mature leaves. Most CsDof genes responded to drought stress. These results provide information on the Dof gene family in tea, offer new insights into the function of CsDof genes in a perennial species, and lay the foundation for further analysis of their functions.
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Affiliation(s)
- Qian Yu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China.,State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Chen Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China.,State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Jiucheng Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China.,State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Yueyue Tian
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China.,State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Hanyue Wang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China.,State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Yue Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China.,State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Zhengqun Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China.,State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Qinzeng Xiang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China.,State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Xiaoyang Han
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China.,State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
| | - Lixia Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an, China.,State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, China
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Wang Y, Bailey DC, Yin S, Dong X. Characterizing rhizome bud dormancy in Polygonatum kingianum: Development of novel chill models and determination of dormancy release mechanisms by weighted correlation network analysis. PLoS One 2020; 15:e0231867. [PMID: 32353065 PMCID: PMC7192456 DOI: 10.1371/journal.pone.0231867] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/02/2020] [Indexed: 12/25/2022] Open
Abstract
This study was conducted to explore specific chill models and the mechanisms underlying rhizome bud dormancy break in Polygonatum kingianum. Rhizome buds were subjected to various chilling temperatures for different duration and then transferred to warm conditions for germination and subsequent evaluation of their response to temperature and chilling requirements. A CUkingianum model was constructed to describe the contribution of low temperature to the chill unit, and it was suggested that 2.97°C was the optimum temperature and that 11.54°C was the upper limit for bud release. The CASkingianum model showed the relationship between chilling accumulation and sprouting percentage; therefore, rhizome bud development could be predicted through the model. Weighted correlation network analysis (WGCNA) of transcriptomic data of endo-, eco- and nondormant rhizome buds generated 33 gene modules, 6 of which were significantly related to bud sprouting percentage. In addition, 7 significantly matched transcription factors (TFs) were identified from the promoters of 17 "real" hub genes, and DAG2 was the best matched TF that bound to AAAG element to regulate gene expression. The current study is valuable for developing a highly efficient strategy for seedling cultivation and provides strong candidates for key genes related to rhizome bud dormancy in P. kingianum.
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Affiliation(s)
- Yue Wang
- Department of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Donovan C Bailey
- Department of Biology, New Mexico State University, Las Cruces, New Mexico State, United States of America
| | - Shikai Yin
- Department of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Xuehui Dong
- Department of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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Xiong R, Liu C, Xu M, Wei SS, Huang JQ, Tang H. Transcriptomic analysis of flower induction for long-day pitaya by supplementary lighting in short-day winter season. BMC Genomics 2020; 21:329. [PMID: 32349680 PMCID: PMC7191803 DOI: 10.1186/s12864-020-6726-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 04/12/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pitayas are currently attracting considerable interest as a tropical fruit with numerous health benefits. However, as a long-day plant, pitaya plants cannot flower in the winter season from November to April in Hainan, China. To harvest pitayas with high economic value in the winter season, it is necessary to provide supplementary lighting at night to induce flowering. To further explore the molecular regulating mechanisms of flower induction in pitaya plants exposed to supplementary lighting, we used de novo RNA sequencing-based transcriptomic analysis for four stages of pitaya plants subjected to light induction. RESULTS We assembled 68,113 unigenes in total, comprising 29,782 unigenes with functional annotations in the NR database, 20,716 annotations in SwissProt, 18,088 annotations in KOG, and 11,059 annotations in KEGG. Comparisons between different samples revealed different numbers of significantly differentially expressed genes (DEGs). A number of DEGs involved in energy metabolism-related processes and plant hormone signaling were detected. Moreover, we identified many CONSTANS-LIKE, FLOWERING LOCUS T, and other DEGs involved in the direct regulation of flowering including CDF and TCP, which function as typical transcription factor genes in the flowering process. At the transcriptomic level, we verified 13 DEGs with different functions in the time-course response to light-induced flowering by quantitative reverse-transcription PCR analysis. CONCLUSIONS The identified DEGs may include some key genes controlling the pitaya floral-induction network, the flower induction and development is very complicated, and it involves photoperiod perception and different phytohormone signaling. These findings will increase our understanding to the molecular mechanism of floral regulation of long-day pitaya plants in short-day winter season induced by supplementary lighting.
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Affiliation(s)
- Rui Xiong
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, No. 58 Renmin Avenue, Haikou, 570228, Hainan, P. R. China
| | - Chengli Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, No. 58 Renmin Avenue, Haikou, 570228, Hainan, P. R. China
| | - Min Xu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, No. 58 Renmin Avenue, Haikou, 570228, Hainan, P. R. China
| | - Shuang-Shuang Wei
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, No. 58 Renmin Avenue, Haikou, 570228, Hainan, P. R. China
| | - Jia-Quan Huang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, No. 58 Renmin Avenue, Haikou, 570228, Hainan, P. R. China
| | - Hua Tang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, No. 58 Renmin Avenue, Haikou, 570228, Hainan, P. R. China.
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Ritonga FN, Chen S. Physiological and Molecular Mechanism Involved in Cold Stress Tolerance in Plants. PLANTS (BASEL, SWITZERLAND) 2020; 9:E560. [PMID: 32353940 PMCID: PMC7284489 DOI: 10.3390/plants9050560] [Citation(s) in RCA: 120] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/18/2020] [Accepted: 04/21/2020] [Indexed: 01/26/2023]
Abstract
Previous studies have reported that low temperature (LT) constrains plant growth and restricts productivity in temperate regions. However, the underlying mechanisms are complex and not well understood. Over the past ten years, research on the process of adaptation and tolerance of plants during cold stress has been carried out. In molecular terms, researchers prioritize research into the field of the ICE-CBF-COR signaling pathway which is believed to be the important key to the cold acclimation process. Inducer of CBF Expression (ICE) is a pioneer of cold acclimation and plays a central role in C-repeat binding (CBF) cold induction. CBFs activate the expression of COR genes via binding to cis-elements in the promoter of COR genes. An ICE-CBF-COR signaling pathway activates the appropriate expression of downstream genes, which encodes osmoregulation substances. In this review, we summarize the recent progress of cold stress tolerance in plants from molecular and physiological perspectives and other factors, such as hormones, light, and circadian clock. Understanding the process of cold stress tolerance and the genes involved in the signaling network for cold stress is essential for improving plants, especially crops.
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Affiliation(s)
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China;
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