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Yuan H, Cheng M, Wang R, Wang Z, Fan F, Wang W, Si F, Gao F, Li S. miR396b/GRF6 module contributes to salt tolerance in rice. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2079-2092. [PMID: 38454780 PMCID: PMC11258987 DOI: 10.1111/pbi.14326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 03/09/2024]
Abstract
Salinity, as one of the most challenging environmental factors restraining crop growth and yield, poses a severe threat to global food security. To address the rising food demand, it is urgent to develop crop varieties with enhanced yield and greater salt tolerance by delving into genes associated with salt tolerance and high-yield traits. MiR396b/GRF6 module has previously been demonstrated to increase rice yield by shaping the inflorescence architecture. In this study, we revealed that miR396b/GRF6 module can significantly improve salt tolerance of rice. In comparison with the wild type, the survival rate of MIM396 and OE-GRF6 transgenic lines increased by 48.0% and 74.4%, respectively. Concurrent with the increased salt tolerance, the transgenic plants exhibited reduced H2O2 accumulation and elevated activities of ROS-scavenging enzymes (CAT, SOD and POD). Furthermore, we identified ZNF9, a negative regulator of rice salt tolerance, as directly binding to the promoter of miR396b to modulate the expression of miR396b/GRF6. Combined transcriptome and ChIP-seq analysis showed that MYB3R serves as the downstream target of miR396b/GRF6 in response to salt tolerance, and overexpression of MYB3R significantly enhanced salt tolerance. In conclusion, this study elucidated the potential mechanism underlying the response of the miR396b/GRF6 network to salt stress in rice. These findings offer a valuable genetic resource for the molecular breeding of high-yield rice varieties endowed with stronger salt tolerance.
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Affiliation(s)
- Huanran Yuan
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of EducationCollege of Life Sciences, Wuhan UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
| | - Mingxing Cheng
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of EducationCollege of Life Sciences, Wuhan UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
| | - Ruihua Wang
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of EducationCollege of Life Sciences, Wuhan UniversityWuhanChina
| | - Zhikai Wang
- College of Life Science, Yangtze UniversityJingzhouChina
| | - Fengfeng Fan
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of EducationCollege of Life Sciences, Wuhan UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
| | - Wei Wang
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of EducationCollege of Life Sciences, Wuhan UniversityWuhanChina
| | - Fengfeng Si
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of EducationCollege of Life Sciences, Wuhan UniversityWuhanChina
| | - Feng Gao
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of EducationCollege of Life Sciences, Wuhan UniversityWuhanChina
| | - Shaoqing Li
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of EducationCollege of Life Sciences, Wuhan UniversityWuhanChina
- Hubei Hongshan LaboratoryWuhanChina
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Khisti M, Avuthu T, Yogendra K, Kumar Valluri V, Kudapa H, Reddy PS, Tyagi W. Genome-wide identification and expression profiling of growth‑regulating factor (GRF) and GRF‑interacting factor (GIF) gene families in chickpea and pigeonpea. Sci Rep 2024; 14:17178. [PMID: 39060385 PMCID: PMC11282205 DOI: 10.1038/s41598-024-68033-2] [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: 01/19/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
The growth-regulating factor (GRF) and GRF-interacting factor (GIF) families encode plant-specific transcription factors and play vital roles in plant development and stress response processes. Although GRF and GIF genes have been identified in various plant species, there have been no reports of the analysis and identification of the GRF and GIF transcription factor families in chickpea (Cicer arietinum) and pigeonpea (Cajanus cajan). The present study identified seven CaGRFs, eleven CcGRFs, four CaGIFs, and four CcGIFs. The identified proteins were grouped into eight and three clades for GRFs and GIFs, respectively based on their phylogenetic relationships. A comprehensive in-silico analysis was performed to determine chromosomal location, sub-cellular localization, and types of regulatory elements present in the putative promoter region. Synteny analysis revealed that GRF and GIF genes showed diploid-polyploid topology in pigeonpea, but not in chickpea. Tissue-specific expression data at the vegetative and reproductive stages of the plant showed that GRFs and GIFs were strongly expressed in tissues like embryos, pods, and seeds, indicating that GRFs and GIFs play vital roles in plant growth and development. This research characterized GRF and GIF families and hints at their primary roles in the chickpea and pigeonpea growth and developmental process. Our findings provide potential gene resources and vital information on GRF and GIF gene families in chickpea and pigeonpea, which will help further understand the regulatory role of these gene families in plant growth and development.
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Affiliation(s)
- Mitesh Khisti
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Tejaswi Avuthu
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Kalenahalli Yogendra
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Vinod Kumar Valluri
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Himabindu Kudapa
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Palakolanu Sudhakar Reddy
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India
| | - Wricha Tyagi
- Research Program-Accelerated Crop Improvement, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Patancheru, Telangana, 502324, India.
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Sha G, Cheng J, Wang X, Xue Q, Zhang H, Zhai R, Yang C, Wang Z, Xu L. PbbHLH137 interacts with PbGIF1 to regulate pear fruit development by promoting cell expansion to increase fruit size. PHYSIOLOGIA PLANTARUM 2024; 176:e14451. [PMID: 39075941 DOI: 10.1111/ppl.14451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/16/2024] [Accepted: 07/07/2024] [Indexed: 07/31/2024]
Abstract
The regulation of fruit development is a complex process and a core issue in the fruit tree industry. To investigate the role of PbGIF1 in pear fruit development, we identified a transcription factor PbbHLH137 that regulates pear (Pyrus bretschneideri) fruit development by screening a yeast library constructed from fruit cDNA. Yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BiFC), and split luciferase complementation (split-LUC) assays were performed to confirm the PbbHLH137-PbGIF1 interaction. By tracing the complete fruit development process, we found that PbbHLH137 expression was closely related to fruit size and highly involved at the late pear fruit development stage. Transgenic experiments showed that heterologous expression of PbbHLH137 or PbGIF1 promoted fruit enlargement. PbbHLH137 promoted mainly the expansion of fruit cell volume, whereas PbGIF1 mainly increased the number of cells. Further LUC experiments demonstrated that PbGIF1 promoted the transcriptional activation ability of PbbHLH137. Our work identified PbbHLH137 as a transcription factor that regulates fruit development, and showed that PbGIF1 played an ongoing role during fruit development, making it a candidate gene for genetic improvement of pear fruit development.
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Affiliation(s)
- Guangya Sha
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Jingjing Cheng
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Xue Wang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Qiyang Xue
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Haiqi Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Rui Zhai
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Chengquan Yang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Zhigang Wang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Lingfei Xu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province, China
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Cui D, Song Y, Jiang W, Ye H, Wang S, Yuan L, Liu B. Genome-wide characterization of the GRF transcription factors in potato ( Solanum tuberosum L.) and expression analysis of StGRF genes during potato tuber dormancy and sprouting. FRONTIERS IN PLANT SCIENCE 2024; 15:1417204. [PMID: 38978523 PMCID: PMC11228316 DOI: 10.3389/fpls.2024.1417204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Accepted: 06/03/2024] [Indexed: 07/10/2024]
Abstract
Growth-regulating factors (GRFs) are transcription factors that play a pivotal role in plant growth and development. This study identifies 12 Solanum tuberosum GRF transcription factors (StGRFs) and analyzes their physicochemical properties, phylogenetic relationships, gene structures and gene expression patterns using bioinformatics. The StGRFs exhibit a length range of 266 to 599 amino acids, with a molecular weight of 26.02 to 64.52 kDa. The majority of StGRFs possess three introns. The promoter regions contain a plethora of cis-acting elements related to plant growth and development, as well as environmental stress and hormone response. All the members of the StGRF family contain conserved WRC and QLQ domains, with the sequences of these two conserved domain modules exhibiting high levels of conservation. Transcriptomic data indicates that StGRFs play a significant role in the growth and development of stamens, roots, young tubers, and other tissues or organs in potatoes. Furthermore, a few StGRFs exhibit differential expression patterns in response to Phytophthora infestans, chemical elicitors, heat, salt, and drought stresses, as well as multiple hormone treatments. The results of the expression analysis indicate that StGRF1, StGRF2, StGRF5, StGRF7, StGRF10 and StGRF12 are involved in the process of tuber sprouting, while StGRF4 and StGRF9 may play a role in tuber dormancy. These findings offer valuable insights that can be used to investigate the roles of StGRFs during potato tuber dormancy and sprouting.
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Affiliation(s)
- Danni Cui
- Shenzhen Research Institute, Northwest A&F University, Shenzhen, China
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, China
| | - Yin Song
- Shenzhen Research Institute, Northwest A&F University, Shenzhen, China
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, China
| | - Weihao Jiang
- Shenzhen Research Institute, Northwest A&F University, Shenzhen, China
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, China
| | - Han Ye
- Shenzhen Research Institute, Northwest A&F University, Shenzhen, China
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, China
| | - Shipeng Wang
- Shenzhen Research Institute, Northwest A&F University, Shenzhen, China
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, China
| | - Li Yuan
- Shenzhen Research Institute, Northwest A&F University, Shenzhen, China
| | - Bailin Liu
- Shenzhen Research Institute, Northwest A&F University, Shenzhen, China
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, China
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Patil BL, Tripathi S. Differential expression of microRNAs in response to Papaya ringspot virus infection in differentially responding genotypes of papaya ( Carica papaya L.) and its wild relative. FRONTIERS IN PLANT SCIENCE 2024; 15:1398437. [PMID: 38966149 PMCID: PMC11222417 DOI: 10.3389/fpls.2024.1398437] [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: 03/09/2024] [Accepted: 05/29/2024] [Indexed: 07/06/2024]
Abstract
Papaya ringspot virus (PRSV) is one of the most devastating viruses of papaya that has significantly hampered papaya production across the globe. Although PRSV resistance is known in some of its wild relatives, such as Vasconcellea cauliflora and in some of the improved papaya genotypes, the molecular basis of this resistance mechanism has not been studied and understood. Plant microRNAs are an important class of small RNAs that regulate the gene expression in several plant species against the invading plant pathogens. These miRNAs are known to manifest the expression of genes involved in resistance against plant pathogens, through modulation of the plant's biochemistry and physiology. In this study we made an attempt to study the overall expression pattern of small RNAs and more specifically the miRNAs in different papaya genotypes from India, that exhibit varying levels of tolerance or resistance to PRSV. Our study found that the expression of some of the miRNAs was differentially regulated in these papaya genotypes and they had entirely different miRNA expression profile in healthy and PRSV infected symptomatic plants. This data may help in improvement of papaya cultivars for resistance against PRSV through new breeding initiatives or biotechnological approaches such as genome editing.
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Affiliation(s)
| | - Savarni Tripathi
- ICAR-Indian Agricultural Research Institute, Regional Station, Pune, India
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Nardeli SM, Arge LWP, Artico S, de Moura SM, Tschoeke DA, de Freitas Guedes FA, Grossi-de-Sa MF, Martinelli AP, Alves-Ferreira M. Global gene expression profile and functional analysis reveal the conservation of reproduction-associated gene networks in Gossypium hirsutum. PLANT REPRODUCTION 2024; 37:215-227. [PMID: 38183442 DOI: 10.1007/s00497-023-00491-6] [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: 05/31/2023] [Accepted: 11/29/2023] [Indexed: 01/08/2024]
Abstract
KEY MESSAGE Lastly, the bZIP gene family encompasses genes that have been reported to play a role in flower development, such as bZIP14 (FD). Notably, bZIP14 is essential for Flowering Locus T (FT) initiation of floral development in Arabidopsis (Abe et al. 2005). Cotton (Gossypium hirsutum L.) is the world's most extensively cultivated fiber crop. However, its reproductive development is poorly characterized at the molecular level. Thus, this study presents a detailed transcriptomic analysis of G. hirsutum at three different reproductive stages. We provide evidence that more than 64,000 genes are active in G. hirsutum during flower development, among which 94.33% have been assigned to functional terms and specific pathways. Gene set enrichment analysis (GSEA) revealed that the biological process categories of floral organ development, pollen exine formation, and stamen development were enriched among the genes expressed during the floral development of G. hirsutum. Furthermore, we identified putative Arabidopsis homologs involved in the G. hirsutum gene regulatory network (GRN) of pollen and flower development, including transcription factors such as WUSCHEL (WUS), INNER NO OUTER (INO), AGAMOUS-LIKE 66 (AGL66), SPOROCYTELESS/NOZZLE (SPL/NZZ), DYSFUNCTIONAL TAPETUM 1 (DYT1), ABORTED MICROSPORES (AMS), and ASH1-RELATED 3 (ASHR3), which are known crucial genes for plant reproductive success. The cotton MADS-box protein-protein interaction pattern resembles the previously described patterns for AGAMOUS (AG), SEEDSTICK (STK), SHATTERPROOF (SHP), and SEPALLATA3 (SEP3) homolog proteins from Arabidopsis. In addition to serving as a resource for comparative flower development studies, this work highlights the changes in gene expression profiles and molecular networks underlying stages that are valuable for cotton breeding improvement.
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Affiliation(s)
- Sarah Muniz Nardeli
- Laboratório de Genética Molecular e Biotecnologia Vegetal, Universidade Federal do Rio de Janeiro-UFRJ, Rio de Janeiro, RJ, Brazil
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Luis Willian Pacheco Arge
- Laboratório de Genética Molecular e Biotecnologia Vegetal, Universidade Federal do Rio de Janeiro-UFRJ, Rio de Janeiro, RJ, Brazil
| | - Sinara Artico
- Laboratório de Genética Molecular e Biotecnologia Vegetal, Universidade Federal do Rio de Janeiro-UFRJ, Rio de Janeiro, RJ, Brazil
| | - Stéfanie Menezes de Moura
- Laboratório de Genética Molecular e Biotecnologia Vegetal, Universidade Federal do Rio de Janeiro-UFRJ, Rio de Janeiro, RJ, Brazil
- Embrapa Genetic Resources and Biotechnology-Embrapa, Brasília, DF, Brazil
| | - Diogo Antonio Tschoeke
- Laboratório de Microbiologia, Universidade Federal do Rio de Janeiro-UFRJ, Rio de Janeiro, RJ, Brazil
| | - Fernanda Alves de Freitas Guedes
- Laboratório de Genética Molecular e Biotecnologia Vegetal, Universidade Federal do Rio de Janeiro-UFRJ, Rio de Janeiro, RJ, Brazil
| | - Maria Fatima Grossi-de-Sa
- Embrapa Genetic Resources and Biotechnology-Embrapa, Brasília, DF, Brazil
- Catholic University of Brasília, Brasília, DF, Brazil
- National Institute of Science and Technology-INCT PlantStress Biotech, Embrapa, Brasília, DF, Brazil
| | | | - Marcio Alves-Ferreira
- Laboratório de Genética Molecular e Biotecnologia Vegetal, Universidade Federal do Rio de Janeiro-UFRJ, Rio de Janeiro, RJ, Brazil.
- National Institute of Science and Technology-INCT PlantStress Biotech, Embrapa, Brasília, DF, Brazil.
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Faiz Z, Parveen S, Saeed S, Tayyab M, Sultana M, Hussain M, Shafqat Z. Comparative genomic studies on the TGF-β superfamily in blue whale. Mamm Genome 2024; 35:228-240. [PMID: 38467865 DOI: 10.1007/s00335-024-10031-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/29/2024] [Indexed: 03/13/2024]
Abstract
TGF-β supergene family has a wide range of physiological functions including cell adhesion, motility, proliferation, apoptosis, and differentiation. We systematically analyzed and characterized the TGF-β gene superfamily from the whole blue whale (Balaenoptera musculus) genome, using comparative genomic and evolutionary analysis. We identified 30 TGF-β genes and were split into two subgroups, BMP-like and TGF-like. All TGF-β proteins demonstrating a basic nature, with the exception of BMP1, BMP2, BMP10, GDF2, MSTN, and NODAL modulator, had acidic characteristics. All the blue whale (B. musculus) TGF-β proteins, excluding BMP1, are thermostable based on aliphatic index. The instability index showed all proteins except the NODAL modulator was unstable. TGF-β proteins showed a hydrophilic character, with the exception of GDF1 and INHBC. Moreover, all the detected TGF-β genes showed evolutionary conserved nature. A segmental duplication was indicated by TGF-β gene family, and the Ka/Ks ratio showed that the duplicated gene pairs were subjected to selection pressure, indicating both purifying and positive selection pressure. Two possible recombination breakpoints were also predicted. This study provides insights into the genetic characterization and evolutionary aspects of the TGF-β superfamily in blue whales (B. musculus).
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Affiliation(s)
- Zunaira Faiz
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
| | - Shakeela Parveen
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan.
| | - Saba Saeed
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
| | - Muhammad Tayyab
- Department of Zoology, Government College University Faisalabad, Faisalabad, Punjab, Pakistan
| | - Mehwish Sultana
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
| | - Muhammad Hussain
- Department of Veterinary and Animal Sciences, University of Veterinary and Animal Sciences, Lahore, Punjab, Pakistan
| | - Zainab Shafqat
- Department of Zoology, The Government Sadiq College Women University, Bahawalpur, 63100, Punjab, Pakistan
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Yang Z, Zhao M, Zhang X, Gu L, Li J, Ming F, Wang M, Wang Z. MIR396-GRF/GIF enhances in planta shoot regeneration of Dendrobium catenatum. BMC Genomics 2024; 25:543. [PMID: 38822270 PMCID: PMC11143658 DOI: 10.1186/s12864-024-10360-9] [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: 01/08/2024] [Accepted: 04/29/2024] [Indexed: 06/02/2024] Open
Abstract
Recent studies on co-transformation of the growth regulator, TaGRF4-GIF1 chimera (Growth Regulating Factor 4-GRF Interacting Factor 1), in cultivated wheat varieties (Triticum aestivum), showed improved regeneration efficiency, marking a significant breakthrough. Here, a simple and reproducible protocol using the GRF4-GIF1 chimera was established and tested in the medicinal orchid Dendrobium catenatum, a monocot orchid species. TaGRF4-GIF1 from T. aestivum and DcGRF4-GIF1 from D. catenatum were reconstructed, with the chimeras significantly enhancing the regeneration efficiency of D. catenatum through in planta transformation. Further, mutating the microRNA396 (miR396) target sites in TaGRF4 and DcGRF4 improved regeneration efficiency. The target mimicry version of miR396 (MIM396) not only boosted shoot regeneration but also enhanced plant growth. Our methods revealed a powerful tool for the enhanced regeneration and genetic transformation of D. catenatum.
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Affiliation(s)
- Zhenyu Yang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, the National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, the National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Meili Zhao
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, the National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, the National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
| | - Xiaojie Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, the National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, the National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
- Xinjiang Key Laboratory of Grassland Resources and Ecology, College of Grassland Sciences, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Lili Gu
- Xinjiang Key Laboratory of Grassland Resources and Ecology, College of Grassland Sciences, Xinjiang Agricultural University, Urumqi, 830052, China
| | - Jian Li
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, the National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, the National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China
| | - Feng Ming
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
| | - Meina Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, the National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China.
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, the National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China.
| | - Zhicai Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, the National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China.
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, the National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen, 518114, China.
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Xu M, Li L, Yan J, Li D, Liu Y, Zhang W, Liu Y. Blocking miR396 activity by overexpression MIM396 improved switchgrass tiller number and biomass yield. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:69. [PMID: 38802880 PMCID: PMC11131217 DOI: 10.1186/s13068-024-02514-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 05/07/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND MicroRNA396 (miR396) plays an important role in the regulation of plant growth and development by repressing the expression level of its target growth-regulating factor (GRF) family genes. In our previous study, we found that overexpression of miR396 negatively regulated both tillering and biomass yield in switchgrass (Panicum virgatum L.). We, therefore, speculated that blocking the expression of miR396 could enhance switchgrass tillering and biomass yield. Here, we produced transgenic switchgrass plants overexpressing a target mimicry form of miR396 (MIM396) in wild type (WT) and Os-MIR319b overexpressing switchgrass plant (with higher enzymatic hydrolysis efficiency, but reduced tillering), in which the expression of miR396 was blocked. The phenotype and biological yields of these plants were analyzed. RESULTS Blocking miR396 to improve its target PvGRFs expression in switchgrass improved the tiller number and dry weight of transgenic plants. Further morphological analysis revealed that MIM396 plants increased the number of aerial branches and basal tillers compared to those of wild-type plants. The enzymatic efficiency of MIM396 plants was reduced; however, the total sugar production per plant was still significantly higher than that of wild-type plants due to the increase in biomass. In addition, blocking miR396 in a transgenic switchgrass plant overexpressing Os-MIR319b (TG21-Ms) significantly increased the PvGRF1/3/5 expression level and tiller number and biomass yield. The miR156-target gene PvSPL4, playing a negative role in aerial and basal buds outgrowth, showed significant downregulated in MIM396 and TG21-Ms. Those results indicate that miR396-PvGRFs, through disrupting the PvSPL4 expression, are involved in miR319-PvPCFs in regulating tiller number, at least partly. CONCLUSIONS MIM396 could be used as a molecular tool to improving tiller number and biomass yield in switchgrass wild type and miR319b transgenic plants. This finding may be applied to other graminaceous plants to regulate plant biological yield.
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Affiliation(s)
- Mingzhi Xu
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Lin Li
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jianping Yan
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Dayong Li
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, 100097, People's Republic of China
| | - Yaling Liu
- National Center of Pratacultural Technology Innovation (Under Preparation), Hohhot, 010010, China
| | - Wanjun Zhang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yanrong Liu
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China.
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10
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Wang P, Wang Z, Cao H, He J, Qin C, He L, Liu B, Wang J, Kong L, Ren W, Liu X, Ma W. Genome-wide identification and expression pattern analysis of the GRF transcription factor family in Astragalus mongholicus. Mol Biol Rep 2024; 51:618. [PMID: 38705956 DOI: 10.1007/s11033-024-09581-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/22/2024] [Indexed: 05/07/2024]
Abstract
BACKGROUND Astragalus membranaceus is a plant of the Astragalus genus, which is used as a traditional Chinese herbal medicine with extremely high medicinal and edible value. Astragalus mongholicus, as one of the representative medicinal materials with the same origin of medicine and food, has a rising market demand for its raw materials, but the quality is different in different production areas. Growth-regulating factors (GRF) are transcription factors unique to plants that play important roles in plant growth and development. Up to now, there is no report about GRF in A. mongholicus. METHODS AND RESULTS This study conducted a genome-wide analysis of the AmGRF gene family, identifying a total of nine AmGRF genes that were classified into subfamily V based on phylogenetic relationships. In the promoter region of the AmGRF gene, we successfully predicted cis-elements that respond to abiotic stress, growth, development, and hormone production in plants. Based on transcriptomic data and real-time quantitative polymerase chain reaction (qPCR) validation, the results showed that AmGRFs were expressed in the roots, stems, and leaves, with overall higher expression in leaves, higher expression of AmGRF1 and AmGRF8 in roots, and high expression levels of AmGRF1 and AmGRF9 in stems. CONCLUSIONS The results of this study provide a theoretical basis for the further exploration of the functions of AmGRFs in plant growth and development.
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Affiliation(s)
- Panpan Wang
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Zhen Wang
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Huiyan Cao
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Jiajun He
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Chen Qin
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Lianqing He
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Bo Liu
- Library, Harbin Cambridge University, Harbin, 150069, China
| | - Jiamei Wang
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
- Equipment department, Heilongjiang University of Chinese Medicine, Haerbin, 150040, China
| | - Lingyang Kong
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Weichao Ren
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, 150040, China.
| | - Xiubo Liu
- Jiamusi College, Heilongjiang University of Chinese Medicine, Jiamusi, 154007, China.
| | - Wei Ma
- School of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, 150040, China.
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11
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Xu P, Zhong Y, Xu A, Liu B, Zhang Y, Zhao A, Yang X, Ming M, Cao F, Fu F. Application of Developmental Regulators for Enhancing Plant Regeneration and Genetic Transformation. PLANTS (BASEL, SWITZERLAND) 2024; 13:1272. [PMID: 38732487 PMCID: PMC11085514 DOI: 10.3390/plants13091272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/26/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
Establishing plant regeneration systems and efficient genetic transformation techniques plays a crucial role in plant functional genomics research and the development of new crop varieties. The inefficient methods of transformation and regeneration of recalcitrant species and the genetic dependence of the transformation process remain major obstacles. With the advancement of plant meristematic tissues and somatic embryogenesis research, several key regulatory genes, collectively known as developmental regulators, have been identified. In the field of plant genetic transformation, the application of developmental regulators has recently garnered significant interest. These regulators play important roles in plant growth and development, and when applied in plant genetic transformation, they can effectively enhance the induction and regeneration capabilities of plant meristematic tissues, thus providing important opportunities for improving genetic transformation efficiency. This review focuses on the introduction of several commonly used developmental regulators. By gaining an in-depth understanding of and applying these developmental regulators, it is possible to further enhance the efficiency and success rate of plant genetic transformation, providing strong support for plant breeding and genetic engineering research.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Fangfang Fu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; (P.X.); (Y.Z.); (A.X.); (B.L.); (Y.Z.); (A.Z.); (X.Y.); (M.M.); (F.C.)
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12
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Li P, He Y, Xiao L, Quan M, Gu M, Jin Z, Zhou J, Li L, Bo W, Qi W, Huang R, Lv C, Wang D, Liu Q, El-Kassaby YA, Du Q, Zhang D. Temporal dynamics of genetic architecture governing leaf development in Populus. THE NEW PHYTOLOGIST 2024; 242:1113-1130. [PMID: 38418427 DOI: 10.1111/nph.19649] [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: 09/10/2023] [Accepted: 02/13/2024] [Indexed: 03/01/2024]
Abstract
Leaf development is a multifaceted and dynamic process orchestrated by a myriad of genes to shape the proper size and morphology. The dynamic genetic network underlying leaf development remains largely unknown. Utilizing a synergistic genetic approach encompassing dynamic genome-wide association study (GWAS), time-ordered gene co-expression network (TO-GCN) analyses and gene manipulation, we explored the temporal genetic architecture and regulatory network governing leaf development in Populus. We identified 42 time-specific and 18 consecutive genes that displayed different patterns of expression at various time points. We then constructed eight TO-GCNs that covered the cell proliferation, transition, and cell expansion stages of leaf development. Integrating GWAS and TO-GCN, we postulated the functions of 27 causative genes for GWAS and identified PtoGRF9 as a key player in leaf development. Genetic manipulation via overexpression and suppression of PtoGRF9 revealed its primary influence on leaf development by modulating cell proliferation. Furthermore, we elucidated that PtoGRF9 governs leaf development by activating PtoHB21 during the cell proliferation stage and attenuating PtoLD during the transition stage. Our study provides insights into the dynamic genetic underpinnings of leaf development and understanding the regulatory mechanism of PtoGRF9 in this dynamic process.
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Affiliation(s)
- Peng Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yuling He
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Liang Xiao
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Mingyang Quan
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Mingyue Gu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Zhuoying Jin
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jiaxuan Zhou
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Lianzheng Li
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Wenhao Bo
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Weina Qi
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Rui Huang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Chenfei Lv
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Dan Wang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Qing Liu
- CSIRO Agriculture and Food, Black Mountain, Canberra, ACT, 2601, Australia
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, Forest Sciences Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Qingzhang Du
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Deqiang Zhang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
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13
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Wang R, Zhu Y, Zhao D. Genome-Wide Identification and Expression Analysis of Growth-Regulating Factors in Eucommia ulmoides Oliver (Du-Zhong). PLANTS (BASEL, SWITZERLAND) 2024; 13:1185. [PMID: 38732399 PMCID: PMC11085888 DOI: 10.3390/plants13091185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/20/2024] [Accepted: 04/21/2024] [Indexed: 05/13/2024]
Abstract
The roots, stems, leaves, and seeds of Eucommia ulmoides contain a large amount of trans-polyisoprene (also known as Eu-rubber), which is considered to be an important laticiferous plant with valuable industrial applications. Eu-rubber used in industry is mainly extracted from leaves. Therefore, it is of great significance to identify genes related to regulating the leaf size of E. ulmoides. Plant growth-regulating factors (GRFs) play important roles in regulating leaf size, and their functions are highly conserved across different plant species. However, there have been very limited reports on EuGRFs until now. In this study, eight canonical EuGRFs with both QLQ and WRC domains and two putative eul-miR396s were identified in the chromosome-level genome of E. ulmoides. It is found that, unlike AtGRFs, all EuGRFs contain the miR396s binding site in the terminal of WRC domains. These EuGRFs were distributed on six chromosomes in the genome of E. ulmoides. Collinearity analysis of the E. ulmoides genome revealed that EuGRF1 and EuGRF3 exhibit collinear relationships with EuGRF2, suggesting that those three genes may have emerged via gene replication events. The collinear relationship between EuGRFs, AtGRFs, and OsGRFs showed that EuGRF5 and EuGRF8 had no collinear members in Arabidopsis and rice. Almost all EuGRFs show a higher expression level in growing and developing tissues, and most EuGRF promoters process phytohormone-response and stress-induced cis-elements. Moreover, we found the expression of EuGRFs was significantly induced by gibberellins (GA3) in three hours, and the height of E. ulmoides seedlings was significantly increased one week after GA3 treatment. The findings in this study provide potential candidate genes for further research and lay the foundation for further exploring the molecular mechanism underlying E. ulmoides development in response to GA3.
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Affiliation(s)
- Ruoruo Wang
- Plant Conservation Technology Center, Guizhou Key Laboratory of Agricultural Biotechnology, Biotechnology Institute of Guizhou Province, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Ying Zhu
- Plant Conservation Technology Center, Guizhou Key Laboratory of Agricultural Biotechnology, Biotechnology Institute of Guizhou Province, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Degang Zhao
- Plant Conservation Technology Center, Guizhou Key Laboratory of Agricultural Biotechnology, Biotechnology Institute of Guizhou Province, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
- Ministry of Agriculture and Rural Affairs, Key Laboratory of Crop Genetic Resources and Germplasm Innovation in Karst Region, Guiyang 550006, China
- The Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China
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14
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Luo X, Zhang Y, Zhou M, Liu K, Zhang S, Ye D, Tang C, Cao J. Overexpression of HbGRF4 or HbGRF4-HbGIF1 Chimera Improves the Efficiency of Somatic Embryogenesis in Hevea brasiliensis. Int J Mol Sci 2024; 25:2921. [PMID: 38474173 DOI: 10.3390/ijms25052921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Transgenic technology is a crucial tool for gene functional analysis and targeted genetic modification in the para rubber tree (Hevea brasiliensis). However, low efficiency of plant regeneration via somatic embryogenesis remains a bottleneck of successful genetic transformation in H. brasiliensis. Enhancing expression of GROWTH-REGULATING FACTOR 4 (GRF4)-GRF-INTERACTING FACTOR 1 (GIF1) has been reported to significantly improve shoot and embryo regeneration in multiple crops. Here, we identified endogenous HbGRF4 and HbGIF1 from the rubber clone Reyan7-33-97, the expressions of which dramatically increased along with somatic embryo (SE) production. Intriguingly, overexpression of HbGRF4 or HbGRF4-HbGIF1 markedly enhanced the efficiency of embryogenesis in two H. brasiliensis callus lines with contrasting rates of SE production. Transcriptional profiling revealed that the genes involved in jasmonic acid response were up-regulated, whereas those in ethylene biosynthesis and response as well as the S-adenosylmethionine-dependent methyltransferase activity were down-regulated in HbGRF4- and HbGRF4-HbGIF1-overexpressing H. brasiliensis embryos. These findings open up a new avenue for improving SE production in rubber tree, and help to unravel the underlying mechanisms of HbGRF4-enhanced somatic embryogenesis.
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Affiliation(s)
- Xiaomei Luo
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| | - Yi Zhang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
- National Key Laboratory for Biological Breeding of Tropical Crops, Hainan University, Haikou 570228, China
- Natural Rubber Cooperative Innovation Center of Hainan Province and Ministry of Education of PRC, Hainan University, Haikou 570228, China
| | - Miaomiao Zhou
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| | - Kaiye Liu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
- National Key Laboratory for Biological Breeding of Tropical Crops, Hainan University, Haikou 570228, China
- Natural Rubber Cooperative Innovation Center of Hainan Province and Ministry of Education of PRC, Hainan University, Haikou 570228, China
| | - Shengmin Zhang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
- National Key Laboratory for Biological Breeding of Tropical Crops, Hainan University, Haikou 570228, China
- Natural Rubber Cooperative Innovation Center of Hainan Province and Ministry of Education of PRC, Hainan University, Haikou 570228, China
| | - De Ye
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
- National Key Laboratory for Biological Breeding of Tropical Crops, Hainan University, Haikou 570228, China
- Natural Rubber Cooperative Innovation Center of Hainan Province and Ministry of Education of PRC, Hainan University, Haikou 570228, China
| | - Chaorong Tang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
- National Key Laboratory for Biological Breeding of Tropical Crops, Hainan University, Haikou 570228, China
- Natural Rubber Cooperative Innovation Center of Hainan Province and Ministry of Education of PRC, Hainan University, Haikou 570228, China
| | - Jie Cao
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
- National Key Laboratory for Biological Breeding of Tropical Crops, Hainan University, Haikou 570228, China
- Natural Rubber Cooperative Innovation Center of Hainan Province and Ministry of Education of PRC, Hainan University, Haikou 570228, China
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15
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Viana JPG, Avalos A, Zhang Z, Nelson R, Hudson ME. Common signatures of selection reveal target loci for breeding across soybean populations. THE PLANT GENOME 2024; 17:e20426. [PMID: 38263616 DOI: 10.1002/tpg2.20426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 11/15/2023] [Accepted: 11/21/2023] [Indexed: 01/25/2024]
Abstract
Understanding the underlying genetic bases of yield-related selection and distinguishing these changes from genetic drift are critical for both improved understanding and future success of plant breeding. Soybean [Glycine max (L.) Merr.] is a key species for world food security, yet knowledge of the mechanism of selective breeding in soybean, such as the century-long program of artificial selection in U.S. soybean germplasm, is currently limited to certain genes and loci. Here, we identify genome-wide signatures of selection in separate populations of soybean subjected to artificial selection for increased yield by multiple breeding programs in the United States. We compared the alternative soybean breeding population (AGP) created by USDA-ARS to the conventional public soybean lines (CGP) developed at three different stages of breeding (ancestral, intermediate, and elite) to identify shared signatures of selection and differentiate these from drift. The results showed a strong selection for specific haplotypes identified by single site frequency and haplotype homozygosity methods. A set of common selection signatures was identified in both AGP and CGP that supports the hypothesis that separate breeding programs within similar environments coalesce on the fixation of the same key haplotypes. Signatures unique to each breeding program were observed. These results raise the possibility that selection analysis can allow the identification of favorable alleles to enhance directed breeding approaches.
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Affiliation(s)
- João Paulo Gomes Viana
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Arián Avalos
- U. S. Department of Agriculture, Honeybee Breeding, Genetics, and Physiology Research, Baton Rouge, Louisiana, USA
| | - Zhihai Zhang
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Randall Nelson
- USDA-ARS, Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Matthew E Hudson
- DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1102 S Goodwin Ave, Urbana, Illinois, 61801, USA
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16
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Espindula E, Passaglia LMP. Maize-Azospirillum brasilense interaction: accessing maize's miRNA expression under the effect of an inhibitor of indole-3-acetic acid production by the plant. Braz J Microbiol 2024; 55:101-109. [PMID: 38214876 PMCID: PMC10920601 DOI: 10.1007/s42770-023-01236-3] [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: 09/14/2023] [Accepted: 12/26/2023] [Indexed: 01/13/2024] Open
Abstract
MicroRNA (miRNA) is a class of non-coding RNAs. They play essential roles in plants' physiology, as in the regulation of plant development, response to biotic and abiotic stresses, and symbiotic processes. This work aimed to better understand the importance of maize's miRNA during Azospirillum-plant interaction when the plant indole-3-acetic acid (IAA) production was inhibited with yucasin, an inhibitor of the TAM/YUC pathway. Twelve cDNA libraries from a previous Dual RNA-Seq experiment were used to analyze gene expression using a combined analysis approach. miRNA coding genes (miR) and their predicted mRNA targets were identified among the differentially expressed genes. Statistical differences among the groups indicate that Azospirillum brasilense, yucasin, IAA concentration, or all together could influence the expression of several maize's miRNAs. The miRNA's probable targets were identified, and some of them were observed to be differentially expressed. Dcl4, myb122, myb22, and morf3 mRNAs were probably regulated by their respective miRNAs. Other probable targets were observed responding to the IAA level, the bacterium, or all of them. A. brasilense was able to influence the expression of some maize's miRNA, for example, miR159f, miR164a, miR169j, miR396c, and miR399c. The results allow us to conclude that the bacterium can influence directly or indirectly the expression of some of the identified mRNA targets, probably due to an IAA-independent pathway, and that they are somehow involved in the previously observed physiological effects.
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Affiliation(s)
- Eliandro Espindula
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Centro Politécnico, Curitiba, PR, Brazil
| | - Luciane Maria Pereira Passaglia
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves 9500, Porto Alegre, RS, 91501-970, Brazil.
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17
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Li J, Pan W, Zhang S, Ma G, Li A, Zhang H, Liu L. A rapid and highly efficient sorghum transformation strategy using GRF4-GIF1/ternary vector system. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1604-1613. [PMID: 38038993 DOI: 10.1111/tpj.16575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023]
Abstract
Sorghum is an important crop for food, forage, wine and biofuel production. To enhance its transformation efficiency without negative developmental by-effects, we investigated the impact of GRF4-GIF1 chimaera and GRF5 on sorghum transformation. Both GRF4-GIF1 and GRF5 effectively improved the transformation efficiency of sorghum and accelerated the transformation process of sorghum to less than 2 months which was not observed when using BBM-WUS. As agrobacterium effectors increase the ability of T-DNA transfer into plant cells, we checked whether ternary vector system can additively enhance sorghum transformation. The combination of GRF4-GIF1 with helper plasmid pVS1-VIR2 achieved the highest transformation efficiency, reaching 38.28%, which is 7.71-fold of the original method. Compared with BBM-WUS, overexpressing GRF4-GIF1 caused no noticeable growth defects in sorghum. We further developed a sorghum CRISPR/Cas9 gene-editing tool based on this GRF4-GIF1/ternary vector system, which achieved an average gene mutation efficiency of 41.36%, and null mutants were created in the T0 generation.
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Affiliation(s)
- Junpeng Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, 266237, Qingdao, China
| | - Wenbo Pan
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, 261325, Weifang, China
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, Ministry of Education & Guangdong Provincial Key Laboratory of Laser Life Science, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Shuai Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, 266237, Qingdao, China
| | - Guojing Ma
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, 266237, Qingdao, China
| | - Aixia Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, 266237, Qingdao, China
| | - Huawei Zhang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, 261325, Weifang, China
| | - Lijing Liu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, 266237, Qingdao, China
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18
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Zhou H, Song X, Lu MZ. Growth-regulating factor 15-mediated vascular cambium differentiation positively regulates wood formation in hybrid poplar ( Populus alba × P. glandulosa). FRONTIERS IN PLANT SCIENCE 2024; 15:1343312. [PMID: 38425797 PMCID: PMC10902170 DOI: 10.3389/fpls.2024.1343312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/01/2024] [Indexed: 03/02/2024]
Abstract
Introduction Hybrid poplars are industrial trees in China. An understanding of the molecular mechanism underlying wood formation in hybrid poplars is necessary for molecular breeding. Although the division and differentiation of vascular cambial cells is important for secondary growth and wood formation, the regulation of this process is largely unclear. Methods In this study, mPagGRF15 OE and PagGRF15-SRDX transgenic poplars were generated to investigate the function of PagGRF15. RNA-seq and qRT-PCR were conducted to analyze genome-wide gene expression, while ChIP‒seq and ChIP-PCR were used to identified the downstream genes regulated by PagGRF15. Results and discussion We report that PagGRF15 from hybrid poplar (Populus alba × P. glandulosa), a growth-regulating factor, plays a critical role in the regulation of vascular cambium activity. PagGRF15 was expressed predominantly in the cambial zone of vascular tissue. Overexpression of mPagGRF15 (the mutated version of GRF15 in the miR396 target sequence) in Populus led to decreased plant height and internode number. Further stem cross sections showed that the mPagGRF15 OE plants exhibited significant changes in vascular pattern with an increase in xylem and a reduction in phloem. In addition, cambium cell files were decreased in the mPagGRF15 OE plants. However, dominant suppression of the downstream genes of PagGRF15 using PagGRF15-SRDX showed an opposite phenotype. Based on the RNA-seq and ChIP-seq results, combining qRT-PCR and ChIP-PCR analysis, candidate genes, such as WOX4b, PXY and GID1.3, were obtained and found to be mainly involved in cambial activity and xylem differentiation. Accordingly, we speculated that PagGRF15 functions as a positive regulator mediating xylem differentiation by repressing the expression of the WOX4a and PXY genes to set the pace of cambial activity. In contrast, PagGRF15 mediated the GA signaling pathway by upregulating GID1.3 expression to stimulate xylem differentiation. This study provides valuable information for further studies on vascular cambium differentiation mechanisms and genetic improvement of the specific gravity of wood in hybrid poplars.
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Affiliation(s)
- Houjun Zhou
- The Engineering Research Institute of Agriculture and Forestry, Ludong University, Yantai, China
| | - Xueqin Song
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Meng-Zhu Lu
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
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Yadav A, Mathan J, Dubey AK, Singh A. The Emerging Role of Non-Coding RNAs (ncRNAs) in Plant Growth, Development, and Stress Response Signaling. Noncoding RNA 2024; 10:13. [PMID: 38392968 PMCID: PMC10893181 DOI: 10.3390/ncrna10010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Plant species utilize a variety of regulatory mechanisms to ensure sustainable productivity. Within this intricate framework, numerous non-coding RNAs (ncRNAs) play a crucial regulatory role in plant biology, surpassing the essential functions of RNA molecules as messengers, ribosomal, and transfer RNAs. ncRNAs represent an emerging class of regulators, operating directly in the form of small interfering RNAs (siRNAs), microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs). These ncRNAs exert control at various levels, including transcription, post-transcription, translation, and epigenetic. Furthermore, they interact with each other, contributing to a variety of biological processes and mechanisms associated with stress resilience. This review primarily concentrates on the recent advancements in plant ncRNAs, delineating their functions in growth and development across various organs such as root, leaf, seed/endosperm, and seed nutrient development. Additionally, this review broadens its scope by examining the role of ncRNAs in response to environmental stresses such as drought, salt, flood, heat, and cold in plants. This compilation offers updated information and insights to guide the characterization of the potential functions of ncRNAs in plant growth, development, and stress resilience in future research.
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Affiliation(s)
- Amit Yadav
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA;
| | - Jyotirmaya Mathan
- Sashi Bhusan Rath Government Autonomous Women’s College, Brahmapur 760001, India;
| | - Arvind Kumar Dubey
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
| | - Anuradha Singh
- Department of Plant, Soil and Microbial Science, Michigan State University, East Lansing, MI 48824, USA
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20
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Kumar S, Sharma N, Sopory SK, Sanan-Mishra N. miRNAs and genes as molecular regulators of rice grain morphology and yield. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108363. [PMID: 38281341 DOI: 10.1016/j.plaphy.2024.108363] [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: 07/03/2023] [Revised: 12/07/2023] [Accepted: 01/10/2024] [Indexed: 01/30/2024]
Abstract
Rice is one of the most consumed crops worldwide and the genetic and molecular basis of its grain yield attributes are well understood. Various studies have identified different yield-related parameters in rice that are regulated by the microRNAs (miRNAs). MiRNAs are endogenous small non-coding RNAs that silence gene expression during or after transcription. They control a variety of biological or genetic activities in plants including growth, development and response to stress. In this review, we have summarized the available information on the genetic control of panicle architecture and grain yield (number and morphology) in rice. The miRNA nodes that are associated with their regulation are also described while focussing on the central role of miR156-SPL node to highlight the co-regulation of two master regulators that determine the fate of panicle development. Since abiotic stresses are known to negatively affect yield, the impact of abiotic stress induced alterations on the levels of these miRNAs are also discussed to highlight the potential of miRNAs for regulating crop yields.
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Affiliation(s)
- Sudhir Kumar
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
| | - Neha Sharma
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
| | - Sudhir K Sopory
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
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21
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de Oliveira Cabral SK, de Freitas MB, Stadnik MJ, Kulcheski FR. Emerging roles of plant microRNAs during Colletotrichum spp. infection. PLANTA 2024; 259:48. [PMID: 38285194 DOI: 10.1007/s00425-023-04318-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 12/23/2023] [Indexed: 01/30/2024]
Abstract
MAIN CONCLUSION This review provides valuable insights into plant molecular regulatory mechanisms during fungus attacks, highlighting potential miRNA candidates for future disease management. Plant defense responses to biotic stress involve intricate regulatory mechanisms, including post-transcriptional regulation of genes mediated by microRNAs (miRNAs). These small RNAs play a vital role in the plant's innate immune system, defending against viral, bacterial, and fungal attacks. Among the plant pathogenic fungi, Colletotrichum spp. are notorious for causing anthracnose, a devastating disease affecting economically important crops worldwide. Understanding the molecular machinery underlying the plant immune response to Colletotrichum spp. is crucial for developing tools to reduce production losses. In this comprehensive review, we examine the current understanding of miRNAs associated with plant defense against Colletotrichum spp. We summarize the modulation patterns of miRNAs and their respective target genes. Depending on the function of their targets, miRNAs can either contribute to host resistance or susceptibility. We explore the multifaceted roles of miRNAs during Colletotrichum infection, including their involvement in R-gene-dependent immune system responses, hormone-dependent defense mechanisms, secondary metabolic pathways, methylation regulation, and biosynthesis of other classes of small RNAs. Furthermore, we employ an integrative approach to correlate the identified miRNAs with various strategies and distinct phases of fungal infection. This study provides valuable insights into the current understanding of plant miRNAs and their regulatory mechanisms during fungus attacks.
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Affiliation(s)
- Sarah Kirchhofer de Oliveira Cabral
- Group of Plant Molecular Biology, Center of Biological Sciences, Federal University of Santa Catarina, Florianópolis, Brazil
- Post-Graduation Program in Cell and Developmental Biology, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Mateus Brusco de Freitas
- Laboratory of Plant Pathology, Center of Agricultural Sciences, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Marciel João Stadnik
- Laboratory of Plant Pathology, Center of Agricultural Sciences, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Franceli Rodrigues Kulcheski
- Group of Plant Molecular Biology, Center of Biological Sciences, Federal University of Santa Catarina, Florianópolis, Brazil.
- Post-Graduation Program in Cell and Developmental Biology, Federal University of Santa Catarina, Florianópolis, Brazil.
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22
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Chen X, Zhang J, Wang S, Cai H, Yang M, Dong Y. Genome-wide molecular evolution analysis of the GRF and GIF gene families in Plantae (Archaeplastida). BMC Genomics 2024; 25:74. [PMID: 38233778 PMCID: PMC10795294 DOI: 10.1186/s12864-024-10006-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 01/11/2024] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND Plant growth-regulating factors (GRFs) and GRF-interacting factors (GIFs) interact with each other and collectively have important regulatory roles in plant growth, development, and stress responses. Therefore, it is of great significance to explore the systematic evolution of GRF and GIF gene families. However, our knowledge and understanding of the role of GRF and GIF genes during plant evolution has been fragmentary. RESULTS In this study, a large number of genomic and transcriptomic datasets of algae, mosses, ferns, gymnosperms and angiosperms were used to systematically analyze the evolution of GRF and GIF genes during the evolution of plants. The results showed that GRF gene first appeared in the charophyte Klebsormidium nitens, whereas the GIF genes originated relatively early, and these two gene families were mainly expanded by segmental duplication events after plant terrestrialization. During the process of evolution, the protein sequences and functions of GRF and GIF family genes are relatively conservative. As cooperative partner, GRF and GIF genes contain the similar types of cis-acting elements in their promoter regions, which enables them to have similar transcriptional response patterns, and both show higher levels of expression in reproductive organs and tissues and organs with strong capacity for cell division. Based on protein-protein interaction analysis and verification, we found that the GRF-GIF protein partnership began to be established in pteridophytes and is highly conserved across different terrestrial plants. CONCLUSIONS These results provide a foundation for further exploration of the molecular evolution and biological functions of GRF and GIF genes.
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Affiliation(s)
- Xinghao Chen
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, People's Republic of China
| | - Jun Zhang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, People's Republic of China
| | - Shijie Wang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, People's Republic of China
| | - Hongyu Cai
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, People's Republic of China
| | - Minsheng Yang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China.
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, People's Republic of China.
| | - Yan Dong
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China.
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, 071000, Baoding, People's Republic of China.
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Liu C, Dong K, Du H, Wang X, Sun J, Hu Q, Luo H, Sun X. AsHSP26.2, a creeping bentgrass chloroplast small heat shock protein positively regulates plant development. PLANT CELL REPORTS 2024; 43:32. [PMID: 38195772 DOI: 10.1007/s00299-023-03109-3] [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: 09/09/2023] [Accepted: 11/10/2023] [Indexed: 01/11/2024]
Abstract
KEY MESSAGE The creeping bentgrass small heat shock protein AsHSP26.2 positively regulates plant growth and is a novel candidate for use in crop genetic engineering for enhanced biomass production and grain yield. Small heat shock proteins (sHSPs), a family of proteins with high level of diversity, significantly influence plant stress tolerance and plant development. We have cloned a creeping bentgrass chloroplast-localized sHSP gene, AsHSP26.2 responsive to IAA, GA and 6-BA stimulation. Transgenic creeping bentgrass overexpressing AsHSP26.2 exhibited significantly enhanced plant growth with increased stolon number and length as well as enlarged leaf blade width and leaf sheath diameters, but inhibited leaf trichomes initiation and development in the abaxial epidermis. These phenotypes are completely opposite to those displayed in the transgenic plants overexpressing AsHSP26.8, another chloroplast sHSP26 isoform that contains additional seven amino acids (AEGQGDG) between the consensus regions III and IV (Sun et al., Plant Cell Environ 44:1769-1787, 2021). Furthermore, AsHSP26.2 overexpression altered phytohormone biosynthesis and signaling transduction, resulting in elevated auxin and gibberellins (GA) accumulation. The results obtained provide novel insights implicating the sHSPs in plant growth and development regulation, and strongly suggest AsHSP26.2 to be a novel candidate for use in crop genetic engineering for enhanced plant biomass production and grain yield.
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Affiliation(s)
- Chang Liu
- College of Agronomy, Hebei Agricultural University, Baoding, Hebei, 071001, People's Republic of China
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, 071001, People's Republic of China
- Key Laboratory of Crop Growth Regulation of Hebei Province, Hebei Agricultural University, Baoding, Hebei, 071001, People's Republic of China
| | - Kangting Dong
- College of Agronomy, Hebei Agricultural University, Baoding, Hebei, 071001, People's Republic of China
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, 071001, People's Republic of China
- Key Laboratory of Crop Growth Regulation of Hebei Province, Hebei Agricultural University, Baoding, Hebei, 071001, People's Republic of China
| | - Hui Du
- College of Agronomy, Hebei Agricultural University, Baoding, Hebei, 071001, People's Republic of China
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, 071001, People's Republic of China
- Key Laboratory of Crop Growth Regulation of Hebei Province, Hebei Agricultural University, Baoding, Hebei, 071001, People's Republic of China
| | - Xiaodong Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, 071001, People's Republic of China
- College of Plant Protection, Hebei Agricultural University, Baoding, 071000, China
| | - Jianmiao Sun
- College of Agronomy, Hebei Agricultural University, Baoding, Hebei, 071001, People's Republic of China
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, 071001, People's Republic of China
- Key Laboratory of Crop Growth Regulation of Hebei Province, Hebei Agricultural University, Baoding, Hebei, 071001, People's Republic of China
| | - Qian Hu
- Department of Genetics and Biochemistry, Clemson University, 110 Biosystems Research Complex, Clemson, SC, 29634, USA
| | - Hong Luo
- Department of Genetics and Biochemistry, Clemson University, 110 Biosystems Research Complex, Clemson, SC, 29634, USA.
| | - Xinbo Sun
- College of Agronomy, Hebei Agricultural University, Baoding, Hebei, 071001, People's Republic of China.
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, 071001, People's Republic of China.
- Key Laboratory of Crop Growth Regulation of Hebei Province, Hebei Agricultural University, Baoding, Hebei, 071001, People's Republic of China.
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24
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Fu MK, He YN, Yang XY, Tang X, Wang M, Dai WS. Genome-wide identification of the GRF family in sweet orange (Citrus sinensis) and functional analysis of the CsGRF04 in response to multiple abiotic stresses. BMC Genomics 2024; 25:37. [PMID: 38184538 PMCID: PMC10770916 DOI: 10.1186/s12864-023-09952-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 12/28/2023] [Indexed: 01/08/2024] Open
Abstract
BACKGROUND Citrus is one of the most valuable fruits worldwide and an economic pillar industry in southern China. Nevertheless, it frequently suffers from undesirable environmental stresses during the growth cycle, which severely restricts the growth, development and yield of citrus. In plants, the growth-regulating factor (GRF) family of transcription factors (TF) is extensively distributed and plays an vital part in plant growth and development, hormone response, as well as stress adaptation. However, the systematic identification and functional analysis of GRF TFs in citrus have not been reported. RESULTS Here, a genome-wide identification of GRF TFs was performed in Citrus sinensis, 9 members of CsGRFs were systematically identified and discovered to be scattered throughout 5 chromosomes. Subsequently, physical and chemical properties, phylogenetic relationships, structural characteristics, gene duplication events, collinearity and cis-elements of promoter were elaborately analyzed. In particular, the expression patterns of the CsGRF genes in response to multiple phytohormone and abiotic stress treatments were investigated. Predicated on this result, CsGRF04, which exhibited the most differential expression pattern under multiple phytohormone and abiotic stress treatments was screened out. Virus-induced gene silencing (VIGS) technology was utilized to obtain gene silenced plants for CsGRF04 successfully. After the three stress treatments of high salinity, low temperature and drought, the CsGRF04-VIGS lines showed significantly reduced resistance to high salinity and low temperature stresses, but extremely increased resistance to drought stress. CONCLUSIONS Taken together, our findings systematically analyzed the genomic characterization of GRF family in Citrus sinensis, and excavated a CsGRF04 with potential functions under multiple abiotic stresses. Our study lay a foundation for further study on the function of CsGRFs in abiotic stress and hormone signaling response.
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Affiliation(s)
- Ming-Kang Fu
- College of Life Sciences, Gannan Normal University, National Navel Orange Engineering Research Center, Ganzhou, 341000, Jiangxi, China
| | - Ying-Na He
- College of Life Sciences, Gannan Normal University, National Navel Orange Engineering Research Center, Ganzhou, 341000, Jiangxi, China
| | - Xiao-Yue Yang
- College of Life Sciences, Gannan Normal University, National Navel Orange Engineering Research Center, Ganzhou, 341000, Jiangxi, China
| | - Xi Tang
- College of Life Sciences, Gannan Normal University, National Navel Orange Engineering Research Center, Ganzhou, 341000, Jiangxi, China
| | - Min Wang
- College of Life Sciences, Gannan Normal University, National Navel Orange Engineering Research Center, Ganzhou, 341000, Jiangxi, China
| | - Wen-Shan Dai
- College of Life Sciences, Gannan Normal University, National Navel Orange Engineering Research Center, Ganzhou, 341000, Jiangxi, China.
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Yuan HY, Kagale S, Ferrie AMR. Multifaceted roles of transcription factors during plant embryogenesis. FRONTIERS IN PLANT SCIENCE 2024; 14:1322728. [PMID: 38235196 PMCID: PMC10791896 DOI: 10.3389/fpls.2023.1322728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024]
Abstract
Transcription factors (TFs) are diverse groups of regulatory proteins. Through their specific binding domains, TFs bind to their target genes and regulate their expression, therefore TFs play important roles in various growth and developmental processes. Plant embryogenesis is a highly regulated and intricate process during which embryos arise from various sources and undergo development; it can be further divided into zygotic embryogenesis (ZE) and somatic embryogenesis (SE). TFs play a crucial role in the process of plant embryogenesis with a number of them acting as master regulators in both ZE and SE. In this review, we focus on the master TFs involved in embryogenesis such as BABY BOOM (BBM) from the APETALA2/Ethylene-Responsive Factor (AP2/ERF) family, WUSCHEL and WUSCHEL-related homeobox (WOX) from the homeobox family, LEAFY COTYLEDON 2 (LEC2) from the B3 family, AGAMOUS-Like 15 (AGL15) from the MADS family and LEAFY COTYLEDON 1 (LEC1) from the Nuclear Factor Y (NF-Y) family. We aim to present the recent progress pertaining to the diverse roles these master TFs play in both ZE and SE in Arabidopsis, as well as other plant species including crops. We also discuss future perspectives in this context.
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Affiliation(s)
| | | | - Alison M. R. Ferrie
- Aquatic and Crop Resource Development Research Center, National Research Council Canada, Saskatoon, SK, Canada
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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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Kishore Sahoo R, Jeughale KP, Sarkar S, Selvaraj S, Singh NR, Swain N, Balasubramaniasai C, Chidambaranathan P, Katara JL, Nayak AK, Samantaray S. Growing Conditions and Varietal Ecologies Differently Regulates the Growth-regulating-factor (GRFs) Gene Family in Rice. IRANIAN JOURNAL OF BIOTECHNOLOGY 2024; 22:e3697. [PMID: 38827337 PMCID: PMC11139448 DOI: 10.30498/ijb.2024.394984.3697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 12/31/2023] [Indexed: 06/04/2024]
Abstract
Background Growth-regulating factors (GRFs) are crucial in rice for controlling plant growth and development. Among the rice cultivation practices, aerobic methods are water efficient but result in significant yield reduction relative to non-aerobic cultivation. Therefore, mechanistic insights into aerobic rice cultivation are important for improving the aerobic performance of rice. Objectives This study aimed to examine the evolution of GRFs in different rice species, analyse the phenotypic differences between aerobic and non-aerobic conditions in three rice varieties, and assess the expression of GRFs in these varieties under both aerobic and non-aerobic conditions. Materials and Methods This study comprehensively examined the GRFs gene family in 11 rice species (Oryza barthii, Oryza brachyantha, Oryza glaberrima, Oryza glumipatula, Oryza sativa subsp. indica, Oryza longistaminata, Oryza meridionalis, Oryza nivara, Oryza punctata, Oryza rufipogon, Oryza sativa subsp. japonica) focusing on phylogenetic analysis. Additionally, the expression patterns of 12 GRFs were investigated in three distinct genotypes of O. sativa subsp. indica rice, under both non-aerobic and aerobic conditions. Results Three major phylogenetic clades were formed based on conserved motifs in the 123 GRFs proteins in eleven rice species. Further, novel motifs were identified especially in O. longistaminata indicative of the species level evolutionary differences in rice. Among the trait performance, the number of tillers was reduced by ~ 36% under aerobic conditions, but the reduction was found to be less in CR Dhan 201, an aerobic variety. Besides, three GRFs namely GRF3, GRF4, and GRF7 were found to be distinct in expression between aerobic and non-aerobic conditions. Conclusion Three GRF genes namely GRF3, GRF4, and GRF7 could be associated with the aerobic adaptation in rice.
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Affiliation(s)
- Raj Kishore Sahoo
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, India
- Department of Botany, Ravenshaw University, Cuttack, India
| | | | - Suman Sarkar
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, India
| | | | | | - Nibedita Swain
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, India
| | | | | | - Jawahar Lal Katara
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, India
| | - Amaresh Kumar Nayak
- Crop Production Division, ICAR-National Rice Research Institute, Cuttack, India
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Zhu S, Wang H, Xue Q, Zou H, Liu W, Xue Q, Ding XY. Genome-wide identification and expression analysis of growth-regulating factors in Dendrobium officinale and Dendrobium chrysotoxum. PeerJ 2023; 11:e16644. [PMID: 38111654 PMCID: PMC10726744 DOI: 10.7717/peerj.16644] [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: 08/16/2023] [Accepted: 11/20/2023] [Indexed: 12/20/2023] Open
Abstract
Background Dendrobium, one of the largest genera in Orchidaceae, is popular not only for its aesthetic appeal but for its significant medicinal value. Growth-regulating factors (GRFs) play an essential role in plant growth and development. However, there is still a lack of information about the evolution and biological function analysis of the GRF gene family among Dendrobiumspecies. Methods Growth-regulating factors from Dendrobium officinale Kimura et Migo and Dendrobium chrysotoxum Lindl. were identified by HMMER and BLAST. Detailed bioinformatics analysis was conducted to explore the evolution and function of GRF gene family in D. officinale and D. chrysotoxum using genomic data, transcriptome data and qRT-PCR technology. Results Here, we evaluated the evolution of the GRF gene family based on the genome sequences of D. officinale and D. chrysotoxum. Inferred from phylogenetic trees, the GRF genes were classified into two clades, and each clade contains three subclades. Sequence comparison analysis revealed relatively conserved gene structures and motifs among members of the same subfamily, indicating a conserved evolution of GRF genes within Dendrobiumspecies. However, considering the distribution of orthologous DoGRFs and DcGRFs, and the differences in the number of GRFs among species, we suggest that the GRF gene family has undergone different evolutionary processes. A total of 361 cis-elements were detected, with 33, 141, and 187 related to plant growth and development, stress, and hormones, respectively. The tissue-specific expression of GRFs showed that DoGRF8 may have a significant function in the stem elongation of D. officinale. Moreover, four genes were up-regulated under Methyl-jasmonic acid/methyl jasmonate (MeJA) treatment, showing that DoGRFs and DcGRFs play a crucial role in stress response. These findings provide valuable information for further investigations into the evolution and function of GRF genes in D. officinale and D. chrysotoxum.
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Affiliation(s)
- Shuying Zhu
- Huzhou College, School of Life and Health Sciences, Huzhou, Zhejiang, China
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, Jiangsu, China
| | - Hongman Wang
- Nanjing Normal University, College of Life Sciences, Nanjing, Jiangsu, China
| | - Qiqian Xue
- Nanjing Normal University, College of Life Sciences, Nanjing, Jiangsu, China
| | - Huasong Zou
- Huzhou College, School of Life and Health Sciences, Huzhou, Zhejiang, China
| | - Wei Liu
- Nanjing Normal University, College of Life Sciences, Nanjing, Jiangsu, China
| | - Qingyun Xue
- Nanjing Normal University, College of Life Sciences, Nanjing, Jiangsu, China
| | - Xiao-Yu Ding
- Jiangsu Provincial Engineering Research Center for Technical Industrialization for Dendrobiums, Nanjing, Jiangsu, China
- Nanjing Normal University, College of Life Sciences, Nanjing, Jiangsu, China
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Lu J, Wang Z, Li J, Zhao Q, Qi F, Wang F, Xiaoyang C, Tan G, Wu H, Deyholos MK, Wang N, Liu Y, Zhang J. Genome-Wide Analysis of Flax ( Linum usitatissimum L.) Growth-Regulating Factor (GRF) Transcription Factors. Int J Mol Sci 2023; 24:17107. [PMID: 38069430 PMCID: PMC10707037 DOI: 10.3390/ijms242317107] [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: 10/07/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
Flax is an important cash crop globally with a variety of commercial uses. It has been widely used for fiber, oil, nutrition, feed and in composite materials. Growth regulatory factor (GRF) is a transcription factor family unique to plants, and is involved in regulating many processes of growth and development. Bioinformatics analysis of the GRF family in flax predicted 17 LuGRF genes, which all contained the characteristic QLQ and WRC domains. Equally, 15 of 17 LuGRFs (88%) are predicted to be regulated by lus-miR396 miRNA. Phylogenetic analysis of GRFs from flax and several other well-characterized species defined five clades; LuGRF genes were found in four clades. Most LuGRF gene promoters contained cis-regulatory elements known to be responsive to hormones and stress. The chromosomal locations and collinearity of LuGRF genes were also analyzed. The three-dimensional structure of LuGRF proteins was predicted using homology modeling. The transcript expression data indicated that most LuGRF family members were highly expressed in flax fruit and embryos, whereas LuGRF3, LuGRF12 and LuGRF16 were enriched in response to salt stress. Real-time quantitative fluorescent PCR (qRT-PCR) showed that both LuGRF1 and LuGRF11 were up-regulated under ABA and MeJA stimuli, indicating that these genes were involved in defense. LuGRF1 was demonstrated to be localized to the nucleus as expected for a transcription factor. These results provide a basis for further exploration of the molecular mechanism of LuGRF gene function and obtaining improved flax breeding lines.
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Affiliation(s)
- Jianyu Lu
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Zhenhui Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Jinxi Li
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Qian Zhao
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Fan Qi
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Fu Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Chunxiao Xiaoyang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Guofei Tan
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Hanlu Wu
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Michael K. Deyholos
- Department of Biology, University of British Columbia, Okanagan, Kelowna, BC V5K1K5, Canada;
| | - Ningning Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
| | - Yingnan Liu
- Institute of Natural Resources and Ecology, Heilongjiang Academy of Science, Harbin 150040, China
| | - Jian Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China; (J.L.); (Z.W.); (J.L.); (Q.Z.); (F.Q.); (F.W.); (C.X.); (G.T.); wuhan (H.W.); (N.W.)
- Department of Biology, University of British Columbia, Okanagan, Kelowna, BC V5K1K5, Canada;
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Bull T, Khakhar A. Design principles for synthetic control systems to engineer plants. PLANT CELL REPORTS 2023; 42:1875-1889. [PMID: 37789180 DOI: 10.1007/s00299-023-03072-z] [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: 02/21/2023] [Accepted: 09/10/2023] [Indexed: 10/05/2023]
Abstract
KEY MESSAGE Synthetic control systems have led to significant advancement in the study and engineering of unicellular organisms, but it has been challenging to apply these tools to multicellular organisms like plants. The ability to predictably engineer plants will enable the development of novel traits capable of alleviating global problems, such as climate change and food insecurity. Engineering predictable multicellular phenotypes will require the development of synthetic control systems that can precisely regulate how the information encoded in genomes is translated into phenotypes. Many efficient control systems have been developed for unicellular organisms. However, it remains challenging to use such tools to study or engineer multicellular organisms. Plants are a good chassis within which to develop strategies to overcome these challenges, thanks to their capacity to withstand large-scale reprogramming without lethality. Additionally, engineered plants have great potential for solving major societal problems. Here we briefly review the progress of control system development in unicellular organisms, and how that information can be leveraged to characterize control systems in plants. Further, we discuss strategies for developing control systems designed to regulate the expression of transgenes or endogenous loci and generate dosage-dependent or discrete traits. Finally, we discuss the utility that mathematical models of biological processes have for control system deployment.
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Affiliation(s)
- Tawni Bull
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Arjun Khakhar
- Department of Biology, Colorado State University, Fort Collins, CO, USA.
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Sun P, Nishiyama S, Li H, Mai Y, Han W, Suo Y, Liang C, Du H, Diao S, Wang Y, Yuan J, Zhang Y, Tao R, Li F, Fu J. Genetic insights into the dissolution of dioecy in diploid persimmon Diospyros oleifera Cheng. BMC PLANT BIOLOGY 2023; 23:606. [PMID: 38030968 PMCID: PMC10688080 DOI: 10.1186/s12870-023-04610-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/15/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND Dioecy, a sexual system of single-sexual (gynoecious/androecious) individuals, is rare in flowering plants. This rarity may be a result of the frequent transition from dioecy into systems with co-sexual individuals. RESULTS In this study, co-sexual expression (monoecy and hermaphroditic development), previously thought to be polyploid-specific in Diospyros species, was identified in the diploid D. oleifeara historically. We characterized potential genetic mechanisms that underlie the dissolution of dioecy to monoecy and andro(gyno)monoecy, based on multiscale genome-wide investigations of 150 accessions of Diospyros oleifera. We found all co-sexual plants, including monoecious and andro(gyno)monoecious individuals, possessed the male determinant gene OGI, implying the presence of genetic factors controlling gynoecia development in genetically male D. oleifera. Importantly, discrepancies in the OGI/MeGI module were found in diploid monoecious D. oleifera compared with polyploid monoecious D. kaki, including no Kali insertion on the promoter of OGI, no different abundance of smRNAs targeting MeGI (a counterpart of OGI), and no different expression of MeGI between female and male floral buds. On the contrary, in both single- and co-sexual plants, female function was expressed in the presence of a genome-wide decrease in methylation levels, along with sexually distinct regulatory networks of smRNAs and their targets. Furthermore, a genome-wide association study (GWAS) identified a genomic region and a DUF247 gene cluster strongly associated with the monoecious phenotype and several regions that may contribute to andromonoecy. CONCLUSIONS Collectively, our findings demonstrate stable breakdown of the dioecious system in D. oleifera, presumably also a result of genomic features of the Y-linked region.
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Affiliation(s)
- Peng Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Soichiro Nishiyama
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwakecho, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Huawei Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Yini Mai
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Weijuan Han
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Yujing Suo
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huilong Du
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Songfeng Diao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Yiru Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Jiaying Yuan
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Yue Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwakecho, Sakyo-Ku, Kyoto, 606-8502, Japan.
| | - Fangdong Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China.
| | - Jianmin Fu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China.
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Gasparis S, Miłoszewski MM. Genetic Basis of Grain Size and Weight in Rice, Wheat, and Barley. Int J Mol Sci 2023; 24:16921. [PMID: 38069243 PMCID: PMC10706642 DOI: 10.3390/ijms242316921] [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: 10/19/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Grain size is a key component of grain yield in cereals. It is a complex quantitative trait controlled by multiple genes. Grain size is determined via several factors in different plant development stages, beginning with early tillering, spikelet formation, and assimilates accumulation during the pre-anthesis phase, up to grain filling and maturation. Understanding the genetic and molecular mechanisms that control grain size is a prerequisite for improving grain yield potential. The last decade has brought significant progress in genomic studies of grain size control. Several genes underlying grain size and weight were identified and characterized in rice, which is a model plant for cereal crops. A molecular function analysis revealed most genes are involved in different cell signaling pathways, including phytohormone signaling, transcriptional regulation, ubiquitin-proteasome pathway, and other physiological processes. Compared to rice, the genetic background of grain size in other important cereal crops, such as wheat and barley, remains largely unexplored. However, the high level of conservation of genomic structure and sequences between closely related cereal crops should facilitate the identification of functional orthologs in other species. This review provides a comprehensive overview of the genetic and molecular bases of grain size and weight in wheat, barley, and rice, focusing on the latest discoveries in the field. We also present possibly the most updated list of experimentally validated genes that have a strong effect on grain size and discuss their molecular function.
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Affiliation(s)
- Sebastian Gasparis
- Plant Breeding and Acclimatization Institute—National Research Institute in Radzików, 05-870 Błonie, Poland;
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33
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Zanatta CB, Hoepers AM, Nodari RO, Agapito-Tenfen SZ. Specificity Testing for NGT PCR-Based Detection Methods in the Context of the EU GMO Regulations. Foods 2023; 12:4298. [PMID: 38231759 DOI: 10.3390/foods12234298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/07/2023] [Accepted: 11/20/2023] [Indexed: 01/19/2024] Open
Abstract
The term new genomic techniques (NGTs) is an umbrella term used to describe a variety of techniques that can alter the genetic material of an organism and that have emerged or have been developed since 2001, when the existing genetically modified organism (GMO) legislation was adopted. The analytical framework used to detect GMOs in Europe is an established single harmonized procedure that is mandatory for the authorization of GM food and feed, thus generating a reliable, transparent, and effective labeling scheme for GMO products. However, NGT products can challenge the implementation and enforcement of the current regulatory system in the EU, relating in particular to the detection of NGT products that contain no foreign genetic material. Consequently, the current detection methods might fail to meet the minimum performance requirements. Although existing detection methods may be able to detect and quantify even small alterations in the genome, this does not necessarily confirm the distinction between products resulting from NGTs subject to the GMO legislation and other products. Therefore, this study provides a stepwise approach for the in silico prediction of PCR systems' specificity by testing a bioinformatics pipeline for amplicon and primer set searches in current genomic databases. In addition, it also empirically tested the PCR system evaluated during the in silico analysis. Two mutant genotypes produced by CRISPR-Cas9 in Arabidopsis thaliana were used as a case study. Overall, our results demonstrate that the single PCR system developed for identifying a nucleotide insertion in the grf1-3 genotype has multiple matches in the databases, which do not enable the discrimination of this mutated event. Empirical assays further support this demonstration. In contrast, the second mutated genotype, grf8-61, which contains a -3 bp deletion, did not yield any matches in the sequence variant database. However, the primer sequences were not efficient during the empirical assay. Our approach represents a first step in decision making for analytical methods for NGT detection, identification, and quantification in light of the European labeling regulations.
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Affiliation(s)
- Caroline Bedin Zanatta
- Department of Crop Science, Federal University of Santa Catarina, Florianópolis 88034000, Brazil
| | - Aline Martins Hoepers
- Department of Crop Science, Federal University of Santa Catarina, Florianópolis 88034000, Brazil
| | - Rubens Onofre Nodari
- Department of Crop Science, Federal University of Santa Catarina, Florianópolis 88034000, Brazil
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Zhang M, Li H, Zhu H, Zhao H, Zhang K, Ge W. Molecular Mechanisms of the miR396b- GRF1 Module Underlying Rooting Regulation in Acer rubrum L.. Evol Bioinform Online 2023; 19:11769343231211071. [PMID: 38020534 PMCID: PMC10655668 DOI: 10.1177/11769343231211071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023] Open
Abstract
Rooting and root development in Acer rubrum have important effects on overall growth. A. rubrum does not take root easily in natural conditions. In this study, the mechanisms of the miR396b-GRF1 module underlying rooting regulation in A. rubrum were studied. The subcellular localization and transcriptional activation of miR396b and its target gene growth regulating factor 1 (GRF1) were investigated. These experiments showed that GRF1 was localized in the nucleus and had transcriptional activation activity. Functional validation experiments in transgenic plants demonstrated that overexpression of Ar-miR396b inhibited adventitious root growth, whereas overexpression of ArGRF1 increased adventitious root growth. These results help clarify the molecular regulatory mechanisms underlying adventitious root growth in A. rubrum and provide some new insights into the rooting rate in this species.
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Affiliation(s)
- Manyu Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, People’s Republic of China
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, People’s Republic of China
| | - Huiju Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, People’s Republic of China
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, People’s Republic of China
| | - Huiyu Zhu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, People’s Republic of China
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, People’s Republic of China
| | - Hewen Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, People’s Republic of China
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, People’s Republic of China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, People’s Republic of China
| | - Kezhong Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, People’s Republic of China
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, People’s Republic of China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, People’s Republic of China
| | - Wei Ge
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, People’s Republic of China
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, People’s Republic of China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, People’s Republic of China
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Angulo J, Astin CP, Bauer O, Blash KJ, Bowen NM, Chukwudinma NJ, DiNofrio AS, Faletti DO, Ghulam AM, Gusinde-Duffy CM, Horace KJ, Ingram AM, Isaack KE, Jeong G, Kiser RJ, Kobylanski JS, Long MR, Manning GA, Morales JM, Nguyen KH, Pham RT, Phillips MH, Reel TW, Seo JE, Vo HD, Wukoson AM, Yeary KA, Zheng GY, Lukowitz W. CRISPR/Cas9 mutagenesis of the Arabidopsis GROWTH-REGULATING FACTOR (GRF) gene family. Front Genome Ed 2023; 5:1251557. [PMID: 37908969 PMCID: PMC10613670 DOI: 10.3389/fgeed.2023.1251557] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 09/29/2023] [Indexed: 11/02/2023] Open
Abstract
Genome editing in plants typically relies on T-DNA plasmids that are mobilized by Agrobacterium-mediated transformation to deliver the CRISPR/Cas machinery. Here, we introduce a series of CRISPR/Cas9 T-DNA vectors for minimal settings, such as teaching labs. Gene-specific targeting sequences can be inserted as annealed short oligonucleotides in a single straightforward cloning step. Fluorescent markers expressed in mature seeds enable reliable selection of transgenic or transgene-free individuals using a combination of inexpensive LED lamps and colored-glass alternative filters. Testing these tools on the Arabidopsis GROWTH-REGULATING FACTOR (GRF) genes, we were able to create a collection of predicted null mutations in all nine family members with little effort. We then explored the effects of simultaneously targeting two, four and eight GRF genes on the rate of induced mutations at each target locus. In our hands, multiplexing was associated with pronounced disparities: while mutation rates at some loci remained consistently high, mutation rates at other loci dropped dramatically with increasing number of single guide RNA species, thereby preventing a systematic mutagenesis of the family.
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Affiliation(s)
- Juan Angulo
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | | | - Olivia Bauer
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Kelan J. Blash
- Division of Biology, University of Georgia, Athens, GA, United States
| | - Natalee M. Bowen
- Division of Biology, University of Georgia, Athens, GA, United States
| | | | | | - Donald O. Faletti
- Division of Biology, University of Georgia, Athens, GA, United States
| | - Alexa M. Ghulam
- Division of Biology, University of Georgia, Athens, GA, United States
| | | | - Kamaria J. Horace
- Division of Biology, University of Georgia, Athens, GA, United States
| | - Andrew M. Ingram
- Division of Biology, University of Georgia, Athens, GA, United States
| | - Kylie E. Isaack
- Division of Biology, University of Georgia, Athens, GA, United States
| | - Geon Jeong
- Division of Biology, University of Georgia, Athens, GA, United States
| | - Randolph J. Kiser
- Division of Biology, University of Georgia, Athens, GA, United States
| | - Jason S. Kobylanski
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Madeline R. Long
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Grace A. Manning
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Julie M. Morales
- Division of Biology, University of Georgia, Athens, GA, United States
| | - Kevin H. Nguyen
- Division of Biology, University of Georgia, Athens, GA, United States
| | - Robin T. Pham
- Division of Biology, University of Georgia, Athens, GA, United States
| | - Monthip H. Phillips
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Tanner W. Reel
- Division of Biology, University of Georgia, Athens, GA, United States
| | - Jenny E. Seo
- Division of Biology, University of Georgia, Athens, GA, United States
| | - Hiep D. Vo
- Division of Biology, University of Georgia, Athens, GA, United States
| | | | - Kathryn A. Yeary
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Grace Y. Zheng
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Wolfgang Lukowitz
- Department of Plant Biology, University of Georgia, Athens, GA, United States
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Hamid R, Jacob F, Ghorbanzadeh Z, Jafari L, Alishah O. Dynamic roles of small RNAs and DNA methylation associated with heterosis in allotetraploid cotton (Gossypium hirsutum L.). BMC PLANT BIOLOGY 2023; 23:488. [PMID: 37828433 PMCID: PMC10571366 DOI: 10.1186/s12870-023-04495-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023]
Abstract
BACKGROUND Heterosis is a complex phenomenon wherein the hybrids outperform their parents. Understanding the underlying molecular mechanism by which hybridization leads to higher yields in allopolyploid cotton is critical for effective breeding programs. Here, we integrated DNA methylation, transcriptomes, and small RNA profiles to comprehend the genetic and molecular basis of heterosis in allopolyploid cotton at three developmental stages. RESULTS Transcriptome analysis revealed that numerous DEGs responsive to phytohormones (auxin and salicylic acid) were drastically altered in F1 hybrid compared to the parental lines. DEGs involved in energy metabolism and plant growth were upregulated, whereas DEGs related to basal defense were downregulated. Differences in homoeologous gene expression in F1 hybrid were greatly reduced after hybridization, suggesting that higher levels of parental expression have a vital role in heterosis. Small RNAome and methylome studies showed that the degree of DNA methylation in hybrid is higher when compared to the parents. A substantial number of allele-specific expression genes were found to be strongly regulated by CG allele-specific methylation levels. The hybrid exhibited higher 24-nt-small RNA (siRNA) expression levels than the parents. The regions in the genome with increased levels of 24-nt-siRNA were chiefly related to genes and their flanking regulatory regions, demonstrating a possible effect of these molecules on gene expression. The transposable elements correlated with siRNA clusters in the F1 hybrid had higher methylation levels but lower expression levels, which suggest that these non-additively expressed siRNA clusters, reduced the activity of transposable elements through DNA methylation in the hybrid. CONCLUSIONS These multi-omics data provide insights into how changes in epigenetic mechanisms and gene expression patterns can lead to heterosis in allopolyploid cotton. This makes heterosis a viable tool in cotton breeding.
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Affiliation(s)
- Rasmieh Hamid
- Department of Plant Breeding, Cotton Research Institute of Iran (CRII), Agricultural Research, Education and Extension Organization (AREEO), Gorgan, Iran.
| | - Feba Jacob
- Centre for Plant Biotechnology and Molecular Biology, Kerala Agricultural University, Thrissur, India
| | - Zahra Ghorbanzadeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Leila Jafari
- Horticultural Science Department, Faculty of Agriculture and Natural Resources, University of Hormozgan, Bandar Abbas, Iran
- Research Group of Agroecology in Dryland Areas, University of Hormozgan, Bandar Abbas, Iran
| | - Omran Alishah
- Department of Plant Breeding, Cotton Research Institute of Iran (CRII), Agricultural Research, Education and Extension Organization (AREEO), Gorgan, Iran
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Favreau B, Gaal C, Pereira de Lima I, Droc G, Roques S, Sotillo A, Guérard F, Cantonny V, Gakière B, Leclercq J, Lafarge T, de Raissac M. A multi-level approach reveals key physiological and molecular traits in the response of two rice genotypes subjected to water deficit at the reproductive stage. PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2023; 4:229-257. [PMID: 37822730 PMCID: PMC10564380 DOI: 10.1002/pei3.10121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 07/20/2023] [Accepted: 07/31/2023] [Indexed: 10/13/2023]
Abstract
Rice is more vulnerable to drought than maize, wheat, and sorghum because its water requirements remain high throughout the rice life cycle. The effects of drought vary depending on the timing, intensity, and duration of the events, as well as on the rice genotype and developmental stage. It can affect all levels of organization, from genes to the cells, tissues, and/or organs. In this study, a moderate water deficit was applied to two contrasting rice genotypes, IAC 25 and CIRAD 409, during their reproductive stage. Multi-level transcriptomic, metabolomic, physiological, and morphological analyses were performed to investigate the complex traits involved in their response to drought. Weighted gene network correlation analysis was used to identify the specific molecular mechanisms regulated by each genotype, and the correlations between gene networks and phenotypic traits. A holistic analysis of all the data provided a deeper understanding of the specific mechanisms regulated by each genotype, and enabled the identification of gene markers. Under non-limiting water conditions, CIRAD 409 had a denser shoot, but shoot growth was slower despite better photosynthetic performance. Under water deficit, CIRAD 409 was weakly affected regardless of the plant level analyzed. In contrast, IAC 25 had reduced growth and reproductive development. It regulated transcriptomic and metabolic activities at a high level, and activated a complex gene regulatory network involved in growth-limiting processes. By comparing two contrasting genotypes, the present study identified the regulation of some fundamental processes and gene markers, that drive rice development, and influence its response to water deficit, in particular, the importance of the biosynthetic and regulatory pathways for cell wall metabolism. These key processes determine the biological and mechanical properties of the cell wall and thus influence plant development, organ expansion, and turgor maintenance under water deficit. Our results also question the genericity of the antagonism between morphogenesis and organogenesis observed in the two genotypes.
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Affiliation(s)
- Bénédicte Favreau
- CIRAD, UMR AGAP InstitutMontpellierFrance
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut AgroMontpellierFrance
| | - Camille Gaal
- CIRAD, UMR AGAP InstitutMontpellierFrance
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut AgroMontpellierFrance
| | | | - Gaétan Droc
- CIRAD, UMR AGAP InstitutMontpellierFrance
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut AgroMontpellierFrance
| | - Sandrine Roques
- CIRAD, UMR AGAP InstitutMontpellierFrance
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut AgroMontpellierFrance
| | - Armel Sotillo
- CIRAD, UMR AGAP InstitutMontpellierFrance
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut AgroMontpellierFrance
| | - Florence Guérard
- Plateforme Métabolisme‐MétabolomeInstitute of Plant Sciences Paris‐Saclay (IPS2), Université Paris‐Saclay, National Committee of Scientific Research (CNRS), National Institute for Research for Agriculture, Food and Environment (INRAE), Université d'Evry, Université de ParisGif‐sur‐YvetteFrance
| | - Valérie Cantonny
- Plateforme Métabolisme‐MétabolomeInstitute of Plant Sciences Paris‐Saclay (IPS2), Université Paris‐Saclay, National Committee of Scientific Research (CNRS), National Institute for Research for Agriculture, Food and Environment (INRAE), Université d'Evry, Université de ParisGif‐sur‐YvetteFrance
| | - Bertrand Gakière
- Plateforme Métabolisme‐MétabolomeInstitute of Plant Sciences Paris‐Saclay (IPS2), Université Paris‐Saclay, National Committee of Scientific Research (CNRS), National Institute for Research for Agriculture, Food and Environment (INRAE), Université d'Evry, Université de ParisGif‐sur‐YvetteFrance
| | - Julie Leclercq
- CIRAD, UMR AGAP InstitutMontpellierFrance
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut AgroMontpellierFrance
| | - Tanguy Lafarge
- CIRAD, UMR AGAP InstitutMontpellierFrance
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut AgroMontpellierFrance
| | - Marcel de Raissac
- CIRAD, UMR AGAP InstitutMontpellierFrance
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut AgroMontpellierFrance
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Du K, Jiang S, Chen H, Xia Y, Guo R, Ling A, Liao T, Wu W, Kang X. Spatiotemporal miRNA and transcriptomic network dynamically regulate the developmental and senescence processes of poplar leaves. HORTICULTURE RESEARCH 2023; 10:uhad186. [PMID: 37899951 PMCID: PMC10611553 DOI: 10.1093/hr/uhad186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 09/07/2023] [Indexed: 10/31/2023]
Abstract
Poplar is an important afforestation and urban greening species. Poplar leaf development occurs in stages, from young to mature and then from mature to senescent; these are accompanied by various phenotypic and physiological changes. However, the associated transcriptional regulatory network is relatively unexplored. We first used principal component analysis to classify poplar leaves at different leaf positions into two stages: developmental maturity (the stage of maximum photosynthetic capacity); and the stage when photosynthetic capacity started to decline and gradually changed to senescence. The two stages were then further subdivided into five intervals by gene expression clustering analysis: young leaves, the period of cell genesis and functional differentiation (L1); young leaves, the period of development and initial formation of photosynthetic capacity (L3-L7); the period of maximum photosynthetic capacity of functional leaves (L9-L13); the period of decreasing photosynthetic capacity of functional leaves (L15-L27); and the period of senescent leaves (L29). Using a weighted co-expression gene network analysis of regulatory genes, high-resolution spatiotemporal transcriptional regulatory networks were constructed to reveal the core regulators that regulate leaf development. Spatiotemporal transcriptome data of poplar leaves revealed dynamic changes in genes and miRNAs during leaf development and identified several core regulators of leaf development, such as GRF5 and MYB5. This in-depth analysis of transcriptional regulation during leaf development provides a theoretical basis for exploring the biological basis of the transcriptional regulation of leaf development and the molecular design of breeding for delaying leaf senescence.
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Affiliation(s)
- Kang Du
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Shenxiu Jiang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Hao Chen
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Yufei Xia
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Ruihua Guo
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Aoyu Ling
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Ting Liao
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100093, China
| | - Wenqi Wu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiangyang Kang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
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Yang L, Ping T, Lu W, Song S, Wang J, Wang Q, Chai G, Bai Y, Chen Y. Genome-wide identification of auxin-responsive microRNAs in the poplar stem. Genes Genomics 2023; 45:1073-1083. [PMID: 37336805 DOI: 10.1007/s13258-023-01385-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 04/01/2023] [Indexed: 06/21/2023]
Abstract
BACKGROUND Wood (secondary xylem) of forests is a material of great economic importance. Wood development is strictly controlled by both the phytohormone auxin and microRNAs (miRNAs). Currently, the regulatory mechanisms underlying wood formation by auxin-associated miRNAs remain unclear. OBJECTIVE This report was designed to identify auxin-responsive miRNAs during wood formation. METHODS Morphological observation of wood development in the poplar stems was performed under the treatment of different concentrations (0 mg/L, CK; 5 mg/L, Low; 10 mg/L, High) of indol-3-butyric acid (IBA). Using a small RNA sequencing strategy, the effect of IBA treatment on miRNAs expression was genome-widely analyzed. RESULTS In this study, we found that wood development of poplar was promoted by low concentration of IBA treatment but inhibited by high concentration of IBA treatment. Stringent bioinformatic analysis led to identification of 118 known and 134 novel miRNAs candidates. Sixty-nine unique developmental-related miRNAs, corresponding to 269 target genes, exhibited specific expression patterns in response to auxin, as was consistent with the influence of auxin application on wood formation. Three novel miRNAs had the most number (≥ 9) of target genes, belonging to SPL, GRF and ARF gene families. The evolutionary relationships and tissue expression patterns of 41 SPL, GRF and ARF genes in poplar were thus analyzed. Of them, four representative members and corresponding miRNAs were confirmed using RT-qPCR. CONCLUSIONS Our results may be helpful for a better understanding of auxin-induced regulation of wood formation in tree species.
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Affiliation(s)
- Lihua Yang
- College of Life Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Tao Ping
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Wenjin Lu
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Sangfa Song
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jianli Wang
- Grass and Science Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Qiao Wang
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Guohua Chai
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, 266109, China
- Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration with Qingdao Agricultural University, Dongying, 257000, China
| | - Yue Bai
- Forestry College, Inner Mongolia Agricultural University, Huhhot, 010018, China.
| | - Yan Chen
- Forestry College, Inner Mongolia Agricultural University, Huhhot, 010018, China.
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, 266109, China.
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Cheng Z, Wen S, Wu Y, Shang L, Wu L, Lyu D, Yu H, Wang J, Jian H. Comparatively Evolution and Expression Analysis of GRF Transcription Factor Genes in Seven Plant Species. PLANTS (BASEL, SWITZERLAND) 2023; 12:2790. [PMID: 37570944 PMCID: PMC10421444 DOI: 10.3390/plants12152790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 07/16/2023] [Accepted: 07/20/2023] [Indexed: 08/13/2023]
Abstract
Growth regulatory factors (GRF) are plant-specific transcription factors that play pivotal roles in growth and various abiotic stresses regulation. However, adaptive evolution of GRF gene family in land plants are still being elucidated. Here, we performed the evolutionary and expression analysis of GRF gene family from seven representative species. Extensive phylogenetic analyses and gene structure analysis revealed that the number of genes, QLQ domain and WRC domain identified in higher plants was significantly greater than those identified in lower plants. Besides, dispersed duplication and WGD/segmental duplication effectively promoted expansion of the GRF gene family. The expression patterns of GRF gene family and target genes were found in multiple floral organs and abundant in actively growing tissues. They were also found to be particularly expressed in response to various abiotic stresses, with stress-related elements in promoters, implying potential roles in floral development and abiotic stress. Our analysis in GRF gene family interaction network indicated the similar results that GRFs resist to abiotic stresses with the cooperation of other transcription factors like GIFs. This study provides insights into evolution in the GRF gene family, together with expression patterns valuable for future functional researches of plant abiotic stress biology.
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Affiliation(s)
- Zhihan Cheng
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400715, China; (Z.C.); (S.W.); (Y.W.); (L.S.); (L.W.); (D.L.); (J.W.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Shiqi Wen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400715, China; (Z.C.); (S.W.); (Y.W.); (L.S.); (L.W.); (D.L.); (J.W.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Yuke Wu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400715, China; (Z.C.); (S.W.); (Y.W.); (L.S.); (L.W.); (D.L.); (J.W.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Lina Shang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400715, China; (Z.C.); (S.W.); (Y.W.); (L.S.); (L.W.); (D.L.); (J.W.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Lin Wu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400715, China; (Z.C.); (S.W.); (Y.W.); (L.S.); (L.W.); (D.L.); (J.W.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing 400715, China
| | - Dianqiu Lyu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400715, China; (Z.C.); (S.W.); (Y.W.); (L.S.); (L.W.); (D.L.); (J.W.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing 400715, China
| | - Hongtao Yu
- Suihua Branch of Heilongjiang Academy of Agriculture Sciences, Suihua 152052, China;
| | - Jichun Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400715, China; (Z.C.); (S.W.); (Y.W.); (L.S.); (L.W.); (D.L.); (J.W.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
| | - Hongju Jian
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Southwest University, Chongqing 400715, China; (Z.C.); (S.W.); (Y.W.); (L.S.); (L.W.); (D.L.); (J.W.)
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land of Southwest University, Chongqing 400715, China
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, Chongqing 400715, China
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Wan L, Wang Z, Zhang X, Zeng H, Ren J, Zhang N, Sun Y, Mi T. Optimised Agrobacterium-Mediated Transformation and Application of Developmental Regulators Improve Regeneration Efficiency in Melons. Genes (Basel) 2023; 14:1432. [PMID: 37510336 PMCID: PMC10378916 DOI: 10.3390/genes14071432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/27/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Melon (Cucumis melo L.) is a protected crop in China with high economic value. Agrobacterium-mediated genetic transformation is a powerful tool to improve agronomic traits and obtain elite germplasm. However, current transformation protocols in melons are inefficient and highly genotype-dependent. To improve transformation in melon, we tested different infiltration methods for Agrobacterium-mediated transformation. Among these methods, micro-brushing and sonication for 20 s, followed by vacuum infiltration at -1.0 kPa for 90 s, resulted in the strongest green fluorescent protein signal and increased the proportion of infected explants. We transformed melon with developmental regulatory genes AtGRF5, AtPLT5, AtBBM, AtWUS, AtWOX5, and AtWIND1 from Arabidopsis and estimated regeneration frequencies as the number of regenerating shoots/total number of inoculated explants in the selection medium. The overexpression of AtGRF5 and AtPLT5 in melon resulted in transformation efficiencies of 42.3% and 33% in ZHF and 45.6% and 32.9% in Z12, respectively, which were significantly higher than those of the control. AtGRF5 and AtPLT5 expression cassettes were added to CRISPR/Cas9 genome-editing vectors to obtain transgenic phytoene desaturase CmPDS knockout mutants. Using AtGRF5 or AtPLT5, multi-allelic mutations were observed at CmPDS target sites in recalcitrant melon genotypes. This strategy enables genotype-flexible transformation and promotes precise genome modification technologies in melons.
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Affiliation(s)
- Lili Wan
- Institute of Crop, Wuhan Academy of Agricultural Sciences, Wuhan 430065, China
| | - Zhuanrong Wang
- Institute of Crop, Wuhan Academy of Agricultural Sciences, Wuhan 430065, China
| | - Xuejun Zhang
- Research Center of Hami Melon, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
- Hainan Sanya Crops Breeding Trial Center, Xinjiang Academy of Agricultural Sciences, Sanya 572019, China
| | - Hongxia Zeng
- Institute of Crop, Wuhan Academy of Agricultural Sciences, Wuhan 430065, China
| | - Jian Ren
- Institute of Crop, Wuhan Academy of Agricultural Sciences, Wuhan 430065, China
| | - Na Zhang
- Institute of Crop, Wuhan Academy of Agricultural Sciences, Wuhan 430065, China
| | - Yuhong Sun
- Institute of Crop, Wuhan Academy of Agricultural Sciences, Wuhan 430065, China
| | - Tang Mi
- Institute of Crop, Wuhan Academy of Agricultural Sciences, Wuhan 430065, China
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Su W, Xu M, Radani Y, Yang L. Technological Development and Application of Plant Genetic Transformation. Int J Mol Sci 2023; 24:10646. [PMID: 37445824 DOI: 10.3390/ijms241310646] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/07/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023] Open
Abstract
Genetic transformation is an important strategy for enhancing plant biomass or resistance in response to adverse environments and population growth by imparting desirable genetic characteristics. Research on plant genetic transformation technology can promote the functional analysis of plant genes, the utilization of excellent traits, and precise breeding. Various technologies of genetic transformation have been continuously discovered and developed for convenient manipulation and high efficiency, mainly involving the delivery of exogenous genes and regeneration of transformed plants. Here, currently developed genetic transformation technologies were expounded and compared. Agrobacterium-mediated gene delivery methods are commonly used as direct genetic transformation, as well as external force-mediated ways such as particle bombardment, electroporation, silicon carbide whiskers, and pollen tubes as indirect ones. The regeneration of transformed plants usually involves the de novo organogenesis or somatic embryogenesis pathway of the explants. Ectopic expression of morphogenetic transcription factors (Bbm, Wus2, and GRF-GIF) can significantly improve plant regeneration efficiency and enable the transformation of some hard-to-transform plant genotypes. Meanwhile, some limitations in these gene transfer methods were compared including genotype dependence, low transformation efficiency, and plant tissue damage, and recently developed flexible approaches for plant genotype transformation are discussed regarding how gene delivery and regeneration strategies can be optimized to overcome species and genotype dependence. This review summarizes the principles of various techniques for plant genetic transformation and discusses their application scope and limiting factors, which can provide a reference for plant transgenic breeding.
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Affiliation(s)
- Wenbin Su
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Mingyue Xu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yasmina Radani
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Liming Yang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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Wang P, Xiao Y, Yan M, Yan Y, Lei X, Di P, Wang Y. Whole-genome identification and expression profiling of growth-regulating factor (GRF) and GRF-interacting factor (GIF) gene families in Panax ginseng. BMC Genomics 2023; 24:334. [PMID: 37328802 PMCID: PMC10276473 DOI: 10.1186/s12864-023-09435-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 06/07/2023] [Indexed: 06/18/2023] Open
Abstract
BACKGROUND Panax ginseng is a perennial herb and one of the most widely used traditional medicines in China. During its long growth period, it is affected by various environmental factors. Past studies have shown that growth-regulating factors (GRFs) and GRF-interacting factors (GIFs) are involved in regulating plant growth and development, responding to environmental stress, and responding to the induction of exogenous hormones. However, GRF and GIF transcription factors in ginseng have not been reported. RESULTS In this study, 20 GRF gene members of ginseng were systematically identified and found to be distributed on 13 chromosomes. The ginseng GIF gene family has only ten members, which are distributed on ten chromosomes. Phylogenetic analysis divided these PgGRFs into six clades and PgGIFs into two clades. In total, 18 of the 20 PgGRFs and eight of the ten PgGIFs are segmental duplications. Most PgGRF and PgGIF gene promoters contain some hormone- and stress- related cis-regulatory elements. Based on the available public RNA-Seq data, the expression patterns of PgGRF and PgGIF genes were analysed from 14 different tissues. The responses of the PgGRF gene to different hormones (6-BA, ABA, GA3, IAA) and abiotic stresses (cold, heat, drought, and salt) were studied. The expression of the PgGRF gene was significantly upregulated under GA3 induction and three weeks of heat treatment. The expression level of the PgGIF gene changed only slightly after one week of heat treatment. CONCLUSIONS The results of this study may be helpful for further study of the function of PgGRF and PgGIF genes and lay a foundation for further study of their role in the growth and development of Panax ginseng.
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Affiliation(s)
- Ping Wang
- State Local Joint Engineering Research Centre of Ginseng Breeding and Application, Jilin Agricultural University, Changchun, 130118, China
| | - Ying Xiao
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Min Yan
- State Local Joint Engineering Research Centre of Ginseng Breeding and Application, Jilin Agricultural University, Changchun, 130118, China
| | - Yan Yan
- State Local Joint Engineering Research Centre of Ginseng Breeding and Application, Jilin Agricultural University, Changchun, 130118, China
| | - Xiujuan Lei
- State Local Joint Engineering Research Centre of Ginseng Breeding and Application, Jilin Agricultural University, Changchun, 130118, China
| | - Peng Di
- State Local Joint Engineering Research Centre of Ginseng Breeding and Application, Jilin Agricultural University, Changchun, 130118, China.
| | - Yingping Wang
- State Local Joint Engineering Research Centre of Ginseng Breeding and Application, Jilin Agricultural University, Changchun, 130118, China.
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Khan SI, Yamada R, Shiroma R, Abe T, Kozaki A. Properties of INDETERMINATE DOMAIN Proteins from Physcomitrium patens: DNA-Binding, Interaction with GRAS Proteins, and Transcriptional Activity. Genes (Basel) 2023; 14:1249. [PMID: 37372429 DOI: 10.3390/genes14061249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
INDETERMINATE DOMAIN (IDD) proteins are plant-specific transcription factors that interact with GRAS proteins, such as DELLA and SHORT ROOT (SHR), to regulate target genes. The combination of IDD and DELLA proteins regulates genes involved in gibberellic acid (GA) synthesis and GA signaling, whereas the combination of IDD with the complex of SHR and SCARECROW, another GRAS protein, regulates genes involved in root tissue formation. Previous bioinformatic research identified seven IDDs, two DELLA, and two SHR genes in Physcomitrium patens, a model organism for non-vascular plants (bryophytes), which lack a GA signaling pathway and roots. In this study, DNA-binding properties and protein-protein interaction of IDDs from P. patens (PpIDD) were analyzed. Our results showed that the DNA-binding properties of PpIDDs were largely conserved between moss and seed plants. Four PpIDDs showed interaction with Arabidopsis DELLA (AtDELLA) proteins but not with PpDELLAs, and one PpIDD showed interaction with PpSHR but not with AtSHR. Moreover, AtIDD10 (JACKDAW) interacted with PpSHR but not with PpDELLAs. Our results indicate that DELLA proteins have modified their structure to interact with IDD proteins during evolution from moss lineage to seed plants, whereas the interaction of IDD and SHR was already present in moss lineage.
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Affiliation(s)
- Saiful Islam Khan
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Ren Yamada
- Department of Biological Science, Faculty of Science, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Ryoichi Shiroma
- Course of Bioscience, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Tatsuki Abe
- Course of Bioscience, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
| | - Akiko Kozaki
- Graduate School of Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
- Department of Biological Science, Faculty of Science, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
- Course of Bioscience, Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, Ohya 836, Suruga-ku, Shizuoka 422-8021, Japan
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Wang X, Jin Z, Ding Y, Guo M. Characterization of HSP70 family in watermelon ( Citrullus lanatus): identification, structure, evolution, and potential function in response to ABA, cold and drought stress. Front Genet 2023; 14:1201535. [PMID: 37323666 PMCID: PMC10265491 DOI: 10.3389/fgene.2023.1201535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023] Open
Abstract
Watermelon (Citrullus lanatus) as a crop with important economic value, is widely cultivated around the world. The heat shock protein 70 (HSP70) family in plant is indispensable under stress conditions. However, no comprehensive analysis of watermelon HSP70 family is reported to date. In this study, 12 ClHSP70 genes were identified from watermelon, which were unevenly located in 7 out of 11 chromosomes and divided into three subfamilies. ClHSP70 proteins were predicted to be localized primarily in cytoplasm, chloroplast, and endoplasmic reticulum. Two pairs of segmental repeats and 1 pair of tandem repeats existed in ClHSP70 genes, and ClHSP70s underwent strong purification selection. There were many abscisic acid (ABA) and abiotic stress response elements in ClHSP70 promoters. Additionally, the transcriptional levels of ClHSP70s in roots, stems, true leaves, and cotyledons were also analyzed. Some of ClHSP70 genes were also strongly induced by ABA. Furthermore, ClHSP70s also had different degrees of response to drought and cold stress. The above data indicate that ClHSP70s may be participated in growth and development, signal transduction and abiotic stress response, laying a foundation for further analysis of the function of ClHSP70s in biological processes.
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Affiliation(s)
- Xinsheng Wang
- School of Wine and Horticulture, Ningxia University, Yinchuan, China
| | - Zhi Jin
- School of Wine and Horticulture, Ningxia University, Yinchuan, China
| | - Yina Ding
- School of Wine and Horticulture, Ningxia University, Yinchuan, China
| | - Meng Guo
- School of Wine and Horticulture, Ningxia University, Yinchuan, China
- Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan, China
- Ningxia Modern Facility Horticulture Engineering Technology Research Center, Yinchuan, Ningxia, China
- Ningxia Facility Horticulture Technology Innovation Center, Ningxia University, Yinchuan, China
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Guo J, Zhao Y, Chu Y, Li Y, Song Y, Pan Q, Qiu Z, Yu B, Zhu Y. Screening Candidate Genes at the Co Locus Conferring to the Columnar Growth Habit in Apple ( Malus × Domestica Borkh.). Genes (Basel) 2023; 14:genes14050964. [PMID: 37239324 DOI: 10.3390/genes14050964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 04/11/2023] [Indexed: 05/28/2023] Open
Abstract
The columnar growth trait of apple (Malus × domestica Borkh.) is genetically controlled by the Columnar (Co) locus on 10 chromosomes, including several candidate genes. Except for MdCo31, other candidate genes at the Co locus are less elucidated. In this study, a strategy of step-by-step screening was adopted to select 11 candidate genes by experimental cloning, transient expression, and genetic transformation. There existed several SNPs in four genes by sequence alignment in columnar and non-columnar apples. Two genes were detected in the nucleus and three genes in the cell membrane, other genes were located in multiple cellular structures by subcellular location. Ectopic expression demonstrated that more branching occurred in MdCo38-OE by upregulating NtPIN1 and NtGA2ox and enlarged leaves in MdCo41-OE tobaccos by upregulating NtCCDs. Transcripts of MdCo38 and MdCo41 were associated with the Co genotypes in apples. The results indicate that MdCo38 and MdCo41 are involved in the columnar growth phenotype in apple, probably through altering polar auxin transport, active gibberellin levels, and strigolactone biosynthesis.
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Affiliation(s)
- Jing Guo
- Department of Pomology, College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, China
| | - Yuan Zhao
- Department of Pomology, College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, China
| | - Yu Chu
- Department of Pomology, College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, China
| | - Yuru Li
- Department of Pomology, College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, China
| | - Yuqi Song
- Department of Pomology, College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, China
| | - Qi Pan
- Department of Pomology, College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, China
| | - Zhannan Qiu
- Department of Pomology, College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, China
| | - Boyang Yu
- Department of Pomology, College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, China
| | - Yuandi Zhu
- Department of Pomology, College of Horticulture, China Agricultural University, Yuanmingyuan West Road No. 2, Haidian District, Beijing 100193, China
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Li L, Zhou B, Liu D, Wu H, Shi Q, Lin S, Yao W. Transcriptomic Complexity of Culm Growth and Development in Different Types of Moso Bamboo. Int J Mol Sci 2023; 24:ijms24087425. [PMID: 37108588 PMCID: PMC10138756 DOI: 10.3390/ijms24087425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/03/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Moso bamboo is capable of both sexual and asexual reproduction during natural growth, resulting in four distinct types of culms: the bamboo shoot-culm, the seedling stem, the leptomorph rhizome, and a long-ignored culm-the outward-rhizome. Sometimes, when the outward rhizomes break through the soil, they continue to grow longitudinally and develop into a new individual. However, the roles of alternative transcription start sites (aTSS) or termination sites (aTTS) as well as alternative splicing (AS) have not been comprehensively studied for their development. To re-annotate the moso bamboo genome and identify genome-wide aTSS, aTTS, and AS in growing culms, we utilized single-molecule long-read sequencing technology. In total, 169,433 non-redundant isoforms and 14,840 new gene loci were identified. Among 1311 lncRNAs, most of which showed a positive correlation with their target mRNAs, one-third of these IncRNAs were preferentially expressed in winter bamboo shoots. In addition, the predominant AS type observed in moso bamboo was intron retention, while aTSS and aTTS events occurred more frequently than AS. Notably, most genes with AS events were also accompanied by aTSS and aTTS events. Outward rhizome growth in moso bamboo was associated with a significant increase in intron retention, possibly due to changes in the growth environment. As different types of moso bamboo culms grow and develop, a significant number of isoforms undergo changes in their conserved domains due to the regulation of aTSS, aTTS, and AS. As a result, these isoforms may play different roles than their original functions. These isoforms then performed different functions from their original roles, contributing to the transcriptomic complexity of moso bamboo. Overall, this study provided a comprehensive overview of the transcriptomic changes underlying different types of moso bamboo culm growth and development.
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Affiliation(s)
- Long Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Binao Zhou
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Dong Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Hongyu Wu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Qianqian Shi
- College of Landscape Architecture and Art, Northwest A&F University, Xianyang 712100, China
| | - Shuyan Lin
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Wenjing Yao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
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Zhou B, Gao X, Zhao F. Integration of mRNA and miRNA Analysis Reveals the Post-Transcriptional Regulation of Salt Stress Response in Hemerocallis fulva. Int J Mol Sci 2023; 24:ijms24087290. [PMID: 37108448 PMCID: PMC10139057 DOI: 10.3390/ijms24087290] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 04/09/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
MicroRNAs (miRNAs) belong to non-coding small RNAs which have been shown to take a regulatory function at the posttranscriptional level in plant growth development and response to abiotic stress. Hemerocallis fulva is an herbaceous perennial plant with fleshy roots, wide distribution, and strong adaptability. However, salt stress is one of the most serious abiotic stresses to limit the growth and production of Hemerocallis fulva. To identify the miRNAs and their targets involved in the salt stress resistance, the salt-tolerant H. fulva with and without NaCl treatment were used as materials, and the expression differences of miRNAs-mRNAs related to salt-tolerance were explored and the cleavage sites between miRNAs and targets were also identified by using degradome sequencing technology. In this study, twenty and three significantly differential expression miRNAs (p-value < 0.05) were identified in the roots and leaves of H. fulva separately. Additionally, 12,691 and 1538 differentially expressed genes (DEGs) were also obtained, respectively, in roots and leaves. Moreover, 222 target genes of 61 family miRNAs were validated by degradome sequencing. Among the DE miRNAs, 29 pairs of miRNA targets displayed negatively correlated expression profiles. The qRT-PCR results also showed that the trends of miRNA and DEG expression were consistent with those of RNA-seq. A gene ontology (GO) enrichment analysis of these targets revealed that the calcium ion pathway, oxidative defense response, microtubule cytoskeleton organization, and DNA binding transcription factor responded to NaCl stress. Five miRNAs, miR156, miR160, miR393, miR166, and miR396, and several hub genes, squamosa promoter-binding-like protein (SPL), auxin response factor 12 (ARF), transport inhibitor response 1-like protein (TIR1), calmodulin-like proteins (CML), and growth-regulating factor 4 (GRF4), might play central roles in the regulation of NaCl-responsive genes. These results indicate that non-coding small RNAs and their target genes that are related to phytohormone signaling, Ca2+ signaling, and oxidative defense signaling pathways are involved in H. fulva's response to NaCl stress.
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Affiliation(s)
- Bo Zhou
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Northeast Forestry University, Ministry of Education, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Xiang Gao
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, China
| | - Fei Zhao
- Horticulture Science and Engineering, Shandong Agricultural University, Taian 271018, China
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Yang S, Xu N, Chen N, Qi J, Salam A, Wu J, Liu Y, Huang L, Liu B, Gan Y. OsUGE1 is directly targeted by OsGRF6 to regulate root hair length in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:108. [PMID: 37039968 DOI: 10.1007/s00122-023-04356-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/04/2023] [Indexed: 05/13/2023]
Abstract
KEY MESSAGE Root hairs are required for water and nutrient acquisition in plants. Here, we report a novel mechanism that OsUGE1 is negatively controlled by OsGRF6 to regulate root hair elongation in rice. Root hairs are tubular outgrowths generated by the root epidermal cells. They effectively enlarge the soil-root contact area and play essential roles for nutrient and water absorption. Here, in this study, we demonstrated that the Oryza sativa UDP-glucose 4-epimerase 1-like (OsUGE1) negatively regulated root hair elongation and was directly targeted by Oryza sativa growth regulating factor 6 (OsGRF6). Knockout mutants of OsUGE1 using CRISPR-Cas9 technology showed longer root hairs than those of wild type. In contrast, overexpression lines of OsUGE1 displayed shorter root hair compared with those of wild type. GUS staining showed that it could specifically express in root hair. Subcellular localization analysis indicates that OsUGE1 is located in endoplasmic reticulum, nucleus and plasma membrane. More importantly, ChIP-qPCR, Yeast-one-hybrid and BiFC experiments revealed that OsGRF6 could bind to the promoter of OsUGE1. Furthermore, knockout mutants of OsGRF6 showed shorter root hair than those of wild type, and OsGRF6 dominantly expressed in root. In addition, the expression level of OsUGE1 is significantly downregulated in Osgrf6 mutant. Taken together, our study reveals a novel pathway that OsUGE1 is negatively controlled by OsGRF6 to regulate root hair elongation in rice.
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Affiliation(s)
- Shuaiqi Yang
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310000, China
| | - Nuo Xu
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310000, China
| | - Nana Chen
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310000, China
| | - Jiaxuan Qi
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310000, China
| | - Abdul Salam
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310000, China
| | - Junyu Wu
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310000, China
| | - Yihua Liu
- College of Agriculture and Forestry Sciences, Linyi University, Linyi, 276000, Shandong, China
| | - Linli Huang
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310000, China
| | - Bohan Liu
- College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Yinbo Gan
- Zhejiang Key Lab of Crop Germplasm, Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310000, China.
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50
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Hertig C, Rutten T, Melzer M, Schippers JHM, Thiel J. Dissection of Developmental Programs and Regulatory Modules Directing Endosperm Transfer Cell and Aleurone Identity in the Syncytial Endosperm of Barley. PLANTS (BASEL, SWITZERLAND) 2023; 12:1594. [PMID: 37111818 PMCID: PMC10142620 DOI: 10.3390/plants12081594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/10/2023] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
Endosperm development in barley starts with the formation of a multinucleate syncytium, followed by cellularization in the ventral part of the syncytium generating endosperm transfer cells (ETCs) as first differentiating subdomain, whereas aleurone (AL) cells will originate from the periphery of the enclosing syncytium. Positional signaling in the syncytial stage determines cell identity in the cereal endosperm. Here, we performed a morphological analysis and employed laser capture microdissection (LCM)-based RNA-seq of the ETC region and the peripheral syncytium at the onset of cellularization to dissect developmental and regulatory programs directing cell specification in the early endosperm. Transcriptome data revealed domain-specific characteristics and identified two-component signaling (TCS) and hormone activities (auxin, ABA, ethylene) with associated transcription factors (TFs) as the main regulatory links for ETC specification. On the contrary, differential hormone signaling (canonical auxin, gibberellins, cytokinin) and interacting TFs control the duration of the syncytial phase and timing of cellularization of AL initials. Domain-specific expression of candidate genes was validated by in situ hybridization and putative protein-protein interactions were confirmed by split-YFP assays. This is the first transcriptome analysis dissecting syncytial subdomains of cereal seeds and provides an essential framework for initial endosperm differentiation in barley, which is likely also valuable for comparative studies with other cereal crops.
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Affiliation(s)
- Christian Hertig
- Department of Physiology and Cell Biology, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland, Germany
| | - Twan Rutten
- Department of Physiology and Cell Biology, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland, Germany
| | - Michael Melzer
- Department of Physiology and Cell Biology, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland, Germany
| | - Jos H. M. Schippers
- Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland, Germany
| | - Johannes Thiel
- Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland, Germany
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