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Zhou C, Liu H, Wang H, Niu S, El-Kassaby YA, Li W. Deciphering the Role of SVP-Like Genes and Their Key Regulation Networks During Reproductive Cone Development in Pinus tabuliformis. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39257299 DOI: 10.1111/pce.15129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 08/02/2024] [Accepted: 08/16/2024] [Indexed: 09/12/2024]
Abstract
Reproductive development plays an essential role in the perpetuation of genetic material and environmental adaptation. In angiosperms, the Short Vegetative Phase (SVP) serves as a flowering repressor, influencing the development of floral organs. In this study, heterologous transformation of Arabidopsis thaliana with SVP-like genes (PtSVL1 and PtSVL2) derived from Pinus tabuliformis significantly impacted stamen formation and pollen fertility, without altering flowering time. Gene co-expression networks revealed that SVP-like and SOC1-like genes function as key coregulatory transcription factors during the initial stages of cone development in P. tabuliformis. Interestingly, the regulatory module of SOC1 regulated by SVP in angiosperms is absent in conifers and conifer SVP-like exercises its function in a form that is physically bound to SOC1-like. Furthermore, combining the yeast one-hybrid scanning with co-expression network analysis, revealed that SPLs and TPSs were the principal downstream target genes of PtSVL1. Notably, the PtSPL16 promoter is positively regulated by PtSVL1, and overexpression of PtSPL16 results in delayed flowering in Arabidopsis, suggesting that the PtSVL1-PtSPL16 module plays a crucial role in regulating reproductive development in conifers. Collectively, these findings enhance our understanding of the roles of SVP-like genes in conifers and the key regulatory networks centred on PtSVL1 during reproductive cone development.
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Affiliation(s)
- Chengcheng Zhou
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Hongmei Liu
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Huili Wang
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Shihui Niu
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
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2
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Huo Q, Song R, Ma Z. Recent advances in exploring transcriptional regulatory landscape of crops. FRONTIERS IN PLANT SCIENCE 2024; 15:1421503. [PMID: 38903438 PMCID: PMC11188431 DOI: 10.3389/fpls.2024.1421503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 05/23/2024] [Indexed: 06/22/2024]
Abstract
Crop breeding entails developing and selecting plant varieties with improved agronomic traits. Modern molecular techniques, such as genome editing, enable more efficient manipulation of plant phenotype by altering the expression of particular regulatory or functional genes. Hence, it is essential to thoroughly comprehend the transcriptional regulatory mechanisms that underpin these traits. In the multi-omics era, a large amount of omics data has been generated for diverse crop species, including genomics, epigenomics, transcriptomics, proteomics, and single-cell omics. The abundant data resources and the emergence of advanced computational tools offer unprecedented opportunities for obtaining a holistic view and profound understanding of the regulatory processes linked to desirable traits. This review focuses on integrated network approaches that utilize multi-omics data to investigate gene expression regulation. Various types of regulatory networks and their inference methods are discussed, focusing on recent advancements in crop plants. The integration of multi-omics data has been proven to be crucial for the construction of high-confidence regulatory networks. With the refinement of these methodologies, they will significantly enhance crop breeding efforts and contribute to global food security.
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Affiliation(s)
| | | | - Zeyang Ma
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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3
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Ma Y, Fu W, Wan S, Li Y, Mao H, Khalid E, Zhang W, Ming R. Gene Regulatory Network Controlling Flower Development in Spinach ( Spinacia oleracea L.). Int J Mol Sci 2024; 25:6127. [PMID: 38892313 PMCID: PMC11173220 DOI: 10.3390/ijms25116127] [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: 04/15/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Spinach (Spinacia oleracea L.) is a dioecious, diploid, wind-pollinated crop cultivated worldwide. Sex determination plays an important role in spinach breeding. Hence, this study aimed to understand the differences in sexual differentiation and floral organ development of dioecious flowers, as well as the differences in the regulatory mechanisms of floral organ development of dioecious and monoecious flowers. We compared transcriptional-level differences between different genders and identified differentially expressed genes (DEGs) related to spinach floral development, as well as sex-biased genes to investigate the flower development mechanisms in spinach. In this study, 9189 DEGs were identified among the different genders. DEG analysis showed the participation of four main transcription factor families, MIKC_MADS, MYB, NAC, and bHLH, in spinach flower development. In our key findings, abscisic acid (ABA) and gibberellic acid (GA) signal transduction pathways play major roles in male flower development, while auxin regulates both male and female flower development. By constructing a gene regulatory network (GRN) for floral organ development, core transcription factors (TFs) controlling organ initiation and growth were discovered. This analysis of the development of female, male, and monoecious flowers in spinach provides new insights into the molecular mechanisms of floral organ development and sexual differentiation in dioecious and monoecious plants in spinach.
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Affiliation(s)
- Yaying Ma
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.M.); (W.F.)
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.W.); (Y.L.); (H.M.); (E.K.)
| | - Wenhui Fu
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.M.); (W.F.)
| | - Suyan Wan
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.W.); (Y.L.); (H.M.); (E.K.)
| | - Yikai Li
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.W.); (Y.L.); (H.M.); (E.K.)
| | - Haoming Mao
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.W.); (Y.L.); (H.M.); (E.K.)
| | - Ehsan Khalid
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.W.); (Y.L.); (H.M.); (E.K.)
| | - Wenping Zhang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
| | - Ray Ming
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (S.W.); (Y.L.); (H.M.); (E.K.)
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4
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Bowman JL, Moyroud E. Reflections on the ABC model of flower development. THE PLANT CELL 2024; 36:1334-1357. [PMID: 38345422 PMCID: PMC11062442 DOI: 10.1093/plcell/koae044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 02/07/2024] [Indexed: 05/02/2024]
Abstract
The formulation of the ABC model by a handful of pioneer plant developmental geneticists was a seminal event in the quest to answer a seemingly simple question: how are flowers formed? Fast forward 30 years and this elegant model has generated a vibrant and diverse community, capturing the imagination of developmental and evolutionary biologists, structuralists, biochemists and molecular biologists alike. Together they have managed to solve many floral mysteries, uncovering the regulatory processes that generate the characteristic spatio-temporal expression patterns of floral homeotic genes, elucidating some of the mechanisms allowing ABC genes to specify distinct organ identities, revealing how evolution tinkers with the ABC to generate morphological diversity, and even shining a light on the origins of the floral gene regulatory network itself. Here we retrace the history of the ABC model, from its genesis to its current form, highlighting specific milestones along the way before drawing attention to some of the unsolved riddles still hidden in the floral alphabet.
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Affiliation(s)
- John L Bowman
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Melbourne, VIC 3800, Australia
| | - Edwige Moyroud
- The Sainsbury Laboratory, Cambridge University, Cambridge CB2 1LR, UK
- Department of Genetics, University of Cambridge, Cambridge CB2 3EJ, UK
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5
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Cao S, Zhao X, Li Z, Yu R, Li Y, Zhou X, Yan W, Chen D, He C. Comprehensive integration of single-cell transcriptomic data illuminates the regulatory network architecture of plant cell fate specification. PLANT DIVERSITY 2024; 46:372-385. [PMID: 38798726 PMCID: PMC11119547 DOI: 10.1016/j.pld.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 03/29/2024] [Indexed: 05/29/2024]
Abstract
Plant morphogenesis relies on precise gene expression programs at the proper time and position which is orchestrated by transcription factors (TFs) in intricate regulatory networks in a cell-type specific manner. Here we introduced a comprehensive single-cell transcriptomic atlas of Arabidopsis seedlings. This atlas is the result of meticulous integration of 63 previously published scRNA-seq datasets, addressing batch effects and conserving biological variance. This integration spans a broad spectrum of tissues, including both below- and above-ground parts. Utilizing a rigorous approach for cell type annotation, we identified 47 distinct cell types or states, largely expanding our current view of plant cell compositions. We systematically constructed cell-type specific gene regulatory networks and uncovered key regulators that act in a coordinated manner to control cell-type specific gene expression. Taken together, our study not only offers extensive plant cell atlas exploration that serves as a valuable resource, but also provides molecular insights into gene-regulatory programs that varies from different cell types.
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Affiliation(s)
- Shanni Cao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xue Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Zhuojin Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Ranran Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Yuqi Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinkai Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Chao He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
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6
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Huang X, Liu L, Qiang X, Meng Y, Li Z, Huang F. Integrative Metabolomic and Transcriptomic Analysis Elucidates That the Mechanism of Phytohormones Regulates Floral Bud Development in Alfalfa. PLANTS (BASEL, SWITZERLAND) 2024; 13:1078. [PMID: 38674487 PMCID: PMC11053841 DOI: 10.3390/plants13081078] [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: 04/06/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024]
Abstract
Floral bud growth influences seed yield and quality; however, the molecular mechanism underlying the development of floral buds in alfalfa (Medicago sativa) is still unclear. Here, we comprehensively analyzed the transcriptome and targeted metabolome across the early, mid, and late bud developmental stages (D1, D2, and D3) in alfalfa. The metabolomic results revealed that gibberellin (GA), auxin (IAA), cytokinin (CK), and jasmonic acid (JA) might play an essential role in the developmental stages of floral bud in alfalfa. Moreover, we identified some key genes associated with GA, IAA, CK, and JA biosynthesis, including CPS, KS, GA20ox, GA3ox, GA2ox, YUCCA6, amid, ALDH, IPT, CYP735A, LOX, AOC, OPR, MFP2, and JMT. Additionally, many candidate genes were detected in the GA, IAA, CK, and JA signaling pathways, including GID1, DELLA, TF, AUX1, AUX/IAA, ARF, GH3, SAUR, AHP, B-ARR, A-ARR, JAR1, JAZ, and MYC2. Furthermore, some TFs related to flower growth were screened in three groups, such as AP2/ERF-ERF, MYB, MADS-M-type, bHLH, NAC, WRKY, HSF, and LFY. The findings of this study revealed the potential mechanism of floral bud differentiation and development in alfalfa and established a theoretical foundation for improving the seed yield of alfalfa.
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Affiliation(s)
| | - Lei Liu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 100081, China; (X.H.); (Y.M.); (Z.L.); (F.H.)
| | - Xiaojing Qiang
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 100081, China; (X.H.); (Y.M.); (Z.L.); (F.H.)
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7
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He H, Chen X, Wang T, Zhang X, Liu Z, Qu S, Gu Z, Huang M, Huang H. Flower development and a functional analysis of related genes in Impatiens uliginosa. FRONTIERS IN PLANT SCIENCE 2024; 15:1370949. [PMID: 38590746 PMCID: PMC10999631 DOI: 10.3389/fpls.2024.1370949] [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: 01/15/2024] [Accepted: 02/26/2024] [Indexed: 04/10/2024]
Abstract
Impatiens uliginosa is a plant of the Impatiens, with peculiar flowers. In this study, we combined morphogenesis and molecular biology to explore its development of flowers. An analysis of basic observational data and paraffin sectioning showed that it took approximately 13 d for the floral organs to differentiate. An analysis of the development of inflorescences and floral organs by scanning electron microscopy showed that the inflorescence of I. uliginosa is a spiral raceme. The floral organs differentiated in the following order: lateral sepals (Ls), posterior sepal (Ps), anterior sepals (As), anterior petal (Ap), lateral petals (Lp), stamens (St) and gynoecium (Gy). I. uliginosa was found to have four sepals, and the connate stamens are caused by the fusion and growth of filament appendages. The results of fluorescence quantification and virus-induced gene silencing showed that I. uliginosa had its own unique model for flower development, and there was functional diversity of IuAP1 and IuDEF. Among them, IuAP1 controls the formation of bract s (Br), regulates the morphogenesis of posterior sepal, controls the anthocyanin precipitation of the anterior petals and the formation of lateral petals. IuDEF regulates the morphogenesis of lateral sepals, the length of development of the spur, and controls the size of yellow flower color plaques of the lateral petals. In this study, the process of flower development and the function of flower development genes of I. uliginosa were preliminarily verified. This study provides basic guidance and new concepts that can be used to study the development of Impatiens flowers.
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Affiliation(s)
- Haihao He
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, China
| | - Xinyi Chen
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, China
| | - Tianye Wang
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, China
| | - Xiaoli Zhang
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, China
| | - Zedong Liu
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, China
| | - Suping Qu
- Flower Research Institute, Yunnan Academy of Agricultural Sciences China, Kunming, China
| | - Zhijia Gu
- Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Meijuan Huang
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, China
| | - Haiquan Huang
- College of Landscape Architecture and Horticulture Sciences, Southwest Research Center for Engineering Technology of Landscape Architecture (State Forestry and Grassland Administration), Yunnan Engineering Research Center for Functional Flower Resources and Industrialization, Research and Development Center of Landscape Plants and Horticulture Flowers, Southwest Forestry University, Kunming, Yunnan, China
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8
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Unnikrishnan DK, Sreeharsha RV, Mudalkar S, Reddy AR. Flowering onset time is regulated by microRNA-mediated trehalose-6-phosphate signaling in Cajanus cajan L . under elevated CO 2. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:483-496. [PMID: 38633268 PMCID: PMC11018574 DOI: 10.1007/s12298-024-01434-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 02/24/2024] [Accepted: 03/05/2024] [Indexed: 04/19/2024]
Abstract
CO2 levels are known to have an impact on plant development and physiology. In the current study, we have investigated the effect of elevated CO2 on flowering and its regulation through miRNA mediated sugar signaling. We also unraveled small RNA transcriptome of pigeonpea under ambient and elevated CO2 conditions and predicted the targets for crucial miRNAs through computational methods. The results have shown that the delayed flowering in pigeonpea under elevated CO2 was due to an imbalance in C:N stoichiometry and differential expression pattern of aging pathway genes, including SQUAMOSA PROMOTER BINDING PROTEIN-LIKE. Furthermore, qRT PCR analysis has revealed the role of miR156 and miR172 in mediating trehalose-6-phosphate dependent flowering regulation. The current study is crucial in understanding the responses of flowering patterns in a legume crop to elevated CO2 which showed a significant impact on its final yields. Also, these findings are crucial in devising effective crop improvement strategies for developing climate resilient crops, including pigeonpea. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-024-01434-9.
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Affiliation(s)
| | | | - Shalini Mudalkar
- Forest College and Research Institute, Hyderabad, Mulugu, Telangana 502279 India
| | - Attipalli R. Reddy
- Department of Plant Sciences, University of Hyderabad, Hyderabad, 500049 India
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9
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Wang L, Niu F, Wang J, Zhang H, Zhang D, Hu Z. Genome-Wide Association Studies Prioritize Genes Controlling Seed Size and Reproductive Period Length in Soybean. PLANTS (BASEL, SWITZERLAND) 2024; 13:615. [PMID: 38475461 DOI: 10.3390/plants13050615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024]
Abstract
Hundred-seed weight (HSW) and reproductive period length (RPL) are two major agronomic traits critical for soybean production and adaptation. However, both traits are quantitatively controlled by multiple genes that have yet to be comprehensively elucidated due to the lack of major genes; thereby, the genetic basis is largely unknown. In the present study, we conducted comprehensive genome-wide association analyses (GWAS) of HSW and RPL with multiple sets of accessions that were phenotyped across different environments. The large-scale analysis led to the identification of sixty-one and seventy-four significant QTLs for HSW and RPL, respectively. An ortholog-based search analysis prioritized the most promising candidate genes for the QTLs, including nine genes (TTG2, BZR1, BRI1, ANT, KLU, EOD1/BB, GPA1, ABA2, and ABI5) for HSW QTLs and nine genes (such as AGL8, AGL9, TOC1, and COL4) and six known soybean flowering time genes (E2, E3, E4, Tof11, Tof12, and FT2b) for RPL QTLs. We also demonstrated that some QTLs were targeted during domestication to drive the artificial selection of both traits towards human-favored traits. Local adaptation likely contributes to the increased genomic diversity of the QTLs underlying RPL. The results provide additional insight into the genetic basis of HSW and RPL and prioritize a valuable resource of candidate genes that merits further investigation to reveal the complex molecular mechanism and facilitate soybean improvement.
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Affiliation(s)
- Le Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Fu'an Niu
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Jinshe Wang
- National Innovation Centre for Bio-Breeding Industry, Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Hengyou Zhang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhenbin Hu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA
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10
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Chow CN, Yang CW, Wu NY, Wang HT, Tseng KC, Chiu YH, Lee TY, Chang WC. PlantPAN 4.0: updated database for identifying conserved non-coding sequences and exploring dynamic transcriptional regulation in plant promoters. Nucleic Acids Res 2024; 52:D1569-D1578. [PMID: 37897338 PMCID: PMC10767843 DOI: 10.1093/nar/gkad945] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/07/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023] Open
Abstract
PlantPAN 4.0 (http://PlantPAN.itps.ncku.edu.tw/) is an integrative resource for constructing transcriptional regulatory networks for diverse plant species. In this release, the gene annotation and promoter sequences were expanded to cover 115 species. PlantPAN 4.0 can help users characterize the evolutionary differences and similarities among cis-regulatory elements; furthermore, this system can now help in identification of conserved non-coding sequences among homologous genes. The updated transcription factor binding site repository contains 3428 nonredundant matrices for 18305 transcription factors; this expansion helps in exploration of combinational and nucleotide variants of cis-regulatory elements in conserved non-coding sequences. Additionally, the genomic landscapes of regulatory factors were manually updated, and ChIP-seq data sets derived from a single-cell green alga (Chlamydomonas reinhardtii) were added. Furthermore, the statistical review and graphical analysis components were improved to offer intelligible information through ChIP-seq data analysis. These improvements included easy-to-read experimental condition clusters, searchable gene-centered interfaces for the identification of promoter regions' binding preferences by considering experimental condition clusters and peak visualization for all regulatory factors, and the 20 most significantly enriched gene ontology functions for regulatory factors. Thus, PlantPAN 4.0 can effectively reconstruct gene regulatory networks and help compare genomic cis-regulatory elements across plant species and experiments.
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Affiliation(s)
- Chi-Nga Chow
- Institute of Tropical Plant Sciences and Microbiology, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan
- School of Molecular Sciences, Arizona State University, Tempe 85281, USA
| | - Chien-Wen Yang
- Institute of Tropical Plant Sciences and Microbiology, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan
| | - Nai-Yun Wu
- Institute of Tropical Plant Sciences and Microbiology, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan
| | - Hung-Teng Wang
- Institute of Tropical Plant Sciences and Microbiology, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan
| | - Kuan-Chieh Tseng
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Yu-Hsuan Chiu
- Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Tainan 701, Taiwan
| | - Tzong-Yi Lee
- Department of Biological Science & Technology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Wen-Chi Chang
- Institute of Tropical Plant Sciences and Microbiology, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan 701, Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
- Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Tainan 701, Taiwan
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11
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Wang J, Ma X, Hu Y, Feng G, Guo C, Zhang X, Ma H. Regulation of micro- and small-exon retention and other splicing processes by GRP20 for flower development. NATURE PLANTS 2024; 10:66-85. [PMID: 38195906 PMCID: PMC10808074 DOI: 10.1038/s41477-023-01605-8] [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: 11/11/2022] [Accepted: 11/29/2023] [Indexed: 01/11/2024]
Abstract
Pre-mRNA splicing is crucial for gene expression and depends on the spliceosome and splicing factors. Plant exons have an average size of ~180 nucleotides and typically contain motifs for interactions with spliceosome and splicing factors. Micro exons (<51 nucleotides) are found widely in eukaryotes and in genes for plant development and environmental responses. However, little is known about transcript-specific regulation of splicing in plants and about the regulators for micro exon splicing. Here we report that glycine-rich protein 20 (GRP20) is an RNA-binding protein and required for splicing of ~2,100 genes including those functioning in flower development and/or environmental responses. Specifically, GRP20 is required for micro-exon retention in transcripts of floral homeotic genes; these micro exons are conserved across angiosperms. GRP20 is also important for small-exon (51-100 nucleotides) splicing. In addition, GRP20 is required for flower development. Furthermore, GRP20 binds to poly-purine motifs in micro and small exons and a spliceosome component; both RNA binding and spliceosome interaction are important for flower development and micro-exon retention. Our results provide new insights into the mechanisms of micro-exon retention in flower development.
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Affiliation(s)
- Jun Wang
- Department of Biology, Eberly College of Science, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Xinwei Ma
- Department of Biology, Eberly College of Science, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Yi Hu
- Department of Biology, Eberly College of Science, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Guanhua Feng
- Department of Biology, Eberly College of Science, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Chunce Guo
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang, China
| | - Xin Zhang
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Eberly College of Science, Pennsylvania State University, University Park, PA, USA
| | - Hong Ma
- Department of Biology, Eberly College of Science, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
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12
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Pelayo MA, Yamaguchi N. Old school, new rules: floral meristem development revealed by 3D gene expression atlases and high-resolution transcription factor-chromatin dynamics. FRONTIERS IN PLANT SCIENCE 2023; 14:1323507. [PMID: 38155851 PMCID: PMC10753784 DOI: 10.3389/fpls.2023.1323507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 11/23/2023] [Indexed: 12/30/2023]
Abstract
The intricate morphology of the flower is primarily established within floral meristems in which floral organs will be defined and from where the developing flower will emerge. Floral meristem development involves multiscale-level regulation, including lineage and positional mechanisms for establishing cell-type identity, and transcriptional regulation mediated by changes in the chromatin environment. However, many key aspects of floral meristem development remain to be determined, such as: 1) the exact role of cellular location in connecting transcriptional inputs to morphological outcomes, and 2) the precise interactions between transcription factors and chromatin regulators underlying the transcriptional networks that regulate the transition from cell proliferation to differentiation during floral meristem development. Here, we highlight recent studies addressing these points through newly developed spatial reconstruction techniques and high-resolution transcription factor-chromatin environment interactions in the model plant Arabidopsis thaliana. Specifically, we feature studies that reconstructed 3D gene expression atlases of the floral meristem. We also discuss how the precise timing of floral meristem specification, floral organ patterning, and floral meristem termination is determined through temporally defined epigenetic dynamics for fine-tuning of gene expression. These studies offer fresh insights into the well-established principles of floral meristem development and outline the potential for further advances in this field in an age of integrated, powerful, multiscale resolution approaches.
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Affiliation(s)
| | - Nobutoshi Yamaguchi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
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13
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Rehman S, Bahadur S, Xia W. An overview of floral regulatory genes in annual and perennial plants. Gene 2023; 885:147699. [PMID: 37567454 DOI: 10.1016/j.gene.2023.147699] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/31/2023] [Accepted: 08/08/2023] [Indexed: 08/13/2023]
Abstract
The floral initiation in angiosperms is a complex process influenced by endogenous and exogenous signals. With this approach, we aim to provide a comprehensive review to integrate this complex floral regulatory process and summarize the regulatory genes and their functions in annuals and perennials. Seven primary paths leading to flowering have been discovered in Arabidopsis under several growth condition that include; photoperiod, ambient temperature, vernalization, gibberellins, autonomous, aging and carbohydrates. These pathways involve a series of interlinked signaling pathways that respond to both internal and external signals, such as light, temperature, hormones, and developmental cues, to coordinate the expression of genes that are involved in flower development. Among them, the photoperiodic pathway was the most important and conserved as some of the fundamental loci and mechanisms are shared even by closely related plant species. The activation of floral regulatory genes such as FLC, FT, LFY, and SOC1 that determine floral meristem identity and the transition to the flowering stage result from the merging of these pathways. Recent studies confirmed that alternative splicing, antisense RNA and epigenetic modification play crucial roles by regulating the expression of genes related to blooming. In this review, we documented recent progress in the floral transition time in annuals and perennials, with emphasis on the specific regulatory mechanisms along with the application of various molecular approaches including overexpression studies, RNA interference and Virus-induced flowering. Furthermore, the similarities and differences between annual and perennial flowering will aid significant contributions to the field by elucidating the mechanisms of perennial plant development and floral initiation regulation.
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Affiliation(s)
- Shazia Rehman
- Sanya Nanfan Research Institution, Hainan University, Haikou 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Saraj Bahadur
- College of Forestry, Hainan University, Haikou 570228 China
| | - Wei Xia
- Sanya Nanfan Research Institution, Hainan University, Haikou 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China.
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14
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Chen G, Mishina K, Wang Q, Zhu H, Tagiri A, Kikuchi S, Sassa H, Oono Y, Komatsuda T. Organ-enriched gene expression during floral morphogenesis in wild barley. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:887-902. [PMID: 37548103 DOI: 10.1111/tpj.16416] [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: 05/31/2023] [Revised: 07/19/2023] [Accepted: 07/23/2023] [Indexed: 08/08/2023]
Abstract
Floral morphology varies considerably between dicots and monocots. The ABCDE model explaining how floral organ development is controlled was formulated using core eudicots and applied to grass crops. Barley (Hordeum. vulgare) has unique floral morphogenesis. Wild barley (H. vulgare ssp. spontaneum), which is the immediate ancestor of cultivated barley (H. vulgare ssp. vulgare), contains a rich reservoir of genetic diversity. However, the wild barley genes involved in floral organ development are still relatively uncharacterized. In this study, we generated an organ-specific transcriptome atlas for wild barley floral organs. Genome-wide transcription profiles indicated that 22 838 protein-coding genes were expressed in at least one organ. These genes were grouped into seven clusters according to the similarities in their expression patterns. Moreover, 5619 genes exhibited organ-enriched expression, 677 of which were members of 47 transcription factor families. Gene ontology analyses suggested that the functions of the genes with organ-enriched expression influence the biological processes in floral organs. The co-expression regulatory network showed that the expression of 690 genes targeted by MADS-box proteins was highly positively correlated with the expression of ABCDE model genes during floral morphogenesis. Furthermore, the expression of 138 genes was specific to the wild barley OUH602 genome and not the Morex genome; most of these genes were highly expressed in the glume, awn, lemma, and palea. This study revealed the global gene expression patterns underlying floral morphogenesis in wild barley. On the basis of the study findings, a molecular mechanism controlling floral morphology in barley was proposed.
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Affiliation(s)
- Gang Chen
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Kohei Mishina
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Qi Wang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture and Rural Affairs, and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China
| | - Hongjing Zhu
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Akemi Tagiri
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Shinji Kikuchi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Hidenori Sassa
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Youko Oono
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Takao Komatsuda
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Jinan, 252100, China
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15
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He Z, Chao H, Zhou X, Ni Q, Hu Y, Yu R, Wang M, Li C, Chen J, Chen Y, Chen Y, Cui C, Zhang L, Chen M, Chen D. A chromosome-level genome assembly provides insights into Cornus wilsoniana evolution, oil biosynthesis, and floral bud development. HORTICULTURE RESEARCH 2023; 10:uhad196. [PMID: 38023476 PMCID: PMC10673659 DOI: 10.1093/hr/uhad196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 09/25/2023] [Indexed: 12/01/2023]
Abstract
Cornus wilsoniana W. is a woody oil plant with high oil content and strong hypolipidemic effects, making it a valuable species for medicinal, landscaping, and ecological purposes in China. To advance genetic research on this species, we employed PacBio together with Hi-C data to create a draft genome assembly for C. wilsoniana. Based on an 11-chromosome anchored chromosome-level assembly, the estimated genome size was determined to be 843.51 Mb. The N50 contig size and N50 scaffold size were calculated to be 4.49 and 78.00 Mb, respectively. Furthermore, 30 474 protein-coding genes were annotated. Comparative genomics analysis revealed that C. wilsoniana diverged from its closest species ~12.46 million years ago (Mya). Furthermore, the divergence between Cornaceae and Nyssaceae occurred >62.22 Mya. We also found evidence of whole-genome duplication events and whole-genome triplication γ, occurring at ~44.90 and 115.86 Mya. We further inferred the origins of chromosomes, which sheds light on the complex evolutionary history of the karyotype of C. wilsoniana. Through transcriptional and metabolic analysis, we identified two FAD2 homologous genes that may play a crucial role in controlling the oleic to linoleic acid ratio. We further investigated the correlation between metabolites and genes and identified 33 MADS-TF homologous genes that may affect flower morphology in C. wilsoniana. Overall, this study lays the groundwork for future research aimed at identifying the genetic basis of crucial traits in C. wilsoniana.
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Affiliation(s)
- Zhenxiang He
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Haoyu Chao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xinkai Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Qingyang Ni
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yueming Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ranran Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Minghuai Wang
- Forest Protection Department, Guangdong Academy of Forestry, Guangzhou 510520, China
| | - Changzhu Li
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410004, China
| | - Jingzhen Chen
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410004, China
| | - Yunzhu Chen
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410004, China
| | - Yong Chen
- Xishan Forest Farm, Dazu District, Chongqing 402360, China
| | - Chunyi Cui
- Longshan Forest Farm, Lechang 512221, China
| | - Liangbo Zhang
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha 410004, China
- Hunan Horticultural Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
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16
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Li Y, Zhao M, Cai K, Liu L, Han R, Pei X, Zhang L, Zhao X. Phytohormone biosynthesis and transcriptional analyses provide insight into the main growth stage of male and female cones Pinus koraiensis. FRONTIERS IN PLANT SCIENCE 2023; 14:1273409. [PMID: 37885661 PMCID: PMC10598626 DOI: 10.3389/fpls.2023.1273409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 09/26/2023] [Indexed: 10/28/2023]
Abstract
The cone is a crucial component of the whole life cycle of gymnosperm and an organ for sexual reproduction of gymnosperms. In Pinus koraiensis, the quantity and development process of male and female cones directly influence seed production, which in turn influences the tree's economic value. There are, however, due to the lack of genetic information and genomic data, the morphological development and molecular mechanism of female and male cones of P. koraiensis have not been analyzed. Long-term phenological observations were used in this study to document the main process of the growth of both male and female cones. Transcriptome sequencing and endogenous hormone levels at three critical developmental stages were then analyzed to identify the regulatory networks that control these stages of cones development. The most significant plant hormones influencing male and female cones growth were discovered to be gibberellin and brassinosteroids, according to measurements of endogenous hormone content. Additionally, transcriptome sequencing allowed the identification of 71,097 and 31,195 DEGs in male and female cones. The synthesis and control of plant hormones during cones growth were discovered via enrichment analysis of key enrichment pathways. FT and other flowering-related genes were discovered in the coexpression network of flower growth development, which contributed to the growth development of male and female cones of P. koraiensis. The findings of this work offer a cutting-edge foundation for understanding reproductive biology and the molecular mechanisms that control the growth development of male and female cones in P. koraiensis.
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Affiliation(s)
- Yan Li
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun, China
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Minghui Zhao
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun, China
| | - Kewei Cai
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun, China
| | - Lin Liu
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun, China
| | - Rui Han
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun, China
| | - Xiaona Pei
- College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Lina Zhang
- School of Information Technology, Jilin Agricultural University, Changchun, China
| | - Xiyang Zhao
- Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun, China
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17
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Li S, Chen H, Hong J, Ye X, Wang J, Chen Y, Zhang L, Su Z, Yang Z. Chlorate-induced molecular floral transition revealed by transcriptomes. Open Life Sci 2023; 18:20220612. [PMID: 37528883 PMCID: PMC10389677 DOI: 10.1515/biol-2022-0612] [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: 10/13/2021] [Revised: 03/25/2023] [Accepted: 04/08/2023] [Indexed: 08/03/2023] Open
Abstract
Flowering in off-season longan (Dimocarpus longan L.) can be induced effectively by the application of potassium chlorate (KClO3), but the mechanism of the physiological induction is largely unknown to decipher its mechanism and identify genes potentially regulating the process, and comparative analysis via RNA-Seq was performed between vegetative and KClO3-induced floral buds. A total of 18,649 differentially expressed genes (DEGs) were identified between control and treated samples. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that DEGs related to plant hormone signal transduction, mitogen-activated protein kinase (MAPK) signaling pathway, starch and sucrose metabolism, and phenylpropanoid biosynthesis were enriched in our data. A total of 29 flowering-related DEGs were identified in our study, such as APETALA1 (AP1), APETALA2 (AP2), AUXIN RESPONSE FACTOR 3/ETTIN (ARF3), SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 8 (SPL8), AGAMOUS (AG), and others. The upregulation of AP2 and SPL genes indicates that the age-related pathway is activated and influences the floral induction in KClO3-induced longan floral buds by coordinated regulation of genes related to AP1, AG, and ARF3. This study provides a valuable resource for studying molecular mechanisms underlying chlorate-induced floral transition in off-season longan, which may benefit the development and production of off-season tropical/subtropical fruit trees.
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Affiliation(s)
- Songgang Li
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, Hainan, China
- College of Horticulture, South China Agricultural University, Guangzhou510642, Guangdong, China
| | - Houbin Chen
- College of Horticulture, South China Agricultural University, Guangzhou510642, Guangdong, China
| | - Jiwang Hong
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, Hainan, China
| | - Xiuxu Ye
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, Hainan, China
| | - Jiabao Wang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, Hainan, China
| | - Yeyuan Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, Hainan, China
| | - Lei Zhang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, Hainan, China
| | - Zuanxian Su
- College of Horticulture, South China Agricultural University, Guangzhou510642, Guangdong, China
| | - Ziqin Yang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou571101, Hainan, China
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18
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Hummel NFC, Zhou A, Li B, Markel K, Ornelas IJ, Shih PM. The trans-regulatory landscape of gene networks in plants. Cell Syst 2023; 14:501-511.e4. [PMID: 37348464 DOI: 10.1016/j.cels.2023.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/21/2023] [Accepted: 05/11/2023] [Indexed: 06/24/2023]
Abstract
The transcriptional effector domains of transcription factors play a key role in controlling gene expression; however, their functional nature is poorly understood, hampering our ability to explore this fundamental dimension of gene regulatory networks. To map the trans-regulatory landscape in a complex eukaryote, we systematically characterized the putative transcriptional effector domains of over 400 Arabidopsis thaliana transcription factors for their capacity to modulate transcription. We demonstrate that transcriptional effector activity can be integrated into gene regulatory networks capable of elucidating the functional dynamics underlying gene expression patterns. We further show how our characterized domains can enhance genome engineering efforts and reveal how plant transcriptional activators share regulatory features conserved across distantly related eukaryotes. Our results provide a framework to systematically characterize the regulatory role of transcription factors at a genome-scale in order to understand the transcriptional wiring of biological systems.
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Affiliation(s)
- Niklas F C Hummel
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94705, USA; Department of Biology, Technische Universität Darmstadt, Darmstadt 64287, Germany
| | - Andy Zhou
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94705, USA
| | - Baohua Li
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94705, USA
| | - Kasey Markel
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94705, USA
| | - Izaiah J Ornelas
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94705, USA
| | - Patrick M Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94705, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
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19
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Thessen AE, Cooper L, Swetnam TL, Hegde H, Reese J, Elser J, Jaiswal P. Using knowledge graphs to infer gene expression in plants. Front Artif Intell 2023; 6:1201002. [PMID: 37384147 PMCID: PMC10298150 DOI: 10.3389/frai.2023.1201002] [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: 04/05/2023] [Accepted: 05/23/2023] [Indexed: 06/30/2023] Open
Abstract
Introduction Climate change is already affecting ecosystems around the world and forcing us to adapt to meet societal needs. The speed with which climate change is progressing necessitates a massive scaling up of the number of species with understood genotype-environment-phenotype (G×E×P) dynamics in order to increase ecosystem and agriculture resilience. An important part of predicting phenotype is understanding the complex gene regulatory networks present in organisms. Previous work has demonstrated that knowledge about one species can be applied to another using ontologically-supported knowledge bases that exploit homologous structures and homologous genes. These types of structures that can apply knowledge about one species to another have the potential to enable the massive scaling up that is needed through in silico experimentation. Methods We developed one such structure, a knowledge graph (KG) using information from Planteome and the EMBL-EBI Expression Atlas that connects gene expression, molecular interactions, functions, and pathways to homology-based gene annotations. Our preliminary analysis uses data from gene expression studies in Arabidopsis thaliana and Populus trichocarpa plants exposed to drought conditions. Results A graph query identified 16 pairs of homologous genes in these two taxa, some of which show opposite patterns of gene expression in response to drought. As expected, analysis of the upstream cis-regulatory region of these genes revealed that homologs with similar expression behavior had conserved cis-regulatory regions and potential interaction with similar trans-elements, unlike homologs that changed their expression in opposite ways. Discussion This suggests that even though the homologous pairs share common ancestry and functional roles, predicting expression and phenotype through homology inference needs careful consideration of integrating cis and trans-regulatory components in the curated and inferred knowledge graph.
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Affiliation(s)
- Anne E. Thessen
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Laurel Cooper
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Tyson L. Swetnam
- BIO5 Institute, University of Arizona, Tucson, AZ, United States
| | - Harshad Hegde
- Environmental Genomics and Systems Biology Division, Berkeley Lab (DOE), Berkeley, CA, United States
| | - Justin Reese
- Environmental Genomics and Systems Biology Division, Berkeley Lab (DOE), Berkeley, CA, United States
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
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20
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Qu Q, Liu N, Su Q, Liu X, Jia H, Liu Y, Sun M, Cao Z, Dong J. MicroRNAs involved in the trans-kingdom gene regulation in the interaction of maize kernels and Fusarium verticillioides. Int J Biol Macromol 2023:125046. [PMID: 37245767 DOI: 10.1016/j.ijbiomac.2023.125046] [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: 01/13/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 05/30/2023]
Abstract
Maize ear rot is a widespread disease and the main pathogen is Fusarium verticillioides. Plant microRNAs (miRNAs) have great effects on disease resistance and it has been reported that maize miRNA participates in defense responses in maize ear rot. However, the trans-kingdom regulation of miRNAs between maize and F. verticillioides remains uncharacterized. In this study, the relationship between miRNA-like RNAs (milRNAs) of F. verticillioides and pathogenicity was investigated, followed by sRNA analysis and degradome sequencing of miRNA profiles and the target genes of maize and F. verticillioides after inoculation. It was found that the milRNA biogenesis positively regulated the pathogenicity of F. verticillioides by knocking out the gene FvDicer2-encoded Dicer-like protein in F. verticillioides. Following inoculation with F. verticillioides, 284 known and 6571 novel miRNAs were obtained in maize, including 28 miRNAs differentially expressed at multiple time points. The target genes of maize differentially expressed miRNAs in F. verticillioides mediated multiple pathways, including autophagy and MAPK signaling pathway. Fifty-one novel F. verticillioides milRNAs were predicted to target 333 genes in maize involved in MAPK signaling pathways, plant hormone signaling transduction and plant-pathogen interaction pathways. Additionally, the miR528b-5p in maize targeted the mRNA of FvTTP which encoded a twice transmembrane protein in F. verticillioides. The FvTTP-knockout mutants displayed decreased pathogenicity and reduced synthesis of fumonisins. Thus, by interfering with the translation of FvTTP, the miR528b-5p inhibited F. verticillioides infection. These findings suggested a novel function of miR528 in resisting F. verticillioides infection. The miRNAs identified in this research and their putative target genes can be used to further elucidate the trans-kingdom functions of microRNAs in plant pathogen interaction.
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Affiliation(s)
- Qing Qu
- Plant Pathogenic Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agriculture University, Baoding 071001, China; State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agriculture University, Baoding 071001, China
| | - Ning Liu
- Plant Pathogenic Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agriculture University, Baoding 071001, China; State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agriculture University, Baoding 071001, China
| | - Qianfu Su
- Jilin Academy of Agricultural Sciences, Jilin 130033, China
| | - Xinfang Liu
- Corn Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, China
| | - Hui Jia
- Plant Pathogenic Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agriculture University, Baoding 071001, China; State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agriculture University, Baoding 071001, China
| | - Yuwei Liu
- Plant Pathogenic Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agriculture University, Baoding 071001, China
| | - Manli Sun
- Plant Pathogenic Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agriculture University, Baoding 071001, China; State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agriculture University, Baoding 071001, China
| | - Zhiyan Cao
- Plant Pathogenic Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agriculture University, Baoding 071001, China; State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agriculture University, Baoding 071001, China.
| | - Jingao Dong
- Plant Pathogenic Mycotoxin and Molecular Plant Pathology Laboratory, Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agriculture University, Baoding 071001, China; State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agriculture University, Baoding 071001, China.
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21
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Mishra S, Chaudhary R, Sharma P. Temporal expression analysis of microRNAs and their target GRAS genes induced by osmotic stress in two contrasting wheat genotypes. Mol Biol Rep 2023:10.1007/s11033-023-08486-2. [PMID: 37179268 DOI: 10.1007/s11033-023-08486-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/25/2023] [Indexed: 05/15/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are important nonprotein-coding genes in plants which participate in almost all biological processes during abiotic and biotic stresses. Understanding how plants respond to various environmental conditions requires the identification of stress-related miRNAs. In recent years, there has been an increased interest in studying miRNA genes and gene expression. Drought is one of the common environmental stresses limiting plant growth and development. Stress-specific miRNAs and their GRAS gene targets were validated to understand the role of miRNAs in response to osmotic stress. RESULTS In this study, expression patterns of the ten stress-responsive miRNAs involved in osmotic stress adaptation were examined in order to undertand the regulation behavior of abiotic stress and miRNAs in two contrasting wheat genotype C-306 (drought tolerant) and WL-711 (drought sensitive). Three miRNAs were discovered to be upregulated under stress, whereas seven miRNAs were showed to be down-regulated as a consequence of the study. In contrast to miRNA, it was also discovered that GRAS genes as their targets were up-regulated during osmotic stress. In addition, the expression level of miR159, miR408 along with their targets, TaGRAS178 and TaGRAS84 increased in response to osmotic stress. Nevertheless, miR408 is highly conserved miRNA that regulates plant growth, development and stress response. As a result, variation in the expression levels of studied miRNAs in the presence of target genes provides a plausible explanation for miRNA-based abiotic stress regulation. A regulatory network of miRNA and their targets revealed that fourteen miRNA interact with 55 GRAS targets from various subfamilies that contribute in the plant growth and development. CONCLUSIONS These findings provide evidence for temporal and variety-specific differential regulation of miRNAs and their targets in wheat in response to osmotic shock, and they may aid in determining the potential.
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Affiliation(s)
- Shefali Mishra
- ICAR-Indian Institute of Wheat and Barley Research, Karnal Agrasain Marg, Karnal, Haryana, 132 001, India
- Deenbandhu Chhotu Ram University of Science and Technology, Murthal, India
| | - Reeti Chaudhary
- Deenbandhu Chhotu Ram University of Science and Technology, Murthal, India
| | - Pradeep Sharma
- ICAR-Indian Institute of Wheat and Barley Research, Karnal Agrasain Marg, Karnal, Haryana, 132 001, India.
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22
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Vandepoele K, Kaufmann K. Characterization of Gene Regulatory Networks in Plants Using New Methods and Data Types. Methods Mol Biol 2023; 2698:1-11. [PMID: 37682465 DOI: 10.1007/978-1-0716-3354-0_1] [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] [Indexed: 09/09/2023]
Abstract
A major question in plant biology is to understand how plant growth, development, and environmental responses are controlled and coordinated by the activities of regulatory factors. Gene regulatory network (GRN) analyses require integrated approaches that combine experimental approaches with computational analyses. A wide range of experimental approaches and tools are now available, such as targeted perturbation of gene activities, quantitative and cell-type specific measurements of dynamic gene activities, and systematic analysis of the molecular 'hard-wiring' of the systems. At the computational level, different tools and databases are available to study regulatory sequences, including intuitive visualizations to explore data-driven gene regulatory networks in different plant species. Furthermore, advanced data integration approaches have recently been developed to efficiently leverage complementary regulatory data types and learn context-specific networks.
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Affiliation(s)
- Klaas Vandepoele
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium.
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium.
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.
| | - Kerstin Kaufmann
- Institute of Biology, Humboldt-Universitaet zu Berlin, Berlin, Germany
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23
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Lan Y, Zhao X, Chen D. The ChIP-Hub Resource: Toward plantEncode. Methods Mol Biol 2023; 2698:221-231. [PMID: 37682478 DOI: 10.1007/978-1-0716-3354-0_14] [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] [Indexed: 09/09/2023]
Abstract
Recent advances in sequencing technologies lead to the generation of an enormous amount of regulome and epigenome data in a variety of plant species. However, a comprehensive standardized resource is so far not available. In this chapter, we present ChIP-Hub, an integrative platform that has been developed based on the ENCODE standards by collecting and reanalyzing regulatory genomic datasets from 41 plant species. The ChIP-hub website is introduced in this chapter, including information on detailed steps of searching, data download, and online analyses, which facilitates users to explore ChIP-Hub. We also provide a cross-species comparison of chromatin accessibility information that gives a thorough view of evolutionary regulatory networks in plants.
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Affiliation(s)
- Yangming Lan
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xue Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.
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24
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Ó'Maoiléidigh D, Thomson B, Wellmer F. Floral Induction Systems for the Study of Arabidopsis Flower Development. Methods Mol Biol 2023; 2686:285-292. [PMID: 37540363 DOI: 10.1007/978-1-0716-3299-4_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Assessing the molecular changes that occur over the course of flower development is hampered by difficulties in isolating sufficient amounts of floral tissue at specific developmental stages. This is especially problematic when investigating molecular events at early stages of Arabidopsis flower development, as floral buds are minute and are initiated sequentially so that a single flower on an inflorescence is at a given developmental stage. Moreover, young floral buds are hidden by older flowers, which presents an additional challenge for dissection. To circumvent these issues, floral induction systems that allow the simultaneous induction of a large number of flowers on the inflorescence of a single plant were developed. To allow the plant community to avail of the full benefits of these systems, we address some common problems that can be encountered when growing these plants and collecting floral buds for analysis.
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Affiliation(s)
| | - Bennett Thomson
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Frank Wellmer
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland.
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25
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Chahtane H, Lai X, Tichtinsky G, Rieu P, Arnoux-Courseaux M, Cancé C, Marondedze C, Parcy F. Flower Development in Arabidopsis. Methods Mol Biol 2023; 2686:3-38. [PMID: 37540352 DOI: 10.1007/978-1-0716-3299-4_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Like in other angiosperms, the development of flowers in Arabidopsis starts right after the floral transition, when the shoot apical meristem (SAM) stops producing leaves and makes flowers instead. On the flanks of the SAM emerge the flower meristems (FM) that will soon differentiate into the four main floral organs, sepals, petals, stamens, and pistil, stereotypically arranged in concentric whorls. Each phase of flower development-floral transition, floral bud initiation, and floral organ development-is under the control of specific gene networks. In this chapter, we describe these different phases and the gene regulatory networks involved, from the floral transition to the floral termination.
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Affiliation(s)
- Hicham Chahtane
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France
- Institut de Recherche Pierre Fabre, Green Mission Pierre Fabre, Conservatoire Botanique Pierre Fabre, Soual, France
| | - Xuelei Lai
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Wuhan, China
| | | | - Philippe Rieu
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | | | - Coralie Cancé
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France
| | - Claudius Marondedze
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France
- Department of Biochemistry, Faculty of Medicine, Midlands State University, Senga, Gweru, Zimbabwe
| | - François Parcy
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France.
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26
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Álvarez-Urdiola R, Matus JT, Riechmann JL. Multi-Omics Methods Applied to Flower Development. Methods Mol Biol 2023; 2686:495-508. [PMID: 37540374 DOI: 10.1007/978-1-0716-3299-4_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Developmental processes in multicellular organisms depend on the proficiency of cells to orchestrate different gene expression programs. Over the past years, several studies of reproductive organ development have considered genomic analyses of transcription factors and global gene expression changes, modeling complex gene regulatory networks. Nevertheless, the dynamic view of developmental processes requires, as well, the study of the proteome in its expression, complexity, and relationship with the transcriptome. In this chapter, we describe a dual extraction method-for protein and RNA-for the characterization of genome expression at proteome level and its correlation to transcript expression data. We also present a shotgun proteomic procedure (LC-MS/MS) followed by a pipeline for the imputation of missing values in mass spectrometry results.
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Affiliation(s)
- Raquel Álvarez-Urdiola
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
| | - José Tomás Matus
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Cerdanyola del Vallès, Barcelona, Spain
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Valencia, Spain
| | - José Luis Riechmann
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Cerdanyola del Vallès, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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27
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Wang L, Xie X, Xu Y, Li Z, Xu G, Cheng L, Yang J, Li L, Pu W, Cao P. Comprehensive analysis of the carboxylesterase gene reveals that NtCXE22 regulates axillary bud growth through strigolactone metabolism in tobacco. FRONTIERS IN PLANT SCIENCE 2022; 13:1019538. [PMID: 36600915 PMCID: PMC9806860 DOI: 10.3389/fpls.2022.1019538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Carboxylesterases (CXE) are a class of hydrolytic enzymes with α/β-folding domains that play a vital role in plant growth, development, stress response, and activation of herbicide-active substances. In this study, 49 Nicotiana tabacum L. CXE genes (NtCXEs) were identified using a sequence homology search. The basic characteristics, phylogenetic evolution, gene structure, subcellular location, promoter cis-elements, and gene expression patterns of the CXE family were systematically analyzed. RNA-seq data and quantitative real-time PCR showed that the expression level of CXEs was associated with various stressors and hormones; gene expression levels were significantly different among the eight tissues examined and at different developmental periods. As a new class of hormones, strigolactones (SLs) are released from the roots of plants and can control the germination of axillary buds.NtCXE7, NtCXE9, NtCXE22, and NtCXE24 were homologous to Arabidopsis SLs hydrolase AtCXE15, and changes in their expression levels were induced by topping and by GR24 (a synthetic analogue of strigolactone). Further examination revealed that NtCXE22-mutant (ntcxe22) plants generated by CRISPR-Cas9 technology had shorter bud outgrowth with lower SLs content. Validation of NtCXE22 was also performed in NtCCD8-OE plants (with fewer axillary buds) and in ntccd8 mutant plants (with more axillary buds). The results suggest that NtCXE22 may act as an efficient SLs hydrolase and affects axillary bud development, thereby providing a feasible method for manipulating endogenous SLs in crops and ornamental plants.
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Affiliation(s)
- Lin Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing, China
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Xiaodong Xie
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Yalong Xu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Zefeng Li
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Guoyun Xu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Lingtong Cheng
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Jun Yang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Lei Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Wenxuan Pu
- Technology Center, China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
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28
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Damerval C, Claudot C, Le Guilloux M, Conde e Silva N, Brunaud V, Soubigou-Taconnat L, Caius J, Delannoy E, Nadot S, Jabbour F, Deveaux Y. Evolutionary analyses and expression patterns of TCP genes in Ranunculales. FRONTIERS IN PLANT SCIENCE 2022; 13:1055196. [PMID: 36531353 PMCID: PMC9752903 DOI: 10.3389/fpls.2022.1055196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
TCP transcription factors play a role in a large number of developmental processes and are at the crossroads of numerous hormonal biosynthetic and signaling pathways. The complete repertoire of TCP genes has already been characterized in several plant species, but not in any species of early diverging eudicots. We focused on the order Ranunculales because of its phylogenetic position as sister group to all other eudicots and its important morphological diversity. Results show that all the TCP genes expressed in the floral transcriptome of Nigella damascena (Ranunculaceae) are the orthologs of the TCP genes previously identified from the fully sequenced genome of Aquilegia coerulea. Phylogenetic analyses combined with the identification of conserved amino acid motifs suggest that six paralogous genes of class I TCP transcription factors were present in the common ancestor of angiosperms. We highlight independent duplications in core eudicots and Ranunculales within the class I and class II subfamilies, resulting in different numbers of paralogs within the main subclasses of TCP genes. This has most probably major consequences on the functional diversification of these genes in different plant clades. The expression patterns of TCP genes in Nigella damascena were consistent with the general suggestion that CIN and class I TCP genes may have redundant roles or take part in same pathways, while CYC/TB1 genes have more specific actions. Our findings open the way for future studies at the tissue level, and for investigating redundancy and subfunctionalisation in TCP genes and their role in the evolution of morphological novelties.
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Affiliation(s)
- Catherine Damerval
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, IDEEV, Gif-sur-Yvette, France
| | - Carmine Claudot
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, IDEEV, Gif-sur-Yvette, France
| | - Martine Le Guilloux
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, IDEEV, Gif-sur-Yvette, France
| | - Natalia Conde e Silva
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, IDEEV, Gif-sur-Yvette, France
| | - Véronique Brunaud
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Ludivine Soubigou-Taconnat
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - José Caius
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Etienne Delannoy
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Sophie Nadot
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Florian Jabbour
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Yves Deveaux
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, Génétique Quantitative et Evolution-Le Moulon, IDEEV, Gif-sur-Yvette, France
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29
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Zhang K, Zhang H, Pan Y, Niu Y, Guo L, Ma Y, Tian S, Wei J, Wang C, Yang X, Fu Y, Qu P, Liu L, Zhang Y, Sun H, Bai Z, Dong J, Li C, Liu X. Cell- and noncell-autonomous AUXIN RESPONSE FACTOR3 controls meristem proliferation and phyllotactic patterns. PLANT PHYSIOLOGY 2022; 190:2335-2349. [PMID: 35972411 PMCID: PMC9706454 DOI: 10.1093/plphys/kiac370] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
In cell-cell communication, noncell-autonomous transcription factors play vital roles in controlling plant stem cell fate. We previously reported that AUXIN RESPONSE FACTOR3 (ARF3), a member of the ARF family with critical roles in floral meristem maintenance and determinacy, has a distinct accumulation pattern that differs from the expression domain of its encoding gene in the shoot apical meristem (SAM). However, the biological meaning of this difference is obscure. Here, we demonstrate that ARF3 expression in Arabidopsis (Arabidopsis thaliana) is mainly activated at the periphery of the SAM by auxin where ARF3 cell autonomously regulates the expression of meristem-organ boundary-specific genes, such as CUP-SHAPED COTYLEDON1-3 (CUC1-3), BLADE ON PETIOLE1-2 (BOP1-2), and TARGETS UNDER ETTIN CONTROL3 (TEC3) to regulate the arrangement of organs in regular pattern, a phenomenon referred to as phyllotaxis. We also show that ARF3 is translocated into the organizing center where it represses cytokinin activity and WUSCHEL expression to regulate meristem activity noncell-autonomously. Therefore, ARF3 acts as a molecular link that mediates the interaction of auxin and cytokinin signaling in the SAM while coordinating the balance between meristem maintenance and organogenesis. Our findings reveal an ARF3-mediated coordination mechanism through cell-cell communication in dynamic SAM maintenance.
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Affiliation(s)
- Ke Zhang
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Hao Zhang
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Yanyun Pan
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Yanxiao Niu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Lin Guo
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang, China
| | - Yuru Ma
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Shijun Tian
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Jiarong Wei
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Cong Wang
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Xiubo Yang
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Yunze Fu
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Ping Qu
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Liantao Liu
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Yongjiang Zhang
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Hongchun Sun
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Zhiying Bai
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Jingao Dong
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Cundong Li
- State Key Laboratory of North China Crop Improvement and Regulation; Key Laboratory of Crop Growth Regulation of Hebei Province, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Xigang Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University; Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang, China
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Ferrari C, Manosalva Pérez N, Vandepoele K. MINI-EX: Integrative inference of single-cell gene regulatory networks in plants. MOLECULAR PLANT 2022; 15:1807-1824. [PMID: 36307979 DOI: 10.1016/j.molp.2022.10.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/30/2022] [Accepted: 10/21/2022] [Indexed: 05/26/2023]
Abstract
Multicellular organisms, such as plants, are characterized by highly specialized and tightly regulated cell populations, establishing specific morphological structures and executing distinct functions. Gene regulatory networks (GRNs) describe condition-specific interactions of transcription factors (TFs) regulating the expression of target genes, underpinning these specific functions. As efficient and validated methods to identify cell-type-specific GRNs from single-cell data in plants are lacking, limiting our understanding of the organization of specific cell types in both model species and crops, we developed MINI-EX (Motif-Informed Network Inference based on single-cell EXpression data), an integrative approach to infer cell-type-specific networks in plants. MINI-EX uses single-cell transcriptomic data to define expression-based networks and integrates TF motif information to filter the inferred regulons, resulting in networks with increased accuracy. Next, regulons are assigned to different cell types, leveraging cell-specific expression, and candidate regulators are prioritized using network centrality measures, functional annotations, and expression specificity. This embedded prioritization strategy offers a unique and efficient means to unravel signaling cascades in specific cell types controlling a biological process of interest. We demonstrate the stability of MINI-EX toward input data sets with low number of cells and its robustness toward missing data, and show that it infers state-of-the-art networks with a better performance compared with other related single-cell network tools. MINI-EX successfully identifies key regulators controlling root development in Arabidopsis and rice, leaf development in Arabidopsis, and ear development in maize, enhancing our understanding of cell-type-specific regulation and unraveling the roles of different regulators controlling the development of specific cell types in plants.
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Affiliation(s)
- Camilla Ferrari
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Nicolás Manosalva Pérez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium.
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Wang Q, Gao G, Chen X, Liu X, Dong B, Wang Y, Zhong S, Deng J, Fang Q, Zhao H. Genetic studies on continuous flowering in woody plant Osmanthus fragrans. FRONTIERS IN PLANT SCIENCE 2022; 13:1049479. [PMID: 36407607 PMCID: PMC9671776 DOI: 10.3389/fpls.2022.1049479] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Continuous flowering is a key horticultural trait in ornamental plants, whereas the specific molecular regulation mechanism remains largely unknown. In sweet osmanthus (Osmanthus fragrans Lour.), plants based on their flowering characteristics are divided into once-flowering (OF) habit and continuous flowering (CF) habit. Here, we first described the flowering phenology shifts of OF and CF habits in sweet osmanthus through paraffin section and microscope assay. Phenotypic characterization showed that CF plants had constant new shoot growth, floral transition, and blooming for 1 year, which might lead to a continuous flowering trait. We performed the transcriptome sequencing of OF and CF sweet osmanthus and analyzed the transcriptional activity of flowering-related genes. Among the genes, three floral integrators, OfFT, OfTFL1, and OfBFT, had a differential expression during the floral transition process in OF and CF habits. The expression patterns of the three genes in 1 year were revealed. The results suggested that their accumulations corresponded to the new shoots occurring and the floral transition process. Function studies suggested that OfFT acted as a flowering activator, whereas OfBFT was a flowering inhibitor. Yeast one-hybrid assay indicated that OfSPL8 was a common upstream transcription factor of OfFT and OfBFT, suggesting the vital role of OfSPL8 in continuous flowering regulation. These results provide a novel insight into the molecular mechanism of continuous flowering.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Qiu Fang
- *Correspondence: Hongbo Zhao, ; Qiu Fang,
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Heisler MG, Jönsson H, Wenkel S, Kaufmann K. Context-specific functions of transcription factors controlling plant development: From leaves to flowers. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102262. [PMID: 35952407 DOI: 10.1016/j.pbi.2022.102262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Plant development is regulated by transcription factors that often act in more than one process and stage of development. Yet the molecular mechanisms that govern the functional diversity and specificity of these proteins remains far from understood. Flower development provides an ideal context to study these mechanisms since the development of distinct floral organs depends on similar but distinct combinations of transcriptional regulators. Recent work also highlights the importance of leaf polarity regulators as additional key factors in flower initiation, floral organ morphogenesis, and possibly floral organ positioning. A detailed understanding of how these factors work in combination will enable us to address outstanding questions in flower development including how distinct shapes and positions of floral organs are generated. Experimental approaches and computer-based modeling will be required to characterize gene-regulatory networks at the level of single cells.
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Affiliation(s)
- Marcus G Heisler
- School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Henrik Jönsson
- Sainsbury Laboratory, University of Cambridge, UK; Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK; Computational Biology and Biological Physics, Lund University, Sweden
| | - Stephan Wenkel
- Department of Plant & Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark
| | - Kerstin Kaufmann
- Humboldt-Universität zu Berlin, Institute of Biology, Philippstr. 13, 10115, Berlin, Germany.
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33
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Mou Z, Wang H, Chen S, Reiter RJ, Zhao D. Molecular mechanisms and evolutionary history of phytomelatonin in flowering. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5840-5850. [PMID: 35443058 DOI: 10.1093/jxb/erac164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 04/15/2022] [Indexed: 06/14/2023]
Abstract
Flowering is a critical stage in plant life history, which is coordinated by environmental signals and endogenous cues. Phytomelatonin is a widely distributed indoleamine present in all living organisms and plays pleiotropic roles in plant growth and development. Recent evidence has established that phytomelatonin could modulate flowering in many species, probably in a concentration-dependent manner. Phytomelatonin seems to associate with floral meristem identification and floral organ formation, and the fluctuation of phytomelatonin might be important for flowering. Regarding the underlying mechanisms, phytomelatonin interacts with the central components of floral gene regulatory networks directly or indirectly, including the MADS-box gene family, phytohormones, and reactive oxygen species (ROS). From an evolutionary point of view, the actions of phytomelatonin in flowering probably evolved during the period of the diversification of flowering plants and could be regarded as a functional extension of its primary activities. The presumed evolutionary history of phytomelatonin-modulated flowering is proposed, presented in the chronological order of the appearance of phytomelatonin and core flowering regulators, namely DELLA proteins, ROS, and phytohormones. Further efforts are needed to address some intriguing aspects, such as the exploration of the association between phytomelatonin and photoperiodic flowering, phytomelatonin-related floral MADS-box genes, the crosstalk between phytomelatonin and phytohormones, as well as its potential applications in agriculture.
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Affiliation(s)
- Zongmin Mou
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
- Biocontrol Engineering Research Center of Plant Disease and Pest, Yunnan University, Kunming, China
- Biocontrol Engineering Research Center of Crop Disease and Pest, Yunnan University, Kunming, China
| | - Houping Wang
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan University, Kunming, China
| | - Suiyun Chen
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
- Biocontrol Engineering Research Center of Plant Disease and Pest, Yunnan University, Kunming, China
- Biocontrol Engineering Research Center of Crop Disease and Pest, Yunnan University, Kunming, China
| | - Russel J Reiter
- Department of Cell Systems and Anatomy, UT Health San Antonio, Long School of Medicine, San Antonio, TX, USA
| | - Dake Zhao
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
- Biocontrol Engineering Research Center of Plant Disease and Pest, Yunnan University, Kunming, China
- Biocontrol Engineering Research Center of Crop Disease and Pest, Yunnan University, Kunming, China
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Liu C, Leng J, Li Y, Ge T, Li J, Chen Y, Guo C, Qi J. A spatiotemporal atlas of organogenesis in the development of orchid flowers. Nucleic Acids Res 2022; 50:9724-9737. [PMID: 36095130 PMCID: PMC9508851 DOI: 10.1093/nar/gkac773] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/19/2022] [Accepted: 08/29/2022] [Indexed: 11/15/2022] Open
Abstract
Development of floral organs exhibits complex molecular mechanisms involving the co-regulation of many genes specialized and precisely functioning in various tissues and developing stages. Advance in spatial transcriptome technologies allows for quantitative measurement of spatially localized gene abundance making it possible to bridge complex scenario of flower organogenesis with genome-wide molecular phenotypes. Here, we apply the 10× Visium technology in the study of the formation of floral organs through development in an orchid plant, Phalaenopsis Big Chili. Cell-types of early floral development including inflorescence meristems, primordia of floral organs and identity determined tissues, are recognized based on spatial expression distribution of thousands of genes in high resolution. In addition, meristematic cells on the basal position of floral organs are found to continuously function in multiple developmental stages after organ initiation. Particularly, the development of anther, which primordium starts from a single spot to multiple differentiated cell-types in later stages including pollinium and other vegetative tissues, is revealed by well-known MADS-box genes and many other downstream regulators. The spatial transcriptome analyses provide comprehensive information of gene activity for understanding the molecular architecture of flower organogenesis and for future genomic and genetic studies of specific cell-types.
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Affiliation(s)
- Chang Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Jing Leng
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yonglong Li
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang, China
| | - Tingting Ge
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang, China
| | - Jinglong Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yamao Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Chunce Guo
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang, China
| | - Ji Qi
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
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Han X, Zhang YW, Liu JY, Zuo JF, Zhang ZC, Guo L, Zhang YM. 4D genetic networks reveal the genetic basis of metabolites and seed oil-related traits in 398 soybean RILs. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:92. [PMID: 36076247 PMCID: PMC9461130 DOI: 10.1186/s13068-022-02191-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/27/2022] [Indexed: 11/10/2022]
Abstract
Background The yield and quality of soybean oil are determined by seed oil-related traits, and metabolites/lipids act as bridges between genes and traits. Although there are many studies on the mode of inheritance of metabolites or traits, studies on multi-dimensional genetic network (MDGN) are limited. Results In this study, six seed oil-related traits, 59 metabolites, and 107 lipids in 398 recombinant inbred lines, along with their candidate genes and miRNAs, were used to construct an MDGN in soybean. Around 175 quantitative trait loci (QTLs), 36 QTL-by-environment interactions, and 302 metabolic QTL clusters, 70 and 181 candidate genes, including 46 and 70 known homologs, were previously reported to be associated with the traits and metabolites, respectively. Gene regulatory networks were constructed using co-expression, protein–protein interaction, and transcription factor binding site and miRNA target predictions between candidate genes and 26 key miRNAs. Using modern statistical methods, 463 metabolite–lipid, 62 trait–metabolite, and 89 trait–lipid associations were found to be significant. Integrating these associations into the above networks, an MDGN was constructed, and 128 sub-networks were extracted. Among these sub-networks, the gene–trait or gene–metabolite relationships in 38 sub-networks were in agreement with previous studies, e.g., oleic acid (trait)–GmSEI–GmDGAT1a–triacylglycerol (16:0/18:2/18:3), gene and metabolite in each of 64 sub-networks were predicted to be in the same pathway, e.g., oleic acid (trait)–GmPHS–d-glucose, and others were new, e.g., triacylglycerol (16:0/18:1/18:2)–GmbZIP123–GmHD-ZIPIII-10–miR166s–oil content. Conclusions This study showed the advantages of MGDN in dissecting the genetic relationships between complex traits and metabolites. Using sub-networks in MGDN, 3D genetic sub-networks including pyruvate/threonine/citric acid revealed genetic relationships between carbohydrates, oil, and protein content, and 4D genetic sub-networks including PLDs revealed the relationships between oil-related traits and phospholipid metabolism likely influenced by the environment. This study will be helpful in soybean quality improvement and molecular biological research. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02191-1.
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Gao Z, Li J, Li L, Yang Y, Li J, Fu C, Zhu D, He H, Cai H, Li L. Structural and Functional Analyses of Hub MicroRNAs in An Integrated Gene Regulatory Network of Arabidopsis. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:747-764. [PMID: 33662619 PMCID: PMC9880815 DOI: 10.1016/j.gpb.2020.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 12/04/2019] [Accepted: 06/14/2020] [Indexed: 01/31/2023]
Abstract
MicroRNAs (miRNAs) are trans-acting small regulatory RNAs that work coordinately with transcription factors (TFs) to shape the repertoire of cellular mRNAs available for translation. Despite our growing knowledge of individual plant miRNAs, their global roles in gene regulatory networks remain mostly unassessed. Based on interactions obtained from public databases and curated from the literature, we reconstructed an integrated miRNA network in Arabidopsis that includes 66 core TFs, 318 miRNAs, and 1712 downstream genes. We found that miRNAs occupy distinct niches and enrich miRNA-containing feed-forward loops (FFLs), particularly those with miRNAs as intermediate nodes. Further analyses revealed that miRNA-containing FFLs coordinate TFs located in different hierarchical layers and that intertwined miRNA-containing FFLs are associated with party and date miRNA hubs. Using the date hub MIR858A as an example, we performed detailed molecular and genetic analyses of three interconnected miRNA-containing FFLs. These analyses revealed individual functions of the selected miRNA-containing FFLs and elucidated how the date hub miRNA fulfills multiple regulatory roles. Collectively, our findings highlight the prevalence and importance of miRNA-containing FFLs, and provide new insights into the design principles and control logics of miRNA regulatory networks governing gene expression programs in plants.
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Affiliation(s)
- Zhaoxu Gao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Jun Li
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Li Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Yanzhi Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Jian Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Chunxiang Fu
- CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Danmeng Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Hang He
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Huaqing Cai
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lei Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China,Corresponding author.
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37
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Galán-Vásquez E, Gómez-García MDC, Pérez-Rueda E. A landscape of gene regulation in the parasitic amoebozoa Entamoeba spp. PLoS One 2022; 17:e0271640. [PMID: 35913975 PMCID: PMC9342746 DOI: 10.1371/journal.pone.0271640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 07/05/2022] [Indexed: 11/27/2022] Open
Abstract
Entamoeba are amoeboid extracellular parasites that represent an important group of organisms for which the regulatory networks must be examined to better understand how genes and functional processes are interrelated. In this work, we inferred the gene regulatory networks (GRNs) in four Entamoeba species, E. histolytica, E. dispar, E. nuttalli, and E. invadens, and the GRN topological properties and the corresponding biological functions were evaluated. From these analyses, we determined that transcription factors (TFs) of E. histolytica, E. dispar, and E. nuttalli are associated mainly with the LIM family, while the TFs in E. invadens are associated with the RRM_1 family. In addition, we identified that EHI_044890 regulates 121 genes in E. histolytica, EDI_297980 regulates 284 genes in E. dispar, ENU1_120230 regulates 195 genes in E. nuttalli, and EIN_249270 regulates 257 genes in E. invadens. Finally, we identified that three types of processes, Macromolecule metabolic process, Cellular macromolecule metabolic process, and Cellular nitrogen compound metabolic process, are the main biological processes for each network. The results described in this work can be used as a basis for the study of gene regulation in these organisms.
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Affiliation(s)
- Edgardo Galán-Vásquez
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, México
- * E-mail: (EG-V); (EP-R)
| | - María del Consuelo Gómez-García
- Laboratorio de Biomedicina Molecular, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Ciudad de México, México
| | - Ernesto Pérez-Rueda
- Unidad Académica Yucatán, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Mérida, Yucatán, México
- * E-mail: (EG-V); (EP-R)
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Hernández MA, Butler JB, Ammitzboll H, Weller JL, Vaillancourt RE, Potts BM. Genetic control of the operculum and capsule morphology of Eucalyptus globulus. ANNALS OF BOTANY 2022; 130:97-108. [PMID: 35652517 PMCID: PMC9295918 DOI: 10.1093/aob/mcac072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIMS The petaline operculum that covers the inner whorls until anthesis and the woody capsule that develops after fertilization are reproductive structures of eucalypts that protect the flower and seeds. Although they are distinct organs, they both develop from flower buds and this common ontogeny suggests shared genetic control. In Eucalyptus globulus their morphology is variable and we aimed to identify the quantitative trait loci (QTL) underlying this variation and determine whether there is common genetic control of these ecologically and taxonomically important reproductive structures. METHODS Samples of opercula and capsules were collected from 206 trees that belong to a large outcrossed F2E. globulus mapping population. The morphological variation in these structures was characterized by measuring six operculum and five capsule traits. QTL analysis was performed using these data and a linkage map consisting of 480 markers. KEY RESULTS A total of 27 QTL were detected for operculum traits and 28 for capsule traits, with the logarithm of odds ranging from 2.8 to 11.8. There were many co-located QTL associated with operculum or capsule traits, generally reflecting allometric relationships. A key finding was five genomic regions where co-located QTL affected both operculum and capsule morphology, and the overall trend for these QTL was to affect elongation of both organs. Some of these QTL appear to have a significant effect on the phenotype, with the strongest QTL explaining 26.4 % of the variation in operculum shape and 16.4 % in capsule shape. Flower bud measurements suggest the expression of these QTL starts during bud development. Several candidate genes were found associated with the QTL and their putative function is discussed. CONCLUSIONS Variation in both operculum and capsule traits in E. globulus is under strong genetic control. Our results suggest that these reproductive structures share a common genetic pathway during flower bud development.
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Affiliation(s)
- Mariano A Hernández
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
- Instituto Nacional de Tecnología Agropecuaria (INTA), Route 27 - Km 38.3, Bella Vista, Corrientes 3432, Argentina
| | | | - Hans Ammitzboll
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - James L Weller
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture
| | - René E Vaillancourt
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Brad M Potts
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
- ARC Training Centre for Forest Value, University of Tasmania, Hobart, Tasmania 7001, Australia
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Fu LY, Zhu T, Zhou X, Yu R, He Z, Zhang P, Wu Z, Chen M, Kaufmann K, Chen D. ChIP-Hub provides an integrative platform for exploring plant regulome. Nat Commun 2022; 13:3413. [PMID: 35701419 PMCID: PMC9197862 DOI: 10.1038/s41467-022-30770-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 05/18/2022] [Indexed: 11/18/2022] Open
Abstract
Plant genomes encode a complex and evolutionary diverse regulatory grammar that forms the basis for most life on earth. A wealth of regulome and epigenome data have been generated in various plant species, but no common, standardized resource is available so far for biologists. Here, we present ChIP-Hub, an integrative web-based platform in the ENCODE standards that bundles >10,000 publicly available datasets reanalyzed from >40 plant species, allowing visualization and meta-analysis. We manually curate the datasets through assessing ~540 original publications and comprehensively evaluate their data quality. As a proof of concept, we extensively survey the co-association of different regulators and construct a hierarchical regulatory network under a broad developmental context. Furthermore, we show how our annotation allows to investigate the dynamic activity of tissue-specific regulatory elements (promoters and enhancers) and their underlying sequence grammar. Finally, we analyze the function and conservation of tissue-specific promoters, enhancers and chromatin states using comparative genomics approaches. Taken together, the ChIP-Hub platform and the analysis results provide rich resources for deep exploration of plant ENCODE. ChIP-Hub is available at https://biobigdata.nju.edu.cn/ChIPHub/ .
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Affiliation(s)
- Liang-Yu Fu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Tao Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xinkai Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Ranran Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Zhaohui He
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Peijing Zhang
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhigui Wu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
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Cheng L, Ma L, Meng L, Shang H, Cao P, Jin J. Genome-Wide Identification and Analysis of the Class III Peroxidase Gene Family in Tobacco (Nicotiana tabacum). Front Genet 2022; 13:916867. [PMID: 35769995 PMCID: PMC9234461 DOI: 10.3389/fgene.2022.916867] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
Class III peroxidases (PODs) are plant-specific enzymes that play significant roles in plant physiological processes and stress responses. However, a comprehensive analysis of the POD gene family in tobacco has not yet been conducted. In this study, 210 non-redundant POD gene members (NtPODs) were identified in tobacco (Nicotiana tabacum) and distributed unevenly throughout 24 tobacco chromosomes. Phylogenetic analysis clustered these genes into six subgroups (I-VI). Gene structure and motif analyses showed the structural and functional diversity among the subgroups. Segmental duplication and purifying selection were the main factors affecting NtPOD gene evolution. Our analyses also suggested that NtPODs might be regulated by miRNAs and cis-acting regulatory elements of transcription factors that are involved in various biological processes. In addition, the expression patterns in different tissues and under various stress treatments were investigated. The results showed that the majority of NtPODs had tissue-specific expression patterns and may be involved in many biotic and abiotic responses. qRT-PCR analyses of different tissues and stress treatments were performed to verify transcriptome patterns. Expression of a green fluorescent protein-NtPOD fusion confirmed the plasma membrane localization of NtPOD121 and NtPOD4. Furthermore, 3D structures provided evidences of membrane-bound peroxidase. These findings provide useful information to better understand the evolution of the NtPOD gene family and lay the foundation for further studies on POD gene function in tobacco.
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Affiliation(s)
- Lingtong Cheng
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Lanxin Ma
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Lijun Meng
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
| | - Haihong Shang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
- *Correspondence: Jingjing Jin, ; Peijian Cao,
| | - Jingjing Jin
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China
- *Correspondence: Jingjing Jin, ; Peijian Cao,
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41
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Bernardi Y, Ponso MA, Belén F, Vegetti AC, Dotto MC. MicroRNA miR394 regulates flowering time in Arabidopsis thaliana. PLANT CELL REPORTS 2022; 41:1375-1388. [PMID: 35333960 DOI: 10.1007/s00299-022-02863-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
miR394 regulates Arabidopsis flowering time in a LCR-independent manner. Arabidopsis plants harboring mutations in theMIR394 genes exhibit early flowering, lower expression of floral repressor FLC and higher expression of floral integrators FT and SOC1. Plant development occurs throughout its entire life cycle and involves a phase transition between vegetative and reproductive phases, leading to the flowering process, fruit formation and ultimately seed production. It has been shown that the microRNA394 (miR394) regulates the accumulation of the transcript coding for LEAF CURLING RESPONSIVENESS, a member of a family of F-Box proteins. The miR394 pathway regulates several processes including leaf morphology and development of the shoot apical meristem during embryogenesis, as well as having been assigned a role in the response to biotic and abiotic stress in Arabidopsis thaliana and other species. Here, we characterized plants harboring mutations in MIR394 precursor genes and demonstrate that mir394a mir394b double mutants display an early flowering phenotype which correlates with a lower expression of FLOWERING LOCUS C earlier in development and higher expression of the floral integrators FLOWERING LOCUS T and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1. Consequently, mutant plants produce fewer branches and exhibit lower seed production. Our work reveals previously unknown developmental aspects regulated by the miR394 pathway, in an LCR-independent manner, contributing to the characterization of the multiple roles of this versatile plant regulatory miRNA.
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Affiliation(s)
- Yanel Bernardi
- Instituto de Ciencias Agropecuarias del Litoral (ICIAGRO-Litoral, UNL-CONICET), Kreder 2805, CP3080, Esperanza, Santa Fe, Argentina
- Instituto Tecnológico de Chascomús (INTECH, CONICET-UNSAM), Chascomús, Argentina
| | - María Agustina Ponso
- Instituto de Ciencias Agropecuarias del Litoral (ICIAGRO-Litoral, UNL-CONICET), Kreder 2805, CP3080, Esperanza, Santa Fe, Argentina
- Instituto Multidisciplinario de Investigación y Transferencia Agroalimentaria y Biotecnológica (IMITAB, UNVM-CONICET). Instituto de Ciencias Básicas, Villa María, Córdoba, Argentina
| | - Federico Belén
- Instituto de Ciencias Agropecuarias del Litoral (ICIAGRO-Litoral, UNL-CONICET), Kreder 2805, CP3080, Esperanza, Santa Fe, Argentina
| | - Abelardo C Vegetti
- Instituto de Ciencias Agropecuarias del Litoral (ICIAGRO-Litoral, UNL-CONICET), Kreder 2805, CP3080, Esperanza, Santa Fe, Argentina
| | - Marcela C Dotto
- Instituto de Ciencias Agropecuarias del Litoral (ICIAGRO-Litoral, UNL-CONICET), Kreder 2805, CP3080, Esperanza, Santa Fe, Argentina.
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Panigrahy M, Panigrahi KCS, Poli Y, Ranga A, Majeed N. Integrated Expression Analysis of Small RNA, Degradome and Microarray Reveals Complex Regulatory Action of miRNA during Prolonged Shade in Swarnaprabha Rice. BIOLOGY 2022; 11:biology11050798. [PMID: 35625525 PMCID: PMC9138629 DOI: 10.3390/biology11050798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 12/22/2022]
Abstract
Prolonged shade during the reproductive stage can result in significant yield losses in rice. For this study, we elucidated the role of microRNAs in prolonged-shade tolerance (~20 days of shade) in a shade-tolerant rice variety, Swarnaprabha (SP), in its reproductive stage using small RNA and degradome sequencing with expression analysis using microarray and qRT-PCR. This study demonstrates that miRNA (miR) regulation for shade-tolerance predominately comprises the deactivation of the miR itself, leading to the upregulation of their targets. Up- and downregulated differentially expressed miRs (DEms) presented drastic differences in the category of targets based on the function and pathway in which they are involved. Moreover, neutrally regulated and uniquely expressed miRs also contributed to the shade-tolerance response by altering the differential expression of their targets, probably due to their differential binding affinities. The upregulated DEms mostly targeted the cell wall, membrane, cytoskeleton, and cellulose synthesis-related transcripts, and the downregulated DEms targeted the transcripts of photosynthesis, carbon and sugar metabolism, energy metabolism, and amino acid and protein metabolism. We identified 16 miRNAs with 21 target pairs, whose actions may significantly contribute to the shade-tolerance phenotype and sustainable yield of SP. The most notable among these were found to be miR5493-OsSLAC and miR5144-OsLOG1 for enhanced panicle size, miR5493-OsBRITTLE1-1 for grain formation, miR6245-OsCsIF9 for decreased stem mechanical strength, miR5487-OsGns9 and miR168b-OsCP1 for better pollen development, and miR172b-OsbHLH153 for hyponasty under shade.
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Affiliation(s)
- Madhusmita Panigrahy
- Biofuel & Bioprocessing Research Centre, Institute of Technical Education and Research, Siksha ‘O’ Anusandhan University, Bhubaneswar 751002, India
- National Institute of Science Education and Research, Homi Bhabha National Institute (HBNI), Khurda 752050, India; (A.R.); (N.M.)
- Correspondence: (M.P.); (K.C.S.P.); Tel.: +91-8762086581 (M.P.); +91-6742494139 (K.C.S.P.)
| | - Kishore Chandra Sekhar Panigrahi
- National Institute of Science Education and Research, Homi Bhabha National Institute (HBNI), Khurda 752050, India; (A.R.); (N.M.)
- Correspondence: (M.P.); (K.C.S.P.); Tel.: +91-8762086581 (M.P.); +91-6742494139 (K.C.S.P.)
| | - Yugandhar Poli
- ICAR-Indian Institute of Rice Research, Rajendra Nagar, Hyderabad 500030, India;
| | - Aman Ranga
- National Institute of Science Education and Research, Homi Bhabha National Institute (HBNI), Khurda 752050, India; (A.R.); (N.M.)
| | - Neelofar Majeed
- National Institute of Science Education and Research, Homi Bhabha National Institute (HBNI), Khurda 752050, India; (A.R.); (N.M.)
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Zhao ML, Zhou ZF, Chen MS, Xu CJ, Xu ZF. An ortholog of the MADS-box gene SEPALLATA3 regulates stamen development in the woody plant Jatropha curcas. PLANTA 2022; 255:111. [PMID: 35478059 DOI: 10.1007/s00425-022-03886-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Overexpression of JcSEP3 causes defective stamen development in Jatropha curcas, in which brassinosteroid and gibberellin signaling pathways may be involved. SEPALLATAs (SEPs), the class E genes of the ABCE model, are required for floral organ determination. In this study, we investigated the role of the JcSEP3 gene in floral organ development in the woody plant Jatropha curcas. Transgenic Jatropha plants overexpressing JcSEP3 displayed abnormal phenotypes such as deficient anthers and pollen, as well as free stamen filaments, whereas JcSEP3-RNA interference (RNAi) transgenic plants had no obvious phenotypic changes, suggesting that JcSEP3 is redundant with other JcSEP genes in Jatropha. Moreover, we compared the transcriptomes of wild-type plants, JcSEP3-overexpressing, and JcSEP3-RNAi transgenic plants. In the JcSEP3-overexpressing transgenic plants, we discovered 25 upregulated genes involved in anther and pollen development, as well as 12 induced genes in brassinosteroid (BR) and gibberellin (GA) signaling pathways. These results suggest that JcSEP3 directly or indirectly regulates stamen development, concomitant with the regulation of BR and GA signaling pathways. Our findings help to understand the roles of SEP genes in stamen development in perennial woody plants.
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Affiliation(s)
- Mei-Li Zhao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Zhi-Fang Zhou
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Mao-Sheng Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China.
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China.
| | - Chuan-Jia Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China
| | - Zeng-Fu Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning, 530004, Guangxi, China.
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Hurgobin B, Lewsey MG. Applications of cell- and tissue-specific 'omics to improve plant productivity. Emerg Top Life Sci 2022; 6:163-173. [PMID: 35293572 PMCID: PMC9023014 DOI: 10.1042/etls20210286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 02/21/2022] [Accepted: 02/25/2022] [Indexed: 01/05/2023]
Abstract
The individual tissues and cell types of plants each have characteristic properties that contribute to the function of the plant as a whole. These are reflected by unique patterns of gene expression, protein and metabolite content, which enable cell-type-specific patterns of growth, development and physiology. Gene regulatory networks act within the cell types to govern the production and activity of these components. For the broader organism to grow and reproduce successfully, cell-type-specific activity must also function within the context of surrounding cell types, which is achieved by coordination of signalling pathways. We can investigate how gene regulatory networks are constructed and function using integrative 'omics technologies. Historically such experiments in plant biological research have been performed at the bulk tissue level, to organ resolution at best. In this review, we describe recent advances in cell- and tissue-specific 'omics technologies that allow investigation at much improved resolution. We discuss the advantages of these approaches for fundamental and translational plant biology, illustrated through the examples of specialised metabolism in medicinal plants and seed germination. We also discuss the challenges that must be overcome for such approaches to be adopted widely by the community.
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Affiliation(s)
- Bhavna Hurgobin
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, AgriBio Building, Bundoora, VIC 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC 3086, Australia
| | - Mathew G. Lewsey
- La Trobe Institute for Agriculture and Food, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, AgriBio Building, Bundoora, VIC 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, VIC 3086, Australia
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45
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Dong X, Guan Y, Zhang Z, Li H. miR390-tasiRNA3-ARF4 pathway is involved in regulating flowering time in woodland strawberry. PLANT CELL REPORTS 2022; 41:921-934. [PMID: 34985575 DOI: 10.1007/s00299-021-02828-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
miR390-tasiRNA3-ARF4 pathway was identified in woodland strawberry. FvemiR390 was involved in the regulation of flowering time, and miR390-tasiRNA3-ARF4 regulated flowering time through FveAP1/FveFUL in woodland strawberry. miRNA is an important type of regulator, and widely involved in plant growth, development and stress response. As a conserved miRNA family, the function of miR390 has been studied in many species, but poorly understood in woodland strawberry. In this study, we found that the members of miR390 family were highly conservative, and FvemiR390a and FvemiR390b have the same mature sequence. Therefore, we chose FveMIR390a to generate FvemiR390 mature sequence for functional studies. Subsequently, the result of transient gene expression assay proved that FvemiR390 negatively regulates FveARF4 through miR390-tasiRNA3-ARF4 pathway. Using transgenic plants, we discovered that the overexpression of FveMIR390a delayed flowering in woodland strawberry. Further studies revealed that the expressions of FveAP1 and FveFUL were lower in transgenic plants, which indicates miR390-tasiRNA3-ARF4 pathway delays flowering time through the FveAP1/FveFUL in woodland strawberry. Moreover, the expression of FvemiR390 responded to exogenous hormones, which also provides a reference for the application of exogenous hormones in regulating the flowering time of woodland strawberry.
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Affiliation(s)
- Xiangxiang Dong
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yuhan Guan
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhihong Zhang
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Analytical and Testing Center, Shenyang Agricultural University, Shenyang, 110866, China
| | - He Li
- Liaoning Key Laboratory of Strawberry Breeding and Cultivation, College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China.
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46
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An Integrated Analysis of Transcriptome and miRNA Sequencing Provides Insights into the Dynamic Regulations during Flower Morphogenesis in Petunia. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8040284] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Published genome sequences can facilitate multiple genome sequencing studies of flower development, which can serve as the basis for later analysis of variation in flower phenotypes. To identify potential regulators related to flower morphology, we captured dynamic expression patterns under five different developmental stages of petunia flowers, a popular bedding plant, using transcriptome and miRNA sequencing. The significant transcription factor (TF) families, including MYB, MADS, and bHLH, were elucidated. MADS-box genes exhibited co-expression patterns with BBR-BPC, GATA, and Dof genes in different modules according to a weighted gene co-expression network analysis. Through miRNA sequencing, a total of 45 conserved and 26 novel miRNAs were identified. According to GO and KEGG enrichment analysis, the carbohydrate metabolic process, photosynthesis, and phenylalanine metabolism were significant at the transcriptomic level, while the response to hormone pathways was significantly enriched by DEmiR-targeted genes. Finally, an miRNA–RNA network was constructed, which suggested the possibility of novel miRNA-mediated regulation pathways being activated during flower development. Overall, the expression data in the present study provide novel insights into the developmental gene regulatory network facilitated by TFs, miRNA, and their target genes.
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House MA, Young LW, Robinson SJ, Booker HM. Transcriptomic Analysis of Early Flowering Signals in ‘Royal’ Flax. PLANTS 2022; 11:plants11070860. [PMID: 35406840 PMCID: PMC9002848 DOI: 10.3390/plants11070860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/11/2022] [Accepted: 03/16/2022] [Indexed: 11/29/2022]
Abstract
Canada is one of the world’s leading producers and exporters of flax seed, with most production occurring in the Prairie Provinces. However, reduced season length and risk of frost restricts production in the northern grain belt of the Canadian Prairies. To expand the growing region of flax and increase production in Canada, flax breeders need to develop earlier-flowering varieties capable of avoiding the risk of abiotic stress. A thorough understanding of flowering control of flax is essential for the efficient breeding of such lines. We identified 722 putative flax flowering genes that span all major flowering-time pathways. Frequently, we found multiple flax homologues for a single Arabidopsis flowering gene. We used RNA sequencing to quantify the expression of genes in the shoot apical meristem (SAM) at 10, 15, 19, and 29 days after planting (dap) using the ‘Royal’ cultivar. We observed the expression of 80% of putative flax flowering genes and the differential expression of only 30%; these included homologues of major flowering regulators, such as SOC1, FUL, and AP1. We also found enrichment of differentially expressed genes (DEGs) in transcription factor (TF) families involved in flowering. Finally, we identified the candidates’ novel flowering genes amongst the uncharacterized flax genes. Our transcriptomic dataset provides a useful resource for investigating the regulatory control of the transition to flowering in flax and for the breeding of northern-adapted varieties.
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Affiliation(s)
- Megan A. House
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada; (M.A.H.); (L.W.Y.)
| | - Lester W. Young
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada; (M.A.H.); (L.W.Y.)
| | - Stephen J. Robinson
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N 0X2, Canada;
| | - Helen M. Booker
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada; (M.A.H.); (L.W.Y.)
- Department of Plant Agriculture, Ontario Agricultural College, University of Guelph, 50 Stone Rd E, Guelph, ON N1G 2W1, Canada
- Correspondence: ; Tel.: +1-519-824-4120 (ext. 56829)
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48
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Yamaguchi N. The epigenetic mechanisms regulating floral hub genes and their potential for manipulation. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1277-1287. [PMID: 34752611 DOI: 10.1093/jxb/erab490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
Gene regulatory networks formed by transcription factors play essential roles in the regulation of gene expression during plant reproductive development. These networks integrate endogenous, phytohormonal, and environmental cues. Molecular genetic, biochemical, and chemical analyses performed mainly in Arabidopsis have identified network hub genes and revealed the contributions of individual components to these networks. Here, I outline current understanding of key epigenetic regulatory circuits identified by research on plant reproduction, and highlight significant recent examples of genetic engineering and chemical applications to modulate the epigenetic regulation of gene expression. Furthermore, I discuss future prospects for applying basic plant science to engineer useful floral traits in a predictable manner as well as the potential side effects.
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Affiliation(s)
- Nobutoshi Yamaguchi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan
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Abstract
Flowering plants produce flowers and one of the most complex floral structures is the pistil or the gynoecium. All the floral organs differentiate from the floral meristem. Various reviews exist on molecular mechanisms controlling reproductive development, but most focus on a short time window and there has been no recent review on the complete developmental time frame of gynoecium and fruit formation. Here, we highlight recent discoveries, including the players, interactions and mechanisms that govern gynoecium and fruit development in Arabidopsis. We also present the currently known gene regulatory networks from gynoecium initiation until fruit maturation.
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Affiliation(s)
- Humberto Herrera-Ubaldo
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-León, Irapuato 36824, Guanajuato, México
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-León, Irapuato 36824, Guanajuato, México
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50
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Li M, Sang M, Wen Z, Meng J, Cheng T, Zhang Q, Sun L. Mapping Floral Genetic Architecture in Prunus mume, an Ornamental Woody Plant. FRONTIERS IN PLANT SCIENCE 2022; 13:828579. [PMID: 35211141 PMCID: PMC8860970 DOI: 10.3389/fpls.2022.828579] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Floral traits are both evolutionarily and economically relevant for ornamental plants. However, their underlying genetic architecture, especially in woody ornamental plants, is still poorly understood. We perform mapping experiments aimed at identifying specific quantitative trait loci (QTLs) that control the size, shape, architecture, color, and timing of flowers in mei (Prunus mume). We find that the narrow region of chromosome 1 (5-15 Mb) contains a number of floral QTLs. Most QTLs detected from this mapping study are annotated to candidate genes that regulate various biological functions toward the floral formation. We identify strong pleiotropic control on different aspects of flower morphology (including shape, petal number, pistil number, petal color, and calyx color) and flower timing, but find different genetic systems that mediate whether a flower produces pistils and how many pistils a flower produces. We find that many floral QTLs display pleiotropic effects on shoot length growth but shoot radial growth, implicating a possible association of floral display with light capture. We conduct a transcriptomic study to characterize the genomic signature of floral QTLs expressed in mei. Our mapping results about the genetic control of floral features make it promising to select superior varieties for mei carrying flowers of ornamental value.
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Affiliation(s)
- Mingyu Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Mengmeng Sang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- School Medicine, Institute of Reproductive Medicine, Nantong University, Nantong, China
| | - Zhenying Wen
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Juan Meng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Lidan Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing, China
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