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Wójcikowska B, Chwiałkowska K, Nowak K, Citerne S, Morończyk J, Wójcik AM, Kiwior-Wesołowska A, Francikowski J, Kwaśniewski M, Gaj MD. Transcriptomic profiling reveals histone acetylation-regulated genes involved in somatic embryogenesis in Arabidopsis thaliana. BMC Genomics 2024; 25:788. [PMID: 39148037 PMCID: PMC11325840 DOI: 10.1186/s12864-024-10623-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 07/15/2024] [Indexed: 08/17/2024] Open
Abstract
BACKGROUND Somatic embryogenesis (SE) exemplifies the unique developmental plasticity of plant cells. The regulatory processes, including epigenetic modifications controlling embryogenic reprogramming of cell transcriptome, have just started to be revealed. RESULTS To identify the genes of histone acetylation-regulated expression in SE, we analyzed global transcriptomes of Arabidopsis explants undergoing embryogenic induction in response to treatment with histone deacetylase inhibitor, trichostatin A (TSA). The TSA-induced and auxin (2,4-dichlorophenoxyacetic acid; 2,4-D)-induced transcriptomes were compared. RNA-seq results revealed the similarities of the TSA- and auxin-induced transcriptomic responses that involve extensive deregulation, mostly repression, of the majority of genes. Within the differentially expressed genes (DEGs), we identified the master regulators (transcription factors - TFs) of SE, genes involved in biosynthesis, signaling, and polar transport of auxin and NITRILASE-encoding genes of the function in indole-3-acetic acid (IAA) biosynthesis. TSA-upregulated TF genes of essential functions in auxin-induced SE, included LEC1/LEC2, FUS3, AGL15, MYB118, PHB, PHV, PLTs, and WUS/WOXs. The TSA-induced transcriptome revealed also extensive upregulation of stress-related genes, including those related to stress hormone biosynthesis. In line with transcriptomic data, TSA-induced explants accumulated salicylic acid (SA) and abscisic acid (ABA), suggesting the role of histone acetylation (Hac) in regulating stress hormone-related responses during SE induction. Since mostly the adaxial side of cotyledon explant contributes to SE induction, we also identified organ polarity-related genes responding to TSA treatment, including AIL7/PLT7, RGE1, LBD18, 40, HB32, CBF1, and ULT2. Analysis of the relevant mutants supported the role of polarity-related genes in SE induction. CONCLUSION The study results provide a step forward in deciphering the epigenetic network controlling embryogenic transition in somatic cells of plants.
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Affiliation(s)
- Barbara Wójcikowska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland.
| | - Karolina Chwiałkowska
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Katarzyna Nowak
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Sylvie Citerne
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), Versailles, 78000, France
| | - Joanna Morończyk
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Anna Maria Wójcik
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Agnieszka Kiwior-Wesołowska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Jacek Francikowski
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Mirosław Kwaśniewski
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Małgorzata Danuta Gaj
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
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McFarland FL, Kaeppler HF. History and current status of embryogenic culture-based tissue culture, transformation and gene editing of maize (Zea mays L.). THE PLANT GENOME 2024:e20451. [PMID: 38600860 DOI: 10.1002/tpg2.20451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/12/2024] [Accepted: 03/20/2024] [Indexed: 04/12/2024]
Abstract
The production of embryogenic callus and somatic embryos is integral to the genetic improvement of crops via genetic transformation and gene editing. Regenerable embryogenic cultures also form the backbone of many micro-propagation processes for crop species. In many species, including maize, the ability to produce embryogenic cultures is highly genotype dependent. While some modern transformation and genome editing methods reduce genotype dependence, these efforts ultimately fall short of producing truly genotype-independent tissue culture methods. Recalcitrant genotypes are still identified in these genotype-flexible processes, and their presence is magnified by the stark contrast with more amenable lines, which may respond more efficiently by orders of magnitude. This review aims to describe the history of research into somatic embryogenesis, embryogenic tissue cultures, and plant transformation, with particular attention paid to maize. Contemporary research into genotype-flexible morphogenic gene-based transformation and genome engineering is also covered in this review. The rapid evolution of plant biotechnology from nascent technologies in the latter half of the 20th century to well-established, work-horse production processes has, and will continue to, fundamentally changed agriculture and plant genetics research.
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Affiliation(s)
- Frank L McFarland
- Department of Plant and Agroecosystem Sciences, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin Crop Innovation Center, University of Wisconsin, Middleton, Wisconsin, USA
| | - Heidi F Kaeppler
- Department of Plant and Agroecosystem Sciences, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin Crop Innovation Center, University of Wisconsin, Middleton, Wisconsin, USA
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3
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Liu Q, Zhang XS, Su YH. Application of Wox2a in transformation of recalcitrant maize genotypes. ABIOTECH 2023; 4:386-388. [PMID: 38106431 PMCID: PMC10721569 DOI: 10.1007/s42994-023-00116-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/31/2023] [Indexed: 12/19/2023]
Abstract
The genetic transformation plays an important role in plant gene functional analysis and its genetic improvement. However, only a limited number of maize germplasms can be routinely transformed. The maize gene Wuschel-like homeobox protein 2a (Wox2a) was shown to play a crucial role in promoting the formation of embryonic cells and enhancing the efficiency of genetic transformation in maize. This commentary discusses the mechanism by which the Wox2a gene contributes to the variation in embryogenic tissue culture response among different maize inbred lines. In addition, the frequency and intensity of Wox2a or Wus2/Bbm vector-induced somatic embryogenesis was also discussed. The application of Wox2a in transformation of recalcitrant maize genotypes could well accelerate the development of maize genetic improvement.
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Affiliation(s)
- Qiangbo Liu
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai’an, 271018 China
| | - Xian Sheng Zhang
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai’an, 271018 China
| | - Ying Hua Su
- National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai’an, 271018 China
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4
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Karami O, de Jong H, Somovilla VJ, Villanueva Acosta B, Sugiarta AB, Ham M, Khadem A, Wennekes T, Offringa R. Structure-activity relationship of 2,4-D correlates auxinic activity with the induction of somatic embryogenesis in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1355-1369. [PMID: 37647363 DOI: 10.1111/tpj.16430] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/19/2023] [Accepted: 08/04/2023] [Indexed: 09/01/2023]
Abstract
2,4-dichlorophenoxyacetic acid (2,4-D) is a synthetic analogue of the plant hormone auxin that is commonly used in many in vitro plant regeneration systems, such as somatic embryogenesis (SE). Its effectiveness in inducing SE, compared to the natural auxin indole-3-acetic acid (IAA), has been attributed to the stress triggered by this compound rather than its auxinic activity. However, this hypothesis has never been thoroughly tested. Here we used a library of forty 2,4-D analogues to test the structure-activity relationship with respect to the capacity to induce SE and auxinic activity in Arabidopsis thaliana. Four analogues induced SE as effectively as 2,4-D and 13 analogues induced SE but were less effective. Based on root growth inhibition and auxin response reporter expression, the 2,4-D analogues were classified into different groups, ranging from very active to not active auxin analogues. A halogen at the 4-position of the aromatic ring was important for auxinic activity, whereas a halogen at the 3-position resulted in reduced activity. Moreover, a small substitution at the carboxylate chain was tolerated, as was extending the carboxylate chain with an even number of carbons. The auxinic activity of most 2,4-D analogues was consistent with their simulated TIR1-Aux/IAA coreceptor binding characteristics. A strong correlation was observed between SE induction efficiency and auxinic activity, which is in line with our observation that 2,4-D-induced SE and stress both require TIR1/AFB auxin co-receptor function. Our data indicate that the stress-related effects triggered by 2,4-D and considered important for SE induction are downstream of auxin signalling.
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Affiliation(s)
- Omid Karami
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Hanna de Jong
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomedical Research, Utrecht University, Universiteitsweg 99, 3584CG, Utrecht, The Netherlands
| | - Victor J Somovilla
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014, Donostia San Sebastián, Spain
| | - Beatriz Villanueva Acosta
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Aldo Bryan Sugiarta
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Marvin Ham
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Azadeh Khadem
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Tom Wennekes
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomedical Research, Utrecht University, Universiteitsweg 99, 3584CG, Utrecht, The Netherlands
| | - Remko Offringa
- Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
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Li L, Sun X, Yu W, Gui M, Qiu Y, Tang M, Tian H, Liang G. Comparative transcriptome analysis of high- and low-embryogenic Hevea brasiliensis genotypes reveals involvement of phytohormones in somatic embryogenesis. BMC PLANT BIOLOGY 2023; 23:489. [PMID: 37828441 PMCID: PMC10571474 DOI: 10.1186/s12870-023-04432-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/31/2023] [Indexed: 10/14/2023]
Abstract
BACKGROUND Rubber plant (Hevea brasiliensis) is one of the major sources of latex. Somatic embryogenesis (SE) is a promising alterative to its propagation by grafting and seed. Phytohormones have been shown to influence SE in different plant species. However, limited knowledge is available on the role of phytohormones in SE in Hevea. The anther cultures of two Hevea genotypes (Yunyan 73477-YT and Reken 628-RT) with contrasting SE rate were established and four stages i.e., anthers (h), anther induced callus (y), callus differentiation state (f), and somatic embryos (p) were studied. UPLC-ESI-MS/MS and transcriptome analyses were used to study phytohormone accumulation and related expression changes in biosynthesis and signaling genes. RESULTS YT showed higher callus induction rate than RT. Of the two genotypes, only YT exhibited successful SE. Auxins, cytokinins (CKs), abscisic acid (ABA), jasmonic acid (JA), salicylic acid (SA), gibberellins (GAs), and ethylene (ETH) were detected in the two genotypes. Indole-3-acetic acid (IAA), CKs, ABA, and ETH had notable differences in the studied stages of the two genotypes. The differentially expressed genes identified in treatment comparisons were majorly enriched in MAPK and phytohormone signaling, biosynthesis of secondary metabolites, and metabolic pathways. The expression changes in IAA, CK, ABA, and ETH biosynthesis and signaling genes confirmed the differential accumulation of respective phytohormones in the two genotypes. CONCLUSION These results suggest potential roles of phytohormones in SE in Hevea.
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Affiliation(s)
- Ling Li
- The Center of Rubber Research, Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Xiaolong Sun
- The Center of Rubber Research, Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Wencai Yu
- The Center of Rubber Research, Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Mingchun Gui
- The Center of Rubber Research, Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Yanfen Qiu
- The Center of Rubber Research, Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Min Tang
- The Center of Rubber Research, Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Hai Tian
- The Center of Rubber Research, Yunnan Institute of Tropical Crops, Xishuangbanna, China
| | - Guoping Liang
- The Center of Rubber Research, Yunnan Institute of Tropical Crops, Xishuangbanna, China.
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McFarland FL, Collier R, Walter N, Martinell B, Kaeppler SM, Kaeppler HF. A key to totipotency: Wuschel-like homeobox 2a unlocks embryogenic culture response in maize (Zea mays L.). PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1860-1872. [PMID: 37357571 PMCID: PMC10440991 DOI: 10.1111/pbi.14098] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/19/2023] [Accepted: 05/28/2023] [Indexed: 06/27/2023]
Abstract
The ability of plant somatic cells to dedifferentiate, form somatic embryos and regenerate whole plants in vitro has been harnessed for both clonal propagation and as a key component of plant genetic engineering systems. Embryogenic culture response is significantly limited, however, by plant genotype in most species. This impedes advancements in both plant transformation-based functional genomics research and crop improvement efforts. We utilized natural variation among maize inbred lines to genetically map somatic embryo generation potential in tissue culture and identify candidate genes underlying totipotency. Using a series of maize lines derived from crosses involving the culturable parent A188 and the non-responsive parent B73, we identified a region on chromosome 3 associated with embryogenic culture response and focused on three candidate genes within the region based on genetic position and expression pattern. Two candidate genes showed no effect when ectopically expressed in B73, but the gene Wox2a was found to induce somatic embryogenesis and embryogenic callus proliferation. Transgenic B73 cells with strong constitutive expression of the B73 and A188 coding sequences of Wox2a were found to produce somatic embryos at similar frequencies, demonstrating that sufficient expression of either allele could rescue the embryogenic culture phenotype. Transgenic B73 plants were regenerated from the somatic embryos without chemical selection and no pleiotropic effects were observed in the Wox2a overexpression lines in the regenerated T0 plants or in the two independent events which produced T1 progeny. In addition to linking natural variation in tissue culture response to Wox2a, our data support the utility of Wox2a in enabling transformation of recalcitrant genotypes.
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Affiliation(s)
- Frank L. McFarland
- Department of AgronomyUniversity of WisconsinMadisonWIUSA
- Wisconsin Crop Innovation CenterUniversity of WisconsinMiddletonWIUSA
| | - Ray Collier
- Department of AgronomyUniversity of WisconsinMadisonWIUSA
| | | | | | - Shawn M. Kaeppler
- Department of AgronomyUniversity of WisconsinMadisonWIUSA
- Wisconsin Crop Innovation CenterUniversity of WisconsinMiddletonWIUSA
| | - Heidi F. Kaeppler
- Department of AgronomyUniversity of WisconsinMadisonWIUSA
- Wisconsin Crop Innovation CenterUniversity of WisconsinMiddletonWIUSA
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7
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Adero M, Tripathi JN, Tripathi L. Advances in Somatic Embryogenesis of Banana. Int J Mol Sci 2023; 24:10999. [PMID: 37446177 DOI: 10.3390/ijms241310999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/19/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
The cultivation of bananas and plantains (Musa spp.) holds significant global economic importance, but faces numerous challenges, which may include diverse abiotic and biotic factors such as drought and various diseases caused by fungi, viruses, and bacteria. The genetic and asexual nature of cultivated banana cultivars makes them unattractive for improvement via traditional breeding. To overcome these constraints, modern biotechnological approaches like genetic modification and genome editing have become essential for banana improvement. However, these techniques rely on somatic embryogenesis, which has only been successfully achieved in a limited number of banana cultivars. Therefore, developing new strategies for improving somatic embryogenesis in banana is crucial. This review article focuses on advancements in banana somatic embryogenesis, highlighting the progress, the various stages of regeneration, cryopreservation techniques, and the molecular mechanisms underlying the process. Furthermore, this article discusses the factors that could influence somatic embryogenesis and explores the prospects for improving the process, especially in recalcitrant banana cultivars. By addressing these challenges and exploring potential solutions, researchers aim to unlock the full potential of somatic embryogenesis as a tool for banana improvement, ultimately benefiting the global banana industry.
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Affiliation(s)
- Mark Adero
- International Institute of Tropical Agriculture (IITA), Nairobi 30709-00100, Kenya
| | | | - Leena Tripathi
- International Institute of Tropical Agriculture (IITA), Nairobi 30709-00100, Kenya
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8
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Xu Y, Shang W, Li L, Song Y, Wang G, Shi L, Shen Y, Sun Y, He S, Wang Z. Transcriptome Landscape Analyses of the Regulatory Network for Zygotic Embryo Development in Paeonia ostii. Int J Mol Sci 2023; 24:10715. [PMID: 37445891 DOI: 10.3390/ijms241310715] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/22/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
Paeonia ostii is a worldwide ornamental flower and an emerging oil crop. Zyotic embryogenesis is a critical process during seed development, and it can provide a basis for improving the efficiency of somatic embryogenesis (SE). In this study, transcriptome sequencing of embryo development was performed to investigate gene expression profiling in P. ostii and identified Differentially expressed genes (DEGs) related to transcription factors, plant hormones, and antioxidant enzymes. The results indicated that IAA (Indole-3-acetic acid), GA (Gibberellin), BR (Brassinosteroid) and ETH (Ethylene) were beneficial to early embryonic morphogenesis, while CTK (Cytokinin) and ABA (Abscisic Acid) promoted embryo morphogenesis and maturation. The antioxidant enzymes' activity was the highest in early embryos and an important participant in embryo formation. The high expression of the genes encoding fatty acid desaturase was beneficial to fast oil accumulation. Representative DEGs were selected and validated using qRT-PCR. Protein-protein interaction network (PPI) was predicted, and six central node proteins, including AUX1, PIN1, ARF6, LAX3, ABCB19, PIF3, and PIF4, were screened. Our results provided new insights into the formation of embryo development and even somatic embryo development in tree peonies.
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Affiliation(s)
- Yufeng Xu
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China
| | - Wenqian Shang
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China
| | - Linda Li
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China
| | - Yinglong Song
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China
| | - Guiqing Wang
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China
| | - Liyun Shi
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China
| | - Yuxiao Shen
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China
| | - Yuke Sun
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China
| | - Songlin He
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China
- Henan Institute of Science and Technology, Xinxiang 453000, China
| | - Zheng Wang
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou 450002, China
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9
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Wang Q, Guo M, Chen J, Duan R. A gene regulatory network inference model based on pseudo-siamese network. BMC Bioinformatics 2023; 24:163. [PMID: 37085776 PMCID: PMC10122305 DOI: 10.1186/s12859-023-05253-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 03/24/2023] [Indexed: 04/23/2023] Open
Abstract
MOTIVATION Gene regulatory networks (GRNs) arise from the intricate interactions between transcription factors (TFs) and their target genes during the growth and development of organisms. The inference of GRNs can unveil the underlying gene interactions in living systems and facilitate the investigation of the relationship between gene expression patterns and phenotypic traits. Although several machine-learning models have been proposed for inferring GRNs from single-cell RNA sequencing (scRNA-seq) data, some of these models, such as Boolean and tree-based networks, suffer from sensitivity to noise and may encounter difficulties in handling the high noise and dimensionality of actual scRNA-seq data, as well as the sparse nature of gene regulation relationships. Thus, inferring large-scale information from GRNs remains a formidable challenge. RESULTS This study proposes a multilevel, multi-structure framework called a pseudo-Siamese GRN (PSGRN) for inferring large-scale GRNs from time-series expression datasets. Based on the pseudo-Siamese network, we applied a gated recurrent unit to capture the time features of each TF and target matrix and learn the spatial features of the matrices after merging by applying the DenseNet framework. Finally, we applied a sigmoid function to evaluate interactions. We constructed two maize sub-datasets, including gene expression levels and GRNs, using existing open-source maize multi-omics data and compared them to other GRN inference methods, including GENIE3, GRNBoost2, nonlinear ordinary differential equations, CNNC, and DGRNS. Our results show that PSGRN outperforms state-of-the-art methods. This study proposed a new framework: a PSGRN that allows GRNs to be inferred from scRNA-seq data, elucidating the temporal and spatial features of TFs and their target genes. The results show the model's robustness and generalization, laying a theoretical foundation for maize genotype-phenotype associations with implications for breeding work.
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Affiliation(s)
- Qian Wang
- School of Electrical and Information Engineering, Beijing University of Civil Engineering and Architecture, Beijing, China
| | - Maozu Guo
- School of Electrical and Information Engineering, Beijing University of Civil Engineering and Architecture, Beijing, China.
| | - Jian Chen
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Ran Duan
- School of Electrical and Information Engineering, Beijing University of Civil Engineering and Architecture, Beijing, China
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10
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Awada R, Lepelley M, Breton D, Charpagne A, Campa C, Berry V, Georget F, Breitler JC, Léran S, Djerrab D, Martinez-Seidel F, Descombes P, Crouzillat D, Bertrand B, Etienne H. Global transcriptome profiling reveals differential regulatory, metabolic and hormonal networks during somatic embryogenesis in Coffea arabica. BMC Genomics 2023; 24:41. [PMID: 36694132 PMCID: PMC9875526 DOI: 10.1186/s12864-022-09098-z] [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: 09/27/2022] [Accepted: 12/22/2022] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Somatic embryogenesis (SE) is one of the most promising processes for large-scale dissemination of elite varieties. However, for many plant species, optimizing SE protocols still relies on a trial and error approach. We report the first global scale transcriptome profiling performed at all developmental stages of SE in coffee to unravel the mechanisms that regulate cell fate and totipotency. RESULTS RNA-seq of 48 samples (12 developmental stages × 4 biological replicates) generated 90 million high quality reads per sample, approximately 74% of which were uniquely mapped to the Arabica genome. First, the statistical analysis of transcript data clearly grouped SE developmental stages into seven important phases (Leaf, Dedifferentiation, Primary callus, Embryogenic callus, Embryogenic cell clusters, Redifferentiation and Embryo) enabling the identification of six key developmental phase switches, which are strategic for the overall biological efficiency of embryo regeneration. Differential gene expression and functional analysis showed that genes encoding transcription factors, stress-related genes, metabolism-related genes and hormone signaling-related genes were significantly enriched. Second, the standard environmental drivers used to control SE, i.e. light, growth regulators and cell density, were clearly perceived at the molecular level at different developmental stages. Third, expression profiles of auxin-related genes, transcription factor-related genes and secondary metabolism-related genes were analyzed during SE. Gene co-expression networks were also inferred. Auxin-related genes were upregulated during dedifferentiation and redifferentiation while transcription factor-related genes were switched on from the embryogenic callus and onward. Secondary metabolism-related genes were switched off during dedifferentiation and switched back on at the onset of redifferentiation. Secondary metabolites and endogenous IAA content were tightly linked with their respective gene expression. Lastly, comparing Arabica embryogenic and non-embryogenic cell transcriptomes enabled the identification of biological processes involved in the acquisition of embryogenic capacity. CONCLUSIONS The present analysis showed that transcript fingerprints are discriminating signatures of cell fate and are under the direct influence of environmental drivers. A total of 23 molecular candidates were successfully identified overall the 12 developmental stages and can be tested in many plant species to optimize SE protocols in a rational way.
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Affiliation(s)
- Rayan Awada
- Nestlé Research - Plant Science Research Unit, Tours, France ,grid.8183.20000 0001 2153 9871UMR DIADE, CIRAD, Montpellier, France ,grid.121334.60000 0001 2097 0141UMR DIADE, Université de Montpellier, CIRAD, Montpellier, IRD France
| | - Maud Lepelley
- Nestlé Research - Plant Science Research Unit, Tours, France
| | - David Breton
- Nestlé Research - Plant Science Research Unit, Tours, France
| | - Aline Charpagne
- grid.419905.00000 0001 0066 4948Nestlé Research, Société Des Produits Nestlé SA, Lausanne, Switzerland ,grid.511382.c0000 0004 7595 5223Sophia Genetics, Genève, Switzerland
| | - Claudine Campa
- grid.121334.60000 0001 2097 0141UMR DIADE, Université de Montpellier, CIRAD, Montpellier, IRD France ,grid.4399.70000000122879528UMR DIADE, IRD, Montpellier, France
| | - Victoria Berry
- Nestlé Research - Plant Science Research Unit, Tours, France
| | - Frédéric Georget
- grid.8183.20000 0001 2153 9871UMR DIADE, CIRAD, Montpellier, France ,grid.121334.60000 0001 2097 0141UMR DIADE, Université de Montpellier, CIRAD, Montpellier, IRD France
| | - Jean-Christophe Breitler
- grid.8183.20000 0001 2153 9871UMR DIADE, CIRAD, Montpellier, France ,grid.121334.60000 0001 2097 0141UMR DIADE, Université de Montpellier, CIRAD, Montpellier, IRD France
| | - Sophie Léran
- grid.8183.20000 0001 2153 9871UMR DIADE, CIRAD, Montpellier, France ,grid.121334.60000 0001 2097 0141UMR DIADE, Université de Montpellier, CIRAD, Montpellier, IRD France
| | - Doâa Djerrab
- grid.8183.20000 0001 2153 9871UMR DIADE, CIRAD, Montpellier, France ,grid.121334.60000 0001 2097 0141UMR DIADE, Université de Montpellier, CIRAD, Montpellier, IRD France
| | - Federico Martinez-Seidel
- grid.418390.70000 0004 0491 976XMax Planck Institute for Molecular Plant Physiology, Golm, Germany ,grid.1008.90000 0001 2179 088XSchool of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Patrick Descombes
- grid.419905.00000 0001 0066 4948Nestlé Research, Société Des Produits Nestlé SA, Lausanne, Switzerland
| | | | - Benoît Bertrand
- grid.8183.20000 0001 2153 9871UMR DIADE, CIRAD, Montpellier, France ,grid.121334.60000 0001 2097 0141UMR DIADE, Université de Montpellier, CIRAD, Montpellier, IRD France
| | - Hervé Etienne
- grid.8183.20000 0001 2153 9871UMR DIADE, CIRAD, Montpellier, France ,grid.121334.60000 0001 2097 0141UMR DIADE, Université de Montpellier, CIRAD, Montpellier, IRD France
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11
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Shen K, Qu M, Zhao P. The Roads to Haploid Embryogenesis. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12020243. [PMID: 36678955 PMCID: PMC9865920 DOI: 10.3390/plants12020243] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/19/2022] [Accepted: 12/30/2022] [Indexed: 05/31/2023]
Abstract
Although zygotic embryogenesis is usually studied in the field of seed biology, great attention has been paid to the methods used to generate haploid embryos due to their applications in crop breeding. These mainly include two methods for haploid embryogenesis: in vitro microspore embryogenesis and in vivo haploid embryogenesis. Although microspore culture systems and maize haploid induction systems were discovered in the 1960s, little is known about the molecular mechanisms underlying haploid formation. In recent years, major breakthroughs have been made in in vivo haploid induction systems, and several key factors, such as the matrilineal (MTL), baby boom (BBM), domain of unknown function 679 membrane protein (DMP), and egg cell-specific (ECS) that trigger in vivo haploid embryo production in both the crops and Arabidopsis models have been identified. The discovery of these haploid inducers indicates that haploid embryogenesis is highly related to gamete development, fertilization, and genome stability in ealry embryos. Here, based on recent efforts to identify key players in haploid embryogenesis and to understand its molecular mechanisms, we summarize the different paths to haploid embryogenesis, and we discuss the mechanisms of haploid generation and its potential applications in crop breeding. Although these haploid-inducing factors could assist egg cells in bypassing fertilization to initiate embryogenesis or trigger genome elimination in zygotes after fertilization to form haploid embryos, the fertilization of central cells to form endosperms is a prerequisite step for haploid formation. Deciphering the molecular and cellular mechanisms for haploid embryogenesis, increasing the haploid induction efficiency, and establishing haploid induction systems in other crops are critical for promoting the application of haploid technology in crop breeding, and these should be addressed in further studies.
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Affiliation(s)
- Kun Shen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Mengxue Qu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Peng Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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12
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Chen B, Li C, Chen Y, Chen S, Xiao Y, Wu Q, Zhong L, Huang K. Proteome profiles during early stage of somatic embryogenesis of two Eucalyptus species. BMC PLANT BIOLOGY 2022; 22:558. [PMID: 36460945 PMCID: PMC9716740 DOI: 10.1186/s12870-022-03956-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Somatic embryogenesis (SE) was recognized as an important tool for plants to propagate. However, our knowledge about the proteins involved in early SE including the callus dedifferentiation is still limited, especially in the economic woody tree - Eucalyptus. RESULTS We used the data-independent acquisition mass-spectrometry to study the different proteome profiles of early SE of two Eucalyptus species-E. camaldulensis (high regeneratively potential) and E. grandis x urophylla (low regenerative potential). Initially, 35,207 peptides and 7,077 proteins were identified in the stem and tissue-culture induced callus of the two Eucalyptus species. MSstat identified 2,078 and 2,807 differentially expressed proteins (DEPs) in early SE of E. camaldulensis and E. grandis x urophylla, respectively. They shared 760 upregulated and 420 downregulated proteins, including 4 transcription factors, 31 ribosomal proteins, 1 histone, 3 zinc finger proteins (ZFPs), 16 glutathione transferases, 10 glucosyltransferases, ARF19, WOX8 and PIN1. These proteins might be involved in the early SE of Eucalyptus. By combining the miRNA and RNA-Seq results, some miRNA ~ gene/protein regulatory networks were identified in early SE of Eucalyptus, such as miR160 ~ TPP2, miR164 ~ UXS2, miR169 ~ COX11 and miR535 ~ Eucgr.E01067. Further, we found SERK, WRKY, ZFP and ABC transporter might be related with high SE potential. CONCLUSIONS Overall, our study identified proteins involved in the early SE and related to the high regeneration potential of Eucalyptus. It greatly enhanced our understanding of the early SE and the SE capacity of Eucalyptus.
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Affiliation(s)
- Bowen Chen
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China
| | - Changrong Li
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China
| | - Yingying Chen
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China
| | - Shengkan Chen
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China
| | - Yufei Xiao
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China
| | - Qi Wu
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China
| | - Lianxiang Zhong
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China
| | - Kaiyong Huang
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Guangxi Forestry Research Institute, 23 Yongwu Road, Nanning, 530002, Guangxi, China.
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13
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Transcriptome Profiling of Different State Callus Induced from Immature Embryo in Maize. J CHEM-NY 2022. [DOI: 10.1155/2022/6237298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Embryogenic and regenerable tissue cultures are widely used in plant transformation. To dissect the molecular mechanism of embryogenesis, we used inbred line A188 as the material; the immature embryo of kernels (15 day after pollination, 15DAP) was isolated and cultured in inducing medium and subjected to RNA-Seq. The results revealed that 5,076 differentially expressed genes (DEGs) were involved in morphological and histological changes and endogenous indole-3-acetic acid (IAA) alteration. Functional analysis showed that the DEGs were related to metabolic pathways and biosynthesis of secondary metabolites. In particular, ARF16 and ARF8 genes of auxin response factors (ARF) were upregulated from EC to IDC and EC to IRC. Meanwhile, BBM2, SERK1, and SERK2 genes of the embryogenic pathway were upregulated, and WIP2 and ESR genes of the wound-inducible were upregulated from EC to IDC and EC to IRC. These changes can improve conversion efficiency from EC to IRC, which is important for elucidating the underlying molecular mechanisms of callus formation.
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14
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Weighted Gene Correlation Network Analysis (WGCNA) of Arabidopsis Somatic Embryogenesis (SE) and Identification of Key Gene Modules to Uncover SE-Associated Hub Genes. Int J Genomics 2022; 2022:7471063. [PMID: 35837132 PMCID: PMC9274236 DOI: 10.1155/2022/7471063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/23/2022] [Indexed: 01/07/2023] Open
Abstract
Somatic embryogenesis (SE), which occurs naturally in many plant species, serves as a model to elucidate cellular and molecular mechanisms of embryo patterning in plants. Decoding the regulatory landscape of SE is essential for its further application. Hence, the present study was aimed at employing Weighted Gene Correlation Network Analysis (WGCNA) to construct a gene coexpression network (GCN) for Arabidopsis SE and then identifying highly correlated gene modules to uncover the hub genes associated with SE that may serve as potential molecular targets. A total of 17,059 genes were filtered from a microarray dataset comprising four stages of SE, i.e., stage I (zygotic embryos), stage II (proliferating tissues at 7 days of induction), stage III (proliferating tissues at 14 days of induction), and stage IV (mature somatic embryos). This included 1,711 transcription factors and 445 EMBRYO DEFECTIVE genes. GCN analysis identified a total of 26 gene modules with the module size ranging from 35 to 3,418 genes using a dynamic cut tree algorithm. The module-trait analysis revealed that four, four, seven, and four modules were associated with stages I, II, III, and IV, respectively. Further, we identified a total of 260 hub genes based on the degree of intramodular connectivity. Validation of the hub genes using publicly available expression datasets demonstrated that at least 78 hub genes are potentially associated with embryogenesis; of these, many genes remain functionally uncharacterized thus far. In silico promoter analysis of these genes revealed the presence of cis-acting regulatory elements, “soybean embryo factor 4 (SEF4) binding site,” and “E-box” of the napA storage-protein gene of Brassica napus; this suggests that these genes may play important roles in plant embryo development. The present study successfully applied WGCNA to construct a GCN for SE in Arabidopsis and identified hub genes involved in the development of somatic embryos. These hub genes could be used as molecular targets to further elucidate the molecular mechanisms underlying SE in plants.
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15
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Liu S, Shi Y, Liu F, Guo Y, Lu M. LaCl 3 treatment improves Agrobacterium-mediated immature embryo genetic transformation frequency of maize. PLANT CELL REPORTS 2022; 41:1439-1448. [PMID: 35376997 DOI: 10.1007/s00299-022-02867-w] [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: 12/14/2021] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
We report an optimized transformation system that uses a LaCl3 pretreatment (a Ca2+ channel blocker) for enhancing Agrobacterium-mediated infection of immature embryos and improving the genetic transformation frequency of maize. Agrobacterium-mediated genetic transformation of immature embryos is important for gene-function studies and molecular breeding of maize. However, the relatively low genetic transformation frequency remains a bottleneck for applicability of this method, especially on commercial scale. We report that pretreatment of immature embryos with LaCl3 (a Ca2+ channel blocker) improves the infection frequency of Agrobacterium tumefaciens, increases the proportion of positive callus, yields more positive regenerated plantlets, and increases the transformation frequency from 8.40 to 17.60% for maize. This optimization is a novel method for improving the frequency of plant genetic transformations mediated by Agrobacterium tumefaciens.
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Affiliation(s)
- Shengnan Liu
- Center for Crop Functional Genomics and Molecular Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yunlu Shi
- Center for Crop Functional Genomics and Molecular Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Fang Liu
- Center for Crop Functional Genomics and Molecular Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yan Guo
- Center for Crop Functional Genomics and Molecular Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Minhui Lu
- Center for Crop Functional Genomics and Molecular Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
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16
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Joshi S, Paul P, Hartman JM, Perry SE. AGL15 Promotion of Somatic Embryogenesis: Role and Molecular Mechanism. FRONTIERS IN PLANT SCIENCE 2022; 13:861556. [PMID: 35419012 PMCID: PMC8996056 DOI: 10.3389/fpls.2022.861556] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
Plants have amazing regenerative properties with single somatic cells, or groups of cells able to give rise to fully formed plants. One means of regeneration is somatic embryogenesis, by which an embryonic structure is formed that "converts" into a plantlet. Somatic embryogenesis has been used as a model for zygotic processes that are buried within layers of maternal tissues. Understanding mechanisms of somatic embryo induction and development are important as a more accessible model for seed development. We rely on seed development not only for most of our caloric intake, but also as a delivery system for engineered crops to meet agricultural challenges. Regeneration of transformed cells is needed for this applied work as well as basic research to understand gene function. Here we focus on a MADS-domain transcription factor, AGAMOUS-Like15 (AGL15) that shows a positive correlation between accumulation levels and capacity for somatic embryogenesis. We relate AGL15 function to other transcription factors, hormones, and epigenetic modifiers involved in somatic embryo development.
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Affiliation(s)
- Sanjay Joshi
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
| | - Priyanka Paul
- Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, United States
| | - Jeanne M. Hartman
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
| | - Sharyn E. Perry
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
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17
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Dal Santo S, De Paoli E, Pagliarani C, Amato A, Celii M, Boccacci P, Zenoni S, Gambino G, Perrone I. Stress responses and epigenomic instability mark the loss of somatic embryogenesis competence in grapevine. PLANT PHYSIOLOGY 2022; 188:490-508. [PMID: 34726761 PMCID: PMC8774814 DOI: 10.1093/plphys/kiab477] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
Somatic embryogenesis (SE) represents the most appropriate tool for next-generation breeding methods in woody plants such as grapevine (Vitis vinifera L.). However, in this species, the SE competence is strongly genotype-dependent and the molecular basis of this phenomenon is poorly understood. We explored the genetic and epigenetic basis of SE in grapevine by profiling the transcriptome, epigenome, and small RNAome of undifferentiated, embryogenic, and non-embryogenic callus tissues derived from two genotypes differing in competence for SE, Sangiovese and Cabernet Sauvignon. During the successful formation of embryonic callus, we observed the upregulation of epigenetic-related transcripts and short interfering RNAs in association with DNA hypermethylation at transposable elements in both varieties. Nevertheless, the switch to nonembryonic development matched the incomplete reinforcement of transposon silencing, and the evidence of such effect was more apparent in the recalcitrant Cabernet Sauvignon. Transcriptomic differences between the two genotypes were maximized already at early stage of culture where the recalcitrant variety expressed a broad panel of genes related to stress responses and secondary metabolism. Our data provide a different angle on the SE molecular dynamics that can be exploited to leverage SE as a biotechnological tool for fruit crop breeding.
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Affiliation(s)
- Silvia Dal Santo
- Department of Biotechnology, University of Verona, Verona 37134, Italy
| | - Emanuele De Paoli
- Department of Agri-Food, Environmental and Animal Sciences, University of Udine, Udine 33100, Italy
| | - Chiara Pagliarani
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino 10135, Italy
| | - Alessandra Amato
- Department of Biotechnology, University of Verona, Verona 37134, Italy
| | - Mirko Celii
- Department of Agri-Food, Environmental and Animal Sciences, University of Udine, Udine 33100, Italy
| | - Paolo Boccacci
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino 10135, Italy
| | - Sara Zenoni
- Department of Biotechnology, University of Verona, Verona 37134, Italy
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino 10135, Italy
| | - Irene Perrone
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Torino 10135, Italy
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18
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Elhiti M, Stasolla C. Transduction of Signals during Somatic Embryogenesis. PLANTS (BASEL, SWITZERLAND) 2022; 11:178. [PMID: 35050066 PMCID: PMC8779037 DOI: 10.3390/plants11020178] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/30/2021] [Accepted: 01/07/2022] [Indexed: 05/05/2023]
Abstract
Somatic embryogenesis (SE) is an in vitro biological process in which bipolar structures (somatic embryos) can be induced to form from somatic cells and regenerate into whole plants. Acquisition of the embryogenic potential in culture is initiated when some competent cells within the explants respond to inductive signals (mostly plant growth regulators, PRGs), and de-differentiate into embryogenic cells. Such cells, "canalized" into the embryogenic developmental pathway, are able to generate embryos comparable in structure and physiology to their in vivo counterparts. Genomic and transcriptomic studies have identified several pathways governing the initial stages of the embryogenic process. In this review, the authors emphasize the importance of the developmental signals required for the progression of embryo development, starting with the de-differentiation of somatic cells and culminating with tissue patterning during the formation of the embryo body. The action and interaction of PGRs are highlighted, along with the participation of master regulators, mostly transcription factors (TFs), and proteins involved in stress responses and the signal transduction required for the initiation of the embryogenic process.
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Affiliation(s)
- Mohamed Elhiti
- Department of Botany, Faculty of Science, Tanta University, Tanta 31527, Egypt;
| | - Claudio Stasolla
- Department of Plant Science, University of Manitoba, Winnipeg, MB R3T2N2, Canada
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19
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Liu B, Sun G, Liu C, Liu S. LEAFY COTYLEDON 2: A Regulatory Factor of Plant Growth and Seed Development. Genes (Basel) 2021; 12:genes12121896. [PMID: 34946844 PMCID: PMC8701892 DOI: 10.3390/genes12121896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/18/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022] Open
Abstract
Transcription factors are key molecules in the regulation of gene expression in all organisms. The transcription factor LEAFY COTYLEDON 2 (LEC2), which belongs to the DNA-binding protein family, contains a B3 domain. The transcription factor is involved in the regulation of important plant biological processes such as embryogenesis, somatic embryo formation, seed storage protein synthesis, fatty acid metabolism, and other important biological processes. Recent studies have shown that LEC2 regulates the formation of lateral roots and influences the embryonic resetting of the parental vernalization state. The orthologs of LEC2 and their regulatory effects have also been identified in some crops; however, their regulatory mechanism requires further investigation. Here, we summarize the most recent findings concerning the effects of LEC2 on plant growth and seed development. In addition, we discuss the potential molecular mechanisms of the action of the LEC2 gene during plant development.
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20
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Wang Y, Li HL, Zhou YK, Guo D, Zhu JH, Peng SQ. Transcriptomes analysis reveals novel insight into the molecular mechanisms of somatic embryogenesis in Hevea brasiliensis. BMC Genomics 2021; 22:183. [PMID: 33711923 PMCID: PMC7953812 DOI: 10.1186/s12864-021-07501-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 03/02/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Somatic embryogenesis (SE) is a promising technology for plant vegetative propagation, which has an important role in tree breeding. Though rubber tree (Hevea brasiliensis Muell. Arg.) SE has been founded, few late SE-related genes have been identified and the molecular regulation mechanisms of late SE are still not well understood. RESULTS In this study, the transcriptomes of embryogenic callus (EC), primary embryo (PE), cotyledonary embryo (CE), abnormal embryo (AE), mature cotyledonary embryo (MCE) and withered abnormal embryo (WAE) were analyzed. A total of 887,852,416 clean reads were generated, 85.92% of them were mapped to the rubber tree genome. The de novo assembly generated 36,937 unigenes. The differentially expressed genes (DEGs) were identified in the pairwise comparisons of CE vs. AE and MCE vs. WAE, respectively. The specific common DEGs were mainly involved in the phytohormones signaling pathway, biosynthesis of phenylpropanoid and starch and sucrose metabolism. Among them, hormone signal transduction related genes were significantly enriched, especially the auxin signaling factors (AUX-like1, GH3.1, SAUR32-like, IAA9-like, IAA14-like, IAA27-like, IAA28-like and ARF5-like). The transcription factors including WRKY40, WRKY70, MYBS3-like, MYB1R1-like, AIL6 and bHLH93-like were characterized as molecular markers for rubber tree late SE. CML13, CML36, CAM-7, SERK1 and LEAD-29-like were also related to rubber tree late SE. In addition, histone modification had crucial roles during rubber tree late SE. CONCLUSIONS This study provides important information to elucidate the molecular regulation during rubber tree late SE.
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Affiliation(s)
- Ying Wang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, No.4 Xueyuan Road, Haikou, 571101, China
| | - Hui-Liang Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, No.4 Xueyuan Road, Haikou, 571101, China
| | - Yong-Kai Zhou
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, No.4 Xueyuan Road, Haikou, 571101, China
- School of Life and Pharmaceutical Sciences, Hainan University, Haikou, 570228, China
| | - Dong Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, No.4 Xueyuan Road, Haikou, 571101, China
| | - Jia-Hong Zhu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, No.4 Xueyuan Road, Haikou, 571101, China
| | - Shi-Qing Peng
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, No.4 Xueyuan Road, Haikou, 571101, China.
- Hainan Academy of Tropical Agricultural Resource, CATAS, Haikou, 571101, China.
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21
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Ko DK, Brandizzi F. A temporal hierarchy underpins the transcription factor-DNA interactome of the maize UPR. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:254-270. [PMID: 33098715 PMCID: PMC7942231 DOI: 10.1111/tpj.15044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 09/18/2020] [Accepted: 09/23/2020] [Indexed: 05/10/2023]
Abstract
Adverse environmental conditions reduce crop productivity and often increase the load of unfolded or misfolded proteins in the endoplasmic reticulum (ER). This potentially lethal condition, known as ER stress, is buffered by the unfolded protein response (UPR), a set of signaling pathways designed to either recover ER functionality or ignite programmed cell death. Despite the biological significance of the UPR to the life of the organism, the regulatory transcriptional landscape underpinning ER stress management is largely unmapped, especially in crops. To fill this significant knowledge gap, we performed a large-scale systems-level analysis of the protein-DNA interaction (PDI) network in maize (Zea mays). Using 23 promoter fragments of six UPR marker genes in a high-throughput enhanced yeast one-hybrid assay, we identified a highly interconnected network of 262 transcription factors (TFs) associated with significant biological traits and 831 PDIs underlying the UPR. We established a temporal hierarchy of TF binding to gene promoters within the same family as well as across different families of TFs. Cistrome analysis revealed the dynamic activities of a variety of cis-regulatory elements (CREs) in ER stress-responsive gene promoters. By integrating the cistrome results into a TF network analysis, we mapped a subnetwork of TFs associated with a CRE that may contribute to UPR management. Finally, we validated the role of a predicted network hub gene using the Arabidopsis system. The PDIs, TF networks, and CREs identified in our work are foundational resources for understanding transcription-regulatory mechanisms in the stress responses and crop improvement.
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Affiliation(s)
- Dae Kwan Ko
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, Michigan, 48824
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, 48824
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, Michigan, 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, 48824
- Correspondence:
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22
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Ding M, Dong H, Xue Y, Su S, Wu Y, Li S, Liu H, Li H, Han J, Shan X, Yuan Y. Transcriptomic analysis reveals somatic embryogenesis-associated signaling pathways and gene expression regulation in maize (Zea mays L.). PLANT MOLECULAR BIOLOGY 2020; 104:647-663. [PMID: 32910317 DOI: 10.1007/s11103-020-01066-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 08/31/2020] [Indexed: 06/11/2023]
Abstract
Transcriptome analysis of maize embryogenic callus and somatic embryos reveals associated genes reprogramming, hormone signaling pathways and transcriptional regulation involved in somatic embryogenesis in maize. Somatic embryos are widely utilized in propagation and genetic engineering of crop plants. In our laboratory, an elite maize inbred line Y423 that could generate intact somatic embryos was obtained and applied to genetic transformation. To enhance our understanding of regulatory mechanisms during maize somatic embryogenesis, we used RNA-based sequencing (RNA-seq) to characterize the transcriptome of immature embryo (IE), embryogenic callus (EC) and somatic embryo (SE) from maize inbred line Y423. The number of differentially expressed genes (DEGs) in three pairwise comparisons (IE-vs-EC, IE-vs-SE and EC-vs-SE) was 5767, 7084 and 1065, respectively. The expression patterns of DEGs were separated into eight major clusters. Somatic embryogenesis associated genes were mainly grouped into cluster A or B with an expression trend toward up-regulation during dedifferentiation. GO annotation and KEGG pathway analysis revealed that DEGs were implicated in plant hormone signal transduction, stress response and metabolic process. Among the differentially expressed transcription factors, the most frequently represented families were associated with the common stress response or related to cell differentiation, embryogenic patterning and embryonic maturation processes. Genes include hormone response/transduction and stress response, as well as several transcription factors were discussed in this study, which may be potential candidates for further analyses regarding their roles in somatic embryogenesis. Furthermore, the temporal expression patterns of candidate genes were analyzed to reveal their roles in somatic embryogenesis. This transcriptomic data provide insights into future functional studies, which will facilitate further dissections of the molecular mechanisms that control maize somatic embryogenesis.
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Affiliation(s)
- Meiqi Ding
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - Haixiao Dong
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - Yingjie Xue
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - Shengzhong Su
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - Ying Wu
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - Shipeng Li
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - Hongkui Liu
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - He Li
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - Junyou Han
- College of Plant Science, Jilin University, Changchun, 130062, China
| | - Xiaohui Shan
- College of Plant Science, Jilin University, Changchun, 130062, China.
| | - Yaping Yuan
- College of Plant Science, Jilin University, Changchun, 130062, China.
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Du X, Fang T, Liu Y, Wang M, Zang M, Huang L, Zhen S, Zhang J, Shi Z, Wang G, Fu J, Liu Y. Global profiling of N 6 -methyladenosine methylation in maize callus induction. THE PLANT GENOME 2020; 13:e20018. [PMID: 33016611 DOI: 10.1002/tpg2.20018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/24/2020] [Accepted: 03/05/2020] [Indexed: 05/26/2023]
Abstract
Callus induction is a dedifferentiation process that accompanies a cell fate transition, and epigenetic regulation plays a crucial role in the process. N6 -methyladenosine (m6A) methylation is an important mechanism in post-transcriptional epigenetic regulation and functions in cell reprogramming. However, the function of m6A methylation during callus induction is still unknown. Here, we performed transcriptome-wide m6A-seq on immature maize embryos after culturing for 2, 4, or 8 days with or without the auxin analogue 2,4-D. A total of 26,794 unique m6A peaks were detected from 17,456 maize genes; and 2,338 specific, 2,4-D-induced m6A peaks (D-specific m6A) were detected only in embryos cultured with 2,4-D. Furthermore, a positive correlation between m6A methylation and mRNA abundance was discovered in the genes with D-specific m6A deposition, especially at the beginning of callus induction. Key genes involved in callus induction, i.e. BABY BOOM and LBD transcription factors, underwent m6A methylation, increasing their transcript levels, thus improving callus induction. These results revealed the importance of m6A methylation during the early stage of callus induction and provided new insights into the molecular mechanism of callus induction at an epitranscriptomic level.
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Affiliation(s)
- Xuemei Du
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ting Fang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Meng Wang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Maosen Zang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Liying Huang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Sihan Zhen
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jie Zhang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Zichen Shi
- Beijing No.4 High School International Campus, China
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junjie Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunjun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Chen Y, Xu X, Liu Z, Zhang Z, XuHan X, Lin Y, Lai Z. Global scale transcriptome analysis reveals differentially expressed genes involve in early somatic embryogenesis in Dimocarpus longan Lour. BMC Genomics 2020; 21:4. [PMID: 31898486 PMCID: PMC6941269 DOI: 10.1186/s12864-019-6393-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/12/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Somatic embryogenesis (SE) is a process of somatic cells that dedifferentiate to totipotent embryonic stem cells and generate embryos in vitro. Longan SE has been established and wildly used as model system for studying embryogenesis in woody plants, SE-related genes had been characterized. In spite of that, a comprehensive overview of SE at a molecular level is still absent. To understand the molecular mechanisms during longan SE, we examined the transcriptome changes by using Illumina HiSeq from the four distinct developmental stages, including non-embryogenic callus (NEC), embryogenic callus (EC), incomplete compact pro-embryogenic cultures (ICpEC), globular embryos (GE). RESULTS RNA-seq of the four samples generated a total of 243.78 million high quality reads, approximately 81.5% of the data were mapped to longan genome. The cDNA libraries of NEC, EC, ICpEC and GE, generated 22,743, 19,745, 21,144, 21,102 expressed transcripts, 1935, 1710, 1816, 1732 novel transcripts, 2645, 366, 505, 588 unique genes, respectively. Comparative transcriptome analysis showed that a total of 10,642, 4180, 5846 and 1785 genes were differentially expressed in the pairwise comparisons of NEC_vs_EC, EC_vs_ICpEC, EC_vs_GE, ICpEC_vs_GE, respectively. Among them, plant hormones signalling related genes were significantly enriched, especially the auxin and cytokinin signalling components. The transcripts of flavonoid biosynthesis related genes were mainly expressed in NEC, while fatty acid biosynthesis related genes mainly accumulated in early SE. In addition, the extracelluar protein encoding genes LTP, CHI, GLP, AGP, EP1 were related to longan SE. Combined with the FPKM value of longan nine tissues transcription, 27 SE specific or preferential genes (LEC1, LEC1-like, PDF1.3, GH3.6, AGL80, PIN1, BBM, WOX9, WOX2, ABI3, et al.) and 28 NEC preferential genes (LEA5, CNOT3, DC2.15, PR1-1, NsLTP2, DIR1, PIP1, PIP2.1, TIP2-1, POD-P7 and POD5 et al.) were characterized as molecular markers for longan early SE. qRT-PCR validation of SE-related genes showed a high correlation between RNA-seq and qRT-PCR data. CONCLUSION This study provides new insights into the role of the transcriptome during early SE in longan. Differentially expressed genes reveal that plant hormones signalling, flavonoid and fatty acid biosynthesis, and extracelluar protein related genes were involved in longan early SE. It could serve as a valuable platform resource for further functional studies addressing embryogenesis in woody plants.
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Affiliation(s)
- Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xiaoping Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhuanxia Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xu XuHan
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Institut de la Recherche Interdisciplinaire de Toulouse, IRIT-ARI, 31300 Toulouse, France
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhongxion Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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25
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Nyaga C, Gowda M, Beyene Y, Muriithi WT, Makumbi D, Olsen MS, Suresh LM, Bright JM, Das B, Prasanna BM. Genome-Wide Analyses and Prediction of Resistance to MLN in Large Tropical Maize Germplasm. Genes (Basel) 2019; 11:genes11010016. [PMID: 31877962 PMCID: PMC7016728 DOI: 10.3390/genes11010016] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 11/16/2022] Open
Abstract
Maize lethal necrosis (MLN), caused by co-infection of maize chlorotic mottle virus and sugarcane mosaic virus, can lead up to 100% yield loss. Identification and validation of genomic regions can facilitate marker assisted breeding for resistance to MLN. Our objectives were to identify marker-trait associations using genome wide association study and assess the potential of genomic prediction for MLN resistance in a large panel of diverse maize lines. A set of 1400 diverse maize tropical inbred lines were evaluated for their response to MLN under artificial inoculation by measuring disease severity or incidence and area under disease progress curve (AUDPC). All lines were genotyped with genotyping by sequencing (GBS) SNPs. The phenotypic variation was significant for all traits and the heritability estimates were moderate to high. GWAS revealed 32 significantly associated SNPs for MLN resistance (at p < 1.0 × 10−6). For disease severity, these significantly associated SNPs individually explained 3–5% of the total phenotypic variance, whereas for AUDPC they explained 3–12% of the total proportion of phenotypic variance. Most of significant SNPs were consistent with the previous studies and assists to validate and fine map the big quantitative trait locus (QTL) regions into few markers’ specific regions. A set of putative candidate genes associated with the significant markers were identified and their functions revealed to be directly or indirectly involved in plant defense responses. Genomic prediction revealed reasonable prediction accuracies. The prediction accuracies significantly increased with increasing marker densities and training population size. These results support that MLN is a complex trait controlled by few major and many minor effect genes.
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Affiliation(s)
- Christine Nyaga
- Department of Agricultural Science and Technology, Kenyatta University, Nairobi 43844-00100, Kenya; (C.N.); (W.T.M.)
- International Maize and Wheat Improvement Centre (CIMMYT), World Agroforestry Centre (ICRAF), United Nations Avenue, Gigiri, Nairobi 1041-00621, Kenya; (Y.B.); (D.M.); (M.S.O.); (L.M.S.); (J.M.B.); (B.D.); (B.M.P.)
| | - Manje Gowda
- International Maize and Wheat Improvement Centre (CIMMYT), World Agroforestry Centre (ICRAF), United Nations Avenue, Gigiri, Nairobi 1041-00621, Kenya; (Y.B.); (D.M.); (M.S.O.); (L.M.S.); (J.M.B.); (B.D.); (B.M.P.)
- Correspondence: ; Tel.: +254-727-019-454
| | - Yoseph Beyene
- International Maize and Wheat Improvement Centre (CIMMYT), World Agroforestry Centre (ICRAF), United Nations Avenue, Gigiri, Nairobi 1041-00621, Kenya; (Y.B.); (D.M.); (M.S.O.); (L.M.S.); (J.M.B.); (B.D.); (B.M.P.)
| | - Wilson T. Muriithi
- Department of Agricultural Science and Technology, Kenyatta University, Nairobi 43844-00100, Kenya; (C.N.); (W.T.M.)
| | - Dan Makumbi
- International Maize and Wheat Improvement Centre (CIMMYT), World Agroforestry Centre (ICRAF), United Nations Avenue, Gigiri, Nairobi 1041-00621, Kenya; (Y.B.); (D.M.); (M.S.O.); (L.M.S.); (J.M.B.); (B.D.); (B.M.P.)
| | - Michael S. Olsen
- International Maize and Wheat Improvement Centre (CIMMYT), World Agroforestry Centre (ICRAF), United Nations Avenue, Gigiri, Nairobi 1041-00621, Kenya; (Y.B.); (D.M.); (M.S.O.); (L.M.S.); (J.M.B.); (B.D.); (B.M.P.)
| | - L. M. Suresh
- International Maize and Wheat Improvement Centre (CIMMYT), World Agroforestry Centre (ICRAF), United Nations Avenue, Gigiri, Nairobi 1041-00621, Kenya; (Y.B.); (D.M.); (M.S.O.); (L.M.S.); (J.M.B.); (B.D.); (B.M.P.)
| | - Jumbo M. Bright
- International Maize and Wheat Improvement Centre (CIMMYT), World Agroforestry Centre (ICRAF), United Nations Avenue, Gigiri, Nairobi 1041-00621, Kenya; (Y.B.); (D.M.); (M.S.O.); (L.M.S.); (J.M.B.); (B.D.); (B.M.P.)
| | - Biswanath Das
- International Maize and Wheat Improvement Centre (CIMMYT), World Agroforestry Centre (ICRAF), United Nations Avenue, Gigiri, Nairobi 1041-00621, Kenya; (Y.B.); (D.M.); (M.S.O.); (L.M.S.); (J.M.B.); (B.D.); (B.M.P.)
| | - Boddupalli M. Prasanna
- International Maize and Wheat Improvement Centre (CIMMYT), World Agroforestry Centre (ICRAF), United Nations Avenue, Gigiri, Nairobi 1041-00621, Kenya; (Y.B.); (D.M.); (M.S.O.); (L.M.S.); (J.M.B.); (B.D.); (B.M.P.)
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Li SN, Cheng P, Bai YQ, Shi Y, Yu JY, Li RC, Zhou RN, Zhang ZG, Wu XX, Chen QS. Analysis of Soybean Somatic Embryogenesis Using Chromosome Segment Substitution Lines and Transcriptome Sequencing. Genes (Basel) 2019; 10:E943. [PMID: 31752416 PMCID: PMC6896167 DOI: 10.3390/genes10110943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 11/05/2019] [Accepted: 11/18/2019] [Indexed: 12/15/2022] Open
Abstract
Soybean is an important cash crop that is widely used as a source of vegetable protein and edible oil. The regeneration ability of soybean directly affects the application of biotechnology. In this study, we used the exogenous hormone 2,4-D to treat immature embryos. Different levels of somatic incidence were selected from the chromosome segment substitution lines (CSSLs) constructed by SN14 and ZYD00006. Transcriptome sequencing of extreme materials was performed, and 2666 differentially expressed genes were obtained. At the same time, a difference table was generated by combining the data on CSSL rearrangement. In the extreme materials, a total of 93 differentially expressed genes were predicted and were then analyzed by cluster analysis and Gene Ontology (GO) annotation. After screening and annotating the target genes, three differentially expressed genes with hormone pathways were identified. The expression patterns of the target genes were verified by real-time quantitative PCR (qRT-PCR). Haplotype polymorphism detection and linkage disequilibrium analysis were performed on the candidate gene Glyma.09g248200. This study provided more information on the regulation network of soybean somatic embryogenesis and regeneration processes, and further identified important genes in the soybean regeneration process and provided a theoretical basis for accelerating the application of biotechnology to soybean for improving its breeding efficiency.
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Affiliation(s)
| | | | | | | | | | | | | | - Zhan-Guo Zhang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China; (S.-N.L.); (P.C.); (Y.-Q.B.); (Y.S.); (J.-Y.Y.); (R.-C.L.); (R.-N.Z.)
| | - Xiao-Xia Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China; (S.-N.L.); (P.C.); (Y.-Q.B.); (Y.S.); (J.-Y.Y.); (R.-C.L.); (R.-N.Z.)
| | - Qing-Shan Chen
- College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, China; (S.-N.L.); (P.C.); (Y.-Q.B.); (Y.S.); (J.-Y.Y.); (R.-C.L.); (R.-N.Z.)
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Zhang H, Chen J, Zhang F, Song Y. Transcriptome analysis of callus from melon. Gene 2019; 684:131-138. [PMID: 30321656 DOI: 10.1016/j.gene.2018.10.037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 09/21/2018] [Accepted: 10/11/2018] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To identify the key genes promoting the differentiation of melon non-embryogenic callus into embryogenic callus. METHODS The transcriptome sequencing analysis was used to analyze the mRNA sequence in embryogenic callus (Z) and non-embryogenic callus (F); transcript mapping, gene expression analysis, cluster analysis, classification analysis and enrichment analysis were then used to detect the differentially expressed genes and enriched pathways. RESULTS The correlation coefficient between sample Z and sample F was 0.929 after transcript mapping. The overall gene expression levels in sample Z were higher as compared with sample F. Furthermore, cluster analysis showed that the expression of genes involved in photosynthesis was increased in sample Z when comparing to F. Besides, the classification of differential Gene Ontology (GO) showed that many metabolic processes were affected with the metabolism enhanced in embryogenic callus. Interestingly, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis further demonstrated the high metabolic activity and active secondary metabolite formation in the embryogenic callus. CONCLUSION The genes associated with photosynthesis, metabolic pathways and biosynthesis of secondary metabolites may promote the differentiation of callus into embryogenic callus.
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Affiliation(s)
- Huijun Zhang
- Anhui Key Laboratory of Plant Resources and Biology, School of Life Science, Huaibei Normal University, No. 100 Dongshan Road, Huaibei 235000, Anhui Province, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture/Northeast Agricultural University, Haerbing 150030, Heilongjiang Province, China
| | - Jinfeng Chen
- College of Horticulture, Nanjing Agricultural University, NO.1 weigang, Nanjing 210095, Jiangsu, China.
| | - Fei Zhang
- Anhui Key Laboratory of Plant Resources and Biology, School of Life Science, Huaibei Normal University, No. 100 Dongshan Road, Huaibei 235000, Anhui Province, China
| | - Yunxian Song
- Anhui Key Laboratory of Plant Resources and Biology, School of Life Science, Huaibei Normal University, No. 100 Dongshan Road, Huaibei 235000, Anhui Province, China
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Du X, Fang T, Liu Y, Huang L, Zang M, Wang G, Liu Y, Fu J. Transcriptome Profiling Predicts New Genes to Promote Maize Callus Formation and Transformation. FRONTIERS IN PLANT SCIENCE 2019; 10:1633. [PMID: 31921272 PMCID: PMC6934073 DOI: 10.3389/fpls.2019.01633] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 11/20/2019] [Indexed: 05/17/2023]
Abstract
Maize transformation is highly based on the formation of embryonic callus, which is mainly derived from scutellum cells of the immature maize embryo. However, only a few genes involved in callus induction have been identified in maize. To reveal the potential genes involved in the callus induction of maize, we carried out a high-throughput RNA sequencing on embryos that were cultured for 0, 1, 2, 4, 6, and 8 days, respectively, on a medium containing or lacking 2,4-dichlorophenoxyacetic acid. In total, 7,525 genes were found to be induced by 2,4-dichlorophenoxyacetic acid and categorized into eight clusters, with clusters 2 and 3 showing an increasing trend related to signal transmission, signal transduction, iron ion binding, and heme binding. Among the induced genes, 659 transcription factors belong to 51 families. An AP2 transcription factors, ZmBBM2, was dramatically and rapidly induced by auxin and further characterization showed that overexpression of ZmBBM2 can promote callus induction and proliferation in three inbred maize lines. Therefore, our comprehensive analyses provide some insight into the early molecular regulations during callus induction and are useful for further identification of the regulators governing callus formation.
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Affiliation(s)
- Xuemei Du
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ting Fang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liying Huang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Maosen Zang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunjun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Yunjun Liu, ; Junjie Fu,
| | - Junjie Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Yunjun Liu, ; Junjie Fu,
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Siddiqui ZH, Abbas ZK, Ansari MW, Khan MN. The role of miRNA in somatic embryogenesis. Genomics 2018; 111:1026-1033. [PMID: 30476555 DOI: 10.1016/j.ygeno.2018.11.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/14/2018] [Accepted: 11/17/2018] [Indexed: 02/04/2023]
Abstract
Somatic embryogenesis (SEG) is one of the best techniques for mass production of economically important plants. It is also used for the study of morphology, anatomy, physiology, genetics and molecular mechanism of embryo development. Somatic Embryos (SE) are bipolar structures that develop from a cell other than a gamete or zygote. SEG reflects the unique developmental potential of plant somatic cells, resulting in the transition of the differentiated somatic cells to embryogenic cells to follow the zygotic embryo stages. There are several biochemical and physiological processes that transformed a single somatic cell to a whole plant. SE studies provide insight into cell mechanisms governing the totipotency process in plants. Previously, in vitro studies have suggested the role of various regulatory genes in embryogenic transition that are triggered by plant hormones in response to stress. The omic studies identify the specific genes, transcripts, and proteins required for somatic embryogenesis development. MicroRNAs (miRNAs) are small, 19-24 nucleotides (nt), non-coding small RNA regulatory molecules controlling a large number of biological processes. In addition to their role in SEG, miRNAs play vital role in plant development, secondary metabolite synthesis and metabolism of macromolecules, hormone signal transduction, and tolerance of plants to biotic and abiotic stresses. During last decade several types of miRNAs involved in SEG have been reported. Among these miRNAs, miR156, miR162, miR166a, miR167, miR168, miR171a/b, miR171c, miR393, miR397 and miR398 played very active role during various stages of SEG. In this review, we highlighted the role of these as well as other miRNAs in some economically important plants.
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Affiliation(s)
- Zahid Hameed Siddiqui
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia.
| | - Zahid Khorshid Abbas
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Mohammad Wahid Ansari
- Department of Botany, Zakir Husain Delhi College, University of Delhi, JLN Marg, New Delhi 110002, India
| | - Mohammad Nasir Khan
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
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30
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BABY BOOM (BBM): a candidate transcription factor gene in plant biotechnology. Biotechnol Lett 2018; 40:1467-1475. [PMID: 30298388 DOI: 10.1007/s10529-018-2613-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 10/04/2018] [Indexed: 10/28/2022]
Abstract
Plants have evolved a number of transcription factors, many of which are implicated in signaling pathways as well as regulating diverse cellular functions. BABY BOOM (BBM), transcription factors of the AP2/ERF family are key regulators of plant cell totipotency. Ectopic expression of the BBM gene, originally identified in Brassica napus, has diverse functions in plant cell proliferation, growth and development without exogenous growth regulators. The BBM gene has been implicated to play an important role as a gene marker in multiple signaling developmental pathways in plant development. This review focuses on recent advances in our understanding of a member of the AP2 family of transcription factor BBM in plant biotechnology including plant embryogenesis, cell proliferation, regeneration, plant transformation and apogamy. Recent discoveries about the BBM gene will inevitably help to unlock the long-standing mysteries of different biological mechanisms of plant cells.
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Bräuning S, Catanach A, Lord JM, Bicknell R, Macknight RC. Comparative transcriptome analysis of the wild-type model apomict Hieracium praealtum and its loss of parthenogenesis (lop) mutant. BMC PLANT BIOLOGY 2018; 18:206. [PMID: 30249189 PMCID: PMC6154955 DOI: 10.1186/s12870-018-1423-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 09/10/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Asexual seed formation (apomixis) has been observed in diverse plant families but is rare in crop plants. The generation of apomictic crops would revolutionize agriculture, as clonal seed production provides a low cost and efficient way to produce hybrid seed. Hieracium (Asteraceae) is a model system for studying the molecular components of gametophytic apomixis (asexual seed reproduction). RESULTS In this study, a reference transcriptome was produced from apomictic Hieracium undergoing the key apomictic events of apomeiosis, parthenogenesis and autonomous endosperm development. In addition, transcriptome sequences from pre-pollination and post-pollination stages were generated from a loss of parthenogenesis (lop) mutant accession that exhibits loss of parthenogenesis and autonomous endosperm development. The transcriptome is composed of 147,632 contigs, 50% of which were annotated with orthologous genes and their probable function. The transcriptome was used to identify transcripts differentially expressed during apomictic and pollination dependent (lop) seed development. Gene Ontology enrichment analysis of differentially expressed transcripts showed that an important difference between apomictic and pollination dependent seed development was the expression of genes relating to epigenetic gene regulation. Genes that mark key developmental stages, i.e. aposporous embryo sac development and seed development, were also identified through their enhanced expression at those stages. CONCLUSION The production of a comprehensive floral reference transcriptome for Hieracium provides a valuable resource for research into the molecular basis of apomixis and the identification of the genes underlying the LOP locus.
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Affiliation(s)
- Sophia Bräuning
- Department of Biochemistry, University of Otago, 710 Cumberland St, Dunedin, 9016 New Zealand
- Department of Botany, University of Otago, 464 Great King St, Dunedin, 9016 New Zealand
| | - Andrew Catanach
- New Zealand Institute for Plant and Food Research, Gerald St, Lincoln, 7608 New Zealand
| | - Janice M. Lord
- Department of Botany, University of Otago, 464 Great King St, Dunedin, 9016 New Zealand
| | - Ross Bicknell
- New Zealand Institute for Plant and Food Research, Gerald St, Lincoln, 7608 New Zealand
| | - Richard C. Macknight
- Department of Biochemistry, University of Otago, 710 Cumberland St, Dunedin, 9016 New Zealand
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Karim R, Tan YS, Singh P, Khalid N, Harikrishna JA. Expression and DNA methylation of SERK, BBM, LEC2 and WUS genes in in vitro cultures of Boesenbergia rotunda (L.) Mansf. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:741-751. [PMID: 30150851 PMCID: PMC6103949 DOI: 10.1007/s12298-018-0566-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 06/01/2018] [Accepted: 06/05/2018] [Indexed: 05/20/2023]
Abstract
The process of somatic embryogenesis and plant regeneration involve changes in gene expression and have been associated with changes in DNA methylation. Here, we report the expression and DNA methylation patterns of SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE (SERK), BABY BOOM (BBM), LEAFY COTYLEDON 2 (LEC2) and WUSCHEL (WUS) in meristematic block of newly emerged shoots from rhizome, embryogenic and non-embryogenic calli, prolonged cell suspension culture, ex vitro leaf, and in vitro leaf of regenerated plants of Boesenbergia rotunda. Among all seven samples, based on qRT-PCR, the highest level of expression of SERK, BBM and LEC2 was in embryogenic callus, while WUS was most highly expressed in meristematic block tissue followed by embryogenic callus. Relatively lower expression was observed in cell suspension culture and watery callus for SERK, LEC2 and WUS and in in vitro leaf for BBM. For gene specific methylation determined by bisulfite sequencing data, embryogenic callus samples had the lowest levels of DNA methylation at CG, CHG and CHH contexts of SERK, LEC2 and WUS. We observed negative correlation between DNA methylation at the CG and CHG contexts and the expression levels of SERK, BBM, LEC2 and WUS. Based on our results, we suggest that relatively higher expression and lower level of DNA methylation of SERK, BBM, LEC2 and WUS are associated with somatic embryogenesis and plant regeneration in B. rotunda.
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Affiliation(s)
- Rezaul Karim
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603 Kuala Lumpur, Malaysia
- Department of Botany, Faculty of Life and Earth Sciences, University of Rajshahi, Rajshahi, 6205 Bangladesh
| | - Yew Seong Tan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Pooja Singh
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Norzulaani Khalid
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Jennifer Ann Harikrishna
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603 Kuala Lumpur, Malaysia
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Salvo S, Cook J, Carlson AR, Hirsch CN, Kaeppler SM, Kaeppler HF. Genetic Fine-Mapping of a Quantitative Trait Locus (QTL) Associated with Embryogenic Tissue Culture Response and Plant Regeneration Ability in Maize ( Zea mays L.). THE PLANT GENOME 2018; 11:170111. [PMID: 30025019 DOI: 10.3835/plantgenome2017.12.0111] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Embryogenic and regenerable tissue cultures are widely utilized in plant transformation, clonal propagation, and biological research applications. Germplasm utilized in those applications are limited, however, due to genotype-dependent culture response. The goal of this study was to identify genomic regions controlling embryogenic and regenerable tissue culture response in the globally important crop, maize ( L.), toward the long-term objective of developing approaches for genotype-independent plant genetic engineering and clonal propagation systems. An inbred maize line, WCIC2, nearly-isogenic to reference inbred B73, was developed by phenotypic selection and molecular marker analysis. WCIC2 has over 50x increase in tissue culture response relative to the recurrent parent, B73. This line was used to genetically fine-map a region on chromosome 3 controlling embryogenic and regenerable tissue culture response to a 23.9 Mb region. WCIC2 and derivatives will be useful materials to enable maize research in a genetic background similar to B73, and our genetic mapping results will advance research to identify causal genes controlling somatic embryo formation and plant regeneration in maize.
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Heritable Epigenomic Changes to the Maize Methylome Resulting from Tissue Culture. Genetics 2018; 209:983-995. [PMID: 29848487 DOI: 10.1534/genetics.118.300987] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 05/26/2018] [Indexed: 12/22/2022] Open
Abstract
DNA methylation can contribute to the maintenance of genome integrity and regulation of gene expression. In most situations, DNA methylation patterns are inherited quite stably. However, changes in DNA methylation can occur at some loci as a result of tissue culture resulting in somaclonal variation. To investigate heritable epigenetic changes as a consequence of tissue culture, a sequence-capture bisulfite sequencing approach was implemented to monitor context-specific DNA methylation patterns in ∼15 Mb of the maize genome for a population of plants that had been regenerated from tissue culture. Plants that have been regenerated from tissue culture exhibit gains and losses of DNA methylation at a subset of genomic regions. There was evidence for a high rate of homozygous changes to DNA methylation levels that occur consistently in multiple independent tissue culture lines, suggesting that some loci are either targeted or hotspots for epigenetic variation. The consistent changes inherited following tissue culture include both gains and losses of DNA methylation and can affect CG, CHG, or both contexts within a region. Only a subset of the tissue culture changes observed in callus plants are observed in the primary regenerants, but the majority of DNA methylation changes present in primary regenerants are passed onto offspring. This study provides insights into the susceptibility of some loci and potential mechanisms that could contribute to altered DNA methylation and epigenetic state that occur during tissue culture in plant species.
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35
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Raji JA, Frame B, Little D, Santoso TJ, Wang K. Agrobacterium- and Biolistic-Mediated Transformation of Maize B104 Inbred. Methods Mol Biol 2018; 1676:15-40. [PMID: 28986902 DOI: 10.1007/978-1-4939-7315-6_2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Genetic transformation of maize inbred genotypes remains non-routine for many laboratories due to variations in cell competency to induce embryogenic callus, as well as the cell's ability to receive and incorporate transgenes into the genome. This chapter describes two transformation protocols using Agrobacterium- and biolistic-mediated methods for gene delivery. Immature zygotic embryos of maize inbred B104, excised from ears harvested 10-14 days post pollination, are used as starting explant material. Disarmed Agrobacterium strains harboring standard binary vectors and the biolistic gun system Bio-Rad PDS-1000/He are used as gene delivery systems. The herbicide resistant bar gene and selection agent bialaphos are used for identifying putative transgenic type I callus events. Using the step-by-step protocols described here, average transformation frequencies (number of bialaphos resistant T0 callus events per 100 explants infected or bombarded) of 4% and 8% can be achieved using the Agrobacterium- and biolistic-mediated methods, respectively. An estimated duration of 16-21 weeks is needed using either protocol from the start of transformation experiments to obtaining putative transgenic plantlets with established roots. In addition to laboratory in vitro procedures, detailed greenhouse protocols for producing immature ears as transformation starting material and caring for transgenic plants for seed production are also described.
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Affiliation(s)
- Jennifer A Raji
- Department of Agronomy, Iowa State University, Ames, IA, 50011-1010, USA.,Center for Plant Transformation, Plant Sciences Institute, Iowa State University, Ames, IA, 50011-1010, USA
| | - Bronwyn Frame
- Department of Agronomy, Iowa State University, Ames, IA, 50011-1010, USA.,Center for Plant Transformation, Plant Sciences Institute, Iowa State University, Ames, IA, 50011-1010, USA
| | - Daniel Little
- Department of Agronomy, Iowa State University, Ames, IA, 50011-1010, USA.,Center for Plant Transformation, Plant Sciences Institute, Iowa State University, Ames, IA, 50011-1010, USA
| | - Tri Joko Santoso
- Department of Agronomy, Iowa State University, Ames, IA, 50011-1010, USA.,Center for Plant Transformation, Plant Sciences Institute, Iowa State University, Ames, IA, 50011-1010, USA.,Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD-IAARD), Bogor, Indonesia
| | - Kan Wang
- Department of Agronomy, Iowa State University, Ames, IA, 50011-1010, USA. .,Center for Plant Transformation, Plant Sciences Institute, Iowa State University, Ames, IA, 50011-1010, USA.
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36
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Bilichak A, Luu J, Jiang F, Eudes F. Identification of BABY BOOM homolog in bread wheat. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.aggene.2017.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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37
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Nejat N, Ramalingam A, Mantri N. Advances in Transcriptomics of Plants. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2018; 164:161-185. [PMID: 29392354 DOI: 10.1007/10_2017_52] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The current global population of 7.3 billion is estimated to reach 9.7 billion in the year 2050. Rapid population growth is driving up global food demand. Additionally, global climate change, environmental degradation, drought, emerging diseases, and salty soils are the current threats to global food security. In order to mitigate the adverse effects of these diverse agricultural productivity constraints and enhance crop yield and stress-tolerance in plants, we need to go beyond traditional and molecular plant breeding. The powerful new tools for genome editing, Transcription Activator-Like Effector Nucleases (TALENs) and Clustered Regulatory Interspaced Short Palindromic Repeats (CRISPR)/Cas systems (CRISPR-Cas9), have been hailed as a quantum leap forward in the development of stress-resistant plants. Plant breeding techniques, however, have several drawbacks. Hence, identification of transcriptional regulatory elements and deciphering mechanisms underlying transcriptional regulation are crucial to avoiding unintended consequences in modified crop plants, which could ultimately have negative impacts on human health. RNA splicing as an essential regulated post-transcriptional process, alternative polyadenylation as an RNA-processing mechanism, along with non-coding RNAs (microRNAs, small interfering RNAs and long non-coding RNAs) have been identified as major players in gene regulation. In this chapter, we highlight new findings on the essential roles of alternative splicing and alternative polyadenylation in plant development and response to biotic and abiotic stresses. We also discuss biogenesis and the functions of microRNAs (miRNAs) and small interfering RNAs (siRNAs) in plants and recent advances in our knowledge of the roles of miRNAs and siRNAs in plant stress response. Graphical Abstract.
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Affiliation(s)
- Naghmeh Nejat
- The Pangenomics Group, School of Science, RMIT University, Melbourne, VIC, Australia
| | - Abirami Ramalingam
- The Pangenomics Group, School of Science, RMIT University, Melbourne, VIC, Australia
| | - Nitin Mantri
- The Pangenomics Group, School of Science, RMIT University, Melbourne, VIC, Australia.
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38
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Góngora-Castillo E, Nic-Can GI, Galaz-Ávalos RM, Loyola-Vargas VM. Elaboration of Transcriptome During the Induction of Somatic Embryogenesis. Methods Mol Biol 2018; 1815:411-427. [PMID: 29981139 DOI: 10.1007/978-1-4939-8594-4_29] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Somatic embryogenesis (SE) is one of the most studied developmental processes due to its applications, such as plant micropropagation, transformation, and germplasm conservation. The use of massive techniques of sequencing, as well as the use of subtractive hybridization and macroarrays, has led to the identification of hundreds of genes involved in the SE process. These have been important developments to study the molecular aspects of the progress of SE. With the advent of the new massive techniques for sequencing RNA, it has been possible to see a more complete picture of whole processes. In this chapter we present a technique to handle the elaboration of the transcriptome from the extraction of RNA until the assembly of the complete transcriptome.
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Affiliation(s)
- Elsa Góngora-Castillo
- CONACYT Research Fellow-Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, Mexico.
| | - Geovanny I Nic-Can
- CONACYT Research Fellow-Campus de Ciencias Exactas e Ingeniería, Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
| | - Rosa M Galaz-Ávalos
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, Mexico
| | - Víctor M Loyola-Vargas
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, Mexico
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39
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Chu Z, Chen J, Sun J, Dong Z, Yang X, Wang Y, Xu H, Zhang X, Chen F, Cui D. De novo assembly and comparative analysis of the transcriptome of embryogenic callus formation in bread wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2017; 17:244. [PMID: 29258440 PMCID: PMC5735865 DOI: 10.1186/s12870-017-1204-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 12/06/2017] [Indexed: 05/26/2023]
Abstract
BACKGROUND During asexual reproduction the embryogenic callus can differentiate into a new plantlet, offering great potential for fostering in vitro culture efficiency in plants. The immature embryos (IMEs) of wheat (Triticum aestivum L.) are more easily able to generate embryogenic callus than mature embryos (MEs). To understand the molecular process of embryogenic callus formation in wheat, de novo transcriptome sequencing was used to generate transcriptome sequences from calli derived from IMEs and MEs after 3d, 6d, or 15d of culture (DC). RESULTS In total, 155 million high quality paired-end reads were obtained from the 6 cDNA libraries. Our de novo assembly generated 142,221 unigenes, of which 59,976 (42.17%) were annotated with a significant Blastx against nr, Pfam, Swissprot, KOG, KEGG, GO and COG/KOG databases. Comparative transcriptome analysis indicated that a total of 5194 differentially expressed genes (DEGs) were identified in the comparisons of IME vs. ME at the three stages, including 3181, 2085 and 1468 DEGs at 3, 6 and 15 DC, respectively. Of them, 283 overlapped in all the three comparisons. Furthermore, 4731 DEGs were identified in the comparisons between stages in IMEs and MEs. Functional analysis revealed that 271transcription factor (TF) genes (10 overlapped in all 3 comparisons of IME vs. ME) and 346 somatic embryogenesis related genes (SSEGs; 35 overlapped in all 3 comparisons of IME vs. ME) were differentially expressed in at least one comparison of IME vs. ME. In addition, of the 283 overlapped DEGs in the 3 comparisons of IME vs. ME, excluding the SSEGs and TFs, 39 possessed a higher rate of involvement in biological processes relating to response to stimuli, in multi-organism processes, reproductive processes and reproduction. Furthermore, 7 were simultaneously differentially expressed in the 2 comparisons between the stages in IMEs, but not MEs, suggesting that they may be related to embryogenic callus formation. The expression levels of genes, which were validated by qRT-PCR, showed a high correlation with the RNA-seq value. CONCLUSIONS This study provides new insights into the role of the transcriptome in embryogenic callus formation in wheat, and will serve as a valuable resource for further studies addressing embryogenic callus formation in plants.
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Affiliation(s)
- Zongli Chu
- Agronomy College/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 People’s Republic of China
- Xinyang Agriculture and Forestry University, Xinyang, 464000 China
| | - Junying Chen
- Agronomy College/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 People’s Republic of China
| | - Junyan Sun
- Xinyang Agriculture and Forestry University, Xinyang, 464000 China
| | - Zhongdong Dong
- Agronomy College/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 People’s Republic of China
| | - Xia Yang
- Agronomy College/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 People’s Republic of China
| | - Ying Wang
- Agronomy College/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 People’s Republic of China
| | - Haixia Xu
- Agronomy College/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 People’s Republic of China
| | - Xiaoke Zhang
- Agronomy College, North West Agriculture and Forestry University, Yangling, 712100 China
| | - Feng Chen
- Agronomy College/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 People’s Republic of China
| | - Dangqun Cui
- Agronomy College/Collaborative Innovation Center of Henan Grain Crops/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046 People’s Republic of China
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40
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Horstman A, Bemer M, Boutilier K. A transcriptional view on somatic embryogenesis. ACTA ACUST UNITED AC 2017; 4:201-216. [PMID: 29299323 PMCID: PMC5743784 DOI: 10.1002/reg2.91] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 09/15/2017] [Accepted: 10/04/2017] [Indexed: 12/12/2022]
Abstract
Somatic embryogenesis is a form of induced plant cell totipotency where embryos develop from somatic or vegetative cells in the absence of fertilization. Somatic embryogenesis can be induced in vitro by exposing explants to stress or growth regulator treatments. Molecular genetics studies have also shown that ectopic expression of specific embryo‐ and meristem‐expressed transcription factors or loss of certain chromatin‐modifying proteins induces spontaneous somatic embryogenesis. We begin this review with a general description of the major developmental events that define plant somatic embryogenesis and then focus on the transcriptional regulation of this process in the model plant Arabidopsis thaliana (arabidopsis). We describe the different somatic embryogenesis systems developed for arabidopsis and discuss the roles of transcription factors and chromatin modifications in this process. We describe how these somatic embryogenesis factors are interconnected and how their pathways converge at the level of hormones. Furthermore, the similarities between the developmental pathways in hormone‐ and transcription‐factor‐induced tissue culture systems are reviewed in the light of our recent findings on the somatic embryo‐inducing transcription factor BABY BOOM.
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Affiliation(s)
- Anneke Horstman
- Bioscience Wageningen University and Research Wageningen The Netherlands.,Laboratory of Molecular Biology Wageningen University and Research Wageningen The Netherlands
| | - Marian Bemer
- Laboratory of Molecular Biology Wageningen University and Research Wageningen The Netherlands
| | - Kim Boutilier
- Bioscience Wageningen University and Research Wageningen The Netherlands
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41
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Kretschmer M, Croll D, Kronstad JW. Maize susceptibility to Ustilago maydis is influenced by genetic and chemical perturbation of carbohydrate allocation. MOLECULAR PLANT PATHOLOGY 2017; 18:1222-1237. [PMID: 27564861 PMCID: PMC6638311 DOI: 10.1111/mpp.12486] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 08/15/2016] [Accepted: 08/25/2016] [Indexed: 05/03/2023]
Abstract
The ability of biotrophic fungi to metabolically adapt to the host environment is a critical factor in fungal diseases of crop plants. In this study, we analysed the transcriptome of maize tumours induced by Ustilago maydis to identify key features underlying metabolic shifts during disease. Among other metabolic changes, this analysis highlighted modifications during infection in the transcriptional regulation of carbohydrate allocation and starch metabolism. We confirmed the relevance of these changes by establishing that symptom development was altered in an id1 (indeterminate1) mutant that showed increased accumulation of sucrose as well as being defective in the vegetative to reproductive transition. We further established the relevance of specific metabolic functions related to carbohydrate allocation by assaying disease in su1 (sugary1) mutant plants with altered starch metabolism and in plants treated with glucose, sucrose and silver nitrate during infection. We propose that specific regulatory and metabolic changes influence the balance between susceptibility and resistance by altering carbon allocation to promote fungal growth or to influence plant defence. Taken together, these studies reveal key aspects of metabolism that are critical for biotrophic adaptation during the maize-U. maydis interaction.
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Affiliation(s)
- Matthias Kretschmer
- Michael Smith Laboratories, University of British ColumbiaVancouverBCV6T 1Z4Canada
| | - Daniel Croll
- Michael Smith Laboratories, University of British ColumbiaVancouverBCV6T 1Z4Canada
- Present address:
Institute of Integrative BiologyETH Zürich8092 ZürichSwitzerland
| | - James W. Kronstad
- Michael Smith Laboratories, University of British ColumbiaVancouverBCV6T 1Z4Canada
- Department of Microbiology and ImmunologyUniversity of British ColumbiaVancouverBCV6T 1Z4Canada
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42
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Liu Y, Zhang HL, Guo HR, Xie L, Zeng RZ, Zhang XQ, Zhang ZS. Transcriptomic and Hormonal Analyses Reveal that YUC-Mediated Auxin Biogenesis Is Involved in Shoot Regeneration from Rhizome in Cymbidium. FRONTIERS IN PLANT SCIENCE 2017; 8:1866. [PMID: 29163591 PMCID: PMC5664085 DOI: 10.3389/fpls.2017.01866] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 10/12/2017] [Indexed: 05/22/2023]
Abstract
Cymbidium, one of the most important orchid genera in horticulture, can be classified into epiphytic and terrestrial species. Generally, epiphytic Cymbidium seedlings can be easily propagated by tissue culture, but terrestrial seedlings are difficult to propagate. To date, the molecular mechanisms underlying the differences in the ease with which terrestrial and epiphytic cymbidiums can be propagated are largely unknown. Using RNA-sequencing, quantitative reverse transcription PCR and enzyme-linked immunosorbent assay, Cymbidium 'Xiaofeng' (CXF), which can be efficiently micropropagated, and terrestrial Cymbidium sinense 'Qijianbaimo' (CSQ), which has a low regeneration ability, were used to explore the molecular mechanisms underlying the micropropagation ability of Cymbidium species. To this end, 447 million clean short reads were generated, and 31,264 annotated unigenes were obtained from 10 cDNA libraries. A total of 1,290 differentially expressed genes (DEGs) were identified between CXF and CSQ during shoot induction. Gene ontology (GO) enrichment analysis indicated that the DEGs were significantly enriched in auxin pathway-related GO terms. Further analysis demonstrated that YUC and GH3 family genes, which play crucial roles in the regulation of auxin/IAA (indole-3-acetic acid) metabolism, acted quickly in response to shoot induction culture in vitro and were closely correlated with variation in shoot regeneration between CXF and CSQ. In addition, the study showed that IAA accumulated rapidly and significantly during shoot induction in CXF compared to that in CSQ; in contrast, no significant changes in other hormones were observed between CXF and CSQ. Furthermore, shoot regeneration in CXF was inhibited by a yucasin-auxin biosynthesis inhibitor, indicating that increased IAA level is required for high-frequency shoot regeneration in CXF. In conclusion, our study revealed that YUC-mediated auxin biogenesis is involved in shoot regeneration from rhizome in Cymbidium.
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Affiliation(s)
| | | | | | | | | | - Xiang-Qian Zhang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Zhi-Sheng Zhang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
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Chen J, Strieder N, Krohn NG, Cyprys P, Sprunck S, Engelmann JC, Dresselhaus T. Zygotic Genome Activation Occurs Shortly after Fertilization in Maize. THE PLANT CELL 2017; 29:2106-2125. [PMID: 28814645 PMCID: PMC5635985 DOI: 10.1105/tpc.17.00099] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 07/19/2017] [Accepted: 08/15/2017] [Indexed: 05/18/2023]
Abstract
The formation of a zygote via the fusion of an egg and sperm cell and its subsequent asymmetric division herald the start of the plant's life cycle. Zygotic genome activation (ZGA) is thought to occur gradually, with the initial steps of zygote and embryo development being primarily maternally controlled, and subsequent steps being governed by the zygotic genome. Here, using maize (Zea mays) as a model plant system, we determined the timing of zygote development and generated RNA-seq transcriptome profiles of gametes, zygotes, and apical and basal daughter cells. ZGA occurs shortly after fertilization and involves ∼10% of the genome being activated in a highly dynamic pattern. In particular, genes encoding transcriptional regulators of various families are activated shortly after fertilization. Further analyses suggested that chromatin assembly is strongly modified after fertilization, that the egg cell is primed to activate the translational machinery, and that hormones likely play a minor role in the initial steps of early embryo development in maize. Our findings provide important insights into gamete and zygote activity in plants, and our RNA-seq transcriptome profiles represent a comprehensive, unique RNA-seq data set that can be used by the research community.
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Affiliation(s)
- Junyi Chen
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, 93053 Regensburg, Germany
| | - Nicholas Strieder
- Institute of Functional Genomics, University of Regensburg, 93053 Regensburg, Germany
| | - Nadia G Krohn
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, 93053 Regensburg, Germany
| | - Philipp Cyprys
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, 93053 Regensburg, Germany
| | - Stefanie Sprunck
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, 93053 Regensburg, Germany
| | - Julia C Engelmann
- Institute of Functional Genomics, University of Regensburg, 93053 Regensburg, Germany
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, 93053 Regensburg, Germany
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44
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Jamaluddin ND, Mohd Noor N, Goh HH. Genome-wide transcriptome profiling of Carica papaya L. embryogenic callus. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:357-368. [PMID: 28461724 PMCID: PMC5391361 DOI: 10.1007/s12298-017-0429-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 02/24/2017] [Accepted: 03/06/2017] [Indexed: 05/22/2023]
Abstract
Genome-wide transcriptome profiling is a powerful tool to study global gene expression patterns in plant development. We report the first transcriptome profile analysis of papaya embryogenic callus to improve our understanding on genes associated with somatic embryogenesis. By using 3' mRNA-sequencing, we generated 6,190,687 processed reads and 47.0% were aligned to papaya genome reference, in which 21,170 (75.4%) of 27,082 annotated genes were found to be expressed but only 41% was expressed at functionally high levels. The top 10% of genes with high transcript abundance were significantly enriched in biological processes related to cell proliferation, stress response, and metabolism. Genes functioning in somatic embryogenesis such as SERK and LEA, hormone-related genes, stress-related genes, and genes involved in secondary metabolite biosynthesis pathways were highly expressed. Transcription factors such as NAC, WRKY, MYB, WUSCHEL, Agamous-like MADS-box protein and bHLH important in somatic embryos of other plants species were found to be expressed in papaya embryogenic callus. Abundant expression of enolase and ADH is consistent with proteome study of papaya somatic embryo. Our study highlights that some genes related to secondary metabolite biosynthesis, especially phenylpropanoid biosynthesis, were highly expressed in papaya embryogenic callus, which might have implication for cell factory applications. The discovery of all genes expressed in papaya embryogenic callus provides an important information into early biological processes during the induction of embryogenesis and useful for future research in other plant species.
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Affiliation(s)
- Nur Diyana Jamaluddin
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM, 43600 Bangi, Selangor Darul Ehsan Malaysia
| | - Normah Mohd Noor
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM, 43600 Bangi, Selangor Darul Ehsan Malaysia
| | - Hoe-Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM, 43600 Bangi, Selangor Darul Ehsan Malaysia
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BEN MAHMOUD K, JEDIDI E, DELPORTE F, MUHOVSKI Y, JEMMALI A, DRUART P. Molecular investigations of the somatic embryogenesis recalcitrancein the cherry (Prunus cerasus L.) rootstock CAB 6P. Turk J Biol 2017. [DOI: 10.3906/biy-1604-105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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Zheng Q, Zheng Y, Ji H, Burnie W, Perry SE. Gene Regulation by the AGL15 Transcription Factor Reveals Hormone Interactions in Somatic Embryogenesis. PLANT PHYSIOLOGY 2016; 172:2374-2387. [PMID: 27794101 PMCID: PMC5129705 DOI: 10.1104/pp.16.00564] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 10/25/2016] [Indexed: 05/02/2023]
Abstract
The MADS box transcription factor Arabidopsis (Arabidopsis thaliana) AGAMOUS-LIKE15 (AGL15) and a putative ortholog from soybean (Glycine max), GmAGL15, are able to promote somatic embryogenesis (SE) in these plants when ectopically expressed. SE is an important means of plant regeneration, but many plants, or even particular cultivars, are recalcitrant for this process. Understanding how (Gm)AGL15 promotes SE by identifying and characterizing direct and indirect downstream regulated genes can provide means to improve regeneration by SE for crop improvement and to perform molecular tests of genes. Conserved transcription factors and the genes they regulate in common between species may provide the most promising avenue to identify targets for SE improvement. We show that (Gm)AGL15 negatively regulates auxin signaling in both Arabidopsis and soybean at many levels of the pathway, including the repression of AUXIN RESPONSE FACTOR6 (ARF6) and ARF8 and TRANSPORT INHIBITOR RESPONSE1 as well as the indirect control of components via direct expression of a microRNA-encoding gene. We demonstrate interaction between auxin and gibberellic acid in the promotion of SE and document an inverse correlation between bioactive gibberellic acid and SE in soybean, a difficult crop to transform. Finally, we relate hormone accumulation to transcript accumulation of important soybean embryo regulatory factors such as ABSCISIC ACID INSENSITIVE3 and FUSCA3 and provide a working model of hormone and transcription factor interaction in the control of SE.
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Affiliation(s)
- Qiaolin Zheng
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky 40546-0312
| | - Yumei Zheng
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky 40546-0312
| | - Huihua Ji
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky 40546-0312
| | - Whitney Burnie
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky 40546-0312
| | - Sharyn E Perry
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky 40546-0312
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Merino I, Abrahamsson M, Sterck L, Craven-Bartle B, Canovas F, von Arnold S. Transcript profiling for early stages during embryo development in Scots pine. BMC PLANT BIOLOGY 2016; 16:255. [PMID: 27863470 PMCID: PMC5116219 DOI: 10.1186/s12870-016-0939-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/28/2016] [Indexed: 05/22/2023]
Abstract
BACKGROUND Characterization of the expression and function of genes regulating embryo development in conifers is interesting from an evolutionary point of view. However, our knowledge about the regulation of embryo development in conifers is limited. During early embryo development in Pinus species the proembyo goes through a cleavage process, named cleavage polyembryony, giving rise to four embryos. One of these embryos develops to a dominant embryo, which will develop further into a mature, cotyledonary embryo, while the other embryos, the subordinate embryos, are degraded. The main goal of this study has been to identify processes that might be important for regulating the cleavage process and for the development of a dominant embryo. RESULTS RNA samples from embryos and megagametophytes at four early developmental stages during seed development in Pinus sylvestris were subjected to high-throughput sequencing. A total of 6.6 million raw reads was generated, resulting in 121,938 transcripts, out of which 36.106 contained ORFs. 18,638 transcripts were differentially expressed (DETs) in embryos and megagametophytes. GO enrichment analysis of transcripts up-regulated in embryos showed enrichment for different cellular processes, while those up-regulated in megagametophytes were enriched for accumulation of storage material and responses to stress. The highest number of DETs was detected during the initiation of the cleavage process. Transcripts related to embryogenic competence, cell wall modifications, cell division pattern, axis specification and response to hormones and stress were highly abundant and differentially expressed during early embryo development. The abundance of representative DETs was confirmed by qRT-PCR analyses. CONCLUSION Based on the processes identified in the GO enrichment analyses and the expression of the selected transcripts we suggest that (i) processes related to embryogenic competence and cell wall loosening are involved in activating the cleavage process; (ii) apical-basal polarization is strictly regulated in dominant embryos but not in the subordinate embryos; (iii) the transition from the morphogenic phase to the maturation phase is not completed in subordinate embryos. This is the first genome-wide transcript expression profiling of the earliest stages during embryo development in a Pinus species. Our results can serve as a framework for future studies to reveal the functions of identified genes.
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Affiliation(s)
- Irene Merino
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7080, 750 07 Uppsala, Sweden
| | - Malin Abrahamsson
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7080, 750 07 Uppsala, Sweden
| | - Lieven Sterck
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, B-9000 Belgium
| | - Blanca Craven-Bartle
- Department of Molecular Biology and Biochemistry, School of Sciences, Campus de Teatinos, Universidad de Malaga, 29071 Malaga, Spain
| | - Francisco Canovas
- Department of Molecular Biology and Biochemistry, School of Sciences, Campus de Teatinos, Universidad de Malaga, 29071 Malaga, Spain
| | - Sara von Arnold
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Box 7080, 750 07 Uppsala, Sweden
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Rocha DI, Pinto DLP, Vieira LM, Tanaka FAO, Dornelas MC, Otoni WC. Cellular and molecular changes associated with competence acquisition during passion fruit somatic embryogenesis: ultrastructural characterization and analysis of SERK gene expression. PROTOPLASMA 2016; 253:595-609. [PMID: 26008651 DOI: 10.1007/s00709-015-0837-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/17/2015] [Indexed: 05/18/2023]
Abstract
The integration of cellular and molecular data is essential for understanding the mechanisms involved in the acquisition of competence by plant somatic cells and the cytological changes that underlie this process. In the present study, we investigated the dynamics and fate of Passiflora edulis Sims cotyledon explants that were committed to somatic embryogenesis by characterizing the associated ultrastructural events and analysing the expression of a putative P. edulis ortholog of the Somatic Embryogenesis Receptor-like Kinase (SERK) gene. Embryogenic calli were obtained from zygotic embryo explants cultured on Murashige and Skoog medium supplemented with 2,4-dichlorophenoxyacetic acid and 6-benzyladenine. Callus formation was initiated by the division of cells derived from the protodermal and subprotodermal cells on the abaxial side of the cotyledons. The isodiametric protodermal cells of the cotyledon explants adopted a columnar shape and became meristematic at the onset of PeSERK expression, which was not initially detected in explant cells. Therefore, we propose that these changes represent the first observable steps towards the acquisition of a competent state within this regeneration system. PeSERK expression was limited to the early stages of somatic embryogenesis; the expression of this gene was confined to proembryogenic zones and was absent in the embryos after the globular stage. Our data also demonstrated that the dynamics of the mobilization of reserve compounds correlated with the differentiation of the embryogenic callus.
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Affiliation(s)
- Diego Ismael Rocha
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Rua Monteiro Lobato 255, Campinas, SP, 13083-862, Brazil
| | - Daniela Lopes Paim Pinto
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà, Pisa, TC, 56127, Italy
| | - Lorena Melo Vieira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Av. P.H. Rolfs, Viçosa, MG, 36570-900, Brazil
| | - Francisco André Ossamu Tanaka
- Departamento de Fitopatologia e Nematologia, Núcleo de Apoio à Pesquisa em Microscopia Eletrônica Aplicada à Agricultura, Universidade de São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Marcelo Carnier Dornelas
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Rua Monteiro Lobato 255, Campinas, SP, 13083-862, Brazil
| | - Wagner Campos Otoni
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Av. P.H. Rolfs, Viçosa, MG, 36570-900, Brazil.
- Departamento de Biologia Vegetal, Laboratório de Cultura de Tecidos/BIOAGRO, Campus Universitário, Universidade Federal de Viçosa, Avenida Peter Henry Rolfs s/n, 36570-900, Viçosa, MG, Brazil.
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Shi X, Zhang C, Liu Q, Zhang Z, Zheng B, Bao M. De novo comparative transcriptome analysis provides new insights into sucrose induced somatic embryogenesis in camphor tree (Cinnamomum camphora L.). BMC Genomics 2016; 17:26. [PMID: 26727885 PMCID: PMC4700650 DOI: 10.1186/s12864-015-2357-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 09/11/2015] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Somatic embryogenesis is a notable illustration of cell totipotency, by which somatic cells undergo dedifferentiation and then differentiate into somatic embryos. Our previous work demonstrated that pretreatment of immature zygotic embryos with 0.5 M sucrose solution for 72 h efficiently induced somatic embryo initiation in camphor tree. To better understand the molecular basis of somatic embryogenesis induced by osmotic stress, de novo transcriptome sequencing of three tissues of camphor tree (immature zygotic embryos, sucrose-pretreated immature zygotic embryos, and somatic embryos induced from sucrose-pretreated zygotic embryos) were conducted using Illumina Hiseq 2000 platform. RESULTS A total of 30.70 G high quality clean reads were obtained from cDNA libraries of the three samples. The overall de novo assembly of cDNA sequence data generated 205592 transcripts, with an average length of 998 bp. 114229 unigenes (55.56 % of all transcripts) with an average length of 680 bp were annotated with gene descriptions, gene ontology terms or metabolic pathways based on Blastx search against Nr, Nt, Swissprot, GO, COG/KOG, and KEGG databases. CEGMA software identified 237 out of 248 ultra-conserved core proteins as 'complete' in the transcriptome assembly, showing a completeness of 95.6 %. A total of 897 genes previously annotated to be potentially involved in somatic embryogenesis were identified. Comparative transcriptome analysis showed that a total of 3335 genes were differentially expressed in the three samples. The differentially expressed genes were divided into six groups based on K-means clustering. Expression level analysis of 52 somatic embryogenesis-related genes indicated a high correlation between RNA-seq and qRT-PCR data. Gene enrichment analysis showed significantly differential expression of genes responding to stress and stimulus. CONCLUSIONS The present work reported a de novo transcriptome assembly and global analysis focused on gene expression changes during initiation and formation of somatic embryos in camphor tree. Differential expression of somatic embryogenesis-related genes indicates that sucrose induced somatic embryogenesis may share or partly share the mechanisms of somatic embryogenesis induced by plant hormones. This study provides comprehensive transcript information and gene expression data for camphor tree. It could also serve as an important platform resource for further functional studies in plant embryogenesis.
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Affiliation(s)
- Xueping Shi
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
| | - Cuijie Zhang
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
| | - Qinhong Liu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
| | - Zhe Zhang
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
| | - Bo Zheng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
| | - Manzhu Bao
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
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Wang W, Li H, Lin X, Yang S, Wang Z, Fang B. Transcriptome analysis identifies genes involved in adventitious branches formation of Gracilaria lichenoides in vitro. Sci Rep 2015; 5:17099. [PMID: 26657019 PMCID: PMC4675990 DOI: 10.1038/srep17099] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 10/26/2015] [Indexed: 11/23/2022] Open
Abstract
Tissue culture could solve the problems associated with Gracilaria cultivation, including the consistent supply of high-quality seed stock, strain improvement, and efficient mass culture of high-yielding commercial strains. However, STC lags behind that of higher plants because of the paucity of genomic information. Transcriptome analysis and the identification of potential unigenes involved in the formation and regeneration of callus or direct induction of ABs are essential. Herein, the CK, EWAB and NPA G. lichenoides transcriptomes were analyzed using the Illumina sequencing platform in first time. A total of 17,922,453,300 nucleotide clean bases were generated and assembled into 21,294 unigenes, providing a total gene space of 400,912,038 nucleotides with an average length of 1,883 and N 50 of 5,055 nucleotides and a G + C content of 52.02%. BLAST analysis resulted in the assignment of 13,724 (97.5%), 3,740 (26.6%), 9,934 (70.6%), 10,611 (75.4%), 9,490 (67.4%), and 7,773 (55.2%) unigenes were annotated to the NR, NT, Swiss-Prot, KEGG, COG, and GO databases, respectively, and the total of annotated unigenes was 14,070. A total of 17,099 transcripts were predicted to possess open reading frames, including 3,238 predicted and 13,861 blasted based on protein databases. In addition, 3,287 SSRs were detected in G.lichenoides, providing further support for genetic variation and marker-assisted selection in the future. Our results suggest that auxin polar transport, auxin signal transduction, crosstalk with other endogenous plant hormones and antioxidant systems, play important roles for ABs formation in G. lichenoides explants in vitro. The present findings will facilitate further studies on gene discovery and on the molecular mechanisms underlying the tissue culture of seaweed.
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Affiliation(s)
- Wenlei Wang
- College of Biochemistry and Engineering, Xiamen University, Xiamen 361005, China
| | - Huanqin Li
- College of Ocean and Earth Sciences, Xiamen University, Xiamen 361005, China
| | - Xiangzhi Lin
- Engineering Research Center of Marine Biological Resource Comprehensive Utilization, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, China
| | - Shanjun Yang
- Engineering Research Center of Marine Biological Resource Comprehensive Utilization, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, China
| | - Zhaokai Wang
- Engineering Research Center of Marine Biological Resource Comprehensive Utilization, Third Institute of Oceanography, State Oceanic Administration, Xiamen 361005, China
| | - Baishan Fang
- College of Biochemistry and Engineering, Xiamen University, Xiamen 361005, China
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