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Izuno A, Maruyama TE, Ueno S, Ujino-Ihara T, Moriguchi Y. Genotype and transcriptome effects on somatic embryogenesis in Cryptomeria japonica. PLoS One 2020; 15:e0244634. [PMID: 33373415 PMCID: PMC7771663 DOI: 10.1371/journal.pone.0244634] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 12/14/2020] [Indexed: 12/31/2022] Open
Abstract
Somatic embryogenesis (SE), which is in vitro regeneration of plant bodies from somatic cells, represents a useful means of clonal propagation and genetic engineering of forest trees. While protocols to obtain calluses and induce regeneration in somatic embryos have been reported for many tree species, the knowledge of molecular mechanisms of SE development is still insufficient to achieve an efficient supply of somatic embryos required for the industrial application. Cryptomeria japonica, a conifer species widely used for plantation forestry in Japan, is one of the tree species waiting for a secure SE protocol; the probability of normal embryo development appears to depend on genotype. To discriminate the embryogenic potential of embryonal masses (EMs) and efficiently obtain normal somatic embryos of C. japonica, we investigated the effects of genotype and transcriptome on the variation in embryogenic potential. Using an induction experiment with 12 EMs each from six genotypes, we showed that embryogenic potential differs between/within genotypes. Comparisons of gene expression profiles among EMs with different embryogenic potentials revealed that 742 differently expressed genes were mainly associated with pattern forming and metabolism. Thus, we suggest that not only genotype but also gene expression profiles can determine success in SE development. Consistent with previous findings for other conifer species, genes encoding leafy cotyledon, wuschel, germin-like proteins, and glutathione-S-transferases are likely to be involved in SE development in C. japonica and indeed highly expressed in EMs with high-embryogenic potential; therefore, these proteins represent candidate markers for distinguishing embryogenic potential.
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Affiliation(s)
- Ayako Izuno
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
- * E-mail:
| | - Tsuyoshi E. Maruyama
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Saneyoshi Ueno
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Tokuko Ujino-Ihara
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | - Yoshinari Moriguchi
- Graduate School of Science and Technology, Niigata University, Niigata, Japan
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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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Reis RS, Vale EDM, Heringer AS, Santa-Catarina C, Silveira V. Putrescine induces somatic embryo development and proteomic changes in embryogenic callus of sugarcane. J Proteomics 2016; 130:170-9. [DOI: 10.1016/j.jprot.2015.09.029] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 08/27/2015] [Accepted: 09/21/2015] [Indexed: 01/29/2023]
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dos Santos ALW, Elbl P, Navarro BV, de Oliveira LF, Salvato F, Balbuena TS, Floh EIS. Quantitative proteomic analysis of Araucaria angustifolia (Bertol.) Kuntze cell lines with contrasting embryogenic potential. J Proteomics 2016; 130:180-9. [DOI: 10.1016/j.jprot.2015.09.027] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 08/26/2015] [Accepted: 09/22/2015] [Indexed: 12/21/2022]
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Tao L, Zhao Y, Wu Y, Wang Q, Yuan H, Zhao L, Guo W, You X. Transcriptome profiling and digital gene expression by deep sequencing in early somatic embryogenesis of endangered medicinal Eleutherococcus senticosus Maxim. Gene 2015; 578:17-24. [PMID: 26657036 DOI: 10.1016/j.gene.2015.11.050] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 11/21/2015] [Accepted: 11/30/2015] [Indexed: 11/19/2022]
Abstract
Somatic embryogenesis (SE) has been studied as a model system to understand molecular events in physiology, biochemistry, and cytology during plant embryo development. In particular, it is exceedingly difficult to access the morphological and early regulatory events in zygotic embryos. To understand the molecular mechanisms regulating early SE in Eleutherococcus senticosus Maxim., we used high-throughput RNA-Seq technology to investigate its transcriptome. We obtained 58,327,688 reads, which were assembled into 75,803 unique unigenes. To better understand their functions, the unigenes were annotated using the Clusters of Orthologous Groups, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes databases. Digital gene expression libraries revealed differences in gene expression profiles at different developmental stages (embryogenic callus, yellow embryogenic callus, global embryo). We obtained a sequencing depth of >5.6 million tags per sample and identified many differentially expressed genes at various stages of SE. The initiation of SE affected gene expression in many KEGG pathways, but predominantly that in metabolic pathways, biosynthesis of secondary metabolites, and plant hormone signal transduction. This information on the changes in the multiple pathways related to SE induction in E. senticosus Maxim. embryogenic tissue will contribute to a more comprehensive understanding of the mechanisms involved in early SE. Additionally, the differentially expressed genes may act as molecular markers and could play very important roles in the early stage of SE. The results are a comprehensive molecular biology resource for investigating SE of E. senticosus Maxim.
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Affiliation(s)
- Lei Tao
- College of Life Sciences, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Yue Zhao
- College of Life Sciences, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Ying Wu
- College of Life Sciences, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Qiuyu Wang
- College of Life Sciences, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Hongmei Yuan
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Lijuan Zhao
- Crop Breeding Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Wendong Guo
- Institute of Natural Resources and Ecology, Heilongjiang Academy of Sciences, Harbin 150040, China
| | - Xiangling You
- College of Life Sciences, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China.
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Salvo SAGD, Hirsch CN, Buell CR, Kaeppler SM, Kaeppler HF. Whole transcriptome profiling of maize during early somatic embryogenesis reveals altered expression of stress factors and embryogenesis-related genes. PLoS One 2014; 9:e111407. [PMID: 25356773 PMCID: PMC4214754 DOI: 10.1371/journal.pone.0111407] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 10/01/2014] [Indexed: 01/09/2023] Open
Abstract
Embryogenic tissue culture systems are utilized in propagation and genetic engineering of crop plants, but applications are limited by genotype-dependent culture response. To date, few genes necessary for embryogenic callus formation have been identified or characterized. The goal of this research was to enhance our understanding of gene expression during maize embryogenic tissue culture initiation. In this study, we highlight the expression of candidate genes that have been previously regarded in the literature as having important roles in somatic embryogenesis. We utilized RNA based sequencing (RNA-seq) to characterize the transcriptome of immature embryo explants of the highly embryogenic and regenerable maize genotype A188 at 0, 24, 36, 48, and 72 hours after placement of explants on tissue culture initiation medium. Genes annotated as functioning in stress response, such as glutathione-S-transferases and germin-like proteins, and genes involved with hormone transport, such as PINFORMED, increased in expression over 8-fold in the study. Maize genes with high sequence similarity to genes previously described in the initiation of embryogenic cultures, such as transcription factors BABY BOOM, LEAFY COTYLEDON, and AGAMOUS, and important receptor-like kinases such as SOMATIC EMBRYOGENESIS RECEPTOR LIKE KINASES and CLAVATA, were also expressed in this time course study. By combining results from whole genome transcriptome analysis with an in depth review of key genes that play a role in the onset of embryogenesis, we propose a model of coordinated expression of somatic embryogenesis-related genes, providing an improved understanding of genomic factors involved in the early steps of embryogenic culture initiation in maize and other plant species.
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Affiliation(s)
- Stella A. G. D. Salvo
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Candice N. Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America
| | - C. Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, Michigan, United States of America
| | - Shawn M. Kaeppler
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Heidi F. Kaeppler
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin, United States of America
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Almeida AM, Parreira JR, Santos R, Duque AS, Francisco R, Tomé DFA, Ricardo CP, Coelho AV, Fevereiro P. A proteomics study of the induction of somatic embryogenesis in Medicago truncatula using 2DE and MALDI-TOF/TOF. PHYSIOLOGIA PLANTARUM 2012; 146:236-49. [PMID: 22497501 DOI: 10.1111/j.1399-3054.2012.01633.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Medicago truncatula is a model legume, whose genome is currently being sequenced. Somatic embryogenesis (SE) is a genotype-dependent character and not yet fully understood. In this study, a proteomic approach was used to compare the induction and expression phases of SE of both the highly embryogenic line M9-10a of M. truncatula cv. Jemalong and its non-embryogenic predecessor line, M9. The statistical analysis between the lines revealed 136 proteins with significant differential expression (P < 0.05). Of these, 5 had a presence/absence pattern in M9 vs M9-10a and 22 showed an at least twofold difference in terms of spot volume, were considered of particular relevance to the SE process and therefore chosen for identification. Spots were excised in gel digested with trypsin and proteins were identified using matrix-assisted laser desorption ionization-time of flight/time of flight. Identified proteins indicated a higher adaptability of the embryogenic line toward the stress imposed by the inducing culture conditions. Also, some proteins were shown to have a dual pattern of expression: peroxidase, pyrophosphatase and aspartate aminotransferase. These proteins showed higher expression during the induction phases of the M9 line, whereas in the embryogenic line had higher expression at stages coinciding with embryo formation.
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Affiliation(s)
- André M Almeida
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal.
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