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      • Record: found
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      Identification and expression analysis of GRAS transcription factors in the wild relative of sweet potato Ipomoea trifida

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          Abstract

          Background

          GRAS gene is an important transcription factor gene family that plays a crucial role in plant growth, development, adaptation to adverse environmental condition. Sweet potato is an important food, vegetable, industrial raw material, and biofuel crop in the world, which plays an essential role in food security in China . However, the function of sweet potato GRAS genes remains unknown.

          Results

          In this study, we identified and characterised 70 GRAS members from Ipomoea trifida, which is the progenitor of sweet potato. The chromosome distribution, phylogenetic tree, exon-intron structure and expression profiles were analysed. The distribution map showed that GRAS genes were randomly located in 15 chromosomes. In combination with phylogenetic analysis and previous reports in Arabidopsis and rice, the GRAS proteins from I. trifida were divided into 11 subfamilies. Gene structure showed that most of the GRAS genes in I. trifida lacked introns. The tissue-specific expression patterns and the patterns under abiotic stresses of ItfGRAS genes were investigated via RNA-seq and further tested by RT-qPCR. Results indicated the potential functions of ItfGRAS during plant development and stress responses.

          Conclusions

          Our findings will further facilitate the functional study of GRAS gene and molecular breeding of sweet potato.

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          Most cited references35

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          [GSDS: a gene structure display server].

          An-Yuan Guo, Qi-Hui Zhu, Xin CHEN … (2007)
          We developed a web server GSDS (Gene Structure Display Server) for drawing gene structure schematic diagrams. Users can submit three types of dataCDS and genomic sequences, NCBI GenBank accession numbers or GIs, exon positions on a gene. GSDS uses this information to obtain the gene structure and draw diagram for it. Users can also designate some special regions to mark on the gene structure diagram. The output result will be PNG or SVG format picture. The corresponding sequence will be shown in a new window by clicking the picture in PNG format. A Chinese version for the main page is also built. The GSDS is available on http://gsds.cbi.pku.edu.cn/.
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            The cold-inducible CBF1 factor-dependent signaling pathway modulates the accumulation of the growth-repressing DELLA proteins via its effect on gibberellin metabolism.

            Patrick Achard, Fan Gong, Soizic Cheminant … (2008)
            Plants have evolved robust mechanisms to respond and adapt to unfavorable environmental conditions, such as low temperature. The C-repeat/drought-responsive element binding factor CBF1/DREB1b gene encodes a transcriptional activator transiently induced by cold that controls the expression of a set of genes responding to low temperature (the CBF regulon). Constitutive expression of CBF1 confers freezing tolerance but also slows growth. Here, we propose that low temperature-induced CBF1 expression restrains growth at least in part by allowing the accumulation of DELLAs, a family of nuclear growth-repressing proteins, the degradation of which is stimulated by gibberellin (GA). We show that cold/CBF1 enhances the accumulation of a green fluorescent protein (GFP)-tagged DELLA protein (GFP-RGA) by reducing GA content through stimulating expression of GA-inactivating GA 2-oxidase genes. Accordingly, transgenic plants that constitutively express CBF1 accumulate less bioactive GA and as a consequence exhibit dwarfism and late flowering. Both phenotypes are suppressed when CBF1 is expressed in a line lacking two DELLA proteins, GA-INSENSITIVE and REPRESSOR OF GA1-3. In addition, we show that DELLAs contribute significantly to CBF1-induced cold acclimation and freezing tolerance by a mechanism that is distinct from the CBF regulon. We conclude that DELLAs are components of the CBF1-mediated cold stress response.
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              F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress.

              Mukesh Jain, Aashima Nijhawan, Rita Arora … (2007)
              F-box proteins constitute a large family in eukaryotes and are characterized by a conserved F-box motif (approximately 40 amino acids). As components of the Skp1p-cullin-F-box complex, F-box proteins are critical for the controlled degradation of cellular proteins. We have identified 687 potential F-box proteins in rice (Oryza sativa), the model monocotyledonous plant, by a reiterative database search. Computational analysis revealed the presence of several other functional domains, including leucine-rich repeats, kelch repeats, F-box associated domain, domain of unknown function, and tubby domain in F-box proteins. Based upon their domain composition, they have been classified into 10 subfamilies. Several putative novel conserved motifs have been identified in F-box proteins, which do not contain any other known functional domain. An analysis of a complete set of F-box proteins in rice is presented, including classification, chromosomal location, conserved motifs, and phylogenetic relationship. It appears that the expansion of F-box family in rice, in large part, might have occurred due to localized gene duplications. Furthermore, comprehensive digital expression analysis of F-box protein-encoding genes has been complemented with microarray analysis. The results reveal specific and/or overlapping expression of rice F-box protein-encoding genes during floral transition as well as panicle and seed development. At least 43 F-box protein-encoding genes have been found to be differentially expressed in rice seedlings subjected to different abiotic stress conditions. The expression of several F-box protein-encoding genes is also influenced by light. The structure and function of F-box proteins in plants is discussed in light of these results and the published information. These data will be useful for prioritization of F-box proteins for functional validation in rice.
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                Author and article information

                Contributors
                Yao Chen: cytjghaohao@163.com
                Panpan Zhu: zhupanpan311@126.com
                Shaoyuan Wu: shaoyuanwu@outlook.com
                Yan Lu: luyan306@126.com
                Jian Sun: sunjian@jsnu.edu.cn
                Qinghe Cao: cqhe75@yahoo.com
                Zongyun Li: zongyunli@jsnu.edu.cn
                Tao Xu: xutao_yr@126.com
                Journal
                Journal ID (nlm-ta): BMC Genomics
                Journal ID (iso-abbrev): BMC Genomics
                Title: BMC Genomics
                Publisher: BioMed Central (London )
                ISSN (Electronic): 1471-2164
                Publication date (Electronic): 29 November 2019
                Publication date PMC-release: 29 November 2019
                Publication date Collection: 2019
                Volume: 20
                Electronic Location Identifier: 911
                Affiliations
                [1 ]ISNI 0000 0000 9698 6425, GRID grid.411857.e, Key lab of phylogeny and comparative genomics of the Jiangsu province, , Jiangsu Normal University, ; Xuzhou, Jiangsu Province, 221116 China
                [2 ]ISNI 0000 0001 0356 9399, GRID grid.14005.30, Department of Plant Biotechnology, College of Agriculture and Life Sciences, , Chonnam National University, ; Gwangju, 500-757 South Korea
                [3 ]Xuzhou Academy of Agricultural Sciences/Sweet Potato Research Institute, Xuzhou, 221121 Jiangsu China
                [4 ]ISNI 000000041936754X, GRID grid.38142.3c, Department of Organismic and Evolutionary Biology, , Harvard University, ; Cambridge, MA 02138 USA
                Article
                Publisher ID: 6316
                DOI: 10.1186/s12864-019-6316-7
                PMC ID: 6884806
                PubMed ID: 31783728
                SO-VID: 3f262ba4-9d5e-4692-807f-d5c78a20c632
                Copyright © © The Author(s). 2019
                License:

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                Date received : 27 March 2019
                Date accepted : 21 November 2019
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 31701481
                Award Recipient :
                Funded by: Natural Science Foundation of Jiangsu Higher Education Institutions of China
                Award ID: 19KJA510010
                Award Recipient :
                Funded by: Jiangsu Overseas Visiting Scholar Program for University Prominent Young & Middle-aged Teachers and Presidents
                Award ID: 2019
                Award Recipient :
                Funded by: Priority Academic Program Development of Jiangsu Higher Education Institutions
                Award ID: PAPD
                Award Recipient :
                Funded by: China Agriculture Research System
                Award ID: CARS-10-B03
                Award Recipient :
                Funded by: National Key R&D Program of China
                Award ID: 2018YFD1000705, 2018YFD1000700
                Award Recipient :
                Categories
                Subject: Research Article
                Custom metadata
                issue-copyright-statement © The Author(s) 2019

                ScienceOpen disciplines: Genetics
                Keywords: gras,transcription factor,sweet potato,ipomoea trifida,expression
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: gras, transcription factor, sweet potato, ipomoea trifida, expression

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