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Shin NR, Shin YH, Kim HS, Park YD. Function Analysis of the PR55/ B Gene Related to Self-Incompatibility in Chinese Cabbage Using CRISPR/Cas9. Int J Mol Sci 2022; 23:ijms23095062. [PMID: 35563453 PMCID: PMC9102814 DOI: 10.3390/ijms23095062] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 02/06/2023] Open
Abstract
Chinese cabbage, a major crop in Korea, shows self-incompatibility (SI). SI is controlled by the type 2A serine/threonine protein phosphatases (PP2As). The PP2A gene is controlled by regulatory subunits that comprise a 36 kDa catalyst C subunit, a 65 kDa regulatory A subunit, and a variety of regulatory B subunits (50–70 kDa). Among them, the PP2A 55 kDa B regulatory subunit (PR55/B) gene located in the A05 chromosome has 13 exons spanning 2.9 kb, and two homologous genes, Bra018924 and Bra014296, were found to be present on the A06 and A08 chromosome, respectively. In this study, we performed a functional analysis of the PR55/B gene using clustered regularly interspaced short palindromic repeats/CRISPR-associated system 9 (CRISPR/Cas9)-mediated gene mutagenesis. CRISPR/Cas9 technology can be used to easily introduce mutations in the target gene. Tentative gene-edited lines were generated by the Agrobacterium-mediated transfer and were selected by PCR and Southern hybridization analysis. Furthermore, pods were confirmed to be formed in flower pollination (FP) as well as bud pollination (BP) in some gene-edited lines. Seed fertility of gene-edited lines indicated that the PR55/B gene plays a key role in SI. Finally, self-compatible T-DNA-free T2 gene-edited plants and edited sequences of target genes were secured. The self-compatible Chinese cabbage developed in this study is expected to contribute to Chinese cabbage breeding.
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Genome-Wide Identification and Analysis of TCP Transcription Factors Involved in the Formation of Leafy Head in Chinese Cabbage. Int J Mol Sci 2018. [PMID: 29538304 PMCID: PMC5877708 DOI: 10.3390/ijms19030847] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Chinese cabbage (Brassica rapa L. ssp. pekinensis) is a widely cultivated and economically important vegetable crop with typical leaf curvature. The TCP (Teosinte branched1, Cycloidea, Proliferating cell factor) family proteins are plant-specific transcription factors (TFs) and play important roles in many plant biological processes, especially in the regulation of leaf curvature. In this study, 39 genes encoding TCP TFs are detected on the whole genome of B. rapa. Based on the phylogenetic analysis of TCPs between Arabidopsis thaliana and Brassica rapa, TCP genes of Chinese cabbage are named from BrTCP1a to BrTCP24b. Moreover, the chromosomal location; phylogenetic relationships among B. rapa, A. thaliana, and rice; gene structures and protein conserved sequence alignment; and conserved domains are analyzed. The expression profiles of BrTCPs are analyzed in different tissues. To understand the role of Chinese cabbage TCP members in regulating the curvature of leaves, the expression patterns of all BrTCP genes are detected at three development stages essential for leafy head formation. Our results provide information on the classification and details of BrTCPs and allow us to better understand the function of TCPs involved in leaf curvature of Chinese cabbage.
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Kim MS, Hong S, Devaraj SP, Im S, Kim JR, Lim YP. Identification and characterization of the leaf specific networks of inner and rosette leaves in Brassica rapa. Biochem Biophys Res Commun 2017. [PMID: 28647368 DOI: 10.1016/j.bbrc.2017.06.123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Inner and rosette leaves of Chinese cabbage (Brassica rapa) have different characteristics in terms of nutritional value, appearance, taste, color and texture. Many researchers have utilized differentially expressed genes for exploring the difference between inner and rosette leaves of Brassica rapa. The functional characteristics of a gene, however, is determined by complex interactions between genes. Hence, a noble network approach is required for elucidating such functional difference that is not captured by gene expression profiles alone. In this study, we measured gene expression in the standard cabbage genome by RNA-Sequencing and constructed rosette and inner leaf networks based on the gene expression profiles. Furthermore, we compared the topological and functional characteristics of these networks. We found significant functional difference between the rosette and inner leaf networks. Specifically, we found that the genes in the rosette leaf network were associated with homeostasis and response to external stimuli whereas the genes in the inner leaf network were mainly related to the glutamine biosynthesis processes and developmental processes with hormones. Overall, the network approach provides an insight into the functional difference of the two leaves.
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Affiliation(s)
- Man-Sun Kim
- Department of Horticulture, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, South Korea.
| | - Seongmin Hong
- Department of Horticulture, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, South Korea.
| | - Sangeeth Prasath Devaraj
- Department of Horticulture, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, South Korea.
| | - Subin Im
- Department of Horticulture, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, South Korea.
| | - Jeong-Rae Kim
- Department of Mathematics, University of Seoul, 163 Seoulsiripdaero, Dongdaemun-gu, Seoul 02504, South Korea.
| | - Yong Pyo Lim
- Department of Horticulture, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, South Korea.
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Kim JS, Kim J, Lee TH, Jun KM, Kim TH, Kim YH, Park HM, Jeon JS, An G, Yoon UH, Nahm BH, Kim YK. FSTVAL: a new web tool to validate bulk flanking sequence tags. PLANT METHODS 2012; 8:19. [PMID: 22709793 PMCID: PMC3439307 DOI: 10.1186/1746-4811-8-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 06/18/2012] [Indexed: 06/01/2023]
Abstract
BACKGROUND Information about a transgene locus is one of the major concerns in transgenic research because expression of the transgene or a gene interrupted by the integration event could be affected. Thus, the flanking sequences obtained from transgenic plants need to be analyzed in terms of genomic context, such as genic and intergenic regions. This process may consist of several steps: 1) elimination of a vector sequence from the flanking sequence, 2) finding the locations in the target genome, and 3) statistics of the integration sites. These steps could be automated for flanking sequences from several dozens of transgenic plants generated in an ordinary targeted gene expression strategy. It would be indispensable in a genome-wide mutagenesis screen using T-DNA or transposons because these projects often generate several thousands of transgenic lines and just as many loci of the transgene among the transgenic plants. RESULTS We present an open access web tool, flanking sequence tags validator (FSTVAL), to manage bulk flanking sequence tags (FSTs). FSTVAL automatically evaluates the FSTs and finds the best mapping positions of the FST against a known genome sequence. The statistics, in terms of genic and intergenic regions, are presented as a table, a distribution map, and a frequency graph along the chromosomes. Currently, 17 plant genome sequences, including Arabidopsis thaliana, Oryza sativa, and Glycine max, are available as reference genomes. We evaluated the utility and accuracy of the tool with 5,144 rice FSTs. The whole process, from uploading the sequences to generating tables of insertions, required a few minutes, with less than 4 clicks in the web environment. CONCLUSIONS Run for 1 year and tested over 1,000 times, we have confirmed FSTVAL efficiently handles bulk FSTs. FSTVAL is freely available without login at http://bioinfo.mju.ac.kr/fstval/.
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Affiliation(s)
- Joung Sug Kim
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyonggido, 449-728, South Korea
| | - Jiye Kim
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyonggido, 449-728, South Korea
| | - Tae-Ho Lee
- Genomics Genetics Institute, GreenGene BioTech Inc. Yongin, Yongin, Kyonggido, 449-728, South Korea
| | - Kyong Mi Jun
- Genomics Genetics Institute, GreenGene BioTech Inc. Yongin, Yongin, Kyonggido, 449-728, South Korea
| | - Tea Hoon Kim
- Genomics Genetics Institute, GreenGene BioTech Inc. Yongin, Yongin, Kyonggido, 449-728, South Korea
| | - Yul-Ho Kim
- Upland Crop Research division, National Institute of Crop Science, Suwon, 441-857, South Korea
| | - Hyang-Mi Park
- Upland Crop Research division, National Institute of Crop Science, Suwon, 441-857, South Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology, Kyung Hee University, Yongin, 446-701, South Korea
| | - Gynheung An
- Graduate School of Biotechnology, Kyung Hee University, Yongin, 446-701, South Korea
| | - Ung-Han Yoon
- National Academy of Agricultural Science, Rural Development Administration, Suwon, 441-707, South Korea
| | - Baek Hie Nahm
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Kyonggido, 449-728, South Korea
- Genomics Genetics Institute, GreenGene BioTech Inc. Yongin, Yongin, Kyonggido, 449-728, South Korea
| | - Yeon-Ki Kim
- Genomics Genetics Institute, GreenGene BioTech Inc. Yongin, Yongin, Kyonggido, 449-728, South Korea
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Gase K, Weinhold A, Bozorov T, Schuck S, Baldwin IT. Efficient screening of transgenic plant lines for ecological research. Mol Ecol Resour 2011; 11:890-902. [PMID: 21518300 DOI: 10.1111/j.1755-0998.2011.03017.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Plants stably transformed to manipulate the expression of genes mediating ecological performance have profoundly altered research in plant ecology. Agrobacterium-mediated transformation remains the most effective method of creating plants harbouring a limited number of transgene integrations of low complexity. For ecological/physiological research, the following requirements must be met: (i) the regenerated plants should have the same ploidy level as the corresponding wild-type plant and (ii) contain a single transgene copy in a homozygous state; (iii) the T-DNA must be completely inserted without vector backbone sequence and all its elements functional; and (iv) the integration should not change the phenotype of the plant by interrupting chromosomal genes or by mutations occurring during the regeneration procedure. The screening process to obtain transformed plants that meet the above criteria is costly and time-consuming, and an optimized screening procedure is presented. We developed a flow chart that optimizes the screening process to efficiently select transformed plants for ecological research. It consists of segregational analyses, which select transgenic T₁ and T₂ generation plants with single T-DNA copies that are homozygous. Indispensable molecular genetic tests (flow cytometry, diagnostic PCRs and Southern blotting) are performed at the earliest and most effective times in the screening process. qPCR to quantify changes in transcript accumulation to confirm gene silencing or overexpression is the last step in the selection process. Because we routinely transform the wild tobacco, Nicotiana attenuata, with constructs that silence or ectopically overexpress ecologically relevant genes, the proposed protocol is supported by examples from this system.
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Affiliation(s)
- Klaus Gase
- Department of Molecular Ecology, Max-Planck-Institute for Chemical Ecology, Hans-Knoell-Strasse 8, 07745 Jena, Germany
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Abe H, Narusaka Y, Sasaki I, Hatakeyama K, Shin-I S, Narusaka M, Fukami-Kobayashi K, Matsumoto S, Kobayashi M. Development of full-length cDNAs from Chinese cabbage (Brassica rapa Subsp. pekinensis) and identification of marker genes for defence response. DNA Res 2011; 18:277-89. [PMID: 21745830 PMCID: PMC3158467 DOI: 10.1093/dnares/dsr018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2011] [Accepted: 05/25/2011] [Indexed: 11/13/2022] Open
Abstract
Arabidopsis belongs to the Brassicaceae family and plays an important role as a model plant for which researchers have developed fine-tuned genome resources. Genome sequencing projects have been initiated for other members of the Brassicaceae family. Among these projects, research on Chinese cabbage (Brassica rapa subsp. pekinensis) started early because of strong interest in this species. Here, we report the development of a library of Chinese cabbage full-length cDNA clones, the RIKEN BRC B. rapa full-length cDNA (BBRAF) resource, to accelerate research on Brassica species. We sequenced 10 000 BBRAF clones and confirmed 5476 independent clones. Most of these cDNAs showed high homology to Arabidopsis genes, but we also obtained more than 200 cDNA clones that lacked any sequence homology to Arabidopsis genes. We also successfully identified several possible candidate marker genes for plant defence responses from our analysis of the expression of the Brassica counterparts of Arabidopsis marker genes in response to salicylic acid and jasmonic acid. We compared gene expression of these markers in several Chinese cabbage cultivars. Our BBRAF cDNA resource will be publicly available from the RIKEN Bioresource Center and will help researchers to transfer Arabidopsis-related knowledge to Brassica crops.
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Affiliation(s)
- Hiroshi Abe
- Experimental Plant Division, Department of Biological Systems, RIKEN BioResource Center, Koyadai, Tsukuba, Ibaraki, Japan.
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