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Xu X, Passalacqua M, Rice B, Demesa-Arevalo E, Kojima M, Takebayashi Y, Harris B, Sakakibara H, Gallavotti A, Gillis J, Jackson D. Large-scale single-cell profiling of stem cells uncovers redundant regulators of shoot development and yield trait variation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.04.583414. [PMID: 38496543 PMCID: PMC10942292 DOI: 10.1101/2024.03.04.583414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Stem cells in plant shoots are a rare population of cells that produce leaves, fruits and seeds, vital sources for food and bioethanol. Uncovering regulators expressed in these stem cells will inform crop engineering to boost productivity. Single-cell analysis is a powerful tool for identifying regulators expressed in specific groups of cells. However, accessing plant shoot stem cells is challenging. Recent single-cell analyses of plant shoots have not captured these cells, and failed to detect stem cell regulators like CLAVATA3 and WUSCHEL . In this study, we finely dissected stem cell-enriched shoot tissues from both maize and arabidopsis for single-cell RNA-seq profiling. We optimized protocols to efficiently recover thousands of CLAVATA3 and WUSCHEL expressed cells. A cross-species comparison identified conserved stem cell regulators between maize and arabidopsis. We also performed single-cell RNA-seq on maize stem cell overproliferation mutants to find additional candidate regulators. Expression of candidate stem cell genes was validated using spatial transcriptomics, and we functionally confirmed roles in shoot development. These candidates include a family of ribosome-associated RNA-binding proteins, and two families of sugar kinase genes related to hypoxia signaling and cytokinin hormone homeostasis. These large-scale single-cell profiling of stem cells provide a resource for mining stem cell regulators, which show significant association with yield traits. Overall, our discoveries advance the understanding of shoot development and open avenues for manipulating diverse crops to enhance food and energy security.
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Rieu P, Arnoux-Courseaux M, Tichtinsky G, Parcy F. Thinking outside the F-box: how UFO controls angiosperm development. THE NEW PHYTOLOGIST 2023; 240:945-959. [PMID: 37664990 DOI: 10.1111/nph.19234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/19/2023] [Indexed: 09/05/2023]
Abstract
The formation of inflorescences and flowers is essential for the successful reproduction of angiosperms. In the past few decades, genetic studies have identified the LEAFY transcription factor and the UNUSUAL FLORAL ORGANS (UFO) F-box protein as two major regulators of flower development in a broad range of angiosperm species. Recent research has revealed that UFO acts as a transcriptional cofactor, redirecting the LEAFY floral regulator to novel cis-elements. In this review, we summarize the various roles of UFO across species, analyze past results in light of new discoveries and highlight the key questions that remain to be solved.
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Affiliation(s)
- Philippe Rieu
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 ave des martyrs, F-38054, Grenoble, France
| | - Moïra Arnoux-Courseaux
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 ave des martyrs, F-38054, Grenoble, France
| | - Gabrielle Tichtinsky
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 ave des martyrs, F-38054, Grenoble, France
| | - François Parcy
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 ave des martyrs, F-38054, Grenoble, France
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3
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Han J, Mendell JT. MicroRNA turnover: a tale of tailing, trimming, and targets. Trends Biochem Sci 2023; 48:26-39. [PMID: 35811249 PMCID: PMC9789169 DOI: 10.1016/j.tibs.2022.06.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/06/2022] [Accepted: 06/13/2022] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) post-transcriptionally repress gene expression by guiding Argonaute (AGO) proteins to target mRNAs. While much is known about the regulation of miRNA biogenesis, miRNA degradation pathways are comparatively poorly understood. Although miRNAs generally exhibit slow turnover, they can be rapidly degraded through regulated mechanisms that act in a context- or sequence-specific manner. Recent work has revealed a particularly important role for specialized target interactions in controlling rates of miRNA degradation. Engagement of these targets is associated with the addition and removal of nucleotides from the 3' ends of miRNAs, a process known as tailing and trimming. Here we review these mechanisms of miRNA modification and turnover, highlighting the contexts in which they impact miRNA stability and discussing important questions that remain unanswered.
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Affiliation(s)
- Jaeil Han
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Joshua T Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA.
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Chahtane H, Lai X, Tichtinsky G, Rieu P, Arnoux-Courseaux M, Cancé C, Marondedze C, Parcy F. Flower Development in Arabidopsis. Methods Mol Biol 2023; 2686:3-38. [PMID: 37540352 DOI: 10.1007/978-1-0716-3299-4_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Like in other angiosperms, the development of flowers in Arabidopsis starts right after the floral transition, when the shoot apical meristem (SAM) stops producing leaves and makes flowers instead. On the flanks of the SAM emerge the flower meristems (FM) that will soon differentiate into the four main floral organs, sepals, petals, stamens, and pistil, stereotypically arranged in concentric whorls. Each phase of flower development-floral transition, floral bud initiation, and floral organ development-is under the control of specific gene networks. In this chapter, we describe these different phases and the gene regulatory networks involved, from the floral transition to the floral termination.
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Affiliation(s)
- Hicham Chahtane
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France
- Institut de Recherche Pierre Fabre, Green Mission Pierre Fabre, Conservatoire Botanique Pierre Fabre, Soual, France
| | - Xuelei Lai
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France
- Huazhong Agricultural University, National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Wuhan, China
| | | | - Philippe Rieu
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | | | - Coralie Cancé
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France
| | - Claudius Marondedze
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France
- Department of Biochemistry, Faculty of Medicine, Midlands State University, Senga, Gweru, Zimbabwe
| | - François Parcy
- CNRS, Université Grenoble Alpes, CEA, INRAE, IRIG, BIG-LPCV, Grenoble, France.
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Li H, You C, Yoshikawa M, Yang X, Gu H, Li C, Cui J, Chen X, Ye N, Zhang J, Wang G. A spontaneous thermo-sensitive female sterility mutation in rice enables fully mechanized hybrid breeding. Cell Res 2022; 32:931-945. [PMID: 36068348 PMCID: PMC9525692 DOI: 10.1038/s41422-022-00711-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 08/08/2022] [Indexed: 11/08/2022] Open
Abstract
Male sterility enables hybrid crop breeding to increase yields and has been extensively studied. But thermo-sensitive female sterility, which is an ideal property that may enable full mechanization in hybrid rice breeding, has rarely been investigated due to the absence of such germplasm. Here we identify the spontaneous thermo-sensitive female sterility 1 (tfs1) mutation that confers complete sterility under regular/high temperature and partial fertility under low temperature as a point mutation in ARGONAUTE7 (AGO7). AGO7 associates with miR390 to form an RNA-Induced Silencing Complex (RISC), which triggers the biogenesis of small interfering RNAs (siRNAs) from TRANS-ACTING3 (TAS3) loci by recruiting SUPPRESSOR OF GENE SILENCING (SGS3) and RNA-DEPENDENT RNA POLYMERASE6 (RDR6) to TAS3 transcripts. These siRNAs are known as tasiR-ARFs as they act in trans to repress auxin response factor genes. The mutant TFS1 (mTFS1) protein is compromised in its ability to load the miR390/miR390* duplex and eject miR390* during RISC formation. Furthermore, tasiR-ARF levels are reduced in tfs1 due to the deficiency in RDR6 but not SGS3 recruitment by mTFS1 RISC under regular/high temperature, while low temperature partially restores mTFS1 function in RDR6 recruitment and tasiR-ARF biogenesis. A miR390 mutant also exhibits female sterility, suggesting that female fertility is controlled by the miR390-AGO7 module. Notably, the tfs1 allele introduced into various elite rice cultivars endows thermo-sensitive female sterility. Moreover, field trials confirm the utility of tfs1 as a restorer line in fully mechanized hybrid rice breeding.
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Affiliation(s)
- Haoxuan Li
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Agriculture, Hunan Agricultural University, Changsha, Hunan, China
| | - Chenjiang You
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Manabu Yoshikawa
- Division of Plant and Microbial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 2-1-2 Kannondai Tsukuba, Ibaraki, Japan
| | - Xiaoyu Yang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, China
| | - Haiyong Gu
- The Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Chuanguo Li
- The Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Jie Cui
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA.
| | - Nenghui Ye
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Agriculture, Hunan Agricultural University, Changsha, Hunan, China.
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
| | - Guanqun Wang
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
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Varshney V, Majee M. Emerging roles of the ubiquitin-proteasome pathway in enhancing crop yield by optimizing seed agronomic traits. PLANT CELL REPORTS 2022; 41:1805-1826. [PMID: 35678849 DOI: 10.1007/s00299-022-02884-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Ubiquitin-proteasome pathway has the potential to modulate crop productivity by influencing agronomic traits. Being sessile, the plant often uses the ubiquitin-proteasome pathway to maintain the stability of different regulatory proteins to survive in an ever-changing environment. The ubiquitin system influences plant reproduction, growth, development, responses to the environment, and processes that control critical agronomic traits. E3 ligases are the major players in this pathway, and they are responsible for recognizing and tagging the targets/substrates. Plants have a variety of E3 ubiquitin ligases, whose functions have been studied extensively, ranging from plant growth to defense strategies. Here we summarize three agronomic traits influenced by ubiquitination: seed size and weight, seed germination, and accessory plant agronomic traits particularly panicle architecture, tillering in rice, and tassels branch number in maize. This review article highlights some recent progress on how the ubiquitin system influences the stability/modification of proteins that determine seed agronomic properties like size, weight, germination and filling, and ultimately agricultural productivity and quality. Further research into the molecular basis of the aforementioned processes might lead to the identification of genes that could be modified or selected for crop development. Likewise, we also propose advances and future perspectives in this regard.
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Affiliation(s)
- Vishal Varshney
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Majee
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Borna RS, Murchie EH, Pyke KA, Roberts JA, Gonzalez‐Carranza ZH. The rice EP3 and OsFBK1 E3 ligases alter plant architecture and flower development, and affect transcript accumulation of microRNA pathway genes and their targets. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:297-309. [PMID: 34543503 PMCID: PMC8753360 DOI: 10.1111/pbi.13710] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/13/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
ERECTA PANICLE 3 (EP3) and ORYZA SATIVA F-BOX KELCH 1 (OsFBK1) proteins share 57% and 54% sequence identity with the Arabidopsis F-box protein HAWAIIAN SKIRT (HWS). Previously we showed that EP3 is a functional orthologue of HWS. Here we demonstrate that OsFBK1 is another functional orthologue of HWS and show the complexity of interaction between EP3 and OsFBK1 genes at different developmental stages of the plant. qRT-PCR expression analyses and studies of EP3-GFP and OsFBK1-RFP promoter reporter lines demonstrate that although EP3 and OsFBK1 expression can be detected in the same tissues some cells exclusively express EP3 or OsFBK1 whilst others co-express both genes. Loss, reduction or gain-of-function lines for EP3 and OsFBK1, show that EP3 and OsFBK1 affect plant architecture, organ size, floral organ number and size, floral morphology, pollen viability, grain size and weight. We have identified the putative orthologue genes of the rice microRNA pathway for ORYZA SATIVA DAWDLE (OsDDL) and ORYZA SATIVA SERRATE (OsSE), and demonstrated that EP3 and OsFBK1 affect their transcript levels as well as those of CROWN ROOT DEFECT 1/ORYZA SATIVA Exportin-5 HASTY (CRD1/OsHST), ORYZA SATIVA DICER-LIKE 1 (OsDCL) and ORYZA SATIVA WEAVY LEAF1 (OsWAF1). We show that EP3 affects OsPri-MIR164, OsNAM1 and OsNAC1 transcript levels. OsNAC1 transcripts are modified by OsFBK1, suggesting two independent regulatory pathways, one via EP3 and OsMIR164 and the other via OsFBK1. Our data propose that EP3 and OsFBK1 conjointly play similar roles in rice to how HWS does in Arabidopsis.
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Affiliation(s)
- Rita S. Borna
- Plant and Crop Sciences DivisionSchool of BiosciencesUniversity of NottinghamNottinghamUK
- Present address:
Department of BotanyUniversity of DhakaDhaka1000Bangladesh
| | - Erik H. Murchie
- Plant and Crop Sciences DivisionSchool of BiosciencesUniversity of NottinghamNottinghamUK
| | - Kevin A. Pyke
- Plant and Crop Sciences DivisionSchool of BiosciencesUniversity of NottinghamNottinghamUK
| | - Jeremy A. Roberts
- Plant and Crop Sciences DivisionSchool of BiosciencesUniversity of NottinghamNottinghamUK
- Present address:
Faculty of Science and EngineeringSchool of Biological & Marine SciencesUniversity of PlymouthDevonUK
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8
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Nagata T, Lombardo F, Ezura H. Complementation of the tomato HWS gene with its Arabidopsis counterpart demonstrates conservation of the gene function between both species. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2021; 38:387-390. [PMID: 34782827 PMCID: PMC8562581 DOI: 10.5511/plantbiotechnology.21.0729a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
The HAWAIIAN SKIRT (HWS) gene was originally described in Arabidopsis for the characteristic fusion of sepals in the mutant. A tomato line mutated in the putative ortholog gene was isolated in a previous study. The tomato hws-1 mutant showed facultative parthenocarpy and produced fruits with elevated Brix, revealing the gene as a hopeful resource for crop improvement. To confirm the orthology relationship between the Arabidopsis and tomato HWS genes, the hws-1 mutant was complemented with either the tomato wild-type genomic fragment or the Arabidopsis sequence of the gene. In both complementation experiments, defective phenotypes of hws-1 are rescued, albeit to different extents. Recovery of these phenotypes, which include parthenocarpic fruit production, increased Brix, loss of leaflet serration, alteration of bud and petal shape, firmly establishes SlHWS as an ortholog of the originally described HWS in Arabidopsis. This work indicates that the function of HWS is likely to be conserved in a wide range of plant species.
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Affiliation(s)
- Toshifumi Nagata
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Fabien Lombardo
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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Lombardo F, Gramazio P, Ezura H. Increase in Phloem Area in the Tomato hawaiian skirt Mutant Is Associated with Enhanced Sugar Transport. Genes (Basel) 2021; 12:genes12060932. [PMID: 34207298 PMCID: PMC8234570 DOI: 10.3390/genes12060932] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/13/2021] [Accepted: 06/15/2021] [Indexed: 11/29/2022] Open
Abstract
The HAWAIIAN SKIRT (HWS) gene has been described in Arabidopsis, rice, tomato and poplar where it seems to perform distinct functions with relatively little overlap. In tomato, alteration of the gene function confers facultative parthenocarpy, thought to be a consequence of changes in the microRNA metabolism. In the rice mutant, improvement in panicle architecture is associated with an increase in grain yield. Knowing that hws tomato fruits show a higher Brix level, it was suspected that vascular bundles might also be altered in this species, in a similar fashion to the rice phenotype. The pedicel structure of the hws-1 line was therefore examined under the microscope and sugar concentrations from phloem exudate were determined in an enzymatic assay. A distinct increase in the phloem area was observed as well as a higher sugar content in mutant phloem exudates, which is hypothesized to contribute to the high Brix level in the mutant fruits. Furthermore, the described phenotype in this study bridges the gap between Arabidopsis and rice phenotypes, suggesting that the modulation of the microRNA metabolism by HWS influences traits of agricultural interest across several species.
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Affiliation(s)
- Fabien Lombardo
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan;
- Correspondence:
| | - Pietro Gramazio
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan;
| | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan;
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba 305-8572, Japan;
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10
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Yuan S, Kawasaki S, Abdellatif IMY, Nishida K, Kondo A, Ariizumi T, Ezura H, Miura K. Efficient base editing in tomato using a highly expressed transient system. PLANT CELL REPORTS 2021; 40:667-676. [PMID: 33550455 DOI: 10.1007/s00299-021-02662-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
KEY MESSAGE Base editing in tomatoes was achieved by transient expression. The Solanaceae plants, particularly the tomato (Solanum lycopersicum), is of huge economic value worldwide. The tomato is a unique model plant for studying the functions of genes related to fruit ripening. Deeper understanding of tomatoes is of great importance for both plant research and the economy. Genome editing technology, such as CRISPR/Cas9, has been used for functional genetic research. However, some challenges, such as low transformation efficiency, remain with this technology. Moreover, the foreign Cas9 and gRNA expression cassettes must be removed to obtain null-segregants In this study, we used a high-level transient expression system to improve the base editing technology. A high-level transient expression system has been established previously using geminiviral replication and a double terminator. The pBYR2HS vector was used for this transient expression system. nCas9-CDA and sgRNA-SlHWS were introduced into this vector, and the protein and RNA were then transiently expressed in tomato tissues by agroinfiltration. The homozygous mutant produced by base editing was obtained in the next generation with an efficiency of about 18%. nCas9-free next-generation plants were 71%. All the homozygous base-edited plants in next generation are nCas9-free. These findings show that the high-level transient expression system is useful for base editing in tomatoes.
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Affiliation(s)
- Shaoze Yuan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Shunsuke Kawasaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Islam M Y Abdellatif
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Keiji Nishida
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, 657-8501, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, 657-8501, Japan
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, 657-8501, Japan
| | - Tohru Ariizumi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Hiroshi Ezura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Kenji Miura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan.
- Tsukuba-Plant Innovation Research Center, University of Tsukuba, Tsukuba, 305-8572, Japan.
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11
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The Landscape of the Genomic Distribution and the Expression of the F-Box Genes Unveil Genome Plasticity in Hexaploid Wheat during Grain Development and in Response to Heat and Drought Stress. Int J Mol Sci 2021; 22:ijms22063111. [PMID: 33803701 PMCID: PMC8002965 DOI: 10.3390/ijms22063111] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/01/2021] [Accepted: 03/15/2021] [Indexed: 11/17/2022] Open
Abstract
FBX proteins are subunits of the SCF complex (Skp1-cullin-FBX) belonging to the E3 ligase family, which is involved in the ubiquitin-proteasome 26S (UPS) pathway responsible for the post-translational protein turnover. By targeting, in a selective manner, key regulatory proteins for ubiquitination and 26S proteasome degradation, FBX proteins play a major role in plant responses to diverse developmental and stress conditions. Although studies on the genomic organization of the FBX gene family in various species have been reported, knowledge related to bread wheat (Triticum aestivum) is scarce and needs to be broadened. Using the latest assembly of the wheat genome, we identified 3670 TaFBX genes distributed non-homogeneously within the three subgenomes (A, B and D) and between the 21 chromosomes, establishing it as one of the richest gene families among plant species. Based on the presence of the five different chromosomal regions previously identified, the present study focused on the genomic distribution of the TaFBX family and the identification of differentially expressed genes during the embryogenesis stages and in response to heat and drought stress. Most of the time, when comparing the expected number of genes (taking into account the formal gene distribution on the entire wheat genome), the TaFBX family harbors a different pattern at the various stratum of observation (subgenome, chromosome, chromosomal regions). We report here that the local gene expansion of the TaFBX family must be the consequence of multiple and complex events, including tandem and small-scale duplications. Regarding the differentially expressed TaFBX genes, while the majority of the genes are localized in the distal chromosomal regions (R1 and R3), differentially expressed genes are more present in the interstitial regions (R2a and R2b) than expected, which could be an indication of the preservation of major genes in those specific chromosomal regions.
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Cambiagno DA, Giudicatti AJ, Arce AL, Gagliardi D, Li L, Yuan W, Lundberg DS, Weigel D, Manavella PA. HASTY modulates miRNA biogenesis by linking pri-miRNA transcription and processing. MOLECULAR PLANT 2021; 14:426-439. [PMID: 33385584 DOI: 10.1016/j.molp.2020.12.019] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/29/2020] [Accepted: 12/28/2020] [Indexed: 05/23/2023]
Abstract
Post-transcriptional gene silencing mediated by microRNAs (miRNAs) modulates numerous developmental and stress response pathways. For the last two decades, HASTY (HST), the ortholog of human EXPORTIN 5, was considered to be a candidate protein that exports plant miRNAs from the nucleus to the cytoplasm. Here, we report that HST functions in the miRNA pathway independent of its cargo-exporting activity in Arabidopsis. We found that Arabidopsis mutants with impaired HST shuttling exhibit normal subcellular distribution of miRNAs. Interestingly, protein-protein interaction and microscopy assays showed that HST directly interacts with the microprocessor core component DCL1 through its N-terminal domain. Moreover, mass spectrometry analysis revealed that HST also interacts independently of its N-terminal domain with the mediator complex subunit MED37. Further experiments revealed that HST could act as a scaffold to facilitate the recruitment of DCL1 to genomic MIRNA loci by stabilizing the DCL1-MED37 complex, which in turn promotes the transcription and proper processing of primary miRNA transcripts (pri-miRNAs). Taken together, these results suggest that HST is likely associated with the formation of the miRNA biogenesis complex at MIRNA genes, promoting the transcription and processing of pri-miRNAs rather than the direct export of processed miRNAs from the nucleus.
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Affiliation(s)
- Damian A Cambiagno
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Axel J Giudicatti
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Agustin L Arce
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Delfina Gagliardi
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina
| | - Lei Li
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Wei Yuan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Derek S Lundberg
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, 3000 Santa Fe, Argentina.
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13
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Zhu W, Li T, Silva JR, Chen J. Conservation and divergence in NaChBac and Na V1.7 pharmacology reveals novel drug interaction mechanisms. Sci Rep 2020; 10:10730. [PMID: 32612253 PMCID: PMC7329812 DOI: 10.1038/s41598-020-67761-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/13/2020] [Indexed: 01/16/2023] Open
Abstract
Voltage-gated Na+ (NaV) channels regulate homeostasis in bacteria and control membrane electrical excitability in mammals. Compared to their mammalian counterparts, bacterial NaV channels possess a simpler, fourfold symmetric structure and have facilitated studies of the structural basis of channel gating. However, the pharmacology of bacterial NaV remains largely unexplored. Here we systematically screened 39 NaV modulators on a bacterial channel (NaChBac) and characterized a selection of compounds on NaChBac and a mammalian channel (human NaV1.7). We found that while many compounds interact with both channels, they exhibit distinct functional effects. For example, the local anesthetics ambroxol and lidocaine block both NaV1.7 and NaChBac but affect activation and inactivation of the two channels to different extents. The voltage-sensing domain targeting toxin BDS-I increases NaV1.7 but decreases NaChBac peak currents. The pore binding toxins aconitine and veratridine block peak currents of NaV1.7 and shift activation (aconitine) and inactivation (veratridine) respectively. In NaChBac, they block the peak current by binding to the pore residue F224. Nonetheless, aconitine has no effect on activation or inactivation, while veratridine only modulates activation of NaChBac. The conservation and divergence in the pharmacology of bacterial and mammalian NaV channels provide insights into the molecular basis of channel gating and will facilitate organism-specific drug discovery.
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Affiliation(s)
- Wandi Zhu
- Biochemical and Cellular Pharmacology, Genentech Inc., 103 DNA Way, South San Francisco, CA, USA. .,Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
| | - Tianbo Li
- Biochemical and Cellular Pharmacology, Genentech Inc., 103 DNA Way, South San Francisco, CA, USA
| | - Jonathan R Silva
- Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Jun Chen
- Biochemical and Cellular Pharmacology, Genentech Inc., 103 DNA Way, South San Francisco, CA, USA.
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14
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Abd-Hamid NA, Ahmad-Fauzi MI, Zainal Z, Ismail I. Diverse and dynamic roles of F-box proteins in plant biology. PLANTA 2020; 251:68. [PMID: 32072251 DOI: 10.1007/s00425-020-03356-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 02/05/2020] [Indexed: 05/23/2023]
Abstract
The SCF complex is a widely studied multi-subunit ring E3 ubiquitin ligase that tags targeted proteins with ubiquitin for protein degradation by the ubiquitin 26S-proteasome system (UPS). The UPS is an important system that generally keeps cellular events tightly regulated by purging misfolded or damaged proteins and selectively degrading important regulatory proteins. The specificity of this post-translational regulation is controlled by F-box proteins (FBPs) via selective recognition of a protein-protein interaction motif at the C-terminal domain. Hence, FBPs are pivotal proteins in determining the plant response in multiple scenarios. It is not surprising that the FBP family is one of the largest protein families in the plant kingdom. In this review, the roles of FBPs, specifically in plants, are compiled to provide insights into their involvement in secondary metabolites, plant stresses, phytohormone signalling, plant developmental processes and miRNA biogenesis.
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Affiliation(s)
- Nur-Athirah Abd-Hamid
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Muhammad-Izzat Ahmad-Fauzi
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Zamri Zainal
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Ismanizan Ismail
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
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15
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Zhang S, Tian Z, Li H, Guo Y, Zhang Y, Roberts JA, Zhang X, Miao Y. Genome-wide analysis and characterization of F-box gene family in Gossypium hirsutum L. BMC Genomics 2019; 20:993. [PMID: 31856713 PMCID: PMC6921459 DOI: 10.1186/s12864-019-6280-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 11/13/2019] [Indexed: 11/18/2022] Open
Abstract
Background F-box proteins are substrate-recognition components of the Skp1-Rbx1-Cul1-F-box protein (SCF) ubiquitin ligases. By selectively targeting the key regulatory proteins or enzymes for ubiquitination and 26S proteasome mediated degradation, F-box proteins play diverse roles in plant growth/development and in the responses of plants to both environmental and endogenous signals. Studies of F-box proteins from the model plant Arabidopsis and from many additional plant species have demonstrated that they belong to a super gene family, and function across almost all aspects of the plant life cycle. However, systematic exploration of F-box family genes in the important fiber crop cotton (Gossypium hirsutum) has not been previously performed. The genome-wide analysis of the cotton F-box gene family is now possible thanks to the completion of several cotton genome sequencing projects. Results In current study, we first conducted a genome-wide investigation of cotton F-box family genes by reference to the published F-box protein sequences from other plant species. 592 F-box protein encoding genes were identified in the Gossypium hirsutume acc.TM-1 genome and, subsequently, we were able to present their gene structures, chromosomal locations, syntenic relationships with their parent species. In addition, duplication modes analysis showed that cotton F-box genes were distributed to 26 chromosomes, with the maximum number of genes being detected on chromosome 5. Although the WGD (whole-genome duplication) mode seems play a dominant role during cotton F-box gene expansion process, other duplication modes including TD (tandem duplication), PD (proximal duplication), and TRD (transposed duplication) also contribute significantly to the evolutionary expansion of cotton F-box genes. Collectively, these bioinformatic analysis suggest possible evolutionary forces underlying F-box gene diversification. Additionally, we also conducted analyses of gene ontology, and expression profiles in silico, allowing identification of F-box gene members potentially involved in hormone signal transduction. Conclusion The results of this study provide first insights into the Gossypium hirsutum F-box gene family, which lays the foundation for future studies of functionality, particularly those involving F-box protein family members that play a role in hormone signal transduction.
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Affiliation(s)
- Shulin Zhang
- State Key Laboratory of Cotton Biology, Institute of Plant Stress Biology, School of Life Sciences, Henan University, Jinming Street, Kaifeng, 475004, China.,College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, 455000, China
| | - Zailong Tian
- State Key Laboratory of Cotton Biology, Institute of Plant Stress Biology, School of Life Sciences, Henan University, Jinming Street, Kaifeng, 475004, China
| | - Haipeng Li
- State Key Laboratory of Cotton Biology, Institute of Plant Stress Biology, School of Life Sciences, Henan University, Jinming Street, Kaifeng, 475004, China
| | - Yutao Guo
- State Key Laboratory of Cotton Biology, Institute of Plant Stress Biology, School of Life Sciences, Henan University, Jinming Street, Kaifeng, 475004, China
| | - Yanqi Zhang
- State Key Laboratory of Cotton Biology, Institute of Plant Stress Biology, School of Life Sciences, Henan University, Jinming Street, Kaifeng, 475004, China
| | - Jeremy A Roberts
- Faculty of Science and Engineering, School of Biological & Marine Sciences, University of Plymouth, Devon, UK
| | - Xuebin Zhang
- State Key Laboratory of Cotton Biology, Institute of Plant Stress Biology, School of Life Sciences, Henan University, Jinming Street, Kaifeng, 475004, China.
| | - Yuchen Miao
- State Key Laboratory of Cotton Biology, Institute of Plant Stress Biology, School of Life Sciences, Henan University, Jinming Street, Kaifeng, 475004, China.
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16
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Mei J, Jiang N, Ren G. The F-box protein HAWAIIAN SKIRT is required for mimicry target-induced microRNA degradation in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:1121-1127. [PMID: 30565372 DOI: 10.1111/jipb.12761] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 12/10/2018] [Indexed: 05/02/2023]
Abstract
Mimicry target-directed microRNA degradation is widespread and highly conserved among eukaryotes. However, little is known about its mechanism of action. In this letter, by using STTM160 (target mimic of miR160) as a reporter, we show that dysfunction of HAWAIIAN SKIRT (HWS) suppresses the pleiotropic phenotype of STTM160. Small RNA sequencing and Northern blot analyses suggested that HWS only affects a subset of microRNAs. Intriguingly, we identified a stable coexistence of miR160/miR399 and their mimicry targets within the AGO1 complex when HWS is compromised, pointing to a possible role of HWS in the clearance of RNA-induced silencing complexes associated with mimicry target.
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Affiliation(s)
- Jun Mei
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ning Jiang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Laboratory of Population & Quantitative Genetics, Institute of Genetics and Biostatistics, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Guodong Ren
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
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17
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Damayanti F, Lombardo F, Masuda JI, Shinozaki Y, Ichino T, Hoshikawa K, Okabe Y, Wang N, Fukuda N, Ariizumi T, Ezura H. Functional Disruption of the Tomato Putative Ortholog of HAWAIIAN SKIRT Results in Facultative Parthenocarpy, Reduced Fertility and Leaf Morphological Defects. FRONTIERS IN PLANT SCIENCE 2019; 10:1234. [PMID: 31681360 PMCID: PMC6801985 DOI: 10.3389/fpls.2019.01234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 09/05/2019] [Indexed: 05/03/2023]
Abstract
A number of plant microRNAs have been demonstrated to regulate developmental processes by integrating internal and environmental cues. Recently, the Arabidopsis thaliana F-box protein HAWAIIAN SKIRT (HWS) gene has been described for its role in miRNA biogenesis. We have isolated in a forward genetic screen a tomato (Solanum lycopersicum) line mutated in the putative ortholog of HWS. We show that the tomato hws-1 mutant exhibits reduction in leaflet serration, leaflet fusion, some degree of floral organ fusion, and alteration in miRNA levels, similarly to the original A. thaliana hws-1 mutant. We also describe novel phenotypes for hws such as facultative parthenocarpy, reduction in fertility and flowering delay. In slhws-1, the parthenocarpy trait is influenced by temperature, with higher parthenocarpy rate in warmer environmental conditions. Conversely, slhws-1 is able to produce seeds when grown in cooler environment. We show that the reduction in seed production in the mutant is mainly due to a defective male function and that the levels of several miRNAs are increased, in accordance with previous HWS studies, accounting for the abnormal leaf and floral phenotypes as well as the altered flowering and fruit development processes. This is the first study of HWS in fleshy fruit plant, providing new insights in the function of this gene in fruit development.
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Affiliation(s)
- Farida Damayanti
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Fabien Lombardo
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Jun-ichiro Masuda
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Yoshihito Shinozaki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Japan
| | - Takuji Ichino
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Research Institute for Sustainable Humanosphere, Kyoto University, Kyoto, Japan
| | - Ken Hoshikawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
| | - Yoshihiro Okabe
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Innovation Center, Nippon Flour Mills Co., Ltd, Atsugi, Japan
| | - Ning Wang
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Japan
| | - Naoya Fukuda
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Japan
| | - Tohru Ariizumi
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Japan
| | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Japan
- *Correspondence: Hiroshi Ezura,
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