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Ahmed MIY, Gorafi YSA, Kamal NM, Balla MY, Tahir ISA, Zheng L, Kawakami N, Tsujimoto H. Mining Aegilops tauschii genetic diversity in the background of bread wheat revealed a novel QTL for seed dormancy. FRONTIERS IN PLANT SCIENCE 2023; 14:1270925. [PMID: 38107013 PMCID: PMC10723804 DOI: 10.3389/fpls.2023.1270925] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/14/2023] [Indexed: 12/19/2023]
Abstract
Due to the low genetic diversity in the current wheat germplasm, gene mining from wild relatives is essential to develop new wheat cultivars that are more resilient to the changing climate. Aegilops tauschii, the D-genome donor of bread wheat, is a great gene source for wheat breeding; however, identifying suitable genes from Ae. tauschii is challenging due to the different morphology and the wide intra-specific variation within the species. In this study, we developed a platform for the systematic evaluation of Ae. tauschii traits in the background of the hexaploid wheat cultivar 'Norin 61' and thus for the identification of QTLs and genes. To validate our platform, we analyzed the seed dormancy trait that confers resistance to preharvest sprouting. We used a multiple synthetic derivative (MSD) population containing a genetic diversity of 43 Ae. tauschii accessions representing the full range of the species. Our results showed that only nine accessions in the population provided seed dormancy, and KU-2039 from Afghanistan had the highest level of seed dormancy. Therefore, 166 backcross inbred lines (BILs) were developed by crossing the synthetic wheat derived from KU-2039 with 'Norin 61' as the recurrent parent. The QTL mapping revealed one novel QTL, Qsd.alrc.5D, associated with dormancy explaining 41.7% of the phenotypic variation and other five unstable QTLs, two of which have already been reported. The Qsd.alrc.5D, identified for the first time within the natural variation of wheat, would be a valuable contribution to breeding after appropriate validation. The proposed platform that used the MSD population derived from the diverse Ae. tauschii gene pool and recombinant inbred lines proved to be a valuable platform for mining new and important QTLs or alleles, such as the novel seed dormancy QTL identified here. Likewise, such a platform harboring genetic diversity from wheat wild relatives could be a useful source for mining agronomically important traits, especially in the era of climate change and the narrow genetic diversity within the current wheat germplasm.
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Affiliation(s)
| | - Yasir Serag Alnor Gorafi
- International Platform for Dryland Research and Education, Tottori University, Tottori, Japan
- Gezira Research Station, Agricultural Research Corporation (ARC), Wad-Medani, Sudan
| | - Nasrein Mohamed Kamal
- Gezira Research Station, Agricultural Research Corporation (ARC), Wad-Medani, Sudan
- Arid Land Research Center, Tottori University, Tottori, Japan
| | - Mohammed Yousif Balla
- Gezira Research Station, Agricultural Research Corporation (ARC), Wad-Medani, Sudan
- Arid Land Research Center, Tottori University, Tottori, Japan
| | - Izzat Sidahmed Ali Tahir
- Gezira Research Station, Agricultural Research Corporation (ARC), Wad-Medani, Sudan
- Arid Land Research Center, Tottori University, Tottori, Japan
| | - Lipeng Zheng
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
| | - Naoto Kawakami
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Japan
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2
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Shen B, Schmidt MA, Collet KH, Liu ZB, Coy M, Abbitt S, Molloy L, Frank M, Everard JD, Booth R, Samadar PP, He Y, Kinney A, Herman EM. RNAi and CRISPR-Cas silencing E3-RING ubiquitin ligase AIP2 enhances soybean seed protein content. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7285-7297. [PMID: 36112496 DOI: 10.1093/jxb/erac376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/15/2022] [Indexed: 06/15/2023]
Abstract
The majority of plant protein in the world's food supply is derived from soybean (Glycine max). Soybean is a key protein source for global animal feed and is incorporated into plant-based foods for people, including meat alternatives. Soybean protein content is genetically variable and is usually inversely related to seed oil content. ABI3-interacting protein 2 (AIP2) is an E3-RING ubiquitin ligase that targets the seed-specific transcription factor ABI3. Silencing both soybean AIP2 genes (AIP2a and AIP2b) by RNAi enhanced seed protein content by up to seven percentage points, with no significant decrease in seed oil content. The protein content enhancement did not alter the composition of the seed storage proteins. Inactivation of either AIP2a or AIP2b by a CRISPR-Cas9-mediated mutation increased seed protein content, and this effect was greater when both genes were inactivated. Transactivation assays in transfected soybean hypocotyl protoplasts indicated that ABI3 changes the expression of glycinin, conglycinin, 2S albumin, and oleosin genes, indicating that AIP2 depletion increased seed protein content by regulating activity of the ABI3 transcription factor protein. These results provide an example of a gene-editing prototype directed to improve global food security and protein availability in soybean that may also be applicable to other protein-source crops.
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Affiliation(s)
- Bo Shen
- Corteva Agriscience, 7250 NW 62nd Ave, PO Box 552, Johnston, IA 50131, USA
| | - Monica A Schmidt
- School of Plant Sciences and Bio5 Institute, 1657 E Helen St, University of Arizona, Tucson, AZ, USA
| | | | - Zhan-Bin Liu
- Corteva Agriscience, 7250 NW 62nd Ave, PO Box 552, Johnston, IA 50131, USA
| | - Monique Coy
- Corteva Agriscience, 7250 NW 62nd Ave, PO Box 552, Johnston, IA 50131, USA
| | - Shane Abbitt
- Corteva Agriscience, 7250 NW 62nd Ave, PO Box 552, Johnston, IA 50131, USA
| | - Lynda Molloy
- Corteva Agriscience, 7250 NW 62nd Ave, PO Box 552, Johnston, IA 50131, USA
| | - Mary Frank
- Corteva Agriscience, 7250 NW 62nd Ave, PO Box 552, Johnston, IA 50131, USA
| | - John D Everard
- Corteva Agriscience, 7250 NW 62nd Ave, PO Box 552, Johnston, IA 50131, USA
| | - Russ Booth
- Corteva Agriscience, 7250 NW 62nd Ave, PO Box 552, Johnston, IA 50131, USA
| | - Partha P Samadar
- School of Plant Sciences and Bio5 Institute, 1657 E Helen St, University of Arizona, Tucson, AZ, USA
| | - Yonghua He
- School of Plant Sciences and Bio5 Institute, 1657 E Helen St, University of Arizona, Tucson, AZ, USA
| | - Anthony Kinney
- Corteva Agriscience, 7250 NW 62nd Ave, PO Box 552, Johnston, IA 50131, USA
| | - Eliot M Herman
- School of Plant Sciences and Bio5 Institute, 1657 E Helen St, University of Arizona, Tucson, AZ, USA
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Park SY, Jung WJ, Bang G, Hwang H, Kim JY. Transcriptome and Proteome Co-Profiling Offers an Understanding of Pre-Harvest Sprouting (PHS) Molecular Mechanisms in Wheat ( Triticum aestivum). PLANTS (BASEL, SWITZERLAND) 2022; 11:2807. [PMID: 36365261 PMCID: PMC9657071 DOI: 10.3390/plants11212807] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/17/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
While wheat (Triticum aestivum L.) is a widely grown and enjoyed crop, the diverse and complex global situation and climate are exacerbating the instability of its supply. In particular, pre-harvest sprouting (PHS) is one of the major abiotic stresses that frequently occurs due to irregular climate conditions, causing serious damage to wheat and its quality. In this study, transcriptomic analysis with RNA-seq and proteomic analysis with LC-MS/MS were performed in PHS-treated spikes from two wheat cultivars presenting PHS sensitivity and tolerance, respectively. A total of 13,154 differentially expressed genes (DEGs) and 706 differentially expressed proteins (DEPs) were identified in four comparison groups between the susceptible/tolerant cultivars. Gene function and correlation analysis were performed to determine the co-profiled genes and proteins affected by PHS treatment. In the functional annotation of each comparative group, similar functions were confirmed in each cultivar under PHS treatment; however, in Keumgang PHS+7 (K7) vs. Woori PHS+7 (W7), functional annotations presented clear differences in the "spliceosome" and "proteasome" pathways. In addition, our results indicate that alternative splicing and ubiquitin-proteasome support the regulation of germination and seed dormancy. This study provides an advanced understanding of the functions involved in transcription and translation related to PHS mechanisms, thus enabling specific proposals for the further analysis of germination and seed dormancy mechanisms and pathways in wheat.
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Affiliation(s)
- Sang Yong Park
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 32439, Korea
| | - Woo Joo Jung
- Institute of Life Science and Natural Resources, Korea University, Seoul 02841, Korea
| | - Geul Bang
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju 28119, Korea
| | - Heeyoun Hwang
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju 28119, Korea
| | - Jae Yoon Kim
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 32439, Korea
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4
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Zhang Y, Zhou J, Zhang Y, Zhang D. The ABI3 Transcription Factor Interaction and Antagonism with Ubiquitin E3 Ligase ScPRT1 in Syntrichia caninervis. Genes (Basel) 2022; 13:genes13050718. [PMID: 35627103 PMCID: PMC9141515 DOI: 10.3390/genes13050718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/17/2022] [Accepted: 04/18/2022] [Indexed: 02/05/2023] Open
Abstract
The ubiquitination pathway has been found to regulate plant responses to environmental stress. However, the role of E3 ubiquitin ligase in desiccation tolerant moss has not yet been elucidated. Previous research has shown that the abscisic acid (ABA) signaling factor ScABI3 can significantly increase desiccation tolerance and reduce ABA sensitivity in the desert moss Syntrichia caninervis. In this study, we identified a RING-type E3 ubiquitin ligase, ScPRT1, and showed that ScABI3 can directly interact with ScPRT1 in vitro and in vivo. Furthermore, we found that the high expression of ScPRT1 can interfere with the transcription of ScABI3 under ABA treatment. Therefore, we speculate that ScPRT1 may degrade ScABI3 through the ubiquitin-26S proteasome system and participate in ABA-dependent signaling in response to ABA-insensitivity or desiccation tolerance in S. caninervis. The findings from our study may enrich our knowledge of the role of E3 ubiquitin ligase in desiccation tolerance and lay a theoretical foundation for an in-depth study of the relationship between ubiquitination modification and ABA signal transduction under environmental stress.
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Affiliation(s)
- Yigong Zhang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (Y.Z.); (J.Z.); (Y.Z.)
| | - Jiyang Zhou
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (Y.Z.); (J.Z.); (Y.Z.)
| | - Yi Zhang
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (Y.Z.); (J.Z.); (Y.Z.)
| | - Daoyuan Zhang
- Xinjiang Key Laboratory of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838099, China
- Correspondence:
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5
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Francki MG, Stainer GS, Walker E, Rebetzke GJ, Stefanova KT, French RJ. Phenotypic Evaluation and Genetic Analysis of Seedling Emergence in a Global Collection of Wheat Genotypes ( Triticum aestivum L.) Under Limited Water Availability. FRONTIERS IN PLANT SCIENCE 2021; 12:796176. [PMID: 35003185 PMCID: PMC8739788 DOI: 10.3389/fpls.2021.796176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
The challenge in establishing an early-sown wheat crop in southern Australia is the need for consistently high seedling emergence when sowing deep in subsoil moisture (>10 cm) or into dry top-soil (4 cm). However, the latter is strongly reliant on a minimum soil water availability to ensure successful seedling emergence. This study aimed to: (1) evaluate 233 Australian and selected international wheat genotypes for consistently high seedling emergence under limited soil water availability when sown in 4 cm of top-soil in field and glasshouse (GH) studies; (2) ascertain genetic loci associated with phenotypic variation using a genome-wide association study (GWAS); and (3) compare across loci for traits controlling coleoptile characteristics, germination, dormancy, and pre-harvest sprouting. Despite significant (P < 0.001) environment and genotype-by-environment interactions within and between field and GH experiments, eight genotypes that included five cultivars, two landraces, and one inbred line had consistently high seedling emergence (mean value > 85%) across nine environments. Moreover, 21 environment-specific quantitative trait loci (QTL) were detected in GWAS analysis on chromosomes 1B, 1D, 2B, 3A, 3B, 4A, 4B, 5B, 5D, and 7D, indicating complex genetic inheritance controlling seedling emergence. We aligned QTL for known traits and individual genes onto the reference genome of wheat and identified 16 QTL for seedling emergence in linkage disequilibrium with coleoptile length, width, and cross-sectional area, pre-harvest sprouting and dormancy, germination, seed longevity, and anthocyanin development. Therefore, it appears that seedling emergence is controlled by multifaceted networks of interrelated genes and traits regulated by different environmental cues.
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Affiliation(s)
- Michael G. Francki
- Department of Primary Industries and Regional Development, South Perth, WA, Australia
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | - Grantley S. Stainer
- Department of Primary Industries and Regional Development, Merredin, WA, Australia
| | - Esther Walker
- Department of Primary Industries and Regional Development, South Perth, WA, Australia
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | - Gregory J. Rebetzke
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Katia T. Stefanova
- Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Robert J. French
- Department of Primary Industries and Regional Development, Merredin, WA, Australia
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He D, Damaris RN, Li M, Khan I, Yang P. Advances on Plant Ubiquitylome-From Mechanism to Application. Int J Mol Sci 2020; 21:E7909. [PMID: 33114409 PMCID: PMC7663383 DOI: 10.3390/ijms21217909] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 10/13/2020] [Accepted: 10/17/2020] [Indexed: 12/11/2022] Open
Abstract
Post-translational modifications (PTMs) of proteins enable modulation of their structure, function, localization and turnover. To date, over 660 PTMs have been reported, among which, reversible PTMs are regarded as the key players in cellular signaling. Signaling mediated by PTMs is faster than re-initiation of gene expression, which may result in a faster response that is particularly crucial for plants due to their sessile nature. Ubiquitylation has been widely reported to be involved in many aspects of plant growth and development and it is largely determined by its target protein. It is therefore of high interest to explore new ubiquitylated proteins/sites to obtain new insights into its mechanism and functions. In the last decades, extensive protein profiling of ubiquitylation has been achieved in different plants due to the advancement in ubiquitylated proteins (or peptides) affinity and mass spectrometry techniques. This obtained information on a large number of ubiquitylated proteins/sites helps crack the mechanism of ubiquitylation in plants. In this review, we have summarized the latest advances in protein ubiquitylation to gain comprehensive and updated knowledge in this field. Besides, the current and future challenges and barriers are also reviewed and discussed.
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Affiliation(s)
- Dongli He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (D.H.); (R.N.D.); (M.L.)
| | - Rebecca Njeri Damaris
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (D.H.); (R.N.D.); (M.L.)
| | - Ming Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (D.H.); (R.N.D.); (M.L.)
| | - Imran Khan
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19014, USA;
| | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China; (D.H.); (R.N.D.); (M.L.)
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7
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He D, Li M, Damaris RN, Bu C, Xue J, Yang P. Quantitative ubiquitylomics approach for characterizing the dynamic change and extensive modulation of ubiquitylation in rice seed germination. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1430-1447. [PMID: 31677306 DOI: 10.1111/tpj.14593] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/26/2019] [Accepted: 10/16/2019] [Indexed: 05/22/2023]
Abstract
During seed germination, cells embark on extensive post-transcriptional and post-translational modifications (PTM), providing a perfect platform to study these events in embryo rebooting from relative quiescenct to highly active state. PR-619, a deubiquitylase inhibitor, delayed the rice seed germination and resulted in the accumulation of ubiquitylated proteins, which indicated the protein ubiquitylation is involved in this process. Using the K-Ɛ-GG antibody enrichment method integrated with high-resolution mass spectrometry, a list of 2576 lysine ubiquitylated (Kub) sites in 1171 proteins was compiled for rice embryos at 0, 12 and 24 h after imbibition (HAI). Of these, the abundance of 1419 Kub sites in 777 proteins changed significantly. Most of them substantially increased within the first 12 HAI, which is similar to the dynamic state previously observed for protein phosphorylation, implying that the first 12 HAI are essential for subsequent switch during rice seed germination. We also quantitatively analyzed the embryo proteome in these samples. Generally, a specific protein's abundance in the ubiquitylome was uncorrelated to that in the proteome. The differentially ubiquitinated proteins were greatly enriched in the categories of protein processing, DNA and RNA processing/regulation related, signaling, and transport. The DiGly footprint of the Kub sites was significantly reduced on K48, a linkage typically associated with proteasome-mediated degradation. These observations suggest ubiquitylation may modulate the protein function more than providing 26S degradation signals in the early stage of rice seed germination. Revealing this comprehensive ubiquitylome greatly increases our understanding of this critical PTM during seed germination.
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Affiliation(s)
- Dongli He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Ming Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Rebecca N Damaris
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Chen Bu
- Jingjie PTM BioLab (Hangzhou) Co. Ltd, Hangzhou, 310018, China
| | - Jianyou Xue
- Jingjie PTM BioLab (Hangzhou) Co. Ltd, Hangzhou, 310018, China
| | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430062, China
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8
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Wang Y, Zhang T, Song X, Zhang J, Dang Z, Pei X, Long Y. Identification and functional analysis of two alternatively spliced transcripts of ABSCISIC ACID INSENSITIVE3 (ABI3) in linseed flax (Linum usitatissimum L.). PLoS One 2018; 13:e0191910. [PMID: 29381737 PMCID: PMC5790255 DOI: 10.1371/journal.pone.0191910] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 01/12/2018] [Indexed: 11/19/2022] Open
Abstract
Alternative splicing is a popular phenomenon in different types of plants. It can produce alternative spliced transcripts that encode proteins with altered functions. Previous studies have shown that one transcription factor, ABSCISIC ACID INSENSITIVE3 (ABI3), which encodes an important component in abscisic acid (ABA) signaling, is subjected to alternative splicing in both mono- and dicotyledons. In the current study, we identified two homologs of ABI3 in the genome of linseed flax. We screened two alternatively spliced flax LuABI3 transcripts, LuABI3-2 and LuABI3-3, and one normal flax LuABI3 transcript, LuABI3-1. Sequence analysis revealed that one of the alternatively spliced transcripts, LuABI3-3, retained a 6 bp intron. RNA accumulation analysis showed that all three transcripts were expressed during seed development, while subcellular localization and transgene experiments showed that LuABI3-3 had no biological function. The two normal transcripts, LuABI3-1 and LuABI3-2, are the important functional isoforms in flax and play significant roles in the ABA regulatory pathway during seed development, germination, and maturation.
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Affiliation(s)
- Yanyan Wang
- MOA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianbao Zhang
- MOA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaxia Song
- MOA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianping Zhang
- Crop Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Zhanhai Dang
- Crop Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Xinwu Pei
- MOA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Long
- MOA Key Laboratory on Safety Assessment (Molecular) of Agri-GMO, Institute of Biotechnology, Chinese Academy of Agricultural Sciences, Beijing, China
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Zhou Y, Chen Z, Cheng M, Chen J, Zhu T, Wang R, Liu Y, Qi P, Chen G, Jiang Q, Wei Y, Luo M, Nevo E, Allaby RG, Liu D, Wang J, Dvorák J, Zheng Y. Uncovering the dispersion history, adaptive evolution and selection of wheat in China. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:280-291. [PMID: 28635103 PMCID: PMC5785339 DOI: 10.1111/pbi.12770] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 06/01/2017] [Accepted: 06/03/2017] [Indexed: 05/18/2023]
Abstract
Wheat was introduced to China approximately 4500 years ago, where it adapted over a span of time to various environments in agro-ecological growing zones. We investigated 717 Chinese and 14 Iranian/Turkish geographically diverse, locally adapted wheat landraces with 27 933 DArTseq (for 717 landraces) and 312 831 Wheat660K (for a subset of 285 landraces) markers. This study highlights the adaptive evolutionary history of wheat cultivation in China. Environmental stresses and independent selection efforts have resulted in considerable genome-wide divergence at the population level in Chinese wheat landraces. In total, 148 regions of the wheat genome show signs of selection in at least one geographic area. Our data show adaptive events across geographic areas, from the xeric northwest to the mesic south, along and among homoeologous chromosomes, with fewer variations in the D genome than in the A and B genomes. Multiple variations in interdependent functional genes such as regulatory and metabolic genes controlling germination and flowering time were characterized, showing clear allelic frequency changes corresponding to the dispersion of wheat in China. Population structure and selection data reveal that Chinese wheat spread from the northwestern Caspian Sea region to South China, adapting during its agricultural trajectory to increasingly mesic and warm climatic areas.
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Affiliation(s)
- Yong Zhou
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Zhongxu Chen
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Mengping Cheng
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Jian Chen
- Chengdu City Institute of ArchaeologyChengduSichuanChina
| | - Tingting Zhu
- Department of Plant SciencesUniversity of CaliforniaDavisCAUSA
| | - Rui Wang
- State Key Lab of CAD&CGZhejiang UniversityHangzhouZhejiangChina
| | - Yaxi Liu
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Pengfei Qi
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Guoyue Chen
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Qiantao Jiang
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Yuming Wei
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
| | - Ming‐Cheng Luo
- Department of Plant SciencesUniversity of CaliforniaDavisCAUSA
| | - Eviatar Nevo
- Institute of EvolutionUniversity of HaifaHaifaIsrael
| | | | - Dengcai Liu
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest ChinaSichuan Agricultural UniversityYaanSichuanChina
| | - Jirui Wang
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest ChinaSichuan Agricultural UniversityYaanSichuanChina
| | - Jan Dvorák
- Department of Plant SciencesUniversity of CaliforniaDavisCAUSA
| | - Youliang Zheng
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuanChina
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest ChinaSichuan Agricultural UniversityYaanSichuanChina
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10
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Lin Y, Liu S, Liu Y, Liu Y, Chen G, Xu J, Deng M, Jiang Q, Wei Y, Lu Y, Zheng Y. Genome-wide association study of pre-harvest sprouting resistance in Chinese wheat founder parents. Genet Mol Biol 2017; 40:620-629. [PMID: 28696481 PMCID: PMC5596365 DOI: 10.1590/1678-4685-gmb-2016-0207] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 02/28/2017] [Indexed: 12/23/2022] Open
Abstract
Pre-harvest sprouting (PHS) is a major abiotic factor affecting grain weight and
quality, and is caused by an early break in seed dormancy. Association mapping (AM)
is used to detect correlations between phenotypes and genotypes based on linkage
disequilibrium (LD) in wheat breeding programs. We evaluated seed dormancy in 80
Chinese wheat founder parents in five environments and performed a genome-wide
association study using 6,057 markers, including 93 simple sequence repeat (SSR),
1,472 diversity array technology (DArT), and 4,492 single nucleotide polymorphism
(SNP) markers. The general linear model (GLM) and the mixed linear model (MLM) were
used in this study, and two significant markers (tPt-7980 and
wPt-6457) were identified. Both markers were located on
Chromosome 1B, with wPt-6457 having been identified in a previously
reported chromosomal position. The significantly associated loci contain essential
information for cloning genes related to resistance to PHS and can be used in wheat
breeding programs.
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Affiliation(s)
- Yu Lin
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Shihang Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Yaxi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Yujiao Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Jie Xu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Qiantao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, P.R. China
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Duong S, Vonapartis E, Li CY, Patel S, Gazzarrini S. The E3 ligase ABI3-INTERACTING PROTEIN2 negatively regulates FUSCA3 and plays a role in cotyledon development in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1555-1567. [PMID: 28369580 PMCID: PMC5441903 DOI: 10.1093/jxb/erx046] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
FUSCA3 (FUS3) is a short-lived B3-domain transcription factor that regulates seed development and phase transitions in Arabidopsis thaliana. The mechanisms controlling FUS3 levels are currently poorly understood. Here we show that FUS3 interacts with the RING E3 ligase ABI3-INTERACTING PROTEIN2 (AIP2). AIP2-green fluorescent protein (GFP) is preferentially expressed in the protoderm during early embryogenesis, similarly to FUS3, suggesting that their interaction is biologically relevant. FUS3 degradation is delayed in the aip2-1 mutant and FUS3-GFP fluorescence is increased in aip2-1, but only during mid-embryogenesis, suggesting that FUS3 is negatively regulated by AIP2 at a specific time during embryogenesis. aip2-1 shows delayed flowering and therefore also functions post-embryonically to regulate developmental phase transitions. Plants overexpressing FUS3 post-embryonically in the L1 layer (ML1p:FUS3) show late flowering and other developmental phenotypes that can be rescued by ML1p:AIP2, further supporting a negative role for AIP2 in FUS3 accumulation. However, additional factors regulate FUS3 levels during embryogenesis, as ML1:AIP2 seeds do not resemble fus3-3. Lastly, targeted expression of a RING-inactive AIP2 variant to the protoderm/L1 layer causes FUS3 and ABI3 overexpression phenotypes and defects in cotyledon development. Taken together, these results indicate that AIP2 targets FUS3 for degradation and plays a role in cotyledon development and flowering time in Arabidopsis.
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Affiliation(s)
- Simon Duong
- Department of Biological Sciences, University of Toronto Scarborough, Toronto M1C 1A4, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto M5S 3G5, Canada
| | - Eliana Vonapartis
- Department of Biological Sciences, University of Toronto Scarborough, Toronto M1C 1A4, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto M5S 3G5, Canada
| | - Cheuk-Yan Li
- Department of Biological Sciences, University of Toronto Scarborough, Toronto M1C 1A4, Canada
| | - Sajedabanu Patel
- Department of Biological Sciences, University of Toronto Scarborough, Toronto M1C 1A4, Canada
| | - Sonia Gazzarrini
- Department of Biological Sciences, University of Toronto Scarborough, Toronto M1C 1A4, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto M5S 3G5, Canada
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Oracz K, Stawska M. Cellular Recycling of Proteins in Seed Dormancy Alleviation and Germination. FRONTIERS IN PLANT SCIENCE 2016; 7:1128. [PMID: 27512405 PMCID: PMC4961694 DOI: 10.3389/fpls.2016.01128] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 07/15/2016] [Indexed: 05/24/2023]
Abstract
Each step of the seed-to-seed cycle of plant development including seed germination is characterized by a specific set of proteins. The continual renewal and/or replacement of these biomolecules are crucial for optimal plant adaptation. As proteins are the main effectors inside the cells, their levels need to be tightly regulated. This is partially achieved by specific proteolytic pathways via multicatalytic protease complexes defined as 20S and 26S proteasomes. In plants, the 20S proteasome is responsible for degradation of carbonylated proteins, while the 26S being a part of ubiquitin-proteasome pathway is known to be involved in proteolysis of phytohormone signaling regulators. On the other hand, the role of translational control of plant development is also well-documented, especially in the context of pollen tube growth and light signaling. Despite the current progress that has been made in seed biology, the sequence of cellular events that determine if the seed can germinate or not are still far from complete understanding. The role and mechanisms of regulation of proteome composition during processes occurring in the plant's photosynthetic tissues have been well-characterized since many years, but in non-photosynthetic seeds it has emerged as a tempting research task only since the last decade. This review discusses the recent discoveries providing insights into the role of protein turnover in seed dormancy alleviation, and germination, with a focus on the control of translation and proteasomal proteolysis. The presented novel data of translatome profiling in seeds highlighted that post-transcriptional regulation of germination results from a timely regulated initiation of translation. In addition, the importance of 26S proteasome in the degradation of regulatory elements of cellular signaling and that of the 20S complex in proteolysis of specific carbonylated proteins in hormonal- and light-dependent processes occurring in seeds is discussed. Based on the current knowledge the model of cellular recycling of proteins in germinating seeds is also proposed.
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Shu K, Meng YJ, Shuai HW, Liu WG, Du JB, Liu J, Yang WY. Dormancy and germination: How does the crop seed decide? PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:1104-12. [PMID: 26095078 DOI: 10.1111/plb.12356] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/07/2015] [Indexed: 05/18/2023]
Abstract
Whether seeds germinate or maintain dormancy is decided upon through very intricate physiological processes. Correct timing of these processes is most important for the plants life cycle. If moist conditions are encountered, a low dormancy level causes pre-harvest sprouting in various crop species, such as wheat, corn and rice, this decreases crop yield and negatively impacts downstream industrial processing. In contrast, a deep level of seed dormancy prevents normal germination even under favourable conditions, resulting in a low emergence rate during agricultural production. Therefore, an optimal seed dormancy level is valuable for modern mechanised agricultural systems. Over the past several years, numerous studies have demonstrated that diverse endogenous and environmental factors regulate the balance between dormancy and germination, such as light, temperature, water status and bacteria in soil, and phytohormones such as ABA (abscisic acid) and GA (gibberellic acid). In this updated review, we highlight recent advances regarding the molecular mechanisms underlying regulation of seed dormancy and germination processes, including the external environmental and internal hormonal cues, and primarily focusing on the staple crop species. Furthermore, future challenges and research directions for developing a full understanding of crop seed dormancy and germination are also discussed.
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Affiliation(s)
- K Shu
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China of Ministry of Agriculture, and Department of Biotechnology, Sichuan Agricultural University, Chengdu, China
| | - Y J Meng
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China of Ministry of Agriculture, and Department of Biotechnology, Sichuan Agricultural University, Chengdu, China
| | - H W Shuai
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China of Ministry of Agriculture, and Department of Biotechnology, Sichuan Agricultural University, Chengdu, China
| | - W G Liu
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China of Ministry of Agriculture, and Department of Biotechnology, Sichuan Agricultural University, Chengdu, China
| | - J B Du
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China of Ministry of Agriculture, and Department of Biotechnology, Sichuan Agricultural University, Chengdu, China
| | - J Liu
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China of Ministry of Agriculture, and Department of Biotechnology, Sichuan Agricultural University, Chengdu, China
| | - W Y Yang
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest China of Ministry of Agriculture, and Department of Biotechnology, Sichuan Agricultural University, Chengdu, China
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Araus JL, Li J, Parry MAJ, Wang J. Phenotyping and other breeding approaches for a New Green Revolution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:422-4. [PMID: 24703237 DOI: 10.1111/jipb.12202] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
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