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Wang Y, Huang ZQ, Tian KD, Li H, Xu C, Xia B, Tan BC. Multiple factors interact in editing of PPR-E+-targeted sites in maize mitochondria and plastids. Plant Commun 2024; 5:100836. [PMID: 38327059 PMCID: PMC11121751 DOI: 10.1016/j.xplc.2024.100836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/09/2024]
Abstract
RNA cytidine-to-uridine editing is essential for plant organellar gene expression. Pentatricopeptide repeat (PPR)-E+ proteins have been proposed to bind to target sites and recruit the cytidine deaminase AtDYW2, facilitated by AtNUWA. Here we analyze the function of ZmNUWA, ZmDYW2A, and ZmDYW2B and their relationships with other editing factors in maize. The zmdyw2a and zmdyw2b single mutants are normal, but the zmdyw2a::zmdyw2b and zmnuwa mutants are severely arrested in seed development. ZmNUWA, ZmDYW2A, and ZmDYW2B are dual localized in mitochondria and plastids. Loss of ZmNUWA decreases the editing at 99 mitochondrial sites and 8 plastid sites. Surprisingly, loss of ZmDYW2A:ZmDYW2B affects almost the same set of sites targeted by PPR-E+ proteins. ZmNUWA interacts with ZmDYW2A and ZmDYW2B, suggesting that ZmNUWA recruits ZmDYW2A/2B in the editing of PPR-E+-targeted sites in maize. Further protein interaction analyses show that ZmNUWA and ZmDYW2A/2B interact with ZmMORF1, ZmMORF8, ZmMORF2, and ZmMORF9 and that ZmOZ1 interacts with ZmORRM1, ZmDYW2A, ZmDYW2B, ZmMORF8, and ZmMORF9. These results suggest that the maize mitochondrial PPR-E+ editosome contains PPR-E+, ZmDYW2A/2B, ZmNUWA, and ZmMORF1/8, whereas the plastid PPR-E+ editosome is composed of PPR-E+, ZmDYW2A/2B, ZmNUWA, ZmMORF2/8/9, ZmORRM1, and ZmOZ1.
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Affiliation(s)
- Yong Wang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Zi-Qin Huang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Kai-Di Tian
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Hao Li
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Chunhui Xu
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Bingyujie Xia
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Bao-Cai Tan
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China.
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Doll NM, Nowack MK. Endosperm cell death: roles and regulation in angiosperms. J Exp Bot 2024:erae052. [PMID: 38364847 DOI: 10.1093/jxb/erae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Indexed: 02/18/2024]
Abstract
Double fertilization in angiosperms results in the formation of a second zygote, the fertilized endosperm. Unlike its embryo sibling, the endosperm is a transient structure that eventually undergoes developmentally controlled programmed cell death (PCD) at specific time points of seed development or germination. The nature of endosperm PCD exhibits a considerable diversity, both across different angiosperm taxa and within distinct endosperm tissues. In endosperm-less species, PCD might cause central cell degeneration as a mechanism preventing the formation of a fertilized endosperm. In most other angiosperms, embryo growth necessitates the elimination of surrounding endosperm cells. Nevertheless, complete elimination of the endosperm is rare, and in most cases, specific endosperm tissues persist. In mature seeds, these persisting cells may be dead, such as the starchy endosperm in cereals, or remain alive to die only during germination, like the cereal aleurone or the endosperm of castor beans. In this review, we explore the current knowledge surrounding the cellular, molecular, and genetic aspects of endosperm PCD, and the influence environmental stresses have on PCD processes. Overall, this review provides an exhaustive overview of endosperm PCD processes in angiosperms, shedding light on its diverse mechanisms and its significance in seed development and seedling establishment.
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Affiliation(s)
- Nicolas M Doll
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center of Plant Systems Biology, Ghent 9052, Belgium
| | - Moritz K Nowack
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center of Plant Systems Biology, Ghent 9052, Belgium
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Fang R, Lv G, Zhang X, Chen J, Chen X, Wang B. Preharvest 24-epibrassinolide treatment prolongs harvest duration and shelf life in sweet corn. Food Chem (Oxf) 2023; 7:100179. [PMID: 37583676 PMCID: PMC10423688 DOI: 10.1016/j.fochms.2023.100179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/17/2023] [Accepted: 08/05/2023] [Indexed: 08/17/2023]
Abstract
Sweet corn is perishable and have limited harvest duration and shelf life due to their quality deterioration. Reactive oxygen species (ROS) are one of the most predominant factors for maintaining quality of sweet corn during and after harvest. Brassinosteroids (BRs) can enhance the activity of antioxidant enzymes and decrease the ROS level in plants. In this study, we found that a bioactive BR (24-epibrassinolide, EBR) treatment before harvest markedly inhibited change of quality indicators (MDA content, weight loss rate, and soluble sugar content) during and after harvest. Further analysis revealed that EBR promoted the activity and transcriptions of antioxidant enzymes, maintaining lower ROS level in kernels. Meanwhile, exogenous EBR increased the expression level of genes controlling sucrose transport in sweet corn kernels. Bioinformatics and binding analysis identified that BR transcription factor ZmBES1/ZmBZR1-10 might potentially bind to and upregulate transcriptions of antioxidant enzyme genes including SOD and POD genes, and sucrose transport-related genes including SUT and SWEET genes. These results indicated that exogenous application of EBR ameliorates quality during and after harvest by improving the antioxidant capacity and photosynthetic assimilates accumulation rate of sweet corn, thus prolonging harvest duration and shelf life in sweet corn.
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Affiliation(s)
- Ruiqiu Fang
- Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Dongyang, Zhejiang 322100, China
| | - Guihua Lv
- Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Dongyang, Zhejiang 322100, China
| | - Xianwen Zhang
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
| | - Jianjian Chen
- Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Dongyang, Zhejiang 322100, China
| | - Xiaolong Chen
- Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Dongyang, Zhejiang 322100, China
| | - Bin Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
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Wei YM, Wang BH, Shao DJ, Yan RY, Wu JW, Zheng GM, Zhao YJ, Zhang XS, Zhao XY. Defective kernel 66 encodes a GTPase essential for kernel development in maize. J Exp Bot 2023; 74:5694-5708. [PMID: 37490479 PMCID: PMC10540730 DOI: 10.1093/jxb/erad289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/24/2023] [Indexed: 07/27/2023]
Abstract
The mitochondrion is a semi-autonomous organelle that provides energy for cell activities through oxidative phosphorylation. In this study, we identified a defective kernel 66 (dek66)-mutant maize with defective kernels. We characterized a candidate gene, DEK66, encoding a ribosomal assembly factor located in mitochondria and possessing GTPase activity (which belongs to the ribosome biogenesis GTPase A family). In the dek66 mutant, impairment of mitochondrial structure and function led to the accumulation of reactive oxygen species and promoted programmed cell death in endosperm cells. Furthermore, the transcript levels of most of the key genes associated with nutrient storage, mitochondrial respiratory chain complex, and mitochondrial ribosomes in the dek66 mutant were significantly altered. Collectively, the results suggest that DEK66 is essential for the development of maize kernels by affecting mitochondrial function. This study provides a reference for understanding the impact of a mitochondrial ribosomal assembly factor in maize kernel development.
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Affiliation(s)
- Yi Ming Wei
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
- College of Life Sciences, Zaozhuang University, Zaozhuang, Shandong 277160, China
| | - Bo Hui Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Dong Jie Shao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
- College of Life Sciences, Zaozhuang University, Zaozhuang, Shandong 277160, China
| | - Ru Yu Yan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Jia Wen Wu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Guang Ming Zheng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Ya Jie Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Xian Sheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
| | - Xiang Yu Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, China
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Long Y, Wang C, Liu C, Li H, Pu A, Dong Z, Wei X, Wan X. Molecular mechanisms controlling grain size and weight and their biotechnological breeding applications in maize and other cereal crops. J Adv Res 2023:S2090-1232(23)00265-5. [PMID: 37739122 DOI: 10.1016/j.jare.2023.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 09/03/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023] Open
Abstract
BACKGROUND Cereal crops are a primary energy source for humans. Grain size and weight affect both evolutionary fitness and grain yield of cereals. Although studies on gene mining and molecular mechanisms controlling grain size and weight are constantly emerging in cereal crops, only a few systematic reviews on the underlying molecular mechanisms and their breeding applications are available so far. AIM OF REVIEW This review provides a general state-of-the-art overview of molecular mechanisms and targeted strategies for improving grain size and weight of cereals as well as insights for future yield-improving biotechnology-assisted breeding. KEY SCIENTIFIC CONCEPTS OF REVIEW In this review, the evolution of research on grain size and weight over the last 20 years is traced based on a bibliometric analysis of 1158 publications and the main signaling pathways and transcriptional factors involved are summarized. In addition, the roles of post-transcriptional regulation and photosynthetic product accumulation affecting grain size and weight in maize and rice are outlined. State-of-the-art strategies for discovering novel genes related to grain size and weight in maize and other cereal crops as well as advanced breeding biotechnology strategies being used for improving yield including marker-assisted selection, genomic selection, transgenic breeding, and genome editing are also discussed.
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Affiliation(s)
- Yan Long
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Cheng Wang
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Chang Liu
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Huangai Li
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Aqing Pu
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Zhenying Dong
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Xun Wei
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Xiangyuan Wan
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China.
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Yang Y, Ritzenhofen K, Otrzonsek J, Xie J, Schallenberg-Rüdinger M, Knoop V. Beyond a PPR-RNA recognition code: Many aspects matter for the multi-targeting properties of RNA editing factor PPR56. PLoS Genet 2023; 19:e1010733. [PMID: 37603555 PMCID: PMC10482289 DOI: 10.1371/journal.pgen.1010733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 09/06/2023] [Accepted: 07/30/2023] [Indexed: 08/23/2023] Open
Abstract
The mitochondrial C-to-U RNA editing factor PPR56 of the moss Physcomitrium patens is an RNA-binding pentatricopeptide repeat protein equipped with a terminal DYW-type cytidine deaminase domain. Transferred into Escherichia coli, PPR56 works faithfully on its two native RNA editing targets, nad3eU230SL and nad4eU272SL, and also converts cytidines into uridines at over 100 off-targets in the bacterial transcriptome. Accordingly, PPR56 is attractive for detailed mechanistic studies in the heterologous bacterial setup, allowing for scoring differential RNA editing activities of many target and protein variants in reasonable time. Here, we report (i) on the effects of numerous individual and combined PPR56 protein and target modifications, (ii) on the spectrum of off-target C-to-U editing in the bacterial background transcriptome for PPR56 and two variants engineered for target re-direction and (iii) on combinations of targets in tandem or separately at the 5'- and 3'-ends of large mRNAs. The latter experimentation finds enhancement of RNA editing at weak targets in many cases, including cox3eU290SF as a new candidate mitogenome target. We conclude that C-to-U RNA editing can be much enhanced by transcript features also outside the region ultimately targeted by PPRs of a plant editing factor, possibly facilitated by its enrichment or scanning along transcripts.
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Affiliation(s)
- Yingying Yang
- IZMB–Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Bonn, Germany
| | - Kira Ritzenhofen
- IZMB–Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Bonn, Germany
| | - Jessica Otrzonsek
- IZMB–Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Bonn, Germany
| | - Jingchan Xie
- IZMB–Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Bonn, Germany
| | | | - Volker Knoop
- IZMB–Institut für Zelluläre und Molekulare Botanik, Abteilung Molekulare Evolution, Universität Bonn, Bonn, Germany
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Tang H, Dong H, Guo X, Cheng M, Li M, Chen Q, Yuan Z, Pu Z, Wang J. Identification of candidate gene for the defective kernel phenotype using bulked segregant RNA and exome capture sequencing methods in wheat. Front Plant Sci 2023; 14:1173861. [PMID: 37342127 PMCID: PMC10277647 DOI: 10.3389/fpls.2023.1173861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 05/03/2023] [Indexed: 06/22/2023]
Abstract
Wheat is a significant source of protein and starch worldwide. The defective kernel (Dek) mutant AK-3537, displaying a large hollow area in the endosperm and shrunken grain, was obtained through ethyl methane sulfonate (EMS) treatment of the wheat cultivar Aikang 58 (AK58). The mode of inheritance of the AK-3537 grain Dek phenotype was determined to be recessive with a specific statistical significance level. We used bulked segregant RNA-seq (BSR-seq), BSA-based exome capture sequencing (BSE-seq), and the ΔSNP-index algorithm to identify candidate regions for the grain Dek phenotype. Two major candidate regions, DCR1 (Dek candidate region 1) and DCR2, were identified on chromosome 7A between 279.98 and 287.93 Mb and 565.34 and 568.59 Mb, respectively. Based on transcriptome analysis and previous reports, we designed KASP genotyping assays based on SNP variations in the candidate regions and speculated that the candidate gene is TraesCS7A03G0625900 (HMGS-7A), which encodes a 3-hydroxy-3-methylglutaryl-CoA synthase. One SNP variation located at position 1,049 in the coding sequence (G>A) causes an amino acid change from Gly to Asp. The research suggests that functional changes in HMGS-7A may affect the expression of key enzyme genes involved in wheat starch syntheses, such as GBSSII and SSIIIa.
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Affiliation(s)
- Hao Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Huixue Dong
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Xiaojiang Guo
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Mengping Cheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Maolian Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Qian Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Zhongwei Yuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Zhien Pu
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest China, Sichuan Agricultural University, Chengdu, China
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Sharma V, Gangurde SS, Nayak SN, Gowda AS, Sukanth B, Mahadevaiah SS, Manohar SS, Choudhary RS, Anitha T, Malavalli SS, Srikanth S, Bajaj P, Sharma S, Varshney RK, Latha P, Janila P, Bhat RS, Pandey MK. Genetic mapping identified three hotspot genomic regions and candidate genes controlling heat tolerance-related traits in groundnut. Front Plant Sci 2023; 14:1182867. [PMID: 37287715 PMCID: PMC10243373 DOI: 10.3389/fpls.2023.1182867] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/12/2023] [Indexed: 06/09/2023]
Abstract
Groundnut productivity and quality have been impeded by rising temperatures in semi-arid environments. Hence, understanding the effects and molecular mechanisms of heat stress tolerance will aid in tackling yield losses. In this context, a recombinant inbred line (RIL) population was developed and phenotyped for eight seasons at three locations for agronomic, phenological, and physiological traits under heat stress. A genetic map was constructed using genotyping-by-sequencing with 478 single-nucleotide polymorphism (SNP) loci spanning a map distance of 1,961.39 cM. Quantitative trait locus (QTL) analysis using phenotypic and genotypic data identified 45 major main-effect QTLs for 21 traits. Intriguingly, three QTL clusters (Cluster-1-Ah03, Cluster-2-Ah12, and Cluster-3-Ah20) harbor more than half of the major QTLs (30/45, 66.6%) for various heat tolerant traits, explaining 10.4%-38.6%, 10.6%-44.6%, and 10.1%-49.5% of phenotypic variance, respectively. Furthermore, important candidate genes encoding DHHC-type zinc finger family protein (arahy.J0Y6Y5), peptide transporter 1 (arahy.8ZMT0C), pentatricopeptide repeat-containing protein (arahy.4A4JE9), Ulp1 protease family (arahy.X568GS), Kelch repeat F-box protein (arahy.I7X4PC), FRIGIDA-like protein (arahy.0C3V8Z), and post-illumination chlorophyll fluorescence increase (arahy.92ZGJC) were the underlying three QTL clusters. The putative functions of these genes suggested their involvement in seed development, regulating plant architecture, yield, genesis and growth of plants, flowering time regulation, and photosynthesis. Our results could provide a platform for further fine mapping, gene discovery, and developing markers for genomics-assisted breeding to develop heat-tolerant groundnut varieties.
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Affiliation(s)
- Vinay Sharma
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University (CCSU), Meerut, India
| | - Sunil S. Gangurde
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Spurthi N. Nayak
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Anjan S. Gowda
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - B.S. Sukanth
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | | | - Surendra S. Manohar
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | | | - T. Anitha
- Regional Agricultural Research Station, Acharya N G Ranga Agricultural University (ANGRAU), Tirupati, India
| | - Sachin S. Malavalli
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - S.N. Srikanth
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Prasad Bajaj
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University (CCSU), Meerut, India
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Putta Latha
- Regional Agricultural Research Station, Acharya N G Ranga Agricultural University (ANGRAU), Tirupati, India
| | - Pasupuleti Janila
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Ramesh S. Bhat
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Manish K. Pandey
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
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Krishnappa G, Khan H, Krishna H, Devate NB, Kumar S, Mishra CN, Parkash O, Kumar S, Kumar M, Mamrutha HM, Singh GP, Singh G. Genome-Wide Association Study for Grain Protein, Thousand Kernel Weight, and Normalized Difference Vegetation Index in Bread Wheat (Triticum aestivum L.). Genes (Basel) 2023; 14:637. [PMID: 36980909 PMCID: PMC10048783 DOI: 10.3390/genes14030637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
Genomic regions governing grain protein content (GPC), 1000 kernel weight (TKW), and normalized difference vegetation index (NDVI) were studied in a set of 280 bread wheat genotypes. The genome-wide association (GWAS) panel was genotyped using a 35K Axiom array and phenotyped in three environments. A total of 26 marker-trait associations (MTAs) were detected on 18 chromosomes covering the A, B, and D subgenomes of bread wheat. The GPC showed the maximum MTAs (16), followed by NDVI (6), and TKW (4). A maximum of 10 MTAs was located on the B subgenome, whereas, 8 MTAs each were mapped on the A and D subgenomes. In silico analysis suggest that the SNPs were located on important putative candidate genes such as NAC domain superfamily, zinc finger RING-H2-type, aspartic peptidase domain, folylpolyglutamate synthase, serine/threonine-protein kinase LRK10, pentatricopeptide repeat, protein kinase-like domain superfamily, cytochrome P450, and expansin. These candidate genes were found to have different roles including regulation of stress tolerance, nutrient remobilization, protein accumulation, nitrogen utilization, photosynthesis, grain filling, mitochondrial function, and kernel development. The effects of newly identified MTAs will be validated in different genetic backgrounds for further utilization in marker-aided breeding.
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Li J, Wang K, Yang Y, Lu Y, Cui K, Ji Y, Ma L, Cheng K, Ostersetzer-Biran O, Li F, Qu G, Zhu B, Fu D, Luo Y, Zhu H. SlRIP1b is a global organellar RNA editing factor, required for normal fruit development in tomato plants. New Phytol 2023; 237:1188-1203. [PMID: 36345265 DOI: 10.1111/nph.18594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/26/2022] [Indexed: 06/16/2023]
Abstract
RNA editing in plant organelles involves numerous C-U conversions, which often restore evolutionarily conserved codons and may generate new translation initiation and termination codons. These RNA maturation events rely on a subset of nuclear-encoded protein cofactors. Here, we provide evidence of the role of SlRIP1b on RNA editing of mitochondrial transcripts in tomato (Solanum lycopersicum) plants. SlRIP1b is a RIP/MORF protein that was originally identified as an interacting partner of the organellar editing factor SlORRM4. Mutants of SlRIP1b, obtained by CRISPR/Cas9 strategy, exhibited abnormal carpel development and grew into fruit with more locules. RNA-sequencing revealed that SlRIP1b affects the C-U editing of numerous mitochondrial pre-RNA transcripts and in particular altered RNA editing of various cytochrome c maturation (CCM)-related genes. The slrip1b mutants display increased H2 O2 and aberrant mitochondrial morphologies, which are associated with defects in cytochrome c biosynthesis and assembly of respiratory complex III. Taken together, our results indicate that SlRIP1b is a global editing factor that plays a key role in CCM and oxidative phosphorylation system biogenesis during fruit development in tomato plants. These data provide important insights into the molecular roles of organellar RNA editing factors during fruit development.
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Affiliation(s)
- Jinyan Li
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Keru Wang
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yongfang Yang
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yao Lu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Kaicheng Cui
- Key Lab of Horticultural Plant Biology (MOE), College of Horticultural and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yajing Ji
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Liqun Ma
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Ke Cheng
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Feng Li
- Key Lab of Horticultural Plant Biology (MOE), College of Horticultural and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guiqin Qu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Benzhong Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Daqi Fu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yunbo Luo
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Hongliang Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
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11
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Wang C, Li H, Long Y, Dong Z, Wang J, Liu C, Wei X, Wan X. A Systemic Investigation of Genetic Architecture and Gene Resources Controlling Kernel Size-Related Traits in Maize. Int J Mol Sci 2023; 24:ijms24021025. [PMID: 36674545 PMCID: PMC9865405 DOI: 10.3390/ijms24021025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 12/31/2022] [Accepted: 01/04/2023] [Indexed: 01/07/2023] Open
Abstract
Grain yield is the most critical and complex quantitative trait in maize. Kernel length (KL), kernel width (KW), kernel thickness (KT) and hundred-kernel weight (HKW) associated with kernel size are essential components of yield-related traits in maize. With the extensive use of quantitative trait locus (QTL) mapping and genome-wide association study (GWAS) analyses, thousands of QTLs and quantitative trait nucleotides (QTNs) have been discovered for controlling these traits. However, only some of them have been cloned and successfully utilized in breeding programs. In this study, we exhaustively collected reported genes, QTLs and QTNs associated with the four traits, performed cluster identification of QTLs and QTNs, then combined QTL and QTN clusters to detect consensus hotspot regions. In total, 31 hotspots were identified for kernel size-related traits. Their candidate genes were predicted to be related to well-known pathways regulating the kernel developmental process. The identified hotspots can be further explored for fine mapping and candidate gene validation. Finally, we provided a strategy for high yield and quality maize. This study will not only facilitate causal genes cloning, but also guide the breeding practice for maize.
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Affiliation(s)
- Cheng Wang
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Huangai Li
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Yan Long
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Zhenying Dong
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Jianhui Wang
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Chang Liu
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Xun Wei
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
- Correspondence: (X.W.); (X.W.); Tel.: +86-189-1087-6260 (X.W.); +86-186-0056-1850 (X.W.)
| | - Xiangyuan Wan
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
- Correspondence: (X.W.); (X.W.); Tel.: +86-189-1087-6260 (X.W.); +86-186-0056-1850 (X.W.)
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12
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Wang Y, Li H, Huang ZQ, Ma B, Yang YZ, Xiu ZH, Wang L, Tan BC. Maize PPR-E proteins mediate RNA C-to-U editing in mitochondria by recruiting the trans deaminase PCW1. Plant Cell 2023; 35:529-551. [PMID: 36200865 PMCID: PMC9806569 DOI: 10.1093/plcell/koac298] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/11/2022] [Indexed: 05/24/2023]
Abstract
RNA C-to-U editing in organelles is essential for plant growth and development; however, the underlying mechanism is not fully understood. Here, we report that pentatricopeptide repeat (PPR)-E subclass proteins carry out RNA C-to-U editing by recruiting the trans deaminase PPR motifs, coiled-coil, and DYW domain-containing protein 1 (PCW1) in maize (Zea mays) mitochondria. Loss-of-function of bZIP and coiled-coil domain-containing PPR 1 (bCCP1) or PCW1 arrests seed development in maize. bCCP1 encodes a bZIP and coiled-coil domain-containing PPR protein, and PCW1 encodes an atypical PPR-DYW protein. bCCP1 is required for editing at 66 sites in mitochondria and PCW1 is required for editing at 102 sites, including the 66 sites that require bCCP1. The PCW1-mediated editing sites are exclusively associated with PPR-E proteins. bCCP1 interacts with PCW1 and the PPR-E protein Empty pericarp7 (EMP7). Two multiple organellar RNA editing factor (MORF) proteins, ZmMORF1 and ZmMORF8, interact with PCW1, EMP7, and bCCP1. ZmMORF8 enhanced the EMP7-PCW1 interaction in a yeast three-hybrid assay. C-to-U editing at the ccmFN-1553 site in maize required EMP7, bCCP1, and PCW1. These results suggest that PPR-E proteins function in RNA editing by recruiting the trans deaminase PCW1 and bCCP1, and MORF1/8 assist this recruitment through protein-protein interactions.
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Affiliation(s)
- Yong Wang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Hao Li
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Zi-Qin Huang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Bing Ma
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Yan-Zhuo Yang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Zhi-Hui Xiu
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Le Wang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Bao-Cai Tan
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
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13
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Fang R, Chen X, Zhang X, Wang B. Comparative transcriptome analyses shed light on the regulation of harvest duration and shelf life in sweet corn. Food Res Int 2023; 163:112188. [PMID: 36596131 DOI: 10.1016/j.foodres.2022.112188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/11/2022] [Accepted: 11/15/2022] [Indexed: 11/21/2022]
Abstract
Harvest duration and postharvest shelf life are two of the most important characters for sweet corn. However, the regulatory mechanism remains unclear. We performed a comparative transcriptome analysis of long harvest-duration and shelf-life sweet corn (LHS) and short harvest-duration and shelf-life field corn (SHS) at three stages, i.e. 10 days after pollination (10DAP), 22 days after pollination (22DAP), and 7 days after harvest (7DAH). We have observed the major transcriptome changes accompanying the harvest process in LHS corn. Gene expression pattern analysis and differentially expressed genes (DEGs) functional enrichments suggested an association between ROS metabolism in kernels with harvest duration and postharvest shelf life. The genes encoding cytochrome P450, peroxidase, peroxiredoxin, glutathione peroxidase, and glutathione S-transferase were upregulated specifically in LHS kernels during and after harvest compared to SHS kernels. These novel findings reveal a new regulatory mechanism of corn post-harvest shelf life and should be useful for extending harvest duration and shelf life for sweet corn.
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Affiliation(s)
- Ruiqiu Fang
- Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Dongyang, Zhejiang 322100, China.
| | - Xiaolong Chen
- Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Dongyang, Zhejiang 322100, China
| | - Xianwen Zhang
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China
| | - Bin Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang 310021, China.
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14
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Singh L, Dhillon GS, Kaur S, Dhaliwal SK, Kaur A, Malik P, Kumar A, Gill RK, Kaur S. Genome-wide Association Study for Yield and Yield-Related Traits in Diverse Blackgram Panel (Vigna mungo L. Hepper) Reveals Novel Putative Alleles for Future Breeding Programs. Front Genet 2022; 13:849016. [PMID: 35899191 PMCID: PMC9310006 DOI: 10.3389/fgene.2022.849016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 06/20/2022] [Indexed: 11/29/2022] Open
Abstract
Blackgram (Vigna mungo L. Hepper) is an important tropical and sub-tropical short-duration legume that is rich in dietary protein and micronutrients. Producing high-yielding blackgram varieties is hampered by insufficient genetic variability, absence of suitable ideotypes, low harvest index and susceptibility to biotic-abiotic stresses. Seed yield, a complex trait resulting from the expression and interaction of multiple genes, necessitates the evaluation of diverse germplasm for the identification of novel yield contributing traits. Henceforth, a panel of 100 blackgram genotypes was evaluated at two locations (Ludhiana and Gurdaspur) across two seasons (Spring 2019 and Spring 2020) for 14 different yield related traits. A wide range of variability, high broad-sense heritability and a high correlation of grain yield were observed for 12 out of 14 traits studied among all environments. Investigation of population structure in the panel using a set of 4,623 filtered SNPs led to identification of four sub-populations based on ad-hoc delta K and Cross entropy value. Using Farm CPU model and Mixed Linear Model algorithms, a total of 49 significant SNP associations representing 42 QTLs were identified. Allelic effects were found to be statistically significant at 37 out of 42 QTLs and 50 known candidate genes were identified in 24 of QTLs.
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Affiliation(s)
- Lovejit Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | | | - Sarabjit Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Sandeep Kaur Dhaliwal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Amandeep Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Palvi Malik
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Ashok Kumar
- Regional Research Station, Punjab Agricultural University, Gurdaspur, India
| | - Ranjit Kaur Gill
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
- *Correspondence: Satinder Kaur,
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15
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Wang Z, Chen W, Zhang S, Lu J, Chen R, Fu J, Gu R, Wang G, Wang J, Cui Y. Dek504 Encodes a Mitochondrion-Targeted E+-Type Pentatricopeptide Repeat Protein Essential for RNA Editing and Seed Development in Maize. Int J Mol Sci 2022; 23:2513. [PMID: 35269656 DOI: 10.3390/ijms23052513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/20/2022] [Accepted: 02/22/2022] [Indexed: 12/21/2022] Open
Abstract
In flowering plants, RNA editing is a post-transcriptional process that selectively deaminates cytidines (C) to uridines (U) in organellar transcripts. Pentatricopeptide repeat (PPR) proteins have been identified as site-specific recognition factors for RNA editing. Here, we report the map-based cloning and molecular characterization of the defective kernel mutant dek504 in maize. Loss of Dek504 function leads to delayed embryogenesis and endosperm development, which produce small and collapsed kernels. Dek504 encodes an E+-type PPR protein targeted to the mitochondria, which is required for RNA editing of mitochondrial NADH dehydrogenase 3 at the nad3-317 and nad3-44 sites. Biochemical analysis of mitochondrial protein complexes revealed a significant reduction in the mitochondrial NADH dehydrogenase complex I activity, indicating that the alteration of the amino acid sequence at nad3-44 and nad3-317 through RNA editing is essential for NAD3 function. Moreover, the amino acids are highly conserved in monocots and eudicots, whereas the events of C-to-U editing are not conserved in flowering plants. Thus, our results indicate that Dek504 is essential for RNA editing of nad3, which is critical for NAD3 function, mitochondrial complex I stability, and seed development in maize.
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16
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Zhang H, Zang J, Huo Y, Zhang Z, Chen H, Chen X, Liu J. Identification of the Potential Genes Regulating Seed Germination Speed in Maize. Plants (Basel) 2022; 11:plants11040556. [PMID: 35214886 PMCID: PMC8879924 DOI: 10.3390/plants11040556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 05/02/2023]
Abstract
Seed germination is the crucial stage in plant life cycle. Rapid and uniform germination plays an essential role in plant development and grain yield improvement. However, the molecular mechanism underlying seed germination speed is largely unknown due to the complexity of the dynamic process and the difficulty in phenotyping. Here, we conducted a time-series comparative transcriptome study of two elite maize inbred lines, 72-3 and F9721, with striking difference in seed germination speed, and identified a major locus underlying maize germination speed through genome-wide association analysis (GWAS) of an F2 segregation population. Comparative transcriptome study identified 12 h after imbibition (HAI) as the critical stage responsible for the variation in germination speed. The differentially expressed genes (DEGs) between 72-3 and F9721 were mainly enriched in metabolic pathways, biosynthesis of secondary metabolites, oxidoreductase activity pathways, hormone signal transduction, and amino acid transporter activity pathways. GWAS revealed that germination speed was controlled by a major locus on chromosome 1 with the leading SNP as AX-91332814, explaining 10.63% of phenotypic variation. A total of 87 proposed protein-coding genes surrounding the locus were integrated with DEGs. Combined with evidence from the gene expression database and gene synteny with other model species, we finally anchored three genes as the likely candidates regulating germination speed in maize. This study provides clues for the further exploration of genes controlling the maize seed germination speed, thus facilitating breeding of rapid germinated elite lines through marker assistant selection.
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Affiliation(s)
- Huairen Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (H.Z.); (J.Z.); (Y.H.); (Z.Z.); (H.C.)
| | - Jie Zang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (H.Z.); (J.Z.); (Y.H.); (Z.Z.); (H.C.)
| | - Yanqing Huo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (H.Z.); (J.Z.); (Y.H.); (Z.Z.); (H.C.)
| | - Zhaogui Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (H.Z.); (J.Z.); (Y.H.); (Z.Z.); (H.C.)
| | - Huabang Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (H.Z.); (J.Z.); (Y.H.); (Z.Z.); (H.C.)
| | - Xunji Chen
- Institute of Biotech & Nuclear, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
- Correspondence: (X.C.); (J.L.); Tel.: +86-991-4527003 (X.C.); +86-010-64801561 (J.L.)
| | - Juan Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (H.Z.); (J.Z.); (Y.H.); (Z.Z.); (H.C.)
- Correspondence: (X.C.); (J.L.); Tel.: +86-991-4527003 (X.C.); +86-010-64801561 (J.L.)
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17
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Qin T, Zhao P, Sun J, Zhao Y, Zhang Y, Yang Q, Wang W, Chen Z, Mai T, Zou Y, Liu G, Hao W. Research Progress of PPR Proteins in RNA Editing, Stress Response, Plant Growth and Development. Front Genet 2021; 12:765580. [PMID: 34733319 PMCID: PMC8559896 DOI: 10.3389/fgene.2021.765580] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
RNA editing is a posttranscriptional phenomenon that includes gene processing and modification at specific nucleotide sites. RNA editing mainly occurs in the genomes of mitochondria and chloroplasts in higher plants. In recent years, pentatricopeptide repeat (PPR) proteins, which may act as trans-acting factors of RNA editing have been identified, and the study of PPR proteins has become a research focus in molecular biology. The molecular functions of these proteins and their physiological roles throughout plant growth and development are widely studied. In this minireview, we summarize the current knowledge of the PPR family, hoping to provide some theoretical reference for future research and applications.
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Affiliation(s)
- Tengfei Qin
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, China
| | - Pei Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jialiang Sun
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, China
| | - Yuping Zhao
- Beijing River and Lake Management Office, Beijing, China
| | - Yaxin Zhang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, China
| | - Qiuyue Yang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, China
| | - Weipeng Wang
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, China
| | - Zhuanqing Chen
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, China
| | - Tengfei Mai
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, China
| | - Yingying Zou
- Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Sciences and Technology, Xinxiang, China
| | - Guoxiang Liu
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Wei Hao
- College of Medical Technology, Beihua University, Jilin City, China
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18
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Li X, Sun M, Liu S, Teng Q, Li S, Jiang Y. Functions of PPR Proteins in Plant Growth and Development. Int J Mol Sci 2021; 22:11274. [PMID: 34681932 PMCID: PMC8537650 DOI: 10.3390/ijms222011274] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/14/2021] [Accepted: 10/16/2021] [Indexed: 01/04/2023] Open
Abstract
Pentatricopeptide repeat (PPR) proteins form a large protein family in land plants, with hundreds of different members in angiosperms. In the last decade, a number of studies have shown that PPR proteins are sequence-specific RNA-binding proteins involved in multiple aspects of plant organellar RNA processing, and perform numerous functions in plants throughout their life cycle. Recently, computational and structural studies have provided new insights into the working mechanisms of PPR proteins in RNA recognition and cytidine deamination. In this review, we summarized the research progress on the functions of PPR proteins in plant growth and development, with a particular focus on their effects on cytoplasmic male sterility, stress responses, and seed development. We also documented the molecular mechanisms of PPR proteins in mediating RNA processing in plant mitochondria and chloroplasts.
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Affiliation(s)
- Xiulan Li
- School of Life Sciences, Qufu Normal University, Qufu 273165, China; (M.S.); (S.L.); (Q.T.); (S.L.)
| | | | | | | | | | - Yueshui Jiang
- School of Life Sciences, Qufu Normal University, Qufu 273165, China; (M.S.); (S.L.); (Q.T.); (S.L.)
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19
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Zhao Y, Xu W, Zhang Y, Sun S, Wang L, Zhong S, Zhao X, Liu B. PPR647 Protein Is Required for Chloroplast RNA Editing, Splicing and Chloroplast Development in Maize. Int J Mol Sci 2021; 22:ijms222011162. [PMID: 34681824 PMCID: PMC8537648 DOI: 10.3390/ijms222011162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 11/16/2022] Open
Abstract
Chloroplasts play an essential role in plant growth and development. Any factors affecting chloroplast development will lead to abnormal plant growth. Here, we characterized a new maize mutant, albino seedling mutant 81647 (as-81647), which exhibits an entirely albino phenotype in leaves and eventually died before the three-leaf stage. Transmission electron microscopy (TEM) demonstrated that the chloroplast thylakoid membrane was impaired and the granum lamellae significantly decreased in as-81647. Map-based cloning and transgenic analysis confirmed that PPR647 encodes a new chloroplast protein consisting of 11 pentratricopeptide repeat domains. Quantitative real-time PCR (qRT-PCR) assays and transcriptome analysis (RNA-seq) showed that the PPR647 mutation significantly disrupted the expression of PEP-dependent plastid genes. In addition, RNA splicing and RNA editing of multiple chloroplast genes showed severe defects in as-81647. These results indicated that PPR647 is crucial for RNA editing, RNA splicing of chloroplast genes, and plays an essential role in chloroplast development.
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Affiliation(s)
- Yan Zhao
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China; (Y.Z.); (W.X.); (Y.Z.); (S.S.); (L.W.); (S.Z.)
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an 271018, China;
| | - Wei Xu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China; (Y.Z.); (W.X.); (Y.Z.); (S.S.); (L.W.); (S.Z.)
| | - Yongzhong Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China; (Y.Z.); (W.X.); (Y.Z.); (S.S.); (L.W.); (S.Z.)
| | - Shilei Sun
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China; (Y.Z.); (W.X.); (Y.Z.); (S.S.); (L.W.); (S.Z.)
| | - Lijing Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China; (Y.Z.); (W.X.); (Y.Z.); (S.S.); (L.W.); (S.Z.)
| | - Shiyi Zhong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China; (Y.Z.); (W.X.); (Y.Z.); (S.S.); (L.W.); (S.Z.)
| | - Xiangyu Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an 271018, China;
| | - Baoshen Liu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an 271018, China; (Y.Z.); (W.X.); (Y.Z.); (S.S.); (L.W.); (S.Z.)
- Correspondence: ; Tel.: +86-0538-8242226
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Dou X, Zhou Z, Zhao L. Identification and expression analysis of miRNAs in germination and seedling growth of Tibetan hulless barley. Genomics 2021; 113:3735-49. [PMID: 34517091 DOI: 10.1016/j.ygeno.2021.08.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 01/30/2023]
Abstract
Germination and seedling growth are crucial for plant development and agricultural production. While, the regulatory mechanisms during these processes in Tibetan hulless barley (Hordeum vulgare L. var. nudum) are not well understood. Given the regulatory roles of microRNAs (miRNAs) in crop plants and the irreplaceability of barley in the highland area of China, we herein presented a genome-wide survey of miRNAs to reveal a potential regulatory network in the early developmental stages of two Tibetan hulless barleys, from which a total of 156 miRNAs was identified including 35 known and 121 novel ones. Six of the identified novel miRNAs were further experimentally validated. According to the evolutionary analysis, miR156, miR166, miR168, and miR171 were conserved across Tibetan hulless barleys and eight other seed plants. Expression profiles of ten known miRNAs showed that they were involved in phytohormone signaling, carbohydrate and lipid metabolism, as well as juvenile-adult transition during barley development. Moreover, a total of 1280 genes targeted by 101 miRNAs were predicted from both barley libraries. Three genes (PLN03212, MATE eukaryotic, and GRAS) were validated via the RNA ligase-mediated 5'-rapid amplification of cDNA ends (RLM-5' RACE) to be the targets of hvu-miR159a, hvu-miR166a, and hvu-miR171-3p, respectively. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of putative targets, the most abundant pathways were related to "metabolism". These results revealed that miRNA-target pairs participating in the regulation of multigene expression and the embryonic development of Tibetan hulless barleys were controlled by complex mechanisms involving the concordant expression of different miRNAs and feedback loops among miRNAs as well as their targets. The study provides insight into the regulatory network of barley miRNAs for better understanding of miRNA functions during germination and seedling growth.
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Wei YM, Ren ZJ, Wang BH, Zhang L, Zhao YJ, Wu JW, Li LG, Zhang XS, Zhao XY. A nitrate transporter encoded by ZmNPF7.9 is essential for maize seed development. Plant Sci 2021; 308:110901. [PMID: 34034862 DOI: 10.1016/j.plantsci.2021.110901] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 06/12/2023]
Abstract
Nitrogen is an essential macronutrient for plants and regulates many aspects of plant growth and development. Nitrate is one of the major forms of nitrogen in plants. However, the role of nitrate uptake and allocation in seed development is not fully understood. Here, we identified the maize (Zea mays) small-kernel mutant zmnpf7.9 and characterized the candidate gene, ZmNPF7.9, which was the same gene as nitrate transport 1.5 (NRT1.5) in maize. This gene is specifically expressed in the basal endosperm transfer layer cells of maize endosperm. Dysfunction of ZmNPF7.9 resulted in delayed endosperm development, abnormal starch deposition and decreased hundred-grain weight. Functional analysis of cRNA-injected Xenopus oocytes showed that ZmNPF7.9 is a low-affinity, pH-dependent bidirectional nitrate transporter. Moreover, the amount of nitrate in mature seeds of the zmnpf7.9 mutant was reduced. These suggest that ZmNPF7.9 is involved in delivering nitrate from maternal tissues to the developing endosperm. Moreover, most of the key genes associated with glycolysis/gluconeogenesis, carbon fixation, carbon metabolism and biosynthesis of amino acids pathways in the zmnpf7.9 mutant were significantly down-regulated. Thus, our results demonstrate that ZmNPF7.9 plays a specific role in seed development and grain weight by regulating nutrition transport and metabolism, which might provide useful information for maize genetic improvement.
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Affiliation(s)
- Yi Ming Wei
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Zhi Jie Ren
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Bo Hui Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Lin Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Ya Jie Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Jia Wen Wu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Le Gong Li
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Xian Sheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China; College of Life Sciences, Capital Normal University, Beijing, 100048, China.
| | - Xiang Yu Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China; College of Life Sciences, Capital Normal University, Beijing, 100048, China.
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Zhang K, Wang F, Liu B, Xu C, He Q, Cheng W, Zhao X, Ding Z, Zhang W, Zhang K, Li K. ZmSKS13, a cupredoxin domain-containing protein, is required for maize kernel development via modulation of redox homeostasis. New Phytol 2021; 229:2163-2178. [PMID: 33034042 DOI: 10.1111/nph.16988] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 09/24/2020] [Indexed: 06/11/2023]
Abstract
The SKU5 similar (SKS) genes encode a family of multi-copper-oxidase-like proteins with cupredoxin domains similar to those in laccase and ascorbate oxidase. Although SKS proteins are known to function in root growth and cotyledon vascular patterning in Arabidopsis, their role in plant reproductive processes is poorly understood. Here, we identified a seed mutant of maize (Zea mays), generated by ethyl methane sulfonate (EMS) mutagenesis, that we designated defective kernel-zk1 (dek-zk1). The mutant produced small, shriveled kernels with an aberrant basal endosperm transfer layer (BETL) and placento-chalazal (PC) layer and irregular starch granules. Map-based cloning revealed that Dek-zk1 encodes an SKU5 similar 13 (GenBank: ONM36900.1), so it was named ZmSKS13. ZmSKS13 comprises a paralogous pair with Zm00001d012524, but the transcript abundance of ZmSKS13 in developing kernels is 15 times higher than that of Zm00001d012524, resulting in dek-zk1 mutation conveying a distinct kernel phenotype. ZmSKS13 loss of function led to overaccumulation of reactive oxygen species (ROS) and severe DNA damage in the nucellus and BETL and PC layer cells, and exogenous antioxidants significantly alleviated the defects of the mutant kernels. Our results thus demonstrate that ZmSKS13 is a novel regulator that plays a crucial role in kernel development in maize through the modulation of ROS homeostasis.
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Affiliation(s)
- Ke Zhang
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Fei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Baiyu Liu
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Changzheng Xu
- School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Qiuxia He
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, 250103, China
| | - Wen Cheng
- Maize Institute of Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250100, China
| | - Xiangyu Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Zhaohua Ding
- Maize Institute of Shandong Academy of Agricultural Sciences, Jinan, Shandong, 250100, China
| | - Wei Zhang
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Kewei Zhang
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Kunpeng Li
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
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Abstract
Maize (Zea mays) is a leading cereal crop in the world. The maize kernel is the storage organ and the harvest portion of this crop and is closely related to its yield and quality. The development of maize kernel is initiated by the double fertilization event, leading to the formation of a diploid embryo and a triploid endosperm. The embryo and endosperm are then undergone independent developmental programs, resulting in a mature maize kernel which is comprised of a persistent endosperm, a large embryo, and a maternal pericarp. Due to the well-characterized morphogenesis and powerful genetics, maize kernel has long been an excellent model for the study of cereal kernel development. In recent years, with the release of the maize reference genome and the development of new genomic technologies, there has been an explosive expansion of new knowledge for maize kernel development. In this review, we overviewed recent progress in the study of maize kernel development, with an emphasis on genetic mapping of kernel traits, transcriptome analysis during kernel development, functional gene cloning of kernel mutants, and genetic engineering of kernel traits.
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Affiliation(s)
- Dawei Dai
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, 200444 China
| | - Zeyang Ma
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
| | - Rentao Song
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 China
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Ren RC, Yan XW, Zhao YJ, Wei YM, Lu X, Zang J, Wu JW, Zheng GM, Ding XH, Zhang XS, Zhao XY. The novel E-subgroup pentatricopeptide repeat protein DEK55 is responsible for RNA editing at multiple sites and for the splicing of nad1 and nad4 in maize. BMC Plant Biol 2020; 20:553. [PMID: 33297963 PMCID: PMC7727260 DOI: 10.1186/s12870-020-02765-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 12/01/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Pentatricopeptide repeat (PPR) proteins compose a large protein family whose members are involved in both RNA processing in organelles and plant growth. Previous reports have shown that E-subgroup PPR proteins are involved in RNA editing. However, the additional functions and roles of the E-subgroup PPR proteins are unknown. RESULTS In this study, we developed and identified a new maize kernel mutant with arrested embryo and endosperm development, i.e., defective kernel (dek) 55 (dek55). Genetic and molecular evidence suggested that the defective kernels resulted from a mononucleotide alteration (C to T) at + 449 bp within the open reading frame (ORF) of Zm00001d014471 (hereafter referred to as DEK55). DEK55 encodes an E-subgroup PPR protein within the mitochondria. Molecular analyses showed that the editing percentage of 24 RNA editing sites decreased and that of seven RNA editing sites increased in dek55 kernels, the sites of which were distributed across 14 mitochondrial gene transcripts. Moreover, the splicing efficiency of nad1 introns 1 and 4 and nad4 intron 1 significantly decreased in dek55 compared with the wild type (WT). These results indicate that DEK55 plays a crucial role in RNA editing at multiple sites as well as in the splicing of nad1 and nad4 introns. Mutation in the DEK55 gene led to the dysfunction of mitochondrial complex I. Moreover, yeast two-hybrid assays showed that DEK55 interacts with two multiple organellar RNA-editing factors (MORFs), i.e., ZmMORF1 (Zm00001d049043) and ZmMORF8 (Zm00001d048291). CONCLUSIONS Our results demonstrated that a mutation in the DEK55 gene affects the mitochondrial function essential for maize kernel development. Our results also provide novel insight into the molecular functions of E-subgroup PPR proteins involved in plant organellar RNA processing.
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Affiliation(s)
- Ru Chang Ren
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, PR China
| | - Xu Wei Yan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, PR China
| | - Ya Jie Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, PR China
| | - Yi Ming Wei
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, PR China
| | - Xiaoduo Lu
- Institute of Molecular Breeding for Maize, Qilu Normal University, Jinan, 250200, PR China
| | - Jie Zang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, PR China
| | - Jia Wen Wu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, PR China
| | - Guang Ming Zheng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, PR China
| | - Xin Hua Ding
- State Key Laboratory of Crop Biology, College of Plant Protection, Shandong Agricultural University, Taian, Shandong, 271018, PR China
| | - Xian Sheng Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, PR China
| | - Xiang Yu Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, PR China.
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Dai D, Jin L, Huo Z, Yan S, Ma Z, Qi W, Song R. Maize pentatricopeptide repeat protein DEK53 is required for mitochondrial RNA editing at multiple sites and seed development. J Exp Bot 2020; 71:6246-6261. [PMID: 32710615 DOI: 10.1093/jxb/eraa348] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/21/2020] [Indexed: 05/21/2023]
Abstract
Pentatricopeptide repeat (PPR) proteins were identified as site-specific recognition factors for RNA editing in plant mitochondria and plastids. In this study, we characterized maize (Zea mays) kernel mutant defective kernel 53 (dek53), which has an embryo lethal and collapsed endosperm phenotype. Dek53 encodes an E-subgroup PPR protein, which possesses a short PLS repeat region of only seven repeats. Subcellular localization analysis indicated that DEK53 is localized in the mitochondrion. Strand- and transcript-specific RNA-seq analysis showed that the dek53 mutation affected C-to-U RNA editing at more than 60 mitochondrial C targets. Biochemical analysis of mitochondrial protein complexes revealed a significant reduction in the assembly of mitochondrial complex III in dek53. Transmission electron microscopic examination showed severe morphological defects of mitochondria in dek53 endosperm cells. In addition, yeast two-hybrid and luciferase complementation imaging assays indicated that DEK53 can interact with the mitochondrion-targeted non-PPR RNA editing factor ZmMORF1, suggesting that DEK53 might be a functional component of the organellar RNA editosome.
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Affiliation(s)
- Dawei Dai
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, China
| | - Lifang Jin
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, China
| | - Zhenzhen Huo
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, China
| | - Shumei Yan
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, China
| | - Zeyang Ma
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Weiwei Qi
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, China
| | - Rentao Song
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Joint International Research Laboratory of Crop Molecular Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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