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Song T, Huo Q, Li C, Wang Q, Cheng L, Qi W, Ma Z, Song R. The biosynthesis of storage reserves and auxin is coordinated by a hierarchical regulatory network in maize endosperm. THE NEW PHYTOLOGIST 2024. [PMID: 38962989 DOI: 10.1111/nph.19949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 06/19/2024] [Indexed: 07/05/2024]
Abstract
Grain filling in maize (Zea mays) is intricately linked to cell development, involving the regulation of genes responsible for the biosynthesis of storage reserves (starch, proteins, and lipids) and phytohormones. However, the regulatory network coordinating these biological functions remains unclear. In this study, we identified 1744 high-confidence target genes co-regulated by the transcription factors (TFs) ZmNAC128 and ZmNAC130 (ZmNAC128/130) through chromatin immunoprecipitation sequencing coupled with RNA-seq analysis in the zmnac128/130 loss-of-function mutants. We further constructed a hierarchical regulatory network using DNA affinity purification sequencing analysis of downstream TFs regulated by ZmNAC128/130. In addition to target genes involved in the biosynthesis of starch and zeins, we discovered novel target genes of ZmNAC128/130 involved in the biosynthesis of lipids and indole-3-acetic acid (IAA). Consistently, the number of oil bodies, as well as the contents of triacylglycerol, and IAA were significantly reduced in zmnac128/130. The hierarchical regulatory network centered by ZmNAC128/130 revealed a significant overlap between the direct target genes of ZmNAC128/130 and their downstream TFs, particularly in regulating the biosynthesis of storage reserves and IAA. Our results indicated that the biosynthesis of storage reserves and IAA is coordinated by a multi-TFs hierarchical regulatory network in maize endosperm.
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Affiliation(s)
- Teng Song
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Qiang Huo
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Chaobin Li
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Qun Wang
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Lijun Cheng
- Shanghai Key Laboratory of Bio-Energy Crops, Plant Science Center, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Weiwei Qi
- 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 Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Rentao Song
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
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He J, Wang J, Zhang Z. Toward unveiling transcriptome dynamics and regulatory modules at the maternal/filial interface of developing maize kernel. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2124-2140. [PMID: 38551088 DOI: 10.1111/tpj.16733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/21/2024] [Accepted: 03/12/2024] [Indexed: 06/14/2024]
Abstract
The basal region of maize (Zea mays) kernels, which includes the pedicel, placenta-chalazal, and basal endosperm transfer layers, serves as the maternal/filial interface for nutrient transfer from the mother plant to the developing seed. However, transcriptome dynamics of this maternal/filial interface remain largely unexplored. To address this gap, we conducted high-temporal-resolution RNA sequencing of the basal and upper kernel regions between 4 and 32 days after pollination and deeply analyzed transcriptome dynamics of the maternal/filial interface. Utilizing 790 specifically and highly expressed genes in the basal region, we performed the gene ontology (GO) term and weighted gene co-expression network analyses. In the early-stage basal region, we identified five MADS-box transcription factors (TFs) as hubs. Their homologs have been demonstrated as pivotal regulators at the maternal/filial interface of rice or Arabidopsis, suggesting their potential roles in maize kernel development. In the filling-stage basal region, numerous GO terms associated with transcriptional regulation and transporters are significantly enriched. Furthermore, we investigated the molecular function of three hub TFs. Through genome-wide DNA affinity purification sequencing combined with promoter transactivation assays, we suggested that these three TFs act as regulators of 10 basal-specific transporter genes involved in the transfer of sugars, amino acids, and ions. This study provides insights into transcriptomic dynamic and regulatory modules of the maternal/filial interface. In the future, genetic investigation of these hub regulators must advance our understanding of maternal/filial interface development and function.
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Affiliation(s)
- Juan He
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Jincang Wang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Zhiyong Zhang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
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Blum JE, Kong R, Schulman E, Chen FM, Upadhyay R, Romero-Meza G, Littman DR, Fischbach MA, Nagashima K, Sattely ES. Discovery and characterization of dietary antigens in oral tolerance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.26.593976. [PMID: 38853977 PMCID: PMC11160622 DOI: 10.1101/2024.05.26.593976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Food antigens elicit immune tolerance through the action of regulatory T cells (Tregs) in the intestine. Although antigens that trigger common food allergies are known, the epitopes that mediate tolerance to most foods have not been described. Here, we identified murine T cell receptors specific for maize, wheat, and soy, and used expression cloning to de-orphan their cognate epitopes. All of the epitopes derive from seed storage proteins that are resistant to degradation and abundant in the edible portion of the plant. Multiple unrelated T cell clones were specific for an epitope at the C-terminus of 19 kDa alpha-zein, a protein from maize kernel. An MHC tetramer loaded with this antigen revealed that zein-specific T cells are predominantly Tregs localized to the intestine. These cells, which develop concurrently with weaning, constitute up to 2% of the peripheral Treg pool. Bulk and single-cell RNA sequencing revealed that these cells express higher levels of immunosuppressive markers and chemokines compared to other Tregs. These data suggest that immune tolerance to plant-derived foods is focused on a specific class of antigens with common features, and they reveal the functional properties of naturally occurring food-specific Tregs.
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Affiliation(s)
- Jamie E. Blum
- Department of Chemical Engineering; Stanford University; Stanford, CA 94305 USA
- Howard Hughes Medical Institute; Stanford University; Stanford, CA 94305 USA and New York University School of Medicine; New York, NY USA
| | - Ryan Kong
- Department of Chemical Engineering; Stanford University; Stanford, CA 94305 USA
| | - E.A. Schulman
- Howard Hughes Medical Institute; Stanford University; Stanford, CA 94305 USA and New York University School of Medicine; New York, NY USA
| | - Francis M. Chen
- Department of Cell Biology, New York University School of Medicine; New York, NY 10016, USA
| | - Rabi Upadhyay
- Department of Cell Biology, New York University School of Medicine; New York, NY 10016, USA
- Perlmutter Cancer Center, New York University Langone Health; New York, NY 10016 USA
| | - Gabriela Romero-Meza
- Howard Hughes Medical Institute; Stanford University; Stanford, CA 94305 USA and New York University School of Medicine; New York, NY USA
- Department of Cell Biology, New York University School of Medicine; New York, NY 10016, USA
| | - Dan R. Littman
- Howard Hughes Medical Institute; Stanford University; Stanford, CA 94305 USA and New York University School of Medicine; New York, NY USA
- Department of Cell Biology, New York University School of Medicine; New York, NY 10016, USA
| | - Michael A. Fischbach
- Department of Bioengineering; Stanford University; Stanford, CA 94305 USA
- Department of Microbiology and Immunology; Stanford University School of Medicine, Stanford University, Stanford CA 94305 USA
- ChEM-H Institute, Stanford University; Stanford, CA 94305 USA
- Chan Zuckerberg Biohub; San Francisco, CA, USA
| | - Kazuki Nagashima
- Department of Bioengineering; Stanford University; Stanford, CA 94305 USA
- Department of Microbiology and Immunology; Stanford University School of Medicine, Stanford University, Stanford CA 94305 USA
- ChEM-H Institute, Stanford University; Stanford, CA 94305 USA
| | - Elizabeth S. Sattely
- Department of Chemical Engineering; Stanford University; Stanford, CA 94305 USA
- Howard Hughes Medical Institute; Stanford University; Stanford, CA 94305 USA and New York University School of Medicine; New York, NY USA
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Hsieh JWA, Lin PY, Wang CT, Lee YJ, Chang P, Lu RJH, Chen PY, Wang CJR. Establishing an optimized ATAC-seq protocol for the maize. FRONTIERS IN PLANT SCIENCE 2024; 15:1370618. [PMID: 38863553 PMCID: PMC11165127 DOI: 10.3389/fpls.2024.1370618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/07/2024] [Indexed: 06/13/2024]
Abstract
The advent of next-generation sequencing in crop improvement offers unprecedented insights into the chromatin landscape closely linked to gene activity governing key traits in plant development and adaptation. Particularly in maize, its dynamic chromatin structure is found to collaborate with massive transcriptional variations across tissues and developmental stages, implying intricate regulatory mechanisms, which highlights the importance of integrating chromatin information into breeding strategies for precise gene controls. The depiction of maize chromatin architecture using Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) provides great opportunities to investigate cis-regulatory elements, which is crucial for crop improvement. In this context, we developed an easy-to-implement ATAC-seq protocol for maize with fewer nuclei and simple equipment. We demonstrate a streamlined ATAC-seq protocol with four key steps for maize in which nuclei purification can be achieved without cell sorting and using only a standard bench-top centrifuge. Our protocol, coupled with the bioinformatic analysis, including validation by read length periodicity, key metrics, and correlation with transcript abundance, provides a precise and efficient assessment of the maize chromatin landscape. Beyond its application to maize, our testing design holds the potential to be applied to other crops or other tissues, especially for those with limited size and amount, establishing a robust foundation for chromatin structure studies in diverse crop species.
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Affiliation(s)
- Jo-Wei Allison Hsieh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
| | - Pei-Yu Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chi-Ting Wang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Jing Lee
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Pearl Chang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Tropical Agriculture and International Cooperation/Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Rita Jui-Hsien Lu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
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Peng D, Pan S, Du X, Chen E, He J, Zhang Z. Central Roles of ZmNAC128 and ZmNAC130 in Nutrient Uptake and Storage during Maize Grain Filling. Genes (Basel) 2024; 15:663. [PMID: 38927600 PMCID: PMC11203180 DOI: 10.3390/genes15060663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 05/14/2024] [Accepted: 05/17/2024] [Indexed: 06/28/2024] Open
Abstract
Grain filling is critical for determining yield and quality, raising the question of whether central coordinators exist to facilitate the uptake and storage of various substances from maternal to filial tissues. The duplicate NAC transcription factors ZmNAC128 and ZmNAC130 could potentially serve as central coordinators. By analyzing differentially expressed genes from zmnac128 zmnac130 mutants across different genetic backgrounds and growing years, we identified 243 highly and differentially expressed genes (hdEGs) as the core target genes. These 243 hdEGs were associated with storage metabolism and transporters. ZmNAC128 and ZmNAC130 play vital roles in storage metabolism, and this study revealed two additional starch metabolism-related genes, sugary enhancer1 and hexokinase1, as their direct targets. A key finding of this study was the inclusion of 17 transporter genes within the 243 hdEGs, with significant alterations in the levels of more than 10 elements/substances in mutant kernels. Among them, six out of the nine upregulated transporter genes were linked to the transport of heavy metals and metalloids (HMMs), which was consistent with the enrichment of cadmium, lead, and arsenic observed in mutant kernels. Interestingly, the levels of Mg and Zn, minerals important to biofortification efforts, were reduced in mutant kernels. In addition to their direct involvement in sugar transport, ZmNAC128 and ZmNAC130 also activate the expression of the endosperm-preferential nitrogen and phosphate transporters ZmNPF1.1 and ZmPHO1;2. This coordinated regulation limits the intake of HMMs, enhances biofortification, and facilitates the uptake and storage of essential nutrients.
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Affiliation(s)
- Di Peng
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China; (D.P.); (S.P.); (X.D.); (E.C.)
| | - Shuxing Pan
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China; (D.P.); (S.P.); (X.D.); (E.C.)
| | - Xin Du
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China; (D.P.); (S.P.); (X.D.); (E.C.)
| | - Erwang Chen
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China; (D.P.); (S.P.); (X.D.); (E.C.)
| | - Junjun He
- South Subtropical Crop Research Institute, Chinese Academy of Tropical Agricultural Science, Zhanjiang 524091, China;
| | - Zhiyong Zhang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China; (D.P.); (S.P.); (X.D.); (E.C.)
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Chen J, Hu Y, Zhao T, Huang C, Chen J, He L, Dai F, Chen S, Wang L, Jin S, Zhang T. Comparative transcriptomic analysis provides insights into the genetic networks regulating oil differential production in oil crops. BMC Biol 2024; 22:110. [PMID: 38735918 PMCID: PMC11089805 DOI: 10.1186/s12915-024-01909-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 05/02/2024] [Indexed: 05/14/2024] Open
Abstract
BACKGROUND Plants differ more than threefold in seed oil contents (SOCs). Soybean (Glycine max), cotton (Gossypium hirsutum), rapeseed (Brassica napus), and sesame (Sesamum indicum) are four important oil crops with markedly different SOCs and fatty acid compositions. RESULTS Compared to grain crops like maize and rice, expanded acyl-lipid metabolism genes and relatively higher expression levels of genes involved in seed oil synthesis (SOS) in the oil crops contributed to the oil accumulation in seeds. Here, we conducted comparative transcriptomics on oil crops with two different SOC materials. In common, DIHYDROLIPOAMIDE DEHYDROGENASE, STEAROYL-ACYL CARRIER PROTEIN DESATURASE, PHOSPHOLIPID:DIACYLGLYCEROL ACYLTRANSFERASE, and oil-body protein genes were both differentially expressed between the high- and low-oil materials of each crop. By comparing functional components of SOS networks, we found that the strong correlations between genes in "glycolysis/gluconeogenesis" and "fatty acid synthesis" were conserved in both grain and oil crops, with PYRUVATE KINASE being the common factor affecting starch and lipid accumulation. Network alignment also found a conserved clique among oil crops affecting seed oil accumulation, which has been validated in Arabidopsis. Differently, secondary and protein metabolism affected oil synthesis to different degrees in different crops, and high SOC was due to less competition of the same precursors. The comparison of Arabidopsis mutants and wild type showed that CINNAMYL ALCOHOL DEHYDROGENASE 9, the conserved regulator we identified, was a factor resulting in different relative contents of lignins to oil in seeds. The interconnection of lipids and proteins was common but in different ways among crops, which partly led to differential oil production. CONCLUSIONS This study goes beyond the observations made in studies of individual species to provide new insights into which genes and networks may be fundamental to seed oil accumulation from a multispecies perspective.
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Affiliation(s)
- Jinwen Chen
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, Zhejiang, China
| | - Yan Hu
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, Zhejiang, China
- Hainan Institute of Zhejiang University, Sanya, 572025, Hainan, China
| | - Ting Zhao
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, Zhejiang, China
| | - Chujun Huang
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, Zhejiang, China
| | - Jiani Chen
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, Zhejiang, China
| | - Lu He
- Hainan Institute of Zhejiang University, Sanya, 572025, Hainan, China
| | - Fan Dai
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, Zhejiang, China
| | - Shuqi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Luyao Wang
- Hainan Institute of Zhejiang University, Sanya, 572025, Hainan, China
| | - Shangkun Jin
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, Zhejiang, China
| | - Tianzhen Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, Zhejiang, China.
- Hainan Institute of Zhejiang University, Sanya, 572025, Hainan, China.
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7
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Yang T, Huang Y, Liao L, Wang S, Zhang H, Pan J, Huang Y, Li X, Chen D, Liu T, Lu X, Wu Y. Sucrose-associated SnRK1a1-mediated phosphorylation of Opaque2 modulates endosperm filling in maize. MOLECULAR PLANT 2024; 17:788-806. [PMID: 38615195 DOI: 10.1016/j.molp.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 01/29/2024] [Accepted: 04/10/2024] [Indexed: 04/15/2024]
Abstract
During maize endosperm filling, sucrose not only serves as a source of carbon skeletons for storage-reserve synthesis but also acts as a stimulus to promote this process. However, the molecular mechanisms underlying sucrose and endosperm filling are poorly understood. In this study, we found that sucrose promotes the expression of endosperm-filling hub gene Opaque2 (O2), coordinating with storage-reserve accumulation. We showed that the protein kinase SnRK1a1 can attenuate O2-mediated transactivation, but sucrose can release this suppression. Biochemical assays revealed that SnRK1a1 phosphorylates O2 at serine 41 (S41), negatively affecting its protein stability and transactivation ability. We observed that mutation of SnRK1a1 results in larger seeds with increased kernel weight and storage reserves, while overexpression of SnRK1a1 causes the opposite effect. Overexpression of the native O2 (O2-OE), phospho-dead (O2-SA), and phospho-mimetic (O2-SD) variants all increased 100-kernel weight. Although O2-SA seeds exhibit smaller kernel size, they have higher accumulation of starch and proteins, resulting in larger vitreous endosperm and increased test weight. O2-SD seeds display larger kernel size but unchanged levels of storage reserves and test weight. O2-OE seeds show elevated kernel dimensions and nutrient storage, like a mixture of O2-SA and O2-SD seeds. Collectively, our study discovers a novel regulatory mechanism of maize endosperm filling. Identification of S41 as a SnRK1-mediated phosphorylation site in O2 offers a potential engineering target for enhancing storage-reserve accumulation and yield in maize.
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Affiliation(s)
- Tao Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
| | - Yunqin Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Longyu Liao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Shanshan Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Haoyu Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Jingying Pan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Yongcai Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Xiaoling Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Di Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Tao Liu
- Institute of Molecular Breeding for Maize, Qilu Normal University, Jinan, China
| | - Xiaoduo Lu
- Institute of Molecular Breeding for Maize, Qilu Normal University, Jinan, China
| | - Yongrui Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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Ma B, Cao X, Li X, Bian Z, Zhang QQ, Fang Z, Liu J, Li Q, Liu Q, Zhang L, He Z. Two ABCI family transporters, OsABCI15 and OsABCI16, are involved in grain-filling in rice. J Genet Genomics 2024; 51:492-506. [PMID: 37913986 DOI: 10.1016/j.jgg.2023.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/03/2023]
Abstract
Seed development is critical for plant reproduction and crop yield, with panicle seed-setting rate, grain-filling, and grain weight being key seed characteristics for yield improvement. However, few genes are known to regulate grain filling. Here, we identify two adenosine triphosphate (ATP)-binding cassette (ABC)I-type transporter genes, OsABCI15 and OsABCI16, involved in rice grain-filling. Both genes are highly expressed in developing seeds, and their proteins are localized to the plasma membrane and cytosol. Interestingly, knockout of OsABCI15 and OsABCI16 results in a significant reduction in seed-setting rate, caused predominantly by the severe empty pericarp phenotype, which differs from the previously reported low seed-setting phenotype resulting from failed pollination. Further analysis indicates that OsABCI15 and OsABCI16 participate in ion homeostasis and likely export ions between filial tissues and maternal tissues during grain filling. Importantly, overexpression of OsABCI15 and OsABCI16 enhances the seed-setting rate and grain yield in transgenic plants and decreases ion accumulation in brown rice. Moreover, the OsABCI15/16 orthologues in maize exhibit a similar role in kernel development, as demonstrated by their disruption in transgenic maize. Therefore, our findings reveal the important roles of two ABC transporters in cereal grain filling, highlighting their value in crop yield improvement.
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Affiliation(s)
- Bin Ma
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, Jiangsu 225009, China; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Xiubiao Cao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xiaoyuan Li
- Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang 310024, China
| | - Zhong Bian
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Qi-Qi Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zijun Fang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jiyun Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qun Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qiaoquan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, Jiangsu 225009, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Lin Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, Jiangsu 225009, China.
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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Li J, Gu W, Yang Z, Chen J, Yi F, Li T, Li J, Zhou Y, Guo Y, Song W, Lai J, Zhao H. ZmELP1, an Elongator complex subunit, is required for the maintenance of histone acetylation and RNA Pol II phosphorylation in maize kernels. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1251-1268. [PMID: 38098341 PMCID: PMC11022810 DOI: 10.1111/pbi.14262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/20/2023] [Accepted: 11/26/2023] [Indexed: 01/26/2024]
Abstract
The Elongator complex was originally identified as an interactor of hyperphosphorylated RNA polymerase II (RNAPII) in yeast and has histone acetyltransferase (HAT) activity. However, the genome-wide regulatory roles of Elongator on transcriptional elongation and histone acetylation remain unclear. We characterized a maize miniature seed mutant, mn7 and map-based cloning revealed that Mn7 encodes one of the subunits of the Elongator complex, ZmELP1. ZmELP1 deficiency causes marked reductions in the kernel size and weight. Molecular analyses showed that ZmELP1 interacts with ZmELP3, which is required for H3K14 acetylation (H3K14ac), and Elongator complex subunits interact with RNA polymerase II (RNAPII) C-terminal domain (CTD). Genome-wide analyses indicated that loss of ZmELP1 leads to a significant decrease in the deposition of H3K14ac and the CTD of phosphorylated RNAPII on Ser2 (Ser2P). These chromatin changes positively correlate with global transcriptomic changes. ZmELP1 mutation alters the expression of genes involved in transcriptional regulation and kernel development. We also showed that the decrease of Ser2P depends on the deposition of Elongator complex-mediated H3K14ac. Taken together, our results reveal an important role of ZmELP1 in the H3K14ac-dependent transcriptional elongation, which is critical for kernel development.
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Affiliation(s)
- Jianrui Li
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Wei Gu
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
- Crop Breeding, Cultivation Research Institution/CIMMYT‐China Specialty Maize Research Center, Shanghai Engineering Research Center of Specialty Maize, Shanghai Key Laboratory of Agricultural Genetics and BreedingShanghai Academy of Agricultural SciencesShanghaiChina
| | - Zhijia Yang
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Jian Chen
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Fei Yi
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
- Engineering Research Center of Plant Growth Regulator, Ministry of Education, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Tong Li
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Jingrui Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Yue Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking‐Tsinghua Center for Life SciencesPeking UniversityBeijingChina
| | - Yan Guo
- State Key Laboratory of Plant Environmental Resilience, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Weibin Song
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Jinsheng Lai
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
| | - Haiming Zhao
- State Key Laboratory of Maize Bio‐breeding, National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and BreedingChina Agricultural UniversityBeijingChina
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10
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Fang H, Shan T, Gu H, Chen J, Qi Y, Li Y, Saeed M, Yuan J, Li P, Wang B. Identification and characterization of ACR gene family in maize for salt stress tolerance. FRONTIERS IN PLANT SCIENCE 2024; 15:1381056. [PMID: 38745920 PMCID: PMC11091409 DOI: 10.3389/fpls.2024.1381056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024]
Abstract
Background Members of the ACR gene family are commonly involved in various physiological processes, including amino acid metabolism and stress responses. In recent decades, significant progress has been made in the study of ACR genes in plants. However, little is known about their characteristics and function in maize. Methods In this study, ACR genes were identified from the maize genome, and their molecular characteristics, gene structure, gene evolution, gene collinearity analysis, cis-acting elements were analyzed. qRT-PCR technology was used to verify the expression patterns of the ZmACR gene family in different tissues under salt stress. In addition, Ectopic expression technique of ZmACR5 in Arabidopsis thaliana was utilized to identify its role in response to salt stress. Results A total of 28 ZmACR genes were identified, and their molecular characteristics were extensively described. Two gene pairs arising from segmented replication events were detected in maize, and 18 collinear gene pairs were detected between maize and 3 other species. Through phylogenetic analysis, three subgroups were revealed, demonstrating distinct divergence between monocotyledonous and dicotyledonous plants. Analysis of ZmACR cis-acting elements revealed the optional involvement of ZmACR genes in light response, hormone response and stress resistance. Expression analysis of 8 ZmACR genes under salt treatment clearly revealed their role in the response to salt stress. Ectopic overexpression of ZmACR5 in Arabidopsis notably reduced salt tolerance compared to that of the wild type under salt treatment, suggesting that ZmACR5 has a negative role in the response to salt stress. Conclusion Taken together, these findings confirmed the involvement of ZmACR genes in regulating salt stress and contributed significantly to our understanding of the molecular function of ACR genes in maize, facilitating further research in this field.
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Affiliation(s)
- Hui Fang
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Tingyu Shan
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Haijing Gu
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Junyu Chen
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Yingxiao Qi
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Yexiong Li
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Muhammad Saeed
- Department of Agricultural Sciences, Government College University, Faisalabad, Pakistan
| | | | - Ping Li
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, Jiangsu, China
| | - Baohua Wang
- Ministry of Agricultural Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region, School of Life Sciences, Nantong University, Nantong, Jiangsu, China
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11
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Deng M, Zeng Q, Liu S, Jin M, Luo H, Luo J. Combining association with linkage mapping to dissect the phenolamides metabolism of the maize kernel. FRONTIERS IN PLANT SCIENCE 2024; 15:1376405. [PMID: 38681218 PMCID: PMC11047430 DOI: 10.3389/fpls.2024.1376405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/02/2024] [Indexed: 05/01/2024]
Abstract
Phenolamides are important secondary metabolites in plant species. They play important roles in plant defense responses against pathogens and insect herbivores, protection against UV irradiation and floral induction and development. However, the accumulation and variation in phenolamides content in diverse maize lines and the genes responsible for their biosynthesis remain largely unknown. Here, we combined genetic mapping, protein regulatory network and bioinformatics analysis to further enhance the understanding of maize phenolamides biosynthesis. Sixteen phenolamides were identified in multiple populations, and they were all significantly correlated with one or several of 19 phenotypic traits. By linkage mapping, 58, 58, 39 and 67 QTLs, with an average of 3.9, 3.6, 3.6 and 4.2 QTLs for each trait were mapped in BBE1, BBE2, ZYE1 and ZYE2, explaining 9.47%, 10.78%, 9.51% and 11.40% phenotypic variation for each QTL on average, respectively. By GWAS, 39 and 36 significant loci were detected in two different environments, 3.3 and 2.8 loci for each trait, explaining 10.00% and 9.97% phenotypic variation for each locus on average, respectively. Totally, 58 unique candidate genes were identified, 31% of them encoding enzymes involved in amine and derivative metabolic processes. Gene Ontology term analysis of the 358 protein-protein interrelated genes revealed significant enrichment in terms relating to cellular nitrogen metabolism, amine metabolism. GRMZM2G066142, GRMZM2G066049, GRMZM2G165390 and GRMZM2G159587 were further validated involvement in phenolamides biosynthesis. Our results provide insights into the genetic basis of phenolamides biosynthesis in maize kernels, understanding phenolamides biosynthesis and its nutritional content and ability to withstand biotic and abiotic stress.
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Affiliation(s)
- Min Deng
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Qingping Zeng
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Songqin Liu
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Min Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Hongbing Luo
- College of Agronomy, Hunan Agricultural University, Changsha, China
| | - Jingyun Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
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12
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Zhang J, Yue Y, Hu M, Yi F, Chen J, Lai J, Xin B. Dynamic transcriptome landscape of maize pericarp development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:1574-1591. [PMID: 37970738 DOI: 10.1111/tpj.16548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 10/09/2023] [Accepted: 11/05/2023] [Indexed: 11/17/2023]
Abstract
As a maternal tissue, the pericarp supports and protects for other components of seed, such as embryo and endosperm. Despite the importance of maize pericarp in seed, the genome-wide transcriptome pattern throughout maize pericarp development has not been well characterized. Here, we developed RNA-seq transcriptome atlas of B73 maize pericarp development based on 21 samples from 5 days before fertilization (DBP5) to 32 days after fertilization (DAP32). A total of 25 346 genes were detected in programming pericarp development, including 1887 transcription factors (TFs). Together with pericarp morphological changes, the global clustering of gene expression revealed four developmental stages: undeveloped, thickening, expansion and strengthening. Coexpression analysis provided further insights on key regulators in functional transition of four developmental stages. Combined with non-seed, embryo, endosperm, and nucellus transcriptome data, we identified 598 pericarp-specific genes, including 75 TFs, which could elucidate key mechanisms and regulatory networks of pericarp development. Cell wall related genes were identified that reflected their crucial role in the maize pericarp structure building. In addition, key maternal proteases or TFs related with programmed cell death (PCD) were proposed, suggesting PCD in the maize pericarp was mediated by vacuolar processing enzymes (VPE), and jasmonic acid (JA) and ethylene-related pathways. The dynamic transcriptome atlas provides a valuable resource for unraveling the genetic control of maize pericarp development.
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Affiliation(s)
- Jihong Zhang
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, P. R. China
| | - Yang Yue
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, P. R. China
| | - Mingjian Hu
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, P. R. China
| | - Fei Yi
- Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing, P. R. China
| | - Jian Chen
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, P. R. China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, P. R. China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, P. R. China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, P. R. China
| | - Beibei Xin
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, P. R. China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, P. R. China
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Ma B, Liu H, Xiu ZH, Yang HH, Wang H, Wang Y, Tan BC. Defective kernel 58 encodes an Rrp15p domain-containing protein essential to ribosome biogenesis and seed development in maize. THE NEW PHYTOLOGIST 2024; 241:1662-1675. [PMID: 38058237 DOI: 10.1111/nph.19460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 11/08/2023] [Indexed: 12/08/2023]
Abstract
Ribosome biogenesis is a highly dynamic and orchestrated process facilitated by hundreds of ribosomal biogenesis factors and small nucleolar RNAs. While many of the advances are derived from studies in yeast, ribosome biogenesis remains largely unknown in plants despite its importance to plant growth and development. Through characterizing the maize (Zea mays) defective kernel and embryo-lethal mutant dek58, we show that DEK58 encodes an Rrp15p domain-containing protein with 15.3% identity to yeast Rrp15. Over-expression of DEK58 rescues the mutant phenotype. DEK58 is localized in the nucleolus. Ribosome profiling and RNA gel blot analyses show that the absence of DEK58 reduces ribosome assembly and impedes pre-rRNA processing, accompanied by the accumulation of nearly all the pre-rRNA processing intermediates and the production of an aberrant processing product P-25S*. DEK58 interacts with ZmSSF1, a maize homolog of the yeast Ssf1 in the 60S processome. DEK58 and ZmSSF1 interact with ZmCK2α, a putative component of the yeast UTP-C complex involved in the small ribosomal subunit processome. These results demonstrate that DEK58 is essential to seed development in maize. It functions in the early stage of pre-rRNA processing in ribosome biogenesis, possibly through interacting with ZmSSF1 and ZmCK2α in maize.
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Affiliation(s)
- Bing Ma
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Hui Liu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Zhi-Hui Xiu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Huan-Huan Yang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Hongqiu Wang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yong Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Bao-Cai Tan
- The 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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14
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Li H, Che R, Zhu J, Yang X, Li J, Fernie AR, Yan J. Multi-omics-driven advances in the understanding of triacylglycerol biosynthesis in oil seeds. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:999-1017. [PMID: 38009661 DOI: 10.1111/tpj.16545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 11/01/2023] [Indexed: 11/29/2023]
Abstract
Vegetable oils are rich sources of polyunsaturated fatty acids and energy as well as valuable sources of human food, animal feed, and bioenergy. Triacylglycerols, which are comprised of three fatty acids attached to a glycerol backbone, are the main component of vegetable oils. Here, we review the development and application of multiple-level omics in major oilseeds and emphasize the progress in the analysis of the biological roles of key genes underlying seed oil content and quality in major oilseeds. Finally, we discuss future research directions in functional genomics research based on current omics and oil metabolic engineering strategies that aim to enhance seed oil content and quality, and specific fatty acids components according to either human health needs or industrial requirements.
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Affiliation(s)
- Hui Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Ronghui Che
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Jiantang Zhu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China
| | - Xiaohong Yang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Jiansheng Li
- National Maize Improvement Center of China, China Agricultural University, Beijing, 100193, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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15
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Yuan Y, Huo Q, Zhang Z, Wang Q, Wang J, Chang S, Cai P, Song KM, Galbraith DW, Zhang W, Huang L, Song R, Ma Z. Decoding the gene regulatory network of endosperm differentiation in maize. Nat Commun 2024; 15:34. [PMID: 38167709 PMCID: PMC10762121 DOI: 10.1038/s41467-023-44369-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
The persistent cereal endosperm constitutes the majority of the grain volume. Dissecting the gene regulatory network underlying cereal endosperm development will facilitate yield and quality improvement of cereal crops. Here, we use single-cell transcriptomics to analyze the developing maize (Zea mays) endosperm during cell differentiation. After obtaining transcriptomic data from 17,022 single cells, we identify 12 cell clusters corresponding to five endosperm cell types and revealing complex transcriptional heterogeneity. We delineate the temporal gene-expression pattern from 6 to 7 days after pollination. We profile the genomic DNA-binding sites of 161 transcription factors differentially expressed between cell clusters and constructed a gene regulatory network by combining the single-cell transcriptomic data with the direct DNA-binding profiles, identifying 181 regulons containing genes encoding transcription factors along with their high-confidence targets, Furthermore, we map the regulons to endosperm cell clusters, identify cell-cluster-specific essential regulators, and experimentally validated three predicted key regulators. This study provides a framework for understanding cereal endosperm development and function at single-cell resolution.
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Affiliation(s)
- Yue Yuan
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
| | - Qiang Huo
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Ziru Zhang
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Qun Wang
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Juanxia Wang
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Shuaikang Chang
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Peng Cai
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Karen M Song
- Department of Biology, Trinity College of Arts and Sciences, Duke University, Durham, NC, 27708, USA
| | - David W Galbraith
- School of Plant Sciences and Bio5 Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Weixiao Zhang
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Long Huang
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Rentao Song
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572025, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China.
| | - Zeyang Ma
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572025, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China.
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16
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Shen X, Xiao B, Kaderbek T, Lin Z, Tan K, Wu Q, Yuan L, Lai J, Zhao H, Song W. Dynamic transcriptome landscape of developing maize ear. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1856-1870. [PMID: 37731154 DOI: 10.1111/tpj.16457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/19/2023] [Accepted: 08/26/2023] [Indexed: 09/22/2023]
Abstract
Seed number and harvesting ability in maize (Zea mays L.) are primarily determined by the architecture of female inflorescence, namely the ear. Therefore, ear morphogenesis contributes to grain yield and as such is one of the key target traits during maize breeding. However, the molecular networks of this highly dynamic and complex grain-bearing inflorescence remain largely unclear. As a first step toward characterizing these networks, we performed a high-spatio-temporal-resolution investigation of transcriptomes using 130 ear samples collected from developing ears with length from 0.1 mm to 19.0 cm. Comparisons of these mRNA populations indicated that these spatio-temporal transcriptomes were clearly separated into four distinct stages stages I, II, III, and IV. A total of 23 793 genes including 1513 transcription factors (TFs) were identified in the investigated developing ears. During the stage I of ear morphogenesis, 425 genes were predicted to be involved in a co-expression network established by eight hub TFs. Moreover, 9714 ear-specific genes were identified in the seven kinds of meristems. Additionally, 527 genes including 59 TFs were identified as especially expressed in ear and displayed high temporal specificity. These results provide a high-resolution atlas of gene activity during ear development and help to unravel the regulatory modules associated with the differentiation of the ear in maize.
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Affiliation(s)
- Xiaomeng Shen
- State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing, 100193, P.R. China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, P.R. China
| | - Bing Xiao
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, P.R. China
| | - Tangnur Kaderbek
- State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing, 100193, P.R. China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, P.R. China
| | - Zhen Lin
- State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing, 100193, P.R. China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, P.R. China
| | - Kaiwen Tan
- State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing, 100193, P.R. China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, P.R. China
| | - Qingyu Wu
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, The Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, P. R. China
| | - Lixing Yuan
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, P.R. China
| | - Jinsheng Lai
- State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing, 100193, P.R. China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, P.R. China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, P.R. China
| | - Haiming Zhao
- State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing, 100193, P.R. China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, P.R. China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, P.R. China
| | - Weibin Song
- State Key Laboratory of Maize Bio-breeding, China Agricultural University, Beijing, 100193, P.R. China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, P.R. China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, P.R. China
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Fu Y, Xiao W, Tian L, Guo L, Ma G, Ji C, Huang Y, Wang H, Wu X, Yang T, Wang J, Wang J, Wu Y, Wang W. Spatial transcriptomics uncover sucrose post-phloem transport during maize kernel development. Nat Commun 2023; 14:7191. [PMID: 37938556 PMCID: PMC10632454 DOI: 10.1038/s41467-023-43006-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 10/30/2023] [Indexed: 11/09/2023] Open
Abstract
Maize kernels are complex biological systems composed of three genetic sources, namely maternal tissues, progeny embryos, and progeny endosperms. The lack of gene expression profiles with spatial information has limited the understanding of the specific functions of each cell population, and hindered the exploration of superior genes in kernels. In our study, we conduct microscopic sectioning and spatial transcriptomics analysis during the grain filling stage of maize kernels. This enables us to visualize the expression patterns of all genes through electronical RNA in situ hybridization, and identify 11 cell populations and 332 molecular marker genes. Furthermore, we systematically elucidate the spatial storage mechanisms of the three major substances in maize kernels: starch, protein, and oil. These findings provide valuable insights into the functional genes that control agronomic traits in maize kernels.
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Affiliation(s)
- Yuxin Fu
- College of Life Science, Shanghai Normal University, 100 Guilin Road, Shanghai, 200233, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Shanghai, 200032, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wenxin Xiao
- College of Life Science, Shanghai Normal University, 100 Guilin Road, Shanghai, 200233, China
| | - Lang Tian
- College of Life Science, Shanghai Normal University, 100 Guilin Road, Shanghai, 200233, China
| | - Liangxing Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Shanghai, 200032, China
| | - Guangjin Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Chen Ji
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongcai Huang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Shanghai, 200032, China
- State key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Haihai Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Shanghai, 200032, China
| | - Xingguo Wu
- College of Life Science, Shanghai Normal University, 100 Guilin Road, Shanghai, 200233, China
| | - Tao Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Shanghai, 200032, China
- State key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiechen Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Shanghai, 200032, China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- State key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yongrui Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology & Ecology, Shanghai, 200032, China.
| | - Wenqin Wang
- College of Life Science, Shanghai Normal University, 100 Guilin Road, Shanghai, 200233, China.
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Tourdot E, Mauxion JP, Gonzalez N, Chevalier C. Endoreduplication in plant organogenesis: a means to boost fruit growth. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6269-6284. [PMID: 37343125 DOI: 10.1093/jxb/erad235] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023]
Abstract
Endoreduplication is the major source of somatic endopolyploidy in higher plants, and leads to variation in cell ploidy levels due to iterative rounds of DNA synthesis in the absence of mitosis. Despite its ubiquitous occurrence in many plant organs, tissues, and cells, the physiological meaning of endoreduplication is not fully understood, although several roles during plant development have been proposed, mostly related to cell growth, differentiation, and specialization via transcriptional and metabolic reprogramming. Here, we review recent advances in our knowledge of the molecular mechanisms and cellular characteristics of endoreduplicated cells, and provide an overview of the multi-scale effects of endoreduplication on supporting growth in plant development. In addition, the effects of endoreduplication in fruit development are discussed, since it is highly prominent during fruit organogenesis where it acts as a morphogenetic factor supporting rapid fruit growth, as illustrated by case of the model fleshy fruit, tomato (Solanum lycopersicum).
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Affiliation(s)
- Edouard Tourdot
- Université de Bordeaux, INRAE, UMR1332 Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
| | - Jean-Philippe Mauxion
- Université de Bordeaux, INRAE, UMR1332 Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
| | - Nathalie Gonzalez
- Université de Bordeaux, INRAE, UMR1332 Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
| | - Christian Chevalier
- Université de Bordeaux, INRAE, UMR1332 Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
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19
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Chen E, Yu H, He J, Peng D, Zhu P, Pan S, Wu X, Wang J, Ji C, Chao Z, Xu Z, Wu Y, Chao D, Wu Y, Zhang Z. The transcription factors ZmNAC128 and ZmNAC130 coordinate with Opaque2 to promote endosperm filling in maize. THE PLANT CELL 2023; 35:4066-4090. [PMID: 37542515 PMCID: PMC10615213 DOI: 10.1093/plcell/koad215] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/26/2023] [Accepted: 07/12/2023] [Indexed: 08/07/2023]
Abstract
Endosperm filling in maize (Zea mays), which involves nutrient uptake and biosynthesis of storage reserves, largely determines grain yield and quality. However, much remains unclear about the synchronization of these processes. Here, we comprehensively investigated the functions of duplicate NAM, ATAF1/2, and CUC2 (NAC)-type transcription factors, namely, ZmNAC128 and ZmNAC130, in endosperm filling. The gene-edited double mutant zmnac128 zmnac130 exhibits a poorly filled kernel phenotype such that the kernels have an inner cavity. RNA sequencing and protein abundance analysis revealed that the expression of many genes involved in the biosynthesis of zein and starch is reduced in the filling endosperm of zmnac128 zmnac130. Further, DNA affinity purification and sequencing combined with chromatin-immunoprecipitation quantitative PCR and promoter transactivation assays demonstrated that ZmNAC128 and ZmNAC130 are direct regulators of 3 (16-, 27-, and 50-kD) γ-zein genes and 6 important starch metabolism genes (Brittle2 [Bt2], pullulanase-type starch debranching enzyme [Zpu1], granule-bound starch synthase 1 [GBSS1], starch synthase 1 [SS1], starch synthase IIa [SSIIa], and sucrose synthase 1 [Sus1]). ZmNAC128 and ZmNAC130 recognize an additional cis-element in the Opaque2 (O2) promoter to regulate its expression. The triple mutant zmnac128 zmnac130 o2 exhibits extremely poor endosperm filling, which results in more than 70% of kernel weight loss. ZmNAC128 and ZmNAC130 regulate the expression of the transporter genes sugars that will eventually be exported transporter 4c (ZmSWEET4c), sucrose and glucose carrier 1 (ZmSUGCAR1), and yellow stripe-like2 (ZmYSL2) and in turn facilitate nutrient uptake, while O2 plays a supporting role. In conclusion, ZmNAC128 and ZmNAC130 cooperate with O2 to facilitate endosperm filling, which involves nutrient uptake in the basal endosperm transfer layer (BETL) and the synthesis of zeins and starch in the starchy endosperm (SE).
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Affiliation(s)
- Erwang Chen
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027,China
| | - Huiqin Yu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027,China
| | - Juan He
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027,China
| | - Di Peng
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027,China
| | - Panpan Zhu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027,China
| | - Shuxing Pan
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027,China
| | - Xu Wu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027,China
| | - Jincang Wang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027,China
| | - Chen Ji
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032,China
| | - Zhenfei Chao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032,China
| | - Zhuopin Xu
- Anhui Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031,China
| | - Yuejin Wu
- Anhui Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031,China
| | - Daiyin Chao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032,China
| | - Yongrui Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032,China
| | - Zhiyong Zhang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027,China
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20
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Barros JAS, Chatt EC, Augustine RC, McLoughlin F, Li F, Otegui MS, Vierstra RD. Autophagy during maize endosperm development dampens oxidative stress and promotes mitochondrial clearance. PLANT PHYSIOLOGY 2023; 193:1395-1415. [PMID: 37335933 PMCID: PMC10517192 DOI: 10.1093/plphys/kiad340] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/10/2023] [Accepted: 05/10/2023] [Indexed: 06/21/2023]
Abstract
The selective turnover of macromolecules by autophagy provides a critical homeostatic mechanism for recycling cellular constituents and for removing superfluous and damaged organelles, membranes, and proteins. To better understand how autophagy impacts seed maturation and nutrient storage, we studied maize (Zea mays) endosperm in its early and middle developmental stages via an integrated multiomic approach using mutants impacting the core macroautophagy factor AUTOPHAGY (ATG)-12 required for autophagosome assembly. Surprisingly, the mutant endosperm in these developmental windows accumulated normal amounts of starch and Zein storage proteins. However, the tissue acquired a substantially altered metabolome, especially for compounds related to oxidative stress and sulfur metabolism, including increases in cystine, dehydroascorbate, cys-glutathione disulfide, glucarate, and galactarate, and decreases in peroxide and the antioxidant glutathione. While changes in the associated transcriptome were mild, the proteome was strongly altered in the atg12 endosperm, especially for increased levels of mitochondrial proteins without a concomitant increase in mRNA abundances. Although fewer mitochondria were seen cytologically, a heightened number appeared dysfunctional based on the accumulation of dilated cristae, consistent with attenuated mitophagy. Collectively, our results confirm that macroautophagy plays a minor role in the accumulation of starch and storage proteins during maize endosperm development but likely helps protect against oxidative stress and clears unneeded/dysfunctional mitochondria during tissue maturation.
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Affiliation(s)
- Jessica A S Barros
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Elizabeth C Chatt
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Robert C Augustine
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Fionn McLoughlin
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Faqiang Li
- Department of Genetics, University of Wisconsin, Madison, WI 53706, USA
| | - Marisa S Otegui
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin, Madison, WI 53706, USA
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
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21
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Cai Q, Jiao F, Wang Q, Zhang E, Song X, Pei Y, Li J, Zhao M, Guo X. Multiomics comparative analysis of the maize large grain mutant tc19 identified pathways related to kernel development. BMC Genomics 2023; 24:537. [PMID: 37697229 PMCID: PMC10496403 DOI: 10.1186/s12864-023-09567-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/08/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND The mechanism of grain development in elite maize breeding lines has not been fully elucidated. Grain length, grain width and grain weight are key components of maize grain yield. Previously, using the Chinese elite maize breeding line Chang7-2 and its large grain mutant tc19, we characterized the grain size developmental difference between Chang7-2 and tc19 and performed transcriptomic analysis. RESULTS In this paper, using Chang7-2 and tc19, we performed comparative transcriptomic, proteomic and metabolomic analyses at different grain development stages. Through proteomics analyses, we found 2884, 505 and 126 differentially expressed proteins (DEPs) at 14, 21 and 28 days after pollination, respectively. Through metabolomics analysis, we identified 51, 32 and 36 differentially accumulated metabolites (DAMs) at 14, 21 and 28 days after pollination, respectively. Through multiomics comparative analysis, we showed that the phenylpropanoid pathways are influenced at transcriptomic, proteomic and metabolomic levels in all the three grain developmental stages. CONCLUSION We identified several genes in phenylpropanoid biosynthesis, which may be related to the large grain phenotype of tc19. In summary, our results provided new insights into maize grain development.
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Affiliation(s)
- Qing Cai
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Fuchao Jiao
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
- The Characteristic Laboratory of Crop Germplasm Innovation and Application, Provincial Department of Education, College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qianqian Wang
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Enying Zhang
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xiyun Song
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yuhe Pei
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jun Li
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Meiai Zhao
- College of Life Sciences, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xinmei Guo
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China.
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22
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Yang Y, Wen X, Wu Z, Wang K, Zhu Y. Large-scale long terminal repeat insertions produced a significant set of novel transcripts in cotton. SCIENCE CHINA. LIFE SCIENCES 2023; 66:1711-1724. [PMID: 37079218 DOI: 10.1007/s11427-022-2341-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/03/2023] [Indexed: 04/21/2023]
Abstract
Genomic analysis has revealed that the 1,637-Mb Gossypium arboreum genome contains approximately 81% transposable elements (TEs), while only 57% of the 735-Mb G. raimondii genome is occupied by TEs. In this study, we investigated whether there were unknown transcripts associated with TE or TE fragments and, if so, how these new transcripts were evolved and regulated. As sequence depths increased from 4 to 100 G, a total of 10,284 novel intergenic transcripts (intergenic genes) were discovered. On average, approximately 84% of these intergenic transcripts possibly overlapped with the long terminal repeat (LTR) insertions in the otherwise untranscribed intergenic regions and were expressed at relatively low levels. Most of these intergenic transcripts possessed no transcription activation markers, while the majority of the regular genic genes possessed at least one such marker. Genes without transcription activation markers formed their+1 and -1 nucleosomes more closely (only (117±1.4)bp apart), while twice as big spaces (approximately (403.5±46.0) bp apart) were detected for genes with the activation markers. The analysis of 183 previously assembled genomes across three different kingdoms demonstrated systematically that intergenic transcript numbers in a given genome correlated positively with its LTR content. Evolutionary analysis revealed that genic genes originated during one of the whole-genome duplication events around 137.7 million years ago (MYA) for all eudicot genomes or 13.7 MYA for the Gossypium family, respectively, while the intergenic transcripts evolved around 1.6 MYA, resultant of the last LTR insertion. The characterization of these low-transcribed intergenic transcripts can facilitate our understanding of the potential biological roles played by LTRs during speciation and diversifications.
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Affiliation(s)
- Yan Yang
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
| | - Xingpeng Wen
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhiguo Wu
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Kun Wang
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yuxian Zhu
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China.
- College of Life Sciences, Wuhan University, Wuhan, 430072, China.
- Hubei Hongshan Laboratory, Wuhan, 430072, China.
- TaiKang Center for Life and Medical Sciences, RNA Institute, Remin Hospital, Wuhan University, Wuhan, 430072, China.
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23
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Piya S, Pantalone V, Zadegan SB, Shipp S, Lakhssassi N, Knizia D, Krishnan HB, Meksem K, Hewezi T. Soybean gene co-expression network analysis identifies two co-regulated gene modules associated with nodule formation and development. MOLECULAR PLANT PATHOLOGY 2023; 24:628-636. [PMID: 36975024 DOI: 10.1111/mpp.13327] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 05/18/2023]
Abstract
Gene co-expression network analysis is an efficient systems biology approach for the discovery of novel gene functions and trait-associated gene modules. To identify clusters of functionally related genes involved in soybean nodule formation and development, we performed a weighted gene co-expression network analysis. Two nodule-specific modules (NSM-1 and NSM-2, containing 304 and 203 genes, respectively) were identified. The NSM-1 gene promoters were significantly enriched in cis-binding elements for ERF, MYB, and C2H2-type zinc transcription factors, whereas NSM-2 gene promoters were enriched in cis-binding elements for TCP, bZIP, and bHLH transcription factors, suggesting a role of these regulatory factors in the transcriptional activation of nodule co-expressed genes. The co-expressed gene modules included genes with potential novel roles in nodulation, including those involved in xylem development, transmembrane transport, the ethylene signalling pathway, cytoskeleton organization, cytokinesis and regulation of the cell cycle, regulation of meristem initiation and growth, transcriptional regulation, DNA methylation, and histone modifications. Functional analysis of two co-expressed genes using TILLING mutants provided novel insight into the involvement of unsaturated fatty acid biosynthesis and folate metabolism in nodule formation and development. The identified gene co-expression modules provide valuable resources for further functional genomics studies to dissect the genetic basis of nodule formation and development in soybean.
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Affiliation(s)
- Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, 37996, USA
| | - Vince Pantalone
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, 37996, USA
| | | | - Sarah Shipp
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, 37996, USA
| | - Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, Illinois, 62901, USA
| | - Dounya Knizia
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, Illinois, 62901, USA
| | - Hari B Krishnan
- Plant Science Division, University of Missouri, Columbia, Missouri, USA
- Plant Genetics Research, USDA Agricultural Research Service, Columbia, Missouri, USA
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, Illinois, 62901, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, 37996, USA
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24
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Murphy KM, Dowd T, Khalil A, Char SN, Yang B, Endelman BJ, Shih PM, Topp C, Schmelz EA, Zerbe P. A dolabralexin-deficient mutant provides insight into specialized diterpenoid metabolism in maize. PLANT PHYSIOLOGY 2023; 192:1338-1358. [PMID: 36896653 PMCID: PMC10231366 DOI: 10.1093/plphys/kiad150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 01/19/2023] [Accepted: 02/02/2023] [Indexed: 06/01/2023]
Abstract
Two major groups of specialized metabolites in maize (Zea mays), termed kauralexins and dolabralexins, serve as known or predicted diterpenoid defenses against pathogens, herbivores, and other environmental stressors. To consider the physiological roles of the recently discovered dolabralexin pathway, we examined dolabralexin structural diversity, tissue-specificity, and stress-elicited production in a defined biosynthetic pathway mutant. Metabolomics analyses support a larger number of dolabralexin pathway products than previously known. We identified dolabradienol as a previously undetected pathway metabolite and characterized its enzymatic production. Transcript and metabolite profiling showed that dolabralexin biosynthesis and accumulation predominantly occur in primary roots and show quantitative variation across genetically diverse inbred lines. Generation and analysis of CRISPR-Cas9-derived loss-of-function Kaurene Synthase-Like 4 (Zmksl4) mutants demonstrated dolabralexin production deficiency, thus supporting ZmKSL4 as the diterpene synthase responsible for the conversion of geranylgeranyl pyrophosphate precursors into dolabradiene and downstream pathway products. Zmksl4 mutants further display altered root-to-shoot ratios and root architecture in response to water deficit. Collectively, these results demonstrate dolabralexin biosynthesis via ZmKSL4 as a committed pathway node biochemically separating kauralexin and dolabralexin metabolism, and suggest an interactive role of maize dolabralexins in plant vigor during abiotic stress.
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Affiliation(s)
- Katherine M Murphy
- Department of Plant Biology, University of California-Davis, Davis, CA 95616, USA
| | - Tyler Dowd
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Ahmed Khalil
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Si Nian Char
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| | - Bing Yang
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| | - Benjamin J Endelman
- Department of Plant Biology, University of California-Davis, Davis, CA 95616, USA
| | - Patrick M Shih
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA 94720, USA
| | | | - Eric A Schmelz
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093, USA
| | - Philipp Zerbe
- Department of Plant Biology, University of California-Davis, Davis, CA 95616, USA
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25
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Wang Y, Shi D, Zhu H, Yin H, Wang G, Yang A, Song Z, Jing Q, Shuai B, Xu N, Yang J, Chen H, Wang G. Revisiting maize Brittle endosperm-2 reveals new insights in BETL development and starchy endosperm filling. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 332:111727. [PMID: 37149228 DOI: 10.1016/j.plantsci.2023.111727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/18/2023] [Accepted: 05/03/2023] [Indexed: 05/08/2023]
Abstract
Rerouting the starch biosynthesis pathway in maize can generate specialty types, like sweet corn and waxy corn, with a drastically increasing global demand. Hence, a fine-tuning of starch metabolism is relevant to create diverse maize cultivars for end-use applications. Here, we characterized a new maize brittle endosperm mutant, referred to as bt1774, which exhibited decreased starch content but a dramatic increase of soluble sugars at maturity. Both endosperm and embryo development was impaired in bt1774 relative to the wild-type (WT), with a prominently arrested basal endosperm transfer layer (BETL). Map-based cloning revealed that BRITTLE ENDOSPERM2 (Bt2), which encodes a small subunit of ADP-glucose pyrophosphorylase (AGPase), is the causal gene for bt1774. A MuA2 element was found to be inserted into intron 2 of Bt2, leading to a severe decrease of its expression, in bt1774. This is in line with the irregular and loosely packed starch granules in the mutant. Transcriptome of endosperm at grain filling stage identified 1, 013 differentially expressed genes in bt1774, which were notably enriched in the BETL compartment, including ZmMRP1, Miniature1, MEG1, and BETLs. Gene expression of the canonical starch biosynthesis pathway was marginally disturbed in Bt1774. Combined with the residual 60% of starch in this nearly null mutant of Bt2, this data strongly suggests that an AGPase-independent pathway compensates for starch synthesis in the endosperm. Consistent with the BETL defects, zein accumulation was impaired in bt1774. Co-expression network analysis revealed that Bt2 probably has a role in intracellular signal transduction, besides starch synthesis. Altogether, we propose that Bt2 is likely involved in carbohydrate flux and balance, thus regulating both the BETL development and the starchy endosperm filling.
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Affiliation(s)
- Yongyan Wang
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT-China (Henan) Joint Center of Wheat and Maize, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Dongsheng Shi
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
| | - Hui Zhu
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT-China (Henan) Joint Center of Wheat and Maize, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Hanxue Yin
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT-China (Henan) Joint Center of Wheat and Maize, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Gaoyang Wang
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT-China (Henan) Joint Center of Wheat and Maize, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Anqi Yang
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT-China (Henan) Joint Center of Wheat and Maize, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhixuan Song
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT-China (Henan) Joint Center of Wheat and Maize, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Qingquan Jing
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT-China (Henan) Joint Center of Wheat and Maize, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Bilian Shuai
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Ningkun Xu
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT-China (Henan) Joint Center of Wheat and Maize, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Jianping Yang
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT-China (Henan) Joint Center of Wheat and Maize, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Hongyu Chen
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT-China (Henan) Joint Center of Wheat and Maize, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China.
| | - Guifeng Wang
- National Key Laboratory of Wheat and Maize Crops Science, CIMMYT-China (Henan) Joint Center of Wheat and Maize, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China.
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26
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Katral A, Hossain F, Gopinath I, Chand G, Mehta BK, Kamboj MC, Zunjare RU, Yadava DK, Muthusamy V. Genetic dissection of embryo size and weight related traits for enhancement of kernel oil in maize. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 197:107668. [PMID: 37003215 DOI: 10.1016/j.plaphy.2023.107668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/01/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
Embryo is a key determinant of kernel-oil in maize. Higher calorific value of maize kernel is attributed to increment in kernel-oil and it stores in specialised structure called embryo. Understanding the genetic behaviour of embryo size and weight related-traits is inevitable task for genetic improvement of kernel-oil. Here, the six-basic generations (P1, P2, F1, F2, BC1P1 and BC1P2) of three crosses (CRPBIO-962 × EC932601, CRPBIO-973 × CRPBIO-966 and CRPBIO-966 × CRPBIO-979) between contrasting embryo-sized maize inbreds were field evaluated at three locations to decipher the genetics of twenty embryo, kernel and embryo-to-kernel related-traits through generation-mean-analysis (GMA). Combined ANOVA revealed the significance of all the traits among generations; however, location and generation × location were found to be non-significant (P > 0.05) for most of the traits. Significance (P < 0.05) of scaling and joint-scaling tests revealed the presence of non-allelic interactions. Elucidation of six-parameters disclosed the predominance of dominance main-effect (h) and dominance × dominance interaction-effect (l) for most of traits. The signs of (h) and (l) indicated the prevalence of duplicate-epistasis type across crosses and locations. Thus, the population improvement approaches along with heterosis breeding method could be effective for improvement of these traits. Quantitative inheritance pattern was observed for all the traits with high broad-sense heritability and better-stability across locations. The study also predicted one to three major-gene blocks/QTLs for embryo-traits and up to 11 major-gene blocks/QTLs for embryo-to-kernel traits. These findings could provide deep insights to strategize extensive breeding methods to improve embryo traits for enhancing kernel-oil in sustainable manner.
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Affiliation(s)
| | - Firoz Hossain
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Gulab Chand
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Brijesh K Mehta
- ICAR-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Mehar C Kamboj
- Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
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27
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Yu B, Gao P, Song J, Yang H, Qin L, Yu X, Song H, Coulson J, Bekkaoui Y, Akhov L, Han X, Cram D, Wei Y, Zaharia LI, Zou J, Konkin D, Quilichini TD, Fobert P, Patterson N, Datla R, Xiang D. Spatiotemporal transcriptomics and metabolic profiling provide insights into gene regulatory networks during lentil seed development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 36965062 DOI: 10.1111/tpj.16205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/13/2023] [Accepted: 03/20/2023] [Indexed: 06/18/2023]
Abstract
Lentil (Lens culinaris Medik.) is a nutritious legume with seeds rich in protein, minerals and an array of diverse specialized metabolites. The formation of a seed requires regulation and tight coordination of developmental programs to form the embryo, endosperm and seed coat compartments, which determines the structure and composition of mature seed and thus its end-use quality. Understanding the molecular and cellular events and metabolic processes of seed development is essential for improving lentil yield and seed nutritional value. However, such information remains largely unknown, especially at the seed compartment level. In this study, we generated high-resolution spatiotemporal gene expression profiles in lentil embryo, seed coat and whole seeds from fertilization through maturation. Apart from anatomic differences between the embryo and seed coat, comparative transcriptomics and weighted gene co-expression network analysis revealed embryo- and seed coat-specific genes and gene modules predominant in specific tissues and stages, which highlights distinct genetic programming. Furthermore, we investigated the dynamic profiles of flavonoid, isoflavone, phytic acid and saponin in seed compartments across seed development. Coupled with transcriptome data, we identified sets of candidate genes involved in the biosynthesis of these metabolites. The global view of the transcriptional and metabolic changes of lentil seed tissues throughout development provides a valuable resource for dissecting the genetic control of secondary metabolism and development of molecular tools for improving seed nutritional quality.
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Affiliation(s)
- Bianyun Yu
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Peng Gao
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Jingpu Song
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Hui Yang
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Li Qin
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4L8, Canada
| | - Xiaoyu Yu
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4L8, Canada
| | - Halim Song
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Justin Coulson
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Yasmina Bekkaoui
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Leonid Akhov
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Xiumei Han
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Dustin Cram
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Yangdou Wei
- College of Art & Science, University of Saskatchewan, 9 Campus Drive, Saskatoon, SK, S7N 5A5, Canada
| | - L Irina Zaharia
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Jitao Zou
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - David Konkin
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Teagen D Quilichini
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Pierre Fobert
- Aquatic and Crop Resource Development, National Research Council Canada, Ottawa, Ontario, K1A 0R6, Canada
| | - Nii Patterson
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Raju Datla
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4L8, Canada
| | - Daoquan Xiang
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
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28
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Gao J, Zhang L, Du H, Dong Y, Zhen S, Wang C, Wang Q, Yang J, Zhang P, Zheng X, Li Y. An ARF24-ZmArf2 module influences kernel size in different maize haplotypes. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36866706 DOI: 10.1111/jipb.13473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 02/28/2023] [Indexed: 06/19/2023]
Abstract
Members of the ADP-ribosylation factor family, which are GTP-binding proteins, are involved in metabolite transport, cell division, and expansion. Although there has been a significant amount of research on small GTP-binding proteins, their roles and functions in regulating maize kernel size remain elusive. Here, we identified ZmArf2 as a maize ADP-ribosylation factor-like family member that is highly conserved during evolution. Maize zmarf2 mutants showed a characteristic smaller kernel size. Conversely, ZmArf2 overexpression increased maize kernel size. Furthermore, heterologous expression of ZmArf2 dramatically elevated Arabidopsis and yeast growth by promoting cell division. Using expression quantitative trait loci (eQTL) analysis, we determined that ZmArf2 expression levels in various lines were mainly associated with variation at the gene locus. The promoters of ZmArf2 genes could be divided into two types, pS and pL, that were significantly associated with both ZmArf2 expression levels and kernel size. In yeast-one-hybrid screening, maize Auxin Response Factor 24 (ARF24) is directly bound to the ZmArf2 promoter region and negatively regulated ZmArf2 expression. Notably, the pS and pL promoter types each contained an ARF24 binding element: an auxin response element (AuxRE) in pS and an auxin response region (AuxRR) in pL, respectively. ARF24 binding affinity to AuxRR was much higher compared with AuxRE. Overall, our results establish that the small G-protein ZmArf2 positively regulates maize kernel size and reveals the mechanism of its expression regulation.
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Affiliation(s)
- Jie Gao
- State Key Laboratory of Wheat and Maize Crop Science, Henan Maize Engineering Technology Joint Center, College of Agronomy, and Center for Crop Genome Engineering, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, 450046, China
| | - Long Zhang
- State Key Laboratory of Wheat and Maize Crop Science, Henan Maize Engineering Technology Joint Center, College of Agronomy, and Center for Crop Genome Engineering, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, 450046, China
| | - Haonan Du
- State Key Laboratory of Wheat and Maize Crop Science, Henan Maize Engineering Technology Joint Center, College of Agronomy, and Center for Crop Genome Engineering, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yongbin Dong
- State Key Laboratory of Wheat and Maize Crop Science, Henan Maize Engineering Technology Joint Center, College of Agronomy, and Center for Crop Genome Engineering, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, 450046, China
| | - Sihan Zhen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chen Wang
- State Key Laboratory of Wheat and Maize Crop Science, Henan Maize Engineering Technology Joint Center, College of Agronomy, and Center for Crop Genome Engineering, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, 450046, China
| | - Qilei Wang
- State Key Laboratory of Wheat and Maize Crop Science, Henan Maize Engineering Technology Joint Center, College of Agronomy, and Center for Crop Genome Engineering, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, 450046, China
| | - Jingyu Yang
- State Key Laboratory of Wheat and Maize Crop Science, Henan Maize Engineering Technology Joint Center, College of Agronomy, and Center for Crop Genome Engineering, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, 450046, China
| | - Paifeng Zhang
- State Key Laboratory of Wheat and Maize Crop Science, Henan Maize Engineering Technology Joint Center, College of Agronomy, and Center for Crop Genome Engineering, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xu Zheng
- State Key Laboratory of Wheat and Maize Crop Science, Henan Maize Engineering Technology Joint Center, College of Agronomy, and Center for Crop Genome Engineering, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yuling Li
- State Key Laboratory of Wheat and Maize Crop Science, Henan Maize Engineering Technology Joint Center, College of Agronomy, and Center for Crop Genome Engineering, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, 450046, China
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29
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Wan W, Wu Y, Hu D, Ye F, Wu X, Qi X, Liang H, Zhou H, Xue J, Xu S, Zhang X. Genome-wide association analysis of kernel nutritional quality in two natural maize populations. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:18. [PMID: 37313300 PMCID: PMC10248675 DOI: 10.1007/s11032-023-01360-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 02/05/2023] [Indexed: 06/15/2023]
Abstract
As one of the three staple crops, nutritional traits in maize are important for human and animal nutrition. Grain quality-related traits are closely related to grain commercial value. Understanding the genetic basis of quality-related traits in maize would be helpful for breeding high-quality maize varieties. In this study, two association panels (AM122 and AM180) were subjected to genome-wide association analysis of grain quality-related traits, including protein content, oil content, starch content, and fiber content. In total, 98 SNPs (P < 1 × 10-4) were identified to be significantly associated with these four grain quality-related traits. By integrating two sets of public transcriptome data, 31 genes located in 200 kb regions flanking the associated SNP showed high expression during kernel development and were differentially expressed in two maize inbred lines, KA225 and KB035, with significantly different quality. These genes might regulate maize grain quality by participating in plant hormone processes, autophagy processes, and others. All these results could provide important reference information for breeding high‑quality maize varieties. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01360-w.
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Affiliation(s)
- Wenting Wan
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Ying Wu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Die Hu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Fan Ye
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Xiaopeng Wu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Xingyue Qi
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Hangyu Liang
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Haiyang Zhou
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Jiquan Xue
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Shutu Xu
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
| | - Xinghua Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
- Maize Engineering Technology Research Centre, Yangling, 712100 Shaanxi China
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30
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Zhou Q, Fu Z, Li M, Shen Q, Sun C, Feng Y, Liu Y, Jiang J, Qin T, Mao T, Hearne SJ, Wang G, Tang J. Maize tubulin folding cofactor B is required for cell division and cell growth through modulating microtubule homeostasis. THE NEW PHYTOLOGIST 2023. [PMID: 36843261 DOI: 10.1111/nph.18839] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Tubulin folding cofactors (TFCs) are required for tubulin folding, α/β tubulin heterodimer formation, and microtubule (MT) dynamics in yeast and mammals. However, the functions of their plant counterparts remain to be characterized. We identified a natural maize crumpled kernel mutant, crk2, which exhibits reductions in endosperm cell number and size, as well as embryo/seedling lethality. Map-based cloning and functional complementation confirmed that ZmTFCB is causal for the mutation. ZmTFCB is targeted mainly to the cytosol. It facilitates α-tubulin folding and heterodimer formation through sequential interactions with the cytosolic chaperonin-containing TCP-1 ε subunit ZmCCT5 and ZmTFCE, thus affecting the organization of both the spindle and phragmoplast MT array and the cortical MT polymerization and array formation, which consequently mediated cell division and cell growth. We detected a physical association between ZmTFCB and the maize MT plus-end binding protein END-BINDING1 (ZmEB1), indicating that ZmTFCB1 may modulate MT dynamics by sequestering ZmEB1. Our data demonstrate that ZmTFCB is required for cell division and cell growth through modulating MT homeostasis, an evolutionarily conserved machinery with some species-specific divergence.
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Affiliation(s)
- Qingqian Zhou
- National Key Laboratory of Wheat and Maize Crops Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zhiyuan Fu
- National Key Laboratory of Wheat and Maize Crops Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Mengyuan Li
- National Key Laboratory of Wheat and Maize Crops Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Qingwen Shen
- National Key Laboratory of Wheat and Maize Crops Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Canran Sun
- National Key Laboratory of Wheat and Maize Crops Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yijian Feng
- National Key Laboratory of Wheat and Maize Crops Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yang Liu
- National Key Laboratory of Wheat and Maize Crops Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Jianjun Jiang
- National Key Laboratory of Wheat and Maize Crops Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Tao Qin
- College of Grassland Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Tonglin Mao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Sarah Jane Hearne
- CIMMYT, KM 45 Carretera Mexico-Veracruz, El Batan, Texcoco, Estado de México, 56237, Mexico
| | - Guifeng Wang
- National Key Laboratory of Wheat and Maize Crops Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crops Science/Collaborative Innovation Center of Henan Grain Crops/College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
- The Shennong Laboratory, Zhengzhou, Henan, 450002, China
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31
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Li X, Wu J, Yi F, Lai J, Chen J. High temporal-resolution transcriptome landscapes of maize embryo sac and ovule during early seed development. PLANT MOLECULAR BIOLOGY 2023; 111:233-248. [PMID: 36508138 DOI: 10.1007/s11103-022-01318-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 10/07/2022] [Indexed: 06/18/2023]
Abstract
Here we provided a high temporal-resolution transcriptome atlas of maize embryo sac and ovule to reveal the gene activity dynamic during early seed development. The early maize (Zea mays) seed development is initiated from double fertilization in the embryo sac and needs to undergo a highly dynamic and complex development process to form the differentiated embryo and endosperm. Despite the importance of maize seed for food, feed, and biofuel, many regulators responsible for controlling its early development are not known yet. Here, we reported a high temporal-resolution transcriptome atlas of embryo sac and ovule based on 44 time point samples collected within the first four days of seed development. A total of 25,187 genes including 1598 transcription factors (TFs) involved in early seed development were detected. Global comparisons of the expressions of these genes revealed five distinct development stages of early seed, which are mainly related to double fertilization, asymmetric cell division of the zygote, as well as coenocyte formation, cellularization and differentiation in endosperm. We identified 3327 seed-specific genes, which more than one thousand seed-specific genes with main expressions during early seed development were newly identified here, including 859 and 186 genes predominantly expressed in the embryo sac and ovule, respectively. Combined with the published transcriptome data of seed, we uncovered the dominant auxin biosynthesis, transport and signaling related genes at different development stages and subregions of seed. These results are helpful for understanding the genetic control of early seed development.
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Affiliation(s)
- Xinchen Li
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, People's Republic of China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, People's Republic of China
| | - Jian Wu
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Fei Yi
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, People's Republic of China
- Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing, People's Republic of China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, People's Republic of China
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, People's Republic of China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, People's Republic of China
| | - Jian Chen
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, People's Republic of China.
- Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, People's Republic of China.
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, People's Republic of China.
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32
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Yao D, Wang J, Peng W, Zhang B, Wen X, Wan X, Wang X, Li X, Ma J, Liu X, Fan Y, Sun G. Transcriptomic profiling of wheat stem during meiosis in response to freezing stress. FRONTIERS IN PLANT SCIENCE 2023; 13:1099677. [PMID: 36714719 PMCID: PMC9878610 DOI: 10.3389/fpls.2022.1099677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
Low temperature injury in spring has seriously destabilized the production and grain quality of common wheat. However, the molecular mechanisms underlying spring frost tolerance remain elusive. In this study, we investigated the response of a frost-tolerant wheat variety Zhongmai8444 to freezing stress at the meiotic stage. Transcriptome profiles over a time course were subsequently generated by high-throughput sequencing. Our results revealed that the prolonged freezing temperature led to the significant reductions in plant height and seed setting rate. Cell wall thickening in the vascular tissue was also observed in the stems. RNA-seq analyses demonstrated the identification of 1010 up-regulated and 230 down-regulated genes shared by all time points of freezing treatment. Enrichment analysis revealed that gene activity related to hormone signal transduction and cell wall biosynthesis was significantly modulated under freezing. In addition, among the identified differentially expressed genes, 111 transcription factors belonging to multiple gene families exhibited dynamic expression pattern. This study provided valuable gene resources beneficial for the breeding of wheat varieties with improved spring frost tolerance.
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Affiliation(s)
- Danyu Yao
- National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Juan Wang
- National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wentao Peng
- National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agricultural Science and Engineering, Liaocheng University, Liaocheng, Shandong, China
| | - Bowen Zhang
- National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agronomy, Jilin Agricultural University, Changchun, Jilin, China
| | - Xiaolan Wen
- National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, Hebei, China
| | - Xiaoneng Wan
- National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiuyuan Wang
- National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agricultural Science and Engineering, Liaocheng University, Liaocheng, Shandong, China
| | - Xinchun Li
- National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Ma
- College of Agronomy, Jilin Agricultural University, Changchun, Jilin, China
| | - Xiaofen Liu
- College of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, Hebei, China
| | - Yinglun Fan
- College of Agricultural Science and Engineering, Liaocheng University, Liaocheng, Shandong, China
| | - Guozhong Sun
- National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Yang T, Wu X, Wang W, Wu Y. Regulation of seed storage protein synthesis in monocot and dicot plants: A comparative review. MOLECULAR PLANT 2023; 16:145-167. [PMID: 36495013 DOI: 10.1016/j.molp.2022.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/27/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Seeds are a major source of nutrients for humans and animal livestock worldwide. With improved living standards, high nutritional quality has become one of the main targets for breeding. Storage protein content in seeds, which is highly variable depending on plant species, serves as a pivotal criterion of seed nutritional quality. In the last few decades, our understanding of the molecular genetics and regulatory mechanisms of storage protein synthesis has greatly advanced. Here, we systematically and comprehensively summarize breakthroughs on the conservation and divergence of storage protein synthesis in dicot and monocot plants. With regard to storage protein accumulation, we discuss evolutionary origins, developmental processes, characteristics of main storage protein fractions, regulatory networks, and genetic modifications. In addition, we discuss potential breeding strategies to improve storage protein accumulation and provide perspectives on some key unanswered problems that need to be addressed.
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Affiliation(s)
- Tao Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Xingguo Wu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200233, China
| | - Wenqin Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200233, China
| | - Yongrui Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
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34
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Ning L, Wang Y, Shi X, Zhou L, Ge M, Liang S, Wu Y, Zhang T, Zhao H. Nitrogen-dependent binding of the transcription factor PBF1 contributes to the balance of protein and carbohydrate storage in maize endosperm. THE PLANT CELL 2023; 35:409-434. [PMID: 36222567 PMCID: PMC9806651 DOI: 10.1093/plcell/koac302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Fluctuations in nitrogen (N) availability influence protein and starch levels in maize (Zea mays) seeds, yet the underlying mechanism is not well understood. Here, we report that N limitation impacted the expression of many key genes in N and carbon (C) metabolism in the developing endosperm of maize. Notably, the promoter regions of those genes were enriched for P-box sequences, the binding motif of the transcription factor prolamin-box binding factor 1 (PBF1). Loss of PBF1 altered accumulation of starch and proteins in endosperm. Under different N conditions, PBF1 protein levels remained stable but PBF1 bound different sets of target genes, especially genes related to the biosynthesis and accumulation of N and C storage products. Upon N-starvation, the absence of PBF1 from the promoters of some zein genes coincided with their reduced expression, suggesting that PBF1 promotes zein accumulation in the endosperm. In addition, PBF1 repressed the expression of sugary1 (Su1) and starch branching enzyme 2b (Sbe2b) under normal N supply, suggesting that, under N-deficiency, PBF1 redirects the flow of C skeletons for zein toward the formation of C compounds. Overall, our study demonstrates that PBF1 modulates C and N metabolism during endosperm development in an N-dependent manner.
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Affiliation(s)
| | | | - Xi Shi
- Institute of Crop Germplasm and Biotechnology, Jiangsu Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, China
| | - Ling Zhou
- Institute of Crop Germplasm and Biotechnology, Jiangsu Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, China
| | - Min Ge
- Institute of Crop Germplasm and Biotechnology, Jiangsu Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, China
| | - Shuaiqiang Liang
- Institute of Crop Germplasm and Biotechnology, Jiangsu Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, China
| | - Yibo Wu
- Institute of Crop Germplasm and Biotechnology, Jiangsu Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, China
| | - Tifu Zhang
- Institute of Crop Germplasm and Biotechnology, Jiangsu Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, 210014, China
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35
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Conservation Study of Imprinted Genes in Maize Triparental Heterozygotic Kernels. Int J Mol Sci 2022; 23:ijms232315424. [PMID: 36499766 PMCID: PMC9735609 DOI: 10.3390/ijms232315424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 12/12/2022] Open
Abstract
Genomic imprinting is a classic epigenetic phenomenon related to the uniparental expression of genes. Imprinting variability exists in seeds and can contribute to observed parent-of-origin effects on seed development. Here, we conducted allelic expression of the embryo and endosperm from four crosses at 11 days after pollination (DAP). First, the F1 progeny of B73(♀) × Mo17(♂) and the inducer line CAU5 were used as parents to obtain reciprocal crosses of BM-C/C-BM. Additionally, the F1 progeny of Mo17(♀) × B73(♂) and CAU5 were used as parents to obtain reciprocal crosses of MB-C/C-MB. In total, 192 and 181 imprinted genes were identified in the BM-C/C-BM and MB-C/C-MB crosses, respectively. Then, by comparing the allelic expression of these imprinted genes in the reciprocal crosses of B73 and CAU5 (BC/CB), fifty-one Mo17-added non-conserved genes were identified as exhibiting imprinting variability. Fifty-one B73-added non-conserved genes were also identified by comparing the allelic expression of imprinted genes identified in BM-C/C-BM, MB-C/C-MB and MC/CM crosses. Specific Gene Ontology (GO) terms were not enriched in B73-added/Mo17-added non-conserved genes. Interestingly, the imprinting status of these genes was less conserved across other species. The cis-element distribution, tissue expression and subcellular location were similar between the B73-added/Mo17-added conserved and B73-added/Mo17-added non-conserved imprinted genes. Finally, genotypic and phenotypic analysis of one non-conserved gene showed that the mutation and overexpression of this gene may affect embryo and kernel size, which indicates that these non-conserved genes may also play an important role in kernel development. The findings of this study will be helpful for elucidating the imprinting mechanism of genes involved in maize kernel development.
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36
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Huang Y, Wang H, Zhu Y, Huang X, Li S, Wu X, Zhao Y, Bao Z, Qin L, Jin Y, Cui Y, Ma G, Xiao Q, Wang Q, Wang J, Yang X, Liu H, Lu X, Larkins BA, Wang W, Wu Y. THP9 enhances seed protein content and nitrogen-use efficiency in maize. Nature 2022; 612:292-300. [PMID: 36385527 DOI: 10.1038/s41586-022-05441-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 10/12/2022] [Indexed: 11/17/2022]
Abstract
Teosinte, the wild ancestor of maize (Zea mays subsp. mays), has three times the seed protein content of most modern inbreds and hybrids, but the mechanisms that are responsible for this trait are unknown1,2. Here we use trio binning to create a contiguous haplotype DNA sequence of a teosinte (Zea mays subsp. parviglumis) and, through map-based cloning, identify a major high-protein quantitative trait locus, TEOSINTE HIGH PROTEIN 9 (THP9), on chromosome 9. THP9 encodes an asparagine synthetase 4 enzyme that is highly expressed in teosinte, but not in the B73 inbred, in which a deletion in the tenth intron of THP9-B73 causes incorrect splicing of THP9-B73 transcripts. Transgenic expression of THP9-teosinte in B73 significantly increased the seed protein content. Introgression of THP9-teosinte into modern maize inbreds and hybrids greatly enhanced the accumulation of free amino acids, especially asparagine, throughout the plant, and increased seed protein content without affecting yield. THP9-teosinte seems to increase nitrogen-use efficiency, which is important for promoting a high yield under low-nitrogen conditions.
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Affiliation(s)
- Yongcai Huang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences, Shanghai, China
| | - Haihai Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences, Shanghai, China
| | - Yidong Zhu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences, Shanghai, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Xing Huang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences, Shanghai, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Shuai Li
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xingguo Wu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yao Zhao
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Zhigui Bao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Li Qin
- Institute of Molecular Breeding for Maize, Qilu Normal University, Jinan, China
| | - Yongbo Jin
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yahui Cui
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Guangjin Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences, Shanghai, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Qiao Xiao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences, Shanghai, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Qiong Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences, Shanghai, China
| | - Jiechen Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences, Shanghai, China
| | - Xuerong Yang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Hongjun Liu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Xiaoduo Lu
- Institute of Molecular Breeding for Maize, Qilu Normal University, Jinan, China
| | - Brian A Larkins
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Wenqin Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China.
| | - Yongrui Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology Chinese Academy of Sciences, Shanghai, China.
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37
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Hu M, Li Y, Zhang X, Song W, Jin W, Huang W, Zhao H. Maize sterility gene DRP1 encodes a desiccation-related protein that is critical for Ubisch bodies and pollen exine development. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6800-6815. [PMID: 35922377 DOI: 10.1093/jxb/erac331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 07/30/2022] [Indexed: 06/15/2023]
Abstract
Desiccation tolerance is a remarkable feature of pollen, seeds, and resurrection-type plants. Exposure to desiccation stress can cause sporophytic defects, resulting in male sterility. Here, we report the novel maize sterility gene DRP1 (Desiccation-Related Protein 1), which was identified by bulked-segregant analysis sequencing and encodes a desiccation-related protein. Loss of function of DRP1 results in abnormal Ubisch bodies, defective tectum of the pollen exine, and complete male sterility. Our results suggest that DRP1 may facilitate anther dehydration to maintain appropriate water status. DRP1 is a secretory protein that is specifically expressed in the tapetum and microspore from the tetrad to the uninucleate microspore stage. Differentially expressed genes in drp1 are enriched in Gene Ontology terms for pollen exine formation, polysaccharide catabolic process, extracellular region, and response to heat. In addition, DRP1 is a target of selection that appears to have played an important role in the spread of maize from tropical/subtropical to temperate regions. Taken together, our results suggest that DRP1 encodes a desiccation-related protein whose loss of function causes male sterility. Our findings provide a potential genetic resource that may be used to design crops for heterosis utilization.
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Affiliation(s)
- Mingjian Hu
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
- State Key Laboratory of Wheat and Maize Crop Science and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Yunfei Li
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Xiangbo Zhang
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Weibin Song
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Weiwei Jin
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
- College of Agronomy & Resources and Environment, Tianjin Agricultural University, Tianjin, China
| | - Wei Huang
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Haiming Zhao
- State Key Laboratory of Plant Physiology and Biochemistry and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
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38
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Yang B, Wang J, Yu M, Zhang M, Zhong Y, Wang T, Liu P, Song W, Zhao H, Fastner A, Suter M, Rentsch D, Ludewig U, Jin W, Geiger D, Hedrich R, Braun DM, Koch KE, McCarty DR, Wu WH, Li X, Wang Y, Lai J. The sugar transporter ZmSUGCAR1 of the nitrate transporter 1/peptide transporter family is critical for maize grain filling. THE PLANT CELL 2022; 34:4232-4254. [PMID: 36047828 PMCID: PMC9614462 DOI: 10.1093/plcell/koac256] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 07/31/2022] [Indexed: 05/07/2023]
Abstract
Maternal-to-filial nutrition transfer is central to grain development and yield. nitrate transporter 1/peptide transporter (NRT1-PTR)-type transporters typically transport nitrate, peptides, and ions. Here, we report the identification of a maize (Zea mays) NRT1-PTR-type transporter that transports sucrose and glucose. The activity of this sugar transporter, named Sucrose and Glucose Carrier 1 (SUGCAR1), was systematically verified by tracer-labeled sugar uptake and serial electrophysiological studies including two-electrode voltage-clamp, non-invasive microelectrode ion flux estimation assays in Xenopus laevis oocytes and patch clamping in HEK293T cells. ZmSUGCAR1 is specifically expressed in the basal endosperm transfer layer and loss-of-function mutation of ZmSUGCAR1 caused significantly decreased sucrose and glucose contents and subsequent shrinkage of maize kernels. Notably, the ZmSUGCAR1 orthologs SbSUGCAR1 (from Sorghum bicolor) and TaSUGCAR1 (from Triticum aestivum) displayed similar sugar transport activities in oocytes, supporting the functional conservation of SUGCAR1 in closely related cereal species. Thus, the discovery of ZmSUGCAR1 uncovers a type of sugar transporter essential for grain development and opens potential avenues for genetic improvement of seed-filling and yield in maize and other grain crops.
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Affiliation(s)
- Bo Yang
- State Key Laboratory of Plant Physiology and Biochemistry (SKLPPB) and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Jing Wang
- State Key Laboratory of Plant Physiology and Biochemistry (SKLPPB) and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Miao Yu
- State Key Laboratory of Plant Physiology and Biochemistry (SKLPPB), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Meiling Zhang
- State Key Laboratory of Plant Physiology and Biochemistry (SKLPPB) and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Yanting Zhong
- The Key Laboratory of Plant–Soil Interactions (MOE), Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Tianyi Wang
- National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Peng Liu
- Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Weibin Song
- State Key Laboratory of Plant Physiology and Biochemistry (SKLPPB) and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Haiming Zhao
- State Key Laboratory of Plant Physiology and Biochemistry (SKLPPB) and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Astrid Fastner
- Institute of Plant Sciences, University of Bern, Bern 3013, Switzerland
| | - Marianne Suter
- Institute of Plant Sciences, University of Bern, Bern 3013, Switzerland
| | - Doris Rentsch
- Institute of Plant Sciences, University of Bern, Bern 3013, Switzerland
| | - Uwe Ludewig
- Institute of Crop Science, Nutritional Crop Physiology (340h), University of Hohenheim, Stuttgart 70593, Germany
| | - Weiwei Jin
- National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Dietmar Geiger
- Department of Molecular Plant Physiology and Biophysics, Julius-von-Sachs-Institute for Biosciences, University of Würzburg, Würzburg 97082, Germany
| | - Rainer Hedrich
- Department of Molecular Plant Physiology and Biophysics, Julius-von-Sachs-Institute for Biosciences, University of Würzburg, Würzburg 97082, Germany
| | - David M Braun
- Division of Biological Sciences, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, 116 Tucker Hall, Columbia, Missouri 65211, USA
| | - Karen E Koch
- Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Donald R McCarty
- Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Wei-Hua Wu
- State Key Laboratory of Plant Physiology and Biochemistry (SKLPPB), College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Xuexian Li
- The Key Laboratory of Plant–Soil Interactions (MOE), Department of Plant Nutrition, College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Yi Wang
- State Key Laboratory of Plant Physiology and Biochemistry (SKLPPB), College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry (SKLPPB) and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
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39
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Dai D, Mudunkothge JS, Galli M, Char SN, Davenport R, Zhou X, Gustin JL, Spielbauer G, Zhang J, Barbazuk WB, Yang B, Gallavotti A, Settles AM. Paternal imprinting of dosage-effect defective1 contributes to seed weight xenia in maize. Nat Commun 2022; 13:5366. [PMID: 36100609 PMCID: PMC9470594 DOI: 10.1038/s41467-022-33055-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Historically, xenia effects were hypothesized to be unique genetic contributions of pollen to seed phenotype, but most examples represent standard complementation of Mendelian traits. We identified the imprinted dosage-effect defective1 (ded1) locus in maize (Zea mays) as a paternal regulator of seed size and development. Hypomorphic alleles show a 5–10% seed weight reduction when ded1 is transmitted through the male, while homozygous mutants are defective with a 70–90% seed weight reduction. Ded1 encodes an R2R3-MYB transcription factor expressed specifically during early endosperm development with paternal allele bias. DED1 directly activates early endosperm genes and endosperm adjacent to scutellum cell layer genes, while directly repressing late grain-fill genes. These results demonstrate xenia as originally defined: Imprinting of Ded1 causes the paternal allele to set the pace of endosperm development thereby influencing grain set and size. Xenia effects describe the genetic contribution of pollen to seed phenotypes. Here the authors show that paternal imprinting of Ded1 contributes to the xenia effect in maize by setting the pace of endosperm development.
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Affiliation(s)
- Dawei Dai
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Janaki S Mudunkothge
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Mary Galli
- Waksman Institute, Rutgers University, Piscataway, NJ, 08854, USA
| | - Si Nian Char
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Ruth Davenport
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Xiaojin Zhou
- Crop Functional Genome Research Center, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jeffery L Gustin
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA.,United States Department of Agriculture, Urbana, IL, 61801, USA
| | - Gertraud Spielbauer
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Junya Zhang
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - W Brad Barbazuk
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.,Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Andrea Gallavotti
- Waksman Institute, Rutgers University, Piscataway, NJ, 08854, USA.,Department of Plant Biology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - A Mark Settles
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA. .,Bioengineering Branch, NASA Ames Research Center, Moffett Field, CA, 94035, USA.
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40
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Zhang Y, Yang L, Hu H, Yang J, Cui J, Wei G, Xu J. Transcriptome and metabolome changes in Chinese cedar during cold acclimation reveal the roles of flavonoids in needle discoloration and cold resistance. TREE PHYSIOLOGY 2022; 42:1858-1875. [PMID: 35451493 DOI: 10.1093/treephys/tpac046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
Cryptomeria fortunei growth and development are usually affected by low temperatures. Despite the evergreen nature of this species, most needles turn yellowish-brown in cold winters. The underlying discoloration mechanisms that cause this phenomenon in response to cold acclimation remain poorly understood. Here, we measured the pigment content and ultrastructure of normal wild-type (Wt) and evergreen mutant (GM) C. fortunei needles and performed integrated transcriptomic and metabolomic analyses to explore potential discoloration mechanisms. The results showed that the needle chlorophyll content of these two genotypes decreased in winter. Wt needles showed greater decrease in the chlorophyll content and local destruction of chloroplast ultrastructure and contained larger amounts of flavonoids than GM needles, as shown by metabolomics analysis. We subsequently identified key differentially expressed genes in the flavonoid biosynthesis pathway and observed significantly upregulated flavonol synthase expression in Wt needles compared with GM needles that significantly increased the anthoxanthin (flavones and flavonols) content, which is likely a key factor underlying the difference in needle color between these two genotypes. Therefore, flavonoid metabolism may play important roles in the cold resistance and needle discoloration of C. fortunei, and our results provide an excellent foundation for the molecular mechanism of C. fortunei in response to cold stress.
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Affiliation(s)
- Yingting Zhang
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Liwei Yang
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Hailiang Hu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Junjie Yang
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Jiebing Cui
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Guangqian Wei
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Jin Xu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
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easyMF: A Web Platform for Matrix Factorization-Based Gene Discovery from Large-scale Transcriptome Data. Interdiscip Sci 2022; 14:746-758. [PMID: 35585280 DOI: 10.1007/s12539-022-00522-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 01/22/2023]
Abstract
With the development of high-throughput experimental technologies, large-scale RNA sequencing (RNA-Seq) data have been and continue to be produced, but have led to challenges in extracting relevant biological knowledge hidden in the produced high-dimensional gene expression matrices. Here, we develop easyMF ( https://github.com/cma2015/easyMF ), a web platform that can facilitate functional gene discovery from large-scale transcriptome data using matrix factorization (MF) algorithms. Compared with existing MF-based software packages, easyMF exhibits several promising features, such as greater functionality, flexibility and ease of use. The easyMF platform is equipped using the Big-Data-supported Galaxy system with user-friendly graphic user interfaces, allowing users with little programming experience to streamline transcriptome analysis from raw reads to gene expression, carry out multiple-scenario MF analysis, and perform multiple-way MF-based gene discovery. easyMF is also powered with the advanced packing technology to enhance ease of use under different operating systems and computational environments. We illustrated the application of easyMF for seed gene discovery from temporal, spatial, and integrated RNA-Seq datasets of maize (Zea mays L.), resulting in the identification of 3,167 seed stage-specific, 1,849 seed compartment-specific, and 774 seed-specific genes, respectively. The present results also indicated that easyMF can prioritize seed-related genes with superior prediction performance over the state-of-art network-based gene prioritization system MaizeNet. As a modular, containerized and open-source platform, easyMF can be further customized to satisfy users' specific demands of functional gene discovery and deployed as a web service for broad applications.
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Povilus RA, Friedman WE. Transcriptomes across fertilization and seed development in the water lily Nymphaea thermarum (Nymphaeales): evidence for epigenetic patterning during reproduction. PLANT REPRODUCTION 2022; 35:161-178. [PMID: 35184212 DOI: 10.1007/s00497-022-00438-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
The first record of gene expression during seed development within the Nymphaeales provides evidence for a variety of biological processes, including dynamic epigenetic patterning during sexual reproduction in the water lily Nymphaea thermarum. Studies of gene expression during seed development have been performed for a growing collection of species from a phylogenetically broad sampling of flowering plants (angiosperms). However, angiosperm lineages whose origins predate the divergence of monocots and eudicots have been largely overlooked. In order to provide a new resource for understanding the early evolution of seed development in flowering plants, we sequenced transcriptomes of whole ovules and seeds from three key stages of reproductive development in the waterlily Nymphaea thermarum, an experimentally tractable member of the Nymphaeales. We first explore patterns of gene expression, beginning with mature ovules and continuing through fertilization into early- and mid-stages of seed development. We find patterns of gene expression that corroborate histological/morphological observations of seed development in this species, such as expression of genes involved in starch synthesis and transcription factors that have been associated with embryo and endosperm development in other species. We also find evidence for processes that were previously not known to be occurring during seed development in this species, such as epigenetic modification. We then examine the expression of genes associated with patterning DNA and histone methylation-processes that are essential for seed development in distantly related and structurally diverse monocots and eudicots. Around 89% of transcripts putatively homologous to DNA and histone methylation modifiers are expressed during seed development in N. thermarum, including homologs of genes known to pattern imprinting-related epigenetic modifications. Our results suggest that dynamic epigenetic patterning is a deeply conserved aspect of angiosperm seed development.
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Affiliation(s)
- Rebecca A Povilus
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | - William E Friedman
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
- Arnold Arboretum of Harvard University, 1300 Centre Street, Boston, MA, 02131, USA.
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Jiang L, Liu C, Fan Y, Wu Q, Ye X, Li Q, Wan Y, Sun Y, Zou L, Xiang D, Lv Z. Dynamic transcriptome analysis suggests the key genes regulating seed development and filling in Tartary buckwheat (Fagopyrum tataricum Garetn.). Front Genet 2022; 13:990412. [PMID: 36072657 PMCID: PMC9441574 DOI: 10.3389/fgene.2022.990412] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Tartary buckwheat is highly attractive for the richness of nutrients and quality, yet post-embryonic seed abortion greatly halts the yield. Seed development is crucial for determining grain yield, whereas the molecular basis and regulatory network of Tartary buckwheat seed development and filling is not well understood at present. Here, we assessed the transcriptional dynamics of filling stage Tartary buckwheat seeds at three developmental stages by RNA sequencing. Among the 4249 differentially expressed genes (DEGs), genes related to seed development were identified. Specifically, 88 phytohormone biosynthesis signaling genes, 309 TFs, and 16 expansin genes participating in cell enlargement, 37 structural genes involved in starch biosynthesis represented significant variation and were candidate key seed development genes. Cis-element enrichment analysis indicated that the promoters of differentially expressed expansin genes and starch biosynthesis genes are rich of hormone-responsive (ABA-, AUX-, ET-, and JA-), and seed growth-related (MYB, MYC and WRKY) binding sites. The expansin DEGs showed strong correlations with DEGs in phytohormone pathways and transcription factors (TFs). In total, phytohormone ABA, AUX, ET, BR and CTK, and related TFs could substantially regulate seed development in Tartary buckwheat through targeting downstream expansin genes and structural starch biosynthetic genes. This transcriptome data could provide a theoretical basis for improving yield of Tartary buckwheat.
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Affiliation(s)
- Liangzhen Jiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Changying Liu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Yu Fan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Qi Wu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Xueling Ye
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Yan Wan
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Yanxia Sun
- College of Tourism and Culture Industry, Chengdu University, Chengdu, China
| | - Liang Zou
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, China
| | - Dabing Xiang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industralization, College of Food and Biological Engineering, Chengdu University, Chengdu, China
- *Correspondence: Dabing Xiang, ; Zhibin Lv,
| | - Zhibin Lv
- Department of Medical Instruments and Information, College of Biomedical Engineering, Sichuan University, Chengdu, China
- *Correspondence: Dabing Xiang, ; Zhibin Lv,
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44
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Guo Y, Chen Y, Zhang J, Li J, Fan K, Chen R, Liu Y, Zheng J, Fu J, Gu R, Wang G, Cui Y, Du X, Wang J. Epigenetic Mutation in a Tubulin-Folding Cofactor B (ZmTFCB) Gene Arrests Kernel Development in Maize. PLANT & CELL PHYSIOLOGY 2022; 63:1156-1167. [PMID: 35771678 DOI: 10.1093/pcp/pcac092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/26/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Epialleles, the heritable epigenetic variants that are not caused by changes in DNA sequences, can broaden genetic and phenotypic diversity and benefit to crop breeding, but very few epialleles related to agricultural traits have been identified in maize. Here, we cloned a small kernel mutant, smk-wl10, from maize, which encoded a tubulin-folding cofactor B (ZmTFCB) protein. Expression of the ZmTFCB gene decreased in the smk-wl10 mutant, which arrested embryo, endosperm and basal endosperm transfer layer developments. Overexpression of ZmTFCB could complement the defective phenotype of smk-wl10. No nucleotide sequence variation in ZmTFCB could be found between smk-wl10 and wild type (WT). Instead, we detected hypermethylation of nucleotide CHG (where H is A, C or T nucleotide) sequence contexts and increased level of histone H3K9me2 methylation in the upstream sequence of ZmTFCB in smk-wl10 compared with WT, which might respond to the attenuating transcription of ZmTFCB. In addition, yeast two-hybrid and bimolecular fluorescence complementation assays identified a strong interaction between ZmTFCB and its homolog ZmTFCE. Thus, our work identifies a novel epiallele of the maize ZmTFCB gene, which might represent a common phenomenon in the epigenetic regulation of important traits such as kernel development in maize.
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Affiliation(s)
- Yingmei Guo
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Yan Chen
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Jie Zhang
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jiankun Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kaijian Fan
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rongrong Chen
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yunjun Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jun Zheng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Junjie Fu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Riliang Gu
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Guoying Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yu Cui
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xuemei Du
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jianhua Wang
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
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Fei X, Wang Y, Zheng Y, Shen X, E L, Ding J, Lai J, Song W, Zhao H. Identification of two new QTLs of maize (Zea mays L.) underlying kernel row number using the HNAU-NAM1 population. BMC Genomics 2022; 23:593. [PMID: 35971070 PMCID: PMC9380338 DOI: 10.1186/s12864-022-08793-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 07/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Maize kernel row number (KRN) is one of the most important yield traits and has changed greatly during maize domestication and selection. Elucidating the genetic basis of KRN will be helpful to improve grain yield in maize. RESULTS Here, we measured KRN in four environments using a nested association mapping (NAM) population named HNAU-NAM1 with 1,617 recombinant inbred lines (RILs) that were derived from 12 maize inbred lines with a common parent, GEMS41. Then, five consensus quantitative trait loci (QTLs) distributing on four chromosomes were identified in at least three environments along with the best linear unbiased prediction (BLUP) values by the joint linkage mapping (JLM) method. These QTLs were further validated by the separate linkage mapping (SLM) and genome-wide association study (GWAS) methods. Three KRN genes cloned through the QTL assay were found in three of the five consensus QTLs, including qKRN1.1, qKRN2.1 and qKRN4.1. Two new QTLs of KRN, qKRN4.2 and qKRN9.1, were also identified. On the basis of public RNA-seq and genome annotation data, five genes highly expressed in ear tissue were considered candidate genes contributing to KRN. CONCLUSIONS This study carried out a comprehensive analysis of the genetic architecture of KRN by using a new NAM population under multiple environments. The present results provide solid information for understanding the genetic components underlying KRN and candidate genes in qKRN4.2 and qKRN9.1. Single-nucleotide polymorphisms (SNPs) closely linked to qKRN4.2 and qKRN9.1 could be used to improve inbred yield during molecular breeding in maize.
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Affiliation(s)
- Xiaohong Fei
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, 100193, People's Republic of China.,Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, People's Republic of China.,Longping Agriculture Science Co. Ltd, Beijing, 100004, People's Republic of China
| | - Yifei Wang
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, 100193, People's Republic of China.,Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Yunxiao Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, 100193, People's Republic of China.,Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Xiaomeng Shen
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, 100193, People's Republic of China.,Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Lizhu E
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, 100193, People's Republic of China.,Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Junqiang Ding
- State Key Laboratory of Wheat and Maize Crop Science and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, 450046, People's Republic of China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, 100193, People's Republic of China.,Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Weibin Song
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, 100193, People's Republic of China. .,Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, People's Republic of China.
| | - Haiming Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, 100193, People's Republic of China. .,Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, 100193, People's Republic of China.
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46
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Royo J, Muñiz LM, Gómez E, Añazco-Guenkova AM, Hueros G. Distinct Hormone Signalling-Modulation Activities Characterize Two Maize Endosperm-Specific Type-A Response Regulators. PLANTS 2022; 11:plants11151992. [PMID: 35956471 PMCID: PMC9370639 DOI: 10.3390/plants11151992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/22/2022] [Accepted: 07/27/2022] [Indexed: 11/23/2022]
Abstract
ZmTCRR1 and 2 are type-A response regulators expressed in the maize endosperm transfer cells (TC). While type-B response regulators transcriptionally control canonical type-A response regulators, as part of the cytokinin signal transduction mechanism, the ZmTCRRs are regulated by ZmMRP1, a master regulator of TC identity. In addition, the corresponding proteins are not detected in the TC, accumulating in the inner endosperm cells instead. These features suggest these molecules are not involved in classical, cell-autonomous, cytokinin signalling pathways. Using transgenic Arabidopsis plants ectopically expressing these genes, we have shown that ZmTCRR1 and 2 can modulate auxin and cytokinin signalling, respectively. In Arabidopsis, the ectopic expression of ZmTCRR2 blocked, almost completely, cytokinin perception. Given the conservation of these signalling pathways at the molecular level, our results suggest that the ZmTCRRs modulate cytokinin and auxin perception in the inner endosperm cells.
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47
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Li H, Luo L, Wang Y, Zhang J, Huang Y. Genome-Wide Characterization and Phylogenetic Analysis of GSK Genes in Maize and Elucidation of Their General Role in Interaction with BZR1. Int J Mol Sci 2022; 23:ijms23158056. [PMID: 35897632 PMCID: PMC9330802 DOI: 10.3390/ijms23158056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 07/08/2022] [Accepted: 07/20/2022] [Indexed: 02/01/2023] Open
Abstract
Glycogen synthase kinase-3 (GSK-3) is a nonreceptor serine/threonine protein kinase that is involved in diverse processes, including cell development, photomorphogenesis, biotic and abiotic stress responses, and hormone signaling. In contrast with the deeply researched GSK family in Arabidopsis and rice, maize GSKs’ common bioinformatic features and protein functions are poorly understood. In this study, we identified 11 GSK genes in the maize (Zea mays L.) genome via homologous alignment, which we named Zeama;GSKs (ZmGSKs). The results of ZmGSK protein sequences, conserved motifs, and gene structures showed high similarities with each other. The phylogenetic analyses showed that a total of 11 genes from maize were divided into four clades. Furthermore, semi-quantitative RT-PCR analysis of the GSKs genes showed that ZmGSK1, ZmGSK2, ZmGSK4, ZmGSK5, ZmGSK8, ZmGSK9, ZmGSK10, and ZmGSK11 were expressed in all tissues; ZmGSK3, ZmGSK6, and ZmGSK7 were expressed in a specific organization. In addition, GSK expression profiles under hormone treatments demonstrated that the ZmGSK genes were induced under BR conditions, except for ZmGSK2 and ZmGSK5. ZmGSK genes were regulated under ABA conditions, except for ZmGSK1 and ZmGSK8. Finally, using the yeast two-hybrid and BiFC assay, we determined that clads II (ZmGSK1, ZmGSK4, ZmGSK7, ZmGSK8, and ZmGSK11) could interact with ZmBZR1. The results suggest that clade II of ZmGSKs is important for BR signaling and that ZmGSK1 may play a dominant role in BR signaling as the counterpart to BIN2. This study provides a foundation for the further study of GSK3 functions and could be helpful in devising strategies for improving maize.
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Affiliation(s)
- Hui Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (H.L.); (L.L.); (Y.W.)
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Luo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (H.L.); (L.L.); (Y.W.)
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Yayun Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (H.L.); (L.L.); (Y.W.)
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Junjie Zhang
- College of Life Science, Sichuan Agricultural University, Ya’an 625014, China
- Correspondence: (J.Z.); (Y.H.); Tel.: +86-13908160283 (Y.H.)
| | - Yubi Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (H.L.); (L.L.); (Y.W.)
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (J.Z.); (Y.H.); Tel.: +86-13908160283 (Y.H.)
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Wang W, Ren Z, Li L, Du Y, Zhou Y, Zhang M, Li Z, Yi F, Duan L. Meta-QTL analysis explores the key genes, especially hormone related genes, involved in the regulation of grain water content and grain dehydration rate in maize. BMC PLANT BIOLOGY 2022; 22:346. [PMID: 35842577 PMCID: PMC9287936 DOI: 10.1186/s12870-022-03738-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Low grain water content (GWC) at harvest of maize (Zea mays L.) is essential for mechanical harvesting, transportation and storage. Grain drying rate (GDR) is a key determinant of GWC. Many quantitative trait locus (QTLs) related to GDR and GWC have been reported, however, the confidence interval (CI) of these QTLs are too large and few QTLs has been fine-mapped or even been cloned. Meta-QTL (MQTL) analysis is an effective method to integrate QTLs information in independent populations, which helps to understand the genetic structure of quantitative traits. RESULTS In this study, MQTL analysis was performed using 282 QTLs from 25 experiments related GDR and GWC. Totally, 11 and 34 MQTLs were found to be associated with GDR and GWC, respectively. The average CI of GDR and GWC MQTLs was 24.44 and 22.13 cM which reduced the 57 and 65% compared to the average QTL interval for initial GDR and GWC QTL, respectively. Finally, 1494 and 5011 candidate genes related to GDR and GWC were identified in MQTL intervals, respectively. Among these genes, there are 48 genes related to hormone metabolism. CONCLUSIONS Our studies combined traditional QTL analyses, genome-wide association study and RNA-seq to analysis major locus for regulating GWC in maize.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education &College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Zhaobin Ren
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education &College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Lu Li
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education &College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Yiping Du
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education &College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Yuyi Zhou
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education &College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Mingcai Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education &College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Zhaohu Li
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education &College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
| | - Fei Yi
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education &College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China.
| | - Liusheng Duan
- State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education &College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing, 100193, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
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49
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Han Y, Hu M, Ma X, Yan G, Wang C, Jiang S, Lai J, Zhang M. Exploring key developmental phases and phase-specific genes across the entirety of anther development in maize. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1394-1410. [PMID: 35607822 PMCID: PMC10360140 DOI: 10.1111/jipb.13276] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Anther development from stamen primordium to pollen dispersal is complex and essential to sexual reproduction. How this highly dynamic and complex developmental process is controlled genetically is not well understood, especially for genes involved in specific key developmental phases. Here we generated RNA sequencing libraries spanning 10 key stages across the entirety of anther development in maize (Zea mays). Global transcriptome analyses revealed distinct phases of cell division and expansion, meiosis, pollen maturation, and mature pollen, for which we detected 50, 245, 42, and 414 phase-specific marker genes, respectively. Phase-specific transcription factor genes were significantly enriched in the phase of meiosis. The phase-specific expression of these marker genes was highly conserved among the maize lines Chang7-2 and W23, indicating they might have important roles in anther development. We explored a desiccation-related protein gene, ZmDRP1, which was exclusively expressed in the tapetum from the tetrad to the uninucleate microspore stage, by generating knockout mutants. Notably, mutants in ZmDRP1 were completely male-sterile, with abnormal Ubisch bodies and defective pollen exine. Our work provides a glimpse into the gene expression dynamics and a valuable resource for exploring the roles of key phase-specific genes that regulate anther development.
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Affiliation(s)
- Yingjia Han
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Mingjian Hu
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center of China Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Xuxu Ma
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
| | - Ge Yan
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunyu Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Siqi Jiang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center of China Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Mei Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China
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Sergeeva EM, Larichev KT, Salina EA, Kochetov AV. Starch metabolism in potato <i>Solanum tuberosum</i> L. Vavilovskii Zhurnal Genet Selektsii 2022; 26:250-263. [PMID: 35774362 PMCID: PMC9168746 DOI: 10.18699/vjgb-22-32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 11/19/2022] Open
Abstract
Starch is a major storage carbohydrate in plants. It is an important source of calories in the human and animal diet. Also, it is widely used in various industries. Native starch consists of water-insoluble semicrystalline granules formed by natural glucose polymers amylose and amylopectin. The physicochemical properties of starch are determined by the amylose:amylopectin ratio in the granule and degrees of their polymerization and phosphorylation. Potato Solanum tuberosum L. is one of the main starch-producing crops. Growing industrial needs necessitate the breeding of plant varieties with increased starch content and specified starch properties. This task demands detailed information on starch metabolism in the producing plant. It is a complex process, requiring the orchestrated work of many enzymes, transporter and targeting proteins, transcription factors, and other regulators. Two types of starch are recognized with regard to their biological functions. Transitory starch is synthesized in chloroplasts of photosynthetic organs and degraded in the absence of light, providing carbohydrates for cell needs. Storage starch is synthesized and stored in amyloplasts of storage organs: grains and tubers. The main enzymatic reactions of starch biosynthesis and degradation, as well as carbohydrate transport and metabolism, are well known in the case of transitory starch of the model plant Arabidopsis thaliana. Less is known about features of starch metabolism in storage organs, in particular, potato tubers. Several issues remain obscure: the roles of enzyme isoforms and different regulatory factors in tissues at various plant developmental stages and under different environmental conditions; alternative enzymatic processes; targeting and transport proteins. In this review, the key enzymatic reactions of plant carbohydrate metabolism, transitory and storage starch biosynthesis,
and starch degradation are discussed, and features specific for potato are outlined. Attention is also paid to the
known regulatory factors affecting starch metabolism
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Affiliation(s)
- E. M. Sergeeva
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - K. T. Larichev
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - E. A. Salina
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - A. V. Kochetov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
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