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Bente H, Köhler C. Molecular basis and evolutionary drivers of endosperm-based hybridization barriers. PLANT PHYSIOLOGY 2024; 195:155-169. [PMID: 38298124 PMCID: PMC11060687 DOI: 10.1093/plphys/kiae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/05/2024] [Accepted: 01/06/2024] [Indexed: 02/02/2024]
Abstract
The endosperm, a transient seed tissue, plays a pivotal role in supporting embryo growth and germination. This unique feature sets flowering plants apart from gymnosperms, marking an evolutionary innovation in the world of seed-bearing plants. Nevertheless, the importance of the endosperm extends beyond its role in providing nutrients to the developing embryo by acting as a versatile protector, preventing hybridization events between distinct species and between individuals with different ploidy. This phenomenon centers on growth and differentiation of the endosperm and the speed at which both processes unfold. Emerging studies underscore the important role played by type I MADS-box transcription factors, including the paternally expressed gene PHERES1. These factors, along with downstream signaling pathways involving auxin and abscisic acid, are instrumental in regulating endosperm development and, consequently, the establishment of hybridization barriers. Moreover, mutations in various epigenetic regulators mitigate these barriers, unveiling a complex interplay of pathways involved in their formation. In this review, we discuss the molecular underpinnings of endosperm-based hybridization barriers and their evolutionary drivers.
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Affiliation(s)
- Heinrich Bente
- Department of Plant Reproductive Biology and Epigenetics, Max Planck Institute of Molecular Plant Physiology, Potsdam 14476, Germany
| | - Claudia Köhler
- Department of Plant Reproductive Biology and Epigenetics, Max Planck Institute of Molecular Plant Physiology, Potsdam 14476, Germany
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
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2
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Dharni JS, Shi Y, Zhang C, Petersen C, Walia H, Staswick P. Growth and transcriptional response of wheat and rice to the tertiary amine BMVE. FRONTIERS IN PLANT SCIENCE 2024; 14:1273620. [PMID: 38269141 PMCID: PMC10806070 DOI: 10.3389/fpls.2023.1273620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 12/04/2023] [Indexed: 01/26/2024]
Abstract
Introduction Seed vigor is largely a product of sound seed development, maturation processes, genetics, and storage conditions. It is a crucial factor impacting plant growth and crop yield and is negatively affected by unfavorable environmental conditions, which can include drought and heat as well as cold wet conditions. The latter leads to slow germination and increased seedling susceptibility to pathogens. Prior research has shown that a class of plant growth regulators called substituted tertiary amines (STAs) can enhance seed germination, seedling growth, and crop productivity. However, inconsistent benefits have limited STA adoption on a commercial scale. Methods We developed a novel seed treatment protocol to evaluate the efficacy of 2-(N-methyl benzyl aminoethyl)-3-methyl butanoate (BMVE), which has shown promise as a crop seed treatment in field trials. Transcriptomic analysis of rice seedlings 24 h after BMVE treatment was done to identify the molecular basis for the improved seedling growth. The impact of BMVE on seed development was also evaluated by spraying rice panicles shortly after flower fertilization and subsequently monitoring the impact on seed traits. Results BMVE treatment of seeds 24 h after imbibition consistently improved wheat and rice seedling shoot and root growth in lab conditions. Treated wheat seedlings grown to maturity in a greenhouse also resulted in higher biomass than controls, though only under drought conditions. Treated seedlings had increased levels of transcripts involved in reactive oxygen species scavenging and auxin and gibberellic acid signaling. Conversely, several genes associated with increased reactive oxygen species/ROS load, abiotic stress responses, and germination hindering processes were reduced. BMVE spray increased both fresh and mature seed weights relative to the control for plants exposed to 96 h of heat stress. BMVE treatment during seed development also benefited germination and seedling growth in the next generation, under both ambient and heat stress conditions. Discussion The optimized experimental conditions we developed provide convincing evidence that BMVE does indeed have efficacy in plant growth enhancement. The results advance our understanding of how STAs work at the molecular level and provide insights for their practical application to improve crop growth.
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Affiliation(s)
- Jaspinder Singh Dharni
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
| | - Yu Shi
- School of Biological Sciences, University of Nebraska, Lincoln, NE, United States
| | - Chi Zhang
- School of Biological Sciences, University of Nebraska, Lincoln, NE, United States
| | | | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
| | - Paul Staswick
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
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3
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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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4
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Wang T, Chang Y, Zhao K, Dong Q, Yang J. Maize RNA 3'-terminal phosphate cyclase-like protein promotes 18S pre-rRNA cleavage and is important for kernel development. THE PLANT CELL 2022; 34:1957-1979. [PMID: 35167702 PMCID: PMC9048941 DOI: 10.1093/plcell/koac052] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Plant ribosomes contain four specialized ribonucleic acids, the 5S, 5.8S, 18S, and 25S ribosomal RNAs (rRNAs). Maturation of the latter three rRNAs requires cooperative processing of a single transcript by several endonucleases and exonucleases at specific sites. In maize (Zea mays), the exact nucleases and components required for rRNA processing remain poorly understood. Here, we characterized a conserved RNA 3'-terminal phosphate cyclase (RCL)-like protein, RCL1, that functions in 18S rRNA maturation. RCL1 is highly expressed in the embryo and endosperm during early seed development. Loss of RCL1 function resulted in lethality due to aborted embryo cell differentiation. We also observed pleiotropic defects in the rcl1 endosperm, including abnormal basal transfer cell layer growth and aleurone cell identity, and reduced storage reserve accumulation. The rcl1 seeds had lower levels of mature 18S rRNA and the related precursors were altered in abundance compared with wild type. Analysis of transcript levels and protein accumulation in rcl1 revealed that the observed lower levels of zein and starch synthesis enzymes mainly resulted from effects at the transcriptional and translational levels, respectively. These results demonstrate that RCL1-mediated 18S pre-rRNA processing is essential for ribosome function and messenger RNA translation during maize seed development.
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Affiliation(s)
- Tao Wang
- School of Life Sciences, The National Engineering Laboratory of Crop Resistance Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Yumei Chang
- School of Life Sciences, The National Engineering Laboratory of Crop Resistance Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Kai Zhao
- School of Life Sciences, The National Engineering Laboratory of Crop Resistance Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Qing Dong
- Anhui Academy of Agricultural Sciences, Hefei 230031, China
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5
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Nagata H, Ono A, Tonosaki K, Kawakatsu T, Sato Y, Yano K, Kishima Y, Kinoshita T. Temporal changes in transcripts of miniature inverted-repeat transposable elements during rice endosperm development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1035-1047. [PMID: 35128739 PMCID: PMC9314911 DOI: 10.1111/tpj.15698] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/19/2022] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
The repression of transcription from transposable elements (TEs) by DNA methylation is necessary to maintain genome integrity and prevent harmful mutations. However, under certain circumstances, TEs may escape from the host defense system and reactivate their transcription. In Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), DNA demethylases target the sequences derived from TEs in the central cell, the progenitor cell for the endosperm in the female gametophyte. Genome-wide DNA demethylation is also observed in the endosperm after fertilization. In the present study, we used a custom microarray to survey the transcripts generated from TEs during rice endosperm development and at selected time points in the embryo as a control. The expression patterns of TE transcripts are dynamically up- and downregulated during endosperm development, especially those of miniature inverted-repeat TEs (MITEs). Some TE transcripts were directionally controlled, whereas the other DNA transposons and retrotransposons were not. We also discovered the NUCLEAR FACTOR Y binding motif, CCAAT, in the region near the 5' terminal inverted repeat of Youren, one of the transcribed MITEs in the endosperm. Our results uncover dynamic changes in TE activity during endosperm development in rice.
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Affiliation(s)
- Hiroki Nagata
- Kihara Institute for Biological Research, Yokohama City University641‐12 MaiokaTotsuka, YokohamaKanagawa244‐0813Japan
| | - Akemi Ono
- Kihara Institute for Biological Research, Yokohama City University641‐12 MaiokaTotsuka, YokohamaKanagawa244‐0813Japan
| | - Kaoru Tonosaki
- Kihara Institute for Biological Research, Yokohama City University641‐12 MaiokaTotsuka, YokohamaKanagawa244‐0813Japan
- Faculty of AgricultureIwate University3‐18‐8 UedaMoriokaIwate020‐8550Japan
| | - Taiji Kawakatsu
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization3‐1‐3 Kan‐nondaiTsukubaIbaraki305‐8604Japan
| | - Yutaka Sato
- Genetic Strains Research CenterNational Institute of GeneticsMishima, Shizuoka411‐8540Japan
| | - Kentaro Yano
- Department of Life SciencesSchool of Agriculture, Meiji University1‐1‐1 Higashi‐mitaKawasaki214‐8571Japan
| | - Yuji Kishima
- Research Faculty of AgricultureHokkaido UniversityKita‐9 Nishi‐9Kita‐ku, Sapporo060‐8589Japan
| | - Tetsu Kinoshita
- Kihara Institute for Biological Research, Yokohama City University641‐12 MaiokaTotsuka, YokohamaKanagawa244‐0813Japan
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6
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Song J, Xie X, Cui Y, Zou J. Endosperm-Embryo Communications: Recent Advances and Perspectives. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112511. [PMID: 34834874 PMCID: PMC8625250 DOI: 10.3390/plants10112511] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 05/22/2023]
Abstract
Seed maturation depends on well-coordinated communications between the processes of endosperm and embryo development. The endosperm is considered to be destined to support embryo development and the timing of endosperm cellularization is critical for embryo growth. Recent findings suggest that the endosperm development and the onset of embryo maturation are two independent processes during seed development. Meanwhile, it is lately reported that several mobile regulators originating from the endosperm are needed to ensure proper embryo growth and seed maturation. In this opinion article, we highlight processes on how endosperm communicates with embryo during seed development and discuss some intriguing questions in light of the latest advancements.
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Affiliation(s)
- Jingpu Song
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, SK S7N 0W9, Canada;
- Correspondence:
| | - Xin Xie
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada; (X.X.); (Y.C.)
- Department of Biology, Western University, London, ON N6A 3K7, Canada
| | - Yuhai Cui
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada; (X.X.); (Y.C.)
- Department of Biology, Western University, London, ON N6A 3K7, Canada
| | - Jitao Zou
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, SK S7N 0W9, Canada;
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7
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Zhou YF, Zhang YC, Sun YM, Yu Y, Lei MQ, Yang YW, Lian JP, Feng YZ, Zhang Z, Yang L, He RR, Huang JH, Cheng Y, Liu YW, Chen YQ. The parent-of-origin lncRNA MISSEN regulates rice endosperm development. Nat Commun 2021; 12:6525. [PMID: 34764271 PMCID: PMC8585977 DOI: 10.1038/s41467-021-26795-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 10/22/2021] [Indexed: 11/09/2022] Open
Abstract
The cereal endosperm is a major factor determining seed size and shape. However, the molecular mechanisms of endosperm development are not fully understood. Long noncoding RNAs (lncRNAs) function in various biological processes. Here we show a lncRNA, MISSEN, that plays an essential role in early endosperm development in rice (Oryza sativa). MISSEN is a parent-of-origin lncRNA expressed in endosperm, and negatively regulates endosperm development, leading to a prominent dent and bulge in the seed. Mechanistically, MISSEN functions through hijacking a helicase family protein (HeFP) to regulate tubulin function during endosperm nucleus division and endosperm cellularization, resulting in abnormal cytoskeletal polymerization. Finally, we revealed that the expression of MISSEN is inhibited by histone H3 lysine 27 trimethylation (H3K27me3) modification after pollination. Therefore, MISSEN is the first lncRNA identified as a regulator in endosperm development, highlighting the potential applications in rice breeding.
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Affiliation(s)
- Yan-Fei Zhou
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yu-Chan Zhang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yu-Meng Sun
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yang Yu
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Meng-Qi Lei
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yu-Wei Yang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Jian-Ping Lian
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yan-Zhao Feng
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Zhi Zhang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Lu Yang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Rui-Rui He
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Jia-Hui Huang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yu Cheng
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yu-Wei Liu
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China
| | - Yue-Qin Chen
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, 510275, Guangzhou, China. .,MOE Key Laboratory of Gene Function and Regulation, Sun Yat-sen University, 510275, Guangzhou, China.
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8
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Yoon J, Cho L, Kim S, Tun W, Peng X, Pasriga R, Moon S, Hong W, Ji H, Jung K, Jeon J, An G. CTP synthase is essential for early endosperm development by regulating nuclei spacing. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2177-2191. [PMID: 34058048 PMCID: PMC8541778 DOI: 10.1111/pbi.13644] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/04/2021] [Accepted: 05/22/2021] [Indexed: 06/12/2023]
Abstract
Cereal grain endosperms are an important source of human nutrition. Nuclear division in early endosperm development plays a major role in determining seed size; however, this development is not well understood. We identified the rice mutant endospermless 2 (enl2), which shows defects in the early stages of endosperm development. These phenotypes arise from mutations in OsCTPS1 that encodes a cytidine triphosphate synthase (CTPS). Both wild-type and mutant endosperms were normal at 8 h after pollination (HAP). In contrast, at 24 HAP, enl2 endosperm had approximately 10-16 clumped nuclei while wild-type nuclei had increased in number and migrated to the endosperm periphery. Staining of microtubules in endosperm at 24 HAP revealed that wild-type nuclei were evenly distributed by microtubules while the enl2-2 nuclei were tightly packed due to their reduction in microtubule association. In addition, OsCTPS1 interacts with tubulins; thus, these observations suggest that OsCTPS1 may be involved in microtubule formation. OsCTPS1 transiently formed macromolecular structures in the endosperm during early developmental stages, further supporting the idea that OsCTPS1 may function as a structural component during endosperm development. Finally, overexpression of OsCTPS1 increased seed weight by promoting endosperm nuclear division, suggesting that this trait could be used to increase grain yield.
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Affiliation(s)
- Jinmi Yoon
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
- Department of Plant BioscienceCollege of Natural Resources and Life SciencePusan National UniversityMiryangRepublic of Korea
| | - Lae‐Hyeon Cho
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
- Department of Plant BioscienceCollege of Natural Resources and Life SciencePusan National UniversityMiryangRepublic of Korea
| | - Sung‐Ryul Kim
- Gene Identification and Validation GroupGenetic Design and Validation UnitInternational Rice Research Institute (IRRI)Metro ManilaPhilippines
| | - Win Tun
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Xin Peng
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
- Institution of Genomics and BioinformaticsSouth China Agricultural UniversityGuangzhouChina
| | - Richa Pasriga
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Sunok Moon
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Woo‐Jong Hong
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Hyeonso Ji
- National Institute of Agricultural Sciences, Rural Development AdministrationJeonjuRepublic of Korea
| | - Ki‐Hong Jung
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Jong‐Seong Jeon
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
| | - Gynheung An
- Crop Biotech Institute and Graduate School of BiotechnologyKyung Hee UniversityYonginRepublic of Korea
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Morgan EJ, Čertner M, Lučanová M, Deniz U, Kubíková K, Venon A, Kovářík O, Lafon Placette C, Kolář F. Disentangling the components of triploid block and its fitness consequences in natural diploid-tetraploid contact zones of Arabidopsis arenosa. THE NEW PHYTOLOGIST 2021; 232:1449-1462. [PMID: 33768528 DOI: 10.1111/nph.17357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/15/2021] [Indexed: 06/12/2023]
Abstract
Hybrid seed inviability (HSI) is an important mechanism of reproductive isolation and speciation. HSI varies in strength among populations of diploid species but it remains to be tested whether similar processes affect natural variation in HSI within ploidy-variable species (triploid block). Here we used extensive endosperm, seed and F1 -hybrid phenotyping to explore HSI variation within a diploid-autotetraploid species. By leveraging 12 population pairs from three ploidy contact zones, we tested for the effect of interploidy crossing direction (parent of origin), ploidy divergence and spatial arrangement in shaping reproductive barriers in a naturally relevant context. We detected strong parent-of-origin effects on endosperm development, F1 germination and survival, which was also reflected in the rates of triploid formation in the field. Endosperm cellularization failure was least severe and F1 -hybrid performance was slightly better in the primary contact zone, with genetically closest diploid and tetraploid lineages. We demonstrated overall strong parent-of-origin effects on HSI in a ploidy variable species, which translate to fitness effects and contribute to interploidy reproductive isolation in a natural context. Subtle intraspecific variation in these traits suggests the fitness consequences of HSI are predominantly a constitutive property of the species regardless of the evolutionary background of its populations.
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Affiliation(s)
- Emma J Morgan
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01, Czech Republic
| | - Martin Čertner
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01, Czech Republic
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, CZ-252 43, Czech Republic
| | - Magdalena Lučanová
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01, Czech Republic
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, CZ-252 43, Czech Republic
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 31, České Budějovice, CZ-370 05, Czech Republic
| | - Utku Deniz
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01, Czech Republic
| | - Kateřina Kubíková
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01, Czech Republic
| | - Anthony Venon
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01, Czech Republic
| | - Oleg Kovářík
- Datamole Inc., Vítězné Náměstí 2, Prague, CZ-160 00, Czech Republic
| | - Clément Lafon Placette
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01, Czech Republic
| | - Filip Kolář
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, Prague, CZ-128 01, Czech Republic
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, Průhonice, CZ-252 43, Czech Republic
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10
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Xiao W, Hu S, Zou X, Cai R, Liao R, Lin X, Yao R, Guo X. Lectin receptor-like kinase LecRK-VIII.2 is a missing link in MAPK signaling-mediated yield control. PLANT PHYSIOLOGY 2021; 187:303-320. [PMID: 34618128 PMCID: PMC8418426 DOI: 10.1093/plphys/kiab241] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 05/01/2021] [Indexed: 05/13/2023]
Abstract
The energy allocation for vegetative and reproductive growth is regulated by developmental signals and environmental cues, which subsequently affects seed output. However, the molecular mechanism underlying how plants coordinate yield-related traits to control yield in changing source-sink relationships remains largely unknown. Here, we discovered the lectin receptor-like kinase LecRK-VIII.2 as a specific receptor-like kinase that coordinates silique number, seed size, and seed number to determine seed yield in Arabidopsis (Arabidopsis thaliana). The lecrk-VIII.2 mutants develop smaller seeds, but more siliques and seeds, leading to increased yield. In contrast, the plants overexpressing LecRK-VIII.2 form bigger seeds, but less siliques and seeds, which results in similar yield to that of wild-type plants. Interestingly, LecRK-VIII.2 promotes the growth of the rosette, root, and stem by coordinating the source-sink relationship. Additionally, LecRK-VIII.2 positively regulates cell expansion and proliferation in the seed coat, and maternally controls seed size. The genetic and biochemical analyses demonstrated that LecRK-VIII.2 acts upstream of the mitogen-activated protein kinase (MAPK) gene MPK6 to regulate silique number, seed size, and seed number. Collectively, these findings uncover LecRK-VIII.2 as an upstream component of the MAPK signaling pathway to control yield-related traits and suggest its potential for crop improvement aimed at developing plants with stable yield, a robust root system, and improved lodging resistance.
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Affiliation(s)
- Wenjun Xiao
- College of Biology, Hunan University, Changsha 410082, China
| | - Shuai Hu
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaoxiao Zou
- College of Biology, Hunan University, Changsha 410082, China
| | - Ruqiong Cai
- College of Biology, Hunan University, Changsha 410082, China
| | - Rui Liao
- College of Biology, Hunan University, Changsha 410082, China
| | - Xiaoxia Lin
- College of Biology, Hunan University, Changsha 410082, China
| | - Ruifeng Yao
- College of Biology, Hunan University, Changsha 410082, China
| | - Xinhong Guo
- College of Biology, Hunan University, Changsha 410082, China
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11
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Zielińska KM, Kaźmierczak A, Michalska E. Short-term cell death in tissues of Pulsatilla vernalis seeds from natural and ex situ conserved populations. Sci Rep 2021; 11:16840. [PMID: 34413338 PMCID: PMC8376884 DOI: 10.1038/s41598-021-95668-2] [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: 04/29/2021] [Accepted: 07/28/2021] [Indexed: 11/30/2022] Open
Abstract
Pulsatilla vernalis is a IUCN listed species that occurs in mountain and lowland habitats. The seeds collected from different populations are remarkably diverse in their viability depending on locality or year of collection. We aim to analyse seed viability, among others, by investigation of the percentage of alive, dying, and dead cells in embryos and endosperm when comparing the seeds from a wild lowland population and ex situ cultivation of plants of lowland and Alpine origin. The cell death was detected by staining with two fluorescence probes, one penetrating only the changed nuclear membranes, the other penetrating also the unchanged cells. 54.5% of Alpine origin seeds were presumably capable of germination if they were sown after collection, however, four months later only 36.4% had healthy embryos. In the case of lowland wild plants it was 31.8% and 18.2%, and from ex situ, 27.3% and 13.6%, respectively. 27.3% of Alpine origin seeds had embryo in torpedo stage (9.1% in the case of lowland seeds). Mean weight of the former was 2.9 mg (2.0 mg in lowland ones). Our results confirm the significance of seed origin and seed weight on viability, and that Pulsatilla seeds have a short ‘germination time window’.
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Affiliation(s)
- Katarzyna M Zielińska
- Department of Geobotany and Plant Ecology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha Str. 12/16, 90-237, Lodz, Poland.
| | - Andrzej Kaźmierczak
- Department of Cytophysiology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha Str. 12/16, 90-237, Lodz, Poland
| | - Ewa Michalska
- Department of Geobotany and Plant Ecology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha Str. 12/16, 90-237, Lodz, Poland
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12
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Chatterjee D, Wittmeyer K, Lee TF, Cui J, Yennawar NH, Yennawar HP, Meyers BC, Chopra S. Maize unstable factor for orange1 is essential for endosperm development and carbohydrate accumulation. PLANT PHYSIOLOGY 2021; 186:1932-1950. [PMID: 33905500 PMCID: PMC8331166 DOI: 10.1093/plphys/kiab183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/07/2021] [Indexed: 06/12/2023]
Abstract
Maize (Zea mays L.) Ufo1-1 is a spontaneous dominant mutation of the unstable factor for orange1 (ufo1). We recently cloned ufo1, which is a Poaceae-specific gene highly expressed during seed development in maize. Here, we have characterized Ufo1-1 and a loss-of-function Ds insertion allele (ufo1-Dsg) to decipher the role of ufo1 in maize. We found that both ufo1 mutant alleles impact sugars and hormones, and have defects in the basal endosperm transfer layer (BETL) and adjacent cell types. The Ufo1-1 BETL had reduced cell elongation and cell wall ingrowth, resulting in cuboidal shaped transfer cells. In contrast, the ufo1-Dsg BETL cells showed a reduced overall size with abnormal wall ingrowth. Expression analysis identified the impact of ufo1 on several genes essential for BETL development. The overexpression of Ufo1-1 in various tissues leads to ectopic phenotypes, including abnormal cell organization and stomata subsidiary cell defects. Interestingly, pericarp and leaf transcriptomes also showed that as compared with wild type, Ufo1-1 had ectopic expression of endosperm development-specific genes. This study shows that Ufo1-1 impacts the expression patterns of a wide range of genes involved in various developmental processes.
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Affiliation(s)
- Debamalya Chatterjee
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Kameron Wittmeyer
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Tzuu-fen Lee
- The Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Jin Cui
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Neela H Yennawar
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Hemant P Yennawar
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Blake C Meyers
- The Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 65201, USA
| | - Surinder Chopra
- Department of Plant Science, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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13
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Köhler C, Dziasek K, Del Toro-De León G. Postzygotic reproductive isolation established in the endosperm: mechanisms, drivers and relevance. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200118. [PMID: 33866810 DOI: 10.1098/rstb.2020.0118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The endosperm is a developmental innovation of angiosperms that supports embryo growth and germination. Aside from this essential reproductive function, the endosperm fuels angiosperm evolution by rapidly establishing reproductive barriers between incipient species. Specifically, the endosperm prevents hybridization of newly formed polyploids with their non-polyploid progenitors, a phenomenon termed the triploid block. Furthermore, recently diverged diploid species are frequently reproductively isolated by endosperm-based hybridization barriers. Current genetic approaches have revealed a prominent role for epigenetic processes establishing these barriers. In particular, imprinted genes, which are expressed in a parent-of-origin-specific manner, underpin the interploidy barrier in the model species Arabidopsis. We will discuss the mechanisms establishing hybridization barriers in the endosperm, the driving forces for these barriers and their impact for angiosperm evolution. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Claudia Köhler
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Katarzyna Dziasek
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
| | - Gerardo Del Toro-De León
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala 75007, Sweden
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14
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Tonosaki K, Ono A, Kunisada M, Nishino M, Nagata H, Sakamoto S, Kijima ST, Furuumi H, Nonomura KI, Sato Y, Ohme-Takagi M, Endo M, Comai L, Hatakeyama K, Kawakatsu T, Kinoshita T. Mutation of the imprinted gene OsEMF2a induces autonomous endosperm development and delayed cellularization in rice. THE PLANT CELL 2021; 33:85-103. [PMID: 33751094 PMCID: PMC8136911 DOI: 10.1093/plcell/koaa006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 10/29/2020] [Indexed: 05/22/2023]
Abstract
In angiosperms, endosperm development comprises a series of developmental transitions controlled by genetic and epigenetic mechanisms that are initiated after double fertilization. Polycomb repressive complex 2 (PRC2) is a key component of these mechanisms that mediate histone H3 lysine 27 trimethylation (H3K27me3); the action of PRC2 is well described in Arabidopsis thaliana but remains uncertain in cereals. In this study, we demonstrate that mutation of the rice (Oryza sativa) gene EMBRYONIC FLOWER2a (OsEMF2a), encoding a zinc-finger containing component of PRC2, causes an autonomous endosperm phenotype involving proliferation of the central cell nuclei with separate cytoplasmic domains, even in the absence of fertilization. Detailed cytological and transcriptomic analyses revealed that the autonomous endosperm can produce storage compounds, starch granules, and protein bodies specific to the endosperm. These events have not been reported in Arabidopsis. After fertilization, we observed an abnormally delayed developmental transition in the endosperm. Transcriptome and H3K27me3 ChIP-seq analyses using endosperm from the emf2a mutant identified downstream targets of PRC2. These included >100 transcription factor genes such as type-I MADS-box genes, which are likely required for endosperm development. Our results demonstrate that OsEMF2a-containing PRC2 controls endosperm developmental programs before and after fertilization.
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Affiliation(s)
- Kaoru Tonosaki
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama, Kanagawa 244-0813, Japan
- Department of Plant Biology and Genome Center, University of California, Davis, CA 95616, USA
- Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
- Author for correspondence: (T.Ki.), (K.T.)
| | - Akemi Ono
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama, Kanagawa 244-0813, Japan
| | - Megumi Kunisada
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama, Kanagawa 244-0813, Japan
| | - Megumi Nishino
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama, Kanagawa 244-0813, Japan
| | - Hiroki Nagata
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama, Kanagawa 244-0813, Japan
| | - Shingo Sakamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8562, Japan
| | - Saku T Kijima
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8562, Japan
| | - Hiroyasu Furuumi
- Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Ken-Ichi Nonomura
- Plant Cytogenetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yutaka Sato
- Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Masaru Ohme-Takagi
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Masaki Endo
- Division of Applied Genetics, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
| | - Luca Comai
- Department of Plant Biology and Genome Center, University of California, Davis, CA 95616, USA
| | - Katsunori Hatakeyama
- Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Taiji Kawakatsu
- Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
| | - Tetsu Kinoshita
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Totsuka, Yokohama, Kanagawa 244-0813, Japan
- Author for correspondence: (T.Ki.), (K.T.)
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15
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Chen MX, Lu CC, Sun PC, Nie YX, Tian Y, Hu QJ, Das D, Hou XX, Gao B, Chen X, Liu SX, Zheng CC, Zhao XY, Dai L, Zhang J, Liu YG. Comprehensive transcriptome and proteome analyses reveal a novel sodium chloride responsive gene network in maize seed tissues during germination. PLANT, CELL & ENVIRONMENT 2021; 44:88-101. [PMID: 32677712 DOI: 10.1111/pce.13849] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/25/2020] [Accepted: 05/12/2020] [Indexed: 05/20/2023]
Abstract
Germination is a plant developmental process by which radicle of mature seeds start to penetrate surrounding barriers for seedling establishment and multiple environmental factors have been shown to affect it. Little is known how high salinity affects seed germination of C4 plant, Zea mays. Preliminary germination assay suggested that isolated embryo alone was able to germinate under 200 mM NaCl treatment, whereas the intact seeds were highly repressed. We hypothesized that maize endosperm may function in perception and transduction of salt signal to surrounding tissues such as embryo, showing a completely different response to that in Arabidopsis. Since salt response involves ABA, we analysed in vivo ABA distribution and quantity and the result demonstrated that ABA level in isolated embryo under NaCl treatment failed to increase in comparison with the water control, suggesting that the elevation of ABA level is an endosperm dependent process. Subsequently, by using advanced profiling techniques such as RNA sequencing and SWATH-MS-based quantitative proteomics, we found substantial differences in post-transcriptional and translational changes between salt-treated embryo and endosperm. In summary, our results indicate that these regulatory mechanisms, such as alternative splicing, are likely to mediate early responses to salt stress during maize seed germination.
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Affiliation(s)
- Mo-Xian Chen
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
- Southern Regional Collaborative Innovation Centre for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Chong-Chong Lu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Peng-Cheng Sun
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Yong-Xin Nie
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Yuan Tian
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Qi-Juan Hu
- Department of Biology, Hong Kong Baptist University, Shatin, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Debatosh Das
- Department of Biology, Hong Kong Baptist University, Shatin, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Xuan-Xuan Hou
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Bei Gao
- Department of Biology, Hong Kong Baptist University, Shatin, Hong Kong
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Xi Chen
- Wuhan Institute of Biotechnology, Wuhan, China
| | - Shou-Xu Liu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Cheng-Chao Zheng
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Xiang-Yu Zhao
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jianhua Zhang
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
- Department of Biology, Hong Kong Baptist University, Shatin, Hong Kong
| | - Ying-Gao Liu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, China
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16
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Qi D, Wen Q, Meng Z, Yuan S, Guo H, Zhao H, Cui S. OsLFR is essential for early endosperm and embryo development by interacting with SWI/SNF complex members in Oryza sativa. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:901-916. [PMID: 32808364 DOI: 10.1111/tpj.14967] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 07/09/2020] [Accepted: 07/29/2020] [Indexed: 05/26/2023]
Abstract
Rice (Oryza sativa L.) endosperm provides the developing embryo with nutrients and provides human beings with a staple food. The embryo eventually develops into a new sporophyte generation. Despite their important roles, the molecular mechanisms underlying early-stage endosperm and embryo development remain elusive. Here, we established the fundamental functions of rice OsLFR, an ortholog of the Arabidopsis SWI/SNF chromatin-remodeling complex (CRC) component LFR. OsLFR was expressed primarily in the rice spikelets and seeds, and the OsLFR protein was localized to the nucleus. We conducted genetic, cellular and molecular analyses of loss-of-function mutants and transgenic rescue lines. OsLFR depletion resulted in homozygous lethality in the early seed stage through endosperm and embryo defects, which could be successfully recovered by the OsLFR genomic sequence. Cytological observations revealed that the oslfr endosperm had relatively fewer free nuclei, had abnormal and arrested cellularization, and demonstrated premature programed cell death: the embryo was reduced in size and failed to differentiate. Transcriptome profiling showed that many genes, involved in DNA replication, cell cycle, cell wall assembly and cell death, were differentially expressed in a knockout mutant of OsLFR (oslfr-1), which was consistent with the observed seed defects. Protein-protein interaction analysis showed that OsLFR physically interacts with several putative rice SWI/SNF CRC components. Our findings demonstrate that OsLFR, possibly as one component of the SWI/SNF CRC, is an essential regulator of rice seed development, and provide further insights into the regulatory mechanism of early-stage rice endosperm and embryo development.
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Affiliation(s)
- Dongmei Qi
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Qingqing Wen
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Ze Meng
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Shan Yuan
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Hong Guo
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Hongtao Zhao
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Sujuan Cui
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
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17
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Zhao H, Qin Y, Xiao Z, Li Q, Yang N, Pan Z, Gong D, Sun Q, Yang F, Zhang Z, Wu Y, Xu C, Qiu F. Loss of Function of an RNA Polymerase III Subunit Leads to Impaired Maize Kernel Development. PLANT PHYSIOLOGY 2020; 184:359-373. [PMID: 32591429 PMCID: PMC7479876 DOI: 10.1104/pp.20.00502] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 06/15/2020] [Indexed: 05/03/2023]
Abstract
Kernel size is an important factor determining grain yield. Although a number of genes affecting kernel development in maize (Zea mays) have been identified by analyzing kernel mutants, most of the corresponding mutants cannot be used in maize breeding programs due to low germination or incomplete seed development. Here, we characterized small kernel7, a recessive small-kernel mutant with a mutation in the gene encoding the second-largest subunit of RNA polymerase III (RNAPΙΙΙ; NRPC2). A frame shift in ZmNRPC2 leads to a premature stop codon, resulting in significantly reduced levels of transfer RNAs and 5S ribosomal RNA, which are transcribed by RNAPΙΙΙ. Loss-of-function nrpc2 mutants created by CRISPR/CAS9 showed significantly reduced kernel size due to altered endosperm cell size and number. ZmNRPC2 affects RNAPIII activity and the expression of genes involved in cell proliferation and endoreduplication to control kernel development via physically interacting with RNAPIII subunits RPC53 and AC40, transcription factor class C1 and Floury3. Notably, unlike the semidominant negative mutant floury3, which has defects in starchy endosperm, small kernel7 only affects kernel size but not the composition of kernel storage proteins. Our findings provide novel insights into the molecular network underlying maize kernel size, which could facilitate the genetic improvement of maize in the future.
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Affiliation(s)
- Hailiang Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | | | - Ziyi Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qi Li
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Science Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Ning Yang
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhenyuan Pan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Dianming Gong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qin Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Fang Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongrui Wu
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Science Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Cao Xu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Fazhan Qiu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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18
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Hülle Cells of Aspergillus nidulans with Nuclear Storage and Developmental Backup Functions Are Reminiscent of Multipotent Stem Cells. mBio 2020; 11:mBio.01673-20. [PMID: 32788382 PMCID: PMC7439468 DOI: 10.1128/mbio.01673-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Some aspergilli are among the most cosmopolitan and ecologically dominant fungal species. One pillar of their success is their complex life cycle, which creates specialized cell types for versatile dispersal and regenesis. One of these cell types is unique to aspergilli-the Hülle cells. Despite being known for over a century, the biological and ecological roles of Hülle cells remain largely speculative. Previously reported data on in vivo Hülle cell formation and localization have been conflicting. Our quantification reveals that Hülle cells can occur at all locations on hyphae and that they show cellular activity similar to that seen with adjacent hyphae, indicating that they develop as intricate parts of hyphal tissue. In addition, we show that during sexual development associated with two parental strains, the typically multinucleate Hülle cells can inherit nuclei from both parents, indicating that they may serve as genetic backups. We provide an easy, reproducible method to study Hülle cell biology and germination with which we investigate the 90-year-old puzzle of whether and how Hülle cells germinate. We present clear evidence for the germination of Hülle cells, and we show that Hülle cells grow hyphae that develop into a spore-producing colony. Finally, we show that Hülle cell-derived colonies produce conidiospores faster than spore-derived colonies, providing evidence for an as-yet-undescribed developmental shortcut program in Aspergillus nidulans We propose that Hülle cells represent a unique cell type as specialized hypha-derived sexual tissue with a nucleus storage function and may act as fungal backup stem cells under highly destructive conditions.IMPORTANCE The in vivo identification of Hülle cells in cases of aspergillosis infections in animals and humans illustrates their biological relevance and suggests that they might be involved in pathogenicity. It is striking that aspergilli have developed and maintained a multinucleate nurse cell that is presumably energy-intensive to produce and is usually found only in higher eukaryotes. Our findings shed light on how the understudied Hülle cells might contribute to the success of aspergilli by acting not only as nurse cells under detrimental conditions (sexual development) but also as fungal backup stem cells with the capacity to produce genetically diverse spores in an accelerated manner, thereby substantially contributing to survival in response to predator attack or under otherwise severely destructive conditions. Our study solved the 90-year-old puzzle of Hülle cell germination and provides easy, reproducible methods that will facilitate future studies on biological and ecological roles of Hülle cells in aspergilli.
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19
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Kordyum EL, Mosyakin SL. Endosperm of Angiosperms and Genomic Imprinting. Life (Basel) 2020; 10:E104. [PMID: 32635326 PMCID: PMC7400472 DOI: 10.3390/life10070104] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/28/2020] [Accepted: 06/29/2020] [Indexed: 12/15/2022] Open
Abstract
Modern ideas about the role of epigenetic systems in the regulation of gene expression allow us to understand the mechanisms of vital activities in plants, such as genomic imprinting. It is important that genomic imprinting is known first and foremost for the endosperm, which not only provides an embryo with necessary nutrients, but also plays a special biological role in the formation of seeds and fruits. Available data on genomic imprinting in the endosperm have been obtained only for the triploid endosperm in model plants, which develops after double fertilization in a Polygonum-type embryo sac, the most common type among angiosperms. Here we provide a brief overview of a wide diversity of embryo sacs and endosperm types and ploidy levels, as well as their distribution in the angiosperm families, positioned according to the Angiosperm Phylogeny Group IV (APG IV) phylogenetic classification. Addition of the new, non-model taxa to study gene imprinting in seed development will extend our knowledge about the epigenetic mechanisms underlying angiosperm fertility.
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Affiliation(s)
- Elizabeth L. Kordyum
- Institute of Botany, National Academy of Sciences of Ukraine, 01004 Kyiv, Ukraine; or
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20
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Montini L, Crocoll C, Gleadow RM, Motawia MS, Janfelt C, Bjarnholt N. Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry Imaging of Metabolites during Sorghum Germination. PLANT PHYSIOLOGY 2020; 183:925-942. [PMID: 32350122 PMCID: PMC7333723 DOI: 10.1104/pp.19.01357] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/27/2020] [Indexed: 05/27/2023]
Abstract
Dhurrin is the most abundant cyanogenic glucoside found in sorghum (Sorghum bicolor) where it plays a key role in chemical defense by releasing toxic hydrogen cyanide upon tissue disruption. Besides this well-established function, there is strong evidence that dhurrin plays additional roles, e.g. as a transport and storage form of nitrogen, released via endogenous recycling pathways. However, knowledge about how, when and why dhurrin is endogenously metabolized is limited. We combined targeted metabolite profiling with matrix-assisted laser desorption/ionization-mass spectrometry imaging to investigate accumulation of dhurrin, its recycling products and key general metabolites in four different sorghum lines during 72 h of grain imbibition, germination and early seedling development, as well as the spatial distribution of these metabolites in two of the lines. Little or no dhurrin or recycling products were present in the dry grain, but their de novo biosynthesis started immediately after water uptake. Dhurrin accumulation increased rapidly within the first 24 h in parallel with an increase in free amino acids, a key event in seed germination. The trajectories and final concentrations of dhurrin, the recycling products and free amino acids reached within the experimental period were dependent on genotype. Matrix-assisted laser desorption/ionization-mass spectrometry imaging demonstrated that dhurrin primarily accumulated in the germinating embryo, confirming its function in protecting the emerging tissue against herbivory. The dhurrin recycling products, however, were mainly located in the scutellum and/or pericarp/seed coat region, suggesting unknown key functions in germination.
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Affiliation(s)
- Lucia Montini
- VILLUM Research Center for Plant Plasticity, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark
| | - Christoph Crocoll
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark
| | - Roslyn M Gleadow
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Mohammed Saddik Motawia
- VILLUM Research Center for Plant Plasticity, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark
| | - Christian Janfelt
- Department of Pharmacy, Faculty of Health and Medical Science, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Nanna Bjarnholt
- VILLUM Research Center for Plant Plasticity, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg 1871, Denmark
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21
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Assessment of Genetic Heritability in Rice Breeding Lines Based on Morphological Traits and Caryopsis Ultrastructure. Sci Rep 2020; 10:7830. [PMID: 32385288 PMCID: PMC7210993 DOI: 10.1038/s41598-020-63976-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/03/2020] [Indexed: 11/22/2022] Open
Abstract
Rice (Oryza sativa L) is a most important staple food crop of the world because more than half of the World’s population is dependent on it for their livelihood. Global rice production must be doubled by 2050 to cope up with the situation of population growth. Narrow genetic base in the released varieties has made the improvement in plateaus. Widening the genetic base is necessary to overcome the yield barrier. Hybridization and pre-breeding has been carried out to broaden the genetic base. Heritability and genetic advances were measured in the F5 lines (Tulaipanji × IR64), F3 lines (Tulaipanji × IR64 × PB1460), and F3 lines (Badshabhog × Swarna sub1). Some of the breeding lines were showing promising field performance with high yield potentiality. Wide crosses were performed to widen the genetic base between (Ranjit × O. rufipogon) and (Badshabhog × O. rufipogon) and the heritability pattern of the morphological characteristics in the progeny lines was evaluated. Nutritional quality of the rice grain is totally dependent on the morphology and histological characteristics of the caryopsis which are genetically determined. Caryopses ultrastructural analyses were carried out in seventeen different rice breeding lines through SEM. SEM analysis showed distinguishing ultrastructure in respect to pericarp, testa, aleurone layer, protein bodies and starchy endosperm in the breeding lines with distinctive inheritance pattern. This study provides information about the cross compatibility of the wide hybridization and heritability measures of the morphological traits which may supplement the breeding program to break the yield plateaus.
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22
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Doll NM, Just J, Brunaud V, Caïus J, Grimault A, Depège-Fargeix N, Esteban E, Pasha A, Provart NJ, Ingram GC, Rogowsky PM, Widiez T. Transcriptomics at Maize Embryo/Endosperm Interfaces Identifies a Transcriptionally Distinct Endosperm Subdomain Adjacent to the Embryo Scutellum. THE PLANT CELL 2020; 32:833-852. [PMID: 32086366 PMCID: PMC7145466 DOI: 10.1105/tpc.19.00756] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 02/03/2020] [Accepted: 02/20/2020] [Indexed: 05/23/2023]
Abstract
Seeds are complex biological systems comprising three genetically distinct tissues nested one inside another (embryo, endosperm, and maternal tissues). However, the complexity of the kernel makes it difficult to understand intercompartment interactions without access to spatially accurate information. Here, we took advantage of the large size of the maize (Zea mays) kernel to characterize genome-wide expression profiles of tissues at different embryo/endosperm interfaces. Our analysis identifies specific transcriptomic signatures in two interface tissues compared with whole seed compartments: the scutellar aleurone layer and the newly named endosperm adjacent to scutellum (EAS). The EAS, which appears around 9 d after pollination and persists for around 11 d, is confined to one to three endosperm cell layers adjacent to the embryonic scutellum. Its transcriptome is enriched in genes encoding transporters. The absence of the embryo in an embryo specific mutant can alter the expression pattern of EAS marker genes. The detection of cell death in some EAS cells together with an accumulation of crushed cell walls suggests that the EAS is a dynamic zone from which cell layers in contact with the embryo are regularly eliminated and to which additional endosperm cells are recruited as the embryo grows.
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Affiliation(s)
- Nicolas M Doll
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, F-69342 Lyon, France
| | - Jeremy Just
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, F-69342 Lyon, France
| | - Véronique Brunaud
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, F-91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, F-91405 Orsay, France
| | - José Caïus
- Institute of Plant Sciences Paris-Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, F-91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, F-91405 Orsay, France
| | - Aurélie Grimault
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, F-69342 Lyon, France
| | - Nathalie Depège-Fargeix
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, F-69342 Lyon, France
| | - Eddi Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Gwyneth C Ingram
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, F-69342 Lyon, France
| | - Peter M Rogowsky
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, F-69342 Lyon, France
| | - Thomas Widiez
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, F-69342 Lyon, France
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23
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Qu J, Xu S, Tian X, Li T, Wang L, Zhong Y, Xue J, Guo D. Comparative transcriptomics reveals the difference in early endosperm development between maize with different amylose contents. PeerJ 2019; 7:e7528. [PMID: 31523504 PMCID: PMC6717500 DOI: 10.7717/peerj.7528] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/22/2019] [Indexed: 01/06/2023] Open
Abstract
In seeds, the endosperm is a crucial organ that plays vital roles in supporting embryo development and determining seed weight and quality. Starch is the predominant storage carbohydrate of the endosperm and accounts for ∼70% of the mature maize kernel weight. Nonetheless, because starch biosynthesis is a complex process that is orchestrated by multiple enzymes, the gene regulatory networks of starch biosynthesis, particularly amylose and amylopectin biosynthesis, have not been fully elucidated. Here, through high-throughput RNA sequencing, we developed a temporal transcriptome atlas of the endosperms of high-amylose maize and common maize at 5-, 10-, 15- and 20-day after pollination and found that 21,986 genes are involved in the programming of the high-amylose and common maize endosperm. A coexpression analysis identified multiple sequentially expressed gene sets that are closely correlated with cellular and metabolic programmes and provided valuable insight into the dynamic reprogramming of the transcriptome in common and high-amylose maize. In addition, a number of genes and transcription factors were found to be strongly linked to starch synthesis, which might help elucidate the key mechanisms and regulatory networks underlying amylose and amylopectin biosynthesis. This study will aid the understanding of the spatiotemporal patterns and genetic regulation of endosperm development in different types of maize and provide valuable genetic information for the breeding of starch varieties with different contents.
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Affiliation(s)
- Jianzhou Qu
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.,Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, Shaanxi, China
| | - Shutu Xu
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.,Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, Shaanxi, China
| | - Xiaokang Tian
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.,Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, Shaanxi, China
| | - Ting Li
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.,Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, Shaanxi, China
| | - Licheng Wang
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.,Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, Shaanxi, China
| | - Yuyue Zhong
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.,Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, Shaanxi, China
| | - Jiquan Xue
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.,Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, Shaanxi, China
| | - Dongwei Guo
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.,Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, Shaanxi, China
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24
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Niu L, Ding H, Zhang J, Wang W. Proteomic Analysis of Starch Biosynthesis in Maize Seeds. STARCH-STARKE 2019. [DOI: 10.1002/star.201800294] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Liangjie Niu
- State Key Laboratory of Wheat & Maize Crop ScienceCollege of Life SciencesHenan Agricultural UniversityZhengzhouP. R. China
| | - Huiying Ding
- State Key Laboratory of Wheat & Maize Crop ScienceCollege of Life SciencesHenan Agricultural UniversityZhengzhouP. R. China
| | - Jinghua Zhang
- State Key Laboratory of Wheat & Maize Crop ScienceCollege of Life SciencesHenan Agricultural UniversityZhengzhouP. R. China
| | - Wei Wang
- State Key Laboratory of Wheat & Maize Crop ScienceCollege of Life SciencesHenan Agricultural UniversityZhengzhouP. R. China
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25
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Fei X, Shi J, Liu Y, Niu J, Wei A. The steps from sexual reproduction to apomixis. PLANTA 2019; 249:1715-1730. [PMID: 30963237 DOI: 10.1007/s00425-019-03113-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 02/18/2019] [Indexed: 05/03/2023]
Abstract
In this paper, an interaction model of apomixis-related genes was constructed to analyze the emergence of apomictic types. It is speculated that apomixis technology will be first implemented in gramineous plants. Apomixis (asexual seed formation) is a phenomenon in which a plant bypasses the most fundamental aspects of sexual reproduction-meiosis and fertilization-to form a viable seed. Plants can form seeds without fertilization, and the seed genotype is consistent with the female parent. The development of apomictic technology would be revolutionary for agriculture and for food production as it would reduce costs and breeding times and also avoid many complications typical of sexual reproduction (e.g. incompatibility barriers) and of vegetative propagation (e.g. viral transfer). The application of apomictic reproductive technology has the potential to revolutionize crop breeding. This article reviews recent advances in apomixis in cytology and molecular biology. The general idea of identifying apomixis was proposed and the process of the emergence of non-fusion types was discussed. To better understand the apomixis mechanism, an apomixis regulatory model was established. At the same time, the realization of apomixis technology is proposed, which provides reference for the research and application of apomixis.
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Affiliation(s)
- Xitong Fei
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Jingwei Shi
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Yulin Liu
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Jinshuang Niu
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Anzhi Wei
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China.
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26
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Song W, Zhu J, Zhao H, Li Y, Liu J, Zhang X, Huang L, Lai J. OS1 functions in the allocation of nutrients between the endosperm and embryo in maize seeds. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:706-727. [PMID: 30506638 DOI: 10.1111/jipb.12755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/27/2018] [Indexed: 05/05/2023]
Abstract
Uncovering the genetic basis of seed development will provide useful tools for improving both crop yield and nutritional value. However, the genetic regulatory networks of maize (Zea mays) seed development remain largely unknown. The maize opaque endosperm and small germ 1 (os1) mutant has opaque endosperm and a small embryo. Here, we cloned OS1 and show that it encodes a putative transcription factor containing an RWP-RK domain. Transcriptional analysis indicated that OS1 expression is elevated in early endosperm development, especially in the basal endosperm transfer layer (BETL), conducting zone (CZ), and central starch endosperm (CSE) cells. RNA sequencing (RNA-Seq) analysis of the os1 mutant revealed sharp downregulation of certain genes in specific cell types, including ZmMRP-1 and Meg1 in BETL cells and a majority of zein- and starch-related genes in CSE cells. Using a haploid induction system, we show that wild-type endosperm could rescue the smaller size of os1 embryo, which suggests that nutrients are allocated by the wild-type endosperm. Therefore, our data imply that the network regulated by OS1 accomplishes a key step in nutrient allocation between endosperm and embryo within maize seeds. Identification of this network will help uncover the mechanisms regulating the nutritional balance between endosperm and embryo.
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Affiliation(s)
- Weibin Song
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100094, China
| | - Jinjie Zhu
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100094, China
| | - Haiming Zhao
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100094, China
| | - Yingnan Li
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100094, China
| | - Jiangtao Liu
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100094, China
| | - Xiangbo Zhang
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100094, China
| | - Liangliang Huang
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100094, China
| | - Jinsheng Lai
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100094, China
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27
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Yi F, Gu W, Chen J, Song N, Gao X, Zhang X, Zhou Y, Ma X, Song W, Zhao H, Esteban E, Pasha A, Provart NJ, Lai J. High Temporal-Resolution Transcriptome Landscape of Early Maize Seed Development. THE PLANT CELL 2019; 31:974-992. [PMID: 30914497 PMCID: PMC6533015 DOI: 10.1105/tpc.18.00961] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/06/2019] [Accepted: 03/25/2019] [Indexed: 05/13/2023]
Abstract
The early maize (Zea mays) seed undergoes several developmental stages after double fertilization to become fully differentiated within a short period of time, but the genetic control of this highly dynamic and complex developmental process remains largely unknown. Here, we report a high temporal-resolution investigation of transcriptomes using 31 samples collected at an interval of 4 or 6 h within the first six days of seed development. These time-course transcriptomes were clearly separated into four distinct groups corresponding to the stages of double fertilization, coenocyte formation, cellularization, and differentiation. A total of 22,790 expressed genes including 1415 transcription factors (TFs) were detected in early stages of maize seed development. In particular, 1093 genes including 110 TFs were specifically expressed in the seed and displayed high temporal specificity by expressing only in particular period of early seed development. There were 160, 22, 112, and 569 seed-specific genes predominantly expressed in the first 16 h after pollination, coenocyte formation, cellularization, and differentiation stage, respectively. In addition, network analysis predicted 31,256 interactions among 1317 TFs and 14,540 genes. The high temporal-resolution transcriptome atlas reported here provides an important resource for future functional study to unravel the genetic control of seed development.
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Affiliation(s)
- Fei Yi
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Wei Gu
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
- China Specialty Maize Research Center (CIMMYT), Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Jian Chen
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Ning Song
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Xiang Gao
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Xiangbo Zhang
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yingsi Zhou
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Xuxu Ma
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Weibin Song
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Haiming Zhao
- State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Eddi Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Asher Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Nicholas J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Jinsheng Lai
- State Key Laboratory of Agrobiotechnology 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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28
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Niu S, Zhang G, Li X, Haroon M, Si H, Fan G, Li XQ. Organelle DNA contents and starch accumulation in potato tubers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:205-216. [PMID: 30390131 DOI: 10.1007/s00122-018-3208-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/11/2018] [Indexed: 06/08/2023]
Abstract
Starch contents were found to be positively correlated with organelle/nuclear DNA ratios, suggesting that these ratios are involved in starch accumulation and may serve as a target trait in genetic engineering and a biomarker in breeding for improving the dry matter and starch production in potato. Starch is the main dry matter component of various staple food crops, including potato. Starch synthesis and accumulation is in plastids, uses sugar, consumes cellular energy, and requires active expression of starch synthesis genes. We hypothesized that the plastid/nuclear DNA ratios and mitochondrial/nuclear DNA ratios are involved in this accumulation. We analyzed the dry mater, starch, plastid DNA, mitochondrial DNA, and nuclear DNA in tuber stem ends and tuber bud ends in two potato cultivars and verified the results using whole tubers in nine potato cultivars. Dry matter contents (DMC) and organelle/nuclear DNA ratios increased rapidly during tuber bulking. DMC and starch contents were greater at the tuber stem ends than at the tuber bud ends. Both the comparisons between tuber ends and among whole tubers indicated that DMC and starch contents were positively correlated with both plastid/nuclear DNA ratios and mitochondrial/nuclear DNA ratios. The results suggest that pt/nuc and mt/nuc DNA ratios are important and may serve as a biomarker in selection, genetic engineering, and cytoplasm manipulation, for dry matter and starch accumulation in potato.
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Affiliation(s)
- Suyan Niu
- Institute of Bioengineering, Zhengzhou Normal University, Zhengzhou, 450044, China
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, E3B 4Z7, Canada
- College of Forest, Henan Agricultural University, Zhengzhou, 450002, China
| | - Guodong Zhang
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, E3B 4Z7, Canada
- Gansu Provincial Key Laboratory of Arid land Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, 730070, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xiubao Li
- Rizhao Academy of Agricultural Sciences, Rizhao, 276500, Shandong, China
| | - Muhammad Haroon
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, E3B 4Z7, Canada
| | - Huaijun Si
- Gansu Provincial Key Laboratory of Arid land Crop Science, Gansu Key Laboratory of Crop Genetic and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, 730070, China.
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Guoqiang Fan
- College of Forest, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Xiu-Qing Li
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, E3B 4Z7, Canada.
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Shin HY, Nam KH. RAV1 Negatively Regulates Seed Development by Directly Repressing MINI3 and IKU2 in Arabidopsis. Mol Cells 2018; 41:1072-1080. [PMID: 30518173 PMCID: PMC6315318 DOI: 10.14348/molcells.2018.0259] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/16/2018] [Accepted: 10/01/2018] [Indexed: 11/27/2022] Open
Abstract
A plant-specific B3 domain and AP2 domain-containing transcription factor, RAV1 acts as a negative regulator of growth in many plant species and its transcription was downregulated by BR and ABA. In this study, we found that RAV1-overexpressing transgenic plants showed abnormally developed ovules, resulting in reduced seed size, weight, and number in a silique. Interestingly, the endogenous expression of RAV1 fluctuated during seed development; it remained low during the early stage of seed development and sharply increased in the seed maturation stage. In plants, seed development is a complex process that requires coordinated growth of the embryo, endosperm, and maternal integuments. Among many genes that are associated with endosperm proliferation and embryo development, three genes consisting of SHB1, MINI3, and IKU2 form a small unit positively regulating this process, and their expression was regulated by BR and ABA. Using the floral stage-specific RNAs, we found that the expression of MINI3 and IKU2, the two downstream genes of the SHB1-MINI3-IKU2 cascade in the seed development pathway, were particularly reduced in the RAV1-overexpressing transgenic plants. We further determined that RAV1 directly binds to the promoter of MINI3 and IKU2, resulting in their repression. Direct treatment with brassinolide (BL) improved seed development of RAV1-overexpressing plants, but treatment with ABA severely worsened it. Overall, these results suggest that RAV1 is an additional negative player in the early stages of seed development, during which ABA and BR signaling are coordinated.
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Affiliation(s)
- Hyun-young Shin
- Department of Biological Sciences, Sookmyung Women’s University, Seoul,
Korea
| | - Kyoung Hee Nam
- Department of Biological Sciences, Sookmyung Women’s University, Seoul,
Korea
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30
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Zhang S, Zhan J, Yadegari R. Maize opaque mutants are no longer so opaque. PLANT REPRODUCTION 2018; 31:319-326. [PMID: 29978299 PMCID: PMC6105308 DOI: 10.1007/s00497-018-0344-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 06/23/2018] [Indexed: 05/02/2023]
Abstract
The endosperm of angiosperms is a zygotic seed organ that stores nutrient reserves to support embryogenesis and seed germination. Cereal endosperm is also a major source of human calories and an industrial feedstock. Maize opaque endosperm mutants commonly exhibit opaque, floury kernels, along with other abnormal seed and/or non-seed phenotypes. The opaque endosperm phenotype is sometimes accompanied by a soft kernel texture and increased nutritional quality, including a higher lysine content, which are valuable agronomic traits that have drawn attention of maize breeders. Recently, an increasing number of genes that underlie opaque mutants have been cloned, and their characterization has begun to shed light on the molecular basis of the opaque endosperm phenotype. These mutants are categorized by disruption of genes encoding zein or non-zein proteins localized to protein bodies, enzymes involved in endosperm metabolic processes, or transcriptional regulatory proteins associated with endosperm storage programs.
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Affiliation(s)
- Shanshan Zhang
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Junpeng Zhan
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Ramin Yadegari
- School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.
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31
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Xiu Y, Wu G, Tang W, Peng Z, Bu X, Chao L, Yin X, Xiong J, Zhang H, Zhao X, Ding J, Ma L, Wang H, van Staden J. Oil biosynthesis and transcriptome profiles in developing endosperm and oil characteristic analyses in Paeonia ostii var. lishizhenii. JOURNAL OF PLANT PHYSIOLOGY 2018; 228:121-133. [PMID: 29902680 DOI: 10.1016/j.jplph.2018.05.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 05/31/2018] [Accepted: 05/31/2018] [Indexed: 05/21/2023]
Abstract
Paeonia ostii var. lishizhenii, a well-known medicinal and horticultural plant, is indigenous to China. Recent studies have shown that its seed has a high oil content, and it was approved as a novel resource of edible oil with a high level of α-linolenic acid by the Chinese Government. This study measured the seed oil contents and fatty acid components of P. ostii var. lishizhenii and six other peonies, P. suffruticosa, P. ludlowii, P. decomposita, P. rockii, and P. lactiflora Pall. 'Heze' and 'Gansu'. The results show that P. ostii var. lishizhenii exhibits the average oil characteristics of tested peonies, with an oil content of 21.3%, α-linolenic acid 43.8%, and unsaturated fatty acids around 92.1%. Hygiene indicators for the seven peony seed oils met the Chinese national food standards. P. ostii var. lishizhenii seeds were used to analyze transcriptome gene regulation networks on endosperm development and oil biosynthesis. In total, 124,117 transcripts were obtained from six endosperm developing stages (S0-S5). The significant changes in differential expression genes (DEGs) clarify three peony endosperm developmental phases: the endosperm cell mitotic phase (S0-S1), the TAG biosynthesis phase (S1-S4), and the mature phase (S5). The DEGs in plant hormone signal transduction, DNA replication, cell division, differentiation, transcription factors, and seed dormancy pathways regulate the endosperm development process. Another 199 functional DEGs participate in glycolysis, pentose phosphate pathway, citrate cycle, FA biosynthesis, TAG assembly, and other pathways. A key transcription factor (WRI1) and some important target genes (ACCase, FATA, LPCAT, FADs, and DGAT etc.) were found in the comprehensive genetic networks of oil biosynthesis.
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Affiliation(s)
- Yu Xiu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; College of Forestry, Beijing Forestry University, Beijing 100083, China.
| | - Guodong Wu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China.
| | - Wensi Tang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China.
| | | | - Xiangpan Bu
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China.
| | - Longjun Chao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; Beijing Peonature Biotechnology Co., Ltd., Beijing, 101301, China.
| | - Xue Yin
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China.
| | - Jiannan Xiong
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China.
| | - Haiwu Zhang
- Forestry Institute of Tibet Autonomous Region, Lhasa 850000, China.
| | | | - Jing Ding
- Jiangsu Guosetianxiang Oil Peony Science and Technology Development Co., Ltd., Changzhou 213000, China.
| | - Lvyi Ma
- College of Forestry, Beijing Forestry University, Beijing 100083, China.
| | - Huafang Wang
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China.
| | - Johannes van Staden
- Research Centre for Plant Growth and Development, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, Private Bag X01, Scottsville, 3209, South Africa.
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32
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Qu J, Xu S, Zhang Z, Chen G, Zhong Y, Liu L, Zhang R, Xue J, Guo D. Evolutionary, structural and expression analysis of core genes involved in starch synthesis. Sci Rep 2018; 8:12736. [PMID: 30143668 PMCID: PMC6109180 DOI: 10.1038/s41598-018-30411-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 07/30/2018] [Indexed: 01/29/2023] Open
Abstract
Starch is the main storage carbohydrate in plants and an important natural resource for food, feed and industrial raw materials. However, the details regarding the pathway for starch biosynthesis and the diversity of biosynthetic enzymes involved in this process are poorly understood. This study uses a comprehensive phylogenetic analysis of 74 sequenced plant genomes to revisit the evolutionary history of the genes encoding ADP-glucose pyrophosphorylase (AGPase), starch synthase (SS), starch branching enzyme (SBE) and starch de-branching enzyme (DBE). Additionally, the protein structures and expression patterns of these four core genes in starch biosynthesis were studied to determine their functional differences. The results showed that AGPase, SS, SBE and DBE have undergone complicated evolutionary processes in plants and that gene/genome duplications are responsible for the observed differences in isoform numbers. A structure analysis of these proteins suggested that the deletion/mutation of amino acids in some active sites resulted in not only structural variation but also sub-functionalization or neo-functionalization. Expression profiling indicated that AGPase-, SS-, SBE- and DBE-encoding genes exhibit spatio-temporally divergent expression patterns related to the composition of functional complexes in starch biosynthesis. This study provides a comprehensive atlas of the starch biosynthetic pathway, and these data should support future studies aimed at increasing understanding of starch biosynthesis and the functional evolutionary divergence of AGPase, SS, SBE, and DBE in plants.
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Affiliation(s)
- Jianzhou Qu
- The key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100, Shaanxi, China
| | - Shutu Xu
- The key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100, Shaanxi, China
| | - Zhengquan Zhang
- The key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100, Shaanxi, China
| | - Guangzhou Chen
- The key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100, Shaanxi, China
| | - Yuyue Zhong
- The key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100, Shaanxi, China
| | - Linsan Liu
- The key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100, Shaanxi, China
| | - Renhe Zhang
- The key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100, Shaanxi, China
| | - Jiquan Xue
- The key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100, Shaanxi, China.
| | - Dongwei Guo
- The key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
- Maize Engineering Technology Research Centre of Shaanxi Province, Yangling, 712100, Shaanxi, China.
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Quantitative Spatiotemporal Oil Body Ultrastructure Helps to Verify the Distinct Lipid Deposition Patterns in Benzoin Endosperm and Embryo Cells. FORESTS 2018. [DOI: 10.3390/f9050265] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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34
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Zhang S, Wang D, Zhang H, Skaggs MI, Lloyd A, Ran D, An L, Schumaker KS, Drews GN, Yadegari R. FERTILIZATION-INDEPENDENT SEED-Polycomb Repressive Complex 2 Plays a Dual Role in Regulating Type I MADS-Box Genes in Early Endosperm Development. PLANT PHYSIOLOGY 2018; 177. [PMID: 29523711 PMCID: PMC5933120 DOI: 10.1104/pp.17.00534] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Early endosperm development presents a unique system in which to uncover epigenetic regulatory mechanisms because the contributing maternal and paternal genomes possess differential epigenetic modifications. In Arabidopsis (Arabidopsis thaliana), the initiation of endosperm coenocytic growth upon fertilization and the transition to endosperm cellularization are regulated by the FERTILIZATION-INDEPENDENT SEED (FIS)-Polycomb Repressive Complex 2 (PRC2), a putative H3K27 methyltransferase. Here, we address the possible role of the FIS-PRC2 complex in regulating the type I MADS-box gene family, which has been shown previously to regulate early endosperm development. We show that a subclass of type I MADS-box genes (C2 genes) was expressed in distinct domains of the coenocytic endosperm in wild-type seeds. Furthermore, the C2 genes were mostly up-regulated biallelically during the extended coenocytic phase of endosperm development in the FIS-PRC2 mutant background. Using allele-specific expression analysis, we also identified a small subset of C2 genes subjected to FIS-PRC2-dependent maternal or FIS-PRC2-independent paternal imprinting. Our data support a dual role for the FIS-PRC2 complex in the regulation of C2 type I MADS-box genes, as evidenced by a generalized role in the repression of gene expression at both alleles associated with endosperm cellularization and a specialized role in silencing the maternal allele of imprinted genes.
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Affiliation(s)
- Shanshan Zhang
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721
| | - Dongfang Wang
- Biology Department, Spelman College, Atlanta, Georgia 30314
| | - Huajian Zhang
- Department of Biology, University of Utah, Salt Lake City, Utah 84112
| | - Megan I Skaggs
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721
| | - Alan Lloyd
- Department of Biology, University of Utah, Salt Lake City, Utah 84112
| | - Di Ran
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721
- Division of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, Arizona 85724
| | - Lingling An
- Division of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, Arizona 85724
- Department of Agricultural and Biosystems Engineering, University of Arizona, Tucson, Arizona 85721
| | - Karen S Schumaker
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721
| | - Gary N Drews
- Department of Biology, University of Utah, Salt Lake City, Utah 84112
| | - Ramin Yadegari
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721
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35
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Toda E, Ohnishi Y, Okamoto T. An imbalanced parental genome ratio affects the development of rice zygotes. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:2609-2619. [PMID: 29538694 PMCID: PMC5920335 DOI: 10.1093/jxb/ery094] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/06/2018] [Indexed: 05/25/2023]
Abstract
Upon double fertilization, one sperm cell fuses with the egg cell to form a zygote with a 1:1 maternal-to-paternal genome ratio (1m:1p), and another sperm cell fuses with the central cell to form a triploid primary endosperm cell with a 2m:1p ratio, resulting in formation of the embryo and the endosperm, respectively. The endosperm is known to be considerably sensitive to the ratio of the parental genomes. However, the effect of an imbalance of the parental genomes on zygotic development and embryogenesis has not been well studied, because it is difficult to reproduce the parental genome-imbalanced situation in zygotes and to monitor the developmental profile of zygotes without external effects from the endosperm. In this study, we produced polyploid zygotes with an imbalanced parental genome ratio by electro-fusion of isolated rice gametes and observed their developmental profiles. Polyploid zygotes with an excess maternal gamete/genome developed normally, whereas approximately half to three-quarters of polyploid zygotes with a paternal excess showed developmental arrests. These results indicate that paternal and maternal genomes synergistically serve zygote development with distinct functions, and that genes with monoallelic expression play important roles during zygotic development and embryogenesis.
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Affiliation(s)
- Erika Toda
- Department of Biological Sciences, Tokyo Metropolitan University, Minami-osawa, Hachioji, Tokyo, Japan
- Plant Breeding Innovation Laboratory, RIKEN Innovation Center, Tsurumi-ku, Yokohama, Japan
| | - Yukinosuke Ohnishi
- Department of Biological Sciences, Tokyo Metropolitan University, Minami-osawa, Hachioji, Tokyo, Japan
| | - Takashi Okamoto
- Department of Biological Sciences, Tokyo Metropolitan University, Minami-osawa, Hachioji, Tokyo, Japan
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36
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Hu H, He J, Zhao J, Ou X, Li H, Ru Z. Low pH stress responsive transcriptome of seedling roots in wheat (Triticum aestivum L.). Genes Genomics 2018; 40:1199-1211. [PMID: 30315523 DOI: 10.1007/s13258-018-0680-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 02/28/2018] [Indexed: 12/22/2022]
Abstract
Soil acidification is one of major problems limiting crop growth and especially becoming increasingly serious in China owing to excessive use of nitrogen fertilizer. Only the STOP1 of Arabidopsis was identified clearly sensitive to proton rhizotoxicity and the molecular mechanism for proton toxicity tolerance of plants is still poorly understood. The main objective of this study was to investigate the transcriptomic change in plants under the low pH stress. The low pH as a single factor was employed to induce the response of the wheat seedling roots. Wheat cDNA microarray was used to identify differentially expressed genes (DEGs). A total of 1057 DEGs were identified, of which 761 genes were up-regulated and 296 were down-regulated. The greater percentage of up-regulated genes involved in developmental processes, immune system processes, multi-organism processes, positive regulation of biological processes and metabolic processes of the biological processes. The more proportion of down-regulation genes belong to the molecular function category including transporter activity, antioxidant activity and molecular transducer activity and to the extracellular region of the cellular components category. Moreover, most genes among 41 genes involved in ion binding, 17 WAKY transcription factor genes and 17 genes related to transport activity were up-regulated. KEGG analysis showed that the jasmonate signal transduction and flavonoid biosynthesis might play important roles in response to the low pH stress in wheat seedling roots. Based on the data, it is can be deduced that WRKY transcription factors might play a critical role in the transcriptional regulation, and the alkalifying of the rhizosphere might be the earliest response process to low pH stress in wheat seedling roots. These results provide a basis to reveal the molecular mechanism of proton toxicity tolerance in plants.
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Affiliation(s)
- Haiyan Hu
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, Henan, China.
- Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, 453003, Henan, China.
- Henan Engineering Research Center of Crop Genome Editing, Xinxiang, 453003, Henan, China.
| | - Jie He
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, Henan, China
| | - Junjie Zhao
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, Henan, China
| | - Xingqi Ou
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, Henan, China
- Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, 453003, Henan, China
| | - Hongmin Li
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, Henan, China
- Henan Engineering Research Center of Crop Genome Editing, Xinxiang, 453003, Henan, China
| | - Zhengang Ru
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, Henan, China.
- Collaborative Innovation Center of Modern Biological Breeding, Xinxiang, 453003, Henan, China.
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Yang M, Chen L, Wu X, Gao X, Li C, Song Y, Zhang D, Shi Y, Li Y, Li YX, Wang T. Characterization and fine mapping of qkc7.03: a major locus for kernel cracking in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:437-448. [PMID: 29143067 DOI: 10.1007/s00122-017-3012-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/26/2017] [Indexed: 05/20/2023]
Abstract
A major locus conferring kernel cracking in maize was characterized and fine mapped to an interval of 416.27 kb. Meanwhile, combining the results of transcriptomic analysis, the candidate gene was inferred. Seed development requires a proper structural and physiological balance between the maternal tissues and the internal structures of the seeds. In maize, kernel cracking is a disorder in this balance that seriously limits quality and yield and is characterized by a cracked pericarp at the kernel top and endosperm everting. This study elucidated the genetic basis and characterization of kernel cracking. Primarily, a near isogenic line (NIL) with a B73 background exhibited steady kernel cracking across environments. Therefore, deprived mapping populations were developed from this NIL and its recurrent parent B73. A major locus on chromosome 7, qkc7.03, was identified to be associated with the cracking performance. According to a progeny test of recombination events, qkc7.03 was fine mapped to a physical interval of 416.27 kb. In addition, obvious differences were observed in embryo development and starch granule arrangement within the endosperm between the NIL and its recurrent parent upon the occurrence of kernel cracking. Moreover, compared to its recurrent parent, the transcriptome of the NIL showed a significantly down-regulated expression of genes related to zeins, carbohydrate synthesis and MADS-domain transcription factors. The transcriptomic analysis revealed ten annotated genes within the target region of qkc7.03, and only GRMZM5G899476 was differently expressed between the NIL and its recurrent parent, indicating that this gene might be a candidate gene for kernel cracking. The results of this study facilitate the understanding of the potential mechanism underlying kernel cracking in maize.
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Affiliation(s)
- Mingtao Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Lin Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Xun Wu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Xing Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Chunhui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Yanchun Song
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Dengfeng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Yunsu Shi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Yu Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Yong-Xiang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China.
| | - Tianyu Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China.
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38
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Roth M, Florez-Rueda AM, Griesser S, Paris M, Städler T. Incidence and developmental timing of endosperm failure in post-zygotic isolation between wild tomato lineages. ANNALS OF BOTANY 2018; 121:107-118. [PMID: 29280998 PMCID: PMC5786209 DOI: 10.1093/aob/mcx133] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/04/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND AND AIMS Defective hybrid seed development in angiosperms might mediate the rapid establishment of intrinsic post-zygotic isolation between closely related species. Extensive crosses within and among three lineages of wild tomatoes (Solanum section Lycopersicon) were performed to address the incidence, developmental timing and histological manifestations of hybrid seed failure. These lineages encompass different, yet fairly recent, divergence times and both allopatric and partially sympatric pairs. METHODS Mature seeds were scored visually 2 months after hand pollinations, and viable-looking seeds were assessed for germination success. Using histological sections from early-developing seeds from a sub-set of crosses, the growth of three major seed compartments (endosperm, embryo and seed coat) was measured at critical developmental stages up to 21 d after pollination, with a focus on the timing and histological manifestations of endosperm misdevelopment in abortive hybrid seeds. KEY RESULTS For two of three interspecific combinations including the most closely related pair that was also studied histologically, almost all mature seeds appeared 'flat' and proved inviable; histological analyses revealed impaired endosperm proliferation at early globular embryo stages, concomitant with embryo arrest and seed abortion in both cross directions. The third interspecific combination yielded a mixture of flat, inviable and plump, viable seeds; many of the latter germinated and exhibited near-normal juvenile phenotypes or, in some instances, hybrid necrosis and impaired growth. CONCLUSIONS The overall results suggest that near-complete hybrid seed failure can evolve fairly rapidly and without apparent divergence in reproductive phenology/biology. While the evidence accrued here is largely circumstantial, early-acting disruptions of normal endosperm development are most probably the common cause of seed failure regardless of the type of endosperm (nuclear or cellular).
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Affiliation(s)
- Morgane Roth
- Plant Ecological Genetics, Institute of Integrative Biology & Zurich–Basel Plant Science Center, ETH Zurich, Zurich, Switzerland
| | - Ana M Florez-Rueda
- Plant Ecological Genetics, Institute of Integrative Biology & Zurich–Basel Plant Science Center, ETH Zurich, Zurich, Switzerland
| | - Stephan Griesser
- Plant Ecological Genetics, Institute of Integrative Biology & Zurich–Basel Plant Science Center, ETH Zurich, Zurich, Switzerland
| | - Margot Paris
- Plant Ecological Genetics, Institute of Integrative Biology & Zurich–Basel Plant Science Center, ETH Zurich, Zurich, Switzerland
| | - Thomas Städler
- Plant Ecological Genetics, Institute of Integrative Biology & Zurich–Basel Plant Science Center, ETH Zurich, Zurich, Switzerland
- For correspondence. Email
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39
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Yeung EC. A perspective on orchid seed and protocorm development. BOTANICAL STUDIES 2017; 58:33. [PMID: 28779349 PMCID: PMC5544657 DOI: 10.1186/s40529-017-0188-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 07/24/2017] [Indexed: 05/07/2023]
Abstract
This perspective draws attention to the functional organization of orchid seed and protocorm during the course of development. The orchid embryos have a well-organized developmental plan generating a blue-print of a protocorm as they mature. The different phases of embryo development in orchids, i.e. histodifferentiation, storage product synthesis and accumulation, and maturation are essentially similar to other flowering plants. The protocorm is considered as a unique structure designed to establish symbiotic association with mycorrhizal fungi and with the primary goal to form a shoot apical meristem. This perspective brings forth arguments that the processes of embryo and protocorm development are highly programmed events, enhancing survival of orchid seeds and plantlets in their natural habitats. Furthermore, the ability of protocorm cells to divide, makes them ideal explants for micropropagation and transformation studies. Through seed germination and micropropagation using protocorms as explants, orchid conservation efforts are greatly enhanced.
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Affiliation(s)
- Edward C Yeung
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada.
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40
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Zhu M, Zhang M, Xing L, Li W, Jiang H, Wang L, Xu M. Transcriptomic Analysis of Long Non-Coding RNAs and Coding Genes Uncovers a Complex Regulatory Network That Is Involved in Maize Seed Development. Genes (Basel) 2017; 8:genes8100274. [PMID: 29039813 PMCID: PMC5664124 DOI: 10.3390/genes8100274] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 10/03/2017] [Accepted: 10/13/2017] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been reported to be involved in the development of maize plant. However, few focused on seed development of maize. Here, we identified 753 lncRNA candidates in maize genome from six seed samples. Similar to the mRNAs, lncRNAs showed tissue developmental stage specific and differential expression, indicating their putative role in seed development. Increasing evidence shows that crosstalk among RNAs mediated by shared microRNAs (miRNAs) represents a novel layer of gene regulation, which plays important roles in plant development. Functional roles and regulatory mechanisms of lncRNAs as competing endogenous RNAs (ceRNA) in plants, particularly in maize seed development, are unclear. We combined analyses of consistently altered 17 lncRNAs, 840 mRNAs and known miRNA to genome-wide investigate potential lncRNA-mediated ceRNA based on “ceRNA hypothesis”. The results uncovered seven novel lncRNAs as potential functional ceRNAs. Functional analyses based on their competitive coding-gene partners by Gene Ontology (GO) and KEGG biological pathway demonstrated that combined effects of multiple ceRNAs can have major impacts on general developmental and metabolic processes in maize seed. These findings provided a useful platform for uncovering novel mechanisms of maize seed development and may provide opportunities for the functional characterization of individual lncRNA in future studies.
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Affiliation(s)
- Ming Zhu
- School of Life Sciences, Anhui Agricultural University, Hefei 230000, China.
- Biotechnology Research Institute/The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Min Zhang
- Biotechnology Research Institute/The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Lijuan Xing
- Biotechnology Research Institute/The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Wenzong Li
- Biotechnology Research Institute/The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Haiyang Jiang
- School of Life Sciences, Anhui Agricultural University, Hefei 230000, China.
| | - Lei Wang
- Biotechnology Research Institute/The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Miaoyun Xu
- Biotechnology Research Institute/The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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41
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Rangan P, Furtado A, Henry RJ. The transcriptome of the developing grain: a resource for understanding seed development and the molecular control of the functional and nutritional properties of wheat. BMC Genomics 2017; 18:766. [PMID: 29020946 PMCID: PMC5637334 DOI: 10.1186/s12864-017-4154-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 10/02/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Wheat is one of the three major cereals that have been domesticated to feed human populations. The composition of the wheat grain determines the functional properties of wheat including milling efficiency, bread making, and nutritional value. Transcriptome analysis of the developing wheat grain provides key insights into the molecular basis for grain development and quality. RESULTS The transcriptome of 35 genotypes was analysed by RNA-Seq at two development stages (14 and 30 days-post-anthesis, dpa) corresponding to the mid stage of development (stage Z75) and the almost mature seed (stage Z85). At 14dpa, most of the transcripts were associated with the synthesis of the major seed components including storage proteins and starch. At 30dpa, a diverse range of genes were expressed at low levels with a predominance of genes associated with seed defence and stress tolerance. RNA-Seq analysis of changes in expression between 14dpa and 30dpa stages revealed 26,477 transcripts that were significantly differentially expressed at a FDR corrected p-value cut-off at ≤0.01. Functional annotation and gene ontology mapping was performed and KEGG pathway mapping allowed grouping based upon biochemical linkages. This analysis demonstrated that photosynthesis associated with the pericarp was very active at 14dpa but had ceased by 30dpa. Recently reported genes for flour yield in milling and bread quality were found to influence wheat quality largely due to expression patterns at the earlier seed development stage. CONCLUSIONS This study serves as a resource providing an overview of gene expression during wheat grain development at the early (14dpa) and late (30dpa) grain filling stages for use in studies of grain quality and nutritional value and in understanding seed biology.
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Affiliation(s)
- Parimalan Rangan
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, 4072, Australia.,Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia, QLD, 4072, Australia.
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Zhang S, Thakare D, Yadegari R. Laser-Capture Microdissection of Maize Kernel Compartments for RNA-Seq-Based Expression Analysis. Methods Mol Biol 2017; 1676:153-163. [PMID: 28986909 DOI: 10.1007/978-1-4939-7315-6_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Laser-capture microdissection (LCM) enables isolation of single cells or groups of cells for a variety of downstream applications including transcriptome profiling. Recently, this methodology has found a more widespread use particularly with the advent of next-generation sequencing techniques that enable deep profiling of the limited amounts of RNA obtained from fixed or frozen sections. When used with fixed tissues, a major experimental challenge is to balance the tissue integrity needed for microscopic visualization of the cell types of interest with that of the RNA quality necessary for deep profiling. Complex biological structures such as seeds or kernels pose an especially difficult case in this context as in many instances the key internal structures such as the embryo and the endosperm are relatively inaccessible. Here, we present an optimized LCM protocol for maize kernel that has been developed specifically to enable profiling of the early stages of endosperm development using RNA-Seq.
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Affiliation(s)
- Shanshan Zhang
- School of Plant Sciences, University of Arizona, Tucson, Arizona, 85721-0036, USA
| | - Dhiraj Thakare
- School of Plant Sciences, University of Arizona, Tucson, Arizona, 85721-0036, USA
| | - Ramin Yadegari
- School of Plant Sciences, University of Arizona, Tucson, Arizona, 85721-0036, USA.
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Abstract
The maize endosperm consists of three major compartmentalized cell types: the starchy endosperm (SE), the basal endosperm transfer cell layer (BETL), and the aleurone cell layer (AL). Differential genetic programs are activated in each cell type to construct functionally and structurally distinct cells. To compare gene expression patterns involved in maize endosperm cell differentiation, we isolated transcripts from cryo-dissected endosperm specimens enriched with BETL, AL, or SE at 8, 12, and 16 days after pollination (DAP). We performed transcriptome profiling of coding and long noncoding transcripts in the three cell types during differentiation and identified clusters of the transcripts exhibiting spatio-temporal specificities. Our analysis uncovered that the BETL at 12 DAP undergoes the most dynamic transcriptional regulation for both coding and long noncoding transcripts. In addition, our transcriptome analysis revealed spatio-temporal regulatory networks of transcription factors, imprinted genes, and loci marked with histone H3 trimethylated at lysine 27. Our study suggests that various regulatory mechanisms contribute to the genetic networks specific to the functions and structures of the cell types of the endosperm.
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BISPO VANDERSONS, DANTAS LUCASS, CHAVES FILHO ADRIANOB, PINTO ISABELLAF, SILVA RAILMARAPDA, OTSUKA FELIPEA, SANTOS RODRIGOB, SANTOS ALINEC, TRINDADE DANIELLEJ, MATOS HUMBERTOR. Reduction of the DNA damages, Hepatoprotective Effect and Antioxidant Potential of the Coconut Water, ascorbic and Caffeic Acids in Oxidative Stress Mediated by Ethanol. ACTA ACUST UNITED AC 2017; 89:1095-1109. [DOI: 10.1590/0001-3765201720160581] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 01/04/2017] [Indexed: 11/21/2022]
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45
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Abrahamsson M, Valladares S, Merino I, Larsson E, von Arnold S. Degeneration pattern in somatic embryos of Pinus sylvestris L. IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY. PLANT : JOURNAL OF THE TISSUE CULTURE ASSOCIATION 2017; 53:86-96. [PMID: 28553064 PMCID: PMC5423931 DOI: 10.1007/s11627-016-9797-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 12/21/2016] [Indexed: 05/30/2023]
Abstract
Somatic embryos can be used for propagating forest trees vegetatively, which is of great importance for capturing the genetic gain in breeding programs. However, many economically important Pinus species are difficult or impossible to propagate via somatic embryogenesis. In order to get a better understanding of the difficulties to propagate Pinus species via somatic embryogenesis, we are studying the developmental pathway of somatic embryos in different cell lines. In a previous study, we showed that the morphology of early somatic embryos in Scots pine (Pinus sylvestris) differs between cell lines giving rise to normal or abnormal cotyledonary embryos. In this study, we have compared the proliferation and degeneration pattern of early and late embryos in a normal and abnormal cell line. In both cell lines, a high frequency of the embryos degenerated. Among the degenerating embryos, two main degeneration patterns could be distinguished. In the normal cell line, the embryos degenerated similar to how the subordinate embryos are degraded in the seed. In the abnormal cell line, the degeneration of the embryos resulted in a continuous loop of embryo degeneration and differentiation of new embryos. We observed a similar degeneration pattern when embryogenic tissue was initiated from megagametophytes containing zygotic embryos at the stage of cleavage polyembryony. Based on our results, we suggest that the degeneration pattern in abnormal cell lines starts during initiation of embryogenic cultures.
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Affiliation(s)
- Malin Abrahamsson
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7080, 750 07 Uppsala, Sweden
| | - Silvia Valladares
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7080, 750 07 Uppsala, Sweden
- Plant Biotechnology Laboratory, Fundación Promiva, Ctra M501 Km 5,1, 28670 Villaviciosa de Odón, Madrid Spain
| | - Irene Merino
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7080, 750 07 Uppsala, Sweden
| | - Emma Larsson
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7080, 750 07 Uppsala, Sweden
| | - Sara von Arnold
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, P.O. Box 7080, 750 07 Uppsala, Sweden
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46
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Transcriptome Dynamics during Maize Endosperm Development. PLoS One 2016; 11:e0163814. [PMID: 27695101 PMCID: PMC5047526 DOI: 10.1371/journal.pone.0163814] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/14/2016] [Indexed: 11/19/2022] Open
Abstract
The endosperm is a major organ of the seed that plays vital roles in determining seed weight and quality. However, genome-wide transcriptome patterns throughout maize endosperm development have not been comprehensively investigated to date. Accordingly, we performed a high-throughput RNA sequencing (RNA-seq) analysis of the maize endosperm transcriptome at 5, 10, 15 and 20 days after pollination (DAP). We found that more than 11,000 protein-coding genes underwent alternative splicing (AS) events during the four developmental stages studied. These genes were mainly involved in intracellular protein transport, signal transmission, cellular carbohydrate metabolism, cellular lipid metabolism, lipid biosynthesis, protein modification, histone modification, cellular amino acid metabolism, and DNA repair. Additionally, 7,633 genes, including 473 transcription factors (TFs), were differentially expressed among the four developmental stages. The differentially expressed TFs were from 50 families, including the bZIP, WRKY, GeBP and ARF families. Further analysis of the stage-specific TFs showed that binding, nucleus and ligand-dependent nuclear receptor activities might be important at 5 DAP, that immune responses, signalling, binding and lumen development are involved at 10 DAP, that protein metabolic processes and the cytoplasm might be important at 15 DAP, and that the responses to various stimuli are different at 20 DAP compared with the other developmental stages. This RNA-seq analysis provides novel, comprehensive insights into the transcriptome dynamics during early endosperm development in maize.
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47
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Wu X, Liu J, Li D, Liu CM. Rice caryopsis development I: Dynamic changes in different cell layers. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:772-85. [PMID: 26472484 PMCID: PMC5064628 DOI: 10.1111/jipb.12440] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/09/2015] [Indexed: 05/18/2023]
Abstract
Rice caryopsis as one of the most important food sources for humans has a complex structure that is composed of maternal tissues including the pericarp and testa and filial tissues including the endosperm and embryo. Although rice caryopsis studies have been conducted previously, a systematic characterization throughout the entire developmental process is still lacking. In this study, detailed morphological examinations of caryopses were made during the entire 30-day developmental process. We observed some rapid changes in cell differentiation events and cataloged how cellular degeneration processes occurred in maternal tissues. The differentiations of tube cells and cross cells were achieved by 9 days after pollination (DAP). In the testa, the outer integument was degenerated by 3 DAP, while the outer layer of the inner integument degenerated by 7 DAP. In the nucellus, all tissues with the exception of the nucellar projection and the nucellar epidermis degenerated in the first 5 DAP. By 21 DAP, all maternal tissues, including vascular bundles, the nucellar projection and the nucellar epidermal cells were degenerated. In summary, this study provides a complete atlas of the dynamic changes in cell differentiation and degeneration for individual maternal cell layers of rice caryopsis.
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Affiliation(s)
- Xiaoba Wu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jinxin Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Dongqi Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Chun-Ming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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Huang X, Lu Z, Wang X, Ouyang Y, Chen W, Xie K, Wang D, Luo M, Luo J, Yao J. Imprinted gene OsFIE1 modulates rice seed development by influencing nutrient metabolism and modifying genome H3K27me3. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:305-17. [PMID: 27133784 DOI: 10.1111/tpj.13202] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 04/12/2016] [Accepted: 04/25/2016] [Indexed: 05/06/2023]
Abstract
Imprinted Polycomb group (PcG) genes play a critical role in seed development in Arabidopsis. However, the role of the imprinted gene in cereal plants remains obscure. Here, a transgenic approach was conducted to study the function of the imprinted gene Oryza sativa Fertilization-Independent Endosperm 1 (OsFIE1) during seed development in rice (Oryza sativa ssp. japonica 'ZhongHua11'). RNAi of OsFIE1 and homozygous T-DNA insertion mutant osfie1 led to smaller seeds, delayed embryo development, smaller aleurone layer cells, and decreased seed set rate. OsFIE1 was specifically expressed in endosperm, and mRNA of OsFIE1 was also enriched in the inner seed coat together with the corresponding PcG members OsiEZ1 and OsCLF. Meanwhile, the contents of seed storage proteins and Ile, Leu, and Val were decreased, accompanied by the down-regulation of multiple transcription factors, storage protein synthesis and amino acid metabolism-related genes in OsFIE1-RNAi lines and osfie1. Western blot analysis showed that the complex OsFIE1-PcG in endosperm regulated the expression of target genes by genome H3K27me3 modification. We conclude that the OsFIE1-PcG complex, which was enriched in the inner seed coat and endosperm linked the development of embryo and endosperm by influencing transcription factors and nutrient metabolism and induced a highly differential effect when compared with the OsFIE2-PcG complex.
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Affiliation(s)
- Xiaolong Huang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Plant Physiology and Development Regulation, Guizhou Normal University, Guiyang, 550001, China
- School of Life Science, Guizhou Normal University, Guiyang, 550001, China
| | - Zhanhua Lu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xin Wang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Koulong Xie
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dongying Wang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Min Luo
- CSIRO Plant Industry, PO Box 1600, Canberra, ACT, 2601, Australia
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Jialing Yao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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49
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Yang H, Liu X, Xin M, Du J, Hu Z, Peng H, Rossi V, Sun Q, Ni Z, Yao Y. Genome-Wide Mapping of Targets of Maize Histone Deacetylase HDA101 Reveals Its Function and Regulatory Mechanism during Seed Development. THE PLANT CELL 2016; 28:629-45. [PMID: 26908760 PMCID: PMC4826005 DOI: 10.1105/tpc.15.00691] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 02/21/2016] [Indexed: 05/03/2023]
Abstract
Histone deacetylases (HDACs) regulate histone acetylation levels by removing the acetyl group from lysine residues. The maize (Zea mays) HDACHDA101 influences several aspects of development, including kernel size; however, the molecular mechanism by which HDA101 affects kernel development remains unknown. In this study, we find that HDA101 regulates the expression of transfer cell-specific genes, suggesting that their misregulation may be associated with the defects in differentiation of endosperm transfer cells and smaller kernels observed in hda101 mutants. To investigate HDA101 function during the early stages of seed development, we performed genome-wide mapping of HDA101 binding sites. We observed that, like mammalian HDACs, HDA101 mainly targets highly and intermediately expressed genes. Although loss of HDA101 can induce histone hyperacetylation of its direct targets, this often does not involve variation in transcript levels. A small subset of inactive genes that must be negatively regulated during kernel development is also targeted by HDA101 and its loss leads to hyperacetylation and increased expression of these inactive genes. Finally, we report that HDA101 interacts with members of different chromatin remodeling complexes, such as NFC103/MSI1 and SNL1/SIN3-like protein corepressors. Taken together, our results reveal a complex genetic network regulated by HDA101 during seed development and provide insight into the different mechanisms of HDA101-mediated regulation of transcriptionally active and inactive genes.
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Affiliation(s)
- Hua Yang
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, PR China
| | - Xinye Liu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, PR China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, PR China
| | - Jinkun Du
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, PR China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, PR China
| | - HuiRu Peng
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, PR China
| | - Vincenzo Rossi
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Unità di Ricerca per la Maiscoltura, I-24126 Bergamo, Italy
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, PR China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, PR China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology and Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, PR China
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50
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Tai H, Lu X, Opitz N, Marcon C, Paschold A, Lithio A, Nettleton D, Hochholdinger F. Transcriptomic and anatomical complexity of primary, seminal, and crown roots highlight root type-specific functional diversity in maize (Zea mays L.). JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1123-35. [PMID: 26628518 PMCID: PMC4753849 DOI: 10.1093/jxb/erv513] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Maize develops a complex root system composed of embryonic and post-embryonic roots. Spatio-temporal differences in the formation of these root types imply specific functions during maize development. A comparative transcriptomic study of embryonic primary and seminal, and post-embryonic crown roots of the maize inbred line B73 by RNA sequencing along with anatomical studies were conducted early in development. Seminal roots displayed unique anatomical features, whereas the organization of primary and crown roots was similar. For instance, seminal roots displayed fewer cortical cell files and their stele contained more meta-xylem vessels. Global expression profiling revealed diverse patterns of gene activity across all root types and highlighted the unique transcriptome of seminal roots. While functions in cell remodeling and cell wall formation were prominent in primary and crown roots, stress-related genes and transcriptional regulators were over-represented in seminal roots, suggesting functional specialization of the different root types. Dynamic expression of lignin biosynthesis genes and histochemical staining suggested diversification of cell wall lignification among the three root types. Our findings highlight a cost-efficient anatomical structure and a unique expression profile of seminal roots of the maize inbred line B73 different from primary and crown roots.
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Affiliation(s)
- Huanhuan Tai
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| | - Xin Lu
- Experimental Medicine and Therapy Research, University of Regensburg, D-93053 Regensburg, Germany
| | - Nina Opitz
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| | - Caroline Marcon
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| | - Anja Paschold
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
| | - Andrew Lithio
- Department of Statistics, Iowa State University, Ames, IA 50011-1210, USA
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, IA 50011-1210, USA
| | - Frank Hochholdinger
- Institute of Crop Science and Resource Conservation, Crop Functional Genomics, University of Bonn, D-53113 Bonn, Germany
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