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Yuan Y, Huo Q, Zhang Z, Wang Q, Wang J, Chang S, Cai P, Song KM, Galbraith DW, Zhang W, Huang L, Song R, Ma Z. Decoding the gene regulatory network of endosperm differentiation in maize. Nat Commun 2024; 15:34. [PMID: 38167709 PMCID: PMC10762121 DOI: 10.1038/s41467-023-44369-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
The persistent cereal endosperm constitutes the majority of the grain volume. Dissecting the gene regulatory network underlying cereal endosperm development will facilitate yield and quality improvement of cereal crops. Here, we use single-cell transcriptomics to analyze the developing maize (Zea mays) endosperm during cell differentiation. After obtaining transcriptomic data from 17,022 single cells, we identify 12 cell clusters corresponding to five endosperm cell types and revealing complex transcriptional heterogeneity. We delineate the temporal gene-expression pattern from 6 to 7 days after pollination. We profile the genomic DNA-binding sites of 161 transcription factors differentially expressed between cell clusters and constructed a gene regulatory network by combining the single-cell transcriptomic data with the direct DNA-binding profiles, identifying 181 regulons containing genes encoding transcription factors along with their high-confidence targets, Furthermore, we map the regulons to endosperm cell clusters, identify cell-cluster-specific essential regulators, and experimentally validated three predicted key regulators. This study provides a framework for understanding cereal endosperm development and function at single-cell resolution.
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Affiliation(s)
- Yue Yuan
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
| | - Qiang Huo
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Ziru Zhang
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Qun Wang
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Juanxia Wang
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Shuaikang Chang
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Peng Cai
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Karen M Song
- Department of Biology, Trinity College of Arts and Sciences, Duke University, Durham, NC, 27708, USA
| | - David W Galbraith
- School of Plant Sciences and Bio5 Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Weixiao Zhang
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Long Huang
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Rentao Song
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572025, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China.
| | - Zeyang Ma
- State Key Laboratory of Maize Bio-breeding, Frontiers Science Center for Molecular Design Breeding, Joint International Research Laboratory of Crop Molecular Breeding, National Maize Improvement Center, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572025, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China.
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Zheng Y. Molecular mechanisms of maize endosperm transfer cell development. PLANT CELL REPORTS 2022; 41:1171-1180. [PMID: 34689216 DOI: 10.1007/s00299-021-02807-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/14/2021] [Indexed: 05/12/2023]
Abstract
Endosperm transfer cells function as the nutrient transporter, antimicrobic barrier, and signal mediator between filial and maternal tissues. Sugar supply of maternal tissues, sugar demand of filial tissues, and requirement for defence against pathogens are three elemental factors inducing differentiation of endosperm transfer cells. Epigenetic factors, especially MEG1, moderate the key genetic factor ZmMRP-1 to activate endosperm transfer cell-specific genes that control the flange wall ingrowth formation and defensin-like protein secretion in maize. Auxin and cytokinin are primary hormones involved in development of maize endosperm transfer cells. Crosstalk between glucose and hormone signaling regulates endosperm transfer cell development via modifying ZmMRP-1 expression. This review summarizes the current knowledge on maize endosperm transfer cell development, and discusses its potential molecular mechanisms. It is expected to strengthen the theoretical basis for structural and functional optimization of endosperm transfer cells, and yield improvement of kernels in maize.
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Affiliation(s)
- Yankun Zheng
- School of Life Sciences, Anqing Normal University, Anqing, 246133, Anhui, China.
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Povilus RA, Gehring M. Maternal-filial transfer structures in endosperm: A nexus of nutritional dynamics and seed development. CURRENT OPINION IN PLANT BIOLOGY 2022; 65:102121. [PMID: 34801784 DOI: 10.1016/j.pbi.2021.102121] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/09/2021] [Accepted: 09/16/2021] [Indexed: 06/13/2023]
Abstract
Although the ultimate purpose of a seed is the successful establishment of the next generation, seed development involves more than embryo growth. In angiosperms, seed development requires the intimate coordination of three distinct entities - maternal tissue and two offspring, embryo and embryo-nourishing endosperm. Although seeds are cornerstones of many terrestrial ecosystems and human diets, we are only beginning to understand the interactions among seed tissues and the molecular processes and genes that determine them. Recent studies of gene expression and function in distantly related angiosperms, combined with over 100 years of embryological research, have repeatedly highlighted the endosperm associated with maternal-filial boundaries as a central point in seed developmental dynamics. In this review, we highlight evidence that links this zone with nutritional dynamics, developmental signaling, and imprinted gene expression. We suggest that the underappreciated diversity of this specialized endosperm across angiosperms deserves further study from developmental, molecular, and genetic perspectives.
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Affiliation(s)
- Rebecca A Povilus
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | - Mary Gehring
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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Xia X, Zhang HM, Offler CE, Patrick JW. Enzymes contributing to the hydrogen peroxide signal dynamics that regulate wall labyrinth formation in transfer cells. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:219-233. [PMID: 31587068 PMCID: PMC6913738 DOI: 10.1093/jxb/erz443] [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: 07/10/2019] [Accepted: 09/25/2019] [Indexed: 05/31/2023]
Abstract
Transfer cells are characterized by an amplified plasma membrane area supported on a wall labyrinth composed of a uniform wall layer (UWL) from which wall ingrowth (WI) papillae arise. Adaxial epidermal cells of developing Vicia faba cotyledons, when placed in culture, undergo a rapid (hours) trans-differentiation to a functional epidermal transfer cell (ETC) phenotype. The trans-differentiation event is controlled by a signalling cascade comprising auxin, ethylene, apoplasmic reactive oxygen species (apoROS), and cytosolic Ca2+. Apoplasmic hydrogen peroxide (apoH2O2) was confirmed as the apoROS regulating UWL and WI papillae formation. Informed by an ETC-specific transcriptome, a pharmacological approach identified a temporally changing cohort of H2O2 biosynthetic enzymes. The cohort contained a respiratory burst oxidase homologue, polyamine oxidase, copper amine oxidase, and a suite of class III peroxidases. Collectively these generated two consecutive bursts in apoH2O2 production. Spatial organization of biosynthetic/catabolic enzymes was deduced from responses to pharmacologically blocking their activities on the cellular and subcellular distribution of apoH2O2. The findings were consistent with catalase activity constraining the apoH2O2 signal to the outer periclinal wall of the ETCs. Strategic positioning of class III peroxidases in this outer domain shaped subcellular apoH2O2 signatures that differed during assembly of the UWL and WI papillae.
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Affiliation(s)
- Xue Xia
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
- School of Life Sciences, Henan University, Kaifeng, Henan, China
- International Joint Center for Biomedical Innovation, Henan University, Kaifeng, Henan, China
- Key Laboratory of Plant Stress Biology, Henan University, Kaifeng, Henan, China
| | - Hui-Ming Zhang
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Christina E Offler
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - John W Patrick
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
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Zhang HM, Wheeler SL, Xia X, Colyvas K, Offler CE, Patrick JW. Transcript Profiling Identifies Gene Cohorts Controlled by Each Signal Regulating Trans-Differentiation of Epidermal Cells of Vicia faba Cotyledons to a Transfer Cell Phenotype. FRONTIERS IN PLANT SCIENCE 2017; 8:2021. [PMID: 29234338 PMCID: PMC5712318 DOI: 10.3389/fpls.2017.02021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/14/2017] [Indexed: 05/29/2023]
Abstract
Transfer cells (TCs) support high rates of membrane transport of nutrients conferred by a plasma membrane area amplified by lining a wall labyrinth comprised of an uniform wall layer (UWL) upon which intricate wall ingrowth (WI) papillae are deposited. A signal cascade of auxin, ethylene, extracellular hydrogen peroxide (H2O2) and cytosolic Ca2+ regulates wall labyrinth assembly. To identify gene cohorts regulated by each signal, a RNA- sequencing study was undertaken using Vicia faba cotyledons. When cotyledons are placed in culture, their adaxial epidermal cells spontaneously undergo trans-differentiation to epidermal TCs (ETCs). Expressed genes encoding proteins central to wall labyrinth formation (signaling, intracellular organization, cell wall) and TC function of nutrient transport were assembled. Transcriptional profiles identified 9,742 annotated ETC-specific differentially expressed genes (DEGs; Log2fold change > 1; FDR p ≤ 0.05) of which 1,371 belonged to signaling (50%), intracellular organization (27%), cell wall (15%) and nutrient transporters (9%) functional categories. Expression levels of 941 ETC-specific DEGs were found to be sensitive to the known signals regulating ETC trans-differentiation. Significantly, signals acting alone, or in various combinations, impacted similar numbers of ETC-specific DEGs across the four functional gene categories. Amongst the signals acting alone, H2O2 exerted most influence affecting expression levels of 56% of the ETC-specific DEGs followed by Ca2+ (21%), auxin (18%) and ethylene (5%). The dominance by H2O2 was evident across all functional categories, but became more attenuated once trans-differentiation transitioned into WI papillae formation. Amongst the eleven signal combinations, H2O2/Ca2+ elicited the greatest impact across all functional categories accounting for 20% of the ETC-specific DEG cohort. The relative influence of the other signals acting alone, or in various combinations, varied across the four functional categories and two phases of wall labyrinth construction. These transcriptome data provide a powerful information platform from which to examine signal transduction pathways and how these regulate expression of genes encoding proteins engaged in intracellular organization, cell wall construction and nutrient transport.
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Affiliation(s)
- Hui-Ming Zhang
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Simon L. Wheeler
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Xue Xia
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Kim Colyvas
- School of Mathematical and Physical Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Christina E. Offler
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - John W. Patrick
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
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