1
|
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.
Collapse
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.
| |
Collapse
|
2
|
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: 4] [Impact Index Per Article: 2.0] [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.
Collapse
Affiliation(s)
- Yankun Zheng
- School of Life Sciences, Anqing Normal University, Anqing, 246133, Anhui, China.
| |
Collapse
|
3
|
Warman C, Sullivan CM, Preece J, Buchanan ME, Vejlupkova Z, Jaiswal P, Fowler JE. A cost-effective maize ear phenotyping platform enables rapid categorization and quantification of kernels. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:566-579. [PMID: 33476427 DOI: 10.1111/tpj.15166] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 12/30/2020] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
High-throughput phenotyping systems are powerful, dramatically changing our ability to document, measure, and detect biological phenomena. Here, we describe a cost-effective combination of a custom-built imaging platform and deep-learning-based computer vision pipeline. A minimal version of the maize (Zea mays) ear scanner was built with low-cost and readily available parts. The scanner rotates a maize ear while a digital camera captures a video of the surface of the ear, which is then digitally flattened into a two-dimensional projection. Segregating GFP and anthocyanin kernel phenotypes are clearly distinguishable in ear projections and can be manually annotated and analyzed using image analysis software. Increased throughput was attained by designing and implementing an automated kernel counting system using transfer learning and a deep learning object detection model. The computer vision model was able to rapidly assess over 390 000 kernels, identifying male-specific transmission defects across a wide range of GFP-marked mutant alleles. This includes a previously undescribed defect putatively associated with mutation of Zm00001d002824, a gene predicted to encode a vacuolar processing enzyme. Thus, by using this system, the quantification of transmission data and other ear and kernel phenotypes can be accelerated and scaled to generate large datasets for robust analyses.
Collapse
Affiliation(s)
- Cedar Warman
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Christopher M Sullivan
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USA
| | - Justin Preece
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Michaela E Buchanan
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USA
| | - Zuzana Vejlupkova
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Pankaj Jaiswal
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - John E Fowler
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USA
| |
Collapse
|
4
|
Warman C, Sullivan CM, Preece J, Buchanan ME, Vejlupkova Z, Jaiswal P, Fowler JE. A cost-effective maize ear phenotyping platform enables rapid categorization and quantification of kernels. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:566-579. [PMID: 33476427 DOI: 10.1101/2020.07.12.199000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 12/30/2020] [Accepted: 01/13/2021] [Indexed: 05/24/2023]
Abstract
High-throughput phenotyping systems are powerful, dramatically changing our ability to document, measure, and detect biological phenomena. Here, we describe a cost-effective combination of a custom-built imaging platform and deep-learning-based computer vision pipeline. A minimal version of the maize (Zea mays) ear scanner was built with low-cost and readily available parts. The scanner rotates a maize ear while a digital camera captures a video of the surface of the ear, which is then digitally flattened into a two-dimensional projection. Segregating GFP and anthocyanin kernel phenotypes are clearly distinguishable in ear projections and can be manually annotated and analyzed using image analysis software. Increased throughput was attained by designing and implementing an automated kernel counting system using transfer learning and a deep learning object detection model. The computer vision model was able to rapidly assess over 390 000 kernels, identifying male-specific transmission defects across a wide range of GFP-marked mutant alleles. This includes a previously undescribed defect putatively associated with mutation of Zm00001d002824, a gene predicted to encode a vacuolar processing enzyme. Thus, by using this system, the quantification of transmission data and other ear and kernel phenotypes can be accelerated and scaled to generate large datasets for robust analyses.
Collapse
Affiliation(s)
- Cedar Warman
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Christopher M Sullivan
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USA
| | - Justin Preece
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Michaela E Buchanan
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USA
| | - Zuzana Vejlupkova
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Pankaj Jaiswal
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - John E Fowler
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USA
| |
Collapse
|
5
|
Genetic Screens to Target Embryo and Endosperm Pathways in Arabidopsis and Maize. Methods Mol Biol 2020. [PMID: 31975291 DOI: 10.1007/978-1-0716-0342-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The major tissue types and stem-cell niches of plants are established during embryogenesis, and thus knowledge of embryo development is essential for a full understanding of plant development. Studies of seed development are also important for human health, because the nutrients stored in both the embryo and endosperm of plant seeds provide an essential part of our diet. Arabidopsis and maize have evolved different types of seeds, opening a range of experimental opportunities. Development of the Arabidopsis embryo follows an almost invariant pattern, while cell division patterns of maize embryos are variable. Embryo-endosperm interactions are also different between the two species: in Arabidopsis, the endosperm is consumed during seed development, while mature maize seeds contain an enormous endosperm. Genetic screens have provided important insights into seed development in both species. In the genomic era, genetic analysis will continue to provide important tools for understanding embryo and endosperm biology in plants, because single gene functional studies can now be integrated with genome-wide information. Here, we lay out important factors to consider when designing genetic screens to identify new genes or to probe known pathways in seed development. We then highlight the technical details of two previous genetic screens that may serve as useful examples for future experiments.
Collapse
|
6
|
Settles AM. EMS Mutagenesis of Maize Pollen. Methods Mol Biol 2020; 2122:25-33. [PMID: 31975293 DOI: 10.1007/978-1-0716-0342-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Effective mutagenesis is critical for connecting traits of interest to specific plant genes. The development of site-directed mutagenesis and sequenced-indexed genetics resources in maize allows for targeted analysis of individual genes. These reverse genetics approaches have the potential for confirmation bias by only studying candidate genes for association with traits of interest. Genetic screens of induced, random mutations are important for identifying novel loci as well as interacting factors for known mutant loci. Chemical mutagenesis provides very high mutation rates and can be used for a variety of screen designs. This chapter provides an updated protocol for ethyl methanesulfonate (EMS) mutagenesis of maize pollen using paraffin or mineral oil. Mutagenesis occurs in mature pollen causing nonconcordant endosperm and embryo genotypes as well as sectored M1 plants. Considerations for these factors in genetic screens are discussed.
Collapse
Affiliation(s)
- A Mark Settles
- Horticultural Sciences Department and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, USA.
| |
Collapse
|
7
|
Abstract
The plant haploid generation is specified late in higher plant development, and post-meiotic haploid plant cells divide mitotically to produce a haploid gametophyte, in which a subset of cells differentiates into the gametes. The immediate mother of the angiosperm seed is the female gametophyte, also called the embryo sac. In most flowering plants the embryo sac is comprised of two kinds of gametes (egg and central cell) and two kinds of subsidiary cells (antipodals and synergids) all of which descend from a single haploid spore produced by meiosis. The embryo sac develops within a specialized organ of the flower called the ovule, which supports and controls many steps in the development of both the embryo sac and the seed. Double fertilization of the central cell and egg cell by the two sperm cells of a pollen grain produce the endosperm and embryo of the seed, respectively. The endosperm and embryo develop under the influence of their precursor gametes and the surrounding tissues of the ovule and the gametophyte. The final size and pattern of the angiosperm seed then is the result of complex interactions across multiple tissues of three different generations (maternal sporophyte, maternal gametophyte, and the fertilization products) and three different ploidies (haploid gametophyte, diploid parental sporophyte and embryo, and triploid endosperm).
Collapse
|
8
|
Boehlein SK, Liu P, Webster A, Ribeiro C, Suzuki M, Wu S, Guan JC, Stewart JD, Tracy WF, Settles AM, McCarty DR, Koch KE, Hannah LC, Hennen-Bierwagen TA, Myers AM. Effects of long-term exposure to elevated temperature on Zea mays endosperm development during grain fill. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:23-40. [PMID: 30746832 DOI: 10.1111/tpj.14283] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 01/22/2019] [Accepted: 01/23/2019] [Indexed: 05/28/2023]
Abstract
Cereal yields decrease when grain fill proceeds under conditions of prolonged, moderately elevated temperatures. Endosperm-endogenous processes alter both rate and duration of dry weight gain, but underlying mechanisms remain unclear. Heat effects could be mediated by either abnormal, premature cessation of storage compound deposition or accelerated implementation of normal development. This study used controlled environments to isolate temperature as the sole environmental variable during Zea mays kernel-fill, from 12 days after pollination to maturity. Plants subjected to elevated day, elevated night temperatures (38°C day, 28°C night (38/28°C])) or elevated day, normal night (38/17°C), were compared with those from controls grown under normal day and night conditions (28/17°C). Progression of change over time in endosperm tissue was followed to dissect contributions at multiple levels, including transcriptome, metabolome, enzyme activities, product accumulation, and tissue ultrastructure. Integrated analyses indicated that the normal developmental program of endosperm is fully executed under prolonged high-temperature conditions, but at a faster rate. Accelerated development was observed when both day and night temperatures were elevated, but not when daytime temperature alone was increased. Although transcripts for most components of glycolysis and respiration were either upregulated or minimally affected, elevated temperatures decreased abundance of mRNAs related to biosynthesis of starch and storage proteins. Further analysis of 20 central-metabolic enzymes revealed six activities that were reduced under high-temperature conditions, indicating candidate roles in the observed reduction of grain dry weight. Nonetheless, a striking overall resilience of grain filling in the face of elevated temperatures can be attributed to acceleration of normal endosperm development.
Collapse
Affiliation(s)
- Susan K Boehlein
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Peng Liu
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Ashley Webster
- Department of Agronomy, University of Wisconsin, Madison, WI, 53706, USA
| | - Camila Ribeiro
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Masaharu Suzuki
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Shan Wu
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Jiahn-Chou Guan
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Jon D Stewart
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - William F Tracy
- Department of Agronomy, University of Wisconsin, Madison, WI, 53706, USA
| | - A Mark Settles
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Donald R McCarty
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Karen E Koch
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Larkin C Hannah
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Tracie A Hennen-Bierwagen
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Alan M Myers
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| |
Collapse
|
9
|
Bai F, Corll J, Shodja DN, Davenport R, Feng G, Mudunkothge J, Brigolin CJ, Martin F, Spielbauer G, Tseung CW, Siebert AE, Barbazuk WB, Lal S, Settles AM. RNA Binding Motif Protein 48 Is Required for U12 Splicing and Maize Endosperm Differentiation. THE PLANT CELL 2019; 31:715-733. [PMID: 30760564 PMCID: PMC6482629 DOI: 10.1105/tpc.18.00754] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 01/11/2019] [Accepted: 02/13/2019] [Indexed: 05/19/2023]
Abstract
The last eukaryotic common ancestor had two classes of introns that are still found in most eukaryotic lineages. Common U2-type and rare U12-type introns are spliced by the major and minor spliceosomes, respectively. Relatively few splicing factors have been shown to be specific to the minor spliceosome. We found that the maize (Zea mays) RNA binding motif protein 48 (RBM48) is a U12 splicing factor that functions to promote cell differentiation and repress cell proliferation. RBM48 is coselected with the U12 splicing factor, zinc finger CCCH-type, RNA binding motif, and Ser/Arg rich 2/Rough endosperm 3 (RGH3). Protein-protein interactions between RBM48, RGH3, and U2 Auxiliary Factor (U2AF) subunits suggest major and minor spliceosome factors required for intron recognition form complexes with RBM48. Human RBM48 interacts with armadillo repeat containing 7 (ARMC7). Maize RBM48 and ARMC7 have a conserved protein-protein interaction. These data predict that RBM48 is likely to function in U12 splicing throughout eukaryotes and that U12 splicing promotes endosperm cell differentiation in maize.
Collapse
Affiliation(s)
- Fang Bai
- Horticultural Sciences Department, and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611
| | - Jacob Corll
- Department of Biological Sciences, Oakland University, Rochester, Michigan 48309
| | - Donya N Shodja
- Department of Biological Sciences, Oakland University, Rochester, Michigan 48309
| | - Ruth Davenport
- Department of Biology and Genetics Institute, University of Florida, Gainesville, Florida 32611
| | - Guanqiao Feng
- Department of Biology and Genetics Institute, University of Florida, Gainesville, Florida 32611
| | - Janaki Mudunkothge
- Horticultural Sciences Department, and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611
| | - Christian J Brigolin
- Department of Biological Sciences, Oakland University, Rochester, Michigan 48309
| | - Federico Martin
- Horticultural Sciences Department, and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611
| | - Gertraud Spielbauer
- Horticultural Sciences Department, and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611
| | - Chi-Wah Tseung
- Horticultural Sciences Department, and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611
| | - Amy E Siebert
- Department of Biological Sciences, Oakland University, Rochester, Michigan 48309
| | - W Brad Barbazuk
- Department of Biology and Genetics Institute, University of Florida, Gainesville, Florida 32611
| | - Shailesh Lal
- Department of Biological Sciences, Oakland University, Rochester, Michigan 48309
| | - A Mark Settles
- Horticultural Sciences Department, and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611
| |
Collapse
|
10
|
Armenta-Medina A, Gillmor CS. Genetic, molecular and parent-of-origin regulation of early embryogenesis in flowering plants. Curr Top Dev Biol 2019; 131:497-543. [DOI: 10.1016/bs.ctdb.2018.11.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
|
11
|
Gehring M, Satyaki PR. Endosperm and Imprinting, Inextricably Linked. PLANT PHYSIOLOGY 2017; 173:143-154. [PMID: 27895206 PMCID: PMC5210735 DOI: 10.1104/pp.16.01353] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/22/2016] [Indexed: 05/21/2023]
Abstract
Recent developments advance our understanding of imprinted gene expression in plants.
Collapse
Affiliation(s)
- Mary Gehring
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142 (M.G., P.R.S.); and
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (M.G.)
| | - P R Satyaki
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142 (M.G., P.R.S.); and
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (M.G.)
| |
Collapse
|