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Gomez-Cano F, Rodriguez J, Zhou P, Chu YH, Magnusson E, Gomez-Cano L, Krishnan A, Springer NM, de Leon N, Grotewold E. Prioritizing Maize Metabolic Gene Regulators through Multi-Omic Network Integration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.582075. [PMID: 38464086 PMCID: PMC10925184 DOI: 10.1101/2024.02.26.582075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Elucidating gene regulatory networks is a major area of study within plant systems biology. Phenotypic traits are intricately linked to specific gene expression profiles. These expression patterns arise primarily from regulatory connections between sets of transcription factors (TFs) and their target genes. Here, we integrated 46 co-expression networks, 283 protein-DNA interaction (PDI) assays, and 16 million SNPs used to identify expression quantitative trait loci (eQTL) to construct TF-target networks. In total, we analyzed ∼4.6M interactions to generate four distinct types of TF-target networks: co-expression, PDI, trans -eQTL, and cis -eQTL combined with PDIs. To functionally annotate TFs based on their target genes, we implemented three different network integration strategies. We evaluated the effectiveness of each strategy through TF loss-of function mutant inspection and random network analyses. The multi-network integration allowed us to identify transcriptional regulators of several biological processes. Using the topological properties of the fully integrated network, we identified potential functionally redundant TF paralogs. Our findings retrieved functions previously documented for numerous TFs and revealed novel functions that are crucial for informing the design of future experiments. The approach here-described lays the foundation for the integration of multi-omic datasets in maize and other plant systems. GRAPHICAL ABSTRACT
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Romero JM, Serrano-Bueno G, Camacho-Fernández C, Vicente MH, Ruiz MT, Pérez-Castiñeira JR, Pérez-Hormaeche J, Nogueira FTS, Valverde F. CONSTANS, a HUB for all seasons: How photoperiod pervades plant physiology regulatory circuits. THE PLANT CELL 2024; 36:2086-2102. [PMID: 38513610 PMCID: PMC11132886 DOI: 10.1093/plcell/koae090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 02/07/2024] [Accepted: 02/28/2024] [Indexed: 03/23/2024]
Abstract
How does a plant detect the changing seasons and make important developmental decisions accordingly? How do they incorporate daylength information into their routine physiological processes? Photoperiodism, or the capacity to measure the daylength, is a crucial aspect of plant development that helps plants determine the best time of the year to make vital decisions, such as flowering. The protein CONSTANS (CO) constitutes the central regulator of this sensing mechanism, not only activating florigen production in the leaves but also participating in many physiological aspects in which seasonality is important. Recent discoveries place CO in the center of a gene network that can determine the length of the day and confer seasonal input to aspects of plant development and physiology as important as senescence, seed size, or circadian rhythms. In this review, we discuss the importance of CO protein structure, function, and evolutionary mechanisms that embryophytes have developed to incorporate annual information into their physiology.
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Affiliation(s)
- Jose M Romero
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, 41092 Seville, Spain
- Department of Plant Biochemistry and Molecular Biology, Universidad de Sevilla, 41012 Seville, Spain
| | - Gloria Serrano-Bueno
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, 41092 Seville, Spain
- Department of Plant Biochemistry and Molecular Biology, Universidad de Sevilla, 41012 Seville, Spain
| | - Carolina Camacho-Fernández
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, 41092 Seville, Spain
- Department of Plant Biochemistry and Molecular Biology, Universidad de Sevilla, 41012 Seville, Spain
- Universidad Politécnica de Valencia, Vicerrectorado de Investigación, 46022 Valencia, Spain
| | - Mateus Henrique Vicente
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, 41092 Seville, Spain
- Laboratory of Molecular Genetics of Plant Development, Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ), University of São Paulo (USP), Piracicaba, 13418-900 São Paulo, Brazil
| | - M Teresa Ruiz
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, 41092 Seville, Spain
| | - J Román Pérez-Castiñeira
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, 41092 Seville, Spain
- Department of Plant Biochemistry and Molecular Biology, Universidad de Sevilla, 41012 Seville, Spain
| | - Javier Pérez-Hormaeche
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, 41092 Seville, Spain
| | - Fabio T S Nogueira
- Laboratory of Molecular Genetics of Plant Development, Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ), University of São Paulo (USP), Piracicaba, 13418-900 São Paulo, Brazil
| | - Federico Valverde
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, 41092 Seville, Spain
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Hou H, Wu C, Huo J, Liu N, Jiang Y, Sui S, Li Z. Integrated transcriptome and proteome analysis provides insights into CpFPA1 for floral induction in Chimonanthus praecox (Magnoliidae) without FLC in genome. PLANT CELL REPORTS 2024; 43:66. [PMID: 38341387 DOI: 10.1007/s00299-024-03145-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 12/31/2023] [Indexed: 02/12/2024]
Abstract
KEY MESSAGE We used transcriptomic and proteomic association analysis to reveal the critical genes/proteins at three key flower bud differentiation stages and overexpression of CpFPA1 in Arabidopsis resulted in earlier flowering. Wintersweet (Chimonanthus praecox), a rare winter-flowering woody plant, is well known for its unique blooming time, fragrance and long flowering period. However, the molecular mechanism of flowering in C. praecox remains poorly unclear. In this study, we used transcriptomic and proteomic association analysis to reveal the critical genes/proteins at three key flower bud (FB) differentiation stages (FB.Apr, FB.May and FB.Nov) in C. praecox. The results showed that a total of 952 differential expressed genes (DEGs) and 40 differential expressed proteins (DEPs) were identified. Gene ontology (GO) enrichment revealed that DEGs in FB.Apr/FB.May comparison group were mainly involved in metabolic of biological process, cell and cell part of cellular component and catalytic activity of molecular function. In the EuKaryotic Orthologous Groups (KOG) functional classification, DEPs were predicted mainly in the function of general function prediction only (KOG0118), post-translational modification, protein turnover and chaperones. The autonomous pathway genes play an essential role in the floral induction. Based on transcriptome and proteome correlation analysis, six candidate genes associated with the autonomous pathway were identified, including FPA1, FPA2a, FPA2b, FCA, FLK, FY. Furthermore, CpFPA1 was isolated and functionally characterized, and ectopic expression of CpFPA1 in Arabidopsis Columbia (Col-0) resulted in earlier flowering. These data could contribute to understand the function of CpFPA1 for floral induction and provide information for further research on the molecular mechanisms of flowering in wintersweet.
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Affiliation(s)
- Huifang Hou
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Chunyu Wu
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Juntao Huo
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Ning Liu
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Yingjie Jiang
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Shunzhao Sui
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Zhineng Li
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China.
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Liu B, Woods DP, Li W, Amasino RM. INDETERMINATE1-mediated expression of FT family genes is required for proper timing of flowering in Brachypodium distachyon. Proc Natl Acad Sci U S A 2023; 120:e2312052120. [PMID: 37934817 PMCID: PMC10655584 DOI: 10.1073/pnas.2312052120] [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: 07/14/2023] [Accepted: 09/19/2023] [Indexed: 11/09/2023] Open
Abstract
The transition to flowering is a major developmental switch in plants. In many temperate grasses, perception of indicators of seasonal change, such as changing day-length and temperature, leads to expression of FLOWERING LOCUS T1 (FT1) and FT-Like (FTL) genes that are essential for promoting the transition to flowering. However, little is known about the upstream regulators of FT1 and FTL genes in temperate grasses. Here, we characterize the monocot-specific gene INDETERMINATE1 (BdID1) in Brachypodium distachyon and demonstrate that BdID1 is a regulator of FT family genes. Mutations in ID1 impact the ability of the short-day (SD) vernalization, cold vernalization, and long-day (LD) photoperiod pathways to induce certain FTL genes. BdID1 is required for upregulation of FTL9 (FT-LIKE9) expression by the SD vernalization pathway, and overexpression of FTL9 in an id1 background can partially restore the delayed flowering phenotype of id1. We show that BdID1 binds in vitro to the promoter region of FTL genes suggesting that ID1 directly activates FTL expression. Transcriptome analysis shows that BdID1 is required for FT1, FT2, FTL12, and FTL13 expression under inductive LD photoperiods, indicating that BdID1 is a regulator of the FT gene family. Moreover, overexpression of FT1 in the id1 background results in rapid flowering similar to overexpressing FT1 in the wild type, demonstrating that BdID1 is upstream of FT family genes. Interestingly, ID1 negatively regulates a previously uncharacterized FTL gene, FTL4, and we show that FTL4 is a repressor of flowering. Thus, BdID1 is critical for proper timing of flowering in temperate grasses.
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Affiliation(s)
- Bing Liu
- Department of Biochemistry, University of Wisconsin, Madison, WI53706
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI53706
| | - Daniel P. Woods
- Department of Biochemistry, University of Wisconsin, Madison, WI53706
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI53706
- Laboratory of Genetics, University of Wisconsin, Madison, WI53706
| | - Weiya Li
- Department of Biochemistry, University of Wisconsin, Madison, WI53706
| | - Richard M. Amasino
- Department of Biochemistry, University of Wisconsin, Madison, WI53706
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI53706
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Wang X, Yuan D, Liu Y, Liang Y, He J, Yang X, Hang R, Jia H, Mo B, Tian F, Chen X, Liu L. INDETERMINATE1 autonomously regulates phosphate homeostasis upstream of the miR399-ZmPHO2 signaling module in maize. THE PLANT CELL 2023; 35:2208-2231. [PMID: 36943781 PMCID: PMC10226601 DOI: 10.1093/plcell/koad089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/23/2023] [Accepted: 02/25/2023] [Indexed: 05/30/2023]
Abstract
The macronutrient phosphorus is essential for plant growth and development. Plants have evolved multiple strategies to increase the efficiency of phosphate (Pi) acquisition to protect themselves from Pi starvation. However, the crosstalk between Pi homeostasis and plant development remains to be explored. Here, we report that overexpressing microRNA399 (miR399) in maize (Zea mays) is associated with premature senescence after pollination. Knockout of ZmPHO2 (Phosphate 2), a miR399 target, resulted in a similar premature senescence phenotype. Strikingly, we discovered that INDETERMINATE1 (ID1), a floral transition regulator, inhibits the transcription of ZmMIR399 genes by directly binding to their promoters, alleviating the repression of ZmPHO2 by miR399 and ultimately contributing to the maintenance of Pi homeostasis in maize. Unlike ZmMIR399 genes, whose expression is induced by Pi deficiency, ID1 expression was independent of the external inorganic orthophosphate status, indicating that ID1 is an autonomous regulator of Pi homeostasis. Furthermore, we show that ZmPHO2 was under selection during maize domestication and cultivation, resulting in a more sensitive response to Pi starvation in temperate maize than in tropical maize. Our study reveals a direct functional link between Pi-deprivation sensing by the miR399-ZmPHO2 regulatory module and plant developmental regulation by ID1.
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Affiliation(s)
- Xufeng Wang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Dan Yuan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Yanchun Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Yameng Liang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Juan He
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Xiaoyu Yang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518060, China
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Runlai Hang
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Hong Jia
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Feng Tian
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong 518060, China
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Hou Z, Fang C, Liu B, Yang H, Kong F. Origin, variation, and selection of natural alleles controlling flowering and adaptation in wild and cultivated soybean. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:36. [PMID: 37309391 PMCID: PMC10248697 DOI: 10.1007/s11032-023-01382-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/12/2023] [Indexed: 06/14/2023]
Abstract
Soybean (Glycine max) is an economically important crop worldwide, serving as a major source of oil and protein for human consumption and animal feed. Cultivated soybean was domesticated from wild soybean (Glycine soja) which both species are highly sensitive to photoperiod and can grow over a wide geographical range. The extensive ecological adaptation of wild and cultivated soybean has been facilitated by a series of genes represented as quantitative trait loci (QTLs) that control photoperiodic flowering and maturation. Here, we review the molecular and genetic basis underlying the regulation of photoperiodic flowering in soybean. Soybean has experienced both natural and artificial selection during adaptation to different latitudes, resulting in differential molecular and evolutionary mechanisms between wild and cultivated soybean. The in-depth study of natural and artificial selection for the photoperiodic adaptability of wild and cultivated soybean provides an important theoretical and practical basis for enhancing soybean adaptability and yield via molecular breeding. In addition, we discuss the possible origin of wild soybean, current challenges, and future research directions in this important topic.
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Affiliation(s)
- Zhihong Hou
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Chao Fang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Baohui Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Hui Yang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006 China
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7
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Choquette NE, Holland JB, Weldekidan T, Drouault J, de Leon N, Flint-Garcia S, Lauter N, Murray SC, Xu W, Wisser RJ. Environment-specific selection alters flowering-time plasticity and results in pervasive pleiotropic responses in maize. THE NEW PHYTOLOGIST 2023; 238:737-749. [PMID: 36683443 DOI: 10.1111/nph.18769] [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: 08/04/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Crop genetic diversity for climate adaptations is globally partitioned. We performed experimental evolution in maize to understand the response to selection and how plant germplasm can be moved across geographical zones. Initialized with a common population of tropical origin, artificial selection on flowering time was performed for two generations at eight field sites spanning 25° latitude, a 2800 km transect. We then jointly tested all selection lineages across the original sites of selection, for the target trait and 23 other traits. Modeling intergenerational shifts in a physiological reaction norm revealed separate components for flowering-time plasticity. Generalized and local modes of selection altered the plasticity of each lineage, leading to a latitudinal pattern in the responses to selection that were strongly driven by photoperiod. This transformation led to widespread changes in developmental, architectural, and yield traits, expressed collectively in an environment-dependent manner. Furthermore, selection for flowering time alone alleviated a maladaptive syndrome and improved yields for tropical maize in the temperate zone. Our findings show how phenotypic selection can rapidly shift the flowering phenology and plasticity of maize. They also demonstrate that selecting crops to local conditions can accelerate adaptation to climate change.
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Affiliation(s)
- Nicole E Choquette
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - James B Holland
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
- USDA-ARS Plant Science Research Unit, Raleigh, NC, 27695, USA
| | | | - Justine Drouault
- Laboratoire d'Ecophysiologie des Plantes sous Stress Environmentaux, INRAE, University of Montpellier, L'Institut Agro, Montpellier, 34000, France
| | - Natalia de Leon
- Deptartment of Agronomy, University of Wisconsin, Madison, WI, 53706, USA
| | | | - Nick Lauter
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Ames, IA, 50011, USA
| | - Seth C Murray
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Wenwei Xu
- Agricultural Research and Extension Center, Texas A&M AgriLife Research, Lubbock, TX, 79403, USA
| | - Randall J Wisser
- Deptartment of Plant and Soil Sciences, University of Delaware, Newark, DE, 19716, USA
- Laboratoire d'Ecophysiologie des Plantes sous Stress Environmentaux, INRAE, University of Montpellier, L'Institut Agro, Montpellier, 34000, France
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8
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Wang F, Li S, Kong F, Lin X, Lu S. Altered regulation of flowering expands growth ranges and maximizes yields in major crops. FRONTIERS IN PLANT SCIENCE 2023; 14:1094411. [PMID: 36743503 PMCID: PMC9892950 DOI: 10.3389/fpls.2023.1094411] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/04/2023] [Indexed: 06/14/2023]
Abstract
Flowering time influences reproductive success in plants and has a significant impact on yield in grain crops. Flowering time is regulated by a variety of environmental factors, with daylength often playing an important role. Crops can be categorized into different types according to their photoperiod requirements for flowering. For instance, long-day crops include wheat (Triticum aestivum), barley (Hordeum vulgare), and pea (Pisum sativum), while short-day crops include rice (Oryza sativa), soybean (Glycine max), and maize (Zea mays). Understanding the molecular regulation of flowering and genotypic variation therein is important for molecular breeding and crop improvement. This paper reviews the regulation of flowering in different crop species with a particular focus on how photoperiod-related genes facilitate adaptation to local environments.
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Affiliation(s)
| | | | | | - Xiaoya Lin
- *Correspondence: Xiaoya Lin, ; Sijia Lu,
| | - Sijia Lu
- *Correspondence: Xiaoya Lin, ; Sijia Lu,
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Li B, Wang Z, Jiang H, Luo JH, Guo T, Tian F, Rossi V, He Y. ZmCCT10-relayed photoperiod sensitivity regulates natural variation in the arithmetical formation of male germinal cells in maize. THE NEW PHYTOLOGIST 2023; 237:585-600. [PMID: 36266961 DOI: 10.1111/nph.18559] [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: 08/13/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Extensive mutational screening studies have documented genes regulating anther and pollen development. Knowledge concerning how formation of male germinal cell is arithmetically controlled in natural populations, under different environmental conditions, is lacking. We counted pollen number within a single anther and a maize-teosinte BC2 S3 recombinant inbred line population to identify ZmCCT10 as a major determinant of pollen number variation. ZmCCT10 was originally identified as a photoperiod-sensitive negative regulator of flowering. ZmCCT10 inactivation, after transposon insertion within its promoter, is proposed to have accelerated maize spread toward higher latitudes, thus allowing temperate maize to flower under long-day conditions. We showed that the active ZmCCT10 allele decreased pollen formation. As different active and inactive ZmCCT10 alleles have been found in natural maize populations, this represents the first report of a gene controlling pollen number in a crop natural population. These findings suggest that higher pollen number, which provides a competitive advantage in open-pollinated populations, may have been one of the major driving forces for the selection of an inactive ZmCCT10 allele during tropical maize domestication. We provide evidence that ZmCCT10 has opposite effects on cell proliferation of archesporial and tapetum cells and it modulates expression of key regulators during early anther development.
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Affiliation(s)
- Bo Li
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing, 100094, China
| | - Zi Wang
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing, 100094, China
| | - Huan Jiang
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing, 100094, China
| | - Jin-Hong Luo
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing, 100094, China
| | - Ting Guo
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing, 100094, China
| | - Feng Tian
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing, 100094, China
| | - Vincenzo Rossi
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, Bergamo, 24126, Italy
| | - Yan He
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing, 100094, China
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Cardon CH, de Oliveira RR, Lesy V, Ribeiro THC, Fust C, Pereira LP, Colasanti J, Chalfun-Junior A. Expression of coffee florigen CaFT1 reveals a sustained floral induction window associated with asynchronous flowering in tropical perennials. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 325:111479. [PMID: 36181945 DOI: 10.1016/j.plantsci.2022.111479] [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: 07/18/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 06/16/2023]
Abstract
The behavior of florigen(s) and environment-influenced regulatory pathways that control floral initiation in tropical perennials species with complex phenological cycles is poorly understood. Understanding the mechanisms underlying this process is important for food production in the face of climate change, thus, we used Coffea sp. L. (Rubiaceae) as a model to explore this issue. Homologs of FLOWERING LOCUS T (CaFT1) and environment-related regulators CONSTANS (CaCO), PHYTOCHROME INTERACTING FACTOR 4 (CaPIF4) and FLOWERING LOCUS C (CaFLC) were retrieved from coffee genomes and identified through phylogenetic analysis. Overexpression of CaFT1 in Arabidopsis caused early-flowering phenotype and yeast two hybrid studies indicated CaFT1 binding to bZIP floral regulator FD, which suggests that CaFT1 is a coffee florigen. Expression of CaFT1 and other floral regulators, together with carbohydrate analysis, were evaluated over one year using three contrasting genotypes, two C. arabica cultivars and C. canephora. All genotypes showed active and variable CaFT1 transcription from February until October, indicating the potential window for floral induction that reached a maximum in the cold period of June. CaCO expression, as expected, varied over a 24-hour day period and monthly with day length, whereas expression of temperature-responsive homologs, CaFLC and CaPIF4, did not correlate with temperature changes nor CaFT1 expression, suggesting alternative FT regulatory pathways in coffee. Based on our results, we suggest a continuum of floral induction that allows different starting points for floral activation, which explains developmental asynchronicity and prolonged anthesis events in tropical perennial species.
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Affiliation(s)
- Carlos Henrique Cardon
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Minas Gerais, Brazil; Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada.
| | - Raphael Ricon de Oliveira
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Minas Gerais, Brazil.
| | - Victoria Lesy
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada.
| | - Thales Henrique Cherubino Ribeiro
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Minas Gerais, Brazil.
| | - Catherine Fust
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada.
| | - Luísa Peloso Pereira
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Minas Gerais, Brazil.
| | - Joseph Colasanti
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada.
| | - Antonio Chalfun-Junior
- Laboratory of Plant Molecular Physiology, Plant Physiology Sector, Department of Biology, Federal University of Lavras (UFLA), Minas Gerais, Brazil.
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11
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Carvalho RF, Aguiar-Perecin MLR, Clarindo WR, Fristche-Neto R, Mondin M. A Heterochromatic Knob Reducing the Flowering Time in Maize. Front Genet 2022; 12:799681. [PMID: 35280927 PMCID: PMC8908004 DOI: 10.3389/fgene.2021.799681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/22/2021] [Indexed: 11/13/2022] Open
Abstract
Maize flowering time is an important agronomic trait, which has been associated with variations in the genome size and heterochromatic knobs content. We integrated three steps to show this association. Firstly, we selected inbred lines varying for heterochromatic knob composition at specific sites in the homozygous state. Then, we produced homozygous and heterozygous hybrids for knobs. Second, we measured the genome size and flowering time for all materials. Knob composition did not affect the genome size and flowering time. Finally, we developed an association study and identified a knob marker on chromosome 9 showing the strongest association with flowering time. Indeed, modelling allele substitution and dominance effects could offer only one heterochromatic knob locus that could affect flowering time, making it earlier rather than the knob composition.
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Affiliation(s)
- Renata Flávia Carvalho
- “Luiz de Queiroz” College of Agriculture, ESALQ, University of São Paulo, Piracicaba, Brazil
| | | | | | - Roberto Fristche-Neto
- “Luiz de Queiroz” College of Agriculture, ESALQ, University of São Paulo, Piracicaba, Brazil
- International Rice Research Institute (IRRI) - Breeding Analytics and Data, Management Unit, Laguna, Philippines
| | - Mateus Mondin
- “Luiz de Queiroz” College of Agriculture, ESALQ, University of São Paulo, Piracicaba, Brazil
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12
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Su H, Liang J, Abou-Elwafa SF, Cheng H, Dou D, Ren Z, Xie J, Chen Z, Gao F, Ku L, Chen Y. ZmCCT regulates photoperiod-dependent flowering and response to stresses in maize. BMC PLANT BIOLOGY 2021; 21:453. [PMID: 34615461 PMCID: PMC8493678 DOI: 10.1186/s12870-021-03231-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 09/23/2021] [Indexed: 05/30/2023]
Abstract
BACKGROUND Appropriate flowering time is very important to the success of modern agriculture. Maize (Zea mays L.) is a major cereal crop, originated in tropical areas, with photoperiod sensitivity. Which is an important obstacle to the utilization of tropical/subtropical germplasm resources in temperate regions. However, the study on the regulation mechanism of photoperiod sensitivity of maize is still in the early stage. Although it has been previously reported that ZmCCT is involved in the photoperiod response and delays maize flowering time under long-day conditions, the underlying mechanism remains unclear. RESULTS Here, we showed that ZmCCT overexpression delays flowering time and confers maize drought tolerance under LD conditions. Implementing the Gal4-LexA/UAS system identified that ZmCCT has a transcriptional inhibitory activity, while the yeast system showed that ZmCCT has a transcriptional activation activity. DAP-Seq analysis and EMSA indicated that ZmCCT mainly binds to promoters containing the novel motifs CAAAAATC and AAATGGTC. DAP-Seq and RNA-Seq analysis showed that ZmCCT could directly repress the expression of ZmPRR5 and ZmCOL9, and promote the expression of ZmRVE6 to delay flowering under long-day conditions. Moreover, we also demonstrated that ZmCCT directly binds to the promoters of ZmHY5, ZmMPK3, ZmVOZ1 and ZmARR16 and promotes the expression of ZmHY5 and ZmMPK3, but represses ZmVOZ1 and ZmARR16 to enhance stress resistance. Additionally, ZmCCT regulates a set of genes associated with plant development. CONCLUSIONS ZmCCT has dual functions in regulating maize flowering time and stress response under LD conditions. ZmCCT negatively regulates flowering time and enhances maize drought tolerance under LD conditions. ZmCCT represses most flowering time genes to delay flowering while promotes most stress response genes to enhance stress tolerance. Our data contribute to a comprehensive understanding of the regulatory mechanism of ZmCCT in controlling maize flowering time and stress response.
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Affiliation(s)
- Huihui Su
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | - Jiachen Liang
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | | | - Haiyang Cheng
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | - Dandan Dou
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | - Zhenzhen Ren
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | - Jiarong Xie
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | - Zhihui Chen
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | - Fengran Gao
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China
| | - Lixia Ku
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China.
| | - Yanhui Chen
- Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou, 450046, Henan, China.
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13
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Dong MY, Lei L, Fan XW, Li YZ. Analyses of open-access multi-omics data sets reveal genetic and expression characteristics of maize ZmCCT family genes. AOB PLANTS 2021; 13:plab048. [PMID: 34567492 PMCID: PMC8459886 DOI: 10.1093/aobpla/plab048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Flowering in maize (Zea mays) is influenced by photoperiod. The CO, CO-like/COL and TOC1 (CCT) domain protein-encoding genes in maize, ZmCCTs, are particularly important for photoperiod sensitivity. However, little is known about CCT protein-encoding gene number across plant species or among maize inbred lines. Therefore, we analysed CCT protein-encoding gene number across plant species, and characterized ZmCCTs in different inbred lines, including structural variations (SVs), copy number variations (CNVs), expression under stresses, dark-dark (DD) and dark-light (DL) cycles, interaction network and associations with maize quantitative trait loci (QTLs) by referring to the latest v4 genome data of B73. Gene number varied greatly across plant species, more in polyploids than in diploids. The numbers of ZmCCTs identified were 58 in B73, 59 in W22, 48 in Mo17, and 57 in Huangzao4 for temperate maize inbred lines, and 68 in tropical maize inbred line SK. Some ZmCCTs underwent duplications and presented chromosome collinearity. Structural variations and CNVs were found but they had no germplasm specificity. Forty-two ZmCCTs responded to stresses. Expression of 37 ZmCCTs in embryonic leaves during seed germination of maize under DD and DL cycles was roughly divided into five patterns of uphill pattern, downhill-pattern, zigzag-pattern, └-pattern and ⅃-pattern, indicating some of them have a potential to perceive dark and/or dark-light transition. Thirty-three ZmCCTs were co-expressed with 218 other maize genes; and 24 ZmCCTs were associated with known QTLs. The data presented in this study will help inform further functions of ZmCCTs.
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Affiliation(s)
- Ming-You Dong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, P. R. China
| | - Ling Lei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, P. R. China
| | - Xian-Wei Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, P. R. China
| | - You-Zhi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, P. R. China
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14
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Perkins AC, Lynch JP. Increased seminal root number associated with domestication improves nitrogen and phosphorus acquisition in maize seedlings. ANNALS OF BOTANY 2021; 128:453-468. [PMID: 34120166 PMCID: PMC8414917 DOI: 10.1093/aob/mcab074] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 06/11/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Domesticated maize (Zea mays ssp. mays) generally forms between two and six seminal roots, while its wild ancestor, Mexican annual teosinte (Zea mays ssp. parviglumis), typically lacks seminal roots. Maize also produces larger seeds than teosinte, and it generally has higher growth rates as a seedling. Maize was originally domesticated in the tropical soils of southern Mexico, but it was later brought to the Mexican highlands before spreading to other parts of the continent, where it experienced different soil resource constraints. The aims of this study were to understand the impacts of increased seminal root number on seedling nitrogen and phosphorus acquisition and to model how differences in maize and teosinte phenotypes might have contributed to increased seminal root number in domesticated maize. METHODS Seedling root system architectural models of a teosinte accession and a maize landrace were constructed by parameterizing the functional-structural plant model OpenSimRoot using plants grown in mesocosms. Seedling growth was simulated in a low-phosphorus environment, multiple low-nitrogen environments, and at variable planting densities. Models were also constructed to combine individual components of the maize and teosinte phenotypes. KEY RESULTS Seminal roots contributed ~35 % of the nitrogen and phosphorus acquired by maize landrace seedlings in the first 25 d after planting. Increased seminal root number improved plant nitrogen acquisition under low-nitrogen environments with varying precipitation patterns, fertilization rates, soil textures and planting densities. Models suggested that the optimal number of seminal roots for nutrient acquisition in teosinte is constrained by its limited seed carbohydrate reserves. CONCLUSIONS Seminal roots can improve the acquisition of both nitrogen and phosphorus in maize seedlings, and the increase in seed size associated with maize domestication may have facilitated increased seminal root number.
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Affiliation(s)
- Alden C Perkins
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | - Jonathan P Lynch
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
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15
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Minow MAA, Ávila LM, Lukens LN, Rossi V, Colasanti J. Introgressed DNA within a Zea mays near isogenic line displays lower levels of 24nt sRNA expression than the homologous region from the recurrent parent. Genome 2021; 64:1091-1098. [PMID: 34192470 DOI: 10.1139/gen-2021-0007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Near isogenic lines (NILs) are a classical genetic tool used to dissect the actions of an allele when placed in a uniform genetic background. Although the goal of NIL creation is to examine the effects of a single allele in isolation, DNA linked to the allele is invariably retained and can confound any allele specific effects. In addition to genetic variation, highly polymorphic species like Zea mays will contain introgressed polymorphisms encompassing transposable elements (TEs) and the cis acting small RNA (sRNA) that represses them. Through transcriptomics, we described the sRNA and TE transcriptional expression differences between a W22-derived introgression and its homologous B73 region. As anticipated, many sRNA expression differences were found. Unexpectedly, however, 24nt sRNA expression over the introgressed region was low overall compared to both the homologous B73 region and the rest of the genome. Across the introgression, low sRNA expression was accompanied by increased TE transcription. Possible explanations for the observed trends in sRNA and TE expression across the introgression are discussed. These findings support the notion that any introgressed allele is in an epigenetic environment distinct from that found at the allele from the recurrent parent. Additionally, these results suggest that further study of sRNA expression levels during the introgression process is warranted.
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Affiliation(s)
- Mark A A Minow
- University of Guelph, 3653, Molecular and Cellular Biology, 50 Stone Rd East, ON, Guelph, Ontario, Canada, N1G 2W1;
| | - Luis M Ávila
- University of Guelph, 3653, Plant Agriculture Department, Guelph, Ontario, Canada;
| | - Lewis N Lukens
- University of Guelph, Department of Plant Agriculture, Guelph Campus, Guelph, Ontario, Canada, N1G 2W1;
| | - Vincenzo Rossi
- Research Centre for Cereal and Industrial Crops, Bergamo, Italy;
| | - Joseph Colasanti
- University of Guelph, 3653, Department of Molecular and Cellular Biology, Guelph, Ontario, Canada, N1G 2W1;
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16
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Li Q, Liu G, Bao Y, Wu Y, You Q. Evaluation and application of tools for the identification of known microRNAs in plants. APPLICATIONS IN PLANT SCIENCES 2021; 9:e11414. [PMID: 33854848 PMCID: PMC8027368 DOI: 10.1002/aps3.11414] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 02/07/2021] [Indexed: 06/12/2023]
Abstract
MicroRNAs (miRNAs), endogenous non-coding RNA regulators, post-transcriptionally inhibit the expression of their target genes. Several tools have been developed for predicting annotated known miRNAs, but there is no consensus about how to select the most suitable method for any given species. In this study, eight miRNA prediction tools (mirnovo, miRPlant, miRDeep-P2, miRExpress, miRkwood, miRDeep2, miR-PREFeR, and sRNAbench) were selected for evaluation. High-throughput small RNA sequencing data from four plant species (including C3 and C4 species, and both monocots and dicots, i.e., Arabidopsis thaliana, Oryza sativa, Triticum aestivum, and Zea mays) were used for the analysis. The sensitivity, accuracy, area under the curve, consistency, duration, and RAM usage of the known miRNA predictions were evaluated for each tool. The miRNA annotations were obtained using miRBase and sRNAanno. Algorithms, such as random forest, BLAST, and receiver operating characteristic curves, were used to evaluate accuracy. Of the tools evaluated, sRNAbench was found to be the most accurate, miRDeep-P2 was the most sensitive, miRDeep-P2 was the fastest, and miRkwood had the highest memory usage. Due to its large genome size, only three tools were able to successfully predict known miRNAs in wheat (Triticum aestivum). Our results enable us to recommend the tool best suited to a variety of researcher needs, which we hope will reduce confusion and enhance future work.
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Affiliation(s)
- Qinglian Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Co‐Innovation Center for Modern Production Technology of Grain CropsCollege of AgricultureYangzhou UniversityYangzhou225009China
- Jiangsu Xuzhou Sweet Potato Research CenterXuzhou221131China
| | - Guanqing Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Co‐Innovation Center for Modern Production Technology of Grain CropsCollege of AgricultureYangzhou UniversityYangzhou225009China
| | - Yu Bao
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Co‐Innovation Center for Modern Production Technology of Grain CropsCollege of AgricultureYangzhou UniversityYangzhou225009China
| | - Yuechao Wu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Co‐Innovation Center for Modern Production Technology of Grain CropsCollege of AgricultureYangzhou UniversityYangzhou225009China
| | - Qi You
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Co‐Innovation Center for Modern Production Technology of Grain CropsCollege of AgricultureYangzhou UniversityYangzhou225009China
- State Key Laboratory of Cotton BiologyAnyangHenan455000China
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17
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Hostetler AN, Khangura RS, Dilkes BP, Sparks EE. Bracing for sustainable agriculture: the development and function of brace roots in members of Poaceae. CURRENT OPINION IN PLANT BIOLOGY 2021; 59:101985. [PMID: 33418403 DOI: 10.1016/j.pbi.2020.101985] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 11/23/2020] [Accepted: 12/02/2020] [Indexed: 05/28/2023]
Abstract
Optimization of crop production requires root systems to function in water uptake, nutrient use, and anchorage. In maize, two types of nodal roots-subterranean crown and aerial brace roots function in anchorage and water uptake and preferentially express multiple water and nutrient transporters. Brace root development shares genetic control with juvenile-to-adult phase change and flowering time. We present a comprehensive list of the genes known to alter brace roots and explore these as candidates for QTL studies in maize and sorghum. Brace root development and function may be conserved in other members of Poaceae, however research is limited. This work highlights the critical knowledge gap of aerial nodal root development and function and suggests new focus areas for breeding resilient crops.
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Affiliation(s)
- Ashley N Hostetler
- Department of Plant and Soil Sciences and the Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, United States
| | - Rajdeep S Khangura
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, United States
| | - Brian P Dilkes
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, United States
| | - Erin E Sparks
- Department of Plant and Soil Sciences and the Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19711, United States.
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18
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Manechini JRV, Santos PHDS, Romanel E, Brito MDS, Scarpari MS, Jackson S, Pinto LR, Vicentini R. Transcriptomic Analysis of Changes in Gene Expression During Flowering Induction in Sugarcane Under Controlled Photoperiodic Conditions. FRONTIERS IN PLANT SCIENCE 2021; 12:635784. [PMID: 34211482 PMCID: PMC8239368 DOI: 10.3389/fpls.2021.635784] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/12/2021] [Indexed: 05/11/2023]
Abstract
Flowering is of utmost relevance for the agricultural productivity of the sugarcane bioeconomy, but data and knowledge of the genetic mechanisms underlying its photoperiodic induction are still scarce. An understanding of the molecular mechanisms that regulate the transition from vegetative to reproductive growth in sugarcane could provide better control of flowering for breeding. This study aimed to investigate the transcriptome of +1 mature leaves of a sugarcane cultivar subjected to florally inductive and non-inductive photoperiodic treatments to identify gene expression patterns and molecular regulatory modules. We identified 7,083 differentially expressed (DE) genes, of which 5,623 showed significant identity to other plant genes. Functional group analysis showed differential regulation of important metabolic pathways involved in plant development, such as plant hormones (i.e., cytokinin, gibberellin, and abscisic acid), light reactions, and photorespiration. Gene ontology enrichment analysis revealed evidence of upregulated processes and functions related to the response to abiotic stress, photoprotection, photosynthesis, light harvesting, and pigment biosynthesis, whereas important categories related to growth and vegetative development of plants, such as plant organ morphogenesis, shoot system development, macromolecule metabolic process, and lignin biosynthesis, were downregulated. Also, out of 76 sugarcane transcripts considered putative orthologs to flowering genes from other plants (such as Arabidopsis thaliana, Oryza sativa, and Sorghum bicolor), 21 transcripts were DE. Nine DE genes related to flowering and response to photoperiod were analyzed either at mature or spindle leaves at two development stages corresponding to the early stage of induction and inflorescence primordia formation. Finally, we report a set of flowering-induced long non-coding RNAs and describe their level of conservation to other crops, many of which showed expression patterns correlated against those in the functionally grouped gene network.
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Affiliation(s)
- João Ricardo Vieira Manechini
- Laboratório de Biologia de Sistemas, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Paulo Henrique da Silva Santos
- Departamento de Genética e Melhoramento de Plantas, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual de São Paulo (UNESP), Jaboticabal, Brazil
| | - Elisson Romanel
- Laboratório de Genômica de Plantas e Bioenergia (PGEMBL), Departamento de Biotecnologia, Escola de Engenharia de Lorena (EEL), Universidade de São Paulo (USP), Lorena, Brazil
| | - Michael dos Santos Brito
- Instituto de Ciência e Tecnologia, Universidade Federal de São Paulo (UNIFESP), São José dos Campos, Brazil
| | | | - Stephen Jackson
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Luciana Rossini Pinto
- Departamento de Genética e Melhoramento de Plantas, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual de São Paulo (UNESP), Jaboticabal, Brazil
- Centro de Cana, Instituto Agronômico de Campinas (IAC), Ribeirão Preto, Brazil
| | - Renato Vicentini
- Laboratório de Biologia de Sistemas, Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
- *Correspondence: Renato Vicentini,
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19
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Adaptive introgression from maize has facilitated the establishment of teosinte as a noxious weed in Europe. Proc Natl Acad Sci U S A 2020; 117:25618-25627. [PMID: 32989136 DOI: 10.1073/pnas.2006633117] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Global trade has considerably accelerated biological invasions. The annual tropical teosintes, the closest wild relatives of maize, were recently reported as new agricultural weeds in two European countries, Spain and France. Their prompt settlement under climatic conditions differing drastically from that of their native range indicates rapid genetic evolution. We performed a phenotypic comparison of French and Mexican teosintes under European conditions and showed that only the former could complete their life cycle during maize cropping season. To test the hypothesis that crop-to-wild introgression triggered such rapid adaptation, we used single nucleotide polymorphisms to characterize patterns of genetic variation in French, Spanish, and Mexican teosintes as well as in maize germplasm. We showed that both Spanish and French teosintes originated from Zea mays ssp. mexicana race "Chalco," a weedy teosinte from the Mexican highlands. However, introduced teosintes differed markedly from their Mexican source by elevated levels of genetic introgression from the high latitude Dent maize grown in Europe. We identified a clear signature of divergent selection in a region of chromosome 8 introgressed from maize and encompassing ZCN8, a major flowering time gene associated with adaptation to high latitudes. Moreover, herbicide assays and sequencing revealed that French teosintes have acquired herbicide resistance via the introgression of a mutant herbicide-target gene (ACC1) present in herbicide-resistant maize cultivars. Altogether, our results demonstrate that adaptive crop-to-wild introgression has triggered both rapid adaptation to a new climatic niche and acquisition of herbicide resistance, thereby fostering the establishment of an emerging noxious weed.
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20
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Khangura RS, Johal GS, Dilkes BP. Variation in Maize Chlorophyll Biosynthesis Alters Plant Architecture. PLANT PHYSIOLOGY 2020; 184:300-315. [PMID: 32641472 PMCID: PMC7479880 DOI: 10.1104/pp.20.00306] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 06/06/2020] [Indexed: 06/11/2023]
Abstract
Chlorophyll is a tetrapyrrole metabolite essential for photosynthesis in plants. The first committed step of chlorophyll biosynthesis is catalyzed by a multimeric enzyme, magnesium chelatase, the subunit I of which is encoded by the oil yellow1 (oy1) gene in maize (Zea mays). A range of chlorophyll contents and net CO2 assimilation rates can be achieved in maize by combining a semidominant mutant allele of oy1 (Oy1-N1989) and a cis-regulatory modifier named very oil yellow1 (vey1) that varies between different inbred lines. We previously demonstrated that these allelic interactions can delay reproductive maturity. In this study, we demonstrate that multiple gross morphological traits respond to a reduction in chlorophyll. We found that stalk width, number of lateral branches (tillers), and branching of the inflorescence decline with a decrease in chlorophyll level. Chlorophyll deficit suppressed tillering in multiple maize mutants, including teosinte branched1, Tillering1, and grassy tillers1 In contrast to these traits, plant height showed a nonlinear response to chlorophyll levels. Weak suppression of Oy1-N1989 by vey1 B73 resulted in a significant increase in mutant plant height. By contrast, enhancement of the severity of the Oy1-N1989 phenotype by the vey1 Mo17 allele resulted in reduced plant height. We demonstrate that the effects of reduced chlorophyll contents on plant growth and development are complex and depend on the trait being measured. We propose that the lack of chlorophyll exerts growth control via energy balance sensing, which is upstream of the known genetic networks for branching and architecture.
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Affiliation(s)
- Rajdeep S Khangura
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Gurmukh S Johal
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Brian P Dilkes
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
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21
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Maize adaptation across temperate climates was obtained via expression of two florigen genes. PLoS Genet 2020; 16:e1008882. [PMID: 32673315 DOI: 10.1371/journal.pgen.1008882] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 07/28/2020] [Accepted: 05/22/2020] [Indexed: 11/19/2022] Open
Abstract
Expansion of the maize growing area was central for food security in temperate regions. In addition to the suppression of the short-day requirement for floral induction, it required breeding for a large range of flowering time that compensates the effect of South-North gradients of temperatures. Here we show the role of a novel florigen gene, ZCN12, in the latter adaptation in cooperation with ZCN8. Strong eQTLs of ZCN8 and ZCN12, measured in 327 maize lines, accounted for most of the genetic variance of flowering time in platform and field experiments. ZCN12 had a strong effect on flowering time of transgenic Arabidopsis thaliana plants; a path analysis showed that it directly affected maize flowering time together with ZCN8. The allelic composition at ZCN QTLs showed clear signs of selection by breeders. This suggests that florigens played a central role in ensuring a large range of flowering time, necessary for adaptation to temperate areas.
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22
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Ramstein GP, Larsson SJ, Cook JP, Edwards JW, Ersoz ES, Flint-Garcia S, Gardner CA, Holland JB, Lorenz AJ, McMullen MD, Millard MJ, Rocheford TR, Tuinstra MR, Bradbury PJ, Buckler ES, Romay MC. Dominance Effects and Functional Enrichments Improve Prediction of Agronomic Traits in Hybrid Maize. Genetics 2020; 215:215-230. [PMID: 32152047 PMCID: PMC7198274 DOI: 10.1534/genetics.120.303025] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 02/26/2020] [Indexed: 01/04/2023] Open
Abstract
Single-cross hybrids have been critical to the improvement of maize (Zea mays L.), but the characterization of their genetic architectures remains challenging. Previous studies of hybrid maize have shown the contribution of within-locus complementation effects (dominance) and their differential importance across functional classes of loci. However, they have generally considered panels of limited genetic diversity, and have shown little benefit from genomic prediction based on dominance or functional enrichments. This study investigates the relevance of dominance and functional classes of variants in genomic models for agronomic traits in diverse populations of hybrid maize. We based our analyses on a diverse panel of inbred lines crossed with two testers representative of the major heterotic groups in the U.S. (1106 hybrids), as well as a collection of 24 biparental populations crossed with a single tester (1640 hybrids). We investigated three agronomic traits: days to silking (DTS), plant height (PH), and grain yield (GY). Our results point to the presence of dominance for all traits, but also among-locus complementation (epistasis) for DTS and genotype-by-environment interactions for GY. Consistently, dominance improved genomic prediction for PH only. In addition, we assessed enrichment of genetic effects in classes defined by genic regions (gene annotation), structural features (recombination rate and chromatin openness), and evolutionary features (minor allele frequency and evolutionary constraint). We found support for enrichment in genic regions and subsequent improvement of genomic prediction for all traits. Our results suggest that dominance and gene annotations improve genomic prediction across diverse populations in hybrid maize.
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Affiliation(s)
| | - Sara J Larsson
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853
| | - Jason P Cook
- Division of Plant Science, University of Missouri, Columbia, Missouri 56211
| | - Jode W Edwards
- U.S. Department of Agriculture-Agricultural Research Service, Ames, Iowa 50011
| | | | - Sherry Flint-Garcia
- U.S. Department of Agriculture-Agricultural Research Service, University of Missouri, Columbia, Missouri 56211
| | - Candice A Gardner
- U.S. Department of Agriculture-Agricultural Research Service, Ames, Iowa 50011
| | - James B Holland
- U.S. Department of Agriculture-Agricultural Research Service, Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina 27695
| | - Aaron J Lorenz
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68588
| | - Michael D McMullen
- U.S. Department of Agriculture-Agricultural Research Service, University of Missouri, Columbia, Missouri 56211
| | - Mark J Millard
- U.S. Department of Agriculture-Agricultural Research Service, Ames, Iowa 50011
| | | | | | - Peter J Bradbury
- U.S. Department of Agriculture-Agricultural Research Service, Ithaca, New York 14853
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853
- U.S. Department of Agriculture-Agricultural Research Service, Ithaca, New York 14853
| | - M Cinta Romay
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853
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23
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Interaction Between Induced and Natural Variation at oil yellow1 Delays Reproductive Maturity in Maize. G3-GENES GENOMES GENETICS 2020; 10:797-810. [PMID: 31822516 PMCID: PMC7003087 DOI: 10.1534/g3.119.400838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We previously demonstrated that maize (Zea mays) locus very oil yellow1 (vey1) encodes a putative cis-regulatory expression polymorphism at the magnesium chelatase subunit I gene (aka oil yellow1) that strongly modifies the chlorophyll content of the semi-dominant Oy1-N1989 mutants. The vey1 allele of Mo17 inbred line reduces chlorophyll content in the mutants leading to reduced photosynthetic output. Oy1-N1989 mutants in B73 reached reproductive maturity four days later than wild-type siblings. Enhancement of Oy1-N1989 by the Mo17 allele at the vey1 QTL delayed maturity further, resulting in detection of a flowering time QTL in two bi-parental mapping populations crossed to Oy1-N1989. The near isogenic lines of B73 harboring the vey1 allele from Mo17 delayed flowering of Oy1-N1989 mutants by twelve days. Just as previously observed for chlorophyll content, vey1 had no effect on reproductive maturity in the absence of the Oy1-N1989 allele. Loss of chlorophyll biosynthesis in Oy1-N1989 mutants and enhancement by vey1 reduced CO2 assimilation. We attempted to separate the effects of photosynthesis on the induction of flowering from a possible impact of chlorophyll metabolites and retrograde signaling by manually reducing leaf area. Removal of leaves, independent of the Oy1-N1989 mutant, delayed flowering but surprisingly reduced chlorophyll contents of emerging leaves. Thus, defoliation did not completely separate the identity of the signal(s) that regulates flowering time from changes in chlorophyll content in the foliage. These findings illustrate the necessity to explore the linkage between metabolism and the mechanisms that connect it to flowering time regulation.
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Forestan C, Farinati S, Zambelli F, Pavesi G, Rossi V, Varotto S. Epigenetic signatures of stress adaptation and flowering regulation in response to extended drought and recovery in Zea mays. PLANT, CELL & ENVIRONMENT 2020; 43:55-75. [PMID: 31677283 DOI: 10.1111/pce.13660] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 09/03/2019] [Accepted: 09/23/2019] [Indexed: 05/22/2023]
Abstract
During their lifespan, plants respond to a multitude of stressful factors. Dynamic changes in chromatin and concomitant transcriptional variations control stress response and adaptation, with epigenetic memory mechanisms integrating environmental conditions and appropriate developmental programs over the time. Here we analyzed transcriptome and genome-wide histone modifications of maize plants subjected to a mild and prolonged drought stress just before the flowering transition. Stress was followed by a complete recovery period to evaluate drought memory mechanisms. Three categories of stress-memory genes were identified: i) "transcriptional memory" genes, with stable transcriptional changes persisting after the recovery; ii) "epigenetic memory candidate" genes in which stress-induced chromatin changes persist longer than the stimulus, in absence of transcriptional changes; iii) "delayed memory" genes, not immediately affected by the stress, but perceiving and storing stress signal for a delayed response. This last memory mechanism is described for the first time in drought response. In addition, applied drought stress altered floral patterning, possibly by affecting expression and chromatin of flowering regulatory genes. Altogether, we provided a genome-wide map of the coordination between genes and chromatin marks utilized by plants to adapt to a stressful environment, describing how this serves as a backbone for setting stress memory.
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Affiliation(s)
- Cristian Forestan
- Department of Agronomy Animals Food Natural Resources and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020, Legnaro, Italy
| | - Silvia Farinati
- Department of Agronomy Animals Food Natural Resources and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020, Legnaro, Italy
| | - Federico Zambelli
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy
| | - Giulio Pavesi
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy
| | - Vincenzo Rossi
- CREA - Centro di Cerealicoltura e Colture Industriali (CREA-CI), Via Stezzano 24, 24126, Bergamo, Italy
| | - Serena Varotto
- Department of Agronomy Animals Food Natural Resources and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020, Legnaro, Italy
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25
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Liang Y, Liu Q, Wang X, Huang C, Xu G, Hey S, Lin HY, Li C, Xu D, Wu L, Wang C, Wu W, Xia J, Han X, Lu S, Lai J, Song W, Schnable PS, Tian F. ZmMADS69 functions as a flowering activator through the ZmRap2.7-ZCN8 regulatory module and contributes to maize flowering time adaptation. THE NEW PHYTOLOGIST 2019; 221:2335-2347. [PMID: 30288760 DOI: 10.1111/nph.15512] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/14/2018] [Indexed: 05/26/2023]
Abstract
Flowering time is a major determinant of the local adaptation of plants. Although numerous loci affecting flowering time have been mapped in maize, their underlying molecular mechanisms and roles in adaptation remain largely unknown. Here, we report the identification and characterization of MADS-box transcription factor ZmMADS69 that functions as a flowering activator through the ZmRap2.7-ZCN8 regulatory module and contributes to adaptation. We show that ZmMADS69 underlies a quantitative trait locus controlling the difference in flowering time between maize and its wild ancestor, teosinte. Maize ZmMADS69 allele is expressed at a higher level at floral transition and confers earlier flowering than the teosinte allele under long days and short days. Overexpression of ZmMADS69 causes early flowering, while a transposon insertion mutant of ZmMADS69 exhibits delayed flowering. ZmMADS69 shows pleiotropic effects for multiple traits of agronomic importance. ZmMADS69 functions upstream of the flowering repressor ZmRap2.7 to downregulate its expression, thereby relieving the repression of the florigen gene ZCN8 and causing early flowering. Population genetic analyses showed that ZmMADS69 was a target of selection and may have played an important role as maize spread from the tropics to temperate zones. Our findings provide important insights into the regulation and adaptation of flowering time.
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Affiliation(s)
- Yameng Liang
- National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qiang Liu
- Department of Agronomy, Iowa State University, Ames, IA, 50010-3650, USA
| | - Xufeng Wang
- National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Cheng Huang
- National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Guanghui Xu
- National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Stefan Hey
- Department of Agronomy, Iowa State University, Ames, IA, 50010-3650, USA
| | - Hung-Ying Lin
- Department of Agronomy, Iowa State University, Ames, IA, 50010-3650, USA
| | - Cong Li
- National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Dingyi Xu
- National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Lishuan Wu
- National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Chenglong Wang
- National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Weihao Wu
- National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jinliang Xia
- National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Xu Han
- National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Sijia Lu
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Jinsheng Lai
- National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Weibin Song
- National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Patrick S Schnable
- Department of Agronomy, Iowa State University, Ames, IA, 50010-3650, USA
- Department of Plant Genetics & Breeding, China Agricultural University, Beijing, 100193, China
| | - Feng Tian
- National Maize Improvement Center of China, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
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26
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Stephenson E, Estrada S, Meng X, Ourada J, Muszynski MG, Habben JE, Danilevskaya ON. Over-expression of the photoperiod response regulator ZmCCT10 modifies plant architecture, flowering time and inflorescence morphology in maize. PLoS One 2019; 14:e0203728. [PMID: 30726207 PMCID: PMC6364868 DOI: 10.1371/journal.pone.0203728] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 01/11/2019] [Indexed: 11/19/2022] Open
Abstract
Maize originated as a tropical plant that required short days to transition from vegetative to reproductive development. ZmCCT10 [CO, CONSTANS, CO-LIKE and TIMING OF CAB1 (CCT) transcription factor family] is a regulator of photoperiod response and was identified as a major QTL controlling photoperiod sensitivity in maize. We modulated expression of ZmCCT10 in transgenic maize using two constitutive promoters with different expression levels. Transgenic plants over expressing ZmCCT10 with either promoter were delayed in their transition from vegetative to reproductive development but were not affected in their switch from juvenile-to-adult vegetative growth. Strikingly, transgenic plants containing the stronger expressing construct had a prolonged period of vegetative growth accompanied with dramatic modifications to plant architecture that impacted both vegetative and reproductive traits. These plants did not produce ears, but tassels were heavily branched. In more than half of the transgenic plants, tassels were converted into a branched leafy structure resembling phyllody, often composed of vegetative plantlets. Analysis of expression modules controlling the floral transition and meristem identity linked these networks to photoperiod dependent regulation, whereas phase change modules appeared to be photoperiod independent. Results from this study clarified the influence of the photoperiod pathway on vegetative and reproductive development and allowed for the fine-tuning of the maize flowering time model.
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Affiliation(s)
- Elizabeth Stephenson
- CORTEVA Agrisciences, Agriculture Division of DowDuPont; Johnston, Iowa, United States of America
| | - Stacey Estrada
- CORTEVA Agrisciences, Agriculture Division of DowDuPont; Johnston, Iowa, United States of America
| | - Xin Meng
- CORTEVA Agrisciences, Agriculture Division of DowDuPont; Johnston, Iowa, United States of America
| | - Jesse Ourada
- CORTEVA Agrisciences, Agriculture Division of DowDuPont; Johnston, Iowa, United States of America
| | - Michael G. Muszynski
- University of Hawaii at Manoa, Tropical Plant and Soil Sciences, Honolulu, Hawaii; United States of America
| | - Jeffrey E. Habben
- CORTEVA Agrisciences, Agriculture Division of DowDuPont; Johnston, Iowa, United States of America
| | - Olga N. Danilevskaya
- CORTEVA Agrisciences, Agriculture Division of DowDuPont; Johnston, Iowa, United States of America
- * E-mail:
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