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Zhu X, Wang H. Revisiting the role and mechanism of ELF3 in circadian clock modulation. Gene 2024; 913:148378. [PMID: 38490512 DOI: 10.1016/j.gene.2024.148378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/08/2024] [Accepted: 03/12/2024] [Indexed: 03/17/2024]
Abstract
The gene encoding EARLY FLOWERING3 (ELF3) is necessary for photoperiodic flowering and the normal regulation of circadian rhythms. It provides important information at the cellular level to uncover the biological mechanisms that improve plant growth and development. ELF3 interactions with transcription factors such as BROTHER OF LUX ARRHYTHMO (BOA), LIGHT-REGULATED WD1 (LWD1), PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), PHYTOCHROME-INTERACTING FACTOR 7 (PIF7), and LUX ARRHYTHMO (LUX) suggest a role in evening complex (EC) independent pathways, demanding further investigation to elucidate the EC-dependent versus EC-independent mechanisms. The ELF3 regulation of flowering time about photoperiod and temperature variations can also optimize crop cultivation across diverse latitudes. In this review paper, we summarize how ELF3's role in the circadian clock and light-responsive flowering control in crops offers substantial potential for scientific advancement and practical applications in biotechnology and agriculture. Despite its essential role in crop adaptation, very little is known in many important crops. Consequently, comprehensive and targeted research is essential for extrapolating ELF3-related insights from Arabidopsis to other crops, utilizing both computational and experimental methodologies. This research should prioritize investigations into ELF3's protein-protein interactions, post-translational modifications, and genomic targets to elucidate its contribution to accurate circadian clock regulation.
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Affiliation(s)
- Xingzun Zhu
- College of Landscape Architecture, Changchun University, No.1 Weixinglu Changchun, Jilin, China.
| | - Hongtao Wang
- College of Life Sciences, Tonghua Normal University, Tonghua, 950, Yucai Road, China.
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2
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Komura S, Yoshida K, Jinno H, Oono Y, Handa H, Takumi S, Kobayashi F. Identification of the causal mutation in early heading mutant of bread wheat ( Triticum aestivum L.) using MutMap approach. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:41. [PMID: 38779634 PMCID: PMC11106051 DOI: 10.1007/s11032-024-01478-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024]
Abstract
In bread wheat (Triticum aestivum L.), fine-tuning the heading time is essential to maximize grain yield. Photoperiod-1 (Ppd-1) and VERNALIZATION 1 (Vrn-1) are major genes affecting photoperiod sensitivity and vernalization requirements, respectively. These genes have predominantly governed heading timing. However, Ppd-1 and Vrn-1 significantly impact heading dates, necessitating another gene that can slightly modify heading dates for fine-tuning. In this study, we developed an early heading mutant from the ethyl methanesulfonate-mutagenized population of the Japanese winter wheat cultivar "Kitahonami." MutMap analysis identified a nonsense mutation in the clock component gene Wheat PHYTOCLOCK 1/LUX ARRHYTHMO (WPCL-D1) as the probable SNP responsible for the early heading mutant on chromosome 3D. Segregation analysis using F2 and F3 populations confirmed that plants carrying the wpcl-D1 allele headed significantly earlier than those with the functional WPCL-D1. The early heading mutant exhibited increased expression levels of Ppd-1 and circadian clock genes, such as WPCL1 and LATE ELONGATED HYPOCOTYL (LHY). Notably, the transcript accumulation levels of Ppd-A1 and Ppd-D1 were influenced by the copy number of the functional WPCL1 gene. These results suggest that a loss-of-function mutation in WPCL-D1 is the causal mutation for the early heading phenotype. Adjusting the functional copy number of WPCL1 will be beneficial in fine-tuning of heading dates. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01478-5.
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Affiliation(s)
- Shoya Komura
- Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Kentaro Yoshida
- Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Hironobu Jinno
- Hokkaido Research Organization, Kitami Agricultural Experiment Station, Yayoi 52, Kunneppucho, Tokorogun, Hokkaido, 099-1496 Japan
| | - Youko Oono
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, 305-0856 Japan
| | - Hirokazu Handa
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, 305-0856 Japan
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-8522 Japan
| | - Shigeo Takumi
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501 Japan
| | - Fuminori Kobayashi
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, 305-0856 Japan
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3
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Makhoul M, Schlichtermann RH, Ugwuanyi S, Weber SE, Voss-Fels KP, Stahl A, Zetzsche H, Wittkop B, Snowdon RJ, Obermeier C. Novel PHOTOPERIOD-1 gene variants associate with yield-related and root-angle traits in European bread wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:125. [PMID: 38727862 PMCID: PMC11087350 DOI: 10.1007/s00122-024-04634-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/20/2024] [Indexed: 05/13/2024]
Abstract
KEY MESSAGE PHOTOPERIOD-1 homoeologous gene copies play a pivotal role in regulation of flowering time in wheat. Here, we show that their influence also extends to spike and shoot architecture and even impacts root development. The sequence diversity of three homoeologous copies of the PHOTOPERIOD-1 gene in European winter wheat was analyzed by Oxford Nanopore amplicon-based multiplex sequencing and molecular markers in a panel of 194 cultivars representing breeding progress over the past 5 decades. A strong, consistent association with an average 8% increase in grain yield was observed for the PpdA1-Hap1 haplotype across multiple environments. This haplotype was found to be linked in 51% of cultivars to the 2NS/2AS translocation, originally introduced from Aegilops ventricosa, which leads to an overestimation of its effect. However, even in cultivars without the 2NS/2AS translocation, PpdA1-Hap1 was significantly associated with increased grain yield, kernel per spike and kernel per m2 under optimal growth conditions, conferring a 4% yield advantage compared to haplotype PpdA1-Hap4. In contrast to Ppd-B1 and Ppd-D1, the Ppd-A1 gene exhibits novel structural variations and a high number of SNPs, highlighting the evolutionary changes that have occurred in this region over the course of wheat breeding history. Additionally, cultivars carrying the photoperiod-insensitive Ppd-D1a allele not only exhibit earlier heading, but also deeper roots compared to those with photoperiod-sensitive alleles under German conditions. PCR and KASP assays have been developed that can be effectively employed in marker-assisted breeding programs to introduce these favorable haplotypes.
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Affiliation(s)
- Manar Makhoul
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | | | - Samson Ugwuanyi
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Sven E Weber
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Kai P Voss-Fels
- Institute for Grapevine Breeding, Hochschule Geisenheim University, Geisenheim, Germany
| | - Andreas Stahl
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Holger Zetzsche
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Benjamin Wittkop
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Christian Obermeier
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany.
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4
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Li C, Lin H, Debernardi JM, Zhang C, Dubcovsky J. GIGANTEA accelerates wheat heading time through gene interactions converging on FLOWERING LOCUS T1. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:519-533. [PMID: 38184778 DOI: 10.1111/tpj.16622] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/08/2024]
Abstract
Precise regulation of flowering time is critical for cereal crops to synchronize reproductive development with optimum environmental conditions, thereby maximizing grain yield. The plant-specific gene GIGANTEA (GI) plays an important role in the control of flowering time, with additional functions on the circadian clock and plant stress responses. In this study, we show that GI loss-of-function mutants in a photoperiod-sensitive tetraploid wheat background exhibit significant delays in heading time under both long-day (LD) and short-day photoperiods, with stronger effects under LD. However, this interaction between GI and photoperiod is no longer observed in isogenic lines carrying either a photoperiod-insensitive allele in the PHOTOPERIOD1 (PPD1) gene or a loss-of-function allele in EARLY FLOWERING 3 (ELF3), a known repressor of PPD1. These results suggest that the normal circadian regulation of PPD1 is required for the differential effect of GI on heading time in different photoperiods. Using crosses between mutant or transgenic plants of GI and those of critical genes in the flowering regulation pathway, we show that GI accelerates wheat heading time by promoting FLOWERING LOCUS T1 (FT1) expression via interactions with ELF3, VERNALIZATION 2 (VRN2), CONSTANS (CO), and the age-dependent microRNA172-APETALA2 (AP2) pathway, at both transcriptional and protein levels. Our study reveals conserved GI mechanisms between wheat and Arabidopsis but also identifies specific interactions of GI with the distinctive photoperiod and vernalization pathways of the temperate grasses. These results provide valuable knowledge for modulating wheat heading time and engineering new varieties better adapted to a changing environment.
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Affiliation(s)
- Chengxia Li
- Department of Plant Sciences, University of California, Davis, California, 95616, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, 20815, USA
| | - Huiqiong Lin
- Department of Plant Sciences, University of California, Davis, California, 95616, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, 20815, USA
| | - Juan M Debernardi
- Department of Plant Sciences, University of California, Davis, California, 95616, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, 20815, USA
| | - Chaozhong Zhang
- Department of Plant Sciences, University of California, Davis, California, 95616, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, 20815, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, California, 95616, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, 20815, USA
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5
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Yuan L, Avello P, Zhu Z, Lock SCL, McCarthy K, Redmond EJ, Davis AM, Song Y, Ezer D, Pitchford JW, Quint M, Xie Q, Xu X, Davis SJ, Ronald J. Complex epistatic interactions between ELF3, PRR9, and PRR7 regulate the circadian clock and plant physiology. Genetics 2024; 226:iyad217. [PMID: 38142447 PMCID: PMC10917503 DOI: 10.1093/genetics/iyad217] [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: 08/07/2023] [Revised: 08/07/2023] [Accepted: 12/05/2023] [Indexed: 12/26/2023] Open
Abstract
Circadian clocks are endogenous timekeeping mechanisms that coordinate internal physiological responses with the external environment. EARLY FLOWERING3 (ELF3), PSEUDO RESPONSE REGULATOR (PRR9), and PRR7 are essential components of the plant circadian clock and facilitate entrainment of the clock to internal and external stimuli. Previous studies have highlighted a critical role for ELF3 in repressing the expression of PRR9 and PRR7. However, the functional significance of activity in regulating circadian clock dynamics and plant development is unknown. To explore this regulatory dynamic further, we first employed mathematical modeling to simulate the effect of the prr9/prr7 mutation on the elf3 circadian phenotype. These simulations suggested that simultaneous mutations in prr9/prr7 could rescue the elf3 circadian arrhythmia. Following these simulations, we generated all Arabidopsis elf3/prr9/prr7 mutant combinations and investigated their circadian and developmental phenotypes. Although these assays could not replicate the results from the mathematical modeling, our results have revealed a complex epistatic relationship between ELF3 and PRR9/7 in regulating different aspects of plant development. ELF3 was essential for hypocotyl development under ambient and warm temperatures, while PRR9 was critical for root thermomorphogenesis. Finally, mutations in prr9 and prr7 rescued the photoperiod-insensitive flowering phenotype of the elf3 mutant. Together, our results highlight the importance of investigating the genetic relationship among plant circadian genes.
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Affiliation(s)
- Li Yuan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Paula Avello
- Department of Mathematics, University of York, York, YO10 5DD, UK
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Zihao Zhu
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale) 06108, Germany
| | - Sarah C L Lock
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Kayla McCarthy
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Ethan J Redmond
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Amanda M Davis
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Yang Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Daphne Ezer
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Jonathan W Pitchford
- Department of Mathematics, University of York, York, YO10 5DD, UK
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Marcel Quint
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale) 06108, Germany
| | - Qiguang Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Xiaodong Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Seth J Davis
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - James Ronald
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bower Building, University Avenue, Glasgow G12 8QQ, UK
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6
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Helmsorig G, Walla A, Rütjes T, Buchmann G, Schüller R, Hensel G, von Korff M. early maturity 7 promotes early flowering by controlling the light input into the circadian clock in barley. PLANT PHYSIOLOGY 2024; 194:849-866. [PMID: 37951242 PMCID: PMC10828213 DOI: 10.1093/plphys/kiad551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/26/2023] [Indexed: 11/13/2023]
Abstract
Breeding for variation in photoperiod response is crucial to adapt crop plants to various environments. Plants measure changes in day length by the circadian clock, an endogenous timekeeper that allows plants to anticipate changes in diurnal and seasonal light-dark cycles. Here, we describe the early maturity 7 (eam7) locus in barley (Hordeum vulgare), which interacts with PHOTOPERIOD 1 (Ppd-H1) to cause early flowering under non-inductive short days. We identify LIGHT-REGULATED WD 1 (LWD1) as a putative candidate to underlie the eam7 locus in barley as supported by genetic mapping and CRISPR-Cas9-generated lwd1 mutants. Mutations in eam7 cause a significant phase advance and a misregulation of core clock and clock output genes under diurnal conditions. Early flowering was linked to an upregulation of Ppd-H1 during the night and consequent induction of the florigen FLOWERING LOCUS T1 under short days. We propose that EAM7 controls photoperiodic flowering in barley by controlling the light input into the clock and diurnal expression patterns of the major photoperiod response gene Ppd-H1.
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Affiliation(s)
- Gesa Helmsorig
- Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40223 Düsseldorf, Germany
| | - Agatha Walla
- Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40223 Düsseldorf, Germany
| | - Thea Rütjes
- Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40223 Düsseldorf, Germany
| | - Gabriele Buchmann
- Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40223 Düsseldorf, Germany
| | - Rebekka Schüller
- Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40223 Düsseldorf, Germany
| | - Götz Hensel
- Cluster of Excellence on Plant Sciences “SMART Plants for Tomorrow's Needs”, 40223 Düsseldorf, Germany
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-Universität Düsseldorf, 40223 Düsseldorf, Germany
- Division of Molecular Biology, Centre of the Region Hana for Biotechnological and Agriculture Research, Faculty of Science, Palacký University, CZ-779 00 Olomouc, Czech
| | - Maria von Korff
- Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40223 Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences “SMART Plants for Tomorrow's Needs”, 40223 Düsseldorf, Germany
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7
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Expression of Concern: EARLY FLOWERING 3 interactions with PHYTOCHROME B and PHOTOPERIOD1 are critical for the photoperiodic regulation of wheat heading time. PLoS Genet 2023; 19:e1011095. [PMID: 38117765 PMCID: PMC10732402 DOI: 10.1371/journal.pgen.1011095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023] Open
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8
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Gao M, Lu Y, Geng F, Klose C, Staudt AM, Huang H, Nguyen D, Lan H, Lu H, Mockler TC, Nusinow DA, Hiltbrunner A, Schäfer E, Wigge PA, Jaeger KE. Phytochromes transmit photoperiod information via the evening complex in Brachypodium. Genome Biol 2023; 24:256. [PMID: 37936225 PMCID: PMC10631206 DOI: 10.1186/s13059-023-03082-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 10/04/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND Daylength is a key seasonal cue for animals and plants. In cereals, photoperiodic responses are a major adaptive trait, and alleles of clock genes such as PHOTOPERIOD1 (PPD1) and EARLY FLOWERING3 (ELF3) have been selected for in adapting barley and wheat to northern latitudes. How monocot plants sense photoperiod and integrate this information into growth and development is not well understood. RESULTS We find that phytochrome C (PHYC) is essential for flowering in Brachypodium distachyon. Conversely, ELF3 acts as a floral repressor and elf3 mutants display a constitutive long day phenotype and transcriptome. We find that ELF3 and PHYC occur in a common complex. ELF3 associates with the promoters of a number of conserved regulators of flowering, including PPD1 and VRN1. Consistent with observations in barley, we are able to show that PPD1 overexpression accelerates flowering in short days and is necessary for rapid flowering in response to long days. PHYC is in the active Pfr state at the end of the day, but we observe it undergoes dark reversion over the course of the night. CONCLUSIONS We propose that PHYC acts as a molecular timer and communicates information on night-length to the circadian clock via ELF3.
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Affiliation(s)
- Mingjun Gao
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge, CB2 1LR, UK
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Yunlong Lu
- Leibniz-Institut für Gemüse- und Zierpflanzenbau, Theodor-Echtermeyer-Weg 1, Großbeeren, 14979, Germany
| | - Feng Geng
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge, CB2 1LR, UK
| | - Cornelia Klose
- Institut für Biologie II, University of Freiburg, Schaenzlestr. 1, Freiburg, 79104, Germany
| | - Anne-Marie Staudt
- Institut für Biologie II, University of Freiburg, Schaenzlestr. 1, Freiburg, 79104, Germany
| | - He Huang
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Duy Nguyen
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge, CB2 1LR, UK
| | - Hui Lan
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge, CB2 1LR, UK
| | - Han Lu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai, China
| | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | | | - Andreas Hiltbrunner
- Institut für Biologie II, University of Freiburg, Schaenzlestr. 1, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, 79104, Germany
| | - Eberhard Schäfer
- Institut für Biologie II, University of Freiburg, Schaenzlestr. 1, Freiburg, 79104, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schaenzlestr. 18, Freiburg, 79104, Germany
| | - Philip A Wigge
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge, CB2 1LR, UK.
- Leibniz-Institut für Gemüse- und Zierpflanzenbau, Theodor-Echtermeyer-Weg 1, Großbeeren, 14979, Germany.
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, 14476, Germany.
| | - Katja E Jaeger
- Sainsbury Laboratory, University of Cambridge, 47 Bateman St., Cambridge, CB2 1LR, UK.
- Leibniz-Institut für Gemüse- und Zierpflanzenbau, Theodor-Echtermeyer-Weg 1, Großbeeren, 14979, Germany.
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9
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Rodríguez Del Río Á, Monteagudo A, Contreras-Moreira B, Kiss T, Mayer M, Karsai I, Igartua E, Casas AM. Diversity of gene expression responses to light quality in barley. Sci Rep 2023; 13:17143. [PMID: 37816785 PMCID: PMC10564772 DOI: 10.1038/s41598-023-44263-8] [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: 01/06/2023] [Accepted: 10/05/2023] [Indexed: 10/12/2023] Open
Abstract
Light quality influence on barley development is poorly understood. We exposed three barley genotypes with either sensitive or insensitive response to two light sources producing different light spectra, fluorescent bulbs, and metal halide lamps, keeping constant light intensity, duration, and temperature. Through RNA-seq, we identified the main genes and pathways involved in the genotypic responses. A first analysis identified genotypic differences in gene expression of development-related genes, including photoreceptors and flowering time genes. Genes from the vernalization pathway of light quality-sensitive genotypes were affected by fluorescent light. In particular, vernalization-related repressors reacted differently: HvVRN2 did not experience relevant changes, whereas HvOS2 expression increased under fluorescent light. To identify the genes primarily related to light quality responses, and avoid the confounding effect of plant developmental stage, genes influenced by development were masked in a second analysis. Quantitative expression levels of PPD-H1, which influenced HvVRN1 and HvFT1, explained genotypic differences in development. Upstream mechanisms (light signaling and circadian clock) were also altered, but no specific genes linking photoreceptors and the photoperiod pathway were identified. The variety of light-quality sensitivities reveals the presence of possible mechanisms of adaptation of winter and facultative barley to latitudinal variation in light quality, which deserves further research.
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Affiliation(s)
- Álvaro Rodríguez Del Río
- Department of Genetics and Plant Breeding, Aula Dei Experimental Station, CSIC, Avda Montañana 1005, 50059, Zaragoza, Spain
- Centro de Biotecnología y Genómica de Plantas, UPM/INIA-CSIC, Madrid, Spain
| | - Arantxa Monteagudo
- Department of Genetics and Plant Breeding, Aula Dei Experimental Station, CSIC, Avda Montañana 1005, 50059, Zaragoza, Spain
| | - Bruno Contreras-Moreira
- Department of Genetics and Plant Breeding, Aula Dei Experimental Station, CSIC, Avda Montañana 1005, 50059, Zaragoza, Spain
- Fundación ARAID, Zaragoza, Spain
| | - Tibor Kiss
- Centre for Agriculture Research ELKH (ATK), Martonvásár, Hungary
- Center for Research and Development, Food and Wine Center of Excellence, Eszterházy Károly Catholic University, Eger, Hungary
| | - Marianna Mayer
- Centre for Agriculture Research ELKH (ATK), Martonvásár, Hungary
| | - Ildikó Karsai
- Centre for Agriculture Research ELKH (ATK), Martonvásár, Hungary
| | - Ernesto Igartua
- Department of Genetics and Plant Breeding, Aula Dei Experimental Station, CSIC, Avda Montañana 1005, 50059, Zaragoza, Spain.
| | - Ana M Casas
- Department of Genetics and Plant Breeding, Aula Dei Experimental Station, CSIC, Avda Montañana 1005, 50059, Zaragoza, Spain
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10
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Kiseleva AA, Leonova IN, Ageeva EV, Likhenko IE, Salina EA. Identification of genetic loci for early maturity in spring bread wheat using the association analysis and gene dissection. PeerJ 2023; 11:e16109. [PMID: 37842052 PMCID: PMC10569184 DOI: 10.7717/peerj.16109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/25/2023] [Indexed: 10/17/2023] Open
Abstract
Background Early maturity in spring bread wheat is highly desirable in the regions where it enables the plants to evade high temperatures and plant pathogens at the end of the growing season. Methods To reveal the genetic loci responsible for the maturity time association analysis was carried out based on phenotyping for an 11-year period and high-throughput SNP genotyping of a panel of the varieties contrasting for this trait. The expression of candidate genes was verified using qPCR. The association between the SNP markers and the trait was validated using the biparental F2:3 population. Results Our data showed that under long-day conditions, the period from seedling to maturity is mostly influenced by the time from heading to maturity, rather than the heading time. The QTLs associated with the trait were located on 2A, 3B, 4A, 5B, 7A and 7B chromosomes with the 7BL locus being the most significant and promising for its SNPs accelerated the maturity time by about 9 days. Gene dissection in this locus detected a number of candidates, the best being TraesCS7B02G391800 (bZIP9) and TraesCS7B02G412200 (photosystem II reaction center). The two genes are predominantly expressed in the flag leaf while flowering. The effect of the SNPs was verified in F2:3 population and confirmed the association of the 4A, 5B and 7BL loci with the maturity time.
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Affiliation(s)
- Antonina A. Kiseleva
- Laboratory of Plant Molecular Genetics and Cytogenetics, The Federal State Budgetary Institution of Science Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Irina N. Leonova
- Laboratory of Plant Molecular Genetics and Cytogenetics, The Federal State Budgetary Institution of Science Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena V. Ageeva
- Laboratory of Field Crop Breeding and Seed Industry, Siberian Research Institute of Plant Production and Breeding, Branch of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Ivan E. Likhenko
- Laboratory of Field Crop Breeding and Seed Industry, Siberian Research Institute of Plant Production and Breeding, Branch of the Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena A. Salina
- Laboratory of Plant Molecular Genetics and Cytogenetics, The Federal State Budgetary Institution of Science Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Kurchatov Genomics Center, Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
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Zhang J, Xiong H, Burguener GF, Vasquez-Gross H, Liu Q, Debernardi JM, Akhunova A, Garland-Campbell K, Kianian SF, Brown-Guedira G, Pozniak C, Faris JD, Akhunov E, Dubcovsky J. Sequencing 4.3 million mutations in wheat promoters to understand and modify gene expression. Proc Natl Acad Sci U S A 2023; 120:e2306494120. [PMID: 37703281 PMCID: PMC10515147 DOI: 10.1073/pnas.2306494120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/03/2023] [Indexed: 09/15/2023] Open
Abstract
Wheat is an important contributor to global food security, and further improvements are required to feed a growing human population. Functional genetics and genomics tools can help us to understand the function of different genes and to engineer beneficial changes. In this study, we used a promoter capture assay to sequence 2-kb regions upstream of all high-confidence annotated genes from 1,513 mutagenized plants from the tetraploid wheat variety Kronos. We identified 4.3 million induced mutations with an accuracy of 99.8%, resulting in a mutation density of 41.9 mutations per kb. We also remapped Kronos exome capture reads to Chinese Spring RefSeq v1.1, identified 4.7 million mutations, and predicted their effects on annotated genes. Using these predictions, we identified 59% more nonsynonymous substitutions and 49% more truncation mutations than in the original study. To show the biological value of the promoter dataset, we selected two mutations within the promoter of the VRN-A1 vernalization gene. Both mutations, located within transcription factor binding sites, significantly altered VRN-A1 expression, and one reduced the number of spikelets per spike. These publicly available sequenced mutant datasets provide rapid and inexpensive access to induced variation in the promoters and coding regions of most wheat genes. These mutations can be used to understand and modulate gene expression and phenotypes for both basic and commercial applications, where limited governmental regulations can facilitate deployment. These mutant collections, together with gene editing, provide valuable tools to accelerate functional genetic studies in this economically important crop.
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Affiliation(s)
- Junli Zhang
- Department of Plant Sciences, University of California, Davis, CA95616
| | - Hongchun Xiong
- Department of Plant Sciences, University of California, Davis, CA95616
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Germán F. Burguener
- Department of Plant Sciences, University of California, Davis, CA95616
- HHMI, Chevy Chase, MD20815
| | - Hans Vasquez-Gross
- Department of Plant Sciences, University of California, Davis, CA95616
- Nevada Bioinformatics Center, University of Nevada, Reno, NV89557
| | - Qiujie Liu
- Department of Plant Sciences, University of California, Davis, CA95616
- HHMI, Chevy Chase, MD20815
| | - Juan M. Debernardi
- Department of Plant Sciences, University of California, Davis, CA95616
- HHMI, Chevy Chase, MD20815
| | - Alina Akhunova
- Department of Plant Pathology, Kansas State University, Manhattan, KS66506
| | - Kimberly Garland-Campbell
- United States Department of Agriculture - Agricultural Research Service, Wheat Health, Genetics and Quality Research Unit, Pullman, WA99164
| | - Shahryar F. Kianian
- United States Department of Agriculture - Agricultural Research Service, Cereal Disease Laboratory, Saint Paul, MN55108-6086
| | - Gina Brown-Guedira
- United States Department of Agriculture - Agricultural Research Service, Plant Science Research Unit, Raleigh, NC27695
| | - Curtis Pozniak
- Crop Development Centre, University of Saskatchewan, SaskatoonS7N 5A8, Canada
| | - Justin D. Faris
- United States Department of Agriculture - Agricultural Research Service, Cereal Crops Research Unit, Northern Crop Science Laboratory, Fargo, ND58102
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS66506
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA95616
- HHMI, Chevy Chase, MD20815
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Debernardi JM, Burguener G, Bubb K, Liu Q, Queitsch C, Dubcovsky J. Optimization of ATAC-seq in wheat seedling roots using INTACT-isolated nuclei. BMC PLANT BIOLOGY 2023; 23:270. [PMID: 37211599 DOI: 10.1186/s12870-023-04281-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 05/12/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND The genetic information contained in the genome of an organism is organized in genes and regulatory elements that control gene expression. The genomes of multiple plants species have already been sequenced and the gene repertory have been annotated, however, cis-regulatory elements remain less characterized, limiting our understanding of genome functionality. These elements act as open platforms for recruiting both positive- and negative-acting transcription factors, and as such, chromatin accessibility is an important signature for their identification. RESULTS In this work we developed a transgenic INTACT [isolation of nuclei tagged in specific cell types] system in tetraploid wheat for nuclei purifications. Then, we combined the INTACT system together with the assay for transposase-accessible chromatin with sequencing [ATAC-seq] to identify open chromatin regions in wheat root tip samples. Our ATAC-seq results showed a large enrichment of open chromatin regions in intergenic and promoter regions, which is expected for regulatory elements and that is similar to ATAC-seq results obtained in other plant species. In addition, root ATAC-seq peaks showed a significant overlap with a previously published ATAC-seq data from wheat leaf protoplast, indicating a high reproducibility between the two experiments and a large overlap between open chromatin regions in root and leaf tissues. Importantly, we observed overlap between ATAC-seq peaks and cis-regulatory elements that have been functionally validated in wheat, and a good correlation between normalized accessibility and gene expression levels. CONCLUSIONS We have developed and validated an INTACT system in tetraploid wheat that allows rapid and high-quality nuclei purification from root tips. Those nuclei were successfully used to performed ATAC-seq experiments that revealed open chromatin regions in the wheat genome that will be useful to identify cis-regulatory elements. The INTACT system presented here will facilitate the development of ATAC-seq datasets in other tissues, growth stages, and under different growing conditions to generate a more complete landscape of the accessible DNA regions in the wheat genome.
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Affiliation(s)
- Juan M Debernardi
- University of California, Davis, CA, 95616, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
| | - German Burguener
- University of California, Davis, CA, 95616, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Kerry Bubb
- Dept. of Biology, University of Washington, Seattle, WA, 98195, USA
| | - Qiujie Liu
- University of California, Davis, CA, 95616, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | | | - Jorge Dubcovsky
- University of California, Davis, CA, 95616, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
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