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Rehman AU, Iso-Touru T, Junkers J, Rantanen M, Karhu S, Fischer D, Alsheikh M, Hjeltnes SH, Mezzetti B, Davik J, Schulman AH, Hytönen T, Haikonen T. Multi-model GWAS reveals key loci for horticultural traits in reconstructed garden strawberry. PHYSIOLOGIA PLANTARUM 2024; 176:e14440. [PMID: 39030778 DOI: 10.1111/ppl.14440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/08/2024] [Accepted: 06/10/2024] [Indexed: 07/22/2024]
Abstract
The cultivated garden strawberry (Fragaria × ananassa) has a rich history, originating from the hybridization of two wild octoploid strawberry species in the 18th century. Two-step reconstruction of Fragaria × ananassa through controlled crossings between pre-improved selections of its parental species is a promising approach for enriching the breeding germplasm of strawberry for wider adaptability. We created a population of reconstructed strawberry by hybridizing elite selections of F. virginiana and F. chiloensis. A replicated field experiment was conducted to evaluate the population's performance for eleven horticulturally important traits, over multiple years. Population structure analyses based on Fana-50 k SNP array data confirmed pedigree-based grouping of the progenies into four distinct groups. As complex traits are often influenced by environmental variables, and population structure can lead to spurious associations, we tested multiple genome-wide association study (GWAS) models. GWAS uncovered 39 quantitative trait loci (QTL) regions for eight traits distributed across twenty chromosomes, including 11 consistent and 28 putative QTLs. Candidate genes for traits including winter survival, flowering time, runnering vigor, and hermaphrodism were identified within the QTL regions. To our knowledge, this study marks the first comprehensive investigation of adaptive and horticultural traits in a large, multi-familial reconstructed strawberry population using SNP markers.
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Affiliation(s)
- Attiq Ur Rehman
- Natural Resources Institute Finland (Luke), Finland
- Doctoral Program in Plant Sciences, University of Helsinki, Finland
| | | | - Jakob Junkers
- Norwegian Institute of Bioeconomy Research, Ås, Norway
| | | | - Saila Karhu
- Natural Resources Institute Finland (Luke), Finland
| | | | - Muath Alsheikh
- Graminor AS, Norway
- Faculty of Life Sciences, Department of Plant Sciences, Norwegian University of Life Sciences, Ås, Norway
| | | | - Bruno Mezzetti
- Department of Agriculture, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Jahn Davik
- Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Alan H Schulman
- Natural Resources Institute Finland (Luke), Finland
- Viikki Plant Science Centre, Finland
- Institute of Biotechnology, University of Helsinki, Finland
| | - Timo Hytönen
- Viikki Plant Science Centre, Finland
- Department of Agricultural Sciences, University of Helsinki, Finland
| | - Tuuli Haikonen
- Natural Resources Institute Finland (Luke), Finland
- Viikki Plant Science Centre, Finland
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2
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Kohli M, Bansal H, Mishra GP, Dikshit HK, Reddappa SB, Roy A, Sinha SK, Shivaprasad K, Kumari N, Kumar A, Kumar RR, Nair RM, Aski M. Genome-wide association studies for earliness, MYMIV resistance, and other associated traits in mungbean ( Vigna radiata L. Wilczek) using genotyping by sequencing approach. PeerJ 2024; 12:e16653. [PMID: 38288464 PMCID: PMC10823994 DOI: 10.7717/peerj.16653] [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: 08/02/2023] [Accepted: 11/20/2023] [Indexed: 02/01/2024] Open
Abstract
Yellow mosaic disease (YMD) remains a major constraint in mungbean (Vigna radiata (L.)) production; while short-duration genotypes offer multiple crop cycles per year and help in escaping terminal heat stress, especially during summer cultivation. A comprehensive genotyping by sequencing (GBS)-based genome-wide association studies (GWAS) analysis was conducted using 132 diverse mungbean genotypes for traits like flowering time, YMD resistance, soil plant analysis development (SPAD) value, trichome density, and leaf area. The frequency distribution revealed a wide range of values for all the traits. GBS studies identified 31,953 high-quality single nucleotide polymorphism (SNPs) across all 11 mungbean chromosomes and were used for GWAS. Structure analysis revealed the presence of two genetically distinct populations based on ΔK. The linkage disequilibrium (LD) varied throughout the chromosomes and at r2 = 0.2, the mean LD decay was estimated as 39.59 kb. Two statistical models, mixed linear model (MLM) and Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) identified 44 shared SNPs linked with various candidate genes. Notable candidate genes identified include FPA for flowering time (VRADI10G01470; chr. 10), TIR-NBS-LRR for mungbean yellow mosaic India virus (MYMIV) resistance (VRADI09G06940; chr. 9), E3 ubiquitin-protein ligase RIE1 for SPAD value (VRADI07G28100; chr. 11), WRKY family transcription factor for leaf area (VRADI03G06560; chr. 3), and LOB domain-containing protein 21 for trichomes (VRADI06G04290; chr. 6). In-silico validation of candidate genes was done through digital gene expression analysis using Arabidopsis orthologous (compared with Vigna radiata genome). The findings provided valuable insight for marker-assisted breeding aiming for the development of YMD-resistant and early-maturing mungbean varieties.
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Affiliation(s)
- Manju Kohli
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
- Genetics, Indian Agricultural Research Institute, Delhi, Delhi, India
| | - Hina Bansal
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
| | | | | | | | - Anirban Roy
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, Delhi, India
| | - Subodh Kumar Sinha
- Biotechnology, National Institute of Plant Biotechnology, New Delhi, Delhi, India
| | - K.M. Shivaprasad
- Genetics, Indian Agricultural Research Institute, Delhi, Delhi, India
| | - Nikki Kumari
- Genetics, Indian Agricultural Research Institute, Delhi, Delhi, India
| | - Atul Kumar
- Division of Seed Science and Technology, Indian Agricultural Research Institute, New Delhi, Delhi, India
| | - Ranjeet R. Kumar
- Biochemistry, Indian Agricultural Research Institute, New Delhi, Delhi, India
| | | | - Muraleedhar Aski
- Genetics, Indian Agricultural Research Institute, Delhi, Delhi, India
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3
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Patil AB, Kar D, Datta S, Vijay N. Genomic and Transcriptomic Analyses Illuminates Unique Traits of Elusive Night Flowering Jasmine Parijat (Nyctanthes arbor-tristis). PHYSIOLOGIA PLANTARUM 2023; 175:e14119. [PMID: 38148217 DOI: 10.1111/ppl.14119] [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: 08/02/2023] [Accepted: 11/27/2023] [Indexed: 12/28/2023]
Abstract
The night-flowering Jasmine, Nyctanthes arbor-tristis also known as Parijat, is a perennial woody shrub belonging to the family of Oleaceae. It is popular for its fragrant flowers that bloom in the night and is a potent source of secondary metabolites. However, knowledge about its genome and the expression of genes regulating flowering or secondary metabolite accumulation is lacking. In this study, we generated whole genome sequencing data to assemble the first de novo assembly of Parijat and use it for comparative genomics and demographic history reconstruction. The temporal dynamics of effective population size (Ne ) experienced a positive influence of colder climates suggesting the switch to night flowering may have provided an evolutionary advantage. We employed multi-tissue transcriptome sequencing of floral stages/parts to obtain insights into the transcriptional regulation of nocturnal flower development and the production of volatiles/metabolites. Tissue-specific transcripts for mature flowers revealed key players in circadian regulation and flower development, including the auxin pathway and cell wall modifying genes. Furthermore, we identified tissue-specific transcripts responsible for producing numerous secondary metabolites, mainly terpenoids and carotenoids. The diversity and specificity of Terpene Synthase (TPS) and CCDs (Carotenoid Cleavage Deoxygenases) mediate the bio-synthesis of specialised metabolites in Parijat. Our study establishes Parijat as a novel non-model species to understand the molecular mechanisms of nocturnal blooming and secondary metabolite production.
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Affiliation(s)
- Ajinkya Bharatraj Patil
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Madhya Pradesh, India
| | - Debojyoti Kar
- Plant Cell and Developmental Biology Lab, Department of Biological Sciences, IISER Bhopal, Madhya Pradesh, India
| | - Sourav Datta
- Plant Cell and Developmental Biology Lab, Department of Biological Sciences, IISER Bhopal, Madhya Pradesh, India
| | - Nagarjun Vijay
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Madhya Pradesh, India
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4
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Mizuno N, Matsunaka H, Yanaka M, Ishikawa G, Kobayashi F, Nakamura K. Natural variations of wheat EARLY FLOWERING 3 highlight their contributions to local adaptation through fine-tuning of heading time. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:139. [PMID: 37233781 DOI: 10.1007/s00122-023-04386-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023]
Abstract
KEY MESSAGE We identified a large chromosomal deletion containing TaELF-B3 that confers early flowering in wheat. This allele has been preferred in recent wheat breeding in Japan to adapt to the environment. Heading at the appropriate time in each cultivation region can greatly contribute to stabilizing and maximizing yield. Vrn-1 and Ppd-1 are known as the major genes for vernalization requirement and photoperiod sensitivity in wheat. Genotype combinations of Vrn-1 and Ppd-1 can explain the variation in heading time. However, the genes that can explain the remaining variations in heading time are largely unknown. In this study, we aimed to identify the genes conferring early heading using doubled haploid lines derived from Japanese wheat varieties. Quantitative trait locus (QTL) analysis revealed a significant QTL on the long arm of chromosome 1B in multiple growing seasons. Genome sequencing using Illumina short reads and Pacbio HiFi reads revealed a large deletion of a ~ 500 kb region containing TaELF-B3, an orthologue of Arabidopsis clock gene EARLY FLOWERING 3 (ELF3). Plants with the deleted allele of TaELF-B3 (ΔTaELF-B3 allele) headed earlier only under short-day vernalization conditions. Higher expression levels of clock- and clock-output genes, such as Ppd-1 and TaGI, were observed in plants with the ΔTaELF-B3 allele. These results suggest that the deletion of TaELF-B3 causes early heading. Of the TaELF-3 homoeoalleles conferring early heading, the ΔTaELF-B3 allele showed the greatest effect on the early heading phenotype in Japan. The higher allele frequency of the ΔTaELF-B3 allele in western Japan suggests that the ΔTaELF-B3 allele was preferred during recent breeding to adapt to the environment. TaELF-3 homoeologs will help to expand the cultivated area by fine-tuning the optimal timing of heading in each environment.
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Affiliation(s)
- Nobuyuki Mizuno
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.
| | - Hitoshi Matsunaka
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka, 833-0041, Japan
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, 9-4 Shinsei-Minami, Memuro, Kasai, Hokkaido, 082-0081, Japan
| | - Mikiko Yanaka
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka, 833-0041, Japan
| | - Goro Ishikawa
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Fuminori Kobayashi
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Kazuhiro Nakamura
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka, 833-0041, Japan
- Headquarters, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8517, Japan
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5
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Dai Y, Li G, Gao X, Wang S, Li Z, Song C, Zhang S, Li F, Fang Z, Sun R, Zhang H, Zhang S. Identification of long noncoding RNAs involved in plumule-vernalization of Chinese cabbage. FRONTIERS IN PLANT SCIENCE 2023; 14:1147494. [PMID: 36998688 PMCID: PMC10043383 DOI: 10.3389/fpls.2023.1147494] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
Vernalization is a phenomenon in which plants must undergo a period of continuous low temperatures to change from the vegetative growth stage to the reproductive growth stage. Chinese cabbage is a heading vegetable, and flowering time is an essential developmental trait. Premature vernalization leads to premature bolting, which causes a loss of product value and yield. While research into vernalization has provided a wealth of information, a complete understanding of the molecular mechanism for controlling vernalization requirements has not yet been elucidated. In this study, using high-throughput RNA sequencing, we analyzed the plumule-vernalization response of mRNA and long noncoding RNA in the bolting-resistant Chinese cabbage double haploid (DH) line 'Ju Hongxin' (JHX). A total of 3382 lncRNAs were identified, of which 1553 differentially expressed (DE) lncRNAs were characterized as plumule-vernalization responses. The ceRNA network revealed that 280 ceRNA pairs participated in the plumule-vernalization reaction of Chinese cabbage. Through identifying DE lncRNAs in Chinese cabbage and analyzing anti-, cis-, and trans-functional analysis, some candidate lncRNAs related to vernalization promoting flowering of Chinese cabbage and their regulated mRNA genes were found. Moreover, the expression of several critical lncRNAs and their targets was verified using qRT-PCR. Furthermore, we identified the candidate plumule-vernalization-related long noncoding RNAs that regulate BrFLCs in Chinese cabbage, which was interesting and different from previous studies and was a new discovery. Our findings expand the knowledge of lncRNAs in the vernalization of Chinese cabbage, and the identified lncRNAs provide rich resources for future comparative and functional studies.
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Affiliation(s)
- Yun Dai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guoliang Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinyu Gao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shaoxing Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ze Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chao Song
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shifan Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fei Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiyuan Fang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rifei Sun
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hui Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shujiang Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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6
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Roy A, Reddy MH, Sarkar M, Sagolsem D, Murmu SK, Das C, Roy D, Ganguly S, Nath R, Bhattacharyya PK, Sarker A, Bhattacharyya S. A mis-splicing early flowering 3 (elf3) allele of lentil is associated with yield enhancement under terminal heat stress. J Appl Genet 2023; 64:265-273. [PMID: 36821070 DOI: 10.1007/s13353-023-00753-z] [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: 06/25/2022] [Revised: 01/28/2023] [Accepted: 02/13/2023] [Indexed: 02/24/2023]
Abstract
There is a vast scope of area expansion of lentils after harvesting wet rice in South Asia. However, due to the photoperiod effect and terminal heat, the existing short-duration varieties failed to minimize yield loss under late-sown conditions. A mis-splicing causing A/G SNP present in the last nucleotide of exon 3 of early flowering 3 (ELF3) gene (elf3 allele) in a lentil line, L4710, is associated with the photoperiod insensitive flowering and the fast absolute growth rate (AGR). None of the Indian cultivars tested in this study, either early or late, possesses the non-functional elf3 allele. However, the A to G transition in ELF3-exon2 replaces glycine with aspartic acid at the 403rd amino acid in all the Indian varieties tested, compared to the reference sequence of Mediterranean accession, ILL5588. Therefore, targeting A/G SNP of exon 3, a PCR-based codominant marker is developed. The elf3 allele is correlated with the fast AGR and early flowering, but low yield and biomass, in an L4710 × LL56-derived RIL-population, compared to ELF3 carrying alleles when sown on 15th November. However, in a month of delayed sowing (20th December), the same elf3-RILs revealed a higher yield and biomass with slower AGR Moreover, three elf3-carrying lines, grown in delayed condition (20 December) for two consecutive years in three locations, outyielded three popular high-yielding cultivars that carry functional ELF3. Thus, elf3-carrying high-yielding lines could be the breeder's choice to expand and enhance lentil yield in short-season environments and in vast rice fallows of south Asia, where delayed rice harvest occurs frequently.
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Affiliation(s)
- Anirban Roy
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India
| | - M Hemakumar Reddy
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India
| | - Moutushi Sarkar
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India
| | - Diana Sagolsem
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India
| | - Sumit K Murmu
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India
| | - Camellia Das
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India
| | - Debarati Roy
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India
| | - Shamba Ganguly
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India
| | - Rajib Nath
- Department of Agronomy, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India
| | - Prabir K Bhattacharyya
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India
| | - Asutosh Sarker
- ICARDA, South Asia-China Regional Office, New Delhi, 110012, India
| | - Somnath Bhattacharyya
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India.
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7
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Alcantara M, Acosta P, Azatian A, Calderon C, Candray K, Castillo N, Coria-Gomez L, Duran J, Fam J, Hernandez-Segura D, Hidalgo L, Huerta C, Jordan S, Kagan K, Loya K, Martinez E, Musaev K, Navarro R, Nazarians N, Paglia R, Robles G, Simmons T, Smith S, Soudani F, Valenzuela E, Villalobos J, Iftikhar H, Hanzawa Y. Experimental Verification of Inferred Regulatory Interactions of EARLY FLOWERING 3 ( GmELF3-1 ) in Glycine max. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000687. [PMID: 36506349 PMCID: PMC9729981 DOI: 10.17912/micropub.biology.000687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/28/2022] [Accepted: 11/18/2022] [Indexed: 12/15/2022]
Abstract
Understanding the roles of evening complex (EC) genes in the circadian clock of plants can inform how diurnal transcriptional loops in the clock gene network function to regulate key physiological and developmental events, including flowering transition. Gene regulatory interactions among soybean's circadian clock and flowering genes were inferred using time-series RNA-seq data and the network inference algorithmic package CausNet. In this study, we seek to clarify the inferred regulatory interactions of the EC gene GmELF3-1. A gene expression analysis using soybean protoplasts as a transient model indicated regulatory roles of GmELF3-1 in expression of selected flowering genes.
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Affiliation(s)
| | - Patrick Acosta
- Department of Biology, California State University Northridge
| | - Ara Azatian
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Carlos Calderon
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Kevin Candray
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Natalie Castillo
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Luis Coria-Gomez
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Jose Duran
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Justina Fam
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Diego Hernandez-Segura
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Lennix Hidalgo
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Carlos Huerta
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Shane Jordan
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Kimberly Kagan
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Karla Loya
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Eduardo Martinez
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Kirill Musaev
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Roxana Navarro
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Narek Nazarians
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Robert Paglia
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Gabriela Robles
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Taylor Simmons
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Shawn Smith
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Faisel Soudani
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Emily Valenzuela
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Jessica Villalobos
- Department of Biology, BIOL 481 Plant Physiology, California State University Northridge
| | - Hira Iftikhar
- Department of Biology, California State University Northridge
| | - Yoshie Hanzawa
- Department of Biology, California State University Northridge
,
Correspondence to: Yoshie Hanzawa (
)
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8
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Gururaj M, Ohmura A, Ozawa M, Yamano T, Fukuzawa H, Matsuo T. A potential EARLY FLOWERING 3 homolog in Chlamydomonas is involved in the red/violet and blue light signaling pathways for the degradation of RHYTHM OF CHLOROPLAST 15. PLoS Genet 2022; 18:e1010449. [PMID: 36251728 PMCID: PMC9612821 DOI: 10.1371/journal.pgen.1010449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 10/27/2022] [Accepted: 09/26/2022] [Indexed: 11/07/2022] Open
Abstract
Light plays a major role in resetting the circadian clock, allowing the organism to synchronize with the environmental day and night cycle. In Chlamydomonas the light-induced degradation of the circadian clock protein, RHYTHM OF CHLOROPLAST 15 (ROC15), is considered one of the key events in resetting the circadian clock. Red/violet and blue light signals have been shown to reach the clock via different molecular pathways; however, many of the participating components of these pathways are yet to be elucidated. Here, we used a forward genetics approach using a reporter strain that expresses a ROC15-luciferase fusion protein. We isolated a mutant that showed impaired ROC15 degradation in response to a wide range of visible wavelengths and impaired light-induced phosphorylation of ROC15. These results suggest that the effects of different wavelengths converge before acting on ROC15 or at ROC15 phosphorylation. Furthermore, the mutant showed a weakened phase resetting in response to light, but its circadian rhythmicity remained largely unaffected under constant light and constant dark conditions. Surprisingly, the gene disrupted in this mutant was found to encode a protein that possessed a very weak similarity to the Arabidopsis thaliana EARLY FLOWERING 3 (ELF3). Our results suggest that this protein is involved in the many different light signaling pathways to the Chlamydomonas circadian clock. However, it may not influence the transcriptional oscillator of Chlamydomonas to a great extent. This study provides an opportunity to further understand the mechanisms underlying light-induced clock resetting and explore the evolution of the circadian clock architecture in Viridiplantae. Resetting of the circadian clock is crucial for an organism, as it allows the synchronization of its internal processes with the day/night cycle. Environmental signals—such as light and temperature—contribute to this event. In plants, the molecular mechanisms underlying the light-induced resetting of the circadian clock have been well-studied in the streptophyte, Arabidopsis thaliana, and has been explored in some chlorophyte algae such as Ostreococcus tauri and Chlamydomonas reinhardtii. Here, we used a forward genetics approach to examine the light signaling pathway of a process considered critical for the light resetting of the Chlamydomonas clock—light-induced degradation of the circadian clock protein ROC15. We explored various aspects of the isolated mutant, such as the degradation of ROC15 in response to a range of visible wavelengths, the circadian rhythm, and the phase resetting of the rhythm. We show that the effects of different wavelengths of light converge before acting on ROC15 or at ROC15 phosphorylation with the aid of a potential homolog of the Arabidopsis thaliana ELF3. Our findings contradict the existing view that there is no known homolog of ELF3 in chlorophyte algae. This study, therefore, sheds light on the evolutionary aspects of the Viridiplantae circadian clocks and their light resetting.
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Affiliation(s)
- Malavika Gururaj
- Center for Gene Research, Nagoya University, Nagoya, Japan
- Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Ayumi Ohmura
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Mariko Ozawa
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Takashi Yamano
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Hideya Fukuzawa
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Takuya Matsuo
- Center for Gene Research, Nagoya University, Nagoya, Japan
- Graduate School of Science, Nagoya University, Nagoya, Japan
- * E-mail:
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9
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Davis W, Endo M, Locke JCW. Spatially specific mechanisms and functions of the plant circadian clock. PLANT PHYSIOLOGY 2022; 190:938-951. [PMID: 35640123 PMCID: PMC9516738 DOI: 10.1093/plphys/kiac236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 04/22/2022] [Indexed: 06/15/2023]
Abstract
Like many organisms, plants have evolved a genetic network, the circadian clock, to coordinate processes with day/night cycles. In plants, the clock is a pervasive regulator of development and modulates many aspects of physiology. Clock-regulated processes range from the correct timing of growth and cell division to interactions with the root microbiome. Recently developed techniques, such as single-cell time-lapse microscopy and single-cell RNA-seq, are beginning to revolutionize our understanding of this clock regulation, revealing a surprising degree of organ, tissue, and cell-type specificity. In this review, we highlight recent advances in our spatial view of the clock across the plant, both in terms of how it is regulated and how it regulates a diversity of output processes. We outline how understanding these spatially specific functions will help reveal the range of ways that the clock provides a fitness benefit for the plant.
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Affiliation(s)
- William Davis
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Motomu Endo
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara 630-0192, Japan
| | - James C W Locke
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
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10
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Nieto C, Catalán P, Luengo LM, Legris M, López-Salmerón V, Davière JM, Casal JJ, Ares S, Prat S. COP1 dynamics integrate conflicting seasonal light and thermal cues in the control of Arabidopsis elongation. SCIENCE ADVANCES 2022; 8:eabp8412. [PMID: 35984876 PMCID: PMC9390991 DOI: 10.1126/sciadv.abp8412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 07/07/2022] [Indexed: 05/19/2023]
Abstract
As the summer approaches, plants experience enhanced light inputs and warm temperatures, two environmental cues with an opposite morphogenic impact. Key components of this response are PHYTOCHROME B (phyB), EARLY FLOWERING 3 (ELF3), and CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1). Here, we used single and double mutant/overexpression lines to fit a mathematical model incorporating known interactions of these regulators. The fitted model recapitulates thermal growth of all lines used and correctly predicts thermal behavior of others not used in the fit. While thermal COP1 function is accepted to be independent of diurnal timing, our model shows that it acts at temperature signaling only during daytime. Defective response of cop1-4 mutants is epistatic to phyB-9 and elf3-8, indicating that COP1 activity is essential to transduce phyB and ELF3 thermosensory function. Our thermal model provides a unique toolbox to identify best allelic combinations enhancing climate change resilience of crops adapted to different latitudes.
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Affiliation(s)
- Cristina Nieto
- Centro Nacional de Biotecnologia (CNB), CSIC, Darwin 3, 28049 Madrid, Spain
- Centro de Recursos Fitogeneticos y Agricultura Sostenible (CRF-INIA), CSIC, Autovia A2, km 32, 28805 Alcala de Henares, Madrid, Spain
| | - Pablo Catalán
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
- Department of Mathematics, Universidad Carlos III de Madrid, Avenida de la Universidad 30, 28911 Leganes, Madrid, Spain
| | - Luis Miguel Luengo
- Centro Nacional de Biotecnologia (CNB), CSIC, Darwin 3, 28049 Madrid, Spain
- Centro de Investigación en Agrigenomica (CRAG), CSIC-IRTA-UAB-UB, 08193 Cerdanyola, Barcelona, Spain
| | - Martina Legris
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, 1405 Buenos Aires, Argentina
| | | | | | - Jorge J. Casal
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, 1405 Buenos Aires, Argentina
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Facultad de Agronomía, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, 1417 Buenos Aires, Argentina
| | - Saúl Ares
- Centro Nacional de Biotecnologia (CNB), CSIC, Darwin 3, 28049 Madrid, Spain
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
- Corresponding author. (S.A.); (S.P.)
| | - Salomé Prat
- Centro Nacional de Biotecnologia (CNB), CSIC, Darwin 3, 28049 Madrid, Spain
- Centro de Investigación en Agrigenomica (CRAG), CSIC-IRTA-UAB-UB, 08193 Cerdanyola, Barcelona, Spain
- Corresponding author. (S.A.); (S.P.)
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11
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Alexandre Moraes T, Mengin V, Peixoto B, Encke B, Krohn N, Höhne M, Krause U, Stitt M. The circadian clock mutant lhy cca1 elf3 paces starch mobilization to dawn despite severely disrupted circadian clock function. PLANT PHYSIOLOGY 2022; 189:2332-2356. [PMID: 35567528 PMCID: PMC9348821 DOI: 10.1093/plphys/kiac226] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/22/2022] [Indexed: 06/15/2023]
Abstract
Many plants, including Arabidopsis (Arabidopsis thaliana), accumulate starch in the daytime and remobilize it to support maintenance and growth at night. Starch accumulation is increased when carbon is in short supply, for example, in short photoperiods. Mobilization is paced to exhaust starch around dawn, as anticipated by the circadian clock. This diel pattern of turnover is largely robust against loss of day, dawn, dusk, or evening clock components. Here, we investigated diel starch turnover in the triple circadian clock mutant lhy cca1 elf3, which lacks the LATE ELONGATED HYPOCOTYL and the CIRCADIAN CLOCK-ASSOCIATED1 (CCA1) dawn components and the EARLY FLOWERING3 (ELF3) evening components of the circadian clock. The diel oscillations of transcripts for the remaining clock components and related genes like REVEILLE and PHYTOCHROME-INTERACING FACTOR family members exhibited attenuated amplitudes and altered peak time, weakened dawn dominance, and decreased robustness against changes in the external light-dark cycle. The triple mutant was unable to increase starch accumulation in short photoperiods. However, it was still able to pace starch mobilization to around dawn in different photoperiods and growth irradiances and to around 24 h after the previous dawn in T17 and T28 cycles. The triple mutant was able to slow down starch mobilization after a sudden low-light day or a sudden early dusk, although in the latter case it did not fully compensate for the lengthened night. Overall, there was a slight trend to less linear mobilization of starch. Thus, starch mobilization can be paced rather robustly to dawn despite a major disruption of the transcriptional clock. It is proposed that temporal information can be delivered from clock components or a semi-autonomous oscillator.
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Affiliation(s)
| | - Virginie Mengin
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - Bruno Peixoto
- Instituto Gulbenkian de Ciência, Oeiras 2780-156,Portugal
- GREEN-IT Bioresources for Sustainability, ITQB NOVA, Oeiras 2780-157,Portugal
| | - Beatrice Encke
- Systematic Botany and Biodiversity, Humboldt University of Berlin, Berlin D-10115, Germany
| | - Nicole Krohn
- Abteilung für Parodontologie und Synoptische Zahnmedizin, Charité Universitätsmedizin, Berlin 14197, Germany
| | - Melanie Höhne
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Ursula Krause
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
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12
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Nidhi, Kumar P, Pathania D, Thakur S, Sharma M. Environment-mediated mutagenetic interference on genetic stabilization and circadian rhythm in plants. Cell Mol Life Sci 2022; 79:358. [PMID: 35687153 PMCID: PMC11072124 DOI: 10.1007/s00018-022-04368-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/21/2022] [Accepted: 05/07/2022] [Indexed: 12/29/2022]
Abstract
Many mortal organisms on this planet have developed the potential to merge all internal as well as external environmental cues to regulate various processes running inside organisms and in turn make them adaptive to the environment through the circadian clock. This moving rotator controls processes like activation of hormonal, metabolic, or defense pathways, initiation of flowering at an accurate period, and developmental processes in plants to ensure their stability in the environment. All these processes that are under the control of this rotating wheel can be changed either by external environmental factors or by an unpredictable phenomenon called mutation that can be generated by either physical mutagens, chemical mutagens, or by internal genetic interruption during metabolic processes, which alters normal functionality of organisms like innate immune responses, entrainment of the clock, biomass reduction, chlorophyll formation, and hormonal signaling, despite its fewer positive roles in plants like changing plant type, loss of vernalization treatment to make them survivable in different latitudes, and defense responses during stress. In addition, with mutation, overexpression of gene components sometimes supresses mutation effect and promote normal circadian genes abundance in the cell, while sometimes it affects circadian functionality by generating arrhythmicity and shows that not only mutation but overexpression also effects normal functional activities of plant. Therefore, this review mainly summarizes the role of each circadian clock genes in regulating rhythmicity, and shows that how circadian outputs are controlled by mutations as well as overexpression phenomenon.
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Affiliation(s)
- Nidhi
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, 173212, India
| | - Pradeep Kumar
- Central University of Himachal Pradesh, Dharmshala, India
| | - Diksha Pathania
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, 173212, India
| | - Sourbh Thakur
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, Gliwice, Poland
| | - Mamta Sharma
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, 173212, India.
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13
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Venkat A, Muneer S. Role of Circadian Rhythms in Major Plant Metabolic and Signaling Pathways. FRONTIERS IN PLANT SCIENCE 2022; 13:836244. [PMID: 35463437 PMCID: PMC9019581 DOI: 10.3389/fpls.2022.836244] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/23/2022] [Indexed: 05/10/2023]
Abstract
Plants require an endogenous regulatory network and mechanism to cope with diurnal environmental changes and compensate for their sessile nature. Plants use the circadian clock to anticipate diurnal changes. Circadian rhythm predicts a 24-h cycle with 16 h of light and 8 h of darkness in response to abiotic and biotic factors as well as the appropriate temperature. For a plant's fitness, proper growth, and development, these rhythms synchronize the diurnal photoperiodic changes. Input pathway, central oscillator, and output pathway are the three components that make up the endogenous clock. There are also transcriptional and translational feedback loops (TTFLs) in the clock, which are dependent on the results of gene expression. Several physiological processes, such as stress acclimatization, hormone signaling, morphogenesis, carbon metabolism, and defense response, are currently being investigated for their interactions with the circadian clock using phenotypic, genomic, and metabolic studies. This review examines the role of circadian rhythms in the regulation of plant metabolic pathways, such as photosynthesis and carbon metabolism, as well as developmental and degenerative processes, such as flowering and senescence. Furthermore, we summarized signaling pathways related to circadian rhythms, such as defense response and gene regulatory pathways.
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Affiliation(s)
- Ajila Venkat
- Horticulture and Molecular Physiology Lab, School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, India
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Sowbiya Muneer
- Horticulture and Molecular Physiology Lab, School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, India
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14
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Zioutopoulou A, Patitaki E, O’Donnell L, Kaiserli E. Low Fluence Ultraviolet-B Promotes Ultraviolet Resistance 8-Modulated Flowering in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:840720. [PMID: 35432431 PMCID: PMC9009151 DOI: 10.3389/fpls.2022.840720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
Ultraviolet-B (UV-B) irradiation (280-320 nm) is an integral part of sunlight and a pivotal environmental cue that triggers various plant responses, from photoprotection to photomorphogenesis and metabolic processes. UV-B is perceived by ULTRAVIOLET RESISTANCE 8 (UVR8), which orchestrates UV-B signal transduction and transcriptional control of UV-B-responsive genes. However, there is limited information on the molecular mechanism underlying the UV-B- and UVR8-dependent regulation of flowering time in plants. Here, we investigate the role of UV-B and UVR8 in photoperiodic flowering in Arabidopsis thaliana. Our findings suggest that UV-B controls photoperiodic flowering in an ecotype-specific manner and that UVR8 acts as a negative regulator of UV-B-induced flowering. Overall, our research shows that UV-B modulates flowering initiation through the action of UVR8 at the transcriptional level.
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15
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Cai Z, Zhang Y, Tang W, Chen X, Lin C, Liu Y, Ye Y, Wu W, Duan Y. LUX ARRHYTHMO Interacts With ELF3a and ELF4a to Coordinate Vegetative Growth and Photoperiodic Flowering in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:853042. [PMID: 35401642 PMCID: PMC8993510 DOI: 10.3389/fpls.2022.853042] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/22/2022] [Indexed: 05/27/2023]
Abstract
The evening complex (EC) plays a critical role in photoperiod flowering in Arabidopsis. Nevertheless, the underlying functions of individual components and coordinate regulation mechanism of EC genes in rice flowering remain to be elucidated. Here, we characterized the critical role of LUX ARRHYTHMO (LUX) in photoperiod perception and coordinating vegetative growth and flowering in rice. Non-functional alleles of OsLUX extremely extended vegetative phase, leading to photoperiod-insensitive late flowering and great increase of grain yield. OsLUX displayed an obvious diurnal rhythm expression with the peak at dusk and promoted rice flowering via coordinating the expression of genes associated with the circadian clock and the output integrators of photoperiodic flowering. OsLUX combined with OsELF4a and OsELF3a or OsELF3b to form two ECs, of which the OsLUX-OsELF3a-OsELF4a was likely the dominant promoter for photoperiodic flowering. In addition, OsELF4a was also essential for promoting rice flowering. Unlike OsLUX, loss OsELF4a displayed a marginal influence under short-day (SD) condition, but markedly delayed flowering time under long-day (LD) condition. These results suggest that rice EC genes share the function of promoting flowering. This is agreement with the orthologs of SD plant, but opposite to the counterparts of LD species. Taken together, rice EC genes display similar but not identical function in photoperiodic flowering, probably through regulating gene expression cooperative and independent. These findings facilitate our understanding of photoperiodic flowering in plants, especially the SD crops.
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Affiliation(s)
- Zhengzheng Cai
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yudan Zhang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weiqi Tang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuequn Chen
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chenchen Lin
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yang Liu
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanfang Ye
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weiren Wu
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuanlin Duan
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, China
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16
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Evaluating the Effects of the Circadian Clock and Time of Day on Plant Gravitropic Responses. Methods Mol Biol 2022; 2368:301-319. [PMID: 34647263 DOI: 10.1007/978-1-0716-1677-2_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Circadian rhythms are regular oscillations of an organism's physiology with a period of approximately 24 h. In the model plant Arabidopsis thaliana, circadian rhythms regulate a suite of physiological processes, including transcription, photosynthesis, growth, and flowering. The circadian clock and external rhythmic factors have extensive control of the underlying biochemistry and physiology. Therefore, it is critical to consider the time of day when performing gravitropism experiments, even if the circadian clock is not a focus of study. We describe the critical factors and methods to be considered and methods to investigate the possible circadian regulation of gravitropic responses.
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17
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Luo X, Yin M, He Y. Molecular Genetic Understanding of Photoperiodic Regulation of Flowering Time in Arabidopsis and Soybean. Int J Mol Sci 2021; 23:466. [PMID: 35008892 PMCID: PMC8745532 DOI: 10.3390/ijms23010466] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/25/2021] [Accepted: 12/29/2021] [Indexed: 12/15/2022] Open
Abstract
The developmental switch from a vegetative phase to reproduction (flowering) is essential for reproduction success in flowering plants, and the timing of the floral transition is regulated by various environmental factors, among which seasonal day-length changes play a critical role to induce flowering at a season favorable for seed production. The photoperiod pathways are well known to regulate flowering time in diverse plants. Here, we summarize recent progresses on molecular mechanisms underlying the photoperiod control of flowering in the long-day plant Arabidopsis as well as the short-day plant soybean; furthermore, the conservation and diversification of photoperiodic regulation of flowering in these two species are discussed.
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Affiliation(s)
- Xiao Luo
- Peking University Institute of Advanced Agricultural Sciences, Weifang 261325, China
| | - Mengnan Yin
- Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Shanghai 201602, China;
| | - Yuehui He
- Peking University Institute of Advanced Agricultural Sciences, Weifang 261325, China
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences, Peking University, Beijing 100871, China
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18
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Huang Z, Shen F, Chen Y, Cao K, Wang L. Chromosome-scale genome assembly and population genomics provide insights into the adaptation, domestication, and flavonoid metabolism of Chinese plum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1174-1192. [PMID: 34473873 DOI: 10.1111/tpj.15482] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Globally, commercialized plum cultivars are mostly diploid Chinese plums (Prunus salicina Lindl.), also known as Japanese plums, and are one of the most abundant and variable fruit tree species. To advance Prunus genomic research, we present a chromosome-scale P. salicina genome assembly, constructed using an integrated strategy that combines Illumina, Oxford Nanopore, and high-throughput chromosome conformation capture (Hi-C) sequencing. The high-quality genome assembly consists of a 318.6-Mb sequence (contig N50 length of 2.3 Mb) with eight pseudo-chromosomes. The expansion of the P. salicina genome is led by recent segmental duplications and a long terminal repeat burst of approximately 0.2 Mya. This resulted in a significant expansion of gene families associated with flavonoid metabolism and plant resistance, which impacted fruit flavor and increased species adaptability. Population structure and domestication history suggest that Chinese plum may have originated from South China and provides a domestication route with accompanying genomic variations. Selection sweep and genetic diversity analysis enabled the identification of several critical genes associated with flowering time, stress tolerance, and flavonoid metabolism, demonstrating the essential roles of related pathways during domestication. Furthermore, we reconstructed and exploited flavonoid-anthocyanin metabolism using multi-omics analysis in Chinese plum and proposed a complete metabolic pathway. Collectively, our results will facilitate further candidate gene discovery for important agronomic traits in Chinese plum and provide insights into future functional genomic studies and DNA-informed breeding.
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Affiliation(s)
- Zhenyu Huang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Science, Zhengzhou, Henan, 450009, China
| | - Fei Shen
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yuling Chen
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Science, Zhengzhou, Henan, 450009, China
| | - Ke Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Science, Zhengzhou, Henan, 450009, China
| | - Lirong Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Science, Zhengzhou, Henan, 450009, China
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19
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Lagercrantz U, Billhardt A, Rousku SN, Leso M, Reza SH, Eklund DM. DE-ETIOLATED1 has a role in the circadian clock of the liverwort Marchantia polymorpha. THE NEW PHYTOLOGIST 2021; 232:595-609. [PMID: 34320227 DOI: 10.1111/nph.17653] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
Previous studies of plant circadian clock evolution have often relied on clock models and genes defined in Arabidopsis. These studies identified homologues with seemingly conserved function, as well as frequent gene loss. In the present study, we aimed to identify candidate clock genes in the liverwort Marchantia polymorpha using a more unbiased approach. To identify genes with circadian rhythm we sequenced the transcriptomes of gemmalings in a time series in constant light conditions. Subsequently, we performed functional studies using loss-of-function mutants and gene expression reporters. Among the genes displaying circadian rhythm, a homologue to the transcriptional co-repressor Arabidopsis DE-ETIOLATED1 showed high amplitude and morning phase. Because AtDET1 is arrhythmic and associated with the morning gene function of AtCCA1/LHY, that lack a homologue in liverworts, we functionally studied DET1 in M. polymorpha. We found that the circadian rhythm of MpDET1 expression is disrupted in loss-of-function mutants of core clock genes and putative evening-complex genes. MpDET1 knock-down in turn results in altered circadian rhythm of nyctinastic thallus movement and clock gene expression. We could not detect any effect of MpDET1 knock-down on circadian response to light, suggesting that MpDET1 has a yet unknown function in the M. polymorpha circadian clock.
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Affiliation(s)
- Ulf Lagercrantz
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Anja Billhardt
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Sabine N Rousku
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Martina Leso
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Salim Hossain Reza
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - D Magnus Eklund
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre and the Linnean Centre for Plant Biology in Uppsala, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
- Physiological Botany, Department of Organismal Biology, Linnean Centre for Plant Biology in Uppsala, Uppsala University, Ulls Väg 24E, SE-756 51, Uppsala, Sweden
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20
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Wang X, He Y, Wei H, Wang L. A clock regulatory module is required for salt tolerance and control of heading date in rice. PLANT, CELL & ENVIRONMENT 2021; 44:3283-3301. [PMID: 34402093 DOI: 10.1111/pce.14167] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 07/23/2021] [Accepted: 08/10/2021] [Indexed: 05/23/2023]
Abstract
The circadian clock plays multiple roles in plant stress responses and developmental transition phases. Nevertheless, the underlying molecular mechanisms and individual clock components that coordinately regulate important agronomic traits of rice such as salt tolerance and heading date remain to be elucidated. Here, we identify a rice ternary repressive protein complex composed of OsELF4a, OsELF3-1 and OsLUX, which was designated as OsEC1 in analogy to a similar complex in Arabidopsis. OsELF4a physically interacts with OsELF3-1 and OsELF3-2 in nucleus, whilst OsELF3-1 rather than OsELF3-2 strongly interacts with OsLUX, a Myb-domain containing transcriptional factor. Phenotypic analyses show a role for this complex in heading and salt tolerance. The loss-of-function mutants of OsEC1 exhibit lower survival rate under salt stress and late heading date. Transcriptomic profiling together with biochemical assays identified the GIGANTEA homologue OsGI as a direct transcriptional target of OsEC1. Notably, the osgi-101 mutant, generated by CRISPR/Cas9, is salt tolerant and exhibits early heading date in long day conditions. Together, our findings characterized a transcriptional module in rice composed by the OsEC1 repressing OsGI, which links the circadian clock with salt tolerance and control of heading date.
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Affiliation(s)
- Xiling Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuqing He
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hua Wei
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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21
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Ye J, Wang X, Wang W, Yu H, Ai G, Li C, Sun P, Wang X, Li H, Ouyang B, Zhang J, Zhang Y, Han H, Giovannoni JJ, Fei Z, Ye Z. Genome-wide association study reveals the genetic architecture of 27 agronomic traits in tomato. PLANT PHYSIOLOGY 2021; 186:2078-2092. [PMID: 34618111 PMCID: PMC8331143 DOI: 10.1093/plphys/kiab230] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 05/03/2021] [Indexed: 05/05/2023]
Abstract
Tomato (Solanum lycopersicum) is a highly valuable fruit crop, and yield is one of the most important agronomic traits. However, the genetic architecture underlying tomato yield-related traits has not been fully addressed. Based on ∼4.4 million single nucleotide polymorphisms obtained from 605 diverse accessions, we performed a comprehensive genome-wide association study for 27 agronomic traits in tomato. A total of 239 significant associations corresponding to 129 loci, harboring many previously reported and additional genes related to vegetative and reproductive development, were identified, and these loci explained an average of ∼8.8% of the phenotypic variance. A total of 51 loci associated with 25 traits have been under selection during tomato domestication and improvement. Furthermore, a candidate gene, Sl-ACTIVATED MALATE TRANSPORTER15, that encodes an aluminum-activated malate transporter was functionally characterized and shown to act as a pivotal regulator of leaf stomata formation, thereby affecting photosynthesis and drought resistance. This study provides valuable information for tomato genetic research and breeding.
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Affiliation(s)
- Jie Ye
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853, USA
| | - Xin Wang
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853, USA
| | - Wenqian Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Huiyang Yu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Guo Ai
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Changxing Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Pengya Sun
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Xianyu Wang
- College of Agriculture, Guangxi University, Nanning 530004, China
| | - Hanxia Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Bo Ouyang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Junhong Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuyang Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Heyou Han
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - James J Giovannoni
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853, USA
- U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853, USA
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853, USA
- U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853, USA
| | - Zhibiao Ye
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Author for communication:
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22
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Lu Q, Dockter C, Sirijovski N, Zakhrabekova S, Lundqvist U, Gregersen PL, Hansson M. Analysis of barley mutants ert-c.1 and ert-d.7 reveals two loci with additive effect on plant architecture. PLANTA 2021; 254:9. [PMID: 34148131 PMCID: PMC8215040 DOI: 10.1007/s00425-021-03653-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/29/2021] [Indexed: 05/31/2023]
Abstract
Both mutant ert-c.1 and ert-d.7 carry T2-T3 translocations in the Ert-c gene. Principal coordinate analyses revealed the translocation types and translocation breakpoints. Mutant ert-d.7 is an Ert-c Ert-d double mutant. Mutations in the Ert-c and Ert-d loci are among the most common barley mutations affecting plant architecture. The mutants have various degrees of erect and compact spikes, often accompanied with short and stiff culms. In the current study, complementation tests, linkage mapping, principal coordinate analyses and fine mapping were conducted. We conclude that the original ert-d.7 mutant does not only carry an ert-d mutation but also an ert-c mutation. Combined, mutations in Ert-c and Ert-d cause a pyramid-dense spike phenotype, whereas mutations in only Ert-c or Ert-d give a pyramid and dense phenotype, respectively. Associations between the Ert-c gene and T2-T3 translocations were detected in both mutant ert-c.1 and ert-d.7. Different genetic association patterns indicate different translocation breakpoints in these two mutants. Principal coordinate analysis based on genetic distance and screening of recombinants from all four ends of polymorphic regions was an efficient way to narrow down the region of interest in translocation-involved populations. The Ert-c gene was mapped to the marker interval of 2_0801to1_0224 on 3HL near the centromere. The results illuminate a complex connection between two single genes having additive effects on barley spike architecture and will facilitate the identification of the Ert-c and Ert-d genes.
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Affiliation(s)
- Qiongxian Lu
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, 1799, Copenhagen V, Denmark
| | - Christoph Dockter
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, 1799, Copenhagen V, Denmark
| | - Nick Sirijovski
- Department of Biology, Lund University, Sölvegatan 35, 22362, Lund, Sweden
| | | | - Udda Lundqvist
- Nordic Genetic Resource Centre (NordGen), Smedjevägen 3, 23053, Alnarp, Sweden
| | - Per L Gregersen
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Mats Hansson
- Department of Biology, Lund University, Sölvegatan 35, 22362, Lund, Sweden.
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23
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Guo M, Zhang Z, Li S, Lian Q, Fu P, He Y, Qiao J, Xu K, Liu L, Wu M, Du Z, Li S, Wang J, Shao P, Yu Q, Xu G, Li D, Wang Y, Tian S, Zhao J, Feng X, Li R, Jiang W, Zhao X. Genomic analyses of diverse wild and cultivated accessions provide insights into the evolutionary history of jujube. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:517-531. [PMID: 32946650 PMCID: PMC7955879 DOI: 10.1111/pbi.13480] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 07/31/2020] [Accepted: 09/07/2020] [Indexed: 05/07/2023]
Abstract
The Chinese jujube (Ziziphus jujuba Mill.), a member of the Rhamnaceae family, is an important perennial fruit tree crop of substantial economic, ecological and nutritional value, and is also used as a traditional herbal medicine. Here, we report the resequencing of 493 jujube accessions, including 202 wild and 291 cultivated accessions at >16× depth. Our population genomic analyses revealed that the Shanxi-Shaanxi area of China was jujube's primary domestication centre and that jujube was then disseminated into East China before finally extending into South China. Divergence events analysis indicated that Ziziphus acidojujuba and Ziziphus jujuba diverged around 2.7 Mya, suggesting the interesting possibility that a long pre-domestication period may have occurred prior to human intervention. Using the large genetic polymorphism data set, we identified a 15-bp tandem insertion in the promoter of the jujube ortholog of the POLLEN DEFECTIVE IN GUIDANCE 1 (POD1) gene, which was strongly associated with seed-setting rate. Integrating genome-wide association study (GWAS), transcriptome data, expression analysis and transgenic validation in tomato, we identified a DA3/UBIQUITIN-SPECIFIC PROTEASE 14 (UBP14) ortholog, which negatively regulate fruit weight in jujube. We also identified candidate genes, which have likely influenced the selection of fruit sweetness and crispness texture traits among fresh and dry jujubes. Our study not only illuminates the genetic basis of jujube evolution and domestication and provides a deep and rich genomic resource to facilitate both crop improvement and hypothesis-driven basic research, but also identifies multiple agriculturally important genes for this unique perennial tree fruit species.
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Affiliation(s)
- Mingxin Guo
- College of Life SciencesLuoyang Normal UniversityLuoyangChina
- Jujube Research CenterLuoyang Normal UniversityLuoyangChina
| | | | - Shipeng Li
- College of Life SciencesLuoyang Normal UniversityLuoyangChina
- Jujube Research CenterLuoyang Normal UniversityLuoyangChina
| | - Qun Lian
- Genome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Pengcheng Fu
- College of Life SciencesLuoyang Normal UniversityLuoyangChina
| | - Yali He
- College of Life SciencesLuoyang Normal UniversityLuoyangChina
| | - Jinxin Qiao
- College of Life SciencesLuoyang Normal UniversityLuoyangChina
| | - Keke Xu
- College of Life SciencesLuoyang Normal UniversityLuoyangChina
| | - Linpei Liu
- College of Life SciencesLuoyang Normal UniversityLuoyangChina
| | - Miaoyan Wu
- College of Life SciencesLuoyang Normal UniversityLuoyangChina
| | - Zheran Du
- College of Life SciencesLuoyang Normal UniversityLuoyangChina
| | - Sunan Li
- College of Life SciencesLuoyang Normal UniversityLuoyangChina
| | - Junjie Wang
- College of Life SciencesLuoyang Normal UniversityLuoyangChina
| | - Peiyin Shao
- College of Life SciencesLuoyang Normal UniversityLuoyangChina
| | - Qiang Yu
- College of Life SciencesLuoyang Normal UniversityLuoyangChina
| | - Gan Xu
- College of Life SciencesLuoyang Normal UniversityLuoyangChina
| | - Dengke Li
- Pomology InstituteShanxi Academy of Agricultural SciencesTaiguChina
| | - Yongkang Wang
- Pomology InstituteShanxi Academy of Agricultural SciencesTaiguChina
| | - Shan Tian
- College of Life SciencesLuoyang Normal UniversityLuoyangChina
- Jujube Research CenterLuoyang Normal UniversityLuoyangChina
| | - Jing Zhao
- Novogene Bioinformatics InstituteBeijingChina
| | - Xue Feng
- Novogene Bioinformatics InstituteBeijingChina
| | - Ruiqiang Li
- Novogene Bioinformatics InstituteBeijingChina
| | | | - Xusheng Zhao
- College of Life SciencesLuoyang Normal UniversityLuoyangChina
- Jujube Research CenterLuoyang Normal UniversityLuoyangChina
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24
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Bu T, Lu S, Wang K, Dong L, Li S, Xie Q, Xu X, Cheng Q, Chen L, Fang C, Li H, Liu B, Weller JL, Kong F. A critical role of the soybean evening complex in the control of photoperiod sensitivity and adaptation. Proc Natl Acad Sci U S A 2021; 118:e2010241118. [PMID: 33558416 PMCID: PMC7923351 DOI: 10.1073/pnas.2010241118] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Photoperiod sensitivity is a key factor in plant adaptation and crop production. In the short-day plant soybean, adaptation to low latitude environments is provided by mutations at the J locus, which confer extended flowering phase and thereby improve yield. The identity of J as an ortholog of Arabidopsis ELF3, a component of the circadian evening complex (EC), implies that orthologs of other EC components may have similar roles. Here we show that the two soybean homeologs of LUX ARRYTHMO interact with J to form a soybean EC. Characterization of mutants reveals that these genes are highly redundant in function but together are critical for flowering under short day, where the lux1 lux2 double mutant shows extremely late flowering and a massively extended flowering phase. This phenotype exceeds that of any soybean flowering mutant reported to date, and is strongly reminiscent of the "Maryland Mammoth" tobacco mutant that featured in the seminal 1920 study of plant photoperiodism by Garner and Allard [W. W. Garner, H. A. Allard, J. Agric. Res. 18, 553-606 (1920)]. We further demonstrate that the J-LUX complex suppresses transcription of the key flowering repressor E1 and its two homologs via LUX binding sites in their promoters. These results indicate that the EC-E1 interaction has a central role in soybean photoperiod sensitivity, a phenomenon also first described by Garner and Allard. EC and E1 family genes may therefore constitute key targets for customized breeding of soybean varieties with precise flowering time adaptation, either by introgression of natural variation or generation of new mutants by gene editing.
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Affiliation(s)
- Tiantian Bu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Sijia Lu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Kai Wang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Lidong Dong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Shilin Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 475004 Kaifeng, China
| | - Qiguang Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 475004 Kaifeng, China
| | - Xiaodong Xu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, 475004 Kaifeng, China
| | - Qun Cheng
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Liyu Chen
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Chao Fang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Haiyang Li
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
| | - Baohui Liu
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081 Harbin, China
| | - James L Weller
- School of Natural Sciences, University of Tasmania, Hobart, 7001 TAS, Australia
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, 510006 Guangzhou, China;
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, 150081 Harbin, China
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25
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Maric A, Mas P. Chromatin Dynamics and Transcriptional Control of Circadian Rhythms in Arabidopsis. Genes (Basel) 2020; 11:E1170. [PMID: 33036236 PMCID: PMC7601625 DOI: 10.3390/genes11101170] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/01/2020] [Accepted: 10/04/2020] [Indexed: 02/06/2023] Open
Abstract
Circadian rhythms pervade nearly all aspects of plant growth, physiology, and development. Generation of the rhythms relies on an endogenous timing system or circadian clock that generates 24-hour oscillations in multiple rhythmic outputs. At its bases, the plant circadian function relies on dynamic interactive networks of clock components that regulate each other to generate rhythms at specific phases during the day and night. From the initial discovery more than 13 years ago of a parallelism between the oscillations in chromatin status and the transcriptional rhythms of an Arabidopsis clock gene, a number of studies have later expanded considerably our view on the circadian epigenome and transcriptome landscapes. Here, we describe the most recent identification of chromatin-related factors that are able to directly interact with Arabidopsis clock proteins to shape the transcriptional waveforms of circadian gene expression and clock outputs. We discuss how changes in chromatin marks associate with transcript initiation, elongation, and the rhythms of nascent RNAs, and speculate on future interesting research directions in the field.
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Affiliation(s)
- Aida Maric
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain;
| | - Paloma Mas
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain;
- Consejo Superior de Investigaciones Científicas (CSIC), 08028 Barcelona, Spain
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26
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Müller LM, Mombaerts L, Pankin A, Davis SJ, Webb AAR, Goncalves J, von Korff M. Differential Effects of Day/Night Cues and the Circadian Clock on the Barley Transcriptome. PLANT PHYSIOLOGY 2020; 183:765-779. [PMID: 32229608 PMCID: PMC7271788 DOI: 10.1104/pp.19.01411] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 03/04/2020] [Indexed: 05/05/2023]
Abstract
The circadian clock is a complex transcriptional network that regulates gene expression in anticipation of the day/night cycle and controls agronomic traits in plants. However, in crops, how the internal clock and day/night cues affect the transcriptome remains poorly understood. We analyzed the diel and circadian leaf transcriptomes in the barley (Hordeum vulgare) cultivar 'Bowman' and derived introgression lines harboring mutations in EARLY FLOWERING3 (ELF3), LUX ARRHYTHMO1 (LUX1), and EARLY MATURITY7 (EAM7). The elf3 and lux1 mutants exhibited abolished circadian transcriptome oscillations under constant conditions, whereas eam7 maintained oscillations of ≈30% of the circadian transcriptome. However, day/night cues fully restored transcript oscillations in all three mutants and thus compensated for a disrupted oscillator in the arrhythmic barley clock mutants elf3 and lux1 Nevertheless, elf3, but not lux1, affected the phase of the diel oscillating transcriptome and thus the integration of external cues into the clock. Using dynamical modeling, we predicted a structure of the barley circadian oscillator and interactions of its individual components with day/night cues. Our findings provide a valuable resource for exploring the function and output targets of the circadian clock and for further investigations into the diel and circadian control of the barley transcriptome.
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Affiliation(s)
- Lukas M Müller
- Institute for Plant Genetics, Heinrich-Heine University Düsseldorf, Düsseldorf 40225, Germany
- Max-Planck-Institute for Plant Breeding Research, Cologne 50829, Germany
| | | | - Artem Pankin
- Institute for Plant Genetics, Heinrich-Heine University Düsseldorf, Düsseldorf 40225, Germany
- Max-Planck-Institute for Plant Breeding Research, Cologne 50829, Germany
- Cluster of Excellence on Plant Sciences, "SMART Plants for Tomorrow's Needs," Heinrich-Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Seth J Davis
- Max-Planck-Institute for Plant Breeding Research, Cologne 50829, Germany
- Department of Department of Biology, University of York, York YO10 5DD, United Kingdom
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng 15 475004, China
| | - Alex A R Webb
- Circadian Signal Transduction, Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Jorge Goncalves
- Systems Control Group, University of Luxembourg, 1009 Luxembourg
| | - Maria von Korff
- Institute for Plant Genetics, Heinrich-Heine University Düsseldorf, Düsseldorf 40225, Germany
- Max-Planck-Institute for Plant Breeding Research, Cologne 50829, Germany
- Cluster of Excellence on Plant Sciences, "SMART Plants for Tomorrow's Needs," Heinrich-Heine University Düsseldorf, Düsseldorf 40225, Germany
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27
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Lagercrantz U, Billhardt A, Rousku SN, Ljung K, Eklund DM. Nyctinastic thallus movement in the liverwort Marchantia polymorpha is regulated by a circadian clock. Sci Rep 2020; 10:8658. [PMID: 32457350 PMCID: PMC7251115 DOI: 10.1038/s41598-020-65372-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 04/29/2020] [Indexed: 11/24/2022] Open
Abstract
The circadian clock coordinates an organism's growth, development and physiology with environmental factors. One illuminating example is the rhythmic growth of hypocotyls and cotyledons in Arabidopsis thaliana. Such daily oscillations in leaf position are often referred to as sleep movements or nyctinasty. Here, we report that plantlets of the liverwort Marchantia polymorpha show analogous rhythmic movements of thallus lobes, and that the circadian clock controls this rhythm, with auxin a likely output pathway affecting these movements. The mechanisms of this circadian clock are partly conserved as compared to angiosperms, with homologs to the core clock genes PRR, RVE and TOC1 forming a core transcriptional feedback loop also in M. polymorpha.
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Affiliation(s)
- Ulf Lagercrantz
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
- The Linnean Centre for Plant Biology in Uppsala, Uppsala, Sweden
| | - Anja Billhardt
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
- The Linnean Centre for Plant Biology in Uppsala, Uppsala, Sweden
| | - Sabine N Rousku
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
- The Linnean Centre for Plant Biology in Uppsala, Uppsala, Sweden
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umeå, Sweden
| | - D Magnus Eklund
- Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden.
- The Linnean Centre for Plant Biology in Uppsala, Uppsala, Sweden.
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28
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Abstract
Circadian gene expression oscillates over a 24-h period and regulates many genes critical for growth and development in plants. A key component of the circadian clock is the Evening Complex (EC), a transcriptional repressor complex that contains the proteins LUX ARRHYTHMO, EARLY FLOWERING 3, and EARLY FLOWERING 4 (ELF4). By repressing the expression of genes such as PHYTOCHROME INTERACTING FACTOR4 (PIF4), the EC reduces elongation growth. At warmer temperatures, EC activity is lost, promoting thermomorphogenesis via PIF4 expression. The molecular mechanisms underlying EC activity are not well understood. Here, we combined structural studies with extensive in vitro assays to determine the molecular mechanisms of the temperature-dependent EC binding to DNA and demonstrate the critical role of ELF4 in this activity. The Evening Complex (EC), composed of the DNA binding protein LUX ARRHYTHMO (LUX) and two additional proteins EARLY FLOWERING 3 (ELF3) and ELF4, is a transcriptional repressor complex and a core component of the plant circadian clock. In addition to maintaining oscillations in clock gene expression, the EC also participates in temperature and light entrainment, acting as an important environmental sensor and conveying this information to growth and developmental pathways. However, the molecular basis for EC DNA binding specificity and temperature-dependent activity were not known. Here, we solved the structure of the DNA binding domain of LUX in complex with DNA. Residues critical for high-affinity binding and direct base readout were determined and tested via site-directed mutagenesis in vitro and in vivo. Using extensive in vitro DNA binding assays of LUX alone and in complex with ELF3 and ELF4, we demonstrate that, while LUX alone binds DNA with high affinity, the LUX–ELF3 complex is a relatively poor binder of DNA. ELF4 restores binding to the complex. In vitro, the full EC is able to act as a direct thermosensor, with stronger DNA binding at 4 °C and weaker binding at 27 °C. In addition, an excess of ELF4 is able to restore EC binding even at 27 °C. Taken together, these data suggest that ELF4 is a key modulator of thermosensitive EC activity.
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29
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Zha P, Liu S, Li Y, Ma T, Yang L, Jing Y, Lin R. The Evening Complex and the Chromatin-Remodeling Factor PICKLE Coordinately Control Seed Dormancy by Directly Repressing DOG1 in Arabidopsis. PLANT COMMUNICATIONS 2020; 1:100011. [PMID: 33404551 PMCID: PMC7748002 DOI: 10.1016/j.xplc.2019.100011] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 11/23/2019] [Accepted: 11/28/2019] [Indexed: 05/22/2023]
Abstract
Primary seed dormancy is acquired during seed development and maturation, which is important for plant fitness and survival. DELAY OF GERMINATION1 (DOG1) plays a critical role in inducing seed dormancy. DOG1 expression increases rapidly during seed development, but the precise mechanism underlying this process remains elusive. In this study, we showed that mutants with a loss or reduced function of the chromatin-remodeling factor PICKLE (PKL) exhibit increased seed dormancy. PKL associates with DOG1 chromatin and inhibits its transcription. We found that PKL physically interacts with LUX ARRHYTHMO (LUX), a member of the evening complex (EC) of the circadian clock. Furthermore, LUX directly binds to a specific coding sequence of DOG1, and DOG1 acts genetically downstream of PKL and LUX. Mutations in either LUX or EARLY FLOWERING3 (ELF3) encoding another member of the EC led to increased DOG1 expression and enhanced seed dormancy. Surprisingly, these phenotypes were abolished when the parent plants were grown under continuous light. In addition, we observed that loss of function of either PKL or LUX decreased H3K27me3 levels at the DOG1 locus. Taken together, our study reveals a regulatory mechanism in which EC proteins coordinate with PKL to transmit circadian signals for directly regulating DOG1 expression and seed dormancy during seed development.
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Affiliation(s)
- Ping Zha
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Shuangrong Liu
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Li
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tingting Ma
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Liwen Yang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yanjun Jing
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Corresponding author
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30
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Anwer MU, Davis A, Davis SJ, Quint M. Photoperiod sensing of the circadian clock is controlled by EARLY FLOWERING 3 and GIGANTEA. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1397-1410. [PMID: 31694066 DOI: 10.1111/tpj.14604] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/26/2019] [Accepted: 10/28/2019] [Indexed: 05/22/2023]
Abstract
ELF3 and GI are two important components of the Arabidopsis circadian clock. They are not only essential for the oscillator function but are also pivotal in mediating light inputs to the oscillator. Lack of either results in a defective oscillator causing severely compromised output pathways, such as photoperiodic flowering and hypocotyl elongation. Although single loss of function mutants of ELF3 and GI have been well studied, their genetic interaction remains unclear. We generated an elf3 gi double mutant to study their genetic relationship in clock-controlled growth and phase transition phenotypes. We found that ELF3 and GI repress growth differentially during the night and the day, respectively. Circadian clock assays revealed that ELF3 and GI are essential that enable the oscillator to synchronize the endogenous cellular mechanisms to external environmental signals. In their absence, the circadian oscillator fails to synchronize to the light-dark cycles even under diurnal conditions. Consequently, clock-mediated photoperiod-responsive growth and development are completely lost in plants lacking both genes, suggesting that ELF3 and GI together convey photoperiod sensing to the central oscillator. Since ELF3 and GI are conserved across flowering plants and represent important breeding and domestication targets, our data highlight the possibility of developing photoperiod-insensitive crops by adjusting the allelic combination of these two key genes.
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Affiliation(s)
- Muhammad Usman Anwer
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, 06120, Halle (Saale), Germany
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Amanda Davis
- Department of Biology, University of York, Heslington, York, YO10 5DD, United Kingdom
| | - Seth Jon Davis
- Department of Biology, University of York, Heslington, York, YO10 5DD, United Kingdom
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Marcel Quint
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, 06120, Halle (Saale), Germany
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
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Anwer MU, Davis A, Davis SJ, Quint M. Photoperiod sensing of the circadian clock is controlled by EARLY FLOWERING 3 and GIGANTEA. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1397-1410. [PMID: 31694066 DOI: 10.1101/321794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/26/2019] [Accepted: 10/28/2019] [Indexed: 05/27/2023]
Abstract
ELF3 and GI are two important components of the Arabidopsis circadian clock. They are not only essential for the oscillator function but are also pivotal in mediating light inputs to the oscillator. Lack of either results in a defective oscillator causing severely compromised output pathways, such as photoperiodic flowering and hypocotyl elongation. Although single loss of function mutants of ELF3 and GI have been well studied, their genetic interaction remains unclear. We generated an elf3 gi double mutant to study their genetic relationship in clock-controlled growth and phase transition phenotypes. We found that ELF3 and GI repress growth differentially during the night and the day, respectively. Circadian clock assays revealed that ELF3 and GI are essential that enable the oscillator to synchronize the endogenous cellular mechanisms to external environmental signals. In their absence, the circadian oscillator fails to synchronize to the light-dark cycles even under diurnal conditions. Consequently, clock-mediated photoperiod-responsive growth and development are completely lost in plants lacking both genes, suggesting that ELF3 and GI together convey photoperiod sensing to the central oscillator. Since ELF3 and GI are conserved across flowering plants and represent important breeding and domestication targets, our data highlight the possibility of developing photoperiod-insensitive crops by adjusting the allelic combination of these two key genes.
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Affiliation(s)
- Muhammad Usman Anwer
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, 06120, Halle (Saale), Germany
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Amanda Davis
- Department of Biology, University of York, Heslington, York, YO10 5DD, United Kingdom
| | - Seth Jon Davis
- Department of Biology, University of York, Heslington, York, YO10 5DD, United Kingdom
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Marcel Quint
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, 06120, Halle (Saale), Germany
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
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Tong M, Lee K, Ezer D, Cortijo S, Jung J, Charoensawan V, Box MS, Jaeger KE, Takahashi N, Mas P, Wigge PA, Seo PJ. The Evening Complex Establishes Repressive Chromatin Domains Via H2A.Z Deposition. PLANT PHYSIOLOGY 2020; 182:612-625. [PMID: 31712305 PMCID: PMC6945876 DOI: 10.1104/pp.19.00881] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/19/2019] [Indexed: 05/07/2023]
Abstract
The Evening Complex (EC) is a core component of the Arabidopsis (Arabidopsis thaliana) circadian clock, which represses target gene expression at the end of the day and integrates temperature information to coordinate environmental and endogenous signals. Here we show that the EC induces repressive chromatin structure to regulate the evening transcriptome. The EC component ELF3 directly interacts with a protein from the SWI2/SNF2-RELATED (SWR1) complex to control deposition of H2A.Z-nucleosomes at the EC target genes. SWR1 components display circadian oscillation in gene expression with a peak at dusk. In turn, SWR1 is required for the circadian clockwork, as defects in SWR1 activity alter morning-expressed genes. The EC-SWR1 complex binds to the loci of the core clock genes PSEUDO-RESPONSE REGULATOR7 (PRR7) and PRR9 and catalyzes deposition of nucleosomes containing the histone variant H2A.Z coincident with the repression of these genes at dusk. This provides a mechanism by which the circadian clock temporally establishes repressive chromatin domains to shape oscillatory gene expression around dusk.
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Affiliation(s)
- Meixuezi Tong
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Kyounghee Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Daphne Ezer
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Sandra Cortijo
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Jaehoon Jung
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Varodom Charoensawan
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Mathew S Box
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Katja E Jaeger
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Nozomu Takahashi
- Center for Research in Agricultural Genomics, Consortium Consejo Superior de Investigaciones Cientificas-Institute of Agrifood Research and Technology-Universitat Autònoma de Barcelona-Universidad de Barcelona, Parc de Recerca Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallés), Barcelona 08193, Spain
| | - Paloma Mas
- Center for Research in Agricultural Genomics, Consortium Consejo Superior de Investigaciones Cientificas-Institute of Agrifood Research and Technology-Universitat Autònoma de Barcelona-Universidad de Barcelona, Parc de Recerca Universitat Autònoma de Barcelona, Bellaterra (Cerdanyola del Vallés), Barcelona 08193, Spain
- Consejo Superior de Investigaciones Científicas, Barcelona 08193, Spain
| | - Philip A Wigge
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
- Leibniz-Institut für Gemüse- und Zierpflanzenbau, 14979 Großbeeren, Germany
| | - Pil Joon Seo
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea
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Zhang Y, Bo C, Wang L. Novel Crosstalks between Circadian Clock and Jasmonic Acid Pathway Finely Coordinate the Tradeoff among Plant Growth, Senescence and Defense. Int J Mol Sci 2019; 20:ijms20215254. [PMID: 31652760 PMCID: PMC6862349 DOI: 10.3390/ijms20215254] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 01/31/2023] Open
Abstract
Circadian clock not only functions as a cellular time-keeping mechanism, but also acts as a master regulator to coordinate the tradeoff between plant growth and defense in higher plants by timing a few kinds of phytohormone biosynthesis and signaling, including jasmonic acid (JA). Notably, circadian clock and JA pathway have recently been shown to intertwine with each other to ensure and optimize the plant fitness in an ever-changing environment. It has clearly demonstrated that there are multiple crosstalk pathways between circadian clock and JA at both transcriptional and post-transcriptional levels. In this scenario, circadian clock temporally modulates JA-mediated plant development events, herbivory resistance and susceptibility to pathogen. By contrast, the JA signaling regulates clock activity in a feedback manner. In this review, we summarized the cross networks between circadian clock and JA pathway at both transcriptional and post-transcriptional levels. We proposed that the novel crosstalks between circadian clock and JA pathway not only benefit for the understanding the JA-associated circadian outputs including leaf senescence, biotic, and abiotic defenses, but also put timing as a new key factor to investigate JA pathway in the future.
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Affiliation(s)
- Yuanyuan Zhang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Cunpei Bo
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
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34
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Babla M, Cai S, Chen G, Tissue DT, Cazzonelli CI, Chen ZH. Molecular Evolution and Interaction of Membrane Transport and Photoreception in Plants. Front Genet 2019; 10:956. [PMID: 31681411 PMCID: PMC6797626 DOI: 10.3389/fgene.2019.00956] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/06/2019] [Indexed: 12/20/2022] Open
Abstract
Light is a vital regulator that controls physiological and cellular responses to regulate plant growth, development, yield, and quality. Light is the driving force for electron and ion transport in the thylakoid membrane and other membranes of plant cells. In different plant species and cell types, light activates photoreceptors, thereby modulating plasma membrane transport. Plants maximize their growth and photosynthesis by facilitating the coordinated regulation of ion channels, pumps, and co-transporters across membranes to fine-tune nutrient uptake. The signal-transducing functions associated with membrane transporters, pumps, and channels impart a complex array of mechanisms to regulate plant responses to light. The identification of light responsive membrane transport components and understanding of their potential interaction with photoreceptors will elucidate how light-activated signaling pathways optimize plant growth, production, and nutrition to the prevailing environmental changes. This review summarizes the mechanisms underlying the physiological and molecular regulations of light-induced membrane transport and their potential interaction with photoreceptors in a plant evolutionary and nutrition context. It will shed new light on plant ecological conservation as well as agricultural production and crop quality, bringing potential nutrition and health benefits to humans and animals.
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Affiliation(s)
- Mohammad Babla
- School of Science and Health, Western Sydney University, Penrith, NSW, Australia
| | - Shengguan Cai
- School of Science and Health, Western Sydney University, Penrith, NSW, Australia
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Guang Chen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - David T. Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | | | - Zhong-Hua Chen
- School of Science and Health, Western Sydney University, Penrith, NSW, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
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35
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Kanesaka Y, Okada M, Ito S, Oyama T. Monitoring single-cell bioluminescence of Arabidopsis leaves to quantitatively evaluate the efficiency of a transiently introduced CRISPR/Cas9 system targeting the circadian clock gene ELF3. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2019; 36:187-193. [PMID: 31768121 PMCID: PMC6854346 DOI: 10.5511/plantbiotechnology.19.0531a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 05/31/2019] [Indexed: 05/04/2023]
Abstract
The rapid assessment of gene function is crucial in biological research. The CRISPR/Cas9 system is widely used as a tool for targeted gene editing in many organisms including plants. Previously, we established a transient gene expression system for investigating cellular circadian rhythms in duckweed. In this system, circadian reporters and clock gene effectors-such as overexpressors, RNA interference (RNAi), and CRISPR/Cas9-were introduced into duckweed cells using a particle bombardment method. In the present study, we applied the CRISPR/Cas9 system at a single cell level to Arabidopsis thaliana, a model organism in plant biology. To evaluate the mutation induction efficiency of the system, we monitored single-cell bioluminescence after application of the CRISPR/Cas9 system targeting the ELF3 gene, which is essential for robust circadian rhythmicity. We evaluated the mutation induction efficiency by determining the proportion of cells with impaired circadian rhythms. Three single guide RNAs (sgRNAs) were designed, and the proportion of arrhythmic cells following their use ranged from 32 to 91%. A comparison of the mutation induction efficiencies of diploid and tetraploid Arabidopsis suggested that endoreduplication had a slight effect on efficiency. Taken together, our results demonstrate that the transiently introduced CRISPR/Cas9 system is useful for rapidly assessing the physiological function of target genes in Arabidopsis cells.
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Affiliation(s)
| | - Masaaki Okada
- Department of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Shogo Ito
- Department of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Tokitaka Oyama
- Department of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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36
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Abstract
The circadian oscillator is a complex network of interconnected feedback loops that regulates a wide range of physiological processes. Indeed, variation in clock genes has been implicated in an array of plant environmental adaptations, including growth regulation, photoperiodic control of flowering, and responses to abiotic and biotic stress. Although the clock is buffered against the environment, maintaining roughly 24-h rhythms across a wide range of conditions, it can also be reset by environmental cues such as acute changes in light or temperature. These competing demands may help explain the complexity of the links between the circadian clock network and environmental response pathways. Here, we discuss our current understanding of the clock and its interactions with light and temperature-signaling pathways. We also describe different clock gene alleles that have been implicated in the domestication of important staple crops.
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Affiliation(s)
- Nicky Creux
- Department of Plant Biology, University of California, Davis, California 95616, USA
| | - Stacey Harmer
- Department of Plant Biology, University of California, Davis, California 95616, USA
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37
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Thines B, Parlan EV, Fulton EC. Circadian Network Interactions with Jasmonate Signaling and Defense. PLANTS 2019; 8:plants8080252. [PMID: 31357700 PMCID: PMC6724144 DOI: 10.3390/plants8080252] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/21/2019] [Accepted: 07/23/2019] [Indexed: 01/11/2023]
Abstract
Plants experience specific stresses at particular, but predictable, times of the day. The circadian clock is a molecular oscillator that increases plant survival by timing internal processes to optimally match these environmental challenges. Clock regulation of jasmonic acid (JA) action is important for effective defenses against fungal pathogens and generalist herbivores in multiple plant species. Endogenous JA levels are rhythmic and under clock control with peak JA abundance during the day, a time when plants are more likely to experience certain types of biotic stresses. The expression of many JA biosynthesis, signaling, and response genes is transcriptionally controlled by the clock and timed through direct connections with core clock proteins. For example, the promoter of Arabidopsis transcription factor MYC2, a master regulator for JA signaling, is directly bound by the clock evening complex (EC) to negatively affect JA processes, including leaf senescence, at the end of the day. Also, tobacco ZEITLUPE, a circadian photoreceptor, binds directly to JAZ proteins and stimulates their degradation with resulting effects on JA root-based defenses. Collectively, a model where JA processes are embedded within the circadian network at multiple levels is emerging, and these connections to the circadian network suggest multiple avenues for future research.
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Affiliation(s)
- Bryan Thines
- Biology Department, University of Puget Sound, 1500 North Warner St., Tacoma, WA 98416, USA.
| | - Emily V Parlan
- Biology Department, University of Puget Sound, 1500 North Warner St., Tacoma, WA 98416, USA
| | - Elena C Fulton
- Biology Department, University of Puget Sound, 1500 North Warner St., Tacoma, WA 98416, USA
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38
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Lee K, Mas P, Seo PJ. The EC-HDA9 complex rhythmically regulates histone acetylation at the TOC1 promoter in Arabidopsis. Commun Biol 2019; 2:143. [PMID: 31044168 PMCID: PMC6478914 DOI: 10.1038/s42003-019-0377-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 03/06/2019] [Indexed: 12/13/2022] Open
Abstract
Circadian clocks are conserved time-keeper mechanisms in some prokaryotes and higher eukaryotes. Chromatin modification is emerging as key regulatory mechanism for refining core clock gene expression. Rhythmic changes in histone marks are closely associated to the TIMING OF CAB EXPRESSION 1 (TOC1) Arabidopsis clock gene. However, the chromatin-related modifiers responsible for these marks remain largely unknown. Here, we uncover that the chromatin modifier HISTONE DEACETYLASE 9 (HDA9) and the Evening complex (EC) component EARLY FLOWERING 3 (ELF3) directly interact to regulate the declining phase of TOC1 after its peak expression. We found that HDA9 specifically binds to the TOC1 promoter through the interaction with ELF3. The EC-HDA9 complex promotes H3 deacetylation at the TOC1 locus, contributing to suppressing TOC1 expression during the night, the time of EC function. Therefore, we have identified the mechanism by which the circadian clock intertwines with chromatin-related components to shape the circadian waveforms of gene expression in Arabidopsis.
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Affiliation(s)
- Kyounghee Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419 Republic of Korea
| | - Paloma Mas
- Center for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB-UB, Parc de Recerca Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Pil Joon Seo
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419 Republic of Korea
- Department of Chemistry, Seoul National University, Seoul, 08826 Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
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Feke A, Liu W, Hong J, Li MW, Lee CM, Zhou EK, Gendron JM. Decoys provide a scalable platform for the identification of plant E3 ubiquitin ligases that regulate circadian function. eLife 2019; 8:44558. [PMID: 30950791 PMCID: PMC6483598 DOI: 10.7554/elife.44558] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/04/2019] [Indexed: 12/30/2022] Open
Abstract
The circadian clock relies on regulated degradation of clock proteins to maintain rhythmicity. Despite this, we know few components that mediate protein degradation. This is due to high levels of functional redundancy within plant E3 ubiquitin ligase families. In order to overcome this issue and discover E3 ubiquitin ligases that control circadian function, we generated a library of transgenic Arabidopsis plants expressing dominant-negative ‘decoy’ E3 ubiquitin ligases. We determined their effects on the circadian clock and identified dozens of new potential regulators of circadian function. To demonstrate the potency of the decoy screening methodology to overcome redundancy and identify bona fide clock regulators, we performed follow-up studies on MAC3A (PUB59) and MAC3B (PUB60). We show that they redundantly control circadian period by regulating splicing. This work demonstrates the viability of ubiquitin ligase decoys as a screening platform to overcome genetic challenges and discover E3 ubiquitin ligases that regulate plant development. Plants have an internal time keeper known as the circadian clock that operates in 24-hour cycles to coordinate the plants behaviors with the environment. The clock is made of many different proteins and plants carefully control when they make and destroy these proteins to regulate the cycle. Inside plant cells, enzymes known as E3 ubiquitin ligases determine which proteins are destroyed by labelling target proteins with a small tag. Plants have hundreds of different E3 ubiquitin ligases, leading to overlaps in the roles the different enzymes play. These overlaps make it difficult to identify the specific E3 ubiquitin ligases that are involved in a particular process. As a result, only few E3 ubiquitin ligases implicated in the circadian clock have been identified so far. A small weed known as Arabidopsis is often used in research studies because it grows quickly and the genes can be easily manipulated. Here, Feke et al. set out to develop a new tool to identify the specific E3 ubiquitin ligases involved in regulating the circadian clock in Arabidopsis. The team created a library of hundreds of Arabidopsis plants producing different decoy E3 ubiquitin ligases that retained their ability to bind to target proteins but were unable to degrade them. Nearly a quarter of the E3 ligases found in Arabidopsis were represented in this library. The decoy enzymes protected the target proteins from being degraded by the normal E3 ubiquitin ligases, resulting in the library plants having presumably higher levels of these target proteins compared to normal Arabidopsis plants. By tracking circadian rhythms in these plants, the team was able to identify the individual E3 ligases that control the circadian clock. The experiments revealed several E3 ligases that may regulate the circadian clock, including two enzymes called MAC3A and MAC3B. Further experiments demonstrated that MAC3A and MAC3B have similar roles in regulating the circadian clock and can compensate for the absence of the other. The library of Arabidopsis plants generated by Feke et al. is now available for other researchers to use in their studies. In the future this approach could be adapted to make similar libraries for crops and other plants that have even more E3 ligase enzymes than Arabidopsis.
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Affiliation(s)
- Ann Feke
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Wei Liu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Jing Hong
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States.,School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Man-Wah Li
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Chin-Mei Lee
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Elton K Zhou
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | - Joshua M Gendron
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
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40
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Itoh H, Tanaka Y, Izawa T. Genetic Relationship Between Phytochromes and OsELF3-1 Reveals the Mode of Regulation for the Suppression of Phytochrome Signaling in Rice. PLANT & CELL PHYSIOLOGY 2019; 60:549-561. [PMID: 30476313 DOI: 10.1093/pcp/pcy225] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/20/2018] [Indexed: 06/09/2023]
Abstract
EARLY FLOWERING3 (ELF3) functions as a night-time repressor required for sustaining circadian rhythms and co-ordinating growth and development in various plant species. The rice genome carries two ELF3 homologs, namely OsELF3-1 and OsELF3-2. Previous studies have suggested that OsELF3-1 has a predominant role in controlling rice photoperiodic flowering, while also contributing to the transcriptional regulation of rice floral regulators expressed in the morning. However, OsELF3-1 has not been functionally characterized. Here, we observed that the oself3-1 mutation suppresses the photoperiod-insensitive early flowering of photoperiod sensitivity5 (se5), which is a chromophore-deficient rice mutant. Detailed analyses of the se5oself3-1 double mutant revealed the recovery of the phytochrome-dependent expression of Grain number, plant height, and heading date7 (Ghd7), a floral repressor, and Light-harvesting chlorophyll a/b binding protein (Lhcb) genes. Although the oself3-1 mutation recovered Ghd7 expression in the se5 background, there was a lack of Ghd7 expression in the phyAphyBphyC triple mutant background. These observations suggest that OsELF3-1 represses Ghd7 expression by inhibiting the phytochrome signaling pathway. Comparative genome analyses indicated that OsELF3-1 was produced via gene duplication events in Oryza species, and that it is expressed throughout the day. A comparison between the oself3-1 mutant and transgenic rice lines in which OsELF3-1 and OsELF3-2 are simultaneously silenced uncovered a role for OsELF3-1 in addition to the canonical ELF3 function as an evolutionarily conserved role for a night-time repressor that regulates the rice circadian clock. Our study confirmed that an ELF3 paralog, OsELF3-1, had a unique role involving the suppression of phytochrome signaling.
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Affiliation(s)
- Hironori Itoh
- National Agriculture and Food Research Organization, Institute of Crop Science, NARO (NICS), Kannondai 2-1-2, Tsukuba, Japan
- Functional Plant Research Unit, National Institute of Agrobiological Sciences (NIAS), Kannondai, Tsukuba, Japan
| | - Yuri Tanaka
- Functional Plant Research Unit, National Institute of Agrobiological Sciences (NIAS), Kannondai, Tsukuba, Japan
| | - Takeshi Izawa
- Functional Plant Research Unit, National Institute of Agrobiological Sciences (NIAS), Kannondai, Tsukuba, Japan
- Laboratory of Plant Breeding and Genetics, University of Tokyo, Faculty of Agriculture, Bunkyo-ku, Yayoi 1-1-1, Tokyo, Japan
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41
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Abstract
Circadian oscillators are networks of biochemical feedback loops that generate 24-hour rhythms in organisms from bacteria to animals. These periodic rhythms result from a complex interplay among clock components that are specific to the organism, but share molecular mechanisms across kingdoms. A full understanding of these processes requires detailed knowledge, not only of the biochemical properties of clock proteins and their interactions, but also of the three-dimensional structure of clockwork components. Posttranslational modifications and protein–protein interactions have become a recent focus, in particular the complex interactions mediated by the phosphorylation of clock proteins and the formation of multimeric protein complexes that regulate clock genes at transcriptional and translational levels. This review covers the structural aspects of circadian oscillators, and serves as a primer for this exciting realm of structural biology.
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Affiliation(s)
- Reena Saini
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Max-Planck-Institut für Pflanzenzüchtungsforschung, Cologne, Germany
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland
| | - Seth J Davis
- Max-Planck-Institut für Pflanzenzüchtungsforschung, Cologne, Germany. .,Department of Biology, University of York, York, UK.
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Sternberger AL, Bowman MJ, Kruse CPS, Childs KL, Ballard HE, Wyatt SE. Transcriptomics Identifies Modules of Differentially Expressed Genes and Novel Cyclotides in Viola pubescens. FRONTIERS IN PLANT SCIENCE 2019; 10:156. [PMID: 30828342 PMCID: PMC6384259 DOI: 10.3389/fpls.2019.00156] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/29/2019] [Indexed: 05/24/2023]
Abstract
Viola is a large genus with worldwide distribution and many traits not currently exemplified in model plants including unique breeding systems and the production of cyclotides. Here we report de novo genome assembly and transcriptomic analyses of the non-model species Viola pubescens using short-read DNA sequencing data and RNA-Seq from eight diverse tissues. First, V. pubescens genome size was estimated through flow cytometry, resulting in an approximate haploid genome of 455 Mbp. Next, the draft V. pubescens genome was sequenced and assembled resulting in 264,035,065 read pairs and 161,038 contigs with an N50 length of 3,455 base pairs (bp). RNA-Seq data were then assembled into tissue-specific transcripts. Together, the DNA and transcript data generated 38,081 ab initio gene models which were functionally annotated based on homology to Arabidopsis thaliana genes and Pfam domains. Gene expression was visualized for each tissue via principal component analysis and hierarchical clustering, and gene co-expression analysis identified 20 modules of tissue-specific transcriptional networks. Some of these modules highlight genetic differences between chasmogamous and cleistogamous flowers and may provide insight into V. pubescens' mixed breeding system. Orthologous clustering with the proteomes of A. thaliana and Populus trichocarpa revealed 8,531 sequences unique to V. pubescens, including 81 novel cyclotide precursor sequences. Cyclotides are plant peptides characterized by a stable, cyclic cystine knot motif, making them strong candidates for drug scaffolding and protein engineering. Analysis of the RNA-Seq data for these cyclotide transcripts revealed diverse expression patterns both between transcripts and tissues. The diversity of these cyclotides was also highlighted in a maximum likelihood protein cladogram containing V. pubescens cyclotides and published cyclotide sequences from other Violaceae and Rubiaceae species. Collectively, this work provides the most comprehensive sequence resource for Viola, offers valuable transcriptomic insight into V. pubescens, and will facilitate future functional genomics research in Viola and other diverse plant groups.
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Affiliation(s)
- Anne L. Sternberger
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, United States
| | - Megan J. Bowman
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | - Colin P. S. Kruse
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, United States
- Interdisciplinary Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States
| | - Kevin L. Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | - Harvey E. Ballard
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, United States
| | - Sarah E. Wyatt
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, United States
- Interdisciplinary Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States
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Benevenuto RF, Seldal T, Hegland SJ, Rodriguez-Saona C, Kawash J, Polashock J. Transcriptional profiling of methyl jasmonate-induced defense responses in bilberry (Vaccinium myrtillus L.). BMC PLANT BIOLOGY 2019; 19:70. [PMID: 30755189 PMCID: PMC6373060 DOI: 10.1186/s12870-019-1650-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 01/14/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Bilberry (Vaccinium myrtillus L.) is one of the most abundant wild berries in the Northern European ecosystems. This species plays an important ecological role as a food source for many vertebrate and invertebrate herbivores. It is also well-recognized for its bioactive compounds, particularly substances involved in natural defenses against herbivory. These defenses are known to be initiated by leaf damage (e.g. chewing by insects) and mediated by activation of the jasmonic acid (JA) signaling pathway. This pathway can be activated by exogenous application of methyl jasmonate (MeJA), the volatile derivative of JA, which is often used to stimulate plant defense responses in studies of plant-herbivore interactions at ecological, biochemical, and molecular organismal levels. As a proxy for herbivore damage, wild V. myrtillus plants were treated in the field with MeJA and changes in gene expression were compared to untreated plants. RESULTS The de novo transcriptome assembly consisted of 231,887 unigenes. Nearly 71% of the unigenes were annotated in at least one of the databases interrogated. Differentially expressed genes (DEGs), between MeJA-treated and untreated control bilberry plants were identified using DESeq. A total of 3590 DEGs were identified between the treated and control plants, with 2013 DEGs upregulated and 1577 downregulated. The majority of the DEGs identified were associated with primary and secondary metabolism pathways in plants. DEGs associated with growth (e.g. those encoding photosynthesis-related components) and reproduction (e.g. flowering control genes) were frequently down-regulated while those associated with defense (e.g. encoding enzymes involved in biosynthesis of flavonoids, lignin compounds, and deterrent/repellent volatile organic compounds) were up-regulated in the MeJA treated plants. CONCLUSIONS Ecological studies are often limited by controlled conditions to reduce the impact of environmental effects. The results from this study support the hypothesis that bilberry plants, growing in natural conditions, shift resources from growth and reproduction to defenses while in a MeJA-induced state, as when under insect attack. This study highlights the occurrence of this trade-off at the transcriptional level in a realistic field scenario and supports published field observations wherein plant growth is retarded and defenses are upregulated.
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Affiliation(s)
- Rafael Fonseca Benevenuto
- Faculty of Engineering and Science, Western Norway University of Applied Sciences, Sogndal, Norway
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - Tarald Seldal
- Faculty of Engineering and Science, Western Norway University of Applied Sciences, Sogndal, Norway
| | - Stein Joar Hegland
- Faculty of Engineering and Science, Western Norway University of Applied Sciences, Sogndal, Norway
| | - Cesar Rodriguez-Saona
- Rutgers, Department of Entomology, Philip E. Marucci Center for Blueberry and Cranberry Research, The State University of New Jersey, Chatsworth, NJ USA
| | - Joseph Kawash
- Genetic Improvement of Fruits and Vegetables Lab, Philip E. Marucci Center for Blueberry and Cranberry Research, United States Department of Agriculture-Agricultural Research Service, Chatsworth, NJ USA
| | - James Polashock
- Genetic Improvement of Fruits and Vegetables Lab, Philip E. Marucci Center for Blueberry and Cranberry Research, United States Department of Agriculture-Agricultural Research Service, Chatsworth, NJ USA
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Kim YJ, Somers DE. Luciferase-Based Screen for Post-translational Control Factors in the Regulation of the Pseudo-Response Regulator PRR7. FRONTIERS IN PLANT SCIENCE 2019; 10:667. [PMID: 31191580 PMCID: PMC6540683 DOI: 10.3389/fpls.2019.00667] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/02/2019] [Indexed: 05/04/2023]
Abstract
Control of protein turnover is a key post-translational control point in the oscillatory network of the circadian clock. Some elements, such as TOC1 and PRR5 are engaged by a well-described F-box protein, ZEITLUPE, dedicated to their proteolytic turnover to shape their expression profile to a specific time of night. For most other clock components the regulation of their protein abundance is unknown, though turnover is often rapid and often lags the cycling of the respective mRNA. Here we report the design and results of an unbiased genetic screen in Arabidopsis to uncover proteolytic regulatory factors of PSEUDO-RESPONSE REGULATOR 7 (PRR7), a transcriptional repressor that peaks in the late afternoon. We performed EMS mutagenesis on a transgenic line expressing a PRR7::PRR7-luciferase (PRR7-LUC) translational fusion that accurately recapitulates the diurnal and circadian oscillations of the endogenous PRR7 protein. Using continuous luciferase imaging under constant light, we recovered mutants that alter the PRR7-LUC waveform and some that change period. We have identified novel alleles of ELF3 and ELF4, core components of the ELF3-ELF4-LUX Evening Complex (EC), that dampen the oscillation of PRR7-LUC. We report the characterization of two new hypomorphic alleles of ELF3 that help to understand the relationship between molecular potency and phenotype.
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Park HJ, Baek D, Cha JY, Liao X, Kang SH, McClung CR, Lee SY, Yun DJ, Kim WY. HOS15 Interacts with the Histone Deacetylase HDA9 and the Evening Complex to Epigenetically Regulate the Floral Activator GIGANTEA. THE PLANT CELL 2019; 31:37-51. [PMID: 30606777 PMCID: PMC6391688 DOI: 10.1105/tpc.18.00721] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/26/2018] [Accepted: 12/20/2018] [Indexed: 05/18/2023]
Abstract
In plants, seasonal inputs such as photoperiod and temperature modulate the plant's internal genetic program to regulate the timing of the developmental transition from vegetative to reproductive growth. This regulation of the floral transition involves chromatin remodeling, including covalent modification of histones. Here, we report that HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 15 (HOS15), a WD40 repeat protein, associates with a histone deacetylase complex to repress transcription of the GIGANTEA (GI)-mediated photoperiodic flowering pathway in Arabidopsis (Arabidopsis thaliana). Loss of function of HOS15 confers early flowering under long-day conditions because elevated GI expression. LUX ARRHYTHMO (LUX), a DNA binding transcription factor and component of the Evening Complex (EC), is important for the binding of HOS15 to the GI promoter. In wild type, HOS15 associates with the EC components LUX, EARLY FLOWERING 3 (ELF3), and ELF4 and the histone deacetylase HDA9 at the GI promoter, resulting in histone deacetylation and reduced GI expression. In the hos15-2 mutant, the levels of histone acetylation are elevated at the GI promoter, resulting in increased GI expression. Our data suggest that the HOS15-EC-HDA9 histone-modifying complex regulates photoperiodic flowering via the transcriptional repression of GI.
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Affiliation(s)
- Hee Jin Park
- Institute of Glocal Disease Control, Konkuk University, Seoul 05029, Republic of Korea
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Dongwon Baek
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Joon-Yung Cha
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Xueji Liao
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Sang-Ho Kang
- International Technology Cooperation Center, Rural Development Administration, Jeonju, 54875, Republic of Korea
| | - C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Dae-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21Plus), Plant Molecular Biology and Biotechnology Research Center, Research Institute of Life Sciences, Gyeongsang National University, Jinju 52828, Republic of Korea
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Yang LW, Wen XH, Fu JX, Dai SL. ClCRY2 facilitates floral transition in Chrysanthemum lavandulifolium by affecting the transcription of circadian clock-related genes under short-day photoperiods. HORTICULTURE RESEARCH 2018; 5:58. [PMID: 30393540 PMCID: PMC6210193 DOI: 10.1038/s41438-018-0063-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 05/26/2018] [Accepted: 06/04/2018] [Indexed: 05/23/2023]
Abstract
Plants sense photoperiod signals to confirm the optimal flowering time. Previous studies have shown that Cryptochrome2 (CRY2) functions to promote floral transition in the long-day plant (LDP) Arabidopsis; however, the function and molecular mechanism by which CRY2 regulates floral transition in short-day plants (SDPs) is still unclear. In this study, we identified a CRY2 homologous gene, ClCRY2, from Chrysanthemum lavandulifolium, a typical SDP. The morphological changes in the C. lavandulifolium shoot apex and ClFTs expression analysis under SD conditions showed that adult C. lavandulifolium completed the developmental transition from vegetative growth to reproductive growth after eight SDs. Meanwhile, ClCRY2 mRNA exhibited an increasing trend from 0 to 8 d of SD treatment. ClCRY2 overexpression in wild-type (WT) Arabidopsis and C. lavandulifolium resulted in early flowering. The transcript levels of the CONSTANS-like (COL) genes ClCOL1, ClCOL4, and ClCOL5, and FLOWERING LOCUS T (FT) homologous gene ClFT1 were upregulated in ClCRY2 overexpression (ClCRY2-OE) C. lavandulifolium under SD conditions. The transcript levels of some circadian clock-related genes, including PSEUDO-REPONSE REGULATOR 5 (PRR5), ZEITLUPE (ZTL), FLAVIN-BINDING KELCH REPEAT F-BOX 1 (FKF1), and GIGANTEA (GI-1 and GI-2), were upregulated in ClCRY2-OE C. lavandulifolium, while the expression levels of other circadian clock-related genes, such as EARLY FLOWERING 3 (ELF3), ELF4, LATE ELONGATED HYPOCOTYL (LHY), PRR73, and REVEILLE8 (RVE8), were downregulated in ClCRY2-OE C. lavandulifolium under SD conditions. Taken together, the results suggest that ClCRY2 promotes floral transition by fine-tuning the expression of circadian clock-related gene, ClCOLs and ClFT1 in C. lavandulifolium under SD conditions.
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Affiliation(s)
- Li-wen Yang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083 P. R. China
| | - Xiao-hui Wen
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083 P. R. China
| | - Jian-xin Fu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083 P. R. China
| | - Si-lan Dai
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083 P. R. China
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Muchapirei CI, Valentine SL, Roden LC. Plant circadian networks and responses to the environment. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:393-399. [PMID: 32290979 DOI: 10.1071/fp17150] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 10/26/2017] [Indexed: 06/11/2023]
Abstract
There are regular, and therefore predictable, environmental changes on Earth due to the rotation of the planet on its axis and its orbit around the sun. Thus organisms have adapted their metabolism, physiology and behaviour to minimise stresses caused by unfavourable conditions and maximise efficiency of growth. Additionally, most organisms are able to anticipate these changes and accordingly maximise metabolic efficiency and growth, because they have a complex biological time-keeping system commonly referred to as the circadian clock. Multiple pathways in plants are organised in a temporal manner through circadian clock-regulation of gene transcription and post-translational modifications. What is becoming more apparent is the bidirectional nature of interactions between the clock and stress response pathways. Until recently, the focus of many studies had been on the unidirectional, hierarchical control of biological processes by the circadian clock, and impacts on the clock in response to environmental stress had been largely ignored. Studies of interactions of the circadian clock with the environment have primarily been to understand mechanisms of entrainment. We review the evidence and implications of the reciprocal interactions between the clock and the environment.
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Affiliation(s)
- Chenjerai I Muchapirei
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
| | - Shannon-Leigh Valentine
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
| | - Laura C Roden
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
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Song Y, Jiang Y, Kuai B, Li L. CIRCADIAN CLOCK-ASSOCIATED 1 Inhibits Leaf Senescence in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2018; 9:280. [PMID: 29559987 PMCID: PMC5845730 DOI: 10.3389/fpls.2018.00280] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/19/2018] [Indexed: 05/20/2023]
Abstract
Leaf senescence is an integral part of plant development, and the timing and progressing rate of senescence could substantially affect the yield and quality of crops. It has been known that a circadian rhythm synchronized with external environmental cues is critical for the optimal coordination of various physiological and metabolic processes. However, the reciprocal interactions between the circadian clock and leaf senescence in plants remain unknown. Here, through measuring the physiological and molecular senescence related markers of several circadian components mutants, we found that CIRCADIAN CLOCK-ASSOCIATED 1 inhibits leaf senescence. Further molecular and genetic studies revealed that CCA1 directly activates GLK2 and suppresses ORE1 expression to counteract leaf senescence. As plants age, the expression and periodic amplitude of CCA1 declines and thus weakens the inhibition of senescence. Our findings reveal an age-dependent circadian clock component of the process of leaf senescence.
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Characterization of the CCT family and analysis of gene expression in Aegilops tauschii. PLoS One 2017; 12:e0189333. [PMID: 29220383 PMCID: PMC5722339 DOI: 10.1371/journal.pone.0189333] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/22/2017] [Indexed: 01/24/2023] Open
Abstract
Flowering is crucial for reproductive success in flowering plant. The CCT domain-containing genes widely participate in the regulation of flowering process in various plant species. So far, the CCT family in common wheat is largely unknown. Here, we characterized the structure, organization, molecular evolution and expression of the CCT genes in Aegilops tauschii, which is the D genome donor of hexaploid wheat. Twenty-six CCT genes (AetCCT) were identified from the full genome of A. tauschii and these genes were distributed on all 7 chromosomes. Phylogenetic analysis classified these AetCCT genes into 10 subgroups. Thirteen AetCCT members in group A, C, H and G achieved rapid evolution based on evolutionary rate analysis. The AetCCT genes respond to different exogenous hormones and abiotic treatments, the expression of AetCCT4, 7, 8, 11, 12, 16, 17, 19, 21 and 22 showed a significant 24 h rhythm. This study may provide a reference for common wheat's evolution, domestication and evolvement rules, and also help us to understand the ecological adaptability of A. tauschii.
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Huang H, Gehan MA, Huss SE, Alvarez S, Lizarraga C, Gruebbling EL, Gierer J, Naldrett MJ, Bindbeutel RK, Evans BS, Mockler TC, Nusinow DA. Cross-species complementation reveals conserved functions for EARLY FLOWERING 3 between monocots and dicots. PLANT DIRECT 2017; 1:e00018. [PMID: 31245666 PMCID: PMC6508535 DOI: 10.1002/pld3.18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/10/2017] [Accepted: 09/13/2017] [Indexed: 05/03/2023]
Abstract
Plant responses to the environment are shaped by external stimuli and internal signaling pathways. In both the model plant Arabidopsis thaliana (Arabidopsis) and crop species, circadian clock factors are critical for growth, flowering, and circadian rhythms. Outside of Arabidopsis, however, little is known about the molecular function of clock gene products. Therefore, we sought to compare the function of Brachypodium distachyon (Brachypodium) and Setaria viridis (Setaria) orthologs of EARLY FLOWERING 3, a key clock gene in Arabidopsis. To identify both cycling genes and putative ELF3 functional orthologs in Setaria, a circadian RNA-seq dataset and online query tool (Diel Explorer) were generated to explore expression profiles of Setaria genes under circadian conditions. The function of ELF3 orthologs from Arabidopsis, Brachypodium, and Setaria was tested for complementation of an elf3 mutation in Arabidopsis. We find that both monocot orthologs were capable of rescuing hypocotyl elongation, flowering time, and arrhythmic clock phenotypes. Using affinity purification and mass spectrometry, our data indicate that BdELF3 and SvELF3 could be integrated into similar complexes in vivo as AtELF3. Thus, we find that, despite 180 million years of separation, BdELF3 and SvELF3 can functionally complement loss of ELF3 at the molecular and physiological level.
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Affiliation(s)
- He Huang
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | | | | | - Sophie Alvarez
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Present address:
University of Nebraska‐LincolnLincolnNEUSA
| | | | | | - John Gierer
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | - Michael J. Naldrett
- Donald Danforth Plant Science CenterSt. LouisMOUSA
- Present address:
University of Nebraska‐LincolnLincolnNEUSA
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