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Huang Y, Schnurbusch T. The Birth and Death of Floral Organs in Cereal Crops. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:427-458. [PMID: 38424062 DOI: 10.1146/annurev-arplant-060223-041716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Florets of cereal crops are the basic reproductive organs that produce grains for food or feed. The birth of a floret progresses through meristem initiation and floral organ identity specification and maintenance. During these processes, both endogenous and external cues can trigger a premature floral organ death, leading to reproductive failure. Recent advances in different cereal crops have identified both conserved and distinct regulators governing the birth of a floret. However, the molecular underpinnings of floral death are just beginning to be understood. In this review, we first provide a general overview of the current findings in the field of floral development in major cereals and outline different forms of floral deaths, particularly in the Triticeae crops. We then highlight the importance of vascular patterning and photosynthesis in floral development and reproductive success and argue for an expanded knowledge of floral birth-death balance in the context of agroecology.
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Affiliation(s)
- Yongyu Huang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Seeland, Germany; ,
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Seeland, Germany; ,
- Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany
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2
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Cosenza F, Shrestha A, Van Inghelandt D, Casale FA, Wu PY, Weisweiler M, Li J, Wespel F, Stich B. Genetic mapping reveals new loci and alleles for flowering time and plant height using the double round-robin population of barley. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2385-2402. [PMID: 38330219 PMCID: PMC11016846 DOI: 10.1093/jxb/erae010] [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: 05/17/2023] [Accepted: 02/07/2024] [Indexed: 02/10/2024]
Abstract
Flowering time and plant height are two critical determinants of yield potential in barley (Hordeum vulgare). Despite their role in plant physiological regulation, a complete overview of the genetic complexity of flowering time and plant height regulation in barley is still lacking. Using a double round-robin population originated from the crossings of 23 diverse parental inbred lines, we aimed to determine the variance components in the regulation of flowering time and plant height in barley as well as to identify new genetic variants by single and multi-population QTL analyses and allele mining. Despite similar genotypic variance, we observed higher environmental variance components for plant height than flowering time. Furthermore, we detected new QTLs for flowering time and plant height. Finally, we identified a new functional allelic variant of the main regulatory gene Ppd-H1. Our results show that the genetic architecture of flowering time and plant height might be more complex than reported earlier and that a number of undetected, small effect, or low-frequency genetic variants underlie the control of these two traits.
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Affiliation(s)
- Francesco Cosenza
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Asis Shrestha
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Delphine Van Inghelandt
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Federico A Casale
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Po-Ya Wu
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Marius Weisweiler
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Jinquan Li
- Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
| | - Franziska Wespel
- Saatzucht Josef Breun GmbH Co. KG, Amselweg 1, 91074 Herzogenaurach, Germany
| | - Benjamin Stich
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, 40225 Düsseldorf, Germany
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3
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Hansson M, Youssef HM, Zakhrabekova S, Stuart D, Svensson JT, Dockter C, Stein N, Waugh R, Lundqvist U, Franckowiak J. A guide to barley mutants. Hereditas 2024; 161:11. [PMID: 38454479 PMCID: PMC10921644 DOI: 10.1186/s41065-023-00304-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 11/24/2023] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Mutants have had a fundamental impact upon scientific and applied genetics. They have paved the way for the molecular and genomic era, and most of today's crop plants are derived from breeding programs involving mutagenic treatments. RESULTS Barley (Hordeum vulgare L.) is one of the most widely grown cereals in the world and has a long history as a crop plant. Barley breeding started more than 100 years ago and large breeding programs have collected and generated a wide range of natural and induced mutants, which often were deposited in genebanks around the world. In recent years, an increased interest in genetic diversity has brought many historic mutants into focus because the collections are regarded as valuable resources for understanding the genetic control of barley biology and barley breeding. The increased interest has been fueled also by recent advances in genomic research, which provided new tools and possibilities to analyze and reveal the genetic diversity of mutant collections. CONCLUSION Since detailed knowledge about phenotypic characters of the mutants is the key to success of genetic and genomic studies, we here provide a comprehensive description of mostly morphological barley mutants. The review is closely linked to the International Database for Barley Genes and Barley Genetic Stocks ( bgs.nordgen.org ) where further details and additional images of each mutant described in this review can be found.
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Affiliation(s)
- Mats Hansson
- Department of Biology, Lund University, Sölvegatan 35, 22362, Lund, Sweden.
| | - Helmy M Youssef
- Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Halle, 06120, Germany
| | | | - David Stuart
- Department of Biology, Lund University, Sölvegatan 35, 22362, Lund, Sweden
| | - Jan T Svensson
- Nordic Genetic Resource Center (NordGen), Växthusvägen 12, 23456, Alnarp, Sweden
| | - Christoph Dockter
- Carlsberg Research Laboratory, J. C. Jacobsens Gade 4, 1799, Copenhagen V, Denmark
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Stadt Seeland, E06466, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- Division of Plant Sciences, University of Dundee, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- School of Agriculture Food and Wine, Waite Campus, The University of Adelaide, Urrbrae, 5064, Australia
| | - Udda Lundqvist
- Nordic Genetic Resource Center (NordGen), Växthusvägen 12, 23456, Alnarp, Sweden
| | - Jerome Franckowiak
- Department of Agronomy and Plant Genetics, University of Minnesota Twin Cities, 411 Borlaug Hall, 1991 Upper Buford Circle, St Paul, MN, 55108, USA
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4
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Huang Y, Maurer A, Giehl RFH, Zhao S, Golan G, Thirulogachandar V, Li G, Zhao Y, Trautewig C, Himmelbach A, Börner A, Jayakodi M, Stein N, Mascher M, Pillen K, Schnurbusch T. Dynamic Phytomeric Growth Contributes to Local Adaptation in Barley. Mol Biol Evol 2024; 41:msae011. [PMID: 38243866 PMCID: PMC10837018 DOI: 10.1093/molbev/msae011] [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: 06/30/2023] [Revised: 11/03/2023] [Accepted: 01/10/2024] [Indexed: 01/22/2024] Open
Abstract
Vascular plants have segmented body axes with iterative nodes and internodes. Appropriate node initiation and internode elongation are fundamental to plant fitness and crop yield; however, how these events are spatiotemporally coordinated remains elusive. We show that in barley (Hordeum vulgare L.), selections during domestication have extended the apical meristematic phase to promote node initiation, but constrained subsequent internode elongation. In both vegetative and reproductive phases, internode elongation displays a dynamic proximal-distal gradient, and among subpopulations of domesticated barleys worldwide, node initiation and proximal internode elongation are associated with latitudinal and longitudinal gradients, respectively. Genetic and functional analyses suggest that, in addition to their converging roles in node initiation, flowering-time genes have been repurposed to specify the timing and duration of internode elongation. Our study provides an integrated view of barley node initiation and internode elongation and suggests that plant architecture should be recognized as a collection of dynamic phytomeric units in the context of crop adaptive evolution.
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Affiliation(s)
- Yongyu Huang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Andreas Maurer
- Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, 06120 Halle, Germany
| | - Ricardo F H Giehl
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Shuangshuang Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Guy Golan
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | | | - Guoliang Li
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Corinna Trautewig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Murukarthick Jayakodi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Klaus Pillen
- Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, 06120 Halle, Germany
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany
- Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, 06120 Halle, Germany
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Helmsorig G, Walla A, Rütjes T, Buchmann G, Schüller R, Hensel G, von Korff M. early maturity 7 promotes early flowering by controlling the light input into the circadian clock in barley. PLANT PHYSIOLOGY 2024; 194:849-866. [PMID: 37951242 PMCID: PMC10828213 DOI: 10.1093/plphys/kiad551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/26/2023] [Indexed: 11/13/2023]
Abstract
Breeding for variation in photoperiod response is crucial to adapt crop plants to various environments. Plants measure changes in day length by the circadian clock, an endogenous timekeeper that allows plants to anticipate changes in diurnal and seasonal light-dark cycles. Here, we describe the early maturity 7 (eam7) locus in barley (Hordeum vulgare), which interacts with PHOTOPERIOD 1 (Ppd-H1) to cause early flowering under non-inductive short days. We identify LIGHT-REGULATED WD 1 (LWD1) as a putative candidate to underlie the eam7 locus in barley as supported by genetic mapping and CRISPR-Cas9-generated lwd1 mutants. Mutations in eam7 cause a significant phase advance and a misregulation of core clock and clock output genes under diurnal conditions. Early flowering was linked to an upregulation of Ppd-H1 during the night and consequent induction of the florigen FLOWERING LOCUS T1 under short days. We propose that EAM7 controls photoperiodic flowering in barley by controlling the light input into the clock and diurnal expression patterns of the major photoperiod response gene Ppd-H1.
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Affiliation(s)
- Gesa Helmsorig
- Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40223 Düsseldorf, Germany
| | - Agatha Walla
- Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40223 Düsseldorf, Germany
| | - Thea Rütjes
- Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40223 Düsseldorf, Germany
| | - Gabriele Buchmann
- Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40223 Düsseldorf, Germany
| | - Rebekka Schüller
- Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40223 Düsseldorf, Germany
| | - Götz Hensel
- Cluster of Excellence on Plant Sciences “SMART Plants for Tomorrow's Needs”, 40223 Düsseldorf, Germany
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-Universität Düsseldorf, 40223 Düsseldorf, Germany
- Division of Molecular Biology, Centre of the Region Hana for Biotechnological and Agriculture Research, Faculty of Science, Palacký University, CZ-779 00 Olomouc, Czech
| | - Maria von Korff
- Institute of Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40223 Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences “SMART Plants for Tomorrow's Needs”, 40223 Düsseldorf, Germany
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6
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Xie Y, Zhao Y, Chen L, Wang Y, Xue W, Kong D, Li C, Zhou L, Li H, Zhao Y, Wang B, Xu M, Zhao B, Bilska-Kos A, Wang H. ZmELF3.1 integrates the RA2-TSH4 module to repress maize tassel branching. THE NEW PHYTOLOGIST 2024; 241:490-503. [PMID: 37858961 DOI: 10.1111/nph.19329] [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: 03/24/2023] [Accepted: 09/08/2023] [Indexed: 10/21/2023]
Abstract
Tassel branch number (TBN) is a key agronomic trait for adapting to high-density planting and grain yield in maize. However, the molecular regulatory mechanisms underlying tassel branching are still largely unknown. Here, we used molecular and genetic studies together to show that ZmELF3.1 plays a critical role in regulating TBN in maize. Previous studies showed that ZmELF3.1 forms the evening complex through interacting with ZmELF4 and ZmLUX to regulate flowering in maize and that RA2 and TSH4 (ZmSBP2) suppresses and promotes TBN in maize, respectively. In this study, we show that loss-of-function mutants of ZmELF3.1 exhibit a significant increase of TBN. We also show that RA2 directly binds to the promoter of TSH4 and represses its expression, thus leading to reduced TBN. We further demonstrate that ZmELF3.1 directly interacts with both RA2 and ZmELF4.2 to form tri-protein complexes that further enhance the binding of RA2 to the promoter of TSH4, leading to suppressed TSH4 expression and consequently decreased TBN. Our combined results establish a novel functional link between the ELF3-ELF4-RA2 complex and miR156-SPL regulatory module in regulating tassel branching and provide a valuable target for genetic improvement of tassel branching in maize.
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Affiliation(s)
- Yurong Xie
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Hainan Yazhou Bay Seed Lab, Sanya, 572025, China
| | - Yongping Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lihong Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yanli Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Weicong Xue
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Dexin Kong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Changyu Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Linyu Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huiru Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yanfeng Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Baobao Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Hainan Yazhou Bay Seed Lab, Sanya, 572025, China
| | - Miaoyun Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Hainan Yazhou Bay Seed Lab, Sanya, 572025, China
| | - Binbin Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Anna Bilska-Kos
- Plant Breeding and Acclimatization Institute-National Research Institute, Department of Biochemistry and Biotechnology, Radzików, 05-870, Błonie, Poland
| | - Haiyang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
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7
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Zakhrabekova S, Chauhan P, Dockter C, Ealumalai P, Ivanova A, Jørgensen ME, Lu Q, Shoeva O, Werner K, Hansson M. Identification of a candidate dwarfing gene in Pallas, the first commercial barley cultivar generated through mutational breeding. Front Genet 2023; 14:1213815. [PMID: 37470037 PMCID: PMC10352844 DOI: 10.3389/fgene.2023.1213815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/07/2023] [Indexed: 07/21/2023] Open
Abstract
Many induced mutants are available in barley (Hordeum vulgare L.). One of the largest groups of induced mutants is the Erectoides (ert) mutants, which is characterized by a compact and upright spike and a shortened culm. One isolated mutant, ert-k.32, generated by X-ray treatment and registered in 1958 under the named "Pallas", was the first ever induced barley mutant to be released on the market. Its value was improved culm strength and enhanced lodging resistance. In this study, we aimed to identify the casual gene of the ert-k.32 mutant by whole genome sequencing of allelic ert-k mutants. The suggested Ert-k candidate gene, HORVU.MOREX.r3.6HG0574880, is located in the centromeric region of chromosome 6H. The gene product is an alpha/beta hydrolase with a catalytic triad in the active site composed of Ser-167, His-261 and Asp-232. In comparison to proteins derived from the Arabidopsis genome, ErtK is most similar to a thioesterase with de-S-acylation activity. This suggests that ErtK catalyzes post-translational modifications by removing fatty acids that are covalently attached to cysteine residues of target proteins involved in regulation of plant architecture and important commercial traits such as culm stability and lodging resistance.
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Affiliation(s)
| | | | | | | | - Anastasiia Ivanova
- Department of Biology, Lund University, Lund, Sweden
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | | | - Qiongxian Lu
- Carlsberg Research Laboratory, Copenhagen, Denmark
| | - Olesya Shoeva
- Department of Biology, Lund University, Lund, Sweden
- Department of Plant Genetics,Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | | | - Mats Hansson
- Department of Biology, Lund University, Lund, Sweden
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8
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Alvarez MA, Li C, Lin H, Joe A, Padilla M, Woods DP, Dubcovsky J. EARLY FLOWERING 3 interactions with PHYTOCHROME B and PHOTOPERIOD1 are critical for the photoperiodic regulation of wheat heading time. PLoS Genet 2023; 19:e1010655. [PMID: 37163495 PMCID: PMC10171656 DOI: 10.1371/journal.pgen.1010655] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/04/2023] [Indexed: 05/12/2023] Open
Abstract
The photoperiodic response is critical for plants to adjust their reproductive phase to the most favorable season. Wheat heads earlier under long days (LD) than under short days (SD) and this difference is mainly regulated by the PHOTOPERIOD1 (PPD1) gene. Tetraploid wheat plants carrying the Ppd-A1a allele with a large deletion in the promoter head earlier under SD than plants carrying the wildtype Ppd-A1b allele with an intact promoter. Phytochromes PHYB and PHYC are necessary for the light activation of PPD1, and mutations in either of these genes result in the downregulation of PPD1 and very late heading time. We show here that both effects are reverted when the phyB mutant is combined with loss-of-function mutations in EARLY FLOWERING 3 (ELF3), a component of the Evening Complex (EC) in the circadian clock. We also show that the wheat ELF3 protein interacts with PHYB and PHYC, is rapidly modified by light, and binds to the PPD1 promoter in planta (likely as part of the EC). Deletion of the ELF3 binding region in the Ppd-A1a promoter results in PPD1 upregulation at dawn, similar to PPD1 alleles with intact promoters in the elf3 mutant background. The upregulation of PPD1 is correlated with the upregulation of the florigen gene FLOWERING LOCUS T1 (FT1) and early heading time. Loss-of-function mutations in PPD1 result in the downregulation of FT1 and delayed heading, even when combined with the elf3 mutation. Taken together, these results indicate that ELF3 operates downstream of PHYB as a direct transcriptional repressor of PPD1, and that this repression is relaxed both by light and by the deletion of the ELF3 binding region in the Ppd-A1a promoter. In summary, the regulation of the light mediated activation of PPD1 by ELF3 is critical for the photoperiodic regulation of wheat heading time.
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Affiliation(s)
- Maria Alejandra Alvarez
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Chengxia Li
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Huiqiong Lin
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Anna Joe
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Mariana Padilla
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Daniel P Woods
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
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9
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Woods DP, Li W, Sibout R, Shao M, Laudencia-Chingcuanco D, Vogel JP, Dubcovsky J, Amasino RM. PHYTOCHROME C regulation of photoperiodic flowering via PHOTOPERIOD1 is mediated by EARLY FLOWERING 3 in Brachypodium distachyon. PLoS Genet 2023; 19:e1010706. [PMID: 37163541 PMCID: PMC10171608 DOI: 10.1371/journal.pgen.1010706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 03/17/2023] [Indexed: 05/12/2023] Open
Abstract
Daylength sensing in many plants is critical for coordinating the timing of flowering with the appropriate season. Temperate climate-adapted grasses such as Brachypodium distachyon flower during the spring when days are becoming longer. The photoreceptor PHYTOCHROME C is essential for long-day (LD) flowering in B. distachyon. PHYC is required for the LD activation of a suite of genes in the photoperiod pathway including PHOTOPERIOD1 (PPD1) that, in turn, result in the activation of FLOWERING LOCUS T (FT1)/FLORIGEN, which causes flowering. Thus, B. distachyon phyC mutants are extremely delayed in flowering. Here we show that PHYC-mediated activation of PPD1 occurs via EARLY FLOWERING 3 (ELF3), a component of the evening complex in the circadian clock. The extreme delay of flowering of the phyC mutant disappears when combined with an elf3 loss-of-function mutation. Moreover, the dampened PPD1 expression in phyC mutant plants is elevated in phyC/elf3 mutant plants consistent with the rapid flowering of the double mutant. We show that loss of PPD1 function also results in reduced FT1 expression and extremely delayed flowering consistent with results from wheat and barley. Additionally, elf3 mutant plants have elevated expression levels of PPD1, and we show that overexpression of ELF3 results in delayed flowering associated with a reduction of PPD1 and FT1 expression, indicating that ELF3 represses PPD1 transcription consistent with previous studies showing that ELF3 binds to the PPD1 promoter. Indeed, PPD1 is the main target of ELF3-mediated flowering as elf3/ppd1 double mutant plants are delayed flowering. Our results indicate that ELF3 operates downstream from PHYC and acts as a repressor of PPD1 in the photoperiod flowering pathway of B. distachyon.
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Affiliation(s)
- Daniel P. Woods
- Dept. Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Weiya Li
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Richard Sibout
- Institut Jean-Pierre Bourgin, UMR1318 INRAE-AgroParisTech, Versailles Cedex, France
- UR1268 BIA, INRAE, Nantes, France
| | - Mingqin Shao
- DOE Joint Genome Institute, Berkeley, California, United States of America
| | - Debbie Laudencia-Chingcuanco
- USDA-Agricultural Research Service, Western Regional Research Center, Albany, California, United States of America
| | - John P. Vogel
- DOE Joint Genome Institute, Berkeley, California, United States of America
| | - Jorge Dubcovsky
- Dept. Plant Sciences, University of California, Davis, California, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Richard M. Amasino
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, United States of America
- United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin, United States of America
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10
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Zhu Z, Esche F, Babben S, Trenner J, Serfling A, Pillen K, Maurer A, Quint M. An exotic allele of barley EARLY FLOWERING 3 contributes to developmental plasticity at elevated temperatures. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2912-2931. [PMID: 36449391 DOI: 10.1093/jxb/erac470] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 11/28/2022] [Indexed: 06/06/2023]
Abstract
Increase in ambient temperatures caused by climate change affects various morphological and developmental traits of plants, threatening crop yield stability. In the model plant Arabidopsis thaliana, EARLY FLOWERING 3 (ELF3) plays prominent roles in temperature sensing and thermomorphogenesis signal transduction. However, how crop species respond to elevated temperatures is poorly understood. Here, we show that the barley ortholog of AtELF3 interacts with high temperature to control growth and development. We used heterogeneous inbred family (HIF) pairs generated from a segregating mapping population and systematically studied the role of exotic ELF3 variants in barley temperature responses. An exotic ELF3 allele of Syrian origin promoted elongation growth in barley at elevated temperatures, whereas plant area and estimated biomass were drastically reduced, resulting in an open canopy architecture. The same allele accelerated inflorescence development at high temperature, which correlated with early transcriptional induction of MADS-box floral identity genes BM3 and BM8. Consequently, barley plants carrying the exotic ELF3 allele displayed stable total grain number at elevated temperatures. Our findings therefore demonstrate that exotic ELF3 variants can contribute to phenotypic and developmental acclimation to elevated temperatures, providing a stimulus for breeding of climate-resilient crops.
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Affiliation(s)
- Zihao Zhu
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, D-06120, Halle (Saale), Germany
| | - Finn Esche
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, D-06120, Halle (Saale), Germany
| | - Steve Babben
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, D-06120, Halle (Saale), Germany
| | - Jana Trenner
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, D-06120, Halle (Saale), Germany
| | - Albrecht Serfling
- Institute for Resistance Research and Stress Tolerance, Julius Kuehn-Institute, Erwin-Baur-Str. 27, D-06484, Quedlinburg, Germany
| | - Klaus Pillen
- Chair of Plant Breeding, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 3, D-06120, Halle (Saale), Germany
| | - Andreas Maurer
- Chair of Plant Breeding, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 3, D-06120, Halle (Saale), Germany
| | - Marcel Quint
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, D-06120, Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research, Halle-Jena-Leipzig, Puschstrasse 4, D-04103, Leipzig, Germany
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11
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Slafer GA, Casas AM, Igartua E. Sense in sensitivity: difference in the meaning of photoperiod-insensitivity between wheat and barley. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad128. [PMID: 37021554 DOI: 10.1093/jxb/erad128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Indexed: 06/19/2023]
Abstract
The description of long photoperiod sensitivity in wheat and barley is a cause of confusion for researchers working in these crops, usually accustomed to free exchange of physiological and genetic knowledge of such similar crops. Indeed, wheat and barley scientists customarily quote studies of either crop species when researching one of them. Among their numerous similarities the main gene controlling that response is the same in both crops (PPD1; PPD-H1 in barley and PPD-D1 in hexaploid wheat). However, the photoperiod responses are different: (i) the main dominant allele inducing shorter time to anthesis is the insensitive allele in wheat (Ppd-D1a) but the sensitive allele in barley (Ppd-H1) (i.e. sensitivity to photoperiod produces opposite effects on time to heading in wheat and barley), (ii) the main "insensitive" allele in wheat, Ppd-D1a, does confer insensitivity, whilst that of barley reduces the sensitivity but still responds to photoperiod. The different behaviour of PPD1 genes in wheat and barley is put in a common framework based on the similarities and differences of the molecular bases of their mutations, which include polymorphism at gene expression levels, copy number variation, and sequence of coding regions. This common perspective sheds light on a source on confusion for cereal researchers, and prompts us to recommend accounting for the photoperiod sensitivity status of the plant materials when doing research on genetic control of phenology. Finally, we provide advice to facilitate the management of natural PPD1 diversity in breeding programs and suggest targets for further modification through gene editing, based on mutual knowledge on the two crops.
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Affiliation(s)
- Gustavo A Slafer
- Department of Crop and Forest Sciences University of Lleida and AGROTECNIO-CERCA Center, Av. Rovira Roure 191, 25198 Lleida, Spain
- ICREA, Catalonian Institution for Research and Advanced Studies, Spain
| | - Ana M Casas
- Department of Genetics and Plant Production, Aula Dei Experimental Station, EEAD, CSIC, Avda. Montañana 1005, E-50059 Zaragoza, Spain
| | - Ernesto Igartua
- Department of Genetics and Plant Production, Aula Dei Experimental Station, EEAD, CSIC, Avda. Montañana 1005, E-50059 Zaragoza, Spain
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12
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Zahn T, Zhu Z, Ritoff N, Krapf J, Junker A, Altmann T, Schmutzer T, Tüting C, Kastritis PL, Babben S, Quint M, Pillen K, Maurer A. Novel exotic alleles of EARLY FLOWERING 3 determine plant development in barley. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad127. [PMID: 37010230 DOI: 10.1093/jxb/erad127] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Indexed: 06/19/2023]
Abstract
EARLY FLOWERING 3 (ELF3) is an important regulator of various physiological and developmental processes and hence may serve to improve plant adaptation which will be substantial for future plant breeding. To expand the limited knowledge on barley ELF3 in determining agronomic traits, we conducted field studies with heterogeneous inbred families (HIFs) derived from selected lines of the wild barley nested association mapping population HEB-25. During two growing seasons, phenotypes of nearly isogenic HIF sister lines, segregating for exotic and cultivated alleles at the ELF3 locus, were compared for ten developmental and yield-related traits. We determine novel exotic ELF3 alleles and show that HIF lines, carrying the exotic ELF3 allele, accelerated plant development compared to the cultivated ELF3 allele, depending on the genetic background. Remarkably, the most extreme effects on phenology could be attributed to one exotic ELF3 allele differing from the cultivated Barke ELF3 allele in only one SNP. This SNP causes an amino acid substitution (W669G), which predictively has an impact on the protein structure of ELF3, thereby possibly affecting phase separation behaviour and nano-compartment formation of ELF3 and, potentially, also affecting its local cellular interactions causing significant trait differences between HIF sister lines.
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Affiliation(s)
- Tanja Zahn
- Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120, Halle (Saale), Germany
| | - Zihao Zhu
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, 06120, Halle (Saale), Germany
| | - Niklas Ritoff
- Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120, Halle (Saale), Germany
| | - Jonathan Krapf
- Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120, Halle (Saale), Germany
| | - Astrid Junker
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
| | - Thomas Altmann
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Stadt Seeland, Germany
| | - Thomas Schmutzer
- Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120, Halle (Saale), Germany
| | - Christian Tüting
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle (Saale), Germany
| | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle (Saale), Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany
- Biozentrum, Martin Luther University Halle-Wittenberg, Weinbergweg 22, 06120, Halle (Saale), Germany
| | - Steve Babben
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, 06120, Halle (Saale), Germany
| | - Marcel Quint
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 5, 06120, Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Germany
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120, Halle (Saale), Germany
| | - Andreas Maurer
- Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120, Halle (Saale), Germany
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13
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Wittern L, Steed G, Taylor LJ, Ramirez DC, Pingarron-Cardenas G, Gardner K, Greenland A, Hannah MA, Webb AAR. Wheat EARLY FLOWERING 3 affects heading date without disrupting circadian oscillations. PLANT PHYSIOLOGY 2023; 191:1383-1403. [PMID: 36454669 PMCID: PMC9922389 DOI: 10.1093/plphys/kiac544] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 09/23/2022] [Accepted: 11/29/2022] [Indexed: 05/26/2023]
Abstract
Plant breeders have indirectly selected for variation at circadian-associated loci in many of the world's major crops, when breeding to increase yield and improve crop performance. Using an eight-parent Multiparent Advanced Generation Inter-Cross (MAGIC) population, we investigated how variation in circadian clock-associated genes contributes to the regulation of heading date in UK and European winter wheat (Triticum aestivum) varieties. We identified homoeologues of EARLY FLOWERING 3 (ELF3) as candidates for the Earliness per se (Eps) D1 and B1 loci under field conditions. We then confirmed a single-nucleotide polymorphism within the coding region of TaELF3-B1 as a candidate polymorphism underlying the Eps-B1 locus. We found that a reported deletion at the Eps-D1 locus encompassing TaELF3-D1 is, instead, an allele that lies within an introgression region containing an inversion relative to the Chinese Spring D genome. Using Triticum turgidum cv. Kronos carrying loss-of-function alleles of TtELF3, we showed that ELF3 regulates heading, with loss of a single ELF3 homoeologue sufficient to alter heading date. These studies demonstrated that ELF3 forms part of the circadian oscillator; however, the loss of all homoeologues was required to affect circadian rhythms. Similarly, loss of functional LUX ARRHYTHMO (LUX) in T. aestivum, an orthologue of a protein partner of Arabidopsis (Arabidopsis thaliana) ELF3, severely disrupted circadian rhythms. ELF3 and LUX transcripts are not co-expressed at dusk, suggesting that the structure of the wheat circadian oscillator might differ from that of Arabidopsis. Our demonstration that alterations to ELF3 homoeologues can affect heading date separately from effects on the circadian oscillator suggests a role for ELF3 in cereal photoperiodic responses that could be selected for without pleiotropic deleterious alterations to circadian rhythms.
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Affiliation(s)
- Lukas Wittern
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Gareth Steed
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Laura J Taylor
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Dora Cano Ramirez
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | | | - Keith Gardner
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Andy Greenland
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Matthew A Hannah
- BASF, BBCC – Innovation Center Gent, Technologiepark-Zwijnaarde 101, 9052 Gent, Belgium
| | - Alex A R Webb
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
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14
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Wang F, Li S, Kong F, Lin X, Lu S. Altered regulation of flowering expands growth ranges and maximizes yields in major crops. FRONTIERS IN PLANT SCIENCE 2023; 14:1094411. [PMID: 36743503 PMCID: PMC9892950 DOI: 10.3389/fpls.2023.1094411] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/04/2023] [Indexed: 06/14/2023]
Abstract
Flowering time influences reproductive success in plants and has a significant impact on yield in grain crops. Flowering time is regulated by a variety of environmental factors, with daylength often playing an important role. Crops can be categorized into different types according to their photoperiod requirements for flowering. For instance, long-day crops include wheat (Triticum aestivum), barley (Hordeum vulgare), and pea (Pisum sativum), while short-day crops include rice (Oryza sativa), soybean (Glycine max), and maize (Zea mays). Understanding the molecular regulation of flowering and genotypic variation therein is important for molecular breeding and crop improvement. This paper reviews the regulation of flowering in different crop species with a particular focus on how photoperiod-related genes facilitate adaptation to local environments.
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Affiliation(s)
| | | | | | - Xiaoya Lin
- *Correspondence: Xiaoya Lin, ; Sijia Lu,
| | - Sijia Lu
- *Correspondence: Xiaoya Lin, ; Sijia Lu,
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15
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Zhao Y, Zhao B, Xie Y, Jia H, Li Y, Xu M, Wu G, Ma X, Li Q, Hou M, Li C, Xia Z, He G, Xu H, Bai Z, Kong D, Zheng Z, Liu Q, Liu Y, Zhong J, Tian F, Wang B, Wang H. The evening complex promotes maize flowering and adaptation to temperate regions. THE PLANT CELL 2023; 35:369-389. [PMID: 36173348 PMCID: PMC9806612 DOI: 10.1093/plcell/koac296] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 09/16/2022] [Indexed: 05/30/2023]
Abstract
Maize (Zea mays) originated in southern Mexico and has spread over a wide latitudinal range. Maize expansion from tropical to temperate regions has necessitated a reduction of its photoperiod sensitivity. In this study, we cloned a quantitative trait locus (QTL) regulating flowering time in maize and show that the maize ortholog of Arabidopsis thaliana EARLY FLOWERING3, ZmELF3.1, is the causal locus. We demonstrate that ZmELF3.1 and ZmELF3.2 proteins can physically interact with ZmELF4.1/4.2 and ZmLUX1/2, to form evening complex(es; ECs) in the maize circadian clock. Loss-of-function mutants for ZmELF3.1/3.2 and ZmLUX1/2 exhibited delayed flowering under long-day and short-day conditions. We show that EC directly represses the expression of several flowering suppressor genes, such as the CONSTANS, CONSTANS-LIKE, TOC1 (CCT) genes ZmCCT9 and ZmCCT10, ZmCONSTANS-LIKE 3, and the PSEUDORESPONSE REGULATOR (PRR) genes ZmPRR37a and ZmPRR73, thus alleviating their inhibition, allowing florigen gene expression and promoting flowering. Further, we identify two closely linked retrotransposons located in the ZmELF3.1 promoter that regulate the expression levels of ZmELF3.1 and may have been positively selected during postdomestication spread of maize from tropical to temperate regions during the pre-Columbian era. These findings provide insights into circadian clock-mediated regulation of photoperiodic flowering in maize and new targets of genetic improvement for breeding.
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Affiliation(s)
- Yongping Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Binbin Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yurong Xie
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- HainanYazhou Bay Seed Lab, Sanya, 572025, China
| | - Hong Jia
- Department of Plant Genetics and Breeding, State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, China Agricultural University, Beijing, 100193, China
| | - Yongxiang Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 10008, China
| | - Miaoyun Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- HainanYazhou Bay Seed Lab, Sanya, 572025, China
| | - Guangxia Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaojing Ma
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Quanquan Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mei Hou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Changyu Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhanchao Xia
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Gang He
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hua Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhijing Bai
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dexin Kong
- School of Life Sciences, and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Zhigang Zheng
- School of Life Sciences, and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Qing Liu
- School of Life Sciences, and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Yuting Liu
- School of Life Sciences, and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Jinshun Zhong
- School of Life Sciences, and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
| | - Feng Tian
- Department of Plant Genetics and Breeding, State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, China Agricultural University, Beijing, 100193, China
| | - Baobao Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- HainanYazhou Bay Seed Lab, Sanya, 572025, China
| | - Haiyang Wang
- School of Life Sciences, and State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, China
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16
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Yokomizo T, Takahashi Y. Endogenous rhythm variation and adaptation to the tidal environment in the freshwater snail, Semisulcospira reiniana. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1078234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Organisms have endogenous timekeeping system(s) to coordinate their biological processes with environmental cycles, allowing adaptation to external rhythmic changes in their environment. The change in endogenous rhythms could contribute to range expansion in a novel rhythmic environment. We hypothesized that populations of the freshwater snail near estuaries show a circatidal rhythm to synchronize with the tidal cycle. We compared the behavioral and gene expression rhythms between non-tidal and tidal populations of the freshwater snail, Semisulcospira reiniana. Individuals inhabiting tidal areas exhibited a rhythmic activity pattern coordinated with the tidal cycle under both field and laboratory conditions, but individuals inhabiting upstream non-tidal areas showed a circadian activity pattern. The proportion of circadian oscillating genes was greater in non-tidal than in tidal individuals, while that of circatidal oscillating genes was greater in tidal than in non-tidal individuals. Additionally, transcriptome-wide population genetic analyses revealed that these two adjacent populations can be clearly distinguished genetically, though the genetic distance was very small. Our results provide evidence of the shift in an endogenous rhythm via range expansion to a novel rhythmic environment. The changes in a small number of genes and/or phenotypic plasticity may contribute to the difference in the endogenous rhythms between non-tidal and tidal populations.
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17
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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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18
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Trevaskis B, Harris FAJ, Bovill WD, Rattey AR, Khoo KHP, Boden SA, Hyles J. Advancing understanding of oat phenology for crop adaptation. FRONTIERS IN PLANT SCIENCE 2022; 13:955623. [PMID: 36311119 PMCID: PMC9614419 DOI: 10.3389/fpls.2022.955623] [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: 05/29/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Oat (Avena sativa) is an annual cereal grown for forage, fodder and grain. Seasonal flowering behaviour, or phenology, is a key contributor to the success of oat as a crop. As a species, oat is a vernalization-responsive long-day plant that flowers after winter as days lengthen in spring. Variation in both vernalization and daylength requirements broadens adaptation of oat and has been used to breed modern cultivars with seasonal flowering behaviours suited to different regions, sowing dates and farming practices. This review examines the importance of variation in oat phenology for crop adaptation. Strategies to advance understanding of the genetic basis of oat phenology are then outlined. These include the potential to transfer knowledge from related temperate cereals, particularly wheat (Triticum aestivum) and barley (Hordeum vulgare), to provide insights into the potential molecular basis of variation in oat phenology. Approaches that use emerging genomic resources to directly investigate the molecular basis of oat phenology are also described, including application of high-resolution genome-wide diversity surveys to map genes linked to variation in flowering behaviour. The need to resolve the contribution of individual phenology genes to crop performance by developing oat genetic resources, such as near-isogenic lines, is emphasised. Finally, ways that deeper knowledge of oat phenology can be applied to breed improved varieties and to inform on-farm decision-making are outlined.
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Affiliation(s)
- Ben Trevaskis
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food Business Unit, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
| | - Felicity A. J. Harris
- Department of Primary Industries, Pine Gully Road, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - William D. Bovill
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food Business Unit, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
| | | | - Kelvin H. P. Khoo
- School of Agriculture, Food & Wine, Faculty of Sciences, Waite Research Institute, University of Adelaide, Urrbrae, Adelaide, SA, Australia
| | - Scott A. Boden
- School of Agriculture, Food & Wine, Faculty of Sciences, Waite Research Institute, University of Adelaide, Urrbrae, Adelaide, SA, Australia
| | - Jessica Hyles
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food Business Unit, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
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Maeda AE, Nakamichi N. Plant clock modifications for adapting flowering time to local environments. PLANT PHYSIOLOGY 2022; 190:952-967. [PMID: 35266545 PMCID: PMC9516756 DOI: 10.1093/plphys/kiac107] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/09/2022] [Indexed: 05/25/2023]
Abstract
During and after the domestication of crops from ancestral wild plants, humans selected cultivars that could change their flowering time in response to seasonal daylength. Continuous selection of this trait eventually allowed the introduction of crops into higher or lower latitudes and different climates from the original regions where domestication initiated. In the past two decades, numerous studies have found the causal genes or alleles that change flowering time and have assisted in adapting crop species such as barley (Hordeum vulgare), wheat (Triticum aestivum L.), rice (Oryza sativa L.), pea (Pisum sativum L.), maize (Zea mays spp. mays), and soybean (Glycine max (L.) Merr.) to new environments. This updated review summarizes the genes or alleles that contributed to crop adaptation in different climatic areas. Many of these genes are putative orthologs of Arabidopsis (Arabidopsis thaliana) core clock genes. We also discuss how knowledge of the clock's molecular functioning can facilitate molecular breeding in the future.
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Affiliation(s)
- Akari E Maeda
- Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Norihito Nakamichi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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20
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The evening complex integrates photoperiod signals to control flowering in rice. Proc Natl Acad Sci U S A 2022; 119:e2122582119. [PMID: 35733265 DOI: 10.1073/pnas.2122582119] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Plants use photoperiodism to activate flowering in response to a particular daylength. In rice, flowering is accelerated in short-day conditions, and even a brief exposure to light during the dark period (night-break) is sufficient to delay flowering. Although many of the genes involved in controlling flowering in rice have been uncovered, how the long- and short-day flowering pathways are integrated, and the mechanism of photoperiod perception is not understood. While many of the signaling components controlling photoperiod-activated flowering are conserved between Arabidopsis and rice, flowering in these two systems is activated by opposite photoperiods. Here we establish that photoperiodism in rice is controlled by the evening complex (EC). We show that mutants in the EC genes LUX ARRYTHMO (LUX) and EARLY FLOWERING3 (ELF3) paralogs abolish rice flowering. We also show that the EC directly binds and suppresses the expression of flowering repressors, including PRR37 and Ghd7. We further demonstrate that light acts via phyB to cause a rapid and sustained posttranslational modification of ELF3-1. Our results suggest a mechanism by which the EC is able to control both long- and short-day flowering pathways.
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21
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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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22
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Bouché F, Woods DP, Linden J, Li W, Mayer KS, Amasino RM, Périlleux C. EARLY FLOWERING 3 and Photoperiod Sensing in Brachypodium distachyon. FRONTIERS IN PLANT SCIENCE 2022; 12:769194. [PMID: 35069625 PMCID: PMC8770904 DOI: 10.3389/fpls.2021.769194] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/13/2021] [Indexed: 05/26/2023]
Abstract
The proper timing of flowering, which is key to maximize reproductive success and yield, relies in many plant species on the coordination between environmental cues and endogenous developmental programs. The perception of changes in day length is one of the most reliable cues of seasonal change, and this involves the interplay between the sensing of light signals and the circadian clock. Here, we describe a Brachypodium distachyon mutant allele of the evening complex protein EARLY FLOWERING 3 (ELF3). We show that the elf3 mutant flowers more rapidly than wild type plants in short days as well as under longer photoperiods but, in very long (20 h) days, flowering is equally rapid in elf3 and wild type. Furthermore, flowering in the elf3 mutant is still sensitive to vernalization, but not to ambient temperature changes. Molecular analyses revealed that the expression of a short-day marker gene is suppressed in elf3 grown in short days, and the expression patterns of clock genes and flowering time regulators are altered. We also explored the mechanisms of photoperiodic perception in temperate grasses by exposing B. distachyon plants grown under a 12 h photoperiod to a daily night break consisting of a mixture of red and far-red light. We showed that 2 h breaks are sufficient to accelerate flowering in B. distachyon under non-inductive photoperiods and that this acceleration of flowering is mediated by red light. Finally, we discuss advances and perspectives for research on the perception of photoperiod in temperate grasses.
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Affiliation(s)
- Frédéric Bouché
- Laboratory of Plant Physiology, InBioS-PhytoSYSTEMS, Department of Life Sciences, University of Liège, Liège, Belgium
| | - Daniel P. Woods
- Plant Sciences Department, University of California, Davis, Davis, CA, United States
- Laboratory of Genetics, University of Wisconsin, Madison, WI, United States
- Department of Biochemistry, University of Wisconsin, Madison, WI, United States
- United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, United States
- Howard Hughes Medical Institute, Chevy Chase, MD, United States
| | - Julie Linden
- Laboratory of Plant Physiology, InBioS-PhytoSYSTEMS, Department of Life Sciences, University of Liège, Liège, Belgium
| | - Weiya Li
- Department of Biochemistry, University of Wisconsin, Madison, WI, United States
| | - Kevin S. Mayer
- Laboratory of Genetics, University of Wisconsin, Madison, WI, United States
| | - Richard M. Amasino
- Laboratory of Genetics, University of Wisconsin, Madison, WI, United States
- Department of Biochemistry, University of Wisconsin, Madison, WI, United States
- United States Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, United States
| | - Claire Périlleux
- Laboratory of Plant Physiology, InBioS-PhytoSYSTEMS, Department of Life Sciences, University of Liège, Liège, Belgium
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23
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Göransson M, Sigurdardottir TH, Lillemo M, Bengtsson T, Hallsson JH. The Winter-Type Allele of HvCEN Is Associated With Earliness Without Severe Yield Penalty in Icelandic Spring Barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2021; 12:720238. [PMID: 34630467 PMCID: PMC8500236 DOI: 10.3389/fpls.2021.720238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
Icelandic barley genotypes have shown extreme earliness both in flowering and maturity compared to other north European genotypes, whereas earliness is a key trait in adapting barley to northern latitudes. Four genes were partially re-sequenced, which are Ppd-H1, HvCEN, HvELF3, and HvFT1, to better understand the mechanisms underlying this observed earliness. These genes are all known to play a part in the photoperiod response. The objective of this study is to correlate allelic diversity with flowering time and yield data from Icelandic field trials. The resequencing identified two to three alleles at each locus which resulted in 12 haplotype combinations. One haplotype combination containing the winter-type allele of Ppd-H1 correlated with extreme earliness, however, with a severe yield penalty. A winter-type allele in HvCEN in four genotypes correlated with earliness combined with high yield. Our results open the possibility of marker-assisted pyramiding as a rapid way to develop varieties with a shortened time from sowing to flowering under the extreme Icelandic growing conditions and possibly in other arctic or sub-arctic regions.
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Affiliation(s)
- Magnus Göransson
- Faculty of Agriculture, Agricultural University of Iceland, Reykjavík, Iceland
- Department of Plant Science, Norwegian University of Life Sciences, Ås, Norway
| | | | - Morten Lillemo
- Department of Plant Science, Norwegian University of Life Sciences, Ås, Norway
| | - Therése Bengtsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
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24
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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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25
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Abolghasemi R, Haghighi M, Etemadi N, Wang S, Soorni A. Transcriptome architecture reveals genetic networks of bolting regulation in spinach. BMC PLANT BIOLOGY 2021; 21:179. [PMID: 33853527 PMCID: PMC8045288 DOI: 10.1186/s12870-021-02956-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 03/31/2021] [Indexed: 05/09/2023]
Abstract
BACKGROUND Bolting refers to the early flowering stem production on agricultural and horticultural crops before harvesting. Indeed, bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components, which cause a large reduction in the quality and productivity of vegetable crops like spinach. However, little is known about the signaling pathways and molecular functions involved in bolting mechanisms in spinach. The genetic information regarding the transition from vegetative growth to the reproductive stage in spinach would represent an advantage to regulate bolting time and improvement of resistant cultivars to minimize performance loss. RESULTS To investigate the key genes and their genetic networks controlling spinach bolting, we performed RNA-seq analysis on early bolting accession Kashan and late-bolting accession Viroflay at both vegetative and reproductive stages and found a significant number of differentially expressed genes (DEGs) ranging from 195 to 1230 in different comparisons. These genes were mainly associated with the signaling pathways of vernalization, photoperiod/circadian clock, gibberellin, autonomous, and aging pathways. Gene ontology analysis uncovered terms associated with carbohydrate metabolism, and detailed analysis of expression patterns for genes of Fructose-1, 6-bisphosphate aldolase, TREHALOSE-6-PHOSPHATE SYNTHASE 1, FLOWERING PROMOTING FACTOR 1, EARLY FLOWERING, GIGANTEA, and MADS-box proteins revealed their potential roles in the initiating or delaying of bolting. CONCLUSION This study is the first report on identifying bolting and flowering-related genes based on transcriptome sequencing in spinach, which provides insight into bolting control and can be useful for molecular breeding programs and further study in the regulation of the genetic mechanisms related to bolting in other vegetable crops.
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Affiliation(s)
- Reza Abolghasemi
- Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Maryam Haghighi
- Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Nematollah Etemadi
- Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Shui Wang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Aboozar Soorni
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.
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26
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McClung CR. Circadian Clock Components Offer Targets for Crop Domestication and Improvement. Genes (Basel) 2021; 12:genes12030374. [PMID: 33800720 PMCID: PMC7999361 DOI: 10.3390/genes12030374] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 12/31/2022] Open
Abstract
During plant domestication and improvement, farmers select for alleles present in wild species that improve performance in new selective environments associated with cultivation and use. The selected alleles become enriched and other alleles depleted in elite cultivars. One important aspect of crop improvement is expansion of the geographic area suitable for cultivation; this frequently includes growth at higher or lower latitudes, requiring the plant to adapt to novel photoperiodic environments. Many crops exhibit photoperiodic control of flowering and altered photoperiodic sensitivity is commonly required for optimal performance at novel latitudes. Alleles of a number of circadian clock genes have been selected for their effects on photoperiodic flowering in multiple crops. The circadian clock coordinates many additional aspects of plant growth, metabolism and physiology, including responses to abiotic and biotic stresses. Many of these clock-regulated processes contribute to plant performance. Examples of selection for altered clock function in tomato demonstrate that with domestication, the phasing of the clock is delayed with respect to the light–dark cycle and the period is lengthened; this modified clock is associated with increased chlorophyll content in long days. These and other data suggest the circadian clock is an attractive target during breeding for crop improvement.
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Affiliation(s)
- C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
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27
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Rees H, Joynson R, Brown JKM, Hall A. Naturally occurring circadian rhythm variation associated with clock gene loci in Swedish Arabidopsis accessions. PLANT, CELL & ENVIRONMENT 2021; 44:807-820. [PMID: 33179278 PMCID: PMC7986795 DOI: 10.1111/pce.13941] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 05/25/2023]
Abstract
Circadian clocks have evolved to resonate with external day and night cycles. However, these entrainment signals are not consistent everywhere and vary with latitude, climate and seasonality. This leads to divergent selection for clocks which are locally adapted. To investigate the genetic basis for this circadian variation, we used a delayed fluorescence imaging assay to screen 191 naturally occurring Swedish Arabidopsis accessions for their circadian phenotypes. We demonstrate that the period length co-varies with both geography and population sub-structure. Several candidate loci linked to period, phase and relative amplitude error (RAE) were revealed by genome-wide association mapping and candidate genes were investigated using TDNA mutants. We show that natural variation in a single non-synonymous substitution within COR28 is associated with a long-period and late-flowering phenotype similar to that seen in TDNA knock-out mutants. COR28 is a known coordinator of flowering time, freezing tolerance and the circadian clock; all of which may form selective pressure gradients across Sweden. We demonstrate the effect of the COR28-58S SNP in increasing period length through a co-segregation analysis. Finally, we show that period phenotypic tails remain diverged under lower temperatures and follow a distinctive "arrow-shaped" trend indicative of selection for a cold-biased temperature compensation response.
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Affiliation(s)
- Hannah Rees
- Organisms and EcosystemsEarlham Institute, Norwich Research ParkNorwichUK
- Institute of Integrative Biology, University of LiverpoolLiverpoolUK
| | - Ryan Joynson
- Organisms and EcosystemsEarlham Institute, Norwich Research ParkNorwichUK
| | | | - Anthony Hall
- Organisms and EcosystemsEarlham Institute, Norwich Research ParkNorwichUK
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28
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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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29
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Zhao H, Xu D, Tian T, Kong F, Lin K, Gan S, Zhang H, Li G. Molecular and functional dissection of EARLY-FLOWERING 3 (ELF3) and ELF4 in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 303:110786. [PMID: 33487361 DOI: 10.1016/j.plantsci.2020.110786] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 10/31/2020] [Accepted: 11/28/2020] [Indexed: 05/18/2023]
Abstract
The circadian clock is an endogenous timekeeper system that generates biological rhythms of approximately 24 h in most organisms. EARLY FLOWERING 3 (ELF3) and ELF4 were initially identified as negative regulators of flowering time in Arabidopsis thaliana. They were then found to play crucial roles in the circadian clock by integrating environmental light and ambient temperature signals and transmitting them to the central oscillator, thereby regulating various downstream cellular and physiological processes. At dusk, ELF3 acts as a scaffold, interacting with ELF4 and the transcription factor LUX ARRHYTHMO (PHYTOCLOCK1) to form an EVENING COMPLEX (EC). This complex represses the transcription of multiple circadian clock-related genes, thus inhibiting hypocotyl elongation and flowering. Subsequent studies have expanded knowledge about the regulatory roles of the EC in thermomorphogenesis and shade responses. In addition, ELF3 and ELF4 also form multiple complexes with other proteins including chromatin remodeling factors, histone deacetylase, and transcription factors, thus enabling the transcriptional repression of diverse targets. In this review, we summarize the recent advances in elucidating the regulatory mechanisms of ELF3 and ELF4 in plants and discuss directions for future research on ELF3 and ELF4.
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Affiliation(s)
- Hang Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271000, China; College of Life Sciences, Qufu Normal University, Qufu, 273165, China
| | - Di Xu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271000, China
| | - Tian Tian
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271000, China
| | - Fanying Kong
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271000, China
| | - Ke Lin
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271000, China; Department of Biology Science and Technology, Taishan University, Tai'an, 271000, China
| | - Shuo Gan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271000, China
| | - Haisen Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271000, China
| | - Gang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271000, China.
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Gol L, Haraldsson EB, von Korff M. Ppd-H1 integrates drought stress signals to control spike development and flowering time in barley. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:122-136. [PMID: 32459309 PMCID: PMC7816852 DOI: 10.1093/jxb/eraa261] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/21/2020] [Indexed: 05/10/2023]
Abstract
Drought impairs growth and spike development, and is therefore a major cause of yield losses in the temperate cereals barley and wheat. Here, we show that the photoperiod response gene PHOTOPERIOD-H1 (Ppd-H1) interacts with drought stress signals to modulate spike development. We tested the effects of a continuous mild and a transient severe drought stress on developmental timing and spike development in spring barley cultivars with a natural mutation in ppd-H1 and derived introgression lines carrying the wild-type Ppd-H1 allele from wild barley. Mild drought reduced the spikelet number and delayed floral development in spring cultivars but not in the introgression lines with a wild-type Ppd-H1 allele. Similarly, drought-triggered reductions in plant height, and tiller and spike number were more pronounced in the parental lines compared with the introgression lines. Transient severe stress halted growth and floral development; upon rewatering, introgression lines, but not the spring cultivars, accelerated development so that control and stressed plants flowered almost simultaneously. These genetic differences in development were correlated with a differential down-regulation of the flowering promotors FLOWERING LOCUS T1 and the BARLEY MADS-box genes BM3 and BM8. Our findings therefore demonstrate that Ppd-H1 affects developmental plasticity in response to drought in barley.
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Affiliation(s)
- Leonard Gol
- Institute for Plant Genetics, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
- Max-Planck-Institute for Plant Breeding Research, Cologne, Germany
| | - Einar B Haraldsson
- Institute for Plant Genetics, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Maria von Korff
- Institute for Plant Genetics, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
- Max-Planck-Institute for Plant Breeding Research, Cologne, Germany
- Cluster of Excellence on Plant Sciences, ‘SMART Plants for Tomorrows Needs’, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
- Correspondence:
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31
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Brandoli C, Petri C, Egea-Cortines M, Weiss J. Gigantea: Uncovering New Functions in Flower Development. Genes (Basel) 2020; 11:genes11101142. [PMID: 32998354 PMCID: PMC7600796 DOI: 10.3390/genes11101142] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/19/2020] [Accepted: 09/22/2020] [Indexed: 11/16/2022] Open
Abstract
GIGANTEA (GI) is a gene involved in multiple biological functions, which have been analysed and are partially conserved in a series of mono- and dicotyledonous plant species. The identified biological functions include control over the circadian rhythm, light signalling, cold tolerance, hormone signalling and photoperiodic flowering. The latter function is a central role of GI, as it involves a multitude of pathways, both dependent and independent of the gene CONSTANS(CO), as well as on the basis of interaction with miRNA. The complexity of the gene function of GI increases due to the existence of paralogs showing changes in genome structure as well as incidences of sub- and neofunctionalization. We present an updated report of the biological function of GI, integrating late insights into its role in floral initiation, flower development and volatile flower production.
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Affiliation(s)
- Claudio Brandoli
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, 30202 Cartagena, Spain; (C.B.); (M.E.-C.)
| | - Cesar Petri
- Instituto de Hortofruticultura Subtropical y Mediterránea-UMA-CSIC, Departamento de Fruticultura Subtropical y Mediterránea, 29750 Algarrobo-costa, Málaga, Spain;
| | - Marcos Egea-Cortines
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, 30202 Cartagena, Spain; (C.B.); (M.E.-C.)
| | - Julia Weiss
- Genética Molecular, Instituto de Biotecnología Vegetal, Edificio I+D+I, Plaza del Hospital s/n, Universidad Politécnica de Cartagena, 30202 Cartagena, Spain; (C.B.); (M.E.-C.)
- Correspondence: ; Tel.: +34-868-071-078
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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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Matyszczak I, Tominska M, Zakhrabekova S, Dockter C, Hansson M. Analysis of early-flowering genes at barley chromosome 2H expands the repertoire of mutant alleles at the Mat-c locus. PLANT CELL REPORTS 2020; 39:47-61. [PMID: 31541262 PMCID: PMC6960220 DOI: 10.1007/s00299-019-02472-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 09/08/2019] [Indexed: 05/31/2023]
Abstract
Analyses of barley mat-c loss of function mutants reveal deletions, splice-site mutations and nonsynonymous substitutions in a key gene regulating early flowering. Optimal timing of flowering is critical for reproductive success and crop yield improvement. Several major quantitative trait loci for flowering time variation have been identified in barley. In the present study, we analyzed two near-isogenic lines, BW507 and BW508, which were reported to carry two independent early-flowering mutant loci, mat-b.7 and mat-c.19, respectively. Both introgression segments are co-localized in the pericentromeric region of chromosome 2H. We mapped the mutation in BW507 to a 31 Mbp interval on chromosome 2HL and concluded that BW507 has a deletion of Mat-c, which is an ortholog of Antirrhinum majus CENTRORADIALIS (AmCEN) and Arabidopsis thaliana TERMINAL FLOWER1 (AtTFL1). Contrary to previous reports, our data showed that both BW507 and BW508 are Mat-c deficient and none of them are mat-b.7 derived. This work complements previous studies by identifying the uncharacterized mat-c.19 mutant and seven additional mat-c mutants. Moreover, we explored the X-ray structure of AtTFL1 for prediction of the functional effects of nonsynonymous substitutions caused by mutations in Mat-c.
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Affiliation(s)
- Izabela Matyszczak
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, 1799, Copenhagen V, Denmark
| | - Marta Tominska
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, 1799, Copenhagen V, Denmark
- Department of Plant Physiology, Faculty of Biology and Environment Protection, University of Silesia, 40-032, Katowice, Poland
| | - Shakhira Zakhrabekova
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, 1799, Copenhagen V, Denmark
- Department of Biology, Lund University, Sölvegatan 35, SE-22362, Lund, Sweden
| | - Christoph Dockter
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, 1799, Copenhagen V, Denmark
| | - Mats Hansson
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, 1799, Copenhagen V, Denmark.
- Department of Biology, Lund University, Sölvegatan 35, SE-22362, Lund, Sweden.
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Transcriptional Structure of Petunia Clock in Leaves and Petals. Genes (Basel) 2019; 10:genes10110860. [PMID: 31671570 PMCID: PMC6895785 DOI: 10.3390/genes10110860] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 01/20/2023] Open
Abstract
The plant circadian clock coordinates environmental signals with internal processes including secondary metabolism, growth, flowering, and volatile emission. Plant tissues are specialized in different functions, and petals conceal the sexual organs while attracting pollinators. Here we analyzed the transcriptional structure of the petunia (Petunia x hybrida) circadian clock in leaves and petals. We recorded the expression of 13 clock genes in petunia under light:dark (LD) and constant darkness (DD). Under light:dark conditions, clock genes reached maximum expression during the light phase in leaves and the dark period in petals. Under free running conditions of constant darkness, maximum expression was delayed, especially in petals. Interestingly, the rhythmic expression pattern of PhLHY persisted in leaves and petals in LD and DD. Gene expression variability differed among leaves and petals, time of day and photoperiod. The transcriptional noise was higher especially in leaves under constant darkness. We found that PhPRR7, PhPRR5, and PhGI paralogs showed changes in gene structure including exon number and deletions of CCT domain of the PRR family. Our results revealed that petunia petals presented a specialized clock.
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He T, Hill CB, Angessa TT, Zhang XQ, Chen K, Moody D, Telfer P, Westcott S, Li C. Gene-set association and epistatic analyses reveal complex gene interaction networks affecting flowering time in a worldwide barley collection. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5603-5616. [PMID: 31504706 PMCID: PMC6812734 DOI: 10.1093/jxb/erz332] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 08/13/2019] [Indexed: 05/10/2023]
Abstract
Single-marker genome-wide association studies (GWAS) have successfully detected associations between single nucleotide polymorphisms (SNPs) and agronomic traits such as flowering time and grain yield in barley. However, the analysis of individual SNPs can only account for a small proportion of genetic variation, and can only provide limited knowledge on gene network interactions. Gene-based GWAS approaches provide enormous opportunity both to combine genetic information and to examine interactions among genetic variants. Here, we revisited a previously published phenotypic and genotypic data set of 895 barley varieties grown in two years at four different field locations in Australia. We employed statistical models to examine gene-phenotype associations, as well as two-way epistasis analyses to increase the capability to find novel genes that have significant roles in controlling flowering time in barley. Genetic associations were tested between flowering time and corresponding genotypes of 174 putative flowering time-related genes. Gene-phenotype association analysis detected 113 genes associated with flowering time in barley, demonstrating the unprecedented power of gene-based analysis. Subsequent two-way epistasis analysis revealed 19 pairs of gene×gene interactions involved in controlling flowering time. Our study demonstrates that gene-based association approaches can provide higher capacity for future crop improvement to increase crop performance and adaptation to different environments.
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Affiliation(s)
- Tianhua He
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Camilla Beate Hill
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Tefera Tolera Angessa
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Kefei Chen
- SAGI-WEST, Faculty of Science and Engineering, Curtin University, Bentley, WA, Australia
| | | | - Paul Telfer
- Australian Grain Technologies Pty Ltd (AGT), SA, Australia
| | - Sharon Westcott
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Chengdao Li
- Western Barley Genetics Alliance, Western Australian State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
- Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Hubei Jingzhou, China
- Correspondence:
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36
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Lei L, Poets AM, Liu C, Wyant SR, Hoffman PJ, Carter CK, Shaw BG, Li X, Muehlbauer GJ, Katagiri F, Morrell PL. Environmental Association Identifies Candidates for Tolerance to Low Temperature and Drought. G3 (BETHESDA, MD.) 2019; 9:3423-3438. [PMID: 31439717 PMCID: PMC6778781 DOI: 10.1534/g3.119.400401] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/17/2019] [Indexed: 11/24/2022]
Abstract
Barley (Hordeum vulgare ssp. vulgare) is cultivated from the equator to the Arctic Circle. The wild progenitor species, Hordeum vulgare ssp. spontaneum, occupies a relatively narrow latitudinal range (∼30 - 40° N) primarily at low elevation (< 1,500 m). Adaptation to the range of cultivation has occurred over ∼8,000 years. The genetic basis of adaptation is amenable to study through environmental association. An advantage of environmental association in a well-characterized crop is that many loci that contribute to climatic adaptation and abiotic stress tolerance have already been identified. This provides the opportunity to determine if environmental association approaches effectively identify these loci of large effect. Using published genotyping from 7,864 SNPs in 803 barley landraces, we examined allele frequency differentiation across multiple partitions of the data and mixed model associations relative to bioclimatic variables. Using newly generated resequencing data from a subset of these landraces, we tested for linkage disequilibrium (LD) between SNPs queried in genotyping and SNPs in neighboring loci. Six loci previously reported to contribute to adaptive differences in flowering time and abiotic stress in barley and six loci previously identified in other plant species were identified in our analyses. In many cases, patterns of LD are consistent with the causative variant occurring in the immediate vicinity of the queried SNP. The identification of barley orthologs to well-characterized genes may provide a new understanding of the nature of adaptive variation and could permit a more targeted use of potentially adaptive variants in barley breeding and germplasm improvement.
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Affiliation(s)
- Li Lei
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108 and
| | - Ana M Poets
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108 and
| | - Chaochih Liu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108 and
| | - Skylar R Wyant
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108 and
| | - Paul J Hoffman
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108 and
| | - Corey K Carter
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108 and
| | - Brian G Shaw
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108 and
| | - Xin Li
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108 and
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108 and
- Department of Plant and Microbial Biology, Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, Minnesota 55108
| | - Fumiaki Katagiri
- Department of Plant and Microbial Biology, Microbial and Plant Genomics Institute, University of Minnesota, St. Paul, Minnesota 55108
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108 and
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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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Schreiber M, Barakate A, Uzrek N, Macaulay M, Sourdille A, Morris J, Hedley PE, Ramsay L, Waugh R. A highly mutagenised barley ( cv. Golden Promise) TILLING population coupled with strategies for screening-by-sequencing. PLANT METHODS 2019; 15:99. [PMID: 31462905 PMCID: PMC6708184 DOI: 10.1186/s13007-019-0486-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 08/16/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND We developed and characterised a highly mutagenised TILLING population of the barley (Hordeum vulgare) cultivar Golden Promise. Golden Promise is the 'reference' genotype for barley transformation and a primary objective of using this cultivar was to be able to genetically complement observed mutations directly in order to prove gene function. Importantly, a reference genome assembly of Golden Promise has also recently been developed. As our primary interest was to identify mutations in genes involved in meiosis and recombination, to characterise the population we focused on a set of 46 genes from the literature that are possible meiosis gene candidates. RESULTS Sequencing 20 plants from the population using whole exome capture revealed that the mutation density in this population is high (one mutation every 154 kb), and consequently even in this small number of plants we identified several interesting mutations. We also recorded some issues with seed availability and germination. We subsequently designed and applied a simple two-dimensional pooling strategy to identify mutations in varying numbers of specific target genes by Illumina short read pooled-amplicon sequencing and subsequent deconvolution. In parallel we assembled a collection of semi-sterile mutants from the population and used a custom exome capture array targeting the 46 candidate meiotic genes to identify potentially causal mutations. CONCLUSIONS We developed a highly mutagenised barley TILLING population in the transformation competent cultivar Golden Promise. We used novel and cost-efficient screening approaches to successfully identify a broad range of potentially deleterious variants that were subsequently validated by Sanger sequencing. These resources combined with a high-quality genome reference sequence opens new possibilities for efficient functional gene validation.
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Affiliation(s)
- Miriam Schreiber
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA Scotland UK
| | - Abdellah Barakate
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA Scotland UK
| | - Nicola Uzrek
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA Scotland UK
| | - Malcolm Macaulay
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA Scotland UK
| | - Adeline Sourdille
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA Scotland UK
| | - Jenny Morris
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA Scotland UK
| | - Pete E. Hedley
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA Scotland UK
| | - Luke Ramsay
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA Scotland UK
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA Scotland UK
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA Scotland UK
- School of Agriculture and Wine, University of Adelaide, Plant Genome Building, Waite Campus, Urrbrae, Adelaide, SA Australia
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Woodhouse MR, Hufford MB. Parallelism and convergence in post-domestication adaptation in cereal grasses. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180245. [PMID: 31154975 DOI: 10.1098/rstb.2018.0245] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The selection of desirable traits in crops during domestication has been well studied. Many crops share a suite of modified phenotypic characteristics collectively known as the domestication syndrome. In this sense, crops have convergently evolved. Previous work has demonstrated that, at least in some instances, convergence for domestication traits has been achieved through parallel molecular means. However, both demography and selection during domestication may have placed limits on evolutionary potential and reduced opportunities for convergent adaptation during post-domestication migration to new environments. Here we review current knowledge regarding trait convergence in the cereal grasses and consider whether the complexity and dynamism of cereal genomes (e.g., transposable elements, polyploidy, genome size) helped these species overcome potential limitations owing to domestication and achieve broad subsequent adaptation, in many cases through parallel means. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
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Affiliation(s)
- M R Woodhouse
- Iowa State University, Ecology, Evolution, and Organismal Biology , Ames, IA 50011 , USA
| | - M B Hufford
- Iowa State University, Ecology, Evolution, and Organismal Biology , Ames, IA 50011 , USA
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40
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Monteagudo A, Casas AM, Cantalapiedra CP, Contreras-Moreira B, Gracia MP, Igartua E. Harnessing Novel Diversity From Landraces to Improve an Elite Barley Variety. FRONTIERS IN PLANT SCIENCE 2019; 10:434. [PMID: 31031782 PMCID: PMC6470277 DOI: 10.3389/fpls.2019.00434] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 03/22/2019] [Indexed: 05/20/2023]
Abstract
The Spanish Barley Core Collection (SBCC) is a source of genetic variability of potential interest for breeding, particularly for adaptation to Mediterranean environments. Two backcross populations (BC2F5) were developed using the elite cultivar Cierzo as the recurrent parent. The donor parents, namely SBCC042 and SBCC073, were selected from the SBCC lines due to their outstanding yield in drought environments. Flowering time, yield and drought-related traits were evaluated in two field trials in Zaragoza (Spain) during the 2014-15 and 2015-16 seasons and validated in the 2017-18 season. Two hundred sixty-four lines of each population were genotyped with the Barley Illumina iSelect 50k SNP chip. Genetic maps for each population were generated. The map for SBCC042 × Cierzo contains 12,893 SNPs distributed in 9 linkage groups. The map for SBCC073 × Cierzo includes 12,026 SNPs in 7 linkage groups. Both populations shared two QTL hotspots. There are QTLs for flowering time, thousand-kernel weight (TKW), and hectoliter weight on a segment of 23 Mb at ~515 Mb on chromosome 1H, which encompasses the HvFT3 gene. In both populations, flowering was accelerated by the landrace allele, which also increased the TKW. In the same region, better soil coverage was contributed by SBCC042 but coincident with a lower hectoliter weight. The second large hotspot was on chromosome 6H and contained QTLs with wide intervals for grain yield, plant height and TKW. Landrace alleles contributed to increased plant height and TKW and reduced grain yield. Only SBCC042 contributed favorable alleles for "green area," with three significant QTLs that increased ground coverage after winter, which might be exploited as an adaptive trait of this landrace. Some genes of interest found in or very close to the peaks of the QTLs are highlighted. Strategies to deploy the QTLs found for breeding and pre-breeding are proposed.
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Affiliation(s)
| | - Ana M. Casas
- Aula Dei Experimental Station (EEAD-CSIC), Zaragoza, Spain
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Fujino K, Obara M, Ikegaya T. Establishment of adaptability to the northern-limit of rice production. Mol Genet Genomics 2019; 294:729-737. [PMID: 30874890 DOI: 10.1007/s00438-019-01542-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 02/23/2019] [Indexed: 10/27/2022]
Abstract
The domestication of cultivated crops from their wild relatives narrowed down their genetic diversity in a bottleneck effect. Subsequently, the cultivation areas of crops have expanded all over the world into various environmental conditions from the original area along with human migration after domestication. Here, we demonstrated the genetic changes in the adaptation of rice to Hokkaido (41°2-45°3N latitude), Japan, from the tropics of their origin in Asian cultivated rice, Oryza sativa L. Although cultivated rice originated from the tropics, Hokkaido is one of the northern-limits of rice cultivation worldwide. Population genomics focusing on the local populations showed the varieties had genetically distinct classes with limited genetic diversity. In addition, some varieties in the class carried unique genotypes for flowering time, exhibiting extremely early flowering time. Certain mutations in unique genotypes can split off the varieties that are able to grow in Hokkaido. Furthermore, the changes in the genotype for flowering time during rice cultivation in Hokkaido demonstrated novel combinations of genes for flowering time owing to the intensive artificial selection on natural variation and rice breeding programs to achieve stable rice production in Hokkaido.
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Affiliation(s)
- Kenji Fujino
- Hokkaido Agricultural Research Center, National Agricultural Research Organization, Sapporo, 062-8555, Japan.
| | - Mari Obara
- Hokkaido Agricultural Research Center, National Agricultural Research Organization, Sapporo, 062-8555, Japan
| | - Tomohito Ikegaya
- Hokkaido Agricultural Research Center, National Agricultural Research Organization, Sapporo, 062-8555, Japan
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Haas M, Schreiber M, Mascher M. Domestication and crop evolution of wheat and barley: Genes, genomics, and future directions. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:204-225. [PMID: 30414305 DOI: 10.1111/jipb.12737] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 10/27/2018] [Indexed: 05/02/2023]
Abstract
Wheat and barley are two of the founder crops of the agricultural revolution that took place 10,000 years ago in the Fertile Crescent and both crops remain among the world's most important crops. Domestication of these crops from their wild ancestors required the evolution of traits useful to humans, rather than survival in their natural environment. Of these traits, grain retention and threshability, yield improvement, changes to photoperiod sensitivity and nutritional value are most pronounced between wild and domesticated forms. Knowledge about the geographical origins of these crops and the genes responsible for domestication traits largely pre-dates the era of next-generation sequencing, although sequencing will lead to new insights. Molecular markers were initially used to calculate distance (relatedness), genetic diversity and to generate genetic maps which were useful in cloning major domestication genes. Both crops are characterized by large, complex genomes which were long thought to be beyond the scope of whole-genome sequencing. However, advances in sequencing technologies have improved the state of genomic resources for both wheat and barley. The availability of reference genomes for wheat and some of its progenitors, as well as for barley, sets the stage for answering unresolved questions in domestication genomics of wheat and barley.
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Affiliation(s)
- Matthew Haas
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466 Seeland, Germany
| | - Mona Schreiber
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466 Seeland, Germany
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, 06466 Seeland, Germany
- German Center for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
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Göransson M, Hallsson JH, Lillemo M, Orabi J, Backes G, Jahoor A, Hermannsson J, Christerson T, Tuvesson S, Gertsson B, Reitan L, Alsheikh M, Aikasalo R, Isolahti M, Veteläinen M, Jalli M, Krusell L, Hjortshøj RL, Eriksen B, Bengtsson T. Identification of Ideal Allele Combinations for the Adaptation of Spring Barley to Northern Latitudes. FRONTIERS IN PLANT SCIENCE 2019; 10:542. [PMID: 31130971 PMCID: PMC6510284 DOI: 10.3389/fpls.2019.00542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 04/09/2019] [Indexed: 05/02/2023]
Abstract
The northwards expansion of barley production requires adaptation to longer days, lower temperatures and stronger winds during the growing season. We have screened 169 lines of the current barley breeding gene pool in the Nordic region with regards to heading, maturity, height, and lodging under different environmental conditions in nineteen field trials over 3 years at eight locations in northern and central Europe. Through a genome-wide association scan we have linked phenotypic differences observed in multi-environment field trials (MET) to single nucleotide polymorphisms (SNP). We have identified an allele combination, only occurring among a few Icelandic lines, that affects heat sum to maturity and requires 214 growing degree days (GDD) less heat sum to maturity than the most common allele combination in the Nordic spring barley gene pool. This allele combination is beneficial in a cold environment, where autumn frost can destroy a late maturing harvest. Despite decades of intense breeding efforts relying heavily on the same germplasm, our results show that there still exists considerable variation within the current breeding gene pool and we identify ideal allele combinations for regional adaptation, which can facilitate the expansion of cereal cultivation even further northwards.
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Affiliation(s)
- Magnus Göransson
- Faculty of Agricultural and Environmental Sciences, Agricultural University of Iceland, Reykjavik, Iceland
- Department of Plant Sciences, Norwegian University of Life Sciences, Ås, Norway
- *Correspondence: Magnus Göransson, Therése Bengtsson,
| | - Jón Hallsteinn Hallsson
- Faculty of Agricultural and Environmental Sciences, Agricultural University of Iceland, Reykjavik, Iceland
| | - Morten Lillemo
- Department of Plant Sciences, Norwegian University of Life Sciences, Ås, Norway
| | | | - Gunter Backes
- Faculty of Organic Agricultural Sciences, Kassel University, Witzenhausen, Germany
| | - Ahmed Jahoor
- Nordic Seed A/S, Odder, Denmark
- Department of Plant Breeding, The Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Jónatan Hermannsson
- Faculty of Agricultural and Environmental Sciences, Agricultural University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | | | | | | | - Marja Jalli
- Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | | | | | | | - Therése Bengtsson
- Department of Plant Breeding, The Swedish University of Agricultural Sciences, Alnarp, Sweden
- *Correspondence: Magnus Göransson, Therése Bengtsson,
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Zhu C, Peng Q, Fu D, Zhuang D, Yu Y, Duan M, Xie W, Cai Y, Ouyang Y, Lian X, Wu C. The E3 Ubiquitin Ligase HAF1 Modulates Circadian Accumulation of EARLY FLOWERING3 to Control Heading Date in Rice under Long-Day Conditions. THE PLANT CELL 2018; 30:2352-2367. [PMID: 30242038 PMCID: PMC6241267 DOI: 10.1105/tpc.18.00653] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/14/2018] [Accepted: 09/14/2018] [Indexed: 05/21/2023]
Abstract
The ubiquitin 26S proteasome system (UPS) is critical for enabling plants to alter their proteomes to integrate internal and external signals for the photoperiodic induction of flowering. We previously demonstrated that HAF1, a C3HC4 RING domain-containing E3 ubiquitin ligase, is essential to precisely modulate the timing of Heading Date1 accumulation and to ensure appropriate photoperiodic responses under short-day conditions in rice (Oryza sativa). However, how HAF1 mediates flowering under long-day conditions remains unknown. In this study, we show that OsELF3 (EARLY FLOWERING3) is the direct substrate of HAF1 for ubiquitination in vitro and in vivo. HAF1 is required for maintaining the circadian rhythm of OsELF3 accumulation during photoperiodic responses in rice. In addition, the haf1 oself3 double mutant headed as late as oself3 plants under long-day conditions. An amino acid variation (L558S) within the interaction domain of OsELF3 with HAF1 greatly contributes to the variation in heading date among japonica rice accessions. The japonica accessions carrying the OsELF3(L)-type allele are found at higher latitudes, while varieties carrying the OsELF3(S)-type allele are found at lower latitudes. Taken together, our findings suggest that HAF1 precisely modulates the diurnal rhythm of OsELF3 accumulation to ensure the appropriate heading date in rice.
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Affiliation(s)
- Chunmei Zhu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Qiang Peng
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Debao Fu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Dongxia Zhuang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yiming Yu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Min Duan
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yaohui Cai
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Laboratory for Rice, Nanchang 330200, China
| | - Yidang Ouyang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xingming Lian
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Changyin Wu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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González MY, Philipp N, Schulthess AW, Weise S, Zhao Y, Börner A, Oppermann M, Graner A, Reif JC. Unlocking historical phenotypic data from an ex situ collection to enhance the informed utilization of genetic resources of barley (Hordeum sp.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2009-2019. [PMID: 29959470 DOI: 10.1007/s00122-018-3129-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 06/17/2018] [Indexed: 05/11/2023]
Abstract
Key message Historical data generated during seed regeneration are valuable to populate a bio-digital resource center for barley (Hordeum sp.). Precise estimates of trait performance of genetic resources are considered as an intellectually challenging, complex, costly and time-consuming step needed to exploit the phenotypic and genetic diversity maintained in genebanks for breeding and research. Using barley (Hordeum sp.) as a model, we examine strategies to tap into historical data available from regeneration trials. This is a first step toward extending the Federal ex situ Genebank into a bio-digital resource center facilitating an informed choice of barley accessions for research and breeding. Our study is based on historical data of seven decades collected for flowering time, plant height, and thousand grain weight during the regeneration of 12,872 spring and winter barley accessions. Linear mixed models were implemented in conjunction with routines for assessment of data quality. A resampling study highlights the potential risk of biased estimates in second-order statistics when grouping accessions for regeneration according to the year of collection or geographic origin. Based on rigorous quality assessment, we obtained high heritability estimates for the traits under consideration exceeding 0.8. Thus, the best linear unbiased estimations for the three traits are a valuable source to populate a bio-digital resource center for the IPK barley collection. The proposed strategy to leverage historical data from regeneration trials is not crop specific and can be used as a blueprint for other ex situ collections.
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Affiliation(s)
- Maria Y González
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Norman Philipp
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Albert W Schulthess
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Stephan Weise
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Yusheng Zhao
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Andreas Börner
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Markus Oppermann
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Andreas Graner
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany
| | - Jochen C Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Germany.
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Sharma R, Draicchio F, Bull H, Herzig P, Maurer A, Pillen K, Thomas WTB, Flavell AJ. Genome-wide association of yield traits in a nested association mapping population of barley reveals new gene diversity for future breeding. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3811-3822. [PMID: 29767798 PMCID: PMC6054221 DOI: 10.1093/jxb/ery178] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 06/08/2018] [Indexed: 05/05/2023]
Abstract
To explore wild barley as a source of useful alleles for yield improvement in breeding, we have carried out a genome-wide association scan using the nested association mapping population HEB-25, which contains 25 diverse exotic barley genomes superimposed on an ~70% genetic background of cultivated barley. A total of 1420 HEB-25 lines were trialled for nine yield-related grain traits for 2 years in Germany and Scotland, with varying N fertilizer application. The phenotypic data were related to genotype scores for 5398 gene-based single nucleotide polymorphism (SNP) markers. A total of 96 quantitative trait locus (QTL) regions were identified across all measured traits, the majority of which co-localize with known major genes controlling flowering time (Ppd-H2, HvCEN, HvGI, VRN-H1, and VRN-H3) and spike morphology (VRS3, VRS1, VRS4, and INT-C) in barley. Fourteen QTL hotspots, with at least three traits coinciding, were also identified, several of which co-localize with barley orthologues of genes controlling grain dimensions in rice. Most of the allele effects are specific to geographical location and/or exotic parental genotype. This study shows the existence of beneficial alleles for yield-related traits in exotic barley germplasm and provides candidate alleles for future improvement of these traits by the breeder.
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Affiliation(s)
- Rajiv Sharma
- University of Dundee at JHI, Invergowrie, Dundee, UK
| | | | - Hazel Bull
- The James Hutton Institute, Invergowrie, Dundee, UK
| | - Paul Herzig
- Martin-Luther-University Halle-Wittenberg, Halle/Saale, Germany
| | - Andreas Maurer
- Martin-Luther-University Halle-Wittenberg, Halle/Saale, Germany
| | - Klaus Pillen
- Martin-Luther-University Halle-Wittenberg, Halle/Saale, Germany
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Trevaskis B. Developmental Pathways Are Blueprints for Designing Successful Crops. FRONTIERS IN PLANT SCIENCE 2018; 9:745. [PMID: 29922318 PMCID: PMC5996307 DOI: 10.3389/fpls.2018.00745] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 05/15/2018] [Indexed: 05/29/2023]
Abstract
Genes controlling plant development have been studied in multiple plant systems. This has provided deep insights into conserved genetic pathways controlling core developmental processes including meristem identity, phase transitions, determinacy, stem elongation, and branching. These pathways control plant growth patterns and are fundamentally important to crop biology and agriculture. This review describes the conserved pathways that control plant development, using Arabidopsis as a model. Historical examples of how plant development has been altered through selection to improve crop performance are then presented. These examples, drawn from diverse crops, show how the genetic pathways controlling development have been modified to increase yield or tailor growth patterns to suit local growing environments or specialized crop management practices. Strategies to apply current progress in genomics and developmental biology to future crop improvement are then discussed within the broader context of emerging trends in plant breeding. The ways that knowledge of developmental processes and understanding of gene function can contribute to crop improvement, beyond what can be achieved by selection alone, are emphasized. These include using genome re-sequencing, mutagenesis, and gene editing to identify or generate novel variation in developmental genes. The expanding scope for comparative genomics, the possibility to engineer new developmental traits and new approaches to resolve gene-gene or gene-environment interactions are also discussed. Finally, opportunities to integrate fundamental research and crop breeding are highlighted.
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Affiliation(s)
- Ben Trevaskis
- CSIRO Agriculture and Food, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
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Pankin A, Altmüller J, Becker C, von Korff M. Targeted resequencing reveals genomic signatures of barley domestication. THE NEW PHYTOLOGIST 2018; 218:1247-1259. [PMID: 29528492 PMCID: PMC5947139 DOI: 10.1111/nph.15077] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 02/05/2018] [Indexed: 05/18/2023]
Abstract
Barley (Hordeum vulgare) is an established model to study domestication of the Fertile Crescent cereals. Recent molecular data suggested that domesticated barley genomes consist of the ancestral blocks descending from multiple wild barley populations. However, the relationship between the mosaic ancestry patterns and the process of domestication itself remained unclear. To address this knowledge gap, we identified candidate domestication genes using selection scans based on targeted resequencing of 433 wild and domesticated barley accessions. We conducted phylogenetic, population structure, and ancestry analyses to investigate the origin of the domesticated barley haplotypes separately at the neutral and candidate domestication loci. We discovered multiple selective sweeps that occurred on all barley chromosomes during domestication in the background of several ancestral wild populations. The ancestry analyses demonstrated that, although the ancestral blocks of the domesticated barley genomes were descended from all over the Fertile Crescent, the candidate domestication loci originated specifically in its eastern and western parts. These findings provided the first molecular evidence implicating multiple wild or protodomesticated lineages in the process of barley domestication initiated in the Levantine and Zagros clusters of the origin of agriculture.
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Affiliation(s)
- Artem Pankin
- Institute of Plant GeneticsHeinrich‐Heine‐University40225DüsseldorfGermany
- Max Planck Institute for Plant Breeding Research50829CologneGermany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG)University of Cologne50931CologneGermany
| | - Christian Becker
- Cologne Center for Genomics (CCG)University of Cologne50931CologneGermany
| | - Maria von Korff
- Institute of Plant GeneticsHeinrich‐Heine‐University40225DüsseldorfGermany
- Max Planck Institute for Plant Breeding Research50829CologneGermany
- Cluster of Excellence on Plant Sciences ‘From Complex Traits towards Synthetic Modules’Heinrich‐Heine‐University40225DüsseldorfGermany
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Detection of Epistasis for Flowering Time Using Bayesian Multilocus Estimation in a Barley MAGIC Population. Genetics 2017; 208:525-536. [PMID: 29254994 PMCID: PMC5788519 DOI: 10.1534/genetics.117.300546] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/12/2017] [Indexed: 12/16/2022] Open
Abstract
Gene-by-gene interactions, also known as epistasis, regulate many complex traits in different species. With the availability of low-cost genotyping it is now possible to study epistasis on a genome-wide scale. However, identifying genome-wide epistasis is a high-dimensional multiple regression problem and needs the application of dimensionality reduction techniques. Flowering Time (FT) in crops is a complex trait that is known to be influenced by many interacting genes and pathways in various crops. In this study, we successfully apply Sure Independence Screening (SIS) for dimensionality reduction to identify two-way and three-way epistasis for the FT trait in a Multiparent Advanced Generation Inter-Cross (MAGIC) barley population using the Bayesian multilocus model. The MAGIC barley population was generated from intercrossing among eight parental lines and thus, offered greater genetic diversity to detect higher-order epistatic interactions. Our results suggest that SIS is an efficient dimensionality reduction approach to detect high-order interactions in a Bayesian multilocus model. We also observe that many of our findings (genomic regions with main or higher-order epistatic effects) overlap with known candidate genes that have been already reported in barley and closely related species for the FT trait.
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