1
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Li Y, Xiong H, Guo H, Xie Y, Zhao L, Gu J, Li H, Zhao S, Ding Y, Zhou C, Fang Z, Liu L. A gain-of-function mutation at the C-terminus of FT-D1 promotes heading by interacting with 14-3-3A and FDL6 in wheat. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 39276323 DOI: 10.1111/pbi.14474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 07/17/2024] [Accepted: 08/31/2024] [Indexed: 09/16/2024]
Abstract
Vernalization and photoperiod pathways converging at FT1 control the transition to flowering in wheat. Here, we identified a gain-of-function mutation in FT-D1 that results in earlier heading date (HD), and shorter plant height and spike length in the gamma ray-induced eh1 wheat mutant. Knockout of the wild-type and overexpression of the mutated FT-D1 indicate that both alleles are functional to affect HD and plant height. Protein interaction assays demonstrated that the frameshift mutation in FT-D1eh1 exon 3 led to gain-of-function interactions with 14-3-3A and FDL6, thereby enabling the formation of florigen activation complex (FAC) and consequently activating a flowering-related transcriptomic programme. This mutation did not affect FT-D1eh1 interactions with TaNaKR5 or TaFTIP7, both of which could modulate HD, potentially via mediating FT-D1 translocation to the shoot apical meristem. Furthermore, the 'Segment B' external loop is essential for FT-D1 interaction with FDL6, while residue Y85 is required for interactions with TaNaKR5 and TaFTIP7. Finally, the flowering regulatory hub gene, ELF5, was identified as the FT-D1 regulatory target. This study illustrates FT-D1 function in determining wheat HD with a suite of interaction partners and provides genetic resources for tuning HD in elite wheat lines.
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Affiliation(s)
- Yuting Li
- State Key Laboratory of Crop Gene Resources and Breeding/National Engineering Laboratory of Crop Molecular Breeding/CAEA Research and Development Centre on Nuclear Technology Applications for Irradiation Mutation Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Hongchun Xiong
- State Key Laboratory of Crop Gene Resources and Breeding/National Engineering Laboratory of Crop Molecular Breeding/CAEA Research and Development Centre on Nuclear Technology Applications for Irradiation Mutation Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huijun Guo
- State Key Laboratory of Crop Gene Resources and Breeding/National Engineering Laboratory of Crop Molecular Breeding/CAEA Research and Development Centre on Nuclear Technology Applications for Irradiation Mutation Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yongdun Xie
- State Key Laboratory of Crop Gene Resources and Breeding/National Engineering Laboratory of Crop Molecular Breeding/CAEA Research and Development Centre on Nuclear Technology Applications for Irradiation Mutation Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Linshu Zhao
- State Key Laboratory of Crop Gene Resources and Breeding/National Engineering Laboratory of Crop Molecular Breeding/CAEA Research and Development Centre on Nuclear Technology Applications for Irradiation Mutation Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiayu Gu
- State Key Laboratory of Crop Gene Resources and Breeding/National Engineering Laboratory of Crop Molecular Breeding/CAEA Research and Development Centre on Nuclear Technology Applications for Irradiation Mutation Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huiyuan Li
- State Key Laboratory of Crop Gene Resources and Breeding/National Engineering Laboratory of Crop Molecular Breeding/CAEA Research and Development Centre on Nuclear Technology Applications for Irradiation Mutation Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shirong Zhao
- State Key Laboratory of Crop Gene Resources and Breeding/National Engineering Laboratory of Crop Molecular Breeding/CAEA Research and Development Centre on Nuclear Technology Applications for Irradiation Mutation Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuping Ding
- State Key Laboratory of Crop Gene Resources and Breeding/National Engineering Laboratory of Crop Molecular Breeding/CAEA Research and Development Centre on Nuclear Technology Applications for Irradiation Mutation Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chunyun Zhou
- State Key Laboratory of Crop Gene Resources and Breeding/National Engineering Laboratory of Crop Molecular Breeding/CAEA Research and Development Centre on Nuclear Technology Applications for Irradiation Mutation Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhengwu Fang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (co-construction by Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Luxiang Liu
- State Key Laboratory of Crop Gene Resources and Breeding/National Engineering Laboratory of Crop Molecular Breeding/CAEA Research and Development Centre on Nuclear Technology Applications for Irradiation Mutation Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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2
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Gutaker RM, Purugganan MD. Adaptation and the Geographic Spread of Crop Species. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:679-706. [PMID: 38012052 DOI: 10.1146/annurev-arplant-060223-030954] [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: 11/29/2023]
Abstract
Crops are plant species that were domesticated starting about 11,000 years ago from several centers of origin, most prominently the Fertile Crescent, East Asia, and Mesoamerica. From their domestication centers, these crops spread across the globe and had to adapt to differing environments as a result of this dispersal. We discuss broad patterns of crop spread, including the early diffusion of crops associated with the rise and spread of agriculture, the later movement via ancient trading networks, and the exchange between the Old and New Worlds over the last ∼550 years after the European colonization of the Americas. We also examine the various genetic mechanisms associated with the evolutionary adaptation of crops to their new environments after dispersal, most prominently seasonal adaptation associated with movement across latitudes, as well as altitudinal, temperature, and other environmental factors.
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Affiliation(s)
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, New York University, New York, NY, USA;
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Institute for the Study of the Ancient World, New York University, New York, NY, USA
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3
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Gauley A, Pasquariello M, Yoshikawa GV, Alabdullah AK, Hayta S, Smedley MA, Dixon LE, Boden SA. Photoperiod-1 regulates the wheat inflorescence transcriptome to influence spikelet architecture and flowering time. Curr Biol 2024; 34:2330-2343.e4. [PMID: 38781956 PMCID: PMC11149547 DOI: 10.1016/j.cub.2024.04.029] [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: 11/15/2023] [Revised: 03/08/2024] [Accepted: 04/11/2024] [Indexed: 05/25/2024]
Abstract
Photoperiod insensitivity has been selected by breeders to help adapt crops to diverse environments and farming practices. In wheat, insensitive alleles of Photoperiod-1 (Ppd-1) relieve the requirement of long daylengths to flower by promoting expression of floral promoting genes early in the season; however, these alleles also limit yield by reducing the number and fertility of grain-producing florets through processes that are poorly understood. Here, we performed transcriptome analysis of the developing inflorescence using near-isogenic lines that contain either photoperiod-insensitive or null alleles of Ppd-1, during stages when spikelet number is determined and floret development initiates. We report that Ppd-1 influences the stage-specific expression of genes with roles in auxin signaling, meristem identity, and protein turnover, and analysis of differentially expressed transcripts identified bZIP and ALOG transcription factors, namely PDB1 and ALOG1, which regulate flowering time and spikelet architecture. These findings enhance our understanding of genes that regulate inflorescence development and introduce new targets for improving yield potential.
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Affiliation(s)
- Adam Gauley
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK; Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Marianna Pasquariello
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Guilherme V Yoshikawa
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Hartley Grove, Glen Osmond, SA 5064, Australia
| | - Abdul Kader Alabdullah
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Sadiye Hayta
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Mark A Smedley
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Laura E Dixon
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK; Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Scott A Boden
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK; School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Hartley Grove, Glen Osmond, SA 5064, Australia.
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4
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Komura S, Yoshida K, Jinno H, Oono Y, Handa H, Takumi S, Kobayashi F. Identification of the causal mutation in early heading mutant of bread wheat ( Triticum aestivum L.) using MutMap approach. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:41. [PMID: 38779634 PMCID: PMC11106051 DOI: 10.1007/s11032-024-01478-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024]
Abstract
In bread wheat (Triticum aestivum L.), fine-tuning the heading time is essential to maximize grain yield. Photoperiod-1 (Ppd-1) and VERNALIZATION 1 (Vrn-1) are major genes affecting photoperiod sensitivity and vernalization requirements, respectively. These genes have predominantly governed heading timing. However, Ppd-1 and Vrn-1 significantly impact heading dates, necessitating another gene that can slightly modify heading dates for fine-tuning. In this study, we developed an early heading mutant from the ethyl methanesulfonate-mutagenized population of the Japanese winter wheat cultivar "Kitahonami." MutMap analysis identified a nonsense mutation in the clock component gene Wheat PHYTOCLOCK 1/LUX ARRHYTHMO (WPCL-D1) as the probable SNP responsible for the early heading mutant on chromosome 3D. Segregation analysis using F2 and F3 populations confirmed that plants carrying the wpcl-D1 allele headed significantly earlier than those with the functional WPCL-D1. The early heading mutant exhibited increased expression levels of Ppd-1 and circadian clock genes, such as WPCL1 and LATE ELONGATED HYPOCOTYL (LHY). Notably, the transcript accumulation levels of Ppd-A1 and Ppd-D1 were influenced by the copy number of the functional WPCL1 gene. These results suggest that a loss-of-function mutation in WPCL-D1 is the causal mutation for the early heading phenotype. Adjusting the functional copy number of WPCL1 will be beneficial in fine-tuning of heading dates. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01478-5.
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Affiliation(s)
- Shoya Komura
- Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Kentaro Yoshida
- Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Hironobu Jinno
- Hokkaido Research Organization, Kitami Agricultural Experiment Station, Yayoi 52, Kunneppucho, Tokorogun, Hokkaido, 099-1496 Japan
| | - Youko Oono
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, 305-0856 Japan
| | - Hirokazu Handa
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, 305-0856 Japan
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto, 606-8522 Japan
| | - Shigeo Takumi
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501 Japan
| | - Fuminori Kobayashi
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, 305-0856 Japan
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5
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Makhoul M, Schlichtermann RH, Ugwuanyi S, Weber SE, Voss-Fels KP, Stahl A, Zetzsche H, Wittkop B, Snowdon RJ, Obermeier C. Novel PHOTOPERIOD-1 gene variants associate with yield-related and root-angle traits in European bread wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:125. [PMID: 38727862 PMCID: PMC11087350 DOI: 10.1007/s00122-024-04634-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/20/2024] [Indexed: 05/13/2024]
Abstract
KEY MESSAGE PHOTOPERIOD-1 homoeologous gene copies play a pivotal role in regulation of flowering time in wheat. Here, we show that their influence also extends to spike and shoot architecture and even impacts root development. The sequence diversity of three homoeologous copies of the PHOTOPERIOD-1 gene in European winter wheat was analyzed by Oxford Nanopore amplicon-based multiplex sequencing and molecular markers in a panel of 194 cultivars representing breeding progress over the past 5 decades. A strong, consistent association with an average 8% increase in grain yield was observed for the PpdA1-Hap1 haplotype across multiple environments. This haplotype was found to be linked in 51% of cultivars to the 2NS/2AS translocation, originally introduced from Aegilops ventricosa, which leads to an overestimation of its effect. However, even in cultivars without the 2NS/2AS translocation, PpdA1-Hap1 was significantly associated with increased grain yield, kernel per spike and kernel per m2 under optimal growth conditions, conferring a 4% yield advantage compared to haplotype PpdA1-Hap4. In contrast to Ppd-B1 and Ppd-D1, the Ppd-A1 gene exhibits novel structural variations and a high number of SNPs, highlighting the evolutionary changes that have occurred in this region over the course of wheat breeding history. Additionally, cultivars carrying the photoperiod-insensitive Ppd-D1a allele not only exhibit earlier heading, but also deeper roots compared to those with photoperiod-sensitive alleles under German conditions. PCR and KASP assays have been developed that can be effectively employed in marker-assisted breeding programs to introduce these favorable haplotypes.
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Affiliation(s)
- Manar Makhoul
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | | | - Samson Ugwuanyi
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Sven E Weber
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Kai P Voss-Fels
- Institute for Grapevine Breeding, Hochschule Geisenheim University, Geisenheim, Germany
| | - Andreas Stahl
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Holger Zetzsche
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Benjamin Wittkop
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Christian Obermeier
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany.
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6
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Luo X, Liu B, Xie L, Wang K, Xu D, Tian X, Xie L, Li L, Ye X, He Z, Xia X, Yan L, Cao S. The TaSOC1-TaVRN1 module integrates photoperiod and vernalization signals to regulate wheat flowering. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:635-649. [PMID: 37938892 PMCID: PMC10893938 DOI: 10.1111/pbi.14211] [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: 07/30/2022] [Revised: 09/12/2023] [Accepted: 10/12/2023] [Indexed: 11/10/2023]
Abstract
Wheat needs different durations of vernalization, which accelerates flowering by exposure to cold temperature, to ensure reproductive development at the optimum time, as that is critical for adaptability and high yield. TaVRN1 is the central flowering regulator in the vernalization pathway and encodes a MADS-box transcription factor (TF) that usually works by forming hetero- or homo-dimers. We previously identified that TaVRN1 bound to an MADS-box TF TaSOC1 whose orthologues are flowering activators in other plants. The specific function of TaSOC1 and the biological implication of its interaction with TaVRN1 remained unknown. Here, we demonstrated that TaSOC1 was a flowering repressor in the vernalization and photoperiod pathways by overexpression and knockout assays. We confirmed the physical interaction between TaSOC1 and TaVRN1 in wheat protoplasts and in planta, and further validated their genetic interplay. A Flowering Promoting Factor 1-like gene TaFPF1-2B was identified as a common downstream target of TaSOC1 and TaVRN1 through transcriptome and chromatin immunoprecipitation analyses. TaSOC1 competed with TaVRT2, another MADS-box flowering regulator, to bind to TaVRN1; their coding genes synergistically control TaFPF1-2B expression and flowering initiation in response to photoperiod and low temperature. We identified major haplotypes of TaSOC1 and found that TaSOC1-Hap1 conferred earlier flowering than TaSOC1-Hap2 and had been subjected to positive selection in wheat breeding. We also revealed that wheat SOC1 family members were important domestication loci and expanded by tandem and segmental duplication events. These findings offer new insights into the regulatory mechanism underlying flowering control along with useful genetic resources for wheat improvement.
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Affiliation(s)
- Xumei Luo
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Bingyan Liu
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Li Xie
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Ke Wang
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Dengan Xu
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Xiuling Tian
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Lina Xie
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Lingli Li
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Xingguo Ye
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Zhonghu He
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Xianchun Xia
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
| | - Liuling Yan
- Department of Plant and Soil SciencesOklahoma State UniversityStillwaterOKUSA
| | - Shuanghe Cao
- Institute of Crop SciencesChinese Academy of Agricultural Sciences (CAAS)BeijingChina
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7
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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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8
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Zhang Y, Ma Y, Zhang H, Xu J, Gao X, Zhang T, Liu X, Guo L, Zhao D. Environmental F actors coordinate circadian clock function and rhythm to regulate plant development. PLANT SIGNALING & BEHAVIOR 2023; 18:2231202. [PMID: 37481743 PMCID: PMC10364662 DOI: 10.1080/15592324.2023.2231202] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 07/25/2023]
Abstract
Changes in the external environment necessitate plant growth plasticity, with environmental signals such as light, temperature, and humidity regulating growth and development. The plant circadian clock is a biological time keeper that can be "reset" to adjust internal time to changes in the external environment. Exploring the regulatory mechanisms behind plant acclimation to environmental factors is important for understanding how plant growth and development are shaped and for boosting agricultural production. In this review, we summarize recent insights into the coordinated regulation of plant growth and development by environmental signals and the circadian clock, further discussing the potential of this knowledge.
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Affiliation(s)
- Ying Zhang
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- Institute of Biotechnology and Food Science, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Yuru Ma
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Hao Zhang
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Jiahui Xu
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Xiaokuan Gao
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
| | - Tengteng Zhang
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Xigang Liu
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Lin Guo
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
| | - Dan Zhao
- College of Life Sciences, Hengshui University, Hengshui, Hebei, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China
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9
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Chepurnov GY, Ovchinnikova ES, Blinov AG, Chikida NN, Belousova MK, Goncharov NP. Analysis of the Structural Organization and Expression of the Vrn-D1 Gene Controlling Growth Habit (Spring vs. Winter) in Aegilops tauschii Coss. PLANTS (BASEL, SWITZERLAND) 2023; 12:3596. [PMID: 37896059 PMCID: PMC10610194 DOI: 10.3390/plants12203596] [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: 08/30/2023] [Revised: 10/13/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023]
Abstract
The duration of the vegetative period is an important agronomic characteristic of cereal crops. It is mainly influenced by the Vrn (response to vernalization) and Ppd (response to photoperiod) genes. In this work, we searched for alleles of several known genes of these two systems of response to external conditions in 15 accessions of Aegilops tauschii Coss. (syn. Ae. squarrosa L.), with the aim of studying the impact these alleles have on the vegetative period duration and growth habit. As a result, three allelic variants have been found for the Vrn-D1 gene: (i) one intact (winter type), (ii) one with a 5437 bp deletion in the first intron and (iii) one previously undescribed allele with a 3273 bp deletion in the first intron. It has been shown that the spring growth habit of Ae. tauschii can be developed due to the presence of a new allele of the Vrn-D1 gene. Significant differences in expression levels between the new allelic variant of the Vrn-D1 gene and the intact allele vrn-D1 were confirmed by qPCR. The new allele can be introgressed into common wheat to enhance the biodiversity of the spring growth habit and vegetative period duration of plants.
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Affiliation(s)
- Grigory Yurievich Chepurnov
- Early Maturity Genetics Laboratory, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Akademika Lavrentieva Avenue, 10, 630090 Novosibirsk, Russia; (E.S.O.); (A.G.B.)
| | - Ekaterina Sergeevna Ovchinnikova
- Early Maturity Genetics Laboratory, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Akademika Lavrentieva Avenue, 10, 630090 Novosibirsk, Russia; (E.S.O.); (A.G.B.)
| | - Alexander Genadevich Blinov
- Early Maturity Genetics Laboratory, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Akademika Lavrentieva Avenue, 10, 630090 Novosibirsk, Russia; (E.S.O.); (A.G.B.)
| | - Nadezhda Nikolaevna Chikida
- Division of Wheat Genetic Resources, Federal Research Center N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 Saint Petersburg, Russia;
| | - Mariya Khasbulatovna Belousova
- Wheat Laboratory, Dagestan Experimental Station—The Branch of the Federal Research Center N. I. Vavilov All-Russian Institute of Plant Genetic Resources, Vavilovo Village, Derbent District, 368600 Saint Petersburg, Russia;
| | - Nikolay Petrovich Goncharov
- Early Maturity Genetics Laboratory, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Akademika Lavrentieva Avenue, 10, 630090 Novosibirsk, Russia; (E.S.O.); (A.G.B.)
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10
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Graham CA, Paajanen P, Edwards KJ, Dodd AN. Genome-wide circadian gating of a cold temperature response in bread wheat. PLoS Genet 2023; 19:e1010947. [PMID: 37721961 PMCID: PMC10538658 DOI: 10.1371/journal.pgen.1010947] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 09/28/2023] [Accepted: 08/30/2023] [Indexed: 09/20/2023] Open
Abstract
Circadian rhythms coordinate the responses of organisms with their daily fluctuating environments, by establishing a temporal program of gene expression. This schedules aspects of metabolism, physiology, development and behaviour according to the time of day. Circadian regulation in plants is extremely pervasive, and is important because it underpins both productivity and seasonal reproduction. Circadian regulation extends to the control of environmental responses through a regulatory process known as circadian gating. Circadian gating is the process whereby the circadian clock regulates the response to an environmental cue, such that the magnitude of response to an identical cue varies according to the time of day of the cue. Here, we show that there is genome-wide circadian gating of responses to cold temperatures in plants. By using bread wheat as an experimental model, we establish that circadian gating is crucial to the programs of gene expression that underlie the environmental responses of a crop of major socioeconomic importance. Furthermore, we identify that circadian gating of cold temperature responses are distributed unevenly across the three wheat subgenomes, which might reflect the geographical origins of the ancestors of modern wheat.
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Affiliation(s)
- Calum A. Graham
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, Bristol, United Kingdom
| | - Pirita Paajanen
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Keith J. Edwards
- School of Biological Sciences, University of Bristol, Bristol Life Sciences Building, Bristol, United Kingdom
| | - Antony N. Dodd
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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11
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Ning S, Li S, Xu K, Liu D, Ma L, Ma C, Hao M, Zhang L, Chen W, Zhang B, Jiang Y, Huang L, Chen X, Jiang B, Yuan Z, Liu D. Development and Characterization of Near-Isogenic Lines Derived from Synthetic Wheat Revealing the 2 kb Insertion in the PPD-D1 Gene Responsible for Heading Delay and Grain Number Improvement. Int J Mol Sci 2023; 24:10834. [PMID: 37446014 DOI: 10.3390/ijms241310834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/24/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Spikelet number and grain number per spike are two crucial and correlated traits for grain yield in wheat. Photoperiod-1 (Ppd-1) is a key regulator of inflorescence architecture and spikelet formation in wheat. In this study, near-isogenic lines derived from the cross of a synthetic hexaploid wheat and commercial cultivars generated by double top-cross and two-phase selection were evaluated for the number of days to heading and other agronomic traits. The results showed that heading time segregation was conferred by a single incomplete dominant gene PPD-D1, and the 2 kb insertion in the promoter region was responsible for the delay in heading. Meanwhile, slightly delayed heading plants and later heading plants obviously have advantages in grain number and spikelet number of the main spike compared with early heading plants. Utilization of PPD-D1 photoperiod sensitivity phenotype as a potential means to increase wheat yield potential.
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Affiliation(s)
- Shunzong Ning
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Shengke Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Kai Xu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Dongmei Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Ma
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Chunfang Ma
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Lianquan Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Wenjie Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Bo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Yun Jiang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China
| | - Lin Huang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuejiao Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Bo Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhongwei Yuan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Dengcai Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
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12
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Mizuno N, Matsunaka H, Yanaka M, Ishikawa G, Kobayashi F, Nakamura K. Natural variations of wheat EARLY FLOWERING 3 highlight their contributions to local adaptation through fine-tuning of heading time. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:139. [PMID: 37233781 DOI: 10.1007/s00122-023-04386-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023]
Abstract
KEY MESSAGE We identified a large chromosomal deletion containing TaELF-B3 that confers early flowering in wheat. This allele has been preferred in recent wheat breeding in Japan to adapt to the environment. Heading at the appropriate time in each cultivation region can greatly contribute to stabilizing and maximizing yield. Vrn-1 and Ppd-1 are known as the major genes for vernalization requirement and photoperiod sensitivity in wheat. Genotype combinations of Vrn-1 and Ppd-1 can explain the variation in heading time. However, the genes that can explain the remaining variations in heading time are largely unknown. In this study, we aimed to identify the genes conferring early heading using doubled haploid lines derived from Japanese wheat varieties. Quantitative trait locus (QTL) analysis revealed a significant QTL on the long arm of chromosome 1B in multiple growing seasons. Genome sequencing using Illumina short reads and Pacbio HiFi reads revealed a large deletion of a ~ 500 kb region containing TaELF-B3, an orthologue of Arabidopsis clock gene EARLY FLOWERING 3 (ELF3). Plants with the deleted allele of TaELF-B3 (ΔTaELF-B3 allele) headed earlier only under short-day vernalization conditions. Higher expression levels of clock- and clock-output genes, such as Ppd-1 and TaGI, were observed in plants with the ΔTaELF-B3 allele. These results suggest that the deletion of TaELF-B3 causes early heading. Of the TaELF-3 homoeoalleles conferring early heading, the ΔTaELF-B3 allele showed the greatest effect on the early heading phenotype in Japan. The higher allele frequency of the ΔTaELF-B3 allele in western Japan suggests that the ΔTaELF-B3 allele was preferred during recent breeding to adapt to the environment. TaELF-3 homoeologs will help to expand the cultivated area by fine-tuning the optimal timing of heading in each environment.
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Affiliation(s)
- Nobuyuki Mizuno
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan.
| | - Hitoshi Matsunaka
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka, 833-0041, Japan
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, 9-4 Shinsei-Minami, Memuro, Kasai, Hokkaido, 082-0081, Japan
| | - Mikiko Yanaka
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka, 833-0041, Japan
| | - Goro Ishikawa
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Fuminori Kobayashi
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan
| | - Kazuhiro Nakamura
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka, 833-0041, Japan
- Headquarters, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8517, Japan
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13
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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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14
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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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15
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Liu Z, Liu W, Wang Z, Qi K, Xie Z, Zhang S, Wu J, Wang P. Diurnal transcriptome dynamics reveal the photoperiod response of Pyrus. PHYSIOLOGIA PLANTARUM 2023; 175:e13893. [PMID: 36929905 DOI: 10.1111/ppl.13893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/15/2023] [Accepted: 03/14/2023] [Indexed: 06/18/2023]
Abstract
Photoperiod provides a key environmental signal that controls plant growth. Plants have evolved an integrated mechanism for sensing photoperiods with internal clocks to orchestrate physiological events. This mechanism has been identified to enable timely plant growth and improve fitness. Although the components and pathways underlying photoperiod regulation have been described in many species, diurnal patterns of gene expression at the genome-wide level under different photoperiods are rarely reported in perennial fruit trees. To explore the global gene expression in response to photoperiod, pear plants were cultured under long-day (LD) and short-day (SD) conditions. A time-series transcriptomic study was implemented using LD and SD samples collected at 4 h intervals over 2 days. We identified 13,677 rhythmic genes, of which 7639 were identified under LD and 10,557 under SD conditions. Additionally, 4674 genes were differentially expressed in response to photoperiod change. We also characterized the candidate homologs of clock-associated genes in pear. Clock genes were involved in the regulation of many processes throughout the day, including photosynthesis, stress response, hormone dynamics, and secondary metabolism. Strikingly, genes within photosynthesis-related pathways were enriched in both the rhythmic and differential expression analyses. Several key candidate genes were identified to be associated with regulating photosynthesis and improving productivity under different photoperiods. The results suggest that temporal variation in gene expression should not be ignored in pear gene function research. Overall, our work expands the understanding of photoperiod regulation of plant growth, particularly by extending the research to non-model trees.
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Affiliation(s)
- Zhe Liu
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
- Department of Pharmacy, Changzhi Medical College, Changzhi, 046000, China
| | - Weijuan Liu
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhangqing Wang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Kaijie Qi
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhihua Xie
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Shaoling Zhang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Juyou Wu
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Peng Wang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
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16
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Errum A, Rehman N, Uzair M, Inam S, Ali GM, Khan MR. CRISPR/Cas9 editing of wheat Ppd-1 gene homoeologs alters spike architecture and grain morphometric traits. Funct Integr Genomics 2023; 23:66. [PMID: 36840774 DOI: 10.1007/s10142-023-00989-2] [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: 01/13/2023] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 02/26/2023]
Abstract
Mutations in Photoperiod-1 (Ppd-1) gene are known to modify flowering time and yield in wheat. We cloned TaPpd-1 from wheat and found high similarity among the three homoeologs of TaPpd-1. To clarify the characteristics of TaPpd-1 homoeologs in different photoperiod conditions for inflorescence architecture and yield, we used CRISPR/Cas9 system to generate Tappd-1 mutant plants by simultaneous modification of the three homoeologs of wheat Ppd-1. Tappd-1 mutant plants showed no off-target mutations. Four T0-edited lines under short-day length and three lines under long-day length conditions with the mutation frequency of 25% and 21%, respectively. These putative transgenic plants of all the lines were self-fertilized and generated T1 and T2 progenies and were evaluated by phenotypic and expression analysis. Results demonstrated that simultaneously edited TaPpd-1- A1, B1, and D1 homoeologs gene copies in T2_SDL-8-4, T2_SDL-4-5, T2_SDL-3-9, and T2_LDL-10-9 showed similar spike inflorescence, flowering time, and significantly increase in 1000-grain weight, grain area, grain width, grain length, plant height, and spikelets per spike due to mutation in both alleles of Ppd-B1 and Ppd-D1 homoeologs but only spike length was decreased in T2_SDL-8-4, T2_SDL-4-5, and T2_LDL-13-3 mutant lines due to mutation in both alleles of Ppd-A1 homoeolog under both conditions. Our results indicate that all TaPpd1 gene homoeologs influence wheat spike development by affecting both late flowering and earlier flowering but single mutant TaPpd-A1 homoeolog affect lowest as compared to the combination with double mutants of TaPpd-B1 and TaPpd-D1, TaPpd-A1 and TaPpd-B1, and TaPpd-A1 and TaPpd-D1 homoeologs for yield enhancement. Our findings further raised the idea that the relative expression of the various genomic copies of TaPpd-1 homoeologs may have an impact on the spike inflorescence architecture and grain morphometric features in wheat cultivars.
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Affiliation(s)
- Aliya Errum
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan
- PARC Institute of Advanced Studies in Agriculture (PIASA), Islamabad, Pakistan
| | - Nazia Rehman
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan
| | - Safeena Inam
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan
| | | | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan.
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17
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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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18
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Mizuno N, Matsunaka H, Yanaka M, Nakata M, Nakamura K, Nakamaru A, Kiribuchi-Otobe C, Ishikawa G, Chono M, Hatta K, Fujita M, Kobayashi F. Allelic variations of Vrn-1 and Ppd-1 genes in Japanese wheat varieties reveal the genotype-environment interaction for heading time. BREEDING SCIENCE 2022; 72:343-354. [PMID: 36776445 PMCID: PMC9895800 DOI: 10.1270/jsbbs.22017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 08/07/2022] [Indexed: 05/31/2023]
Abstract
The timing of heading is largely affected by environmental conditions. In wheat, Vrn-1 and Ppd-1 have been identified as the major genes involved in vernalization requirement and photoperiod sensitivity, respectively. To compare the effects of Vrn-1 and Ppd-1 alleles on heading time under different environments, we genotyped Vrn-1 and Ppd-1 homoeologues and measured the heading time at Morioka, Tsukuba and Chikugo in Japan for two growing seasons. A total of 128 Japanese and six foreign varieties, classified into four populations based on the 519 genome-wide SNPs, were used for analysis. Varieties with the spring alleles (Vrn-D1a or Vrn-D1b) at the Vrn-D1 locus and insensitive allele (Hapl-I) at the Ppd-D1 locus were found in earlier heading varieties. The effects of Vrn-D1 and Ppd-D1 on heading time were stronger than those of the other Vrn-1 and Ppd-1 homoeologues. Analysis of variance revealed that heading time was significantly affected by the genotype-environment interactions. Some Vrn-1 and Ppd-1 alleles conferred earlier or later heading in specific environments, indicating that the effect of both alleles on the timing of heading depends on the environment. Information on Vrn-1 and Ppd-1 alleles, together with heading time in various environments, provide useful information for wheat breeding.
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Affiliation(s)
- Nobuyuki Mizuno
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Hitoshi Matsunaka
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka 833-0041, Japan
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, 9-4 Shinsei-minami, Memuro, Kasai, Hokkaido 082-0081, Japan
| | - Mikiko Yanaka
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka 833-0041, Japan
| | - Masaru Nakata
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka 833-0041, Japan
| | - Kazuhiro Nakamura
- Kyusyu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 496 Izumi, Chikugo, Fukuoka 833-0041, Japan
| | - Akiko Nakamaru
- Tohoku Agricultural Research Center, National Agriculture and Food Research Organization, 4 Akahira, Shimo-kuriyagawa, Morioka, Iwate 020-0198, Japan
| | - Chikako Kiribuchi-Otobe
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Goro Ishikawa
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Makiko Chono
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Koichi Hatta
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, 9-4 Shinsei-minami, Memuro, Kasai, Hokkaido 082-0081, Japan
| | - Masaya Fujita
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Fuminori Kobayashi
- Institute of Crop Science, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
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19
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Rees H, Rusholme-Pilcher R, Bailey P, Colmer J, White B, Reynolds C, Ward SJ, Coombes B, Graham CA, de Barros Dantas LL, Dodd AN, Hall A. Circadian regulation of the transcriptome in a complex polyploid crop. PLoS Biol 2022; 20:e3001802. [PMID: 36227835 PMCID: PMC9560141 DOI: 10.1371/journal.pbio.3001802] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/18/2022] [Indexed: 11/07/2022] Open
Abstract
The circadian clock is a finely balanced timekeeping mechanism that coordinates programmes of gene expression. It is currently unknown how the clock regulates expression of homoeologous genes in polyploids. Here, we generate a high-resolution time-course dataset to investigate the circadian balance between sets of 3 homoeologous genes (triads) from hexaploid bread wheat. We find a large proportion of circadian triads exhibit imbalanced rhythmic expression patterns, with no specific subgenome favoured. In wheat, period lengths of rhythmic transcripts are found to be longer and have a higher level of variance than in other plant species. Expression of transcripts associated with circadian controlled biological processes is largely conserved between wheat and Arabidopsis; however, striking differences are seen in agriculturally critical processes such as starch metabolism. Together, this work highlights the ongoing selection for balance versus diversification in circadian homoeologs and identifies clock-controlled pathways that might provide important targets for future wheat breeding.
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Affiliation(s)
- Hannah Rees
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | | | - Paul Bailey
- Royal Botanic Gardens Kew, Richmond, Surrey, United Kingdom
| | - Joshua Colmer
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Benjamen White
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Connor Reynolds
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | | | - Benedict Coombes
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Calum A. Graham
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | | | - Antony N. Dodd
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Anthony Hall
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
- * E-mail:
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20
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Wittern LM, Barrero JM, Bovill WD, Verbyla KL, Hughes T, Swain SM, Steed G, Webb AAR, Gardner K, Greenland A, Jacobs J, Frohberg C, Schmidt RC, Cavanagh C, Rohde A, Davey MW, Hannah MA. Overexpression of the WAPO-A1 gene increases the number of spikelets per spike in bread wheat. Sci Rep 2022; 12:14229. [PMID: 35987959 PMCID: PMC9392761 DOI: 10.1038/s41598-022-18614-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/16/2022] [Indexed: 11/09/2022] Open
Abstract
Two homoeologous QTLs for number of spikelets per spike (SPS) were mapped on chromosomes 7AL and 7BL using two wheat MAGIC populations. Sets of lines contrasting for the QTL on 7AL were developed which allowed for the validation and fine mapping of the 7AL QTL and for the identification of a previously described candidate gene, WHEAT ORTHOLOG OF APO1 (WAPO1). Using transgenic overexpression in both a low and a high SPS line, we provide a functional validation for the role of this gene in determining SPS also in hexaploid wheat. We show that the expression levels of this gene positively correlate with SPS in multiple MAGIC founder lines under field conditions as well as in transgenic lines grown in the greenhouse. This work highlights the potential use of WAPO1 in hexaploid wheat for further yield increases. The impact of WAPO1 and SPS on yield depends on other genetic and environmental factors, hence, will require a finely balanced expression level to avoid the development of detrimental pleiotropic phenotypes.
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Affiliation(s)
- Lukas M Wittern
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Jose M Barrero
- Agriculture and Food, Black Mountain Science and Innovation Park, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, 2601, Australia
| | - William D Bovill
- Agriculture and Food, Black Mountain Science and Innovation Park, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, 2601, Australia
| | - Klara L Verbyla
- Agriculture and Food, Black Mountain Science and Innovation Park, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, 2601, Australia
| | - Trijntje Hughes
- Agriculture and Food, Black Mountain Science and Innovation Park, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, 2601, Australia
| | - Steve M Swain
- Agriculture and Food, Black Mountain Science and Innovation Park, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, 2601, Australia
| | - Gareth Steed
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Alex A R Webb
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Keith Gardner
- National Institute of Agricultural Botany (NIAB), Huntingdon Road, Cambridge, CB3 0LE, UK
| | - Andy Greenland
- National Institute of Agricultural Botany (NIAB), Huntingdon Road, Cambridge, CB3 0LE, UK
| | - John Jacobs
- BASF, BBCC - Innovation Center Gent, Technologiepark 101, 9052, Ghent, Belgium
| | - Claus Frohberg
- BASF, BBCC - Innovation Center Gent, Technologiepark 101, 9052, Ghent, Belgium
| | | | - Colin Cavanagh
- BASF Australia Ltd., 28 Freshwater Place, Melbourne, 3006, Australia
| | - Antje Rohde
- BASF, BBCC - Innovation Center Gent, Technologiepark 101, 9052, Ghent, Belgium
| | - Mark W Davey
- BASF, BBCC - Innovation Center Gent, Technologiepark 101, 9052, Ghent, Belgium
| | - Matthew A Hannah
- BASF, BBCC - Innovation Center Gent, Technologiepark 101, 9052, Ghent, Belgium.
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21
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Benaouda S, Dadshani S, Koua P, Léon J, Ballvora A. Identification of QTLs for wheat heading time across multiple-environments. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2833-2848. [PMID: 35776141 PMCID: PMC9325850 DOI: 10.1007/s00122-022-04152-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 06/10/2022] [Indexed: 06/15/2023]
Abstract
KEY MESSAGE The genetic response to changing climatic factors selects consistent across the tested environments and location-specific thermo-sensitive and photoperiod susceptible alleles in lower and higher altitudes, respectively, for starting flowering in winter wheat. Wheat breeders select heading date to match the most favorable conditions for their target environments and this is favored by the extensive genetic variation for this trait that has the potential to be further explored. In this study, we used a germplasm with broad geographic distribution and tested it in multi-location field trials across Germany over three years. The genotypic response to the variation in the climatic parameters depending on location and year uncovered the effect of photoperiod and spring temperatures in accelerating heading date in higher and lower latitudes, respectively. Spring temperature dominates other factors in inducing heading, whereas the higher amount of solar radiation delays it. A genome-wide scan of marker-trait associations with heading date detected two QTL: an adapted allele at locus TaHd102 on chromosome 5A that has a consistent effect on HD in German cultivars in multiple environments and a non-adapted allele at locus TaHd044 on chromosome 3A that accelerates flowering by 5.6 days. TaHd102 and TaHd044 explain 13.8% and 33% of the genetic variance, respectively. The interplay of the climatic variables led to the detection of environment specific association responding to temperature in lower latitudes and photoperiod in higher ones. Another locus TaHd098 on chromosome 5A showed epistatic interactions with 15 known regulators of flowering time when non-adapted cultivars from outside Germany were included in the analysis.
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Affiliation(s)
- Salma Benaouda
- Institute for Crop Science and Resource Conservation, Chair of Plant Breeding, Rheinische Friedrich-Wilhelms-University, Katzenburgweg 5, 53115, Bonn, Germany
| | - Said Dadshani
- Institute for Crop Science and Resource Conservation, Chair of Plant Breeding, Rheinische Friedrich-Wilhelms-University, Katzenburgweg 5, 53115, Bonn, Germany
| | - Patrice Koua
- Institute for Crop Science and Resource Conservation, Chair of Plant Breeding, Rheinische Friedrich-Wilhelms-University, Katzenburgweg 5, 53115, Bonn, Germany
| | - Jens Léon
- Institute for Crop Science and Resource Conservation, Chair of Plant Breeding, Rheinische Friedrich-Wilhelms-University, Katzenburgweg 5, 53115, Bonn, Germany
- Field Lab Campus Klein-Altendorf, Rheinische Friedrich-Wilhelms-University, Bonn, Germany
| | - Agim Ballvora
- Institute for Crop Science and Resource Conservation, Chair of Plant Breeding, Rheinische Friedrich-Wilhelms-University, Katzenburgweg 5, 53115, Bonn, Germany.
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22
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Jalal A, Sun J, Chen Y, Fan C, Liu J, Wang C. Evolutionary Analysis and Functional Identification of Clock-Associated PSEUDO-RESPONSE REGULATOR (PRRs) Genes in the Flowering Regulation of Roses. Int J Mol Sci 2022; 23:ijms23137335. [PMID: 35806340 PMCID: PMC9266954 DOI: 10.3390/ijms23137335] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 01/27/2023] Open
Abstract
Pseudo-response regulators (PRRs) are the important genes for flowering in roses. In this work, clock PRRs were genome-wide identified using Arabidopsis protein sequences as queries, and their evolutionary analyses were deliberated intensively in Rosaceae in correspondence with angiosperms species. To draw a comparative network and flow of clock PRRs in roses, a co-expression network of flowering pathway genes was drawn using a string database, and their functional analysis was studied by silencing using VIGS and protein-to-protein interaction. We revealed that the clock PRRs were significantly expanded in Rosaceae and were divided into three major clades, i.e., PRR5/9 (clade 1), PRR3/7 (clade 2), and TOC1/PRR1 (clade 3), based on their phylogeny. Within the clades, five clock PRRs were identified in Rosa chinensis. Clock PRRs had conserved RR domain and shared similar features, suggesting the duplication occurred during evolution. Divergence analysis indicated the role of duplication events in the expansion of clock PRRs. The diverse cis elements and interaction of clock PRRs with miRNAs suggested their role in plant development. Co-expression network analysis showed that the clock PRRs from Rosa chinensis had a strong association with flowering controlling genes. Further silencing of RcPRR1b and RcPRR5 in Rosa chinensis using VIGS led to earlier flowering, confirming them as negative flowering regulators. The protein-to-protein interactions between RcPRR1a/RcPRR5 and RcCO suggested that RcPRR1a/RcPRR5 may suppress flowering by interfering with the binding of RcCO to the promoter of RcFT. Collectively, these results provided an understanding of the evolutionary profiles as well as the functional role of clock PRRs in controlling flowering in roses.
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23
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Nidhi, Kumar P, Pathania D, Thakur S, Sharma M. Environment-mediated mutagenetic interference on genetic stabilization and circadian rhythm in plants. Cell Mol Life Sci 2022; 79:358. [PMID: 35687153 PMCID: PMC11072124 DOI: 10.1007/s00018-022-04368-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/21/2022] [Accepted: 05/07/2022] [Indexed: 12/29/2022]
Abstract
Many mortal organisms on this planet have developed the potential to merge all internal as well as external environmental cues to regulate various processes running inside organisms and in turn make them adaptive to the environment through the circadian clock. This moving rotator controls processes like activation of hormonal, metabolic, or defense pathways, initiation of flowering at an accurate period, and developmental processes in plants to ensure their stability in the environment. All these processes that are under the control of this rotating wheel can be changed either by external environmental factors or by an unpredictable phenomenon called mutation that can be generated by either physical mutagens, chemical mutagens, or by internal genetic interruption during metabolic processes, which alters normal functionality of organisms like innate immune responses, entrainment of the clock, biomass reduction, chlorophyll formation, and hormonal signaling, despite its fewer positive roles in plants like changing plant type, loss of vernalization treatment to make them survivable in different latitudes, and defense responses during stress. In addition, with mutation, overexpression of gene components sometimes supresses mutation effect and promote normal circadian genes abundance in the cell, while sometimes it affects circadian functionality by generating arrhythmicity and shows that not only mutation but overexpression also effects normal functional activities of plant. Therefore, this review mainly summarizes the role of each circadian clock genes in regulating rhythmicity, and shows that how circadian outputs are controlled by mutations as well as overexpression phenomenon.
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Affiliation(s)
- Nidhi
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, 173212, India
| | - Pradeep Kumar
- Central University of Himachal Pradesh, Dharmshala, India
| | - Diksha Pathania
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, 173212, India
| | - Sourbh Thakur
- Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, Silesian University of Technology, Gliwice, Poland
| | - Mamta Sharma
- School of Biological and Environmental Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, 173212, India.
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24
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Alkhudaydi T, De La lglesia B. Counting spikelets from infield wheat crop images using fully convolutional networks. Neural Comput Appl 2022. [DOI: 10.1007/s00521-022-07392-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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25
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Fait VI, Balashova IA. Distribution of Photoperiod-Insensitive Alleles Ppd-D1a, Ppd-B1a, and Ppd-B1c in Winter Common Wheat Cultivars (Triticum aestivum L.) of Various Origin. CYTOL GENET+ 2022. [DOI: 10.3103/s0095452722020049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Zhang H, Jiao B, Dong F, Liang X, Zhou S, Wang H. Genome-wide identification of CCT genes in wheat (Triticum aestivum L.) and their expression analysis during vernalization. PLoS One 2022; 17:e0262147. [PMID: 34986172 PMCID: PMC8730456 DOI: 10.1371/journal.pone.0262147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 12/17/2021] [Indexed: 11/19/2022] Open
Abstract
Numerous CCT genes are known to regulate various biological processes, such as circadian rhythm regulation, flowering, light signaling, plant development, and stress resistance. The CCT gene family has been characterized in many plants but remains unknown in the major cereal wheat (Triticum aestivum L.). Extended exposure to low temperature (vernalization) is necessary for winter wheat to flower successfully. VERNALIZATION2 (VRN2), a specific CCT-containing gene, has been proved to be strongly associated with vernalization in winter wheat. Mutation of all VRN2 copies in three subgenomes results in the eliminated demands of low temperature in flowering. However, no other CCT genes have been reported to be associated with vernalization to date. The present study screened CCT genes in the whole wheat genome, and preliminarily identified the vernalization related CCT genes through expression analysis. 127 CCT genes were identified in three subgenomes of common wheat through a hidden Markov model-based method. Based on multiple alignment, these genes were grouped into 40 gene clusters, including the duplicated gene clusters TaCMF6 and TaCMF8, each tandemly arranged near the telomere. The phylogenetic analysis classified these genes into eight groups. The transcriptome analysis using leaf tissues collected before, during, and after vernalization revealed 49 upregulated and 31 downregulated CCT genes during vernalization, further validated by quantitative real-time PCR. Among the differentially expressed and well-investigated CCT gene clusters analyzed in this study, TaCMF11, TaCO18, TaPRR95, TaCMF6, and TaCO16 were induced during vernalization but decreased immediately after vernalization, while TaCO1, TaCO15, TaCO2, TaCMF8, and TaPPD1 were stably suppressed during and after vernalization. These data imply that some vernalization related CCT genes other than VRN2 may exist in wheat. This study improves our understanding of CCT genes and provides a foundation for further research on CCT genes related to vernalization in wheat.
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Affiliation(s)
- HongWei Zhang
- College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Bo Jiao
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei, China
| | - FuShuang Dong
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei, China
| | - XinXia Liang
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Shuo Zhou
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei, China
- * E-mail: (SZ); (HBW)
| | - HaiBo Wang
- College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
- Plant Genetic Engineering Center of Hebei Province, Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei, China
- * E-mail: (SZ); (HBW)
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27
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Berezhnaya A, Kiseleva A, Leonova I, Salina E. Allelic Variation Analysis at the Vernalization Response and Photoperiod Genes in Russian Wheat Varieties Identified Two Novel Alleles of Vrn-B3. Biomolecules 2021; 11:biom11121897. [PMID: 34944541 PMCID: PMC8699075 DOI: 10.3390/biom11121897] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/15/2021] [Accepted: 12/15/2021] [Indexed: 11/30/2022] Open
Abstract
Heading time is an important agronomic trait affecting the adaptability and productivity of common wheat. In this study, 95 common wheat varieties from Russia and the late-maturing breeding line ‘Velut’ were tested for allelic diversity of genes having the strongest effect on heading. In this research, allelic variation at the Ppd-D1, Vrn-A1, Vrn-B1, Vrn-D1, and Vrn-B3 loci was tested. The Vrn-B1 and Vrn-B3 loci provided the largest contribution to genetic diversity. We found two novel allelic variants of the Vrn-B3 gene in the studied varieties. Ten varieties carried a 160 bp insertion in the promoter region, and the breeding line ‘Velut’ carried a 1617 bp insertion. These alleles were designated Vrn-B3e and Vrn-B3d, respectively. The analysis of the sequences showed the recent insertion of a retrotransposon homologous to the LTR retrotransposon (RLX_Hvul_Dacia_ RND-1) in the Vrn-B3d allele. Plants with the Vrn-B3e and the ‘Velut’ line with the Vrn-B3d allele headed later than the plants with the wild-type allele; among these plants, ‘Velut’ is the latest maturing wheat variety. Analysis of the gene expression of two groups of lines differing by the Vrn-B3 alleles (Vrn-B3d or vrn-B3) from the F2 population with ‘Velut’ as a parental line did not reveal a significant difference in the expression level between the groups. Additional research is required to study the reasons for the late maturation of the ‘Velut’ line. However, the studied wheat varieties could be used as a potential source of natural variation in genes controlling heading times.
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Affiliation(s)
- Alina Berezhnaya
- The Federal State Budgetary Institution of Science Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia; (A.K.); (I.L.); (E.S.)
- Correspondence: ; Tel.: +7-(383)-363-49-95
| | - Antonina Kiseleva
- The Federal State Budgetary Institution of Science Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia; (A.K.); (I.L.); (E.S.)
- Kurchatov Genomics Center, Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia
| | - Irina Leonova
- The Federal State Budgetary Institution of Science Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia; (A.K.); (I.L.); (E.S.)
| | - Elena Salina
- The Federal State Budgetary Institution of Science Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia; (A.K.); (I.L.); (E.S.)
- Kurchatov Genomics Center, Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia
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28
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Chapman EA, Orford S, Lage J, Griffiths S. Delaying or delivering: identification of novel NAM-1 alleles that delay senescence to extend wheat grain fill duration. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7710-7728. [PMID: 34405865 PMCID: PMC8660559 DOI: 10.1093/jxb/erab368] [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: 02/13/2021] [Accepted: 08/06/2021] [Indexed: 05/03/2023]
Abstract
Senescence is a complex trait under genetic and environmental control, in which resources are remobilized from vegetative tissue into grain. Delayed senescence, or 'staygreen' traits, can confer stress tolerance, with extended photosynthetic activity hypothetically sustaining grain filling. The genetics of senescence regulation are largely unknown, with senescence variation often correlated with phenological traits. Here, we confirm staygreen phenotypes of two Triticum aestivum cv. Paragon ethyl methane sulfonate mutants previously identified during a forward genetic screen and selected for their agronomic performance, similar phenology, and differential senescence phenotypes. Grain filling experiments confirmed a positive relationship between onset of senescence and grain fill duration, reporting an associated ~14% increase in final dry grain weight for one mutant (P<0.05). Recombinant inbred line (RIL) populations segregating for the timing of senescence were developed for trait mapping purposes and phenotyped over multiple years under field conditions. Quantification and comparison of senescence metrics aided RIL selection, facilitating exome capture-enabled bulk segregant analysis (BSA). Using BSA we mapped our two staygreen traits to two independent, dominant, loci of 4.8 and 16.7 Mb in size encompassing 56 and 142 genes, respectively. Combining association analysis with variant effect prediction, we identified single nucleotide polymorphisms encoding self-validating mutations located in NAM-1 homoeologues, which we propose as gene candidates.
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Affiliation(s)
| | - Simon Orford
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Jacob Lage
- KWS-UK, 56 Church Street, Thriplow, Hertfordshire SG8 7RE, UK
| | - Simon Griffiths
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
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29
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Song T, Yu Y, Zhang M, Zhou H, Zhang S, Yu M, Zhou J, Cheng J, Xiang J, Yang S, Zhang X. A Wheat TaTOE1-B1 Transcript TaTOE1-B1-3 Can Delay the Flowering Time of Transgenic Arabidopsis. Int J Mol Sci 2021; 22:12645. [PMID: 34884449 PMCID: PMC8657464 DOI: 10.3390/ijms222312645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 02/02/2023] Open
Abstract
Flowering time is one of the most important agronomic traits in wheat production. A proper flowering time might contribute to the reduction or avoidance of biotic and abiotic stresses, adjust plant architecture, and affect the yield and quality of grain. In this study, TaTOE1-B1 in wheat produced three transcripts (TaTOE1-B1-1, TaTOE1-B1-2, and TaTOE1-B1-3) by alternative splicing. Compared to the longest transcript, TaTOE1-B1-1, TaTOE1-B1-3 has a deletion in the sixth exon (1219-1264 bp). Under long-day conditions, the heterologous overexpression of the TaTOE1-B1-3 gene delayed flowering, prolonged the vegetative growth time, and enlarged the vegetative body of Arabidopsis, but that of TaTOE1-B1-1 did not. As typical AP2 family members, TaTOE1-B1-1 and TaTOE1-B1-3 are mainly located in the nucleus and have transcriptional activation activities; the transcriptional activation region of TaTOE1-B1-3 is located in the C-terminal. In TaTOE1-B1-3 overexpression lines, the expression of flowering-related AtFT and AtSOC1 genes is significantly downregulated. In addition, this study confirms the protein-protein interaction between TaTOE1-B1-3 and TaPIFI, which may play an important role in flowering inhibition. These results provide a theoretical basis for the precise regulation of wheat flowering time.
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Affiliation(s)
- Tianqi Song
- College of Agronomy, Northwest A&F University, Yangling 712100, China; (T.S.); (Y.Y.); (H.Z.); (S.Z.); (M.Y.); (J.Z.); (J.C.)
| | - Yang Yu
- College of Agronomy, Northwest A&F University, Yangling 712100, China; (T.S.); (Y.Y.); (H.Z.); (S.Z.); (M.Y.); (J.Z.); (J.C.)
| | - Mingfei Zhang
- Academy of Agricultural Sciences, Key Laboratory of Agro-Ecological Protection & Exploitation and Utilization of Animal and Plant Resources in Eastern Inner Mongolia, Chifeng University, Chifeng 024000, China;
| | - Hongwei Zhou
- College of Agronomy, Northwest A&F University, Yangling 712100, China; (T.S.); (Y.Y.); (H.Z.); (S.Z.); (M.Y.); (J.Z.); (J.C.)
| | - Shuangxing Zhang
- College of Agronomy, Northwest A&F University, Yangling 712100, China; (T.S.); (Y.Y.); (H.Z.); (S.Z.); (M.Y.); (J.Z.); (J.C.)
| | - Ming Yu
- College of Agronomy, Northwest A&F University, Yangling 712100, China; (T.S.); (Y.Y.); (H.Z.); (S.Z.); (M.Y.); (J.Z.); (J.C.)
| | - Jianfei Zhou
- College of Agronomy, Northwest A&F University, Yangling 712100, China; (T.S.); (Y.Y.); (H.Z.); (S.Z.); (M.Y.); (J.Z.); (J.C.)
| | - Jie Cheng
- College of Agronomy, Northwest A&F University, Yangling 712100, China; (T.S.); (Y.Y.); (H.Z.); (S.Z.); (M.Y.); (J.Z.); (J.C.)
| | - Jishan Xiang
- Academy of Agricultural Sciences, Key Laboratory of Agro-Ecological Protection & Exploitation and Utilization of Animal and Plant Resources in Eastern Inner Mongolia, Chifeng University, Chifeng 024000, China;
| | - Songjie Yang
- School of Modern Agriculture & Biotechnology, Ankang University, Ankang 725000, China;
| | - Xiaoke Zhang
- College of Agronomy, Northwest A&F University, Yangling 712100, China; (T.S.); (Y.Y.); (H.Z.); (S.Z.); (M.Y.); (J.Z.); (J.C.)
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Wu Y, Liu J, Hu G, Xue H, Xu H, Zhao C, Qin R, Cui F, Sun H. Functional Analysis of the "Green Revolution" Gene Photoperiod-1 and Its Selection Trends During Bread Wheat Breeding. FRONTIERS IN PLANT SCIENCE 2021; 12:745411. [PMID: 34858454 PMCID: PMC8631784 DOI: 10.3389/fpls.2021.745411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
Flowering is central to the transformation of plants from vegetative growth to reproductive growth. The circadian clock system enables plants to sense the changes in the external environment and to modify the growth and development process at an appropriate time. Photoperiod-1 (Ppd-1), which is controlled by the output signal of the circadian clock, has played an important role in the wheat "Green Revolution." In the current study, we systematically studied the relationship between Ppd-1 haplotypes and both wheat yield- and quality-related traits, using genome-wide association analysis and transgenic strategies, and found that highly appropriate haplotypes had been selected in the wheat breeding programs. Genome-wide association analysis showed that Ppd-1 is associated with significant differences in yield-related traits in wheat, including spike length (SL), heading date (HD), plant height (PH), and thousand-grain weight (TGW). Ppd-1-Hapl-A1 showed increased SL by 4.72-5.93%, whereas Ppd-1-Hapl-B1 and Ppd-1-Hapl-D1 displayed earlier HD by 0.58-0.75 and 1.24-2.93%, respectively, decreased PH by 5.64-13.08 and 13.62-27.30%, respectively, and increased TGW by 4.89-10.94 and 11.12-21.45%, respectively. Furthermore, the constitutive expression of the Ppd-D1 gene in rice significantly delayed heading date and resulted in reduced plant height, thousand-grain weight, grain width (GW), and total protein content. With reference to 40years of data from Chinese wheat breeding, it was found that the appropriate haplotypes Ppd-1-Hapl-A1, Ppd-1-Hapl-B1, and Ppd-1-Hapl-D1 had all been subjected to directional selection, and that their distribution frequencies had increased from 26.09, 60.00, and 52.00% in landraces to 42.55, 93.62, and 96.23% in wheat cultivars developed in the 2010s. A Ppd-B1 methylation molecular marker was also developed to assist molecular wheat breeding. This research is of significance for fully exploring the function of the Ppd-1 gene and its genetic resource diversity, to effectively use the most appropriate haplotypes and to improve crop yield and sustainability.
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Affiliation(s)
- Yongzhen Wu
- College of Agriculture, Ludong University, Yantai, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, China
| | - Jiahui Liu
- College of Agriculture, Ludong University, Yantai, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, China
| | - Guimei Hu
- College of Agriculture, Ludong University, Yantai, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, China
| | - Huixian Xue
- College of Agriculture, Ludong University, Yantai, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, China
| | - Huiyuan Xu
- College of Agriculture, Ludong University, Yantai, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, China
| | - Chunhua Zhao
- College of Agriculture, Ludong University, Yantai, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, China
| | - Ran Qin
- College of Agriculture, Ludong University, Yantai, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, China
| | - Fa Cui
- College of Agriculture, Ludong University, Yantai, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, China
| | - Han Sun
- College of Agriculture, Ludong University, Yantai, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, China
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31
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Jangra R, Brunetti SC, Wang X, Kaushik P, Gulick PJ, Foroud NA, Wang S, Lee JS. Duplicated antagonistic EPF peptides optimize grass stomatal initiation. Development 2021; 148:271118. [PMID: 34328169 DOI: 10.1242/dev.199780] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/19/2021] [Indexed: 11/20/2022]
Abstract
Peptide signaling has emerged as a key component of plant growth and development, including stomatal patterning, which is crucial for plant productivity and survival. Although exciting progress has been made in understanding EPIDERMAL PATTERNING FACTOR (EPF) signaling in Arabidopsis, the mechanisms by which EPF peptides control different stomatal patterns and morphologies in grasses are poorly understood. Here, by examining expression patterns, overexpression transgenics and cross-species complementation, the antagonistic stomatal ligands orthologous to Arabidopsis AtEPF2 and AtSTOMAGEN/AtEPFL9 peptides were identified in Triticum aestivum (wheat) and the grass model organism Brachypodium distachyon. Application of bioactive BdEPF2 peptides inhibited stomatal initiation, but not the progression or differentiation of stomatal precursors in Brachypodium. Additionally, the inhibitory roles of these EPF peptides during grass stomatal development were suppressed by the contrasting positive action of the BdSTOMAGEN peptide in a dose-dependent manner. These results not only demonstrate how conserved EPF peptides that control different stomatal patterns exist in nature, but also suggest new strategies to improve crop yield through the use of plant-derived antagonistic peptides that optimize stomatal density on the plant epidermis.
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Affiliation(s)
- Raman Jangra
- Department of Biology, Concordia University, Montreal, Quebec, H4B 1R6, Canada
| | - Sabrina C Brunetti
- Department of Biology, Concordia University, Montreal, Quebec, H4B 1R6, Canada
| | - Xutong Wang
- Department of Biology, Concordia University, Montreal, Quebec, H4B 1R6, Canada.,Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
| | - Pooja Kaushik
- Department of Biology, Concordia University, Montreal, Quebec, H4B 1R6, Canada
| | - Patrick J Gulick
- Department of Biology, Concordia University, Montreal, Quebec, H4B 1R6, Canada
| | - Nora A Foroud
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, T1J 4B1, Canada
| | - Shucai Wang
- Laboratory of Plant Molecular Genetics & Crop Gene Editing, School of Life Sciences, Linyi University, Linyi 276000, China
| | - Jin Suk Lee
- Department of Biology, Concordia University, Montreal, Quebec, H4B 1R6, Canada
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32
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Fernández-Calleja M, Casas AM, Igartua E. Major flowering time genes of barley: allelic diversity, effects, and comparison with wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1867-1897. [PMID: 33969431 PMCID: PMC8263424 DOI: 10.1007/s00122-021-03824-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 03/24/2021] [Indexed: 05/10/2023]
Abstract
This review summarizes the allelic series, effects, interactions between genes and with the environment, for the major flowering time genes that drive phenological adaptation of barley. The optimization of phenology is a major goal of plant breeding addressing the production of high-yielding varieties adapted to changing climatic conditions. Flowering time in cereals is regulated by genetic networks that respond predominately to day length and temperature. Allelic diversity at these genes is at the basis of barley wide adaptation. Detailed knowledge of their effects, and genetic and environmental interactions will facilitate plant breeders manipulating flowering time in cereal germplasm enhancement, by exploiting appropriate gene combinations. This review describes a catalogue of alleles found in QTL studies by barley geneticists, corresponding to the genetic diversity at major flowering time genes, the main drivers of barley phenological adaptation: VRN-H1 (HvBM5A), VRN-H2 (HvZCCTa-c), VRN-H3 (HvFT1), PPD-H1 (HvPRR37), PPD-H2 (HvFT3), and eam6/eps2 (HvCEN). For each gene, allelic series, size and direction of QTL effects, interactions between genes and with the environment are presented. Pleiotropic effects on agronomically important traits such as grain yield are also discussed. The review includes brief comments on additional genes with large effects on phenology that became relevant in modern barley breeding. The parallelisms between flowering time allelic variation between the two most cultivated Triticeae species (barley and wheat) are also outlined. This work is mostly based on previously published data, although we added some new data and hypothesis supported by a number of studies. This review shows the wide variety of allelic effects that provide enormous plasticity in barley flowering behavior, which opens new avenues to breeders for fine-tuning phenology of the barley crop.
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Affiliation(s)
- Miriam Fernández-Calleja
- Department of Genetics and Plant Production, Aula Dei Experimental Station, EEAD-CSIC, Avenida Montañana, 1005, 50059, Zaragoza, Spain
| | - Ana M Casas
- Department of Genetics and Plant Production, Aula Dei Experimental Station, EEAD-CSIC, Avenida Montañana, 1005, 50059, Zaragoza, Spain
| | - Ernesto Igartua
- Department of Genetics and Plant Production, Aula Dei Experimental Station, EEAD-CSIC, Avenida Montañana, 1005, 50059, Zaragoza, Spain.
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33
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Yang Y, Zhang X, Wu L, Zhang L, Liu G, Xia C, Liu X, Kong X. Transcriptome profiling of developing leaf and shoot apices to reveal the molecular mechanism and co-expression genes responsible for the wheat heading date. BMC Genomics 2021; 22:468. [PMID: 34162321 PMCID: PMC8220847 DOI: 10.1186/s12864-021-07797-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 06/10/2021] [Indexed: 12/13/2022] Open
Abstract
Background Wheat is one of the most widely planted crops worldwide. The heading date is important for wheat environmental adaptability, as it not only controls flowering time but also determines the yield component in terms of grain number per spike. Results In this research, homozygous genotypes with early and late heading dates derived from backcrossed progeny were selected to conduct RNA-Seq analysis at the double ridge stage (W2.0) and androgynous primordium differentiation stage (W3.5) of the leaf and apical meristem, respectively. In total, 18,352 differentially expressed genes (DEGs) were identified, many of which are strongly associated with wheat heading date genes. Gene Ontology (GO) enrichment analysis revealed that carbohydrate metabolism, trehalose metabolic process, photosynthesis, and light reaction are closely related to the flowering time regulation pathway. Based on MapMan metabolic analysis, the DEGs are mainly involved in the light reaction, hormone signaling, lipid metabolism, secondary metabolism, and nucleotide synthesis. In addition, 1,225 DEGs were annotated to 45 transcription factor gene families, including LFY, SBP, and MADS-box transcription factors closely related to flowering time. Weighted gene co-expression network analysis (WGCNA) showed that 16, 336, 446, and 124 DEGs have biological connections with Vrn1-5 A, Vrn3-7B, Ppd-1D, and WSOC1, respectively. Furthermore, TraesCS2D02G181400 encodes a MADS-MIKC transcription factor and is co-expressed with Vrn1-5 A, which indicates that this gene may be related to flowering time. Conclusions RNA-Seq analysis provided transcriptome data for the wheat heading date at key flower development stages of double ridge (W2.0) and androgynous primordium differentiation (W3.5). Based on the DEGs identified, co-expression networks of key flowering time genes in Vrn1-5 A, Vrn3-7B, WSOC1, and Ppd-1D were established. Moreover, we discovered a potential candidate flowering time gene, TraesCS2D02G181400. Taken together, these results serve as a foundation for further study on the regulatory mechanism of the wheat heading date. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07797-7.
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Affiliation(s)
- Yuxin Yang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Xueying Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Lifen Wu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.,Hebei sub-center of National Maize Improvement Center of China, Key Laboratory of Crop Germplasm Resources of Northern China (Ministry of Education), College of Agronomy, Hebei Agricultural University, 071001, Baoding, China
| | - Lichao Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Guoxiang Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Chuan Xia
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Xu Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Xiuying Kong
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
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34
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Cao S, Luo X, Xu D, Tian X, Song J, Xia X, Chu C, He Z. Genetic architecture underlying light and temperature mediated flowering in Arabidopsis, rice, and temperate cereals. THE NEW PHYTOLOGIST 2021; 230:1731-1745. [PMID: 33586137 DOI: 10.1111/nph.17276] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 01/20/2021] [Indexed: 05/23/2023]
Abstract
Timely flowering is essential for optimum crop reproduction and yield. To determine the best flowering-time genes (FTGs) relevant to local adaptation and breeding, it is essential to compare the interspecific genetic architecture of flowering in response to light and temperature, the two most important environmental cues in crop breeding. However, the conservation and variations of FTGs across species lack systematic dissection. This review summarizes current knowledge on the genetic architectures underlying light and temperature-mediated flowering initiation in Arabidopsis, rice, and temperate cereals. Extensive comparative analyses show that most FTGs are conserved, whereas functional variations in FTGs may be species specific and confer local adaptation in different species. To explore evolutionary dynamics underpinning the conservation and variations in FTGs, domestication and selection of some key FTGs are further dissected. Based on our analyses of genetic control of flowering time, a number of key issues are highlighted. Strategies for modulation of flowering behavior in crop breeding are also discussed. The resultant resources provide a wealth of reference information to uncover molecular mechanisms of flowering in plants and achieve genetic improvement in crops.
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Affiliation(s)
- Shuanghe Cao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xumei Luo
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dengan Xu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiuling Tian
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jie Song
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- International Maize and Wheat Improvement Center China Office, c/o Chinese Academy Agricultural Sciences, Beijing, 100081, China
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35
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Steed G, Ramirez DC, Hannah MA, Webb AAR. Chronoculture, harnessing the circadian clock to improve crop yield and sustainability. Science 2021; 372:372/6541/eabc9141. [PMID: 33926926 DOI: 10.1126/science.abc9141] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Human health is dependent on a plentiful and nutritious supply of food, primarily derived from crop plants. Rhythmic supply of light as a result of the day and night cycle led to the evolution of circadian clocks that modulate most plant physiology, photosynthesis, metabolism, and development. To regulate crop traits and adaptation, breeders have indirectly selected for variation at circadian genes. The pervasive impact of the circadian system on crops suggests that future food production might be improved by modifying circadian rhythms, engineering the timing of transgene expression, and applying agricultural treatments at the most effective time of day. We describe the applied research required to take advantage of circadian biology in agriculture to increase production and reduce inputs.
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Affiliation(s)
- Gareth Steed
- 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
| | - 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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36
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Errum A, Rehman N, Khan MR, Ali GM. Genome-wide characterization and expression analysis of pseudo-response regulator gene family in wheat. Mol Biol Rep 2021; 48:2411-2427. [PMID: 33782785 DOI: 10.1007/s11033-021-06276-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/11/2021] [Indexed: 11/29/2022]
Abstract
Pseudo-response regulator (PRR) gene family members play a significant role in plant circadian clocks, flowering time inflorescence architecture development during transition from vegetative growth phase to reproductive phase. In current study, we analyzed the expression profiling, phylogenetic relationship, and molecular characterization of PRR gene family members of common wheat by using IWGSC Ref seq v1.1 wheat genome database with a coverage rate of 90%. By using bioinformatic approach total 20 candidate gene sequences were identified and divided into six groups and four clades. It was found that mostly genes have same number of exons and introns showed similar features because they originated through duplication events during evolution processes. Although all the proteins have conserved PRR domains, but some are distinct in their sequences suggesting functional divergence. By comparative synteny analysis it was revealed that Group 1, 2, 3 and 11-D of group 4 have duplication events while group 5 and TaPRR9-B,10-D showed conservation with previously identified PRR members from rice. While expression variation of six groups from each analysis matches with each other. Five groups highly expressed in leaf, spike, and roots in pattern like leaf > spike > root at all three stages booting, heading and anthesis of spike development. This suggests that TaPRR genes play important roles in different photoperiod signaling pathways in different organs at different stages of spike development and flowering via unknown pathway. These findings will also provide comprehensive knowledge about future investigations on wheat PRR family members involved in complex network of circadian system for plant development.
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Affiliation(s)
- Aliya Errum
- Pakistan Agriculture Research Council Institute of Advanced Studies in Agriculture, Islamabad, Pakistan
| | - Nazia Rehman
- National Institute of Genomics and Advanced Biotechnology, National Agriculture Research Center, Islamabad, Pakistan. .,Pakistan Agriculture Research Council Institute of Advanced Studies in Agriculture, Islamabad, Pakistan.
| | - Muhammad Ramzan Khan
- National Institute of Genomics and Advanced Biotechnology, National Agriculture Research Center, Islamabad, Pakistan. .,Pakistan Agriculture Research Council Institute of Advanced Studies in Agriculture, Islamabad, Pakistan.
| | - Ghulam Muhammad Ali
- National Institute of Genomics and Advanced Biotechnology, National Agriculture Research Center, Islamabad, Pakistan.,Pakistan Agriculture Research Council Institute of Advanced Studies in Agriculture, Islamabad, Pakistan
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37
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Wheat Developmental Traits as Affected by the Interaction between Eps-7D and Temperature under Contrasting Photoperiods with Insensitive Ppd-D1 Background. PLANTS 2021; 10:plants10030547. [PMID: 33805828 PMCID: PMC7999118 DOI: 10.3390/plants10030547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/01/2021] [Accepted: 03/09/2021] [Indexed: 01/14/2023]
Abstract
Earliness per se (Eps) genes are important to fine tune adaptation, and studying their probable pleiotropic effect on wheat yield traits is worthwhile. In addition, it has been shown that some Eps genes interact with temperature and therefore determining the likely Eps × temperature interaction is needed for each newly identified Eps gene. We studied two NILs differing in the newly identified Eps-7D (carrying insensitive Ppd-D1 in the background) under three temperature regimes (9, 15 and 18 °C) and two photoperiods (12 and 24 h). Eps-7D affected time to anthesis as expected and the Eps-7D-late allele extended both the period before and after terminal spikelet. The interaction effect of Eps-7D × temperature was significant but not cross-over: the magnitude and level of significance of the difference between NILs with the late or early allele was affected by the growing temperature (i.e., difference was least at 18 °C and largest at 9 °C), and the differences caused due to temperature sensitivity were influenced by photoperiod. The rate of leaf initiation was faster in NIL with Eps-7D-early than with the late allele which compensated for the shorter duration of leaf initiation resulting in similar final leaf number between two NILs. Eps-7D-late consistently increased spike fertility through improving floret primordia survival as a consequence of extending the late reproductive phase.
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38
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Liang L, Zhang Z, Cheng N, Liu H, Song S, Hu Y, Zhou X, Zhang J, Xing Y. The transcriptional repressor OsPRR73 links circadian clock and photoperiod pathway to control heading date in rice. PLANT, CELL & ENVIRONMENT 2021; 44:842-855. [PMID: 33377200 DOI: 10.1111/pce.13987] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 05/24/2023]
Abstract
The phase transition from vegetative to reproductive growth is triggered by internal and external signals that participate in circadian clock in plants. We identified a rice floral inhibitor OsPRR73 encoding a CONSTANS protein. Overexpression of OsPRR73 resulted in late heading under both long-day (LD) and short-day (SD) conditions. Knockout mutants led to early heading under LD conditions but no change under SD. OsPRR73 mRNA accumulated at noon and exhibited a robust oscillation under constant light (LL) and constant darkness (DD) conditions. OsPRR73 overexpression exerted negative feedback on endogenous OsPRR73 expression and altered diurnal expressions of key flowering genes and circadian clock genes. OsPRR73 bound to the promoters of the floral gene Ehd1 and the circadian gene OsLHY, and significantly suppressed their expression at dawn. In LL and DD, the oscillatory patterns of the circadian genes OsLHY, OsTOC1, OsGI and OsELF3 were varied in OsPRR73OX and osprr73 mutants. OsPRR73 expression was decreased in osphyb mutants, and overexpression of OsPRR73 complemented the early heading date phenotype of osphyb, indicating OsPRR73 works downstream of OsPhyB. Therefore, OsPRR73 is involved in a feedback loop of the rice clock and connects the photoperiod flowering pathway by binding to the Ehd1 promoter in rice.
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Affiliation(s)
- Liwen Liang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zhanyi Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Niannian Cheng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Haiyang Liu
- College of Agriculture, Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, China
| | - Song Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yong Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xiangchun Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jia Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
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39
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Okada T, Jayasinghe JEARM, Eckermann P, Watson-Haigh NS, Warner P, Williams ME, Albertsen MC, Baumann U, Whitford R. Genetic factors associated with favourable pollinator traits in the wheat cultivar Piko. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:434-447. [PMID: 33332999 DOI: 10.1071/fp20181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
Hybrid breeding in wheat has the potential to boost yields. An efficient hybrid seed production system requires elite pollinators; however, such germplasm is limited among modern cultivars. Piko, a winter wheat (Triticum aestivum L.) cultivar, has been identified as a superior pollinator and has been used in Europe. Piko has favourable pollinator traits for anther extrusion, anther length, pollen mass and hybrid seed set. However, the genetic factors responsible for Piko's favourable traits are largely unknown. Here, we report on the genetic analysis of a Piko-derived F2 mapping population. We confirmed that Piko's Rht-D1a allele for tall stature is associated with large anthers and high anther extrusion. However, Rht-D1 was not found to be associated with anther filament length, confirmed by near isogenic lines. Piko's photoperiod sensitive Ppd-B1b allele shows an association with increased spike length, more spikelets and spike architecture traits, while the insensitive Ppd-B1a allele is linked with high anther extrusion and larger anthers. We identified an anther extrusion quantitative trait locus (QTL) on chromosome 6A that showed significantly biased transmission of the favourable Piko allele amongst F2 progenies. The Piko allele is completely absent in the distal 6AS region and the central 6A region revealed a significantly lower ratio (<8%) of F2 with homozygous Piko alleles. Our study provided further evidence for the effects of Rht-D1 and Ppd-B1 loci on multiple pollinator traits and a novel anther extrusion QTL that exhibits segregation distortion.
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Affiliation(s)
- Takashi Okada
- School of Agriculture, Food and Wine, University of Adelaide, Plant Genomics Centre, Hartley Grove, Urrbrae, SA 5064, Australia; and Present address: The Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide Health and Medical Science Building, North Terrace, Adelaide, SA 5000, Australia; and Corresponding author.
| | - J E A Ridma M Jayasinghe
- School of Agriculture, Food and Wine, University of Adelaide, Plant Genomics Centre, Hartley Grove, Urrbrae, SA 5064, Australia
| | - Paul Eckermann
- School of Agriculture, Food and Wine, University of Adelaide, Plant Genomics Centre, Hartley Grove, Urrbrae, SA 5064, Australia
| | - Nathan S Watson-Haigh
- School of Agriculture, Food and Wine, University of Adelaide, Plant Genomics Centre, Hartley Grove, Urrbrae, SA 5064, Australia
| | - Patricia Warner
- School of Agriculture, Food and Wine, University of Adelaide, Plant Genomics Centre, Hartley Grove, Urrbrae, SA 5064, Australia
| | - Mark E Williams
- Corteva Agriscience, 7250 NW 62nd Avenue, Johnston, IA 50131-1004, USA
| | - Marc C Albertsen
- Corteva Agriscience, 7250 NW 62nd Avenue, Johnston, IA 50131-1004, USA
| | - Ute Baumann
- School of Agriculture, Food and Wine, University of Adelaide, Plant Genomics Centre, Hartley Grove, Urrbrae, SA 5064, Australia
| | - Ryan Whitford
- School of Agriculture, Food and Wine, University of Adelaide, Plant Genomics Centre, Hartley Grove, Urrbrae, SA 5064, Australia
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Basavaraddi PA, Savin R, Wingen LU, Bencivenga S, Przewieslik-Allen AM, Griffiths S, Slafer GA. Interactions between two QTLs for time to anthesis on spike development and fertility in wheat. Sci Rep 2021; 11:2451. [PMID: 33510240 PMCID: PMC7843729 DOI: 10.1038/s41598-021-81857-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/12/2021] [Indexed: 01/30/2023] Open
Abstract
Earliness per se (Eps) genes are reported to be important in fine-tuning flowering time in wheat independently of photoperiod (Ppd) and vernalisation (Vrn). Unlike Ppd and Vrn genes, Eps have relatively small effects and their physiological effect along with chromosomal position are not well defined. We evaluated eight lines derived from crossing two vernalisation insensitive lines, Paragon and Baj (late and early flowering respectively), to study the detailed effects of two newly identified QTLs, Eps-7D and Eps-2B and their interactions under field conditions. The effect of both QTLs was minor and was affected by the allelic status of the other. While the magnitude of effect of these QTLs on anthesis was similar, they are associated with very different profiles of pre-anthesis development which also depends on their interaction. Eps-7D affected both duration before and after terminal spikelet while not affecting final leaf number (FLN) so Eps-7D-early had a faster rate of leaf appearance. Eps-2B acted more specifically in the early reproductive phase and slightly altered FLN without affecting the leaf appearance rate. Both QTLs affected the spike fertility by altering the rate of floret development and mortality. The effect of Eps-2B was very small but consistent in that -late allele tended to produce more fertile florets.
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Affiliation(s)
- Priyanka A. Basavaraddi
- grid.15043.330000 0001 2163 1432Department of Crop and Forest Sciences, University of Lleida-AGROTECNIO Center, Av. R. Roure 191, 25198 Lleida, Spain
| | - Roxana Savin
- grid.15043.330000 0001 2163 1432Department of Crop and Forest Sciences, University of Lleida-AGROTECNIO Center, Av. R. Roure 191, 25198 Lleida, Spain
| | - Luzie U. Wingen
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Stefano Bencivenga
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | | | - Simon Griffiths
- grid.14830.3e0000 0001 2175 7246John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Gustavo A. Slafer
- grid.15043.330000 0001 2163 1432Department of Crop and Forest Sciences, University of Lleida-AGROTECNIO Center, Av. R. Roure 191, 25198 Lleida, Spain ,grid.425902.80000 0000 9601 989XICREA, Catalonian Institution for Research and Advanced Studies, Barcelona, Spain
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Gauley A, Boden SA. Stepwise increases in FT1 expression regulate seasonal progression of flowering in wheat (Triticum aestivum). THE NEW PHYTOLOGIST 2021; 229:1163-1176. [PMID: 32909250 DOI: 10.1111/nph.16910] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/24/2020] [Indexed: 05/28/2023]
Abstract
Flowering is regulated by genes that respond to changing daylengths and temperature, which have been well studied using controlled conditions; however, the molecular processes underpinning flowering in nature remain poorly understood. Here, we investigate the genetic pathways that coordinate flowering and inflorescence development of wheat (Triticum aestivum) as daylengths extend naturally in the field, using lines that contain variant alleles for the key photoperiod gene, Photoperiod-1 (Ppd-1). We found flowering involves a stepwise increase in the expression of FLOWERING LOCUS T1 (FT1), which initiates under day-neutral conditions of early spring. The incremental rise in FT1 expression is overridden in plants that contain a photoperiod-insensitive allele of Ppd-1, which hastens the completion of spikelet development and accelerates flowering time. The accelerated inflorescence development of photoperiod-insensitive lines is promoted by advanced seasonal expression of floral meristem identity genes. The completion of spikelet formation is promoted by FLOWERING LOCUS T2, which regulates spikelet number and is activated by Ppd-1. In wheat, flowering under natural photoperiods is regulated by stepwise increases in the expression of FT1, which responds dynamically to extending daylengths to promote early inflorescence development. This research provides a strong foundation to improve yield potential by fine-tuning the photoperiod-dependent control of inflorescence development.
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Affiliation(s)
- Adam Gauley
- Department of Crop Genetics, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
| | - Scott A Boden
- Department of Crop Genetics, John Innes Centre, Colney Lane, Norwich, NR4 7UH, UK
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA, 5064, Australia
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Li G, Cao C, Yang H, Wang J, Wei W, Zhu D, Gao P, Zhao Y. Molecular cloning and potential role of DiSOC1s in flowering regulation in Davidia involucrata Baill. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 157:453-459. [PMID: 33218844 DOI: 10.1016/j.plaphy.2020.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/04/2020] [Indexed: 06/11/2023]
Abstract
Davidia involucrata Baill. (dove tree) is unique Tertiary relic plant in China, also known as 'living fossil' and 'giant panda'. The MADS-box family gene SOC1 is involved in the regulatory pathway that integrates flowering signals to promote flowering at the optimal time. In this study, we isolated and identified two dove tree SOC1 homologues, named DiSOC1-a and DiSOC1-b. These two sequences possess highly conserved domains MADS-box and SOC1-motif, as well as the semi-conserved region K-box. DiSOC1-a and DiSOC1-b were expressed at varying levels in all tested tissues of dove tree and shared high levels of expression in the flower buds. The expression tendencies of both genes in bract were initially upward and then downward and were highest in young bracts. Neither DiSOC1-a nor DiSOC1-b was expressed in immature leaves. Proteins encoded by DiSOC1-a and DiSOC1-b were located in the nucleus. In addition, ectopic overexpression of both genes in WT Arabidopsis promoted early flowering and the growth of the main bolt. Taken together, these results suggest that DiSOC1-a and DiSOC1-b are involved in the flowering initiation and the main bolt growth process of dove tree. Our results provide a foundation for horticultural breeding to control flowering time of dove tree.
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Affiliation(s)
- Guolin Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Chenxi Cao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Hua Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Jieheng Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Wei Wei
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China
| | - Dahai Zhu
- Administration of LongXi-HongKou National Nature Reserve, No. 24 Donghong Road, Dujiangyan, 611830, China
| | - Ping Gao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China.
| | - Yun Zhao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China.
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Gupta P, Kabbaj H, El Hassouni K, Maccaferri M, Sanchez-Garcia M, Tuberosa R, Bassi FM. Genomic Regions Associated with the Control of Flowering Time in Durum Wheat. PLANTS 2020; 9:plants9121628. [PMID: 33255147 PMCID: PMC7759329 DOI: 10.3390/plants9121628] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/03/2020] [Accepted: 11/05/2020] [Indexed: 01/17/2023]
Abstract
Flowering time is a critical stage for crop development as it regulates the ability of plants to adapt to an environment. To understand the genetic control of flowering time, a genome-wide association study (GWAS) was conducted to identify the genomic regions associated with the control of this trait in durum wheat (Triticum durum Desf.). A total of 96 landraces and 288 modern lines were evaluated for days to heading, growing degree days, and accumulated day length at flowering across 13 environments spread across Morocco, Lebanon, Mauritania, and Senegal. These environments were grouped into four pheno-environments based on temperature, day length, and other climatic variables. Genotyping with a 35K Axiom array generated 7652 polymorphic single nucleotide polymorphisms (SNPs) in addition to 3 KASP markers associated with known flowering genes. In total, 32 significant QTLs were identified in both landraces and modern lines. Some QTLs had a strong association with already known regulatory photoperiod genes, Ppd-A and Ppd-B, and vernalization genes Vrn-A1 and VrnA7. However, these loci explained only 5% to 20% of variance for days to heading. Seven QTLs overlapped between the two germplasm groups in which Q.ICD.Eps-03 and Q.ICD.Vrn-15 consistently affected flowering time in all the pheno-environments, while Q.ICD.Eps-09 and Q.ICD.Ppd-10 were significant only in two pheno-environments and the combined analysis across all environments. These results help clarify the genetic mechanism controlling flowering time in durum wheat and show some clear distinctions to what is known for common wheat (Triticum aestivum L.).
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Affiliation(s)
- Priyanka Gupta
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127 Bologna, Italy; (P.G.); (M.M.); (R.T.)
- International Center for Agricultural Research in the Dry Areas (ICARDA), 10000 Rabat, Morocco; (H.K.); (K.E.H.); (M.S.-G.)
| | - Hafssa Kabbaj
- International Center for Agricultural Research in the Dry Areas (ICARDA), 10000 Rabat, Morocco; (H.K.); (K.E.H.); (M.S.-G.)
| | - Khaoula El Hassouni
- International Center for Agricultural Research in the Dry Areas (ICARDA), 10000 Rabat, Morocco; (H.K.); (K.E.H.); (M.S.-G.)
| | - Marco Maccaferri
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127 Bologna, Italy; (P.G.); (M.M.); (R.T.)
| | - Miguel Sanchez-Garcia
- International Center for Agricultural Research in the Dry Areas (ICARDA), 10000 Rabat, Morocco; (H.K.); (K.E.H.); (M.S.-G.)
| | - Roberto Tuberosa
- Department of Agricultural and Food Sciences, University of Bologna, Viale G Fanin 44, 40127 Bologna, Italy; (P.G.); (M.M.); (R.T.)
| | - Filippo Maria Bassi
- International Center for Agricultural Research in the Dry Areas (ICARDA), 10000 Rabat, Morocco; (H.K.); (K.E.H.); (M.S.-G.)
- Correspondence: ; Tel.: +212-614-402-717
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Kroupin PY, Karlov GI, Bespalova LA, Salina EA, Chernook AG, Watanabe N, Bazhenov MS, Panchenko VV, Nazarova LA, Kovtunenko VY, Divashuk MG. Effects of Rht17 in combination with Vrn-B1 and Ppd-D1 alleles on agronomic traits in wheat in black earth and non-black earth regions. BMC PLANT BIOLOGY 2020; 20:304. [PMID: 33050878 PMCID: PMC7556923 DOI: 10.1186/s12870-020-02514-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Plant height is an important wheat trait that is regulated by multiple genes, among which Rht is of the utmost value. In wheat, Rht-B1p (=Rht17) is a mutant allele of the Rht gene that encodes for a DELLA-protein and results in the development of gibberellin-insensitive plants with a dwarfing phenotype. The pleiotropic effects of dwarfing genes on yield are highly dependent on both the genetic background and the environmental conditions. In Russia, the Central Non-Black Earth Region and Krasnodar Krai are two economically important regions that require differing management for sustainable wheat production for food, feed and industry. The purpose of our study was to compare the pleiotropic effects of Rht-B1p on the main valuable agronomic traits in the F3:4 families of the spring bread wheat Chris Mutant/Novosibirskaya 67 in the genetic background of Vrn-B1a/vrn-B1 (spring/winter phenotype) and Ppd-D1a/Ppd-D1b (insensitivity/sensitivity to photoperiod) alleles in a field experiment in Moscow and Krasnodar Krai. RESULTS Plant height was reduced on average by 21 cm (28%) and 25 cm (30%), respectively; Ppd-D1a slightly strengthened the dwarfing effect in Moscow and mitigated it in Krasnodar Krai. Grain weight of the main spike was reduced by Rht-B1p in Moscow and to lesser extent in Krasnodar; Ppd-D1a and Vrn-B1a tended to partially compensate for this loss in Krasnodar Krai. Thousand grain weight was reduced on average by 5.3 g (16%) and 2.9 g (10%) in Moscow and Krasnodar Krai, respectively, but was partially compensated for by Ppd-D1a in Krasnodar Krai. Harvest index was increased due to Rht-B1p by 6 and 10% in Moscow and Krasnodar Krai, respectively. Rht-B1p resulted in a delay of heading by 1-2 days in Moscow. Ppd-D1a accelerated heading by 1 day and 6 days in Moscow and in Krasnodar Krai, respectively. CONCLUSIONS Rht-B1p could be introduced into wheat breeding along with dwarfing genes such as Rht-B1b and Rht-D1b. Special attention should be paid to its combination with Ppd-D1a and Vrn-B1a as regulators of developmental rates, compensators of adverse effects of Rht-B1p on productivity and enhancers of positive effect of Rht-B1p on harvest index.
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Affiliation(s)
- Pavel Yu Kroupin
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow, 127550, Russia
- Centre for Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya street, 49, Moscow, 127550, Russia
| | - Gennady I Karlov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow, 127550, Russia
- Centre for Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya street, 49, Moscow, 127550, Russia
| | - Ludmila A Bespalova
- Department of Breeding and Seed Production of Wheat and Triticale, National center of grain named after P.P. Lukyanenko, Central Estate of KNIISH, Krasnodar, 350012, Russia
| | - Elena A Salina
- Kurchatov Genomics Center, Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia
| | - Anastasiya G Chernook
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow, 127550, Russia
- Centre for Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya street, 49, Moscow, 127550, Russia
| | - Nobuyoshi Watanabe
- College of Agriculture, Ibaraki University, 3-21-1 Chuo, Ami, Inashiki, Ibaraki, 300-0393, Japan
| | - Mikhail S Bazhenov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow, 127550, Russia
- Centre for Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya street, 49, Moscow, 127550, Russia
| | - Vladimir V Panchenko
- Department of Breeding and Seed Production of Wheat and Triticale, National center of grain named after P.P. Lukyanenko, Central Estate of KNIISH, Krasnodar, 350012, Russia
| | - Lubov A Nazarova
- Kurchatov Genomics Center-ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow, 127550, Russia
| | - Victor Ya Kovtunenko
- Department of Breeding and Seed Production of Wheat and Triticale, National center of grain named after P.P. Lukyanenko, Central Estate of KNIISH, Krasnodar, 350012, Russia
| | - Mikhail G Divashuk
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow, 127550, Russia.
- Centre for Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya street, 49, Moscow, 127550, Russia.
- Kurchatov Genomics Center-ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow, 127550, Russia.
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Hu R, Xiao J, Zhang Q, Gu T, Chang J, Yang G, He G. A light-regulated gene, TaLWD1L-A, affects flowering time in transgenic wheat (Triticum aestivum L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 299:110623. [PMID: 32900433 DOI: 10.1016/j.plantsci.2020.110623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 07/14/2020] [Accepted: 07/23/2020] [Indexed: 06/11/2023]
Abstract
Flowering time is an important agronomic trait that greatly influences plant architecture and grain yield in cereal crops. The present study identified a light-regulated gene, TaLWD1L-A, from hexaploid wheat that encodes a WD40 domain-containing protein. TaLWD1L-A was localized in the nucleus. Phenotypic analysis demonstrated that TaLWD1L-A overexpression in transgenic wheat led to an obvious early flowering phenotype. Upregulation of the floral activator gene TaFT1 caused the early flowering phenotype in transgenic wheat plants. TaLWD1L-A also affected the expression of circadian clock genes, including TaTOC1, TaLHY, TaPRR59, TaPRR73 and TaPRR95, and indirectly regulated the expression of the TaFT1 in transgenic plants by affecting the expression of vernalization-related genes TaVRN1 and TaVRN2 and photoperiod-related genes TaPpd-1 and TaGI. The early flowering phenotype in TaLWD1L-A-overexpressing transgenic lines led to a relatively shorter phenotype and yield reduction. Our results revealed that TaLWD1L-A affected the expression of circadian clock-related genes and played an important role in wheat flowering regulation by influencing the expression of genes related to vernalization and photoperiod pathways.
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Affiliation(s)
- Rui Hu
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Jie Xiao
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Qian Zhang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Ting Gu
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan 430074, China
| | - Junli Chang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan 430074, China.
| | - Guangxiao Yang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan 430074, China.
| | - Guangyuan He
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan 430074, China.
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Shaw LM, Li C, Woods DP, Alvarez MA, Lin H, Lau MY, Chen A, Dubcovsky J. Epistatic interactions between PHOTOPERIOD1, CONSTANS1 and CONSTANS2 modulate the photoperiodic response in wheat. PLoS Genet 2020; 16:e1008812. [PMID: 32658893 PMCID: PMC7394450 DOI: 10.1371/journal.pgen.1008812] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/31/2020] [Accepted: 06/12/2020] [Indexed: 02/06/2023] Open
Abstract
In Arabidopsis, CONSTANS (CO) integrates light and circadian clock signals to promote flowering under long days (LD). In the grasses, a duplication generated two paralogs designated as CONSTANS1 (CO1) and CONSTANS2 (CO2). Here we show that in tetraploid wheat plants grown under LD, combined loss-of-function mutations in the A and B-genome homeologs of CO1 and CO2 (co1 co2) result in a small (3 d) but significant (P<0.0001) acceleration of heading time both in PHOTOPERIOD1 (PPD1) sensitive (Ppd-A1b, functional ancestral allele) and insensitive (Ppd-A1a, functional dominant allele) backgrounds. Under short days (SD), co1 co2 mutants headed 13 d earlier than the wild type (P<0.0001) in the presence of Ppd-A1a. However, in the presence of Ppd-A1b, spikes from both genotypes failed to emerge by 180 d. These results indicate that CO1 and CO2 operate mainly as weak heading time repressors in both LD and SD. By contrast, in ppd1 mutants with loss-of-function mutations in both PPD1 homeologs, the wild type Co1 allele accelerated heading time >60 d relative to the co1 mutant allele under LD. We detected significant genetic interactions among CO1, CO2 and PPD1 genes on heading time, which were reflected in complex interactions at the transcriptional and protein levels. Loss-of-function mutations in PPD1 delayed heading more than combined co1 co2 mutations and, more importantly, PPD1 was able to perceive and respond to differences in photoperiod in the absence of functional CO1 and CO2 genes. Similarly, CO1 was able to accelerate heading time in response to LD in the absence of a functional PPD1. Taken together, these results indicate that PPD1 and CO1 are able to respond to photoperiod in the absence of each other, and that interactions between these two photoperiod pathways at the transcriptional and protein levels are important to fine-tune the flowering response in wheat.
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Affiliation(s)
- Lindsay M. Shaw
- Department of Plant Sciences, University of California, Davis, California, United States of America
- Currently at Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - 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
| | - 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
| | - Maria A. Alvarez
- Department of Plant Sciences, University of California, Davis, California, 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
| | - Mei Y. Lau
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Andrew Chen
- Department of Plant Sciences, University of California, Davis, California, 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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Kippes N, VanGessel C, Hamilton J, Akpinar A, Budak H, Dubcovsky J, Pearce S. Effect of phyB and phyC loss-of-function mutations on the wheat transcriptome under short and long day photoperiods. BMC PLANT BIOLOGY 2020; 20:297. [PMID: 32600268 PMCID: PMC7325275 DOI: 10.1186/s12870-020-02506-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/18/2020] [Indexed: 05/26/2023]
Abstract
BACKGROUND Photoperiod signals provide important cues by which plants regulate their growth and development in response to predictable seasonal changes. Phytochromes, a family of red and far-red light receptors, play critical roles in regulating flowering time in response to changing photoperiods. A previous study showed that loss-of-function mutations in either PHYB or PHYC result in large delays in heading time and in the differential regulation of a large number of genes in wheat plants grown in an inductive long day (LD) photoperiod. RESULTS We found that under non-inductive short-day (SD) photoperiods, phyB-null and phyC-null mutants were taller, had a reduced number of tillers, longer and wider leaves, and headed later than wild-type (WT) plants. The delay in heading between WT and phy mutants was greater in LD than in SD, confirming the importance of PHYB and PHYC in accelerating heading date in LDs. Both mutants flowered earlier in SD than LD, the inverse response to that of WT plants. In both SD and LD photoperiods, PHYB regulated more genes than PHYC. We identified subsets of differentially expressed and alternatively spliced genes that were specifically regulated by PHYB and PHYC in either SD or LD photoperiods, and a smaller set of genes that were regulated in both photoperiods. We found that photoperiod had a contrasting effect on transcript levels of the flowering promoting genes VRN-A1 and PPD-B1 in phyB and phyC mutants compared to the WT. CONCLUSIONS Our study confirms the major role of both PHYB and PHYC in flowering promotion in LD conditions. Transcriptome characterization revealed an unexpected reversion of the wheat LD plants into SD plants in the phyB-null and phyC-null mutants and identified flowering genes showing significant interactions between phytochromes and photoperiod that may be involved in this phenomenon. Our RNA-seq data provides insight into light signaling pathways in inductive and non-inductive photoperiods and a set of candidate genes to dissect the underlying developmental regulatory networks in wheat.
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Affiliation(s)
- Nestor Kippes
- Department of Plant Sciences, University of California, Davis, CA 95616 USA
- Current address: Department of Plant Biology, UC Davis Genome Center, University of California, Davis, CA 95616 USA
| | - Carl VanGessel
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - James Hamilton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | | | | | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA 95616 USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815 USA
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
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Chen Z, Cheng X, Chai L, Wang Z, Du D, Wang Z, Bian R, Zhao A, Xin M, Guo W, Hu Z, Peng H, Yao Y, Sun Q, Ni Z. Pleiotropic QTL influencing spikelet number and heading date in common wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1825-1838. [PMID: 32016554 DOI: 10.1007/s00122-020-03556-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 01/24/2020] [Indexed: 05/23/2023]
Abstract
Three pleiotropic QTL regions associated with spikelet number and heading date were identified, with FT-A1 considered the candidate gene for QTspn/Hd.cau-7A. Spikelet number traits and heading date (HD) play key roles in yield improvement of wheat and its wide adaptation to different environments. Here, we used a Recombinant Inbred Lines population derived from a cross between Yi5029 (5029) and Nongda4332 (4332) to construct a high-density genetic linkage map and identify quantitative trait loci (QTL) associated with total spikelet number per spike (TSPN), fertile spikelet number per spike (FSPN), sterile spikelet number per spike (SSPN) and HD. A total of 22 environmentally stable QTL for TSPN, FSPN, SSPN and HD were identified. Notably, three pleiotropic QTL regions for TSPN and HD were detected on chromosomes 2A, 7A and 7D. The QTL associated with TSPN and HD on chromosome 7AS was designated QTspn/Hd.cau-7A. Furthermore, the candidate gene FT-A1 located in the region of QTspn/Hd.cau-7A had a single-nucleotide polymorphism (T-G) within the third exon, which might be the cause of diversity in spikelet number and HD between the two parents. Additionally, we developed a semi-thermal asymmetric reverse PCR (STARP) marker to analyze the geographical distribution and evolution of FT-A1 (T or G) alleles. This study contributes to our understanding of the molecular mechanisms of the four traits (TSPN, FSPN, SSPN and HD) and provides further insights into the genetic relationship between spikelet number traits and HD in wheat.
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Affiliation(s)
- Zhaoyan Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Xuejiao Cheng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Lingling Chai
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zihao Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Dejie Du
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zhihui Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Ruolin Bian
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Aiju Zhao
- Hebei Crop Genetic Breeding Laboratory, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Weilong Guo
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- National Plant Gene Research Centre, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
- National Plant Gene Research Centre, Beijing, 100193, China.
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Phenology and related traits for wheat adaptation. Heredity (Edinb) 2020; 125:417-430. [PMID: 32457509 PMCID: PMC7784700 DOI: 10.1038/s41437-020-0320-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 05/06/2020] [Accepted: 05/06/2020] [Indexed: 11/09/2022] Open
Abstract
Wheat is a major food crop, with around 765 million tonnes produced globally. The largest wheat producers include the European Union, China, India, Russia, United States, Canada, Pakistan, Australia, Ukraine and Argentina. Cultivation of wheat across such diverse global environments with variation in climate, biotic and abiotic stresses, requires cultivars adapted to a range of growing conditions. One intrinsic way that wheat achieves adaptation is through variation in phenology (seasonal timing of the lifecycle) and related traits (e.g., those affecting plant architecture). It is important to understand the genes that underlie this variation, and how they interact with each other, other traits and the growing environment. This review summarises the current understanding of phenology and developmental traits that adapt wheat to different environments. Examples are provided to illustrate how different combinations of alleles can facilitate breeding of wheat varieties with optimal crop performance for different growing regions or farming systems.
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50
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Royo C, Dreisigacker S, Soriano JM, Lopes MS, Ammar K, Villegas D. Allelic Variation at the Vernalization Response ( Vrn-1) and Photoperiod Sensitivity ( Ppd-1) Genes and Their Association With the Development of Durum Wheat Landraces and Modern Cultivars. FRONTIERS IN PLANT SCIENCE 2020; 11:838. [PMID: 32655598 PMCID: PMC7325763 DOI: 10.3389/fpls.2020.00838] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/26/2020] [Indexed: 05/17/2023]
Abstract
Wheat adaptability to a wide range of environmental conditions is mostly determined by allelic diversity within genes controlling vernalization requirement (Vrn-1) and photoperiod sensitivity (Ppd-1). We characterized a panel of 151 durum wheat Mediterranean landraces and 20 representative locally adapted modern cultivars for their allelic composition at Vrn-1 and Ppd-1 gene using diagnostic molecular markers and studied their association with the time needed to reach six growth stages under field conditions over 6 years. Compared with the more diverse and representative landrace collection, the set of modern cultivars were characterized by a reduction of 50% in the number of allelic variants at the Vrn-A1 and Vrn-B1 genes, and the high frequency of mutant alleles conferring photoperiod insensitivity at Ppd-A1, which resulted on a shorter cycle length. Vrn-A1 played a greater role than Vrn-B1 in regulating crop development (Vrn-A1 > Vrn-B1). The results suggest that mutations in the Vrn-A1 gene may have been the most important in establishing the spring growth habit of Mediterranean landraces and modern durum cultivars. The allele Vrn-A1d, found in 10 landraces, delayed development. The relative effects of single Vrn-A1 alleles on delaying the development of the landraces were vrn-A1 = Vrn-A1d > Vrn-A1b > Vrn-A1c. Allele vrn-B1 was present in all except two landraces and in all modern cultivars. The null allele at Ppd-A1 (a deletion first observed in the French bread wheat cultivar 'Capelle-Desprez') was found for the first time in durum wheat in the present study that identified it in 30 landraces from 13 Mediterranean countries. Allele Ppd-A1a (GS105) was detected in both germplasm types, while the allele Ppd-A1a (GS100) was found only in modern North American and Spanish cultivars. The relative effect of single Ppd-A1 alleles on extending phenological development was Ppd-A1(DelCD) > Ppd-A1b > Ppd-A1a (GS105) > Ppd-A1a (GS100). Sixteen Vrn-1+Ppd-1 allelic combinations were found in landraces and six in modern cultivars, but only three were common to both panels. Differences in the number of days to reach anthesis were 10 days in landraces and 3 days in modern cultivars. Interactive effects between Vrn-1 and Ppd-1 genes were detected.
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Affiliation(s)
- Conxita Royo
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
- *Correspondence: Conxita Royo,
| | | | - Jose Miguel Soriano
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
| | - Marta S. Lopes
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
| | - Karim Ammar
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Dolors Villegas
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
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