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Yoshikawa GV, Boden SA. Finding the right balance: The enduring role of florigens during cereal inflorescence development and their influence on fertility. CURRENT OPINION IN PLANT BIOLOGY 2024; 79:102539. [PMID: 38599051 DOI: 10.1016/j.pbi.2024.102539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 02/23/2024] [Accepted: 03/23/2024] [Indexed: 04/12/2024]
Abstract
Flowering is a vital process in a plant's lifecycle and variation for flowering-time has helped cereals adapt to diverse environments. Much cereal research has focused on understanding how flowering signals, or florigens, regulate the floral transition and timing of ear emergence. However, flowering genes also perform an enduring role during inflorescence development, with genotypes that elicit a weaker flowering signal producing more elaborately branched inflorescences with extra floret-bearing spikelets. While this outcome indicates that variable expression of flowering genes could boost yield potential, further analysis has shown that dampened florigen levels can compromise fertility, negating the benefit of extra grain-producing sites. Here, we discuss ways that florigens contribute to early and late inflorescence development, including their influence on branch/spikelet architecture and fertility. We propose that a deeper understanding of the role for florigens during inflorescence development could be used to balance the effects of florigens throughout flowering to improve productivity.
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Affiliation(s)
- Guilherme V Yoshikawa
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Scott A Boden
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA, 5064, Australia.
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2
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Lee SY, Lee G, Han J, Ha SK, Lee CM, Kang K, Jin M, Suh JP, Jeung JU, Mo Y, Lee HS. GWAS analysis reveals the genetic basis of blast resistance associated with heading date in rice. FRONTIERS IN PLANT SCIENCE 2024; 15:1412614. [PMID: 38835858 PMCID: PMC11148375 DOI: 10.3389/fpls.2024.1412614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 05/06/2024] [Indexed: 06/06/2024]
Abstract
Rice blast is a destructive fungal disease affecting rice plants at various growth stages, significantly threatening global yield stability. Development of resistant rice cultivars stands as a practical means of disease control. Generally, association mapping with a diversity panel powerfully identifies new alleles controlling trait of interest. On the other hand, utilization of a breeding panel has its advantage that can be directly applied in a breeding program. In this study, we conducted a genome-wide association study (GWAS) for blast resistance using 296 commercial rice cultivars with low population structure but large phenotypic diversity. We attempt to answer the genetic basis behind rice blast resistance among early maturing cultivars by subdividing the population based on its Heading date 1 (Hd1) functionality. Subpopulation-specific GWAS using the mixed linear model (MLM) based on blast nursery screening conducted in three years revealed a total of 26 significant signals, including three nucleotide-binding site leucine-rich repeat (NBS-LRR) genes (Os06g0286500, Os06g0286700, and Os06g0287500) located at Piz locus on chromosome 6, and one at the Pi-ta locus (Os12g0281300) on chromosome 12. Haplotype analysis revealed blast resistance associated with Piz locus was exclusively specific to Type 14 hd1 among japonica rice. Our findings provide valuable insights for breeding blast resistant rice and highlight the applicability of our elite cultivar panel to detect superior alleles associated with important agronomic traits.
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Affiliation(s)
- Seung Young Lee
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
- Department of Crop Science and Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Gileung Lee
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Jiheon Han
- Department of Crop Science and Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Su-Kyung Ha
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Chang-Min Lee
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Kyeongmin Kang
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Mina Jin
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Jung-Pil Suh
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Ji-Ung Jeung
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
| | - Youngjun Mo
- Department of Crop Science and Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea
- Institute of Agricultural Science and Technology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Hyun-Sook Lee
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
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3
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Leckie KM, Sawler J, Kapos P, MacKenzie JO, Giles I, Baynes K, Lo J, Baute GJ, Celedon JM. Loss of daylength sensitivity by splice site mutation in Cannabis pseudo-response regulator. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38525679 DOI: 10.1111/tpj.16726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/08/2024] [Accepted: 03/10/2024] [Indexed: 03/26/2024]
Abstract
Photoperiod insensitivity (auto-flowering) in drug-type Cannabis sativa circumvents the need for short day (SD) flowering requirements making outdoor cultivation in high latitudes possible. However, the benefits of photoperiod insensitivity are counterbalanced by low cannabinoid content and poor flower quality in auto-flowering genotypes. Despite recent studies in cannabis flowering, a mechanistic understanding of photoperiod insensitivity is still lacking. We used a combination of genome-wide association study and genetic fine-mapping to identify the genetic cause of auto-flowering in cannabis. We then used gene expression analyses and transient transformation assays to characterize flowering time control. Herein, we identify a splice site mutation within circadian clock gene PSEUDO-RESPONSE REGULATOR 37 (CsPRR37) in auto-flowering cannabis. We show that CsPRR37 represses FT expression and its circadian oscillations transition to a less repressive state during SD as compared to long days (LD). We identify several key circadian clock genes whose expression is altered in auto-flowering cannabis, particularly under non-inductive LD. Research into the pervasiveness of this mutation and others affecting flowering time will help elucidate cannabis domestication history and advance cannabis breeding toward a more sustainable outdoor cultivation system.
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Affiliation(s)
- Keegan M Leckie
- Breeding and Genetics Department, Aurora Cannabis, Inc., 1590 Galbraith Rd, Comox, British Columbia, V9M 4A1, Canada
| | - Jason Sawler
- Breeding and Genetics Department, Aurora Cannabis, Inc., 1590 Galbraith Rd, Comox, British Columbia, V9M 4A1, Canada
| | - Paul Kapos
- Breeding and Genetics Department, Aurora Cannabis, Inc., 1590 Galbraith Rd, Comox, British Columbia, V9M 4A1, Canada
| | - John O MacKenzie
- Breeding and Genetics Department, Aurora Cannabis, Inc., 1590 Galbraith Rd, Comox, British Columbia, V9M 4A1, Canada
| | - Ingrid Giles
- Breeding and Genetics Department, Aurora Cannabis, Inc., 1590 Galbraith Rd, Comox, British Columbia, V9M 4A1, Canada
| | - Katherine Baynes
- Breeding and Genetics Department, Aurora Cannabis, Inc., 1590 Galbraith Rd, Comox, British Columbia, V9M 4A1, Canada
| | - Jessica Lo
- Breeding and Genetics Department, Aurora Cannabis, Inc., 1590 Galbraith Rd, Comox, British Columbia, V9M 4A1, Canada
| | - Gregory J Baute
- Breeding and Genetics Department, Aurora Cannabis, Inc., 1590 Galbraith Rd, Comox, British Columbia, V9M 4A1, Canada
| | - Jose M Celedon
- Breeding and Genetics Department, Aurora Cannabis, Inc., 1590 Galbraith Rd, Comox, British Columbia, V9M 4A1, Canada
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4
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Sun K, Zong W, Xiao D, Wu Z, Guo X, Li F, Song Y, Li S, Wei G, Hao Y, Xu B, Li W, Lin Z, Xie W, Liu YG, Guo J. Effects of the core heading date genes Hd1, Ghd7, DTH8, and PRR37 on yield-related traits in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:227. [PMID: 37851149 DOI: 10.1007/s00122-023-04476-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 10/04/2023] [Indexed: 10/19/2023]
Abstract
KEY MESSAGE We clarify the influence of the genotypes of the heading date genes Hd1, Ghd7, DTH8, and PRR37 and their combinations on yield-related traits and the functional differences between different haplotypes. Heading date is a key agronomic trait in rice (Oryza sativa L.) that determines yield and adaptability to different latitudes. Heading date 1 (Hd1), Grain number, plant height, and heading date 7 (Ghd7), Days to heading on chromosome 8 (DTH8), and PSEUDO-RESPONSE REGULATOR 37 (PRR37) are core rice genes controlling photoperiod sensitivity, and these genes have many haplotypes in rice cultivars. However, the effects of different haplotypes at these genes on yield-related traits in diverse rice materials remain poorly characterized. In this study, we knocked out Hd1, Ghd7, DTH8, or PRR37, alone or together, in indica and japonica varieties and systematically investigated the agronomic traits of each knockout line. Ghd7 and PRR37 increased the number of spikelets and improved yield, and this effect was enhanced with the Ghd7 DTH8 or Ghd7 PRR37 combination, but Hd1 negatively affected yield. We also identified a new weak functional Ghd7 allele containing a mutation that interferes with splicing. Furthermore, we determined that the promotion or inhibition of heading date by different PRR37 haplotypes is related to PRR37 expression levels, day length, and the genetic background. For rice breeding, a combination of functional alleles of Ghd7 and DTH8 or Ghd7 and PRR37 in the hd1 background can be used to increase yield. Our study clarifies the effects of heading date genes on yield-related traits and the functional differences among their different haplotypes, providing valuable information to identify and exploit elite haplotypes for heading date genes to breed high-yielding rice varieties.
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Affiliation(s)
- Kangli Sun
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Wubei Zong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Dongdong Xiao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Zeqiang Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaotong Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Fuquan Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yingang Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Shengting Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Guangliang Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yu Hao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Bingqun Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Weitao Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Zhiwei Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Wenhao Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Jingxin Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
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5
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Zhao H, Huang X, Yang Z, Li F, Ge X. Synergistic optimization of crops by combining early maturation with other agronomic traits. TRENDS IN PLANT SCIENCE 2023; 28:1178-1191. [PMID: 37208203 DOI: 10.1016/j.tplants.2023.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 04/16/2023] [Accepted: 04/24/2023] [Indexed: 05/21/2023]
Abstract
Many newly created early maturing varieties exhibit poor stress resistance and low yield, whereas stress-resistant varieties are typically late maturing. For this reason, the polymerization of early maturity and other desired agronomic qualities requires overcoming the negative connection between early maturity, multi-resistance, and yield, which presents a formidable challenge in current breeding techniques. We review the most salient constraints of early maturity breeding in current crop planting practices and the molecular mechanisms of different maturation timeframes in diverse crops from their origin center to production areas. We explore current breeding tactics and the future direction of crop breeding and the issues that must be resolved to accomplish the polymerization of desirable traits in light of the current obstacles and limitations.
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Affiliation(s)
- Hang Zhao
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; College of Life Sciences, Qufu Normal University, Qufu, 273165, China
| | - Xianzhong Huang
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Chuzhou, China
| | - Zhaoen Yang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Fuguang Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100 Xinjiang, China; Hainan Yazhou Bay Seed Lab, Sanya 572000, Hainan, China.
| | - Xiaoyang Ge
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100 Xinjiang, China; Hainan Yazhou Bay Seed Lab, Sanya 572000, Hainan, China.
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6
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Vicentini G, Biancucci M, Mineri L, Chirivì D, Giaume F, Miao Y, Kyozuka J, Brambilla V, Betti C, Fornara F. Environmental control of rice flowering time. PLANT COMMUNICATIONS 2023; 4:100610. [PMID: 37147799 PMCID: PMC10504588 DOI: 10.1016/j.xplc.2023.100610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 04/14/2023] [Accepted: 04/30/2023] [Indexed: 05/07/2023]
Abstract
Correct measurement of environmental parameters is fundamental for plant fitness and survival, as well as for timing developmental transitions, including the switch from vegetative to reproductive growth. Important parameters that affect flowering time include day length (photoperiod) and temperature. Their response pathways have been best described in Arabidopsis, which currently offers a detailed conceptual framework and serves as a comparison for other species. Rice, the focus of this review, also possesses a photoperiodic flowering pathway, but 150 million years of divergent evolution in very different environments have diversified its molecular architecture. The ambient temperature perception pathway is strongly intertwined with the photoperiod pathway and essentially converges on the same genes to modify flowering time. When observing network topologies, it is evident that the rice flowering network is centered on EARLY HEADING DATE 1, a rice-specific transcriptional regulator. Here, we summarize the most important features of the rice photoperiodic flowering network, with an emphasis on its uniqueness, and discuss its connections with hormonal, temperature perception, and stress pathways.
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Affiliation(s)
- Giulio Vicentini
- Department of Agricultural and Environmental Sciences, University of Milan, via Celoria 2, 20133 Milan, Italy
| | - Marco Biancucci
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
| | - Lorenzo Mineri
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
| | - Daniele Chirivì
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
| | - Francesca Giaume
- Department of Agricultural and Environmental Sciences, University of Milan, via Celoria 2, 20133 Milan, Italy
| | - Yiling Miao
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Vittoria Brambilla
- Department of Agricultural and Environmental Sciences, University of Milan, via Celoria 2, 20133 Milan, Italy
| | - Camilla Betti
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
| | - Fabio Fornara
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy.
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7
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Giaume F, Bono GA, Martignago D, Miao Y, Vicentini G, Toriba T, Wang R, Kong D, Cerise M, Chirivì D, Biancucci M, Khahani B, Morandini P, Tameling W, Martinotti M, Goretti D, Coupland G, Kater M, Brambilla V, Miki D, Kyozuka J, Fornara F. Two florigens and a florigen-like protein form a triple regulatory module at the shoot apical meristem to promote reproductive transitions in rice. NATURE PLANTS 2023; 9:525-534. [PMID: 36973415 DOI: 10.1038/s41477-023-01383-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
Many plant species monitor and respond to changes in day length (photoperiod) for aligning reproduction with a favourable season. Day length is measured in leaves and, when appropriate, leads to the production of floral stimuli called florigens that are transmitted to the shoot apical meristem to initiate inflorescence development1. Rice possesses two florigens encoded by HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1)2. Here we show that the arrival of Hd3a and RFT1 at the shoot apical meristem activates FLOWERING LOCUS T-LIKE 1 (FT-L1), encoding a florigen-like protein that shows features partially differentiating it from typical florigens. FT-L1 potentiates the effects of Hd3a and RFT1 during the conversion of the vegetative meristem into an inflorescence meristem and organizes panicle branching by imposing increasing determinacy to distal meristems. A module comprising Hd3a, RFT1 and FT-L1 thus enables the initiation and balanced progression of panicle development towards determinacy.
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Affiliation(s)
- Francesca Giaume
- Department of Biosciences, University of Milan, Milan, Italy
- Department of Agricultural and Environmental Sciences-Production, Territory, Agroenergy, University of Milan, Milan, Italy
| | - Giulia Ave Bono
- Department of Biosciences, University of Milan, Milan, Italy
| | | | - Yiling Miao
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Giulio Vicentini
- Department of Agricultural and Environmental Sciences-Production, Territory, Agroenergy, University of Milan, Milan, Italy
| | - Taiyo Toriba
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Rui Wang
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Dali Kong
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Martina Cerise
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Daniele Chirivì
- Department of Biosciences, University of Milan, Milan, Italy
| | - Marco Biancucci
- Department of Biosciences, University of Milan, Milan, Italy
| | - Bahman Khahani
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, USA
| | - Piero Morandini
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | | | | | - Daniela Goretti
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - George Coupland
- Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Martin Kater
- Department of Biosciences, University of Milan, Milan, Italy
| | - Vittoria Brambilla
- Department of Agricultural and Environmental Sciences-Production, Territory, Agroenergy, University of Milan, Milan, Italy
| | - Daisuke Miki
- Shanghai Center for Plant Stress Biology, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Fabio Fornara
- Department of Biosciences, University of Milan, Milan, Italy.
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8
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Osnato M. Evolution of flowering time genes in rice: From the paleolithic to the anthropocene. PLANT, CELL & ENVIRONMENT 2023; 46:1046-1059. [PMID: 36411270 DOI: 10.1111/pce.14495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/08/2022] [Accepted: 11/12/2022] [Indexed: 06/16/2023]
Abstract
The evolutionary paths of humans and plants have crossed more than once throughout millennia. While agriculture contributed to the evolution of societies in prehistory, human selection of desirable traits contributed to the evolution of crops during centuries of cultivation. Among cereal crops, rice is currently grown around the globe and represents staple food for almost half of the world population. Over time, rice cultivation has expanded from subtropical to temperate regions thanks to artificial selection of mutants with impaired response to photoperiod. Additional regulatory mechanisms control flowering in response to diverse environmental cues, anticipating or delaying the floral transition to produce seeds in more favourable conditions. Nevertheless, the changing climate is threatening grain production because modern cultivars are sensitive to external fluctuations that go beyond their physiological range. One possibility to guarantee food production could be the exploitation of novel varieties obtained by crossing highly productive Asian rice with stress tolerant African rice. This review explores the genetic basis of the key traits that marked the long journey of rice cultivation from the end of the paleolithic to the anthropocene, with a focus on heading date. By 2050, will rice plants of the future flower in the outer space?
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Affiliation(s)
- Michela Osnato
- Institut de Ciència i Tecnologia Ambientals, Universitat Autónoma de Barcelona (ICTA-UAB), Bellaterra, Spain
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9
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Jadamba C, Vea RL, Ryu JH, Paek NC, Jang S, Chin JH, Yoo SC. GWAS analysis to elucidate genetic composition underlying a photoperiod-insensitive rice population, North Korea. Front Genet 2022; 13:1036747. [PMID: 36568369 PMCID: PMC9768348 DOI: 10.3389/fgene.2022.1036747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/13/2022] [Indexed: 12/12/2022] Open
Abstract
Heading date (Hd) is one of the main factors determining rice production and regional adaptation. To identify the genetic factors involved in the wide regional adaptability of rice, we conducted a genome-wide association study (GWAS) with 190 North Korean rice accessions selected for non-precocious flowering in the Philippines, a low-latitude region. Using both linear mixed models (LMM) and fixed and random model circulating probability unification (FarmCPU), we identified five significant loci for Hd in trials in 2018 and 2019. Among the five lead single nucleotide polymorphisms (SNPs), three were located adjacent to the known Hd genes, Heading date 3a (Hd3a), Heading date 5 (Hd5), and GF14-c. In contrast, three SNPs were located in novel loci with minor effects on heading. Further GWAS analysis for photoperiod insensitivity (PS) revealed no significant genes associated with PS, supporting that this North Korean (NK) population is largely photoperiod-insensitive. Haplotyping analysis showed that more than 80% of the NK varieties harbored nonfunctional alleles of major Hd genes investigated, of which a nonfunctional allele of Heading date 1 (Hd1) was observed in 66% of the varieties. Geographical distribution analysis of Hd allele combination types showed that nonfunctional alleles of floral repressor Hd genes enabled rice cultivation in high-latitude regions. In contrast, Hd1 alleles largely contributed to the wide regional adaptation of rice varieties. In conclusion, an allelic combination of Hd genes is critical for rice cultivation across wide areas.
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Affiliation(s)
- Chuluuntsetseg Jadamba
- Crop Molecular Breeding Laboratory, Department of Plant Life and Environmental Science, Hankyong National University, Anseong, South Korea
| | - Richie L. Vea
- Bureau of Plant Industry, National Seed Quality Control Services, San Mateo, Isabela Philippines
| | - Jung-Hoon Ryu
- Crop Molecular Breeding Laboratory, Department of Plant Life and Environmental Science, Hankyong National University, Anseong, South Korea
| | - Nam-Chon Paek
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Su Jang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Joong Hyoun Chin
- Department of Integrative Biological Sciences and Industry, Sejong University, Seoul, South Korea,*Correspondence: Joong Hyoun Chin, ; Soo-Cheul Yoo,
| | - Soo-Cheul Yoo
- Crop Molecular Breeding Laboratory, Department of Plant Life and Environmental Science, Hankyong National University, Anseong, South Korea,Carbon-Neutral Resources Research Center, Hankyong National University, Seoul, South Korea,*Correspondence: Joong Hyoun Chin, ; Soo-Cheul Yoo,
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10
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Sun K, Huang M, Zong W, Xiao D, Lei C, Luo Y, Song Y, Li S, Hao Y, Luo W, Xu B, Guo X, Wei G, Chen L, Liu YG, Guo J. Hd1, Ghd7, and DTH8 synergistically determine rice heading date and yield-related agronomic traits. J Genet Genomics 2022; 49:437-447. [DOI: 10.1016/j.jgg.2022.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 10/18/2022]
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Mo Y, Lee CM, Park HM, Ha SK, Kim MJ, Kwak J, Lee HS, Lee JH, Jeung JU. Hd1 Allele Types and Their Associations with Major Agronomic Traits in Korean Rice Cultivars. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112408. [PMID: 34834770 PMCID: PMC8619422 DOI: 10.3390/plants10112408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
Optimizing flowering time in crop plants is critical for maximizing yield and quality under target environments. While there is a wide range of heading date variation in Korean rice cultivars, the underlying gene mechanisms are unclear. Here, we sequenced the protein coding regions of Hd1, the major rice heading date gene, from 293 Korean rice cultivars and investigated the associations between Hd1 allele types and major agronomic traits under four different environments. There were four functional Hd1 and five nonfunctional hd1 alleles distributed among the 293 Korean rice cultivars. The effects of the Hd1 allele types were highly significant for days to heading in all four environments, explaining 51.4-65.8% of the phenotypic variation. On average, cultivars carrying nonfunctional hd1 headed 13.7 days earlier than those carrying functional Hd1. While the Hd1 allele types exhibited highly significant effects on culm length and protein content under all four environments, the differences between cultivars carrying Hd1 and hd1 were minimal. The effects of the Hd1 allele types on amylose content were significant in only one of the four environments. Our results provide useful information for fine-tuning rice heading dates by utilizing different Hd1 alleles in rice breeding programs.
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Affiliation(s)
- Youngjun Mo
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (C.-M.L.); (H.-M.P.); (S.-K.H.); (M.-J.K.); (J.K.); (H.-S.L.); (J.-H.L.)
- Department of Crop Science and Biotechnology, Jeonbuk National University, Jeonju 54896, Korea
| | - Chang-Min Lee
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (C.-M.L.); (H.-M.P.); (S.-K.H.); (M.-J.K.); (J.K.); (H.-S.L.); (J.-H.L.)
- Department of Crop Science and Biotechnology, Jeonbuk National University, Jeonju 54896, Korea
| | - Hyang-Mi Park
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (C.-M.L.); (H.-M.P.); (S.-K.H.); (M.-J.K.); (J.K.); (H.-S.L.); (J.-H.L.)
| | - Su-Kyung Ha
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (C.-M.L.); (H.-M.P.); (S.-K.H.); (M.-J.K.); (J.K.); (H.-S.L.); (J.-H.L.)
| | - Mi-Jung Kim
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (C.-M.L.); (H.-M.P.); (S.-K.H.); (M.-J.K.); (J.K.); (H.-S.L.); (J.-H.L.)
| | - Jieun Kwak
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (C.-M.L.); (H.-M.P.); (S.-K.H.); (M.-J.K.); (J.K.); (H.-S.L.); (J.-H.L.)
| | - Hyun-Sook Lee
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (C.-M.L.); (H.-M.P.); (S.-K.H.); (M.-J.K.); (J.K.); (H.-S.L.); (J.-H.L.)
| | - Jeong-Heui Lee
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (C.-M.L.); (H.-M.P.); (S.-K.H.); (M.-J.K.); (J.K.); (H.-S.L.); (J.-H.L.)
| | - Ji-Ung Jeung
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (C.-M.L.); (H.-M.P.); (S.-K.H.); (M.-J.K.); (J.K.); (H.-S.L.); (J.-H.L.)
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12
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Zhou X, Nong C, Wu B, Zhou T, Zhang B, Liu X, Gao G, Mi J, Zhang Q, Liu H, Liu S, Li Z, He Y, Mou T, Guo S, Li S, Yang Y, Zhang Q, Xing Y. Combinations of Ghd7, Ghd8, and Hd1 determine strong heterosis of commercial rice hybrids in diverse ecological regions. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6963-6976. [PMID: 34283218 DOI: 10.1093/jxb/erab344] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
Heterosis of grain yield is closely associated with heading date in crops. Gene combinations of the major heading date genes Ghd7, Ghd8, and Hd1 play important roles in enhancing grain yield and adaptation to ecological regions in rice. However, the predominant three-gene combinations for a specific ecological region remain unclear in both three-line and two-line hybrids. In this study, we sequenced these three genes of 50 cytoplasmic male sterile/maintainer lines, 31 photo-thermo-sensitive genic male sterile lines, and 109 restorer lines. Sequence analysis showed that hybrids carrying strong functional alleles of Ghd7 and Hd1 and non-functional Ghd8 are predominant in three-line hybrids and are recommended for rice production in the subtropics around 30°N/S. Hybrids carrying strong functional Ghd7 and Ghd8 and non-functional Hd1 are predominant in two-line hybrids and are recommended for low latitude areas around 23.5°N/S rich in photothermal resources. Hybrids carrying strong functional Ghd7 and Ghd8 and functional Hd1 were not identified in commercial hybrids in the middle and lower reaches of the Yangtze River, but they have high yield potential in tropical regions because they have the strongest photoperiod sensitivity. Based on these findings, two genic sterile lines, Xiangling 628S and C815S, whose hybrids often head very late, were diagnosed with these three genes, and Hd1 was targeted to be knocked out in Xiangling 628S and replaced with hd1 in C815S. The hybrids developed from both modified sterile lines in turn had appropriate heading dates and significantly improved grain yield. This study provides new insights for breeding design to develop hybrids for various regions.
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Affiliation(s)
- Xiangchun Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Chunxiao Nong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Bi Wu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Tianhao Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Bo Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Xingshao Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Guanjun Gao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Jiaming Mi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Haiyang Liu
- College of Agriculture, Yangtze University, Jingzhou 434023,China
| | - Shisheng Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Zhixin Li
- College of Agriculture, Yangtze University, Jingzhou 434023,China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Tongmin Mou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Sibin Guo
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Naning 530007,China
| | - Shaoqing Li
- College of Life Science, Wuhan University, Wuhan 430072,China
| | - Yuanzhu Yang
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice Breeding, Yuan Longping High-Tech Agriculture Co., Ltd, Changsha 410128,China
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070,China
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13
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Zhang J, Fan X, Hu Y, Zhou X, He Q, Liang L, Xing Y. Global analysis of CCT family knockout mutants identifies four genes involved in regulating heading date in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:913-923. [PMID: 32889758 DOI: 10.1111/jipb.13013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 09/03/2020] [Indexed: 06/11/2023]
Abstract
Many genes encoding CCT domain-containing proteins regulate flowering time. In rice (Oryza sativa), 41 such genes have been identified, but only a few have been shown to regulate heading date. Here, to test whether and how additional CCT family genes regulate heading date in rice, we classified these genes into five groups based on their diurnal expression patterns. The expression patterns of genes in the same subfamily or in close phylogenetic clades tended to be similar. We generated knockout mutants of the entire gene family via CRISPR/Cas9. The heading dates of knockout mutants of only 4 of 14 genes previously shown to regulate heading date were altered, pointing to functional redundancy of CCT family genes in regulating this trait. Analysis of mutants of four other genes showed that OsCCT22, OsCCT38, and OsCCT41 suppress heading under long-day conditions and promote heading under short-day conditions. OsCCT03 promotes heading under both conditions and upregulates the expression of Hd1 and Ehd1, a phenomenon not previously reported for other such genes. To date, at least 18 CCT domain-containing genes involved in regulating heading have been identified, providing diverse, flexible gene combinations for generating rice varieties with a given heading date.
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Affiliation(s)
- Jia Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- College of Life Science, Jiangxi Normal University, Nanchang, 330022, China
| | - Xiaowei Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yong Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiangchun Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qin He
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liwen Liang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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14
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Characterization of the Ghd8 Flowering Time Gene in a Mini-Core Collection of Miscanthus sinensis. Genes (Basel) 2021; 12:genes12020288. [PMID: 33669585 PMCID: PMC7922028 DOI: 10.3390/genes12020288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/10/2021] [Accepted: 02/15/2021] [Indexed: 11/17/2022] Open
Abstract
The optimal flowering time for bioenergy crop Miscanthus is essential for environmental adaptability and biomass accumulation. However, little is known about how genes controlling flowering in other grasses contribute to flowering regulation in Miscanthus. Here, we report on the sequence characterization and gene expression of Miscanthus sinensisGhd8, a transcription factor encoding a HAP3/NF-YB DNA-binding domain, which has been identified as a major quantitative trait locus in rice, with pleiotropic effects on grain yield, heading date and plant height. In M. sinensis, we identified two homoeologous loci, MsiGhd8A located on chromosome 13 and MsiGhd8B on chromosome 7, with one on each of this paleo-allotetraploid species’ subgenomes. A total of 46 alleles and 28 predicted protein sequence types were identified in 12 wild-collected accessions. Several variants of MsiGhd8 showed a geographic and latitudinal distribution. Quantitative real-time PCR revealed that MsiGhd8 expressed under both long days and short days, and MsiGhd8B showed a significantly higher expression than MsiGhd8A. The comparison between flowering time and gene expression indicated that MsiGhd8B affected flowering time in response to day length for some accessions. This study provides insight into the conserved function of Ghd8 in the Poaceae, and is an important initial step in elucidating the flowering regulatory network of Miscanthus.
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15
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Osnato M, Cota I, Nebhnani P, Cereijo U, Pelaz S. Photoperiod Control of Plant Growth: Flowering Time Genes Beyond Flowering. FRONTIERS IN PLANT SCIENCE 2021; 12:805635. [PMID: 35222453 PMCID: PMC8864088 DOI: 10.3389/fpls.2021.805635] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/23/2021] [Indexed: 05/02/2023]
Abstract
Fluctuations in environmental conditions greatly influence life on earth. Plants, as sessile organisms, have developed molecular mechanisms to adapt their development to changes in daylength, or photoperiod. One of the first plant features that comes to mind as affected by the duration of the day is flowering time; we all bring up a clear image of spring blossom. However, for many plants flowering happens at other times of the year, and many other developmental aspects are also affected by changes in daylength, which range from hypocotyl elongation in Arabidopsis thaliana to tuberization in potato or autumn growth cessation in trees. Strikingly, many of the processes affected by photoperiod employ similar gene networks to respond to changes in the length of light/dark cycles. In this review, we have focused on developmental processes affected by photoperiod that share similar genes and gene regulatory networks.
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Affiliation(s)
- Michela Osnato
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
- Institute of Environmental Science and Technology of the Universitat Autònoma de Barcelona, Barcelona, Spain
- *Correspondence: Michela Osnato,
| | - Ignacio Cota
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Poonam Nebhnani
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Unai Cereijo
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Soraya Pelaz
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
- Soraya Pelaz,
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16
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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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17
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Martignago D, Siemiatkowska B, Lombardi A, Conti L. Abscisic Acid and Flowering Regulation: Many Targets, Different Places. Int J Mol Sci 2020; 21:ijms21249700. [PMID: 33353251 PMCID: PMC7767233 DOI: 10.3390/ijms21249700] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/14/2020] [Accepted: 12/17/2020] [Indexed: 12/13/2022] Open
Abstract
Plants can react to drought stress by anticipating flowering, an adaptive strategy for plant survival in dry climates known as drought escape (DE). In Arabidopsis, the study of DE brought to surface the involvement of abscisic acid (ABA) in controlling the floral transition. A central question concerns how and in what spatial context can ABA signals affect the floral network. In the leaf, ABA signaling affects flowering genes responsible for the production of the main florigen FLOWERING LOCUS T (FT). At the shoot apex, FD and FD-like transcription factors interact with FT and FT-like proteins to regulate ABA responses. This knowledge will help separate general and specific roles of ABA signaling with potential benefits to both biology and agriculture.
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18
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Mo Y, Jeong JM, Ha SK, Kim J, Lee C, Lee GP, Jeung JU. Characterization of QTLs and Candidate Genes for Days to Heading in Rice Recombinant Inbred Lines. Genes (Basel) 2020; 11:E957. [PMID: 32825032 PMCID: PMC7565938 DOI: 10.3390/genes11090957] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/17/2020] [Accepted: 08/17/2020] [Indexed: 11/16/2022] Open
Abstract
Understanding the gene mechanisms controlling days to heading (DH) is important in rice breeding for adaption in the target environment. Using a recombinant inbred line population derived from the cross between two japonica rice cultivars, Koshihikari and Baegilmi, we identified three consistent quantitative trait loci (QTLs) for DH for two years, qDH3, qDH6, and qDH7 on chromosomes 3, 6, and 7, respectively. While Baegilmi contributed the allele for early heading at qDH6 and qDH7 with the additive effect of five days each, Koshihikari contributed the allele for early heading at qDH3 with the additive effect of three days. Notably, pyramiding two or more alleles for early heading at these QTLs accelerated heading effectively. Sequencing of Hd16, Hd1, and Ghd7, the previously known heading date genes underlying qDH3, qDH6, and qDH7, respectively, revealed that Baegilmi and Koshihikari carry different alleles at the three genes. Molecular markers were developed to screen the allelic compositions of the three genes among 295 Korean commercial rice cultivars. The results showed that few cultivars carry alleles for early heading at the three genes, highlighting that DH can be further accelerated and fine-tuned in breeding programs by combining the desirable alleles of Hd16, Hd1, and Ghd7.
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Affiliation(s)
- Youngjun Mo
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (J.-M.J.); (S.-K.H.); (J.K.); (C.L.)
| | - Jong-Min Jeong
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (J.-M.J.); (S.-K.H.); (J.K.); (C.L.)
| | - Su-Kyung Ha
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (J.-M.J.); (S.-K.H.); (J.K.); (C.L.)
| | - Jinhee Kim
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (J.-M.J.); (S.-K.H.); (J.K.); (C.L.)
| | - Changmin Lee
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (J.-M.J.); (S.-K.H.); (J.K.); (C.L.)
| | - Gung Pyo Lee
- Department of Integrative Plant Science, Chung-Ang University, Anseong 17546, Korea;
| | - Ji-Ung Jeung
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea; (Y.M.); (J.-M.J.); (S.-K.H.); (J.K.); (C.L.)
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The G123 rice mutant, carrying a mutation in SE13, presents alterations in the expression patterns of photosynthetic and major flowering regulatory genes. PLoS One 2020; 15:e0233120. [PMID: 32421736 PMCID: PMC7233571 DOI: 10.1371/journal.pone.0233120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/28/2020] [Indexed: 12/11/2022] Open
Abstract
Day length is a determinant of flowering time in rice. Phytochromes participate in flowering regulation by measuring the number of daylight hours to which the plant is exposed. Here we describe G123, a rice mutant generated by irradiation, which displays insensitivity to the photoperiod and early flowering under both long day and short day conditions. To detect the mutation responsible for the early flowering phenotype exhibited by G123, we generated an F2 population, derived from crossing with the wild-type, and used a pipeline to detect genomic structural variation, initially developed for human genomes. We detected a deletion in the G123 genome that affects the PHOTOPERIOD SENSITIVITY13 (SE13) gene, which encodes a phytochromobilin synthase, an enzyme implicated in phytochrome chromophore biosynthesis. The transcriptomic analysis, performed by RNA-seq, in the G123 plants indicated an alteration in photosynthesis and other processes related to response to light. The expression patterns of the main flowering regulatory genes, such as Ghd7, Ghd8 and PRR37, were altered in the plants grown under both long day and short day conditions. These findings indicate that phytochromes are also involved in the regulation of these genes under short day conditions, and extend the role of phytochromes in flowering regulation in rice.
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20
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Przelomska NAS, Armstrong CG, Kistler L. Ancient Plant DNA as a Window Into the Cultural Heritage and Biodiversity of Our Food System. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00074] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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21
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Wang P, Gong R, Yang Y, Yu S. Ghd8 controls rice photoperiod sensitivity by forming a complex that interacts with Ghd7. BMC PLANT BIOLOGY 2019; 19:462. [PMID: 31675987 PMCID: PMC6825352 DOI: 10.1186/s12870-019-2053-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 09/24/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Flowering time is one of the most important agronomic characteristics that ultimately determine yield potential and eco-geographical adaptation in crops. Ghd8 and Ghd7, two major flowering genes, have similar functions and large pleiotropic effects in controlling the heading date, plant height and grain yield of rice. However, these gene interactions at the genetic and molecular levels have not been determined to date. RESULTS In this study, we investigated the genetic interaction between Ghd8 and Ghd7 by using a set of near-isogenic lines and a panel of natural germplasm accessions in rice. We found that Ghd8 affected multiple agronomic traits in a functional Ghd7-dependent manner. Both functional Ghd8 and Ghd7 are pivotal for rice photoperiod sensitivity controlled by Hd1 and Hd3a. GHD8 could form a heterotrimeric complex with HD1 and OsHAP5b to activate the transcription of Ghd7 by binding directly to the promoter region of Ghd7, which contains the CCAAT-box motif. CONCLUSIONS The results of this study help to elucidate the genetic and molecular bases of Ghd8 and Ghd7 interactions, indicating that Ghd8 acts upstream of Ghd7 to activate its transcription, which inhibits Hd3a expression and thus affects flowering time and rice adaptation.
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Affiliation(s)
- Peng Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Present Address: Department of Agronomy and Horticulture, University of Nebraska Lincoln, Lincoln, NE, USA
| | - Rong Gong
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ying Yang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Present Address: Department of Agronomy and Horticulture, University of Nebraska Lincoln, Lincoln, NE, USA
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
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22
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Kumar M, Le DT, Hwang S, Seo PJ, Kim HU. Role of the INDETERMINATE DOMAIN Genes in Plants. Int J Mol Sci 2019; 20:ijms20092286. [PMID: 31075826 PMCID: PMC6539433 DOI: 10.3390/ijms20092286] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/03/2019] [Accepted: 05/06/2019] [Indexed: 01/05/2023] Open
Abstract
The INDETERMINATE DOMAIN (IDD) genes comprise a conserved transcription factor family that regulates a variety of developmental and physiological processes in plants. Many recent studies have focused on the genetic characterization of IDD family members and revealed various biological functions, including modulation of sugar metabolism and floral transition, cold stress response, seed development, plant architecture, regulation of hormone signaling, and ammonium metabolism. In this review, we summarize the functions and working mechanisms of the IDD gene family in the regulatory network of metabolism and developmental processes.
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Affiliation(s)
- Manu Kumar
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul 05006, Korea.
| | - Dung Thi Le
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul 05006, Korea.
| | - Seongbin Hwang
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul 05006, Korea.
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul 08826, Korea.
| | - Hyun Uk Kim
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul 05006, Korea.
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23
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Gómez-Ariza J, Brambilla V, Vicentini G, Landini M, Cerise M, Carrera E, Shrestha R, Chiozzotto R, Galbiati F, Caporali E, López Díaz I, Fornara F. A transcription factor coordinating internode elongation and photoperiodic signals in rice. NATURE PLANTS 2019; 5:358-362. [PMID: 30936438 DOI: 10.1038/s41477-019-0401-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 03/05/2019] [Indexed: 05/04/2023]
Abstract
In several plant species, inflorescence formation is accompanied by stem elongation. Both processes are accelerated in rice upon perception of shortening days. Here, we show that PREMATURE INTERNODE ELONGATION 1 (PINE1), encoding a rice zinc-finger transcription factor, reduces the sensitivity of the stem to gibberellin (GA). The florigens reduce PINE1 expression to increase stem responsiveness to GA and promote flowering. These data indicate the existence of a regulatory network coordinating flowering and GA-dependent growth.
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Affiliation(s)
| | - Vittoria Brambilla
- Department of Biosciences, University of Milan, Milan, Italy
- Department of Agricultural and Environmental Sciences-Production, Territory, Agroenergy, University of Milan, Milan, Italy
| | | | - Martina Landini
- Department of Biosciences, University of Milan, Milan, Italy
| | - Martina Cerise
- Department of Biosciences, University of Milan, Milan, Italy
| | - Esther Carrera
- Instituto de Biologıa Molecular y Celular de Plantas (IBMCP), Universidad Politecnica de Valencia-Consejo Superior de Investigaciones Cientıficas (CSIC), Valencia, Spain
| | - Roshi Shrestha
- Department of Biosciences, University of Milan, Milan, Italy
| | - Remo Chiozzotto
- Department of Agricultural and Environmental Sciences-Production, Territory, Agroenergy, University of Milan, Milan, Italy
| | | | | | - Isabel López Díaz
- Instituto de Biologıa Molecular y Celular de Plantas (IBMCP), Universidad Politecnica de Valencia-Consejo Superior de Investigaciones Cientıficas (CSIC), Valencia, Spain
| | - Fabio Fornara
- Department of Biosciences, University of Milan, Milan, Italy.
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24
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Hu Y, Li S, Xing Y. Lessons from natural variations: artificially induced heading date variations for improvement of regional adaptation in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:383-394. [PMID: 30382312 DOI: 10.1007/s00122-018-3225-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 10/25/2018] [Indexed: 05/10/2023]
Abstract
New strategy of breeding by modulating key heading date gene Ehd1 to enhance the variations of heading date regardless of genetic background for better adaptation to local environment in rice. Flowering time (or heading date) is an important quantitative trait in rice (Oryza sativa) that determines its adaptation to specific cultivation areas and growing seasons. However, breeding of flowering time is currently relying on laborious selections and combinations of different alleles of various genes. Here, we cloned a cis-variant allele of Ehd1 that regulated not only heading date but also yield potential. Genetic analysis revealed that Ehd1 acted downstream of Ghd7 as a negative regulator of yield potential, and expression divergence of Ehd1 negatively correlates with phenotype variations including heading date and grain yield. Moreover, regardless of genetic background, manipulations of the expression of a single gene, Ehd1, are sufficient for recreating beneficial heading date variations which could be subjected to the selection of best suitable lines for local environment conditions. Beyond a deeper understanding of transcriptional control of quantitative traits, this study provided an effective and flexible strategy for breeding rice cultivars to maximize grain production for any region of cultivation.
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Affiliation(s)
- Yong Hu
- National Key Laboratory of Crop Genetic Improvement and the National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuangle Li
- National Key Laboratory of Crop Genetic Improvement and the National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement and the National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China.
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25
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Kim SR, Torollo G, Yoon MR, Kwak J, Lee CK, Prahalada GD, Choi IR, Yeo US, Jeong OY, Jena KK, Lee JS. Loss-of-Function Alleles of Heading date 1 ( Hd1) Are Associated With Adaptation of Temperate Japonica Rice Plants to the Tropical Region. FRONTIERS IN PLANT SCIENCE 2018; 9:1827. [PMID: 30619400 PMCID: PMC6295564 DOI: 10.3389/fpls.2018.01827] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/26/2018] [Indexed: 05/11/2023]
Abstract
Adaptation of temperate japonica rice varieties to tropical regions is impeded by extremely early flowering probably due to photoperiod change from long to short. However, constant breeding efforts led to development of temperate japonica varieties adapted to tropical/subtropical regions, but the genetic factor underlying this is still elusive. We analyzed the 45 diverse rice accessions and 12 tropical-adapted temperate japonica lines for the allele types of seven major flowering genes Hd1, OsPPR37, DTH8, Ghd7, Ehd1, RFT1, and Hd3a and flowering time under three different field conditions in temperate and tropical locations. The accessions originated from the tropical/subtropical regions preferred the non-functional alleles of Hd1 and not other flowering genes. The genetic effect analysis of each gene showed that only the functional Hd1 caused early flowering in the tropical location. All 12 temperate japonica breeding lines adapted to the tropics possessed the loss-of-function alleles of Hd1 with no change of other flowering genes compared to common Korean temperate japonica varieties. A phylogenetic analysis using 2,918 SNP data points revealed that the genome status of the 12 breeding lines were very similar to Korean temperate japonica varieties. These results indicate that the functional Hd1 alleles of temperate japonica varieties induced extremely early flowering in the tropics and the non-functional hd1 alleles brought about the adaptation of temperate japonica rice to tropical regions.
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Affiliation(s)
- Sung-Ryul Kim
- Strategic Innovation Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Gideon Torollo
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Mi-Ra Yoon
- National Institute of Crop Science, Rural Development Administration, Jeonju, South Korea
| | - Jieun Kwak
- National Institute of Crop Science, Rural Development Administration, Jeonju, South Korea
| | - Choon-Ki Lee
- National Institute of Crop Science, Rural Development Administration, Jeonju, South Korea
| | - G. D. Prahalada
- Strategic Innovation Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Il-Ryong Choi
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Un-Sang Yeo
- National Institute of Crop Science, Rural Development Administration, Jeonju, South Korea
| | - O-Young Jeong
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
- National Institute of Crop Science, Rural Development Administration, Jeonju, South Korea
| | - Kshirod K. Jena
- Strategic Innovation Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Jeom-Sig Lee
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
- National Institute of Crop Science, Rural Development Administration, Jeonju, South Korea
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26
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Zhu C, Peng Q, Fu D, Zhuang D, Yu Y, Duan M, Xie W, Cai Y, Ouyang Y, Lian X, Wu C. The E3 Ubiquitin Ligase HAF1 Modulates Circadian Accumulation of EARLY FLOWERING3 to Control Heading Date in Rice under Long-Day Conditions. THE PLANT CELL 2018; 30:2352-2367. [PMID: 30242038 PMCID: PMC6241267 DOI: 10.1105/tpc.18.00653] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/14/2018] [Accepted: 09/14/2018] [Indexed: 05/21/2023]
Abstract
The ubiquitin 26S proteasome system (UPS) is critical for enabling plants to alter their proteomes to integrate internal and external signals for the photoperiodic induction of flowering. We previously demonstrated that HAF1, a C3HC4 RING domain-containing E3 ubiquitin ligase, is essential to precisely modulate the timing of Heading Date1 accumulation and to ensure appropriate photoperiodic responses under short-day conditions in rice (Oryza sativa). However, how HAF1 mediates flowering under long-day conditions remains unknown. In this study, we show that OsELF3 (EARLY FLOWERING3) is the direct substrate of HAF1 for ubiquitination in vitro and in vivo. HAF1 is required for maintaining the circadian rhythm of OsELF3 accumulation during photoperiodic responses in rice. In addition, the haf1 oself3 double mutant headed as late as oself3 plants under long-day conditions. An amino acid variation (L558S) within the interaction domain of OsELF3 with HAF1 greatly contributes to the variation in heading date among japonica rice accessions. The japonica accessions carrying the OsELF3(L)-type allele are found at higher latitudes, while varieties carrying the OsELF3(S)-type allele are found at lower latitudes. Taken together, our findings suggest that HAF1 precisely modulates the diurnal rhythm of OsELF3 accumulation to ensure the appropriate heading date in rice.
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Affiliation(s)
- Chunmei Zhu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Qiang Peng
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Debao Fu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Dongxia Zhuang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yiming Yu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Min Duan
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yaohui Cai
- Jiangxi Super-rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, National Engineering Laboratory for Rice, Nanchang 330200, China
| | - Yidang Ouyang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xingming Lian
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Changyin Wu
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
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27
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Coelho CP, Huang P, Lee DY, Brutnell TP. Making Roots, Shoots, and Seeds: IDD Gene Family Diversification in Plants. TRENDS IN PLANT SCIENCE 2018; 23:66-78. [PMID: 29056440 DOI: 10.1016/j.tplants.2017.09.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 09/05/2017] [Accepted: 09/13/2017] [Indexed: 05/27/2023]
Abstract
The INDETERMINATE DOMAIN (IDD) family of transcriptional regulators controls a diversity of processes in a variety of plant tissues and organs and at different stages of plant development. Several recent reports describe the genetic characterization of IDD family members, including those that are likely to regulate C4 kranz anatomy, with implications for the engineering of C4 traits into C3 crops. In this review we summarize the reported functions of IDD members in the regulation of metabolic sensing and leaf, root, seed, and inflorescence development. We also provide an IDD phylogeny for the grasses and suggest future directions and strategies to define the function of IDDs in C4 photosynthesis and other developmental processes.
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Affiliation(s)
- Carla P Coelho
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA. http://twitter.com/coelhopcarla%20
| | - Pu Huang
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
| | - Dong-Yeon Lee
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
| | - Thomas P Brutnell
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA; Laboratory website: https://www.brutnelllab.org/.
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28
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Brambilla V, Martignago D, Goretti D, Cerise M, Somssich M, de Rosa M, Galbiati F, Shrestha R, Lazzaro F, Simon R, Fornara F. Antagonistic Transcription Factor Complexes Modulate the Floral Transition in Rice. THE PLANT CELL 2017; 29:2801-2816. [PMID: 29042404 PMCID: PMC5728136 DOI: 10.1105/tpc.17.00645] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 09/18/2017] [Accepted: 10/16/2017] [Indexed: 05/04/2023]
Abstract
Plants measure day or night lengths to coordinate specific developmental changes with a favorable season. In rice (Oryza sativa), the reproductive phase is initiated by exposure to short days when expression of HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1) is induced in leaves. The cognate proteins are components of the florigenic signal and move systemically through the phloem to reach the shoot apical meristem (SAM). In the SAM, they form a transcriptional activation complex with the bZIP transcription factor OsFD1 to start panicle development. Here, we show that Hd3a and RFT1 can form transcriptional activation or repression complexes also in leaves and feed back to regulate their own transcription. Activation complexes depend on OsFD1 to promote flowering. However, additional bZIPs, including Hd3a BINDING REPRESSOR FACTOR1 (HBF1) and HBF2, form repressor complexes that reduce Hd3a and RFT1 expression to delay flowering. We propose that Hd3a and RFT1 are also active locally in leaves to fine-tune photoperiodic flowering responses.
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Affiliation(s)
- Vittoria Brambilla
- Department of Biosciences, University of Milan, 20133 Milan, Italy
- Department of Agricultural and Environmental Sciences, University of Milan, 20133 Milan, Italy
| | | | - Daniela Goretti
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Martina Cerise
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Marc Somssich
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine University, D-40225 Düsseldorf, Germany
| | | | | | - Roshi Shrestha
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Federico Lazzaro
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Rüdiger Simon
- Institute for Developmental Genetics and Cluster of Excellence on Plant Sciences, Heinrich Heine University, D-40225 Düsseldorf, Germany
| | - Fabio Fornara
- Department of Biosciences, University of Milan, 20133 Milan, Italy
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29
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Dingkuhn M, Pasco R, Pasuquin JM, Damo J, Soulié JC, Raboin LM, Dusserre J, Sow A, Manneh B, Shrestha S, Balde A, Kretzschmar T. Crop-model assisted phenomics and genome-wide association study for climate adaptation of indica rice. 1. Phenology. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4369-4388. [PMID: 28922774 DOI: 10.1093/jxb/erx249] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Phenology and time of flowering are crucial determinants of rice adaptation to climate variation. A previous study characterized flowering responses of 203 diverse indica rices (the ORYTAGE panel) to ten environments in Senegal (six sowing dates) and Madagascar (two years and two altitudes) under irrigation in the field. This study used the physiological phenology model RIDEV V2 to heuristically estimate component traits of flowering such as cardinal temperatures (base temperature (Tbase) and optimum temperature), basic vegetative phase, photoperiod sensitivity and cold acclimation, and to conduct a genome-wide association study for these traits using 16 232 anonymous single-nucleotide polymorphism (SNP) markers. The RIDEV model after genotypic parameter optimization explained 96% of variation in time to flowering for Senegal alone and 91% for Senegal and Madagascar combined. The latter was improved to 94% by including an acclimation parameter reducing Tbase when the crop experienced low temperatures during early vegetative development. Eighteen significant (P<1.0 × 10-5) quantitative trait loci (QTLs) were identified, namely ten for RIDEV parameters and eight for climatic index variables (difference in time to flowering between key environments). Co-localization of QTLs for different traits were rare. RIDEV parameters gave QTLs that were mostly more significant and distinct from QTLs for index variables. Candidate genes were investigated within the estimated 50% linkage disequilibrium regions of 39 kB. In addition to several known flowering network genes, they included genes related to thermal stress adaptation and epigenetic control mechanisms. The peak SNP for a QTL for the crop parameter Tbase (P=2.0 × 10-7) was located within HD3a, a florigen that was recently identified as implicated in flowering under cool conditions.
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Affiliation(s)
- Michael Dingkuhn
- Cirad, Umr AGAP (Dept BIOS) and Upr AIDA (Dept ES), F-34398, Montpellier, France
| | - Richard Pasco
- IRRI, CESD Division, DAPO Box 7777, Metro Manila, Philippines
| | | | - Jean Damo
- IRRI, CESD Division, DAPO Box 7777, Metro Manila, Philippines
| | | | - Louis-Marie Raboin
- Cirad, Umr AGAP (Dept BIOS) and Upr AIDA (Dept ES), F-34398, Montpellier, France
| | - Julie Dusserre
- Cirad, Umr AGAP (Dept BIOS) and Upr AIDA (Dept ES), F-34398, Montpellier, France
| | - Abdoulaye Sow
- Africa Rice Center, Sahel Station, PB 96, St Louis, Senegal
| | | | - Suchit Shrestha
- IRRI, CESD Division, DAPO Box 7777, Metro Manila, Philippines
| | - Alpha Balde
- Africa Rice Center, Sahel Station, PB 96, St Louis, Senegal
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30
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de Montaigu A, Coupland G. The timing of GIGANTEA expression during day/night cycles varies with the geographical origin of Arabidopsis accessions. PLANT SIGNALING & BEHAVIOR 2017. [PMID: 28644109 DOI: 10.1080/15592324.2017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Latitudinal clines in circadian rhythms have consistently been described in various plant species, with the most recent examples appearing in soybean cultivars and in monkey flower natural populations. These latitudinal clines provide evidence that natural variation in circadian rhythms is adaptive, but it is still unclear what adaptive benefits this variation confers, particularly because circadian rhythms are not usually measured in day/night conditions that reflect those experienced by organisms in nature. Here, we report that daily rhythms of GIGANTEA expression respond to day length in a way that depends on the latitude of origin of Arabidopsis accessions. We additionally extend previous findings by confirming that natural variation in GI expression affects growth related traits, and alters the expression of different target genes. The results support the idea that natural variation in daily rhythms of expression have broad effects on plant development and are of potential adaptive value.
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Affiliation(s)
- Amaury de Montaigu
- a Department of Developmental Biology , Max Planck Institute for Plant Breeding Research , Cologne , Germany
| | - George Coupland
- a Department of Developmental Biology , Max Planck Institute for Plant Breeding Research , Cologne , Germany
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31
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de Montaigu A, Coupland G. The timing of GIGANTEA expression during day/night cycles varies with the geographical origin of Arabidopsis accessions. PLANT SIGNALING & BEHAVIOR 2017; 12:e1342026. [PMID: 28644109 PMCID: PMC5586394 DOI: 10.1080/15592324.2017.1342026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 06/06/2017] [Accepted: 06/07/2017] [Indexed: 05/13/2023]
Abstract
Latitudinal clines in circadian rhythms have consistently been described in various plant species, with the most recent examples appearing in soybean cultivars and in monkey flower natural populations. These latitudinal clines provide evidence that natural variation in circadian rhythms is adaptive, but it is still unclear what adaptive benefits this variation confers, particularly because circadian rhythms are not usually measured in day/night conditions that reflect those experienced by organisms in nature. Here, we report that daily rhythms of GIGANTEA expression respond to day length in a way that depends on the latitude of origin of Arabidopsis accessions. We additionally extend previous findings by confirming that natural variation in GI expression affects growth related traits, and alters the expression of different target genes. The results support the idea that natural variation in daily rhythms of expression have broad effects on plant development and are of potential adaptive value.
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Affiliation(s)
- Amaury de Montaigu
- Department of Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - George Coupland
- Department of Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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32
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Deng L, Li L, Zhang S, Shen J, Li S, Hu S, Peng Q, Xiao J, Wu C. Suppressor of rid1 (SID1) shares common targets with RID1 on florigen genes to initiate floral transition in rice. PLoS Genet 2017; 13:e1006642. [PMID: 28234896 PMCID: PMC5345856 DOI: 10.1371/journal.pgen.1006642] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 03/10/2017] [Accepted: 02/17/2017] [Indexed: 11/19/2022] Open
Abstract
The transition from vegetative to reproductive growth is a critical process in the life cycle of higher plants. Previously, we cloned Rice Indeterminate 1 (RID1), which acts as the master switch for the transition from the vegetative to reproductive phase in rice. Although the photoperiod pathway of RID1 inducing expression of the florigen genes Hd3a and RFT1 via Ehd1 has been established, the alternative pathways for the essential flowering transition need to be further examined. Here, we identified a Suppressor of rid1 (SID1), which rescues the never-flowering phenotype of rid1. SID1 encodes an INDETERMINATE DOMAIN (IDD) transcription factor. Mutation in SID1 showed the delayed flowering phenotype. Gain-of-function of SID1, OsIDD1, or OsIDD6 could restore the rid1 to flowering. Further analyses showed SID1 and RID1 directly target the promoter regions of Hd3a and RFT1, two florigen genes in rice. Taken together, our results reveal an autonomous flowering pathway might be mediated by RID1, thereby controlling the phase transition from vegetative to reproductive development in rice. Transition from vegetative to reproductive phase is a critical developmental switch in the life cycle of higher plants. In rice, our previous work suggested Rice Indeterminate 1 (RID1) acts as the master switch for the transition to flowering. Mutation in RID1 results in a never-flowering phenotype. In order to uncover the molecular network regulated by RID1, a Suppressor of rid1 (SID1) was identified in this study. Both SID1 and RID1 encode a plant-specific INDETERMINATE DOMAIN (IDD) transcription factor. Overexpression of SID1, OsIDD1, or OsIDD6 could rescue the never-flowering phenotype of rid1. Molecular data indicate both SID1 and RID1 physically bind the promoters of the florigen genes Hd3a and RFT1 in rice. Thus, we propose that the transition to flowering could be regulated by RID1 through the autonomous pathway, in addition to the photoperiod pathway.
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Affiliation(s)
- Li Deng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Lingmei Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Shuo Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Jianqiang Shen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Shaobo Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Sifan Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Qiang Peng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Jinghua Xiao
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Changyin Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China
- * E-mail:
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33
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Goretti D, Martignago D, Landini M, Brambilla V, Gómez-Ariza J, Gnesutta N, Galbiati F, Collani S, Takagi H, Terauchi R, Mantovani R, Fornara F. Transcriptional and Post-transcriptional Mechanisms Limit Heading Date 1 (Hd1) Function to Adapt Rice to High Latitudes. PLoS Genet 2017; 13:e1006530. [PMID: 28068345 PMCID: PMC5221825 DOI: 10.1371/journal.pgen.1006530] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 12/08/2016] [Indexed: 11/24/2022] Open
Abstract
Rice flowering is controlled by changes in the photoperiod that promote the transition to the reproductive phase as days become shorter. Natural genetic variation for flowering time has been largely documented and has been instrumental to define the genetics of the photoperiodic pathway, as well as providing valuable material for artificial selection of varieties better adapted to local environments. We mined genetic variation in a collection of rice varieties highly adapted to European regions and isolated distinct variants of the long day repressor HEADING DATE 1 (Hd1) that perturb its expression or protein function. Specific variants allowed us to define novel features of the photoperiodic flowering pathway. We demonstrate that a histone fold domain scaffold formed by GRAIN YIELD, PLANT HEIGHT AND HEADING DATE 8 (Ghd8) and several NF-YC subunits can accommodate distinct proteins, including Hd1 and PSEUDO RESPONSE REGULATOR 37 (PRR37), and that the resulting OsNF-Y complex containing Hd1 can bind a specific sequence in the promoter of HEADING DATE 3A (Hd3a). Artificial selection has locally favored an Hd1 variant unable to assemble in such heterotrimeric complex. The causal polymorphism was defined as a single conserved lysine in the CCT domain of the Hd1 protein. Our results indicate how genetic variation can be stratified and explored at multiple levels, and how its description can contribute to the molecular understanding of basic developmental processes. Many plant species flower in response to changes in day length and can be categorized depending on their requirements for long or short days. Rice has tropical origins and normally flowers in response to shortening days. However, artificial selection operated by ancient farmers or modern breeders adapted rice cultivation to several environments, including those typical of temperate regions characterized by long days during the cropping season. Modifications of the genetic network controlling flowering that are causal to such expansion have been the subject of extensive studies, but the full complement of genes that regulate it and the molecular bases of their activity remains unknown. We took advantage of germplasm cultivated in Europe—and highly adapted to flower under long days–to isolate widespread variants of the HEADING DATE 1 (Hd1) gene that limits flowering in temperate areas, and showed that such variants are non-functional and unable to prevent long day flowering. We identified the DNA changes causing the gene to be non-functional and used such mutant alleles as tools to demonstrate that Hd1 can bind a specific DNA sequence in the promoter of a florigenic rice gene. Mining genetic diversity becomes thus instrumental to define the molecular properties of regulatory pathways.
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Affiliation(s)
- Daniela Goretti
- Department of Biosciences, University of Milan, Via Celoria 26, Milan, Italy
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Damiano Martignago
- Department of Biosciences, University of Milan, Via Celoria 26, Milan, Italy
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, United Kingdom
| | - Martina Landini
- Department of Biosciences, University of Milan, Via Celoria 26, Milan, Italy
| | - Vittoria Brambilla
- Department of Biosciences, University of Milan, Via Celoria 26, Milan, Italy
- Department of Agricultural and Environmental Sciences–Production, Territory, Agroenergy, University of Milan, Via Celoria 2, Milan, Italy
| | - Jorge Gómez-Ariza
- Department of Biosciences, University of Milan, Via Celoria 26, Milan, Italy
| | - Nerina Gnesutta
- Department of Biosciences, University of Milan, Via Celoria 26, Milan, Italy
| | - Francesca Galbiati
- Department of Biosciences, University of Milan, Via Celoria 26, Milan, Italy
| | - Silvio Collani
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Hiroki Takagi
- Iwate Biotechnology Research Center and Laboratory of Crop Evolution, Graduate School of Agricultural Sciences, Kyoto University, Mozume, Muko, Kyoto, Japan
| | - Ryohei Terauchi
- Iwate Biotechnology Research Center and Laboratory of Crop Evolution, Graduate School of Agricultural Sciences, Kyoto University, Mozume, Muko, Kyoto, Japan
| | - Roberto Mantovani
- Department of Biosciences, University of Milan, Via Celoria 26, Milan, Italy
| | - Fabio Fornara
- Department of Biosciences, University of Milan, Via Celoria 26, Milan, Italy
- * E-mail:
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Brambilla V, Gomez-Ariza J, Cerise M, Fornara F. The Importance of Being on Time: Regulatory Networks Controlling Photoperiodic Flowering in Cereals. FRONTIERS IN PLANT SCIENCE 2017; 8:665. [PMID: 28491078 PMCID: PMC5405123 DOI: 10.3389/fpls.2017.00665] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 04/11/2017] [Indexed: 05/04/2023]
Abstract
Flowering is the result of the coordination between genetic information and environmental cues. Gene regulatory networks have evolved in plants in order to measure diurnal and seasonal variation of day length (or photoperiod), thus aligning the reproductive phase with the most favorable season of the year. The capacity of plants to discriminate distinct photoperiods classifies them into long and short day species, depending on the conditions that induce flowering. Plants of tropical origin and adapted to short day lengths include rice, maize, and sorghum, whereas wheat and barley were originally domesticated in the Fertile Crescent and are considered long day species. In these and other crops, day length measurement mechanisms have been artificially modified during domestication and breeding to adapt plants to novel areas, to the extent that a wide diversity of responses exists within any given species. Notwithstanding the ample natural and artificial variation of day length responses, some of the basic molecular elements governing photoperiodic flowering are widely conserved. However, as our understanding of the underlying mechanisms improves, it becomes evident that specific regulators exist in many lineages that are not shared by others, while apparently conserved components can be recruited to novel functions during evolution.
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Hori K, Matsubara K, Yano M. Genetic control of flowering time in rice: integration of Mendelian genetics and genomics. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:2241-2252. [PMID: 27695876 DOI: 10.1007/s00122-016-2773-4] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 08/12/2016] [Indexed: 05/20/2023]
Abstract
Integration of previous Mendelian genetic analyses and recent molecular genomics approaches, such as linkage mapping and QTL cloning, dramatically strengthened our current understanding of genetic control of rice flowering time. Flowering time is one of the most important agronomic traits for seed production in rice (Oryza sativa L.). It is controlled mainly by genes associated with photoperiod sensitivity, particularly in short-day plants such as rice. Since the early twentieth century, rice breeders and researchers have been interested in elucidating the genetic basis of flowering time because its modification is important for regional adaptation and yield optimization. Although flowering time is a complex trait controlled by many quantitative trait loci (QTLs), classical genetic studies have shown that many associated genes are inherited in accordance with Mendelian laws. Decoding the rice genome sequence opened a new era in understanding the genetic control of flowering time on the basis of genome-wide mapping and gene cloning. Heading date 1 (Hd1) was the first flowering time QTL to be isolated using natural variation in rice. Recent accumulation of information on rice genome has facilitated the cloning of other QTLs, including those with minor effects on flowering time. This information has allowed us to rediscover some of the flowering genes that were identified by classical Mendelian genetics. The genes characterized so far, including Hd1, have been assigned to specific photoperiod pathways. In this review, we provide an overview of the studies that led to an in-depth understanding of the genetic control of flowering time in rice, and of the current state of improving and fine-tuning this trait for rice breeding.
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Zhang ZH, Cao LY, Chen JY, Zhang YX, Zhuang JY, Cheng SH. Effects of Hd2 in the presence of the photoperiod-insensitive functional allele of Hd1 in rice. Biol Open 2016; 5:1719-1726. [PMID: 27797723 PMCID: PMC5155538 DOI: 10.1242/bio.021071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The role of photoperiod sensitivity (PS) of flowering genes have become well recognized in rice, whereas little attention has been drawn to the non-PS component of these genes, especially to their influence on gene-by-gene interactions. Rice populations in which the photoperiod-sensitive allele at Hd1 has become insensitive to photoperiod but continued to affect heading date (HD) were used in this study to fine-map a quantitative trait locus (QTL) for HD and analyze its genetic relationship to Hd1. The QTL was delimitated to a 96.3-kb region on the distal end of the long arm of chromosome 7. Sequence comparison revealed that this QTL is identical to Hd2. In the near-isogenic line (NIL) populations analyzed, Hd1 and Hd2 were shown to be photoperiod insensitive and have pleiotropic effects for HD, plant height and yield traits. The two genes were found to largely act additively in regulating HD and yield traits. The results indicate that non-PS components of flowering genes involved in photoperiod response play an important role in controlling flowering time and grain yield in rice, which should allow breeders to better manipulate pleiotropic genes for balancing adaptability and high-yielding accumulation. Summary: We show that photoperiod-insensitive components of alleles of Hd1 and Hd2 play an important role in balancing ecological adaptability and high-yield accumulation in rice.
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Affiliation(s)
- Zhen-Hua Zhang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Li-Yong Cao
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Jun-Yu Chen
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Ying-Xin Zhang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Jie-Yun Zhuang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Shi-Hua Cheng
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
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Brambilla V, Fornara F. Y flowering? Regulation and activity of CONSTANS and CCT-domain proteins in Arabidopsis and crop species. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:655-660. [PMID: 27793713 DOI: 10.1016/j.bbagrm.2016.10.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/09/2016] [Accepted: 10/20/2016] [Indexed: 12/21/2022]
Abstract
Changes in day length regulate the proper timing of flowering in several plant species. The genetic architecture of this process is based on CCT-domain proteins, many of which interact with NF-Y subunits to regulate transcription of target genes. In the model plant Arabidopsis thaliana, the CONSTANS CCT-domain protein is a central photoperiodic sensor. We will discuss how the diurnal rhythms of its transcription and protein accumulation are generated, and how the protein engages into multiple complexes to control production of a systemic flowering signal. Regulatory parallels will be drawn between Arabidopsis and major crops that indicate conservation of some CCT/NF-Y modules during plant evolution. This article is part of a Special Issue entitled: Nuclear Factor Y in Development and Disease, edited by Prof. Roberto Mantovani.
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Affiliation(s)
- Vittoria Brambilla
- Department of Agricultural and Environmental Sciences - Production, Territory, Agroenergy, University of Milan, Via Celoria 2, 20133 Milan, Italy
| | - Fabio Fornara
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy.
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Ridge S, Sussmilch FC, Hecht V, Vander Schoor JK, Lee R, Aubert G, Burstin J, Macknight RC, Weller JL. Identification of LATE BLOOMER2 as a CYCLING DOF FACTOR Homolog Reveals Conserved and Divergent Features of the Flowering Response to Photoperiod in Pea. THE PLANT CELL 2016; 28:2545-2559. [PMID: 27670672 PMCID: PMC5134971 DOI: 10.1105/tpc.15.01011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 08/25/2016] [Accepted: 09/23/2016] [Indexed: 05/21/2023]
Abstract
The molecular pathways responsible for the flowering response to photoperiod have been extensively studied in Arabidopsis thaliana and cereals but remain poorly understood in other major plant groups. Here, we describe a dominant mutant at the LATE BLOOMER2 (LATE2) locus in pea (Pisum sativum) that is late-flowering with a reduced response to photoperiod. LATE2 acts downstream of light signaling and the circadian clock to control expression of the main photoperiod-regulated FT gene, FTb2, implying that it plays a primary role in photoperiod measurement. Mapping identified the CYCLING DOF FACTOR gene CDFc1 as a strong candidate for LATE2, and the late2-1D mutant was found to carry a missense mutation in CDFc1 that impairs its capacity to bind to the blue-light photoreceptor FKF1 in yeast two-hybrid assays and delays flowering in Arabidopsis when overexpressed. Arabidopsis CDF genes are important negative regulators of CONSTANS (CO) transcription, but we found no effect of LATE2 on the transcription of pea CO-LIKE genes, nor on genes in any other families previously implicated in the activation of FT in Arabidopsis. Our results reveal an important component of the pea photoperiod response pathway and support the view that regulation of FTb2 expression by photoperiod occurs via a CO-independent mechanism.
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Affiliation(s)
- Stephen Ridge
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Frances C Sussmilch
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Valérie Hecht
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
| | | | - Robyn Lee
- Department of Biochemistry, University of Otago, Dunedin 9054, New Zealand
| | | | | | | | - James L Weller
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
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Galbiati F, Chiozzotto R, Locatelli F, Spada A, Genga A, Fornara F. Hd3a, RFT1 and Ehd1 integrate photoperiodic and drought stress signals to delay the floral transition in rice. PLANT, CELL & ENVIRONMENT 2016; 39:1982-93. [PMID: 27111837 DOI: 10.1111/pce.12760] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 04/10/2016] [Indexed: 05/20/2023]
Abstract
Plants show a high degree of developmental plasticity in response to external cues, including day length and environmental stress. Water scarcity in particular can interfere with photoperiodic flowering, resulting in the acceleration of the switch to reproductive growth in several species, a process called drought escape. However, other strategies are possible and drought stress can also delay flowering, albeit the underlying mechanisms have never been addressed at the molecular level. We investigated these interactions in rice, a short day species in which drought stress delays flowering. A protocol that allows the synchronization of drought with the floral transition was set up to profile the transcriptome of leaves subjected to stress under distinct photoperiods. We identified clusters of genes that responded to drought differently depending on day length. Exposure to drought stress under floral-inductive photoperiods strongly reduced transcription of EARLY HEADING DATE 1 (Ehd1), HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1), primary integrators of day length signals, providing a molecular connection between stress and the photoperiodic pathway. However, phenotypic and transcriptional analyses suggested that OsGIGANTEA (OsGI) does not integrate drought and photoperiodic signals as in Arabidopsis, highlighting molecular differences between long and short day model species.
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Affiliation(s)
- Francesca Galbiati
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy
- Department of Agricultural and Environmental Sciences - Production, Territory, Agroenergy, University of Milan, Via Celoria 2, 20133, Milan, Italy
| | - Remo Chiozzotto
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Bassini 15, 20133, Milan, Italy
| | - Franca Locatelli
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Bassini 15, 20133, Milan, Italy
| | - Alberto Spada
- Department of Agricultural and Environmental Sciences - Production, Territory, Agroenergy, University of Milan, Via Celoria 2, 20133, Milan, Italy
| | - Annamaria Genga
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Bassini 15, 20133, Milan, Italy
| | - Fabio Fornara
- Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milan, Italy
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The Oryza sativa Regulator HDR1 Associates with the Kinase OsK4 to Control Photoperiodic Flowering. PLoS Genet 2016; 12:e1005927. [PMID: 26954091 PMCID: PMC4783006 DOI: 10.1371/journal.pgen.1005927] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 02/19/2016] [Indexed: 11/19/2022] Open
Abstract
Rice is a facultative short-day plant (SDP), and the regulatory pathways for flowering time are conserved, but functionally modified, in Arabidopsis and rice. Heading date 1 (Hd1), an ortholog of Arabidopsis CONSTANS (CO), is a key regulator that suppresses flowering under long-day conditions (LDs), but promotes flowering under short-day conditions (SDs) by influencing the expression of the florigen gene Heading date 3a (Hd3a). Another key regulator, Early heading date 1 (Ehd1), is an evolutionarily unique gene with no orthologs in Arabidopsis, which acts as a flowering activator under both SD and LD by promoting the rice florigen genes Hd3a and RICE FLOWERING LOCUST 1 (RFT1). Here, we report the isolation and characterization of the flowering regulator Heading Date Repressor1 (HDR1) in rice. The hdr1 mutant exhibits an early flowering phenotype under natural LD in a paddy field in Beijing, China (39°54'N, 116°23'E), as well as under LD but not SD in a growth chamber, indicating that HDR1 may functionally regulate flowering time via the photoperiod-dependent pathway. HDR1 encodes a nuclear protein that is most active in leaves and floral organs and exhibits a typical diurnal expression pattern. We determined that HDR1 is a novel suppressor of flowering that upregulates Hd1 and downregulates Ehd1, leading to the downregulation of Hd3a and RFT1 under LDs. We have further identified an HDR1-interacting kinase, OsK4, another suppressor of rice flowering under LDs. OsK4 acts similarly to HDR1, suppressing flowering by upregulating Hd1 and downregulating Ehd1 under LDs, and OsK4 can phosphorylate HD1 with HDR1 presents. These results collectively reveal the transcriptional regulators of Hd1 for the day-length-dependent control of flowering time in rice. In rice, flowering time affects the potential yield, the growing season and regional adaptability. Change in day length is a key seasonal cue for regulating flowering time in rice, a facultative short-day (SD) plant. The photoperiodic pathway of rice contains the evolutionarily conserved Hd1-Hd3a module, which is homologous to the CO-FT module in the long-day (LD) plant Arabidopsis. In this work, we cloned a novel gene, HDR1, that activates Hd1 and represses Ehd1, thereby down-regulating the florigen genes Hd3a and RFT1 to postpone rice flowering. A protein associated with HDR1, OsK4, was also identified, and the resulting complex can interact with HD1 to phosphorylate HD1. We conclude that HDR1 is a novel transcriptional regulator of Hd1 that plays a crucial role in regulating flowering time via the photoperiodic pathway in rice.
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Kazan K, Lyons R. The link between flowering time and stress tolerance. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:47-60. [PMID: 26428061 DOI: 10.1093/jxb/erv441] [Citation(s) in RCA: 206] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Evolutionary success in plants is largely dependent on the successful transition from vegetative to reproductive growth. In the lifetime of a plant, flowering is not only an essential part of the reproductive process but also a critical developmental stage that can be vulnerable to environmental stresses. Exposure to stress during this period can cause substantial yield losses in seed-producing plants. However, it is becoming increasingly evident that altering flowering time is an evolutionary strategy adopted by plants to maximize the chances of reproduction under diverse stress conditions, ranging from pathogen infection to heat, salinity, and drought. Here, recent studies that have revealed new insights into how biotic and abiotic stress signals can be integrated into floral pathways are reviewed. A better understanding of how complex environmental variables affect plant phenology is important for future genetic manipulation of crops to increase productivity under the changing climate.
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Affiliation(s)
- Kemal Kazan
- CSIRO Agriculture, Queensland Bioscience Precinct, Brisbane, Queensland, Australia Queensland Alliance for Agriculture & Food Innovation (QAAFI), The University of Queensland, St Lucia, Brisbane, Queensland 4067, Australia
| | - Rebecca Lyons
- CSIRO Agriculture, Queensland Bioscience Precinct, Brisbane, Queensland, Australia
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