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Rahmati Ishka M, Julkowska M. Tapping into the plasticity of plant architecture for increased stress resilience. F1000Res 2023; 12:1257. [PMID: 38434638 PMCID: PMC10905174 DOI: 10.12688/f1000research.140649.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/24/2023] [Indexed: 03/05/2024] Open
Abstract
Plant architecture develops post-embryonically and emerges from a dialogue between the developmental signals and environmental cues. Length and branching of the vegetative and reproductive tissues were the focus of improvement of plant performance from the early days of plant breeding. Current breeding priorities are changing, as we need to prioritize plant productivity under increasingly challenging environmental conditions. While it has been widely recognized that plant architecture changes in response to the environment, its contribution to plant productivity in the changing climate remains to be fully explored. This review will summarize prior discoveries of genetic control of plant architecture traits and their effect on plant performance under environmental stress. We review new tools in phenotyping that will guide future discoveries of genes contributing to plant architecture, its plasticity, and its contributions to stress resilience. Subsequently, we provide a perspective into how integrating the study of new species, modern phenotyping techniques, and modeling can lead to discovering new genetic targets underlying the plasticity of plant architecture and stress resilience. Altogether, this review provides a new perspective on the plasticity of plant architecture and how it can be harnessed for increased performance under environmental stress.
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Seetharam AS, Yu Y, Bélanger S, Clark LG, Meyers BC, Kellogg EA, Hufford MB. The Streptochaeta Genome and the Evolution of the Grasses. FRONTIERS IN PLANT SCIENCE 2021; 12:710383. [PMID: 34671369 PMCID: PMC8521107 DOI: 10.3389/fpls.2021.710383] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 09/08/2021] [Indexed: 05/15/2023]
Abstract
In this work, we sequenced and annotated the genome of Streptochaeta angustifolia, one of two genera in the grass subfamily Anomochlooideae, a lineage sister to all other grasses. The final assembly size is over 99% of the estimated genome size. We find good collinearity with the rice genome and have captured most of the gene space. Streptochaeta is similar to other grasses in the structure of its fruit (a caryopsis or grain) but has peculiar flowers and inflorescences that are distinct from those in the outgroups and in other grasses. To provide tools for investigations of floral structure, we analyzed two large families of transcription factors, AP2-like and R2R3 MYBs, that are known to control floral and spikelet development in rice and maize among other grasses. Many of these are also regulated by small RNAs. Structure of the gene trees showed that the well documented whole genome duplication at the origin of the grasses (ρ) occurred before the divergence of the Anomochlooideae lineage from the lineage leading to the rest of the grasses (the spikelet clade) and thus that the common ancestor of all grasses probably had two copies of the developmental genes. However, Streptochaeta (and by inference other members of Anomochlooideae) has lost one copy of many genes. The peculiar floral morphology of Streptochaeta may thus have derived from an ancestral plant that was morphologically similar to the spikelet-bearing grasses. We further identify 114 loci producing microRNAs and 89 loci generating phased, secondary siRNAs, classes of small RNAs known to be influential in transcriptional and post-transcriptional regulation of several plant functions.
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Affiliation(s)
- Arun S. Seetharam
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Yunqing Yu
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | | | - Lynn G. Clark
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Blake C. Meyers
- Donald Danforth Plant Science Center, St. Louis, MO, United States
- Division of Plant Sciences, University of Missouri, Columbia, MO, United States
| | | | - Matthew B. Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
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Liu Z, Zhang D, Zhang W, Xiong L, Liu Q, Liu F, Li H, An X, Cui L, Tian D. Molecular Cloning and Expression Profile of Class E Genes Related to Sepal Development in Nelumbo nucifera. PLANTS 2021; 10:plants10081629. [PMID: 34451674 PMCID: PMC8398900 DOI: 10.3390/plants10081629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/20/2021] [Accepted: 07/21/2021] [Indexed: 11/16/2022]
Abstract
The lotus (Nelumbo Adans.) is an important aquatic plant with ornamental, medicinal and edible values and cultural connotations. It has single-, semi-double-, double- and thousand-petalled types of flower shape and is an ideal material for developmental research of flower doubling. The lotus is a basal eudicot species without a morphological difference between the sepals and petals and occupies a critical phylogenetic position in flowering plants. In order to investigate the genetic relationship between the sepals and petals in the lotus, the class E genes which affect sepal formation were focused on and analyzed. Here, SEPALLATA 1(NnSEP1) and its homologous genes AGAMOUS-LIKE MADS-BOXAGL9 (NnAGL9) and MADS-BOX TRANSCRIPTION FACTOR 6-like (NnMADS6-like) of the class E gene family were isolated from the flower buds of the Asian lotus (Nelumbo nucifera Gaertn.). The protein structure, subcellular localization and expression patterns of these three genes were investigated. All three genes were verified to locate in the nucleus and had typical MADS-box characteristics. NnSEP1 and NnMADS6-like were specifically expressed in the sepals, while NnAGL9 was highly expressed in the petals, suggesting that different developmental mechanisms exist in the formation of the sepals and petals in the lotus. The significant functional differences between NnSEP1, NnMADS6-like and NnAGL9 were also confirmed by a yeast two-hybrid assay. These results expand our knowledge on the class E gene family in sepal formation and will benefit fundamental research on the development of floral organs in Nelumbo.
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Affiliation(s)
- Zhuoxing Liu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center of Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Z.L.); (D.Z.); (L.X.); (Q.L.); (H.L.); (X.A.)
- Development Center of Plant Germplam Resources, College of Life Science, Shanghai Normal University, Shanghai 200234, China;
| | - Dasheng Zhang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center of Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Z.L.); (D.Z.); (L.X.); (Q.L.); (H.L.); (X.A.)
| | - Weiwei Zhang
- Department of Plant Science and Technology, Shanghai Vocational College of Agriculture and Forestry, Shanghai 201699, China;
| | - Lei Xiong
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center of Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Z.L.); (D.Z.); (L.X.); (Q.L.); (H.L.); (X.A.)
- Development Center of Plant Germplam Resources, College of Life Science, Shanghai Normal University, Shanghai 200234, China;
| | - Qingqing Liu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center of Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Z.L.); (D.Z.); (L.X.); (Q.L.); (H.L.); (X.A.)
| | - Fengluan Liu
- Development Center of Plant Germplam Resources, College of Life Science, Shanghai Normal University, Shanghai 200234, China;
| | - Hanchun Li
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center of Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Z.L.); (D.Z.); (L.X.); (Q.L.); (H.L.); (X.A.)
| | - Xiangjie An
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center of Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Z.L.); (D.Z.); (L.X.); (Q.L.); (H.L.); (X.A.)
| | - Lijie Cui
- Development Center of Plant Germplam Resources, College of Life Science, Shanghai Normal University, Shanghai 200234, China;
- Correspondence: (L.C.); (D.T.); Tel.: +86-21-37792288-932; Fax: +86-21-57762652
| | - Daike Tian
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center of Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, Shanghai 201602, China; (Z.L.); (D.Z.); (L.X.); (Q.L.); (H.L.); (X.A.)
- Correspondence: (L.C.); (D.T.); Tel.: +86-21-37792288-932; Fax: +86-21-57762652
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Kannan P, Chongloi GL, Majhi BB, Basu D, Veluthambi K, Vijayraghavan U. Characterization of a new rice OsMADS1 null mutant generated by homologous recombination-mediated gene targeting. PLANTA 2021; 253:39. [PMID: 33474591 DOI: 10.1007/s00425-020-03547-3] [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: 08/18/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
A new, stable, null mutant of OsMADS1 generated by homologous recombination-based gene targeting in an indica rice confirms its regulatory role for floral meristem identity, its determinate development and floral organ differentiation. OsMADS1, an E-class MADS-box gene, is an important regulator of rice flower development. Studies of several partial loss-of-function and knockdown mutants show varied floret organ defects and degrees of meristem indeterminacy. The developmental consequences of a true null mutant on floret meristem identity, its determinate development and differentiation of grass-specific organs such as the lemma and palea remain unclear. In this study, we generated an OsMADS1 null mutant by homologous recombination-mediated gene targeting by inserting a selectable marker gene (hpt) in OsMADS1 and replacing parts of its cis-regulatory and coding sequences. A binary vector was constructed with diphtheria toxin A chain gene (DT-A) as a negative marker to eliminate random integrations and the hpt marker for positive selection of homologous recombination. Precise disruption of the endogenous OsMADS1 locus in the rice genome was confirmed by Southern hybridization. The homozygous osmads1ko null mutant displayed severe defects in all floral organs including the lemma and palea. We also noticed striking instances of floral reversion to inflorescence and vegetative states which has not been reported for other mutant alleles of OsMADS1 and further reinforces the role of OsMADS1 in controlling floral meristem determinacy. Our data suggest, OsMADS1 commits and maintains determinate floret development by regulating floral meristem termination, carpel and ovule differentiation genes (OsMADS58, OsMADS13) while its modulation of genes such as OsMADS15, OsIG1 and OsMADS32 could be relevant in the differentiation and development of palea. Further, our study provides an important perspective on developmental stage-dependent modulation of some OsMADS1 target genes.
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Affiliation(s)
- Pachamuthu Kannan
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | | | - Bharat Bhusan Majhi
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Debjani Basu
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Karuppannan Veluthambi
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, 625021, India
| | - Usha Vijayraghavan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, 560012, India.
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Ali Z, Raza Q, Atif RM, Aslam U, Ajmal M, Chung G. Genetic and Molecular Control of Floral Organ Identity in Cereals. Int J Mol Sci 2019; 20:E2743. [PMID: 31167420 PMCID: PMC6600504 DOI: 10.3390/ijms20112743] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 05/25/2019] [Accepted: 05/28/2019] [Indexed: 12/22/2022] Open
Abstract
Grasses represent a major family of monocots comprising mostly cereals. When compared to their eudicot counterparts, cereals show a remarkable morphological diversity. Understanding the molecular basis of floral organ identity and inflorescence development is crucial to gain insight into the grain development for yield improvement purposes in cereals, however, the exact genetic mechanism of floral organogenesis remains elusive due to their complex inflorescence architecture. Extensive molecular analyses of Arabidopsis and other plant genera and species have established the ABCDE floral organ identity model. According to this model, hierarchical combinatorial activities of A, B, C, D, and E classes of homeotic genes regulate the identity of different floral organs with partial conservation and partial diversification between eudicots and cereals. Here, we review the developmental role of A, B, C, D, and E gene classes and explore the recent advances in understanding the floral development and subsequent organ specification in major cereals with reference to model plants. Furthermore, we discuss the evolutionary relationships among known floral organ identity genes. This comparative overview of floral developmental genes and associated regulatory factors, within and between species, will provide a thorough understanding of underlying complex genetic and molecular control of flower development and floral organ identity, which can be helpful to devise innovative strategies for grain yield improvement in cereals.
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Affiliation(s)
- Zulfiqar Ali
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Sharif University of Agriculture, Multan 66000, Pakistan.
| | - Qasim Raza
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
- Molecular Breeding Laboratory, Division of Plant Breeding and Genetics, Rice Research Institute, Kala Shah Kaku 39020, Pakistan.
| | - Rana Muhammad Atif
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
- Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture, Faisalabad 38000, Pakistan.
| | - Usman Aslam
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
| | - Muhammad Ajmal
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam 59626, Korea.
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Chen P, Li R, Zhou R. Comparative phosphoproteomic analysis reveals differentially phosphorylated proteins regulate anther and pollen development in kenaf cytoplasmic male sterility line. Amino Acids 2018; 50:841-862. [DOI: 10.1007/s00726-018-2564-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 03/29/2018] [Indexed: 12/28/2022]
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Grass inflorescence architecture and meristem determinacy. Semin Cell Dev Biol 2017; 79:37-47. [PMID: 29020602 DOI: 10.1016/j.semcdb.2017.10.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/05/2017] [Accepted: 10/06/2017] [Indexed: 11/22/2022]
Abstract
The grass inflorescence is striking not only for its beauty and diversity, but also for its developmental complexity. While models of inflorescence architecture have been proposed in both eudicots and grasses, these are inadequate to fully explain the complex branching events that occur during the development of the grass inflorescence. Key to understanding grass inflorescence architecture is the meristem determinacy/indeterminacy decision, which regulates the number of branching events that occur. Here we review what has been learned about meristem determinacy from grass mutants with defects in inflorescence development. A picture is emerging of a complex network of signaling molecules and meristem identity factors that interact to regulate inflorescence meristem activity, many of which have been modified during crop domestication directly affecting yield traits.
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Khanday I, Das S, Chongloi GL, Bansal M, Grossniklaus U, Vijayraghavan U. Genome-Wide Targets Regulated by the OsMADS1 Transcription Factor Reveals Its DNA Recognition Properties. PLANT PHYSIOLOGY 2016; 172:372-88. [PMID: 27457124 PMCID: PMC5074623 DOI: 10.1104/pp.16.00789] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 07/23/2016] [Indexed: 05/04/2023]
Abstract
OsMADS1 controls rice (Oryza sativa) floral fate and organ development. Yet, its genome-wide targets and the mechanisms underlying its role as a transcription regulator controlling developmental gene expression are unknown. We identify 3112 gene-associated OsMADS1-bound sites in the floret genome. These occur in the vicinity of transcription start sites, within gene bodies, and in intergenic regions. Majority of the bound DNA contained CArG motif variants or, in several cases, only A-tracts. Sequences flanking the binding peak had a higher AT nucleotide content, implying that broader DNA structural features may define in planta binding. Sequences for binding by other transcription factor families like MYC, AP2/ERF, bZIP, etc. are enriched in OsMADS1-bound DNAs. Target genes implicated in transcription, chromatin remodeling, cellular processes, and hormone metabolism were enriched. Combining expression data from OsMADS1 knockdown florets with these DNA binding data, a snapshot of a gene regulatory network was deduced where targets, such as AP2/ERF and bHLH transcription factors and chromatin remodelers form nodes. We show that the expression status of these nodal factors can be altered by inducing the OsMADS1-GR fusion protein and present a model for a regulatory cascade where the direct targets of OsMADS1, OsbHLH108/SPT, OsERF034, and OsHSF24, in turn control genes such as OsMADS32 and OsYABBY5 This cascade, with other similar relationships, cumulatively contributes to floral organ development. Overall, OsMADS1 binds to several regulatory genes and, probably in combination with other factors, controls a gene regulatory network that ensures rice floret development.
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Affiliation(s)
- Imtiyaz Khanday
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India (I.K., G.L.C., U.V.);Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India (S.D., M.B.); andDepartment of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich 8008, Switzerland (U.G.)
| | - Sanjukta Das
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India (I.K., G.L.C., U.V.);Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India (S.D., M.B.); andDepartment of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich 8008, Switzerland (U.G.)
| | - Grace L Chongloi
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India (I.K., G.L.C., U.V.);Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India (S.D., M.B.); andDepartment of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich 8008, Switzerland (U.G.)
| | - Manju Bansal
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India (I.K., G.L.C., U.V.);Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India (S.D., M.B.); andDepartment of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich 8008, Switzerland (U.G.)
| | - Ueli Grossniklaus
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India (I.K., G.L.C., U.V.);Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India (S.D., M.B.); andDepartment of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich 8008, Switzerland (U.G.)
| | - Usha Vijayraghavan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India (I.K., G.L.C., U.V.);Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India (S.D., M.B.); andDepartment of Plant and Microbial Biology and Zurich-Basel Plant Science Center, University of Zurich, Zurich 8008, Switzerland (U.G.)
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Hu Y, Liang W, Yin C, Yang X, Ping B, Li A, Jia R, Chen M, Luo Z, Cai Q, Zhao X, Zhang D, Yuan Z. Interactions of OsMADS1 with Floral Homeotic Genes in Rice Flower Development. MOLECULAR PLANT 2015; 8:1366-84. [PMID: 25917758 DOI: 10.1016/j.molp.2015.04.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 04/05/2015] [Accepted: 04/16/2015] [Indexed: 05/23/2023]
Abstract
During reproductive development, rice plants develop unique flower organs which determine the final grain yield. OsMADS1, one of SEPALLATA-like MADS-box genes, has been unraveled to play critical roles in rice floral organ identity specification and floral meristem determinacy. However, the molecular mechanisms underlying interactions of OsMADS1 with other floral homeotic genes in regulating flower development remains largely elusive. In this work, we studied the genetic interactions of OsMADS1 with B-, C-, and D-class genes along with physical interactions among their proteins. We show that the physical and genetic interactions between OsMADS1 and OsMADS3 are essential for floral meristem activity maintenance and organ identity specification; while OsMADS1 physically and genetically interacts with OsMADS58 in regulating floral meristem determinacy and suppressing spikelet meristem reversion. We provided important genetic evidence to support the neofunctionalization of two rice C-class genes (OsMADS3 and OsMADS58) during flower development. Gene expression profiling and quantitative RT-PCR analyses further revealed that OsMADS1 affects the expression of many genes involved in floral identity and hormone signaling, and chromatin immunoprecipitation (ChIP)-PCR assay further demonstrated that OsMADS17 is a direct target gene of OsMADS1. Taken together, these results reveal that OsMADS1 has diversified regulatory functions in specifying rice floral organ and meristem identity, probably through its genetic and physical interactions with different floral homeotic regulators.
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Affiliation(s)
- Yun Hu
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Wanqi Liang
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Changsong Yin
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Xuelian Yang
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Baozhe Ping
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Anxue Li
- Shanghai Ocean University, Shanghai 201306, China
| | - Ru Jia
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Mingjiao Chen
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Zhijing Luo
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Qiang Cai
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China
| | - Xiangxiang Zhao
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huaian 223300, China
| | - Dabing Zhang
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China; School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA 5064, Australia
| | - Zheng Yuan
- State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 20040, China.
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Li X, Fan T, Song J, Sun W, Xia K, Liao J, Zhang M. Functional conservation and divergence of four ginger AP1/AGL9 MADS-box genes revealed by analysis of their expression and protein-protein interaction, and ectopic expression of AhFUL gene in Arabidopsis. PLoS One 2014; 9:e114134. [PMID: 25461565 PMCID: PMC4252096 DOI: 10.1371/journal.pone.0114134] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 11/03/2014] [Indexed: 11/28/2022] Open
Abstract
Alpinia genus are known generally as ginger-lilies for showy flowers in the ginger family, Zingiberaceae, and their floral morphology diverges from typical monocotyledon flowers. However, little is known about the functions of ginger MADS-box genes in floral identity. In this study, four AP1/AGL9 MADS-box genes were cloned from Alpinia hainanensis, and protein-protein interactions (PPIs) and roles of the four genes in floral homeotic conversion and in floral evolution are surveyed for the first time. AhFUL is clustered to the AP1 lineage, AhSEP4 and AhSEP3b to the SEP lineage, and AhAGL6-like to the AGL6 lineage. The four genes showed conserved and divergent expression patterns, and their encoded proteins were localized in the nucleus. Seven combinations of PPI (AhFUL-AhSEP4, AhFUL-AhAGL6-like, AhFUL-AhSEP3b, AhSEP4-AhAGL6-like, AhSEP4-AhSEP3b, AhAGL6-like-AhSEP3b, and AhSEP3b-AhSEP3b) were detected, and the PPI patterns in the AP1/AGL9 lineage revealed that five of the 10 possible combinations are conserved and three are variable, while conclusions cannot yet be made regarding the other two. Ectopic expression of AhFUL in Arabidopsis thaliana led to early flowering and floral organ homeotic conversion to sepal-like or leaf-like. Therefore, we conclude that the four A. hainanensis AP1/AGL9 genes show functional conservation and divergence in the floral identity from other MADS-box genes.
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Affiliation(s)
- Xiumei Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tian Fan
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Juanjuan Song
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Wei Sun
- Institute of Chinese Materia Medica, Chinese Academy of Chinese Medical Science, Beijing, 100700, China
| | - Kuaifei Xia
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Jingping Liao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Mingyong Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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Shih MC, Chou ML, Yue JJ, Hsu CT, Chang WJ, Ko SS, Liao DC, Huang YT, Chen JJW, Yuan JL, Gu XP, Lin CS. BeMADS1 is a key to delivery MADSs into nucleus in reproductive tissues-De novo characterization of Bambusa edulis transcriptome and study of MADS genes in bamboo floral development. BMC PLANT BIOLOGY 2014; 14:179. [PMID: 24989161 PMCID: PMC4087239 DOI: 10.1186/1471-2229-14-179] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 06/19/2014] [Indexed: 05/09/2023]
Abstract
BACKGROUND The bamboo Bambusa edulis has a long juvenile phase in situ, but can be induced to flower during in vitro tissue culture, providing a readily available source of material for studies on reproductive biology and flowering. In this report, in vitro-derived reproductive and vegetative materials of B. edulis were harvested and used to generate transcriptome databases by use of two sequencing platforms: Illumina and 454. Combination of the two datasets resulted in high transcriptome quality and increased length of the sequence reads. In plants, many MADS genes control flower development, and the ABCDE model has been developed to explain how the genes function together to create the different whorls within a flower. RESULTS As a case study, published floral development-related OsMADS proteins from rice were used to search the B. edulis transcriptome datasets, identifying 16 B. edulis MADS (BeMADS). The BeMADS gene expression levels were determined qRT-PCR and in situ hybridization. Most BeMADS genes were highly expressed in flowers, with the exception of BeMADS34. The expression patterns of these genes were most similar to the rice homologs, except BeMADS18 and BeMADS34, and were highly similar to the floral development ABCDE model in rice. Transient expression of MADS-GFP proteins showed that only BeMADS1 entered leaf nucleus. BeMADS18, BeMADS4, and BeMADS1 were located in the lemma nucleus. When co-transformed with BeMADS1, BeMADS15, 16, 13, 21, 6, and 7 translocated to nucleus in lemmas, indicating that BeMADS1 is a key factor for subcellular localization of other BeMADS. CONCLUSION Our study provides abundant B. edulis transcriptome data and offers comprehensive sequence resources. The results, molecular materials and overall strategy reported here can be used for future gene identification and for further reproductive studies in the economically important crop of bamboo.
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Affiliation(s)
- Ming-Che Shih
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Ming-Lun Chou
- Department of Life Sciences, Tzu Chi University, Hualien, Taiwan
| | - Jin-Jun Yue
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, China
| | - Cheng-Tran Hsu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Wan-Jung Chang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Swee-Suak Ko
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - De-Chih Liao
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-yi, Taiwan
| | - Jeremy JW Chen
- Institute of Biomedical Sciences, National Chung-Hsing University, Taichung, Taiwan
| | - Jin-Ling Yuan
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, China
| | - Xiao-Ping Gu
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, China
| | - Choun-Sea Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
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12
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Durbak AR, Phillips KA, Pike S, O'Neill MA, Mares J, Gallavotti A, Malcomber ST, Gassmann W, McSteen P. Transport of boron by the tassel-less1 aquaporin is critical for vegetative and reproductive development in maize. THE PLANT CELL 2014; 26:2978-95. [PMID: 25035406 PMCID: PMC4145126 DOI: 10.1105/tpc.114.125898] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/11/2014] [Accepted: 06/23/2014] [Indexed: 05/18/2023]
Abstract
The element boron (B) is an essential plant micronutrient, and B deficiency results in significant crop losses worldwide. The maize (Zea mays) tassel-less1 (tls1) mutant has defects in vegetative and inflorescence development, comparable to the effects of B deficiency. Positional cloning revealed that tls1 encodes a protein in the aquaporin family co-orthologous to known B channel proteins in other species. Transport assays show that the TLS1 protein facilitates the movement of B and water into Xenopus laevis oocytes. B content is reduced in tls1 mutants, and application of B rescues the mutant phenotype, indicating that the TLS1 protein facilitates the movement of B in planta. B is required to cross-link the pectic polysaccharide rhamnogalacturonan II (RG-II) in the cell wall, and the percentage of RG-II dimers is reduced in tls1 inflorescences, indicating that the defects may result from altered cell wall properties. Plants heterozygous for both tls1 and rotten ear (rte), the proposed B efflux transporter, exhibit a dosage-dependent defect in inflorescence development under B-limited conditions, indicating that both TLS1 and RTE function in the same biological processes. Together, our data provide evidence that TLS1 is a B transport facilitator in maize, highlighting the importance of B homeostasis in meristem function.
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Affiliation(s)
- Amanda R Durbak
- Division of Biological Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211
| | - Kimberly A Phillips
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Sharon Pike
- Division of Plant Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211
| | - Malcolm A O'Neill
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Jonathan Mares
- Department of Biological Sciences, California State University, Long Beach, California 90840
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Simon T Malcomber
- Department of Biological Sciences, California State University, Long Beach, California 90840
| | - Walter Gassmann
- Division of Plant Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211
| | - Paula McSteen
- Division of Biological Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri 65211
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13
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Lin X, Wu F, Du X, Shi X, Liu Y, Liu S, Hu Y, Theißen G, Meng Z. The pleiotropic SEPALLATA-like gene OsMADS34 reveals that the 'empty glumes' of rice (Oryza sativa) spikelets are in fact rudimentary lemmas. THE NEW PHYTOLOGIST 2014; 202:689-702. [PMID: 24372518 DOI: 10.1111/nph.12657] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 11/22/2013] [Indexed: 05/07/2023]
Abstract
The single floret of the rice (Oryza sativa) spikelet is subtended by a pair of enigmatic organs usually termed 'empty glumes' or 'sterile lemmas'. As the identity of these organs remains essentially unknown, we refer to them as 'organs of unknown identity' (OUIs). Here we present a novel mutant of the rice SEPALLATA-like gene OsMADS34 which develops, in addition to disorganized branches and sterile seeds, elongated OUIs. The function and evolution of OsMADS34 were studied. Morphological and molecular markers indicate that the elongated OUIs have adopted lemma identity. Evolutionary analyses show that the ancestral genes of the OsM34 subclade evolved under positive selection, and that three specific motifs occur in the C-terminal region of proteins in the OsM34 subclade. Yeast two-hybrid assays revealed that the C-terminal region of OsMADS34 plays a crucial role in mediating protein interactions. Sequence analyses for the wild rice Oryza grandiglumis which has elongated OUIs revealed the association of OsMADS34 functionality with OUI identity. Our findings support the hypothesis that OUIs originated from the lemmas of degenerate florets under the negative control of OsMADS34. As OUIs neither are homologues to glumes nor have the identity of lemmas any more, but originated from these organs, we suggest calling them 'rudimentary lemmas'.
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Affiliation(s)
- Xuelei Lin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Feng Wu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiaoqiu Du
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiaowei Shi
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yuan Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Shujun Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yuxin Hu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Günter Theißen
- Department of Genetics, Friedrich Schiller University Jena, D-07743, Jena, Germany
| | - Zheng Meng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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14
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Bartlett ME, Whipple CJ. Protein change in plant evolution: tracing one thread connecting molecular and phenotypic diversity. FRONTIERS IN PLANT SCIENCE 2013; 4:382. [PMID: 24124420 PMCID: PMC3794426 DOI: 10.3389/fpls.2013.00382] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Accepted: 09/06/2013] [Indexed: 05/29/2023]
Abstract
Proteins change over the course of evolutionary time. New protein-coding genes and gene families emerge and diversify, ultimately affecting an organism's phenotype and interactions with its environment. Here we survey the range of structural protein change observed in plants and review the role these changes have had in the evolution of plant form and function. Verified examples tying evolutionary change in protein structure to phenotypic change remain scarce. We will review the existing examples, as well as draw from investigations into domestication, and quantitative trait locus (QTL) cloning studies searching for the molecular underpinnings of natural variation. The evolutionary significance of many cloned QTL has not been assessed, but all the examples identified so far have begun to reveal the extent of protein structural diversity tolerated in natural systems. This molecular (and phenotypic) diversity could come to represent part of natural selection's source material in the adaptive evolution of novel traits. Protein structure and function can change in many distinct ways, but the changes we identified in studies of natural diversity and protein evolution were predicted to fall primarily into one of six categories: altered active and binding sites; altered protein-protein interactions; altered domain content; altered activity as an activator or repressor; altered protein stability; and hypomorphic and hypermorphic alleles. There was also variability in the evolutionary scale at which particular changes were observed. Some changes were detected at both micro- and macroevolutionary timescales, while others were observed primarily at deep or shallow phylogenetic levels. This variation might be used to determine the trajectory of future investigations in structural molecular evolution.
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Affiliation(s)
| | - Clinton J. Whipple
- *Correspondence: Clinton J. Whipple, Biology Department, Brigham Young University, 401 WIDB, Provo, UT 84602, USA e-mail:
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15
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Murai K. Homeotic Genes and the ABCDE Model for Floral Organ Formation in Wheat. PLANTS 2013; 2:379-95. [PMID: 27137382 PMCID: PMC4844379 DOI: 10.3390/plants2030379] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 06/02/2013] [Accepted: 06/18/2013] [Indexed: 12/19/2022]
Abstract
Floral organ formation has been the subject of intensive study for over 20 years, particularly in the model dicot species Arabidopsis thaliana. These studies have led to the establishment of a general model for the development of floral organs in higher plants, the so-called ABCDE model, in which floral whorl-specific combinations of class A, B, C, D, or E genes specify floral organ identity. In Arabidopsis, class A, B, C, D, E genes encode MADS-box transcription factors except for the class A gene APETALA2. Mutation of these genes induces floral organ homeosis. In this review, I focus on the roles of these homeotic genes in bread wheat (Triticum aestivum), particularly with respect to the ABCDE model. Pistillody, the homeotic transformation of stamens into pistil-like structures, occurs in cytoplasmic substitution (alloplasmic) wheat lines that have the cytoplasm of the related wild species Aegilops crassa. This phenomenon is a valuable tool for analysis of the wheat ABCDE model. Using an alloplasmic line, the wheat ortholog of DROOPING LEAF (TaDL), a member of the YABBY gene family, has been shown to regulate pistil specification. Here, I describe the current understanding of the ABCDE model for floral organ formation in wheat.
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Affiliation(s)
- Koji Murai
- Department of Bioscience, Fukui Prefectural University, 4-1-1 Matsuoka-kenjojima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan.
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16
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Tran F, Penniket C, Patel RV, Provart NJ, Laroche A, Rowland O, Robert LS. Developmental transcriptional profiling reveals key insights into Triticeae reproductive development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 74:971-88. [PMID: 23581995 DOI: 10.1111/tpj.12206] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 03/15/2013] [Accepted: 03/22/2013] [Indexed: 05/25/2023]
Abstract
Despite their importance, there remains a paucity of large-scale gene expression-based studies of reproductive development in species belonging to the Triticeae. As a first step to address this deficiency, a gene expression atlas of triticale reproductive development was generated using the 55K Affymetrix GeneChip(®) wheat genome array. The global transcriptional profiles of the anther/pollen, ovary and stigma were analyzed at concurrent developmental stages, and co-expressed as well as preferentially expressed genes were identified. Data analysis revealed both novel and conserved regulatory factors underlying Triticeae floral development and function. This comprehensive resource rests upon detailed gene annotations, and the expression profiles are readily accessible via a web browser.
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Affiliation(s)
- Frances Tran
- Agriculture and Agri-Food Canada, Eastern Cereal and Oilseed Research Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada
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