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Paraiso F, Lin H, Li C, Woods DP, Lan T, Tumelty C, Debernardi JM, Joe A, Dubcovsky J. LEAFY and WAPO1 jointly regulate spikelet number per spike and floret development in wheat. Development 2024; 151:dev202803. [PMID: 39082949 PMCID: PMC11317094 DOI: 10.1242/dev.202803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 06/24/2024] [Indexed: 08/13/2024]
Abstract
In wheat, the transition of the inflorescence meristem to a terminal spikelet (IM→TS) determines the spikelet number per spike (SNS), an important yield component. In this study, we demonstrate that the plant-specific transcription factor LEAFY (LFY) physically and genetically interacts with WHEAT ORTHOLOG OF APO1 (WAPO1) to regulate SNS and floret development. Loss-of-function mutations in either or both genes result in significant and similar reductions in SNS, as a result of a reduction in the rate of spikelet meristem formation per day. SNS is also modulated by significant genetic interactions between LFY and the SQUAMOSA MADS-box genes VRN1 and FUL2, which promote the IM→TS transition. Single-molecule fluorescence in situ hybridization revealed a downregulation of LFY and upregulation of the SQUAMOSA MADS-box genes in the distal part of the developing spike during the IM→TS transition, supporting their opposite roles in the regulation of SNS in wheat. Concurrently, the overlap of LFY and WAPO1 transcription domains in the developing spikelets contributes to normal floret development. Understanding the genetic network regulating SNS is a necessary first step to engineer this important agronomic trait.
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Affiliation(s)
- Francine Paraiso
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Huiqiong Lin
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Chengxia Li
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Daniel P. Woods
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Tianyu Lan
- Institute for Plant Genetics, Heinrich Heine University, Düsseldorf 40225, Germany
| | - Connor Tumelty
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Juan M. Debernardi
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Anna Joe
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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Shivaprasad KM, Dikshit HK, Mishra GP, Sinha SK, Aski M, Kohli M, Mishra DC, Singh AK, Gupta S, Singh A, Tripathi K, Kumar RR, Kumar A, Jha GK, Kumar S, Varshney RK. Delineation of loci governing an extra-earliness trait in lentil (Lens culinaris Medik.) using the QTL-Seq approach. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38923713 DOI: 10.1111/pbi.14415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 04/18/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024]
Abstract
Developing early maturing lentil has the potential to minimize yield losses, mainly during terminal drought. Whole-genome resequencing (WGRS) based QTL-seq identified the loci governing earliness in lentil. The genetic analysis for maturity duration provided a good fit to 3:1 segregation (F2), indicating earliness as a recessive trait. WGRS of Globe Mutant (late parent), late-flowering, and early-flowering bulks (from RILs) has generated 1124.57, 1052.24 million raw and clean reads, respectively. The QTL-Seq identified three QTLs (LcqDTF3.1, LcqDTF3.2, and LcqDTF3.3) on chromosome 3 having 246244 SNPs and 15577 insertions/deletions (InDels) and 13 flowering pathway genes. Of these, 11 exhibited sequence variations between bulks and validation (qPCR) revealed a significant difference in the expression of nine candidate genes (LcGA20oxG, LcFRI, LcLFY, LcSPL13a, Lcu.2RBY.3g060720, Lcu.2RBY.3g062540, Lcu.2RBY.3g062760, LcELF3a, and LcEMF1). Interestingly, the LcELF3a gene showed significantly higher expression in late-flowering genotype and exhibited substantial involvement in promoting lateness. Subsequently, an InDel marker (I-SP-383.9; LcELF3a gene) developed from LcqDTF3.2 QTL region showed 82.35% PVE (phenotypic variation explained) for earliness. The cloning, sequencing, and comparative analysis of the LcELF3a gene from both parents revealed 23 SNPs and InDels. Interestingly, a 52 bp deletion was recorded in the LcELF3a gene of L4775, predicted to cause premature termination of protein synthesis after 4 missense amino acids beyond the 351st amino acid due to the frameshift during translation. The identified InDel marker holds significant potential for breeding early maturing lentil varieties.
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Affiliation(s)
- Kumbarahally Murthigowda Shivaprasad
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
- Indian Council of Forestry Research and Education (ICFRE)-Institute of Forest Biodiversity, Hyderabad, India
| | - Harsh K Dikshit
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Gyan Prakash Mishra
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Subodh Kumar Sinha
- Indian Council of Agricultural Research (ICAR)-National Institute for Plant Biotechnology, New Delhi, India
| | - Muraleedhar Aski
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Manju Kohli
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Dwijesh C Mishra
- Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Amit Kumar Singh
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, New Delhi, India
| | - Soma Gupta
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Akanksha Singh
- South Asia and China Program, International Center for Agricultural Research in the Dry Areas, National Agriculture Science Complex, New Delhi, India
| | - Kuldeep Tripathi
- Germplasm Evaluation Division, National Bureau of Plant Genetic Resources, New Delhi, India
| | - Ranjeet Ranjan Kumar
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, India
| | - Atul Kumar
- Division of Seed Science and Technology, Indian Agricultural Research Institute, New Delhi, India
| | - Girish Kumar Jha
- Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Shiv Kumar
- South Asia and China Program, International Center for Agricultural Research in the Dry Areas, National Agriculture Science Complex, New Delhi, India
| | - Rajeev K Varshney
- Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
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3
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Stevenson DW, Ramakrishnan S, de Santis Alves C, Coelho LA, Kramer M, Goodwin S, Ramos OM, Eshel G, Sondervan VM, Frangos S, Zumajo-Cardona C, Jenike K, Ou S, Wang X, Lee YP, Loke S, Rossetto M, McPherson H, Nigris S, Moschin S, Little DP, Katari MS, Varala K, Kolokotronis SO, Ambrose B, Croft LJ, Coruzzi GM, Schatz M, McCombie WR, Martienssen RA. The genome of the Wollemi pine, a critically endangered "living fossil" unchanged since the Cretaceous, reveals extensive ancient transposon activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.24.554647. [PMID: 37662366 PMCID: PMC10473749 DOI: 10.1101/2023.08.24.554647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
We present the genome of the living fossil, Wollemia nobilis, a southern hemisphere conifer morphologically unchanged since the Cretaceous. Presumed extinct until rediscovery in 1994, the Wollemi pine is critically endangered with less than 60 wild adults threatened by intensifying bushfires in the Blue Mountains of Australia. The 12 Gb genome is among the most contiguous large plant genomes assembled, with extremely low heterozygosity and unusual abundance of DNA transposons. Reduced representation and genome re-sequencing of individuals confirms a relictual population since the last major glacial/drying period in Australia, 120 ky BP. Small RNA and methylome sequencing reveal conservation of ancient silencing mechanisms despite the presence of thousands of active and abundant transposons, including some transferred horizontally to conifers from arthropods in the Jurassic. A retrotransposon burst 8-6 my BP coincided with population decline, possibly as an adaptation enhancing epigenetic diversity. Wollemia, like other conifers, is susceptible to Phytophthora, and a suite of defense genes, similar to those in loblolly pine, are targeted for silencing by sRNAs in leaves. The genome provides insight into the earliest seed plants, while enabling conservation efforts.
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Affiliation(s)
| | | | - Cristiane de Santis Alves
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Laís Araujo Coelho
- Department of Epidemiology and Biostatistics, School of Public Health; Institute for Genomics in Health; Division of Infectious Diseases, Department of Medicine, and Department of Cell Biology, College of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY 11203-2098, USA
| | - Melissa Kramer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | | | - Gil Eshel
- Center for Genomics & Systems Biology, New York University, New York, NY 10003, USA
| | | | - Samantha Frangos
- Center for Genomics & Systems Biology, New York University, New York, NY 10003, USA
| | | | - Katherine Jenike
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Shujun Ou
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Xiaojin Wang
- Purdue University, 610 Purdue Mall, West Lafayette, IN 47907, USA
| | - Yin Peng Lee
- Charles River Laboratories Australia, 17-19 Hi-Tech Ct, Kilsyth VIC 3137, Australia
| | - Stella Loke
- Charles River Laboratories Australia, 17-19 Hi-Tech Ct, Kilsyth VIC 3137, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Royal Botanic Garden Sydney, Sydney, NSW 2000, Australia
| | - Hannah McPherson
- National Herbarium of New South Wales, Australian Botanic Garden, Mount Annan, NSW 2567, Australia
| | - Sebastiano Nigris
- Dipartimento di Biologia, Università degli studi di Padova, via U. Bassi 58/B, 35131 Padova, Italy; and Botanical Garden, Università degli studi di Padova, via Orto Botanico 15, 35123 Padova, Italy
| | - Silvia Moschin
- Dipartimento di Biologia, Università degli studi di Padova, via U. Bassi 58/B, 35131 Padova, Italy; and Botanical Garden, Università degli studi di Padova, via Orto Botanico 15, 35123 Padova, Italy
| | - Damon P. Little
- The New York Botanical Garden, 2900 Southern Boulevard, Bronx, NY 10458, USA
| | - Manpreet S. Katari
- Center for Genomics & Systems Biology, New York University, New York, NY 10003, USA
| | - Kranthi Varala
- Purdue University, 610 Purdue Mall, West Lafayette, IN 47907, USA
| | - Sergios-Orestis Kolokotronis
- Department of Epidemiology and Biostatistics, School of Public Health; Institute for Genomics in Health; Division of Infectious Diseases, Department of Medicine, and Department of Cell Biology, College of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY 11203-2098, USA
| | - Barbara Ambrose
- The New York Botanical Garden, 2900 Southern Boulevard, Bronx, NY 10458, USA
| | - Larry J. Croft
- School of Medicine, Deakin University, Waurn Ponds, Victoria 3216, Australia
| | - Gloria M. Coruzzi
- Center for Genomics & Systems Biology, New York University, New York, NY 10003, USA
| | - Michael Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | | | - Robert A. Martienssen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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Cong L, Ling H, Liu S, Wang A, Zhai R, Yang C, Wang Z, Xu L. 'Yunnan' quince rootstock promoted flower bud formation of 'Abbé Fetel' pear by altering hormone levels and PbAGL9 expression. JOURNAL OF PLANT PHYSIOLOGY 2023; 282:153924. [PMID: 36805518 DOI: 10.1016/j.jplph.2023.153924] [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: 10/23/2022] [Revised: 12/21/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
Flower busd formation is an important plant growth process. It has been reported that dwarfing rootstocks can significantly affect the flower bud formation of scions. In this study, we found the dwarfing rootstock 'Yunnan' quince could significantly increase the flowering rate of 'Abbé Fetel' pear scions. The RNA-sequencing data revealed significant changes in the expression of genes related to hormone pathways. Furthermore, hormone analyses indicated that 'Yunnan' quince significantly decreased the GA3 content and increased the cytokinin/auxin ratio in 'Abbé Fetel' pear apical buds. The hormone contents were consistent with the RNA-sequencing data. Moreover, we found the flower development-related genes PbAGL9 and PbCAL-A1 were significantly upregulated and PbTFL1 was significantly downregulated in 'Abbé Fetel'/'Yunnan' quince apical buds. To further clarify the relationship between hormones and flowering-related genes, a hormone response assay was carried out. We found the expression levels of PbCAl-A1, PbTFL1 and PbAGL9 were regulated by hormones including GA3, CPPU and NAA. Y1H and dual-luciferase assays indicated that PbAGL9 significantly decreased the promoter activity of PbTFL1. In summary, 'Yunnan' quince upregulated PbCAL-A1 and PbAGL9, and downregulated PbTFL1 expression by decreasing the GA3 content and increasing the cytokinin/auxin ratio in 'Abbé Fetel' pear apical buds. Additionally, 'Yunnan' quince down-regulate PbTFL1 by upregulating the expression of PbAGL9, and eventually promoted floral induction in 'Abbé Fetel' pear.
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Affiliation(s)
- Liu Cong
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Hutian Ling
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Shanshan Liu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Azheng Wang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Rui Zhai
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Chengquan Yang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Zhigang Wang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
| | - Lingfei Xu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi Province, 712100, China.
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5
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Strable J, Unger-Wallace E, Aragón Raygoza A, Briggs S, Vollbrecht E. Interspecies transfer of RAMOSA1 orthologs and promoter cis sequences impacts maize inflorescence architecture. PLANT PHYSIOLOGY 2023; 191:1084-1101. [PMID: 36508348 PMCID: PMC9922432 DOI: 10.1093/plphys/kiac559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 06/26/2022] [Indexed: 06/18/2023]
Abstract
Grass inflorescences support floral structures that each bear a single grain, where variation in branch architecture directly impacts yield. The maize (Zea mays) RAMOSA1 (ZmRA1) transcription factor acts as a key regulator of inflorescence development by imposing branch meristem determinacy. Here, we show RA1 transcripts accumulate in boundary domains adjacent to spikelet meristems in sorghum (Sorghum bicolor, Sb) and green millet (Setaria viridis, Sv) inflorescences similar as in the developing maize tassel and ear. To evaluate the functional conservation of syntenic RA1 orthologs and promoter cis sequences in maize, sorghum, and setaria, we utilized interspecies gene transfer and assayed genetic complementation in a common inbred background by quantifying recovery of normal branching in highly ramified ra1-R mutants. A ZmRA1 transgene that includes endogenous upstream and downstream flanking sequences recovered normal tassel and ear branching in ra1-R. Interspecies expression of two transgene variants of the SbRA1 locus, modeled as the entire endogenous tandem duplication or just the nonframeshifted downstream copy, complemented ra1-R branching defects and induced unusual fasciation and branch patterns. The SvRA1 locus lacks conserved, upstream noncoding cis sequences found in maize and sorghum; interspecies expression of a SvRA1 transgene did not or only partially recovered normal inflorescence forms. Driving expression of the SvRA1 coding region by the ZmRA1 upstream region, however, recovered normal inflorescence morphology in ra1-R. These data leveraging interspecies gene transfer suggest that cis-encoded temporal regulation of RA1 expression is a key factor in modulating branch meristem determinacy that ultimately impacts grass inflorescence architecture.
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6
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Wu B, Zhang X, Hu K, Zheng H, Zhang S, Liu X, Ma M, Zhao H. Two alternative splicing variants of a wheat gene TaNAK1, TaNAK1.1 and TaNAK1.2, differentially regulate flowering time and plant architecture leading to differences in seed yield of transgenic Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:1014176. [PMID: 36531344 PMCID: PMC9751850 DOI: 10.3389/fpls.2022.1014176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
In wheat production, appropriate flowering time and ideal plant architecture are the prerequisites for high grain yield. Alternative splicing (AS) is a vital process that regulates gene expression at the post-transcriptional level, and AS events in wheat have been found to be closely related to grain-related traits and abiotic stress tolerance. However, AS events and their biological roles in regulating flowering time and plant architecture in wheat remain unclear. In this study, we report that TaNAK1 undergoes AS, producing three splicing variants. Molecular characterization of TaNAK1 and its splicing variants demonstrated that all three protein isoforms have a conserved NB-ARC domain and a protein kinase domain, but the positions of these two domains and the length of the protein kinase domains are different among them, implying that they may have different three-dimensional structures and therefore have different functions. Further investigations showed that the two splicing variants of TaNAK1, TaNAK1.1 and TaNAK1.2, exhibited different expression patterns during wheat growth and development, while the other one, TaNAK1.3, was not detected. Subcellular localization demonstrated that TaNAK1.1 was mainly localized in the cytoplasm, while TaNAK1.2 was localized in the nucleus and cytoplasm. Both TaNAK1.1 and TaNAK1.2 exhibit protein kinase activity in vitro. Ectopic expression of TaNAK1.1 and TaNAK1.2 in Arabidopsis demonstrated that these two splicing variants play opposite roles in regulating flowering time and plant architecture, resulting in different seed yields. TaNAK1.2 positive regulates the transition from vegetative to reproductive growth, plant height, branching number, seed size, and seed yield of Arabidopsis, while TaNAK1.1 negatively regulates these traits. Our findings provide new gene resource for regulating flowering time and plant architecture in crop breeding for high grain yield.
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Affiliation(s)
| | | | | | | | | | | | - Meng Ma
- *Correspondence: Huixian Zhao, ; Meng Ma,
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Miao Y, Xun Q, Taji T, Tanaka K, Yasuno N, Ding C, Kyozuka J. ABERRANT PANICLE ORGANIZATION2 controls multiple steps in panicle formation through common direct-target genes. PLANT PHYSIOLOGY 2022; 189:2210-2226. [PMID: 35556145 PMCID: PMC9342985 DOI: 10.1093/plphys/kiac216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/18/2022] [Indexed: 05/15/2023]
Abstract
At the transition from vegetative to reproductive growth in rice (Oryza sativa), a developmental program change occurs, resulting in panicle (rice inflorescence) formation. The initial event of the transition is the change of the shoot apical meristem to an inflorescence meristem (IM), accompanied by a rapid increase in the meristem size. Suppression of leaf growth also occurs, resulting in the formation of bracts. The IM generates branch meristems (BMs), indeterminate meristems that reiteratively generate next-order meristems. All meristems eventually acquire a determinate spikelet meristem identity and terminate after producing a floret. ABERRANT PANICLE ORGANIZATION2 (APO2) is the rice ortholog of Arabidopsis (Arabidopsis thaliana) LEAFY (LFY), a plant-specific transcription factor (TF). APO2 is a positive regulator of panicle branch formation. Here, we show that APO2 is also required to increase the meristem size of the IM and suppress bract outgrowth. We identified genes directly and indirectly regulated by APO2 and identified APO2-binding sites. These analyses showed that APO2 directly controls known regulators of panicle development, including SQUAMOSA PROMOTER BINDING PROTEIN LIKE14 and NECK LEAF1. Furthermore, we revealed that a set of genes act as downstream regulators of APO2 in controlling meristem cell proliferation during reproductive transition, bract suppression, and panicle branch formation. Our findings indicate that APO2 acts as a master regulator of rice panicle development by regulating multiple steps in the reproductive transition through directly controlling a set of genes.
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Affiliation(s)
- Yiling Miao
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Qian Xun
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Teruaki Taji
- Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Keisuke Tanaka
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Naoko Yasuno
- Graduate School of Life Sciences, University of Tokyo, Tokyo 113-8654, Japan
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8
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Sidhu GS, Conner JA, Ozias-Akins P. Controlled Induction of Parthenogenesis in Transgenic Rice via Post-translational Activation of PsASGR-BBML. FRONTIERS IN PLANT SCIENCE 2022; 13:925467. [PMID: 35873991 PMCID: PMC9305695 DOI: 10.3389/fpls.2022.925467] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Modern plant breeding programs rely heavily on the generation of homozygous lines, with the traditional process requiring the inbreeding of a heterozygous cross for five to six generations. Doubled haploid (DH) technology, a process of generating haploid plants from an initial heterozygote, followed by chromosome doubling, reduces the process to two generations. Currently established in vitro methods of haploid induction include androgenesis and gynogenesis, while in vivo methods are based on uni-parental genome elimination. Parthenogenesis, embryogenesis from unfertilized egg cells, presents another potential method of haploid induction. PsASGR-BABY BOOM-like, an AP2 transcription factor, induces parthenogenesis in a natural apomictic species, Pennisetum squamulatum (Cenchrus squamulatus) and PsASGR-BBML transgenes promote parthenogenesis in several crop plants, including rice, maize, and pearl millet. The dominant nature of PsASGR-BBML transgenes impedes their use in DH technology. Using a glucocorticoid-based post-translational regulation system and watering with a 100 μM DEX solution before anthesis, PsASGR-BBML can be regulated at the flowering stage to promote parthenogenesis. Conditional expression presents a novel opportunity to use parthenogenetic genes in DH production technology and to elucidate the molecular mechanism underlying parthenogenetic embryogenesis.
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Affiliation(s)
- Gurjot Singh Sidhu
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, United States
| | - Joann A. Conner
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, United States
- Department of Horticulture, University of Georgia, Tifton, GA, United States
| | - Peggy Ozias-Akins
- Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, United States
- Department of Horticulture, University of Georgia, Tifton, GA, United States
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9
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Shimada S, Yanagawa Y, Munesada T, Horii Y, Kuriyama T, Kawashima M, Kondou Y, Yoshizumi T, Mitsuda N, Ohme-Takagi M, Makita Y, Matsui M. A collection of inducible transcription factor-glucocorticoid receptor fusion lines for functional analyses in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:595-607. [PMID: 35510416 DOI: 10.1111/tpj.15796] [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: 08/24/2021] [Revised: 04/12/2022] [Accepted: 05/01/2022] [Indexed: 06/14/2023]
Abstract
Arabidopsis possesses approximately 2000 transcription factors (TFs) in its genome. They play pivotal roles in various biological processes but analysis of their function has been hampered by the overlapping nature of their activities. To uncover clues to their function, we generated inducible TF lines using glucocorticoid receptor (GR) fusion techniques in Arabidopsis. These TF-GR lines each express one of 1255 TFs as a fusion with the GR gene. An average 14 lines of T2 transgenic TF-GR lines were generated for each TF to monitor their function. To evaluate these transcription lines, we induced the TF-GR lines of phytochrome-interacting factor 4, which controls photomorphogenesis, with synthetic glucocorticoid dexamethasone. These phytochrome-interacting factor 4-GR lines showed the phenotype described in a previous report. We performed screening of the other TF-GR lines for TFs involved in light signaling under blue and far-red light conditions and identified 13 novel TF candidates. Among these, we found two lines showing higher anthocyanin accumulation under light conditions and we examined the regulating genes. These results indicate that the TF-GR lines can be used to dissect functionally redundant genes in plants and demonstrate that the TF-GR line collection can be used as an effective tool for functional analysis of TFs.
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Affiliation(s)
- Setsuko Shimada
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Yuki Yanagawa
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, 271-8510, Japan
| | - Takachika Munesada
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- Graduate School of NanoBioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, 236-0027, Japan
| | - Yoko Horii
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Tomoko Kuriyama
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Mika Kawashima
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
| | - Youichi Kondou
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- Department of Biosciences, Kanto Gakuin University College of Science and Engineering, Yokohama, 236-8501, Japan
| | - Takeshi Yoshizumi
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- Faculty of Agriculture, Takasaki University of Health and Welfare, 54 Nakaorui-machi, Takasaki, Gunma, 370-0033, Japan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 4, Higashi 1-1-1, Tsukuba, 305-8562, Japan
| | - Masaru Ohme-Takagi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 4, Higashi 1-1-1, Tsukuba, 305-8562, Japan
- Graduate School of Science and Engineering, Saitama University, Saitama, 338-8570, Japan
| | - Yuko Makita
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
- Graduate School of Engineering, Maebashi Institute of Technology, 460-1, Kamisadori, Maebashi City, Gunma, 371-0816, Japan
| | - Minami Matsui
- Synthetic Genomics Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan
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10
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Abstract
BACKGROUND The LEAFY (LFY) transcription factors are present in algae and across land plants. The available expression and functional data of these genes in embryophytes suggest that LFY genes control a plethora of processes including the first zygotic cell division in bryophytes, shoot cell divisions of the gametophyte and sporophyte in ferns, cone differentiation in gymnosperms and floral meristem identity in flowering plants. However, their putative plesiomorphic role in plant reproductive transition in vascular plants remains untested. RESULTS We perform Maximum Likelihood (ML) phylogenetic analyses for the LFY gene lineage in embryophytes with expanded sampling in lycophytes and ferns. We recover the previously identified seed plant duplication that results in LEAFY and NEEDLY paralogs. In addition, we recover multiple species-specific duplications in ferns and lycophytes and large-scale duplications possibly correlated with the occurrence of whole genome duplication (WGD) events in Equisetales and Salviniales. To test putative roles in diverse ferns and lycophytes we perform LFY expression analyses in Adiantum raddianum, Equisetum giganteum and Selaginella moellendorffii. Our results show that LFY genes are active in vegetative and reproductive tissues, with higher expression in early fertile developmental stages and during sporangia differentiation. CONCLUSIONS Our data point to previously unrecognized roles of LFY genes in sporangia differentiation in lycophytes and ferns and suggests that functions linked to reproductive structure development are not exclusive to seed plant LFY homologs.
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11
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Azpeitia E, Tichtinsky G, Le Masson M, Serrano-Mislata A, Lucas J, Gregis V, Gimenez C, Prunet N, Farcot E, Kater MM, Bradley D, Madueño F, Godin C, Parcy F. Cauliflower fractal forms arise from perturbations of floral gene networks. Science 2021; 373:192-197. [PMID: 34244409 DOI: 10.1126/science.abg5999] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 06/03/2021] [Indexed: 11/02/2022]
Abstract
Throughout development, plant meristems regularly produce organs in defined spiral, opposite, or whorl patterns. Cauliflowers present an unusual organ arrangement with a multitude of spirals nested over a wide range of scales. How such a fractal, self-similar organization emerges from developmental mechanisms has remained elusive. Combining experimental analyses in an Arabidopsis thaliana cauliflower-like mutant with modeling, we found that curd self-similarity arises because the meristems fail to form flowers but keep the "memory" of their transient passage in a floral state. Additional mutations affecting meristem growth can induce the production of conical structures reminiscent of the conspicuous fractal Romanesco shape. This study reveals how fractal-like forms may emerge from the combination of key, defined perturbations of floral developmental programs and growth dynamics.
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Affiliation(s)
- Eugenio Azpeitia
- Laboratoire de Reproduction et Développement des Plantes, Univ. Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, F-69364 Lyon, France
| | - Gabrielle Tichtinsky
- Laboratoire Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, F-38054 Grenoble, France
| | - Marie Le Masson
- Laboratoire Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, F-38054 Grenoble, France
| | - Antonio Serrano-Mislata
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad Politécnica de Valencia (UPV), 46022 Valencia, Spain
| | - Jérémy Lucas
- Laboratoire Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, F-38054 Grenoble, France
| | - Veronica Gregis
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milan, Italy
| | - Carlos Gimenez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad Politécnica de Valencia (UPV), 46022 Valencia, Spain
| | - Nathanaël Prunet
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.,Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Etienne Farcot
- School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Martin M Kater
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milan, Italy
| | - Desmond Bradley
- Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
| | - Francisco Madueño
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC) - Universidad Politécnica de Valencia (UPV), 46022 Valencia, Spain
| | - Christophe Godin
- Laboratoire de Reproduction et Développement des Plantes, Univ. Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, F-69364 Lyon, France.
| | - Francois Parcy
- Laboratoire Physiologie Cellulaire et Végétale, Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, F-38054 Grenoble, France.
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12
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Yamaguchi N. LEAFY, a Pioneer Transcription Factor in Plants: A Mini-Review. FRONTIERS IN PLANT SCIENCE 2021; 12:701406. [PMID: 34290727 PMCID: PMC8287900 DOI: 10.3389/fpls.2021.701406] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/01/2021] [Indexed: 05/25/2023]
Abstract
A subset of eukaryotic transcription factors (TFs) possess the ability to reprogram one cell type into another. Genes important for cellular reprograming are typically located in closed chromatin, which is covered by nucleosomes. Pioneer factors are a special class of TFs that can initially engage their target sites in closed chromatin prior to the engagement with, opening of, or modification of the sites by other factors. Although many pioneer factors are known in animals, a few have been characterized in plants. The TF LEAFY (LFY) acts as a pioneer factor specifying floral fate in Arabidopsis. In response to endogenous and environmental cues, plants produce appropriate floral inducers (florigens). During the vegetative phase, LFY is repressed by the TERMINAL FLOWER 1 (TFL1)-FD complex, which functions as a floral inhibitor, or anti-florigen. The florigen FLOWERING LOCUS T (FT) competes with TFL1 to prevent the binding of the FD TF to the LFY locus. The resulting FT-FD complex functions as a transient stimulus to activate its targets. Once LFY has been transcribed in the appropriate spatiotemporal manner, LFY binds to nucleosomes in closed chromatin regions. Subsequently, LFY opens the chromatin by displacing H1 linker histones and recruiting the SWI/SNF chromatin-remodeling complex. Such local changes permit the binding of other TFs, leading to the expression of the floral meristem identity gene APETALA1. This mini-review describes the latest advances in our understanding of the pioneer TF LFY, providing insight into the establishment of gene expression competence through the shaping of the plant epigenetic landscape.
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13
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Nashima K, Shirasawa K, Ghelfi A, Hirakawa H, Isobe S, Suyama T, Wada T, Kurokura T, Uemachi T, Azuma M, Akutsu M, Kodama M, Nakazawa Y, Namai K. Genome sequence of Hydrangea macrophylla and its application in analysis of the double flower phenotype. DNA Res 2021; 28:5974207. [PMID: 33175097 PMCID: PMC7934569 DOI: 10.1093/dnares/dsaa026] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 11/02/2020] [Indexed: 02/07/2023] Open
Abstract
Owing to its high ornamental value, the double flower phenotype of hydrangea (Hydrangea macrophylla) is one of its most important traits. In this study, genome sequence information was obtained to explore effective DNA markers and the causative genes for double flower production in hydrangea. Single-molecule real-time sequencing data followed by a Hi-C analysis were employed. Two haplotype-phased sequences were obtained from the heterozygous genome of hydrangea. One assembly consisted of 3,779 scaffolds (2.256 Gb in length and N50 of 1.5 Mb), the other also contained 3,779 scaffolds (2.227 Gb in length, and N50 of 1.4 Mb). A total of 36,930 genes were predicted in the sequences, of which 32,205 and 32,222 were found in each haplotype. A pair of 18 pseudomolecules was constructed along with a high-density single-nucleotide polymorphism (SNP) genetic linkage map. Using the genome sequence data, and two F2 populations, the SNPs linked to double flower loci (djo and dsu) were discovered. DNA markers linked to djo and dsu were developed, and these could distinguish the recessive double flower allele for each locus, respectively. The LEAFY gene is a very likely candidate as the causative gene for dsu, since frameshift was specifically observed in the double flower accession with dsu.
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Affiliation(s)
- Kenji Nashima
- Department of Bioagricultural Sciences, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0813Japan
| | - Andrea Ghelfi
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0813Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0813Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0813Japan
| | - Takuro Suyama
- Fukuoka Agriculture and Forestry Research Center, Chikushino, Fukuoka 818-8549, Japan
| | - Takuya Wada
- Fukuoka Agriculture and Forestry Research Center, Chikushino, Fukuoka 818-8549, Japan
| | - Takeshi Kurokura
- Department of Agrobiology and Bioresources, Faculty of Agriculture, Utsunomiya University, Utsunomiya, Tochigi 321-8505, Japan
| | - Tatuya Uemachi
- Department of Biological Resources Management, School of Environmental Science, University of Shiga Prefecture, Hikone, Shiga 522-0057, Japan
| | - Mirai Azuma
- Department of Bioagricultural Sciences, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
| | - Midori Akutsu
- Tochigi Prefectural Agricultural Experimental Station, Utsunomiya, Tochigi 320-0002, Japan
| | - Masaharu Kodama
- Tochigi Prefectural Agricultural Experimental Station, Utsunomiya, Tochigi 320-0002, Japan
| | - Yoshiko Nakazawa
- Tochigi Prefectural Agricultural Experimental Station, Utsunomiya, Tochigi 320-0002, Japan
| | - Kiyoshi Namai
- Tochigi Prefectural Agricultural Experimental Station, Utsunomiya, Tochigi 320-0002, Japan
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14
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Beyond the Genetic Pathways, Flowering Regulation Complexity in Arabidopsis thaliana. Int J Mol Sci 2021; 22:ijms22115716. [PMID: 34071961 PMCID: PMC8198774 DOI: 10.3390/ijms22115716] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/25/2021] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
Flowering is one of the most critical developmental transitions in plants’ life. The irreversible change from the vegetative to the reproductive stage is strictly controlled to ensure the progeny’s success. In Arabidopsis thaliana, seven flowering genetic pathways have been described under specific growth conditions. However, the evidence condensed here suggest that these pathways are tightly interconnected in a complex multilevel regulatory network. In this review, we pursue an integrative approach emphasizing the molecular interactions among the flowering regulatory network components. We also consider that the same regulatory network prevents or induces flowering phase change in response to internal cues modulated by environmental signals. In this sense, we describe how during the vegetative phase of development it is essential to prevent the expression of flowering promoting genes until they are required. Then, we mention flowering regulation under suboptimal growing temperatures, such as those in autumn and winter. We next expose the requirement of endogenous signals in flowering, and finally, the acceleration of this transition by long-day photoperiod and temperature rise signals allowing A. thaliana to bloom in spring and summer seasons. With this approach, we aim to provide an initial systemic view to help the reader integrate this complex developmental process.
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15
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Lai X, Blanc-Mathieu R, GrandVuillemin L, Huang Y, Stigliani A, Lucas J, Thévenon E, Loue-Manifel J, Turchi L, Daher H, Brun-Hernandez E, Vachon G, Latrasse D, Benhamed M, Dumas R, Zubieta C, Parcy F. The LEAFY floral regulator displays pioneer transcription factor properties. MOLECULAR PLANT 2021; 14:829-837. [PMID: 33684542 DOI: 10.1016/j.molp.2021.03.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 01/28/2021] [Accepted: 03/02/2021] [Indexed: 05/23/2023]
Abstract
Pioneer transcription factors (TFs) are a special category of TFs with the capacity to bind to closed chromatin regions in which DNA is wrapped around histones and may be highly methylated. Subsequently, pioneer TFs are able to modify the chromatin state to initiate gene expression. In plants, LEAFY (LFY) is a master floral regulator and has been suggested to act as a pioneer TF in Arabidopsis. Here, we demonstrate that LFY is able to bind both methylated and non-methylated DNA using a combination of in vitro genome-wide binding experiments and structural modeling. Comparisons between regions bound by LFY in vivo and chromatin accessibility data suggest that a subset of LFY bound regions is occupied by nucleosomes. We confirm that LFY is able to bind nucleosomal DNA in vitro using reconstituted nucleosomes. Finally, we show that constitutive LFY expression in seedling tissues is sufficient to induce chromatin accessibility in the LFY direct target genes APETALA1 and AGAMOUS. Taken together, our study suggests that LFY possesses key pioneer TF features that contribute to launching the floral gene expression program.
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Affiliation(s)
- Xuelei Lai
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrs, 38054, Grenoble, France
| | - Romain Blanc-Mathieu
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrs, 38054, Grenoble, France
| | - Loïc GrandVuillemin
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrs, 38054, Grenoble, France
| | - Ying Huang
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Arnaud Stigliani
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrs, 38054, Grenoble, France; The Bioinformatics Centre, Department of Biology and Biotech and Research Innovation Centre, University of Copenhagen, Ole Maaløes Vej 5, DK2200 Copenhagen N, Denmark
| | - Jérémy Lucas
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrs, 38054, Grenoble, France
| | - Emmanuel Thévenon
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrs, 38054, Grenoble, France
| | - Jeanne Loue-Manifel
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrs, 38054, Grenoble, France; Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, 69342 Lyon, France
| | - Laura Turchi
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrs, 38054, Grenoble, France
| | - Hussein Daher
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrs, 38054, Grenoble, France; Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Eugenia Brun-Hernandez
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrs, 38054, Grenoble, France
| | - Gilles Vachon
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrs, 38054, Grenoble, France
| | - David Latrasse
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France; Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 75006 Paris, France
| | - Renaud Dumas
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrs, 38054, Grenoble, France
| | - Chloe Zubieta
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrs, 38054, Grenoble, France
| | - François Parcy
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 17 avenue des martyrs, 38054, Grenoble, France.
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16
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Chai L, Feng B, Liu X, Jiang L, Yuan S, Zhang Z, Li H, Zhang J, Fernando D, Xu C, Cui C, Jiang J, Zheng B, Wu L. Fine Mapping of a Locus Underlying the Ectopic Blade-Like Outgrowths on Leaf and Screening Its Candidate Genes in Rapeseed ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2021; 11:616844. [PMID: 33584757 PMCID: PMC7874103 DOI: 10.3389/fpls.2020.616844] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/01/2020] [Indexed: 06/12/2023]
Abstract
Leaf is an important organ for higher plants, and the shape of it is one of the crucial traits of crops. In this study, we investigated a unique aberrant leaf morphology trait in a mutational rapeseed material, which displayed ectopic blade-like outgrowths on the adaxial side of leaf. The abnormal line 132000B-3 was crossed with the normal line 827-3. Based on the F2 : 3 family, we constructed two DNA pools (normal pool and abnormal pool) by the bulked segregant analysis (BSA) method and performed whole genome re-sequencing (WGR), obtaining the single-nucleotide polymorphism (SNP) and insertion/deletion (InDel) data. The SNP-index method was used to calculate the Δ(SNP/InDel-index), and then an association region was identified on chromosome A10 with a length of 5.5 Mbp, harboring 1048 genes totally. Subsequently, the fine mapping was conducted by using the penta-primer amplification refractory mutation system (PARMS), and the associated region was narrowed down to a 35.1-kbp segment, containing only seven genes. These seven genes were then analyzed according to their annotations and finally, BnA10g0422620 and BnA10g0422610, orthologs of LATE MERISTEM IDENTITY1 (LMI1) gene from Arabidopsis and REDUCED COMPLEXITY (RCO) gene from its relative Cardamine hirsuta, respectively, were identified as the candidate genes responding to this blade-like outgrowth trait in rapeseed. This study provides a novel perspective into the leaf formation in Brassica plants.
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Affiliation(s)
- Liang Chai
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Bin Feng
- Guizhou Oil Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Xun Liu
- School of Biological Sciences, Guizhou Education University, Guiyang, China
| | - Liangcai Jiang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Shu Yuan
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Zhongwei Zhang
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Haojie Li
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Jinfang Zhang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Dilantha Fernando
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada
| | - Chun Xu
- Rape Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Cheng Cui
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Jun Jiang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Benchuan Zheng
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Lintao Wu
- School of Biological Sciences, Guizhou Education University, Guiyang, China
- Rape Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
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17
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Vadde BVL, Roeder AHK. Can the French flag and reaction-diffusion models explain flower patterning? Celebrating the 50th anniversary of the French flag model. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2886-2897. [PMID: 32016398 DOI: 10.1093/jxb/eraa065] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 02/01/2020] [Indexed: 05/25/2023]
Abstract
It has been 50 years since Lewis Wolpert introduced the French flag model proposing the patterning of different cell types based on threshold concentrations of a morphogen diffusing in the tissue. Sixty-seven years ago, Alan Turing introduced the idea of patterns initiating de novo from a reaction-diffusion network. Together these models have been used to explain many patterning events in animal development, so here we take a look at their applicability to flower development. First, although many plant transcription factors move through plasmodesmata from cell to cell, in the flower there is little evidence that they specify fate in a concentration-dependent manner, so they cannot yet be described as morphogens. Secondly, the reaction-diffusion model appears to be a reasonably good description of the formation of spots of pigment on petals, although additional nuances are present. Thirdly, aspects of both of these combine in a new fluctuation-based patterning system creating the scattered pattern of giant cells in Arabidopsis sepals. In the future, more precise imaging and manipulations of the dynamics of patterning networks combined with mathematical modeling will allow us to better understand how the multilayered complex and beautiful patterns of flowers emerge de novo.
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Affiliation(s)
- Batthula Vijaya Lakshmi Vadde
- Weill Institute for Cell and Molecular Biology and School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, NY, USA
| | - Adrienne H K Roeder
- Weill Institute for Cell and Molecular Biology and School of Integrative Plant Science, Section of Plant Biology, Cornell University, Ithaca, NY, USA
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18
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Hassankhah A, Rahemi M, Ramshini H, Sarikhani S, Vahdati K. Flowering in Persian walnut: patterns of gene expression during flower development. BMC PLANT BIOLOGY 2020; 20:136. [PMID: 32245410 PMCID: PMC7118962 DOI: 10.1186/s12870-020-02372-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 03/30/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Flower development and sufficient fruit set are important parameters with respect to walnut yield. Knowledge about flowering genes of fruit trees can help to conduct better molecular breeding programs. Therefore, this study was carried out to investigate the expression pattern of some flowering genes (FT, SOC1, CAL, LFY and TFL1) in Persian walnut (cv. Chandler) during the growing season and winter dormancy. RESULTS The results showed that walnut flower induction and initiation in Shahmirzad, Iran occurred in early June and late September, respectively. After meeting chilling and heat requirement, flower differentiation and anthesis occurred in late-March and mid-April to early-May, respectively. Study of flowering gene expression showed that the expression of the FT gene increased in three stages including before breaking of bud dormancy, from late March to late April (coincided with flower differentiation and anthesis) and from late May to mid-June (coincided with flower induction). Like FT, the expression of SOC1 gene increased during flower induction and initiation (mid-May to early-August) as well as flower anthesis (mid-April to early-May). LFY and CAL genes as floral meristem identity genes are activated by FT and SOC1 genes. In contrast with flowering stimulus genes, TFL1 showed overexpression during winter dormancy which prevented flowering. CONCLUSION The expression of FT gene activated downstream floral meristem identity genes including SOC1, CAL and LFY which consequently led to release bud dormancy as well as flower anthesis and induction. Also, TFL1 as a flowering inhibitor gene in walnut showed overexpression during the bud dormancy. Chilling accumulation reduced TFL1 gene expression and increased the expression of flowering genes which ultimately led to overcome dormancy.
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Affiliation(s)
- Amin Hassankhah
- Department of Horticulture, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Majid Rahemi
- Department of Horticultural Sciences, Faculty of Agriculture, Shiraz University, Shiraz, Iran
| | - Hossein Ramshini
- Department of Agronomy and Plant Breeding Sciences, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Saadat Sarikhani
- Department of Horticulture, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Kourosh Vahdati
- Department of Horticulture, College of Aburaihan, University of Tehran, Tehran, Iran
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Wu S, Han B, Jiao Y. Genetic Contribution of Paleopolyploidy to Adaptive Evolution in Angiosperms. MOLECULAR PLANT 2020; 13:59-71. [PMID: 31678615 DOI: 10.1016/j.molp.2019.10.012] [Citation(s) in RCA: 152] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 10/16/2019] [Accepted: 10/23/2019] [Indexed: 05/20/2023]
Abstract
Ancient whole-genome duplications (WGDs or polyploidy) are prevalent in plants, and some WGDs occurred during the timing of severe global environmental changes. It has been suggested that WGDs may have contributed to plant adaptation. However, this still lacks empirical evidence at the genetic level to support the hypothesis. Here, we investigated the survivors of gene duplicates from multiple ancient WGD events on the major branches of angiosperm phylogeny, and aimed to explore genetic evidence supporting the significance of polyploidy. Duplicated genes co-retained from three waves of independent WGDs (∼120 million years ago [Ma], ∼66, and <20 Ma) were investigated in 25 selected species. Gene families functioning in low temperature and darkness were commonly retained gene duplicates after the eight independently occurring WGDs in many lineages around the Cretaceous-Paleocene boundary, when the global cooling and darkness were the two main stresses. Moreover, the commonly retained duplicates could be key factors which may have contributed to the robustness of the critical stress-related pathways. In addition, genome-wide transcription factors (TFs) functioning in stresses tend to retain duplicates after waves of WGDs, and the coselected gene duplicates in many lineages may play critical roles during severe environmental stresses. Collectively, these results shed new light on the significant contribution of paleopolyploidy to plant adaptation during global environmental changes in the evolutionary history of angiosperms.
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Affiliation(s)
- Shengdan Wu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baocai Han
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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The Striking Flower-in-Flower Phenotype of Arabidopsis thaliana Nossen (No-0) is Caused by a Novel LEAFY Allele. PLANTS 2019; 8:plants8120599. [PMID: 31847079 PMCID: PMC6963406 DOI: 10.3390/plants8120599] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/09/2019] [Accepted: 12/12/2019] [Indexed: 01/19/2023]
Abstract
The transition to reproduction is a crucial step in the life cycle of any organism. In Arabidopsis thaliana the establishment of reproductive growth can be divided into two phases: Firstly, cauline leaves with axillary meristems are formed and internode elongation begins. Secondly, lateral meristems develop into flowers with defined organs. Floral shoots are usually determinate and suppress the development of lateral shoots. Here, we describe a transposon insertion mutant in the Nossen accession with defects in floral development and growth. Most strikingly is the outgrowth of stems from the axillary bracts of the primary flower carrying secondary flowers. Therefore, we named this mutant flower-in-flower (fif). However, the transposon insertion in the annotated gene is not the cause for the fif phenotype. By means of classical and genome sequencing-based mapping, the mutation responsible for the fif phenotype was found to be in the LEAFY gene. The mutation, a G-to-A exchange in the second exon of LEAFY, creates a novel lfy allele and results in a cysteine-to-tyrosine exchange in the α1-helix of LEAFY’s DNA-binding domain. This exchange abolishes target DNA-binding, whereas subcellular localization and homomerization are not affected. To explain the strong fif phenotype against these molecular findings, several hypotheses are discussed.
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RcAP1, a Homolog of APETALA1, is Associated with Flower Bud Differentiation and Floral Organ Morphogenesis in Rosa chinensis. Int J Mol Sci 2019; 20:ijms20143557. [PMID: 31330828 PMCID: PMC6679073 DOI: 10.3390/ijms20143557] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 01/15/2023] Open
Abstract
Rosa chinensis is one of the most popular flower plants worldwide. The recurrent flowering trait greatly enhances the ornamental value of roses, and is the result of the constant formation of new flower buds. Flower bud differentiation has always been a major topic of interest among researchers. The APETALA1 (AP1) MADS-box (Mcm1, Agamous, Deficiens and SRF) transcription factor-encoding gene is important for the formation of the floral meristem and floral organs. However, research on the rose AP1 gene has been limited. Thus, we isolated AP1 from Rosa chinensis ‘Old Blush’. An expression analysis revealed that RcAP1 was not expressed before the floral primordia formation stage in flower buds. The overexpression of RcAP1 in Arabidopsis thaliana resulted in an early-flowering phenotype. Additionally, the virus-induced down-regulation of RcAP1 expression delayed flowering in ‘Old Blush’. Moreover, RcAP1 was specifically expressed in the sepals of floral organs, while its expression was down-regulated in abnormal sepals and leaf-like organs. These observations suggest that RcAP1 may contribute to rose bud differentiation as well as floral organ morphogenesis, especially the sepals. These results may help for further characterization of the regulatory mechanisms of the recurrent flowering trait in rose.
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Gao B, Chen M, Li X, Zhang J. Ancient duplications and grass-specific transposition influenced the evolution of LEAFY transcription factor genes. Commun Biol 2019; 2:237. [PMID: 31263781 PMCID: PMC6588583 DOI: 10.1038/s42003-019-0469-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/17/2019] [Indexed: 12/18/2022] Open
Abstract
The LFY transcription factor gene family are important in the promotion of cell proliferation and floral development. Understanding their evolution offers an insight into floral development in plant evolution. Though a promiscuous transition intermediate and a gene duplication event within the LFY family had been identified previously, the early evolutionary path of this family remained elusive. Here, we reconstructed the LFY family phylogeny using maximum-likelihood and Bayesian inference methods incorporating LFY genes from all major lineages of streptophytes. The well-resolved phylogeny unveiled a high-confidence duplication event before the functional divergence of types I and II LFY genes in the ancestry of liverworts, mosses and tracheophytes, supporting sub-functionalization of an ancestral promiscuous gene. The identification of promiscuous genes in Osmunda suggested promiscuous LFY genes experienced an ancient transient duplication. Genomic synteny comparisons demonstrated a deep genomic positional conservation of LFY genes and an ancestral lineage-specific transposition activity in grasses.
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Affiliation(s)
- Bei Gao
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Moxian Chen
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Xiaoshuang Li
- Key Laboratory of Biogeography and Bioresource, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011 China
| | - Jianhua Zhang
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
- Department of Biology, Faculty of Science, Hong Kong Baptist University, Hong Kong, China
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Birkenbihl RP, Kracher B, Ross A, Kramer K, Finkemeier I, Somssich IE. Principles and characteristics of the Arabidopsis WRKY regulatory network during early MAMP-triggered immunity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:487-502. [PMID: 30044528 DOI: 10.1111/tpj.14043] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/06/2018] [Accepted: 07/10/2018] [Indexed: 05/04/2023]
Abstract
During microbe-associated molecular pattern-triggered immunity more than 5000 Arabidopsis genes are significantly altered in their expression, and the question arises, how such an enormous reprogramming of the transcriptome can be regulated in a safe and robust manner? For the WRKY transcription factors (TFs), which are important regulators of numerous defense responses, it appears that they act in a complex regulatory sub-network rather than in a linear fashion, which would be much more vulnerable to gene function loss either by pathogen-derived effectors or by mutations. In this study we employed RNA-seq, mass spectrometry and chromatin immunoprecipitation-seq to find evidence for and uncover principles and characteristics of this network. Upon flg22-treatment, one can distinguish between two sets of WRKY genes: constitutively expressed and induced WRKY genes. Prior to elicitation the induced WRKY genes appear to be maintained in a repressed state mainly by the constitutively expressed WRKY factors, which themselves appear to be regulated by non-WRKY TFs. Upon elicitation, induced WRKYs rapidly bind to induced WRKY gene promoters and by auto- and cross-regulation build up the regulatory network. Maintenance of this flg22-induced network appears highly robust as removal of three key WRKY factors can be physically and functionally compensated for by other WRKY family members.
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Affiliation(s)
- Rainer P Birkenbihl
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Barbara Kracher
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Annegret Ross
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
| | - Katharina Kramer
- Plant Proteomics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg10, 50829, Cologne, Germany
| | - Iris Finkemeier
- Plant Proteomics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg10, 50829, Cologne, Germany
| | - Imre E Somssich
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829, Cologne, Germany
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Jacob F, Kracher B, Mine A, Seyfferth C, Blanvillain‐Baufumé S, Parker JE, Tsuda K, Schulze‐Lefert P, Maekawa T. A dominant-interfering camta3 mutation compromises primary transcriptional outputs mediated by both cell surface and intracellular immune receptors in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2018; 217:1667-1680. [PMID: 29226970 PMCID: PMC5873390 DOI: 10.1111/nph.14943] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 11/08/2017] [Indexed: 05/15/2023]
Abstract
Pattern recognition receptors (PRRs) and nucleotide-binding domain and leucine-rich repeat (LRR)-containing proteins (NLRs) initiate pattern-triggered immunity (PTI) and effector-triggered immunity (ETI), respectively, each associated with the activation of an overlapping set of defence genes. The regulatory mechanism behind this convergence of PTI- and ETI-mediated defence gene induction remains elusive. We generated transgenic Arabidopsis plants that enable conditional NLR activation without pathogen infection to dissect NLR- and PRR-mediated transcriptional signals. A comparative analysis of over 40 transcriptome datasets linked calmodulin-binding transcription activators (CAMTAs) to the activation of overlapping defence genes in PTI and ETI. We used a dominant camta3 mutant (camta3-D) to assess CAMTA functions in the corresponding transcriptional regulation. Transcriptional regulation by NLRs, although highly similar to PTI responses, can be established independently of pathogen-associated molecular pattern (PAMP) perception, defence phytohormones and host cell death. Conditional expression of the N-terminal coiled-coil domain of the barley MLA (Mildew resistance locus A) NLR is sufficient to trigger similar transcriptional reprogramming as full-length NLRs. CAMTA-binding motifs are overrepresented in the 5' regulatory regions of the identified primary immune response genes, consistent with their altered expression and disease resistance responses in camta3-D plants. We propose that CAMTA-mediated transcriptional regulation defines an early convergence point in NLR- and PRR-mediated signalling.
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Affiliation(s)
- Florence Jacob
- Department of Plant–Microbe InteractionsMax Planck Institute for Plant Breeding Research50829CologneGermany
- Institute of Plant Sciences Paris‐SaclayCentre National de la Recherche ScientifiqueInstitut National de la Recherche AgronomiqueUniversité Paris‐SudUniversité d'EvryUniversité Paris‐DiderotSorbonne Paris‐CitéUniversité Paris‐Saclay91405OrsayFrance
| | - Barbara Kracher
- Department of Plant–Microbe InteractionsMax Planck Institute for Plant Breeding Research50829CologneGermany
| | - Akira Mine
- Department of Plant–Microbe InteractionsMax Planck Institute for Plant Breeding Research50829CologneGermany
| | - Carolin Seyfferth
- Department of Plant–Microbe InteractionsMax Planck Institute for Plant Breeding Research50829CologneGermany
| | | | - Jane E. Parker
- Department of Plant–Microbe InteractionsMax Planck Institute for Plant Breeding Research50829CologneGermany
| | - Kenichi Tsuda
- Department of Plant–Microbe InteractionsMax Planck Institute for Plant Breeding Research50829CologneGermany
| | - Paul Schulze‐Lefert
- Department of Plant–Microbe InteractionsMax Planck Institute for Plant Breeding Research50829CologneGermany
| | - Takaki Maekawa
- Department of Plant–Microbe InteractionsMax Planck Institute for Plant Breeding Research50829CologneGermany
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26
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Detection of Epistasis for Flowering Time Using Bayesian Multilocus Estimation in a Barley MAGIC Population. Genetics 2017; 208:525-536. [PMID: 29254994 PMCID: PMC5788519 DOI: 10.1534/genetics.117.300546] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/12/2017] [Indexed: 12/16/2022] Open
Abstract
Gene-by-gene interactions, also known as epistasis, regulate many complex traits in different species. With the availability of low-cost genotyping it is now possible to study epistasis on a genome-wide scale. However, identifying genome-wide epistasis is a high-dimensional multiple regression problem and needs the application of dimensionality reduction techniques. Flowering Time (FT) in crops is a complex trait that is known to be influenced by many interacting genes and pathways in various crops. In this study, we successfully apply Sure Independence Screening (SIS) for dimensionality reduction to identify two-way and three-way epistasis for the FT trait in a Multiparent Advanced Generation Inter-Cross (MAGIC) barley population using the Bayesian multilocus model. The MAGIC barley population was generated from intercrossing among eight parental lines and thus, offered greater genetic diversity to detect higher-order epistatic interactions. Our results suggest that SIS is an efficient dimensionality reduction approach to detect high-order interactions in a Bayesian multilocus model. We also observe that many of our findings (genomic regions with main or higher-order epistatic effects) overlap with known candidate genes that have been already reported in barley and closely related species for the FT trait.
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27
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Serrano-Mislata A, Goslin K, Zheng B, Rae L, Wellmer F, Graciet E, Madueño F. Regulatory interplay between LEAFY, APETALA1/CAULIFLOWER and TERMINAL FLOWER1: New insights into an old relationship. PLANT SIGNALING & BEHAVIOR 2017; 12:e1370164. [PMID: 28873010 PMCID: PMC5647955 DOI: 10.1080/15592324.2017.1370164] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 08/16/2017] [Indexed: 05/18/2023]
Abstract
The gene regulatory network comprised of LEAFY (LFY), APETALA1 (AP1), the AP1 paralog CAULIFLOWER (CAL), and TERMINAL FLOWER1 (TFL1) is a major determinant of the flowering process in Arabidopsis thaliana. TFL1 activity in the shoot apical meristem provides inflorescence identity while the transcription factors LFY and AP1/CAL confer floral identity to emerging floral primordia. It has been thought that LFY and AP1/CAL control the onset of flowering in part by repressing TFL1 expression in flowers. However, in the June issue of Plant Physiology, we reported that LFY and AP1 act antagonistically in the regulation of several key flowering regulators, including TFL1. Specifically, TFL1 transcription was suppressed by AP1 but promoted by LFY. Here, we present additional evidence for the role of LFY as an activator of TFL1 and propose that this regulatory activity is pivotal for the indeterminate growth of the SAM during the reproductive phase of development.
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Affiliation(s)
- Antonio Serrano-Mislata
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain
- CONTACT Antonio Serrano-Mislata Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), C/Ingeniero Fausto Elio s/n, 46022Valencia, Spain
| | - Kevin Goslin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland
| | - Beibei Zheng
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Liina Rae
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Frank Wellmer
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Emmanuelle Graciet
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland
| | - Francisco Madueño
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain
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28
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Ma Q, Liu X, Franks RG, Xiang QYJ. Alterations of CorTFL1 and CorAP1 expression correlate with major evolutionary shifts of inflorescence architecture in Cornus (Cornaceae) - a proposed model for variation of closed inflorescence forms. THE NEW PHYTOLOGIST 2017; 216:519-535. [PMID: 27662246 DOI: 10.1111/nph.14197] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 08/08/2016] [Indexed: 06/06/2023]
Abstract
TFL1-, AP1- and LFY-like genes are known to be key regulators of inflorescence development. However, it remains to be tested whether the evolutionary modifications of inflorescence morphology result from shifts in their expression patterns. We compared the spatiotemporal expression patterns of CorTFL1, CorAP1 and CorLFY in six closely related Cornus species that display four types of closed inflorescence morphology using quantitative real-time polymerase chain reaction (qRT-PCR) and RNA in situ hybridization. Character mapping on the phylogeny was conducted to identify evolutionary changes and to assess the correlation between changes in gene expression and inflorescence morphology. Results demonstrated variation of gene expression patterns among species and a strong correlation between CorTFL1 expression and the branch index of the inflorescence type. Evolutionary changes in CorTFL1 and CorAP1 expression co-occurred on the phylogeny with the morphological changes underpinning inflorescence divergence. The study found a clear correlation between the expression patterns of CorTFL1 and CorAP1 and the inflorescence architecture in a natural system displaying closed inflorescences. The results suggest a role for the alteration in CorTFL1 and CorAP1 expression during the evolutionary modification of inflorescences in Cornus. We propose that a TFL1-like and AP1-like gene-based model may explain variation of closed inflorescences in Cornus and other lineages.
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Affiliation(s)
- Qing Ma
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695-7612, USA
- Key laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiang Liu
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695-7612, USA
| | - Robert G Franks
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695-7612, USA
| | - Qiu-Yun Jenny Xiang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695-7612, USA
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29
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Goslin K, Zheng B, Serrano-Mislata A, Rae L, Ryan PT, Kwaśniewska K, Thomson B, Ó'Maoiléidigh DS, Madueño F, Wellmer F, Graciet E. Transcription Factor Interplay between LEAFY and APETALA1/CAULIFLOWER during Floral Initiation. PLANT PHYSIOLOGY 2017; 174:1097-1109. [PMID: 28385730 PMCID: PMC5462026 DOI: 10.1104/pp.17.00098] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 04/05/2017] [Indexed: 05/21/2023]
Abstract
The transcription factors LEAFY (LFY) and APETALA1 (AP1), together with the AP1 paralog CAULIFLOWER (CAL), control the onset of flower development in a partially redundant manner. This redundancy is thought to be mediated, at least in part, through the regulation of a shared set of target genes. However, whether these genes are independently or cooperatively regulated by LFY and AP1/CAL is currently unknown. To better understand the regulatory relationship between LFY and AP1/CAL and to obtain deeper insights into the control of floral initiation, we monitored the activity of LFY in the absence of AP1/CAL function. We found that the regulation of several known LFY target genes is unaffected by AP1/CAL perturbation, while others appear to require AP1/CAL activity. Furthermore, we obtained evidence that LFY and AP1/CAL control the expression of some genes in an antagonistic manner. Notably, these include key regulators of floral initiation such as TERMINAL FLOWER1 (TFL1), which had been previously reported to be directly repressed by both LFY and AP1. We show here that TFL1 expression is suppressed by AP1 but promoted by LFY. We further demonstrate that LFY has an inhibitory effect on flower formation in the absence of AP1/CAL activity. We propose that LFY and AP1/CAL act as part of an incoherent feed-forward loop, a network motif where two interconnected pathways or transcription factors act in opposite directions on a target gene, to control the establishment of a stable developmental program for the formation of flowers.
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Affiliation(s)
- Kevin Goslin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland (K.G., B.Z., L.R., P.T.R., K.K., B.T., D.S.Ó., F.W.)
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland (K.G., E.G.); and
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain (A.S.-M., F.M.)
| | - Beibei Zheng
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland (K.G., B.Z., L.R., P.T.R., K.K., B.T., D.S.Ó., F.W.)
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland (K.G., E.G.); and
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain (A.S.-M., F.M.)
| | - Antonio Serrano-Mislata
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland (K.G., B.Z., L.R., P.T.R., K.K., B.T., D.S.Ó., F.W.)
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland (K.G., E.G.); and
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain (A.S.-M., F.M.)
| | - Liina Rae
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland (K.G., B.Z., L.R., P.T.R., K.K., B.T., D.S.Ó., F.W.)
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland (K.G., E.G.); and
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain (A.S.-M., F.M.)
| | - Patrick T Ryan
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland (K.G., B.Z., L.R., P.T.R., K.K., B.T., D.S.Ó., F.W.)
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland (K.G., E.G.); and
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain (A.S.-M., F.M.)
| | - Kamila Kwaśniewska
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland (K.G., B.Z., L.R., P.T.R., K.K., B.T., D.S.Ó., F.W.)
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland (K.G., E.G.); and
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain (A.S.-M., F.M.)
| | - Bennett Thomson
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland (K.G., B.Z., L.R., P.T.R., K.K., B.T., D.S.Ó., F.W.)
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland (K.G., E.G.); and
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain (A.S.-M., F.M.)
| | - Diarmuid S Ó'Maoiléidigh
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland (K.G., B.Z., L.R., P.T.R., K.K., B.T., D.S.Ó., F.W.)
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland (K.G., E.G.); and
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain (A.S.-M., F.M.)
| | - Francisco Madueño
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland (K.G., B.Z., L.R., P.T.R., K.K., B.T., D.S.Ó., F.W.)
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland (K.G., E.G.); and
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain (A.S.-M., F.M.)
| | - Frank Wellmer
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland (K.G., B.Z., L.R., P.T.R., K.K., B.T., D.S.Ó., F.W.);
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland (K.G., E.G.); and
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain (A.S.-M., F.M.)
| | - Emmanuelle Graciet
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland (K.G., B.Z., L.R., P.T.R., K.K., B.T., D.S.Ó., F.W.)
- Department of Biology, National University of Ireland Maynooth, Maynooth, Ireland (K.G., E.G.); and
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain (A.S.-M., F.M.)
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Abstract
Chirality is a key factor in the safety and efficacy of many drug products and thus the production of single enantiomers of drug intermediates and drugs has become important and state of the art in the pharmaceutical industry. There has been an increasing awareness of the enormous potential of microorganisms and enzymes (biocatalysts) for the transformation of synthetic chemicals with high chemo-, regio- and enatioselectivities providing products in high yields and purity. In this article, biocatalytic processes are described for the synthesis of key chiral intermediates for development pharmaceuticals.
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Affiliation(s)
- Ramesh N Patel
- SLRP Associates, LLC, Consultation in Biocatalysis and Biotechnology, 572 Cabot Hill Road, Bridgewater, NJ 08807, USA.
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31
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Gamuyao R, Nagai K, Ayano M, Mori Y, Minami A, Kojima M, Suzuki T, Sakakibara H, Higashiyama T, Ashikari M, Reuscher S. Hormone Distribution and Transcriptome Profiles in Bamboo Shoots Provide Insights on Bamboo Stem Emergence and Growth. PLANT & CELL PHYSIOLOGY 2017; 58:702-716. [PMID: 28204696 DOI: 10.1093/pcp/pcx023] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/01/2017] [Indexed: 05/20/2023]
Abstract
Growth and development are tightly co-ordinated events in the lifetime of living organisms. In temperate bamboo plants, spring is the season when environmental conditions are suitable for the emergence of new shoots. Previous studies demonstrated that bamboo plants undergo an energy-consuming 'fast stem growth' phase. However, the events during the initiation of stem elongation in bamboo are poorly understood. To understand the onset of bamboo stem growth, we performed hormone and transcriptome profiling of tissue regions in newly elongating shoots of the Moso bamboo Phyllostachys edulis. The growth hormones auxins, cytokinins and gibberellins accumulated in the shoot apex, while the stress hormones ABA, salicylic acid (SA) and jasmonic acid (JA) are predominantly found in the lower part of the stem. The mature basal part of the stem showed enrichment of transcripts associated with cell wall metabolism and biosynthesis of phenylpropanoid metabolites, such as lignin. In the young upper stem region, expression of cell formation- and DNA synthesis-related genes was enriched. Moreover, the apical region showed enhanced expression of genes involved in meristem maintenance, leaf differentiation and development, abaxial/adaxial polarity and flowering. Our findings integrate the spatial regulation of hormones and transcriptome programs during the initiation of bamboo stem growth.
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Affiliation(s)
- Rico Gamuyao
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Keisuke Nagai
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Madoka Ayano
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Yoshinao Mori
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Anzu Minami
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Mikiko Kojima
- RIKEN Center for Sustainable Resource Science, Suehiro, Tsurumi, Yokohama, Japan
| | - Takamasa Suzuki
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, Suehiro, Tsurumi, Yokohama, Japan
| | - Tetsuya Higashiyama
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Stefan Reuscher
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
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Liu Y, Zhao Q, Meng N, Song H, Li C, Hu G, Wu J, Lin S, Zhang Z. Over-expression of EjLFY-1 Leads to an Early Flowering Habit in Strawberry ( Fragaria × ananassa) and Its Asexual Progeny. FRONTIERS IN PLANT SCIENCE 2017; 8:496. [PMID: 28443106 PMCID: PMC5385365 DOI: 10.3389/fpls.2017.00496] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/21/2017] [Indexed: 05/18/2023]
Abstract
As a master regulator involved in flower development, LEAFY-like gene has been demonstrated to play a key role in the flowering process regulation of angiosperms. Expression analysis of EjLFY-1, a LEAFY (LFY) homolog of loquat (Eriobotrya japonica Lindl.), indicated its participation in the regulation of flowering in loquat. To verify its function and potential value in the genetic engineering to shorten the juvenile phase, ectopic expression of EjLFY-1 in strawberry (Fragaria × ananassa) was achieved using Agrobacterium-mediated gene transfer of a plant expression vector with the loquat EjLFY-1 gene driven by the CaMV 35S promoter. Totally 59 plantlets were verified to be the transformants. The presence, expression and integration of EjLFY-1 in the transformants were assessed by PCR, quantitative real-time PCR and Southern blot, respectively. Constitutive expression of EjLFY-1 in strawberry accelerated the flowering process in strawberry with the shorten necessary period for flowering induction, development of flower and fruit set. While vegetative growth habits of the transformants in the first cropping season were consistent with the WT ones. Meanwhile, both the flowers and fruits of the transformants were also as same as those of the WT ones. Furthermore, the early-flowering habit was maintained in their asexual progeny, the runner plants. While with continuous asexual propagation, the clones showed a more strengthen early-flowering phenotype, such as the reduced vegetative growth and the abnormal floral organs in individual plantlets. These results demonstrated the function of this gene and at the same time provided us new insights into the utilization potential of such genes in the genetic engineering of perennial fruits.
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Affiliation(s)
- Yuexue Liu
- College of Horticulture, Shenyang Agricultural UniversityShenyang, China
| | - Qian Zhao
- College of Horticulture, Shenyang Agricultural UniversityShenyang, China
| | - Nan Meng
- College of Horticulture, Shenyang Agricultural UniversityShenyang, China
| | - Huwei Song
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, Huaiyin Normal UniversityHuaian, China
| | - Chaochao Li
- College of Horticulture, Shenyang Agricultural UniversityShenyang, China
| | - Guibing Hu
- Institute of Biotechnology in Horticultural Plants, South China Agricultural UniversityGuangzhou, China
| | - Jincheng Wu
- Fujian Provincial Key Laboratory of Ecology-Toxicological Effects and Control Techniques of Emerging Contaminants, Putian UniversityPutian, China
| | - Shunquan Lin
- Institute of Biotechnology in Horticultural Plants, South China Agricultural UniversityGuangzhou, China
- *Correspondence: Zhihong Zhang, Shunquan Lin,
| | - Zhihong Zhang
- College of Horticulture, Shenyang Agricultural UniversityShenyang, China
- *Correspondence: Zhihong Zhang, Shunquan Lin,
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An ortholog of LEAFY in Jatropha curcas regulates flowering time and floral organ development. Sci Rep 2016; 6:37306. [PMID: 27869146 PMCID: PMC5116762 DOI: 10.1038/srep37306] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 10/27/2016] [Indexed: 12/03/2022] Open
Abstract
Jatropha curcas seeds are an excellent biofuel feedstock, but seed yields of Jatropha are limited by its poor flowering and fruiting ability. Thus, identifying genes controlling flowering is critical for genetic improvement of seed yield. We isolated the JcLFY, a Jatropha ortholog of Arabidopsis thaliana LEAFY (LFY), and identified JcLFY function by overexpressing it in Arabidopsis and Jatropha. JcLFY is expressed in Jatropha inflorescence buds, flower buds, and carpels, with highest expression in the early developmental stage of flower buds. JcLFY overexpression induced early flowering, solitary flowers, and terminal flowers in Arabidopsis, and also rescued the delayed flowering phenotype of lfy-15, a LFY loss-of-function Arabidopsis mutant. Microarray and qPCR analysis revealed several flower identity and flower organ development genes were upregulated in JcLFY-overexpressing Arabidopsis. JcLFY overexpression in Jatropha also induced early flowering. Significant changes in inflorescence structure, floral organs, and fruit shape occurred in JcLFY co-suppressed plants in which expression of several flower identity and floral organ development genes were changed. This suggests JcLFY is involved in regulating flower identity, floral organ patterns, and fruit shape, although JcLFY function in Jatropha floral meristem determination is not as strong as that of Arabidopsis.
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Frerichs A, Thoma R, Abdallah AT, Frommolt P, Werr W, Chandler JW. The founder-cell transcriptome in the Arabidopsis apetala1 cauliflower inflorescence meristem. BMC Genomics 2016; 17:855. [PMID: 27809788 PMCID: PMC5093967 DOI: 10.1186/s12864-016-3189-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 10/22/2016] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Although the pattern of lateral organ formation from apical meristems establishes species-specific plant architecture, the positional information that confers cell fate to cells as they transit to the meristem flanks where they differentiate, remains largely unknown. We have combined fluorescence-activated cell sorting and RNA-seq to characterise the cell-type-specific transcriptome at the earliest developmental time-point of lateral organ formation using DORNRÖSCHEN-LIKE::GFP to mark founder-cell populations at the periphery of the inflorescence meristem (IM) in apetala1 cauliflower double mutants, which overproliferate IMs. RESULTS Within the lateral organ founder-cell population at the inflorescence meristem, floral primordium identity genes are upregulated and stem-cell identity markers are downregulated. Additional differentially expressed transcripts are involved in polarity generation and boundary formation, and in epigenetic and post-translational changes. However, only subtle transcriptional reprogramming within the global auxin network was observed. CONCLUSIONS The transcriptional network of differentially expressed genes supports the hypothesis that lateral organ founder-cell specification involves the creation of polarity from the centre to the periphery of the IM and the establishment of a boundary from surrounding cells, consistent with bract initiation. However, contrary to the established paradigm that sites of auxin response maxima pre-pattern lateral organ initiation in the IM, auxin response might play a minor role in the earliest stages of lateral floral initiation.
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Affiliation(s)
- Anneke Frerichs
- Institute of Developmental Biology, University of Cologne, Cologne Biocenter, Zuelpicher Strasse 47b, D-50674, Cologne, Germany
| | - Rahere Thoma
- Present address: Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829, Cologne, Germany
| | - Ali Taleb Abdallah
- CECAD Research Center, University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Peter Frommolt
- CECAD Research Center, University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Wolfgang Werr
- Institute of Developmental Biology, University of Cologne, Cologne Biocenter, Zuelpicher Strasse 47b, D-50674, Cologne, Germany
| | - John William Chandler
- Institute of Developmental Biology, University of Cologne, Cologne Biocenter, Zuelpicher Strasse 47b, D-50674, Cologne, Germany.
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Gene-regulatory networks controlling inflorescence and flower development in Arabidopsis thaliana. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:95-105. [PMID: 27487457 DOI: 10.1016/j.bbagrm.2016.07.014] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 07/21/2016] [Accepted: 07/22/2016] [Indexed: 11/23/2022]
Abstract
Reproductive development in plants is controlled by complex and intricate gene-regulatory networks of transcription factors. These networks integrate the information from endogenous, hormonal and environmental regulatory pathways. Many of the key players have been identified in Arabidopsis and other flowering plant species, and their interactions and molecular modes of action are being elucidated. An emerging theme is that there is extensive crosstalk between different pathways, which can be accomplished at the molecular level by modulation of transcription factor activity or of their downstream targets. In this review, we aim to summarize current knowledge on transcription factors and epigenetic regulators that control basic developmental programs during inflorescence and flower morphogenesis in the model plant Arabidopsis thaliana. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Genome-wide transcriptomic analysis uncovers the molecular basis underlying early flowering and apetalous characteristic in Brassica napus L. Sci Rep 2016; 6:30576. [PMID: 27460760 PMCID: PMC4962316 DOI: 10.1038/srep30576] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 07/04/2016] [Indexed: 11/09/2022] Open
Abstract
Floral transition and petal onset, as two main aspects of flower development, are crucial to rapeseed evolutionary success and yield formation. Currently, very little is known regarding the genetic architecture that regulates flowering time and petal morphogenesis in Brassica napus. In the present study, a genome-wide transcriptomic analysis was performed with an absolutely apetalous and early flowering line, APL01, and a normally petalled line, PL01, using high-throughput RNA sequencing. In total, 13,205 differential expressed genes were detected, of which 6111 genes were significantly down-regulated, while 7094 genes were significantly up-regulated in the young inflorescences of APL01 compared with PL01. The expression levels of a vast number of genes involved in protein biosynthesis were altered in response to the early flowering and apetalous character. Based on the putative rapeseed flowering genes, an early flowering network, mainly comprised of vernalization and photoperiod pathways, was built. Additionally, 36 putative upstream genes possibly governing the apetalous character of line APL01 were identified, and six genes potentially regulating petal origination were obtained by combining with three petal-related quantitative trait loci. These findings will facilitate understanding of the molecular mechanisms underlying floral transition and petal initiation in B. napus.
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Ye L, Wang B, Zhang W, Shan H, Kong H. Gains and Losses of Cis-regulatory Elements Led to Divergence of the Arabidopsis APETALA1 and CAULIFLOWER Duplicate Genes in the Time, Space, and Level of Expression and Regulation of One Paralog by the Other. PLANT PHYSIOLOGY 2016; 171:1055-69. [PMID: 27208240 PMCID: PMC4902614 DOI: 10.1104/pp.16.00320] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 04/04/2016] [Indexed: 05/05/2023]
Abstract
How genes change their expression patterns over time is still poorly understood. Here, by conducting expression, functional, bioinformatic, and evolutionary analyses, we demonstrate that the differences between the Arabidopsis (Arabidopsis thaliana) APETALA1 (AP1) and CAULIFLOWER (CAL) duplicate genes in the time, space, and level of expression were determined by the presence or absence of functionally important transcription factor-binding sites (TFBSs) in regulatory regions. In particular, a CArG box, which is the autoregulatory site of AP1 that can also be bound by the CAL protein, is a key determinant of the expression differences. Because of the CArG box, AP1 is both autoregulated and cross-regulated (by AP1 and CAL, respectively), and its relatively high-level expression is maintained till to the late stages of sepal and petal development. The observation that the CArG box was gained recently further suggests that the autoregulation and cross-regulation of AP1, as well as its function in sepal and petal development, are derived features. By comparing the evolutionary histories of this and other TFBSs, we further indicate that the divergence of AP1 and CAL in regulatory regions has been markedly asymmetric and can be divided into several stages. Specifically, shortly after duplication, when AP1 happened to be the paralog that maintained the function of the ancestral gene, CAL experienced certain degrees of degenerate evolution, in which several functionally important TFBSs were lost. Later, when functional divergence allowed the survival of both paralogs, CAL remained largely unchanged in expression, whereas the functions of AP1 were gradually reinforced by gains of the CArG box and other TFBSs.
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Affiliation(s)
- Lingling Ye
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (L.Y., B.W., W.Z., H.S., H.K.); andUniversity of the Chinese Academy of Sciences, Beijing 100049, China (L.Y., B.W., W.Z.)
| | - Bin Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (L.Y., B.W., W.Z., H.S., H.K.); andUniversity of the Chinese Academy of Sciences, Beijing 100049, China (L.Y., B.W., W.Z.)
| | - Wengen Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (L.Y., B.W., W.Z., H.S., H.K.); andUniversity of the Chinese Academy of Sciences, Beijing 100049, China (L.Y., B.W., W.Z.)
| | - Hongyan Shan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (L.Y., B.W., W.Z., H.S., H.K.); andUniversity of the Chinese Academy of Sciences, Beijing 100049, China (L.Y., B.W., W.Z.)
| | - Hongzhi Kong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (L.Y., B.W., W.Z., H.S., H.K.); andUniversity of the Chinese Academy of Sciences, Beijing 100049, China (L.Y., B.W., W.Z.)
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Tang M, Tao YB, Xu ZF. Ectopic expression of Jatropha curcas APETALA1 (JcAP1) caused early flowering in Arabidopsis, but not in Jatropha. PeerJ 2016; 4:e1969. [PMID: 27168978 PMCID: PMC4860315 DOI: 10.7717/peerj.1969] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 04/03/2016] [Indexed: 11/20/2022] Open
Abstract
Jatropha curcas is a promising feedstock for biofuel production because Jatropha oil is highly suitable for the production of biodiesel and bio-jet fuels. However, Jatropha exhibits a low seed yield as a result of unreliable and poor flowering. APETALA1 (AP1) is a floral meristem and organ identity gene in higher plants. The flower meristem identity genes of Jatropha have not yet been identified or characterized. To better understand the genetic control of flowering in Jatropha, an AP1 homolog (JcAP1) was isolated from Jatropha. An amino acid sequence analysis of JcAP1 revealed a high similarity to the AP1 proteins of other perennial plants. JcAP1 was expressed in inflorescence buds, flower buds, sepals and petals. The highest expression level was observed during the early developmental stage of the flower buds. The overexpression of JcAP1 using the cauliflower mosaic virus (CaMV) 35S promoter resulted in extremely early flowering and abnormal flowers in transgenic Arabidopsis plants. Several flowering genes downstream of AP1 were up-regulated in the JcAP1-overexpressing transgenic plant lines. Furthermore, JcAP1 overexpression rescued the phenotype caused by the Arabidopsis AP1 loss-of-function mutant ap1-11. Therefore, JcAP1 is an ortholog of AtAP1, which plays a similar role in the regulation of flowering in Arabidopsis. However, the overexpression of JcAP1 in Jatropha using the same promoter resulted in little variation in the flowering time and floral organs, indicating that JcAP1 may be insufficient to regulate flowering by itself in Jatropha. This study helps to elucidate the function of JcAP1 and contributes to the understanding of the molecular mechanisms of flower development in Jatropha.
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Affiliation(s)
- Mingyong Tang
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yan-Bin Tao
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences , Menglun, Mengla, Yunnan , China
| | - Zeng-Fu Xu
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences , Menglun, Mengla, Yunnan , China
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Cloning and functional identification of the AcLFY gene in Allium cepa. Biochem Biophys Res Commun 2016; 473:1100-1105. [PMID: 27074580 DOI: 10.1016/j.bbrc.2016.04.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 04/05/2016] [Indexed: 11/21/2022]
Abstract
Onion (Allium cepa L.) is one of the important vegetable crops in the world, usually with a two-year life cycle. The bulbs form in the first year after sowing, then bolting and flowering are induced by low temperature in the following year. Previous studies have shown that LEAFY gene is an inflorescence tissue specific gene, and that it is also the ultimate collection channel of all flowering pathway. In this study, using homologous gene cloning and reverse transcription-PCR (RT-PCR), we isolated an inflorescence meristem specific LEAFY cDNA, AcLFY (JX275962), from onion. AcLFY contains a 1119 bp open reading frame, which encodes a putative protein of 372 amino acids, with ∼70% homology to the daffodils LEAFY and >50% homology to LEAFY proteins from other higher plants. Fluorescence quantitative results showed that AcLFY gene has the highest expression level in inflorescence meristem during early bolting, and is still expressed in leaves after the formation of flower organs. Overexpression of AcLFY gene in Arabidopsis thaliana induced early bolting and flowering, whereas knockdown of the endogenous LEAFY gene by RNAi caused a significant delay in bolting. In addition, transgenic plants also exhibited significant morphological changes in rosette leaves, branches, and plant height.
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40
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Yu H, Huang T. Molecular Mechanisms of Floral Boundary Formation in Arabidopsis. Int J Mol Sci 2016; 17:317. [PMID: 26950117 PMCID: PMC4813180 DOI: 10.3390/ijms17030317] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Revised: 02/21/2016] [Accepted: 02/23/2016] [Indexed: 01/03/2023] Open
Abstract
Boundary formation is a crucial developmental process in plant organogenesis. Boundaries separate cells with distinct identities and act as organizing centers to control the development of adjacent organs. In flower development, initiation of floral primordia requires the formation of the meristem-to-organ (M-O) boundaries and floral organ development depends on the establishment of organ-to-organ (O-O) boundaries. Studies in this field have revealed a suite of genes and regulatory pathways controlling floral boundary formation. Many of these genes are transcription factors that interact with phytohormone pathways. This review will focus on the functions and interactions of the genes that play important roles in the floral boundaries and discuss the molecular mechanisms that integrate these regulatory pathways to control the floral boundary formation.
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Affiliation(s)
- Hongyang Yu
- College of Life Sciences and Oceanography, Shenzhen University, 3688 Nanhai Ave., Shenzhen 518060, China.
- College of Optoelectronic Engineering, Shenzhen University, 3688 Nanhai Ave., Shenzhen 518060, China.
| | - Tengbo Huang
- College of Life Sciences and Oceanography, Shenzhen University, 3688 Nanhai Ave., Shenzhen 518060, China.
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Li P, Zhang G, Gonzales N, Guo Y, Hu H, Park S, Zhao J. Ca(2+) -regulated and diurnal rhythm-regulated Na(+) /Ca(2+) exchanger AtNCL affects flowering time and auxin signalling in Arabidopsis. PLANT, CELL & ENVIRONMENT 2016; 39:377-92. [PMID: 26296956 DOI: 10.1111/pce.12620] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 07/09/2015] [Accepted: 07/30/2015] [Indexed: 05/21/2023]
Abstract
Calcium (Ca(2+) ) is vital for plant growth, development, hormone response and adaptation to environmental stresses, yet the mechanisms regulating plant cytosolic Ca(2+) homeostasis are not fully understood. Here, we characterize an Arabidopsis Ca(2+) -regulated Na(+) /Ca(2+) exchanger AtNCL that regulates Ca(2+) and multiple physiological processes. AtNCL was localized to the tonoplast in yeast and plant cells. AtNCL appeared to mediate sodium (Na(+) ) vacuolar sequestration and meanwhile Ca(2+) release. The EF-hand domains within AtNCL regulated Ca(2+) binding and transport of Ca(2+) and Na(+) . Plants with diminished AtNCL expression were more tolerant to high CaCl2 but more sensitive to both NaCl and auxin; heightened expression of AtNCL rendered plants more sensitive to CaCl2 but tolerant to NaCl. AtNCL expression appeared to be regulated by the diurnal rhythm and suppressed by auxin. DR5::GUS expression and root responses to auxin were altered in AtNCL mutants. The auxin-induced suppression of AtNCL was attenuated in SLR/IAA14 and ARF6/8 mutants. The mutants with altered AtNCL expression also altered flowering time and FT and CO expression; FT may mediate AtNCL-regulated flowering time change. Therefore, AtNCL is a vacuolar Ca(2+) -regulated Na(+) /Ca(2+) exchanger that regulates auxin responses and flowering time.
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Affiliation(s)
- Penghui Li
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430075, China
| | - Gaoyang Zhang
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430075, China
| | - Naomi Gonzales
- Children's Nutrition Research Center, USDA/ARS, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yingqing Guo
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430075, China
- Children's Nutrition Research Center, USDA/ARS, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Honghong Hu
- College of Life Science and technology, Huazhong Agricultural University, Wuhan, 430075, China
| | - Sunghun Park
- Department of Horticulture, Forestry and Recreation Resources, Kansas State University, Manhattan, KS, 66506, USA
| | - Jian Zhao
- College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, 430075, China
- Children's Nutrition Research Center, USDA/ARS, Baylor College of Medicine, Houston, TX, 77030, USA
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Yu Y, Liu Z, Wang L, Kim SG, Seo PJ, Qiao M, Wang N, Li S, Cao X, Park CM, Xiang F. WRKY71 accelerates flowering via the direct activation of FLOWERING LOCUS T and LEAFY in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:96-106. [PMID: 26643131 DOI: 10.1111/tpj.13092] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 11/19/2015] [Accepted: 11/23/2015] [Indexed: 05/03/2023]
Abstract
Flowering is crucial for achieving reproductive success. A large number of well-delineated factors affecting flowering are involved in complex genetic networks in Arabidopsis thaliana. However, the underlying part played by the WRKY transcription factors in this process is not yet clear. Here, we report that WRKY71 is able to accelerate flowering in Arabidopsis. An activation-tagged mutant WRKY71-1D and a constitutive over-expresser of WRKY71 both flowered earlier than the wild type (WT). In contrast, both the RNA interference-based multiple WRKY knock-out mutant (w71w8 + 28RNAi) and the dominant repression line (W71-SRDX) flowered later. Gene expression analysis showed that the transcript abundance of the flowering time integrator gene FLOWERING LOCUS T (FT) and the floral meristem identity genes LEAFY (LFY), APETALA1 (AP1) and FRUITFULL (FUL) were greater in WRKY71-1D than in the WT, but lower in w71w8 + 28RNAi and W71-SRDX. Further, WRKY71 was shown to bind to the W-boxes in the FT and LFY promoters in vitro and in vivo. The suggestion is that WRKY71 activity hastens flowering via the direct activation of FT and LFY.
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Affiliation(s)
- Yanchong Yu
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Zhenhua Liu
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Long Wang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Sang-Gyu Kim
- Molecular Signaling Laboratory, Department of Chemistry, Seoul National University, Seoul, 151-742, Korea
| | - Pil J Seo
- Molecular Signaling Laboratory, Department of Chemistry, Seoul National University, Seoul, 151-742, Korea
| | - Meng Qiao
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Nan Wang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Shuo Li
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, School of Life Sciences, Shandong University, Jinan, 250100, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chung-Mo Park
- Molecular Signaling Laboratory, Department of Chemistry, Seoul National University, Seoul, 151-742, Korea
| | - Fengning Xiang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, School of Life Sciences, Shandong University, Jinan, 250100, China
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Yamaguchi N, Jeong CW, Nole-Wilson S, Krizek BA, Wagner D. AINTEGUMENTA and AINTEGUMENTA-LIKE6/PLETHORA3 Induce LEAFY Expression in Response to Auxin to Promote the Onset of Flower Formation in Arabidopsis. PLANT PHYSIOLOGY 2016; 170:283-93. [PMID: 26537561 PMCID: PMC4704571 DOI: 10.1104/pp.15.00969] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 11/03/2015] [Indexed: 05/06/2023]
Abstract
Proper timing of the onset to flower formation is critical for reproductive success. Monocarpic plants like Arabidopsis (Arabidopsis thaliana) switch from production of branches in the axils of leaves to that of flowers once in their lifecycle, during the meristem identity transition. The plant-specific transcription factor LEAFY (LFY) is necessary and sufficient for this transition. Previously, we reported that the plant hormone auxin induces LFY expression through AUXIN RESPONSE FACTOR5/MONOPTEROS (ARF5/MP). It is not known whether MP is solely responsible for auxin-directed transcriptional activation of LFY. Here, we show that two transcription factors belonging to the AINTEGUMENTA-LIKE/PLETHORA family, AINTEGUMENTA (ANT) and AINTEGUMENTA-LIKE6/PLETHORA3 (AIL6/PLT3), act in parallel with MP to upregulate LFY in response to auxin. ant ail6 mutants display a delay in the meristem identity transition and in LFY induction. ANT and AIL6/PLT3 are expressed prior to LFY and bind to the LFY promoter to control LFY mRNA accumulation. Genetic and promoter/reporter studies suggest that ANT/AIL6 act in parallel with MP to promote LFY induction in response to auxin sensing. Our study highlights the importance of two separate auxin-controlled pathways in the meristem identity transition.
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Affiliation(s)
- Nobutoshi Yamaguchi
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6018 (N.Y., C.W.J., D.W.); andDepartment of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208 (S.N.-W., B.A.K.)
| | - Cheol Woong Jeong
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6018 (N.Y., C.W.J., D.W.); andDepartment of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208 (S.N.-W., B.A.K.)
| | - Staci Nole-Wilson
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6018 (N.Y., C.W.J., D.W.); andDepartment of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208 (S.N.-W., B.A.K.)
| | - Beth A Krizek
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6018 (N.Y., C.W.J., D.W.); andDepartment of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208 (S.N.-W., B.A.K.)
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6018 (N.Y., C.W.J., D.W.); andDepartment of Biological Sciences, University of South Carolina, Columbia, South Carolina 29208 (S.N.-W., B.A.K.)
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Jang S. Functional Characterization of PhapLEAFY, a FLORICAULA/LEAFY Ortholog in Phalaenopsis aphrodite. PLANT & CELL PHYSIOLOGY 2015; 56:2234-47. [PMID: 26493518 DOI: 10.1093/pcp/pcv130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 08/31/2015] [Indexed: 05/05/2023]
Abstract
The plant-specific transcription factor LEAFY (LFY) is considered to be a master regulator of flower development in the model plant, Arabidopsis. This protein plays a dual role in plant growth, integrating signals from the floral inductive pathways and acting as a floral meristem identity gene by activating genes for floral organ development. Although LFY occupies an important position in flower development, the functional divergence of LFY homologs has been demonstrated in several plants including monocots and gymnosperms. In particular, the functional roles of LFY genes from orchid species such as Phalaenopsis that contain unique floral morphologies with distinct expression patterns of floral organ identity genes remain elusive. Here, PhapLFY, an ortholog of Arabidopsis LFY from Phalaenopsis aphrodite subsp. formosana, a Taiwanese native monopodial orchid, was isolated and characterized through analyses of expression and protein activity. PhapLFY transcripts accumulated in the floral primordia of developing inflorescences, and the PhapLFY protein had transcriptional autoactivation activity forming as a homodimer. Furthermore, PhapLFY rescues the aberrant floral phenotypes of Arabidopsis lfy mutants. Overexpression of PhapLFY alone or together with PhapFT1, a P. aphrodite subsp. formosana homolog of Arabidopsis FLOWERING LOCUS T (FT) in rice, caused precocious heading. Consistently, a higher Chl content in the sepals and morphological changes in epidermal cells were observed in the floral organs of PhapLFY knock-down orchids generated by virus-induced gene silencing. Taken together, these results suggest that PhapLFY is functionally distinct from RICE FLORICAULA/LEAFY (RFL) but similar to Arabidopsis LFY based on phenotypes of our transgenic Arabidopsis and rice plants.
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Affiliation(s)
- Seonghoe Jang
- Biotechnology Center in Southern Taiwan (BCST), No. 59, Siraya Blvd, Xinshi Dist., Tainan 74145/Agricultural Biotechnology Research Center, Academia Sinica, No. 128, Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan Institute of Tropical Plant Science, National Cheng Kung University, No. 1 University Road, East Dist., Tainan 70101, Taiwan
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Winter CM, Yamaguchi N, Wu MF, Wagner D. Transcriptional programs regulated by both LEAFY and APETALA1 at the time of flower formation. PHYSIOLOGIA PLANTARUM 2015; 155:55-73. [PMID: 26096587 PMCID: PMC5757833 DOI: 10.1111/ppl.12357] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 06/09/2015] [Indexed: 05/24/2023]
Abstract
Two key regulators of the switch to flower formation and of flower patterning in Arabidopsis are the plant-specific helix-turn-helix transcription factor LEAFY (LFY) and the MADS box transcription factor APETALA1 (AP1). The interactions between these two transcriptional regulators are complex. AP1 is both a direct target of LFY and can act in parallel with LFY. Available genetic and molecular evidence suggests that LFY and AP1 together orchestrate the switch to flower formation and early events during flower morphogenesis by altering transcriptional programs. However, very little is known about target genes regulated by both transcription factors. Here, we performed a meta-analysis of public datasets to identify genes that are likely to be regulated by both LFY and AP1. Our analyses uncovered known and novel direct LFY and AP1 targets with a role in the control of onset of flower formation. It also identified additional families of proteins and regulatory pathways that may be under transcriptional control by both transcription factors. In particular, several of these genes are linked to response to hormones, to transport and to development. Finally, we show that the gibberellin catabolism enzyme ELA1, which was recently shown to be important for the timing of the switch to flower formation, is positively feedback-regulated by AP1. Our study contributes to the elucidation of the regulatory network that leads to formation of a vital plant organ system, the flower.
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Affiliation(s)
- Cara M. Winter
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Nobutoshi Yamaguchi
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Miin-Feng Wu
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
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Zhao JL, Wang YL, Yao DQ, Zhu WY, Chen L, He HL, Pan JS, Cai R. Transcriptome profiling of trichome-less reveals genes associated with multicellular trichome development in Cucumis sativus. Mol Genet Genomics 2015; 290:2007-18. [PMID: 25952908 DOI: 10.1007/s00438-015-1057-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 04/22/2015] [Indexed: 11/28/2022]
Abstract
Trichomes on plants, similar to fine hairs on animal and human bodies, play important roles in plant survival and development. They also represent a useful model for the study of cell differentiation. Although the regulatory gene network of unicellular trichome development in Arabidopsis thaliana has been well studied, the genes that regulate multicellular trichome development remain unclear. We confirmed that Cucumis sativus (cucumber) trichomes are multicellular and unbranched, but identified a spontaneous mutant, trichome-less (tril), which presented a completely glabrous phenotype. We compared the transcriptome profilings of the tril mutant and wild type using the Illumina HiSeq 2000 sequencing technology. A total of 991 genes exhibited differential expression: 518 were up-regulated and 473 were down-regulated. We further identified 62 differentially expressed genes that encoded crucial transcription factors and were subdivided into seven categories: homeodomain, MADS, MYB, and WRKY domains, ethylene-responsive, zinc finger, and other transcription factor genes. We further analyzed the tissue-expression profiles of two candidate genes, GLABRA2-like and ATHB51-like, using qRT-PCR and found that these two genes were specifically expressed in the epidermis and trichomes, respectively. These results and the tril mutant provide useful tools to study the molecular networks associated with multicellular trichome development.
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Affiliation(s)
- Jun-Long Zhao
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Yun-Li Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Dan-Qing Yao
- Shanghai Seed Management Station, 628 Wuzhong Road, Minhang District, Shanghai, 201103, China
| | - Wen-Ying Zhu
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Long Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Huan-Le He
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China
| | - Jun-Song Pan
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China.
| | - Run Cai
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai, 200240, China.
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Wan H, Chang S, Hu JP, Tian YX, Tian XH. Molecular Dynamics Simulations of Ternary Complexes: Comparisons of LEAFY Protein Binding to Different DNA Motifs. J Chem Inf Model 2015; 55:784-94. [PMID: 25734970 DOI: 10.1021/ci500705j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
LEAFY (LFY) is a plant-specific transcription factor, with a variety of roles in different species. LFY contains a conserved DNA-binding domain (DBD) that determines its DNA-binding specificity. Recently, the structures of the dimeric LFY-DBD bound to different DNA motifs were successively solved by X-ray crystallography. In this article, molecular dynamics (MD) simulations are employed to study two crystal structures of DNA-bound LFY protein from angiosperms and the moss Physcomitrella patens, respectively. The comparison of stabilities of the two systems is consistent with the experimental data of binding affinities. The calculation of hydrogen bonds showed that position 312 in LFY determines the difference of DNA-binding specificity. By using principal component analysis (PCA) and free energy landscape (FEL) methods, the open-close conformational change of the dimerization interface was found to be important for the system stability. At the dimerization interface, the protein-protein interaction has multiple influences on the cooperative DNA binding of LFY. The following analysis of DNA structural parameters further revealed that the protein-protein interaction contributes varying roles according to the specific DNA-binding efficiency. We propose that the protein-protein interaction serves a dual function as a connector between LFY monomers and a regulator of DNA-binding specificity. It will improve the robustness and adaptivity of the LFY-DNA ternary structure. This study provides some new insights into the understanding of the dynamics and interaction mechanism of dimeric LFY-DBD bound to DNA at the atomic level.
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Affiliation(s)
- Hua Wan
- †College of Informatics, South China Agricultural University, Guangzhou 510642, China
| | - Shan Chang
- ‡Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Jian-ping Hu
- §Faculty of Biotechnology Industry, Chengdu University, Chengdu 610106, China
| | - Yuan-xin Tian
- ∥School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xu-hong Tian
- †College of Informatics, South China Agricultural University, Guangzhou 510642, China
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Yamaguchi N, Winter CM, Wellmer F, Wagner D. Identification of direct targets of plant transcription factors using the GR fusion technique. Methods Mol Biol 2015; 1284:123-38. [PMID: 25757770 PMCID: PMC5757826 DOI: 10.1007/978-1-4939-2444-8_6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The glucocorticoid receptor-dependent activation of plant transcription factors has proven to be a powerful tool for the identification of their direct target genes. In the absence of the synthetic steroid hormone dexamethasone (dex), transcription factors fused to the hormone-binding domain of the glucocorticoid receptor (TF-GR) are held in an inactive state, due to their cytoplasmic localization. This requires physical interaction with the heat shock protein 90 (HSP90) complex. Hormone binding leads to disruption of the interaction between GR and HSP90 and allows TF-GR fusion proteins to enter the nucleus. Once inside the nucleus, they bind to specific DNA sequences and immediately activate or repress expression of their targets. This system is well suited for the identification of direct target genes of transcription factors in plants, as (A) there is little basal protein activity in the absence of dex, (B) steroid application leads to rapid transcription factor activation, (C) no side effects of dex treatment are observed on the physiology of the plant, and (D) secondary effects of transcription factor activity can be eliminated by simultaneous application of an inhibitor of protein biosynthesis, cycloheximide (cyc). In this chapter, we describe detailed protocols for the preparation of plant material, for dex and cyc treatment, for RNA extraction, and for the PCR-based or genome-wide identification of direct targets of transcription factors fused to GR.
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Affiliation(s)
- Nobutoshi Yamaguchi
- Department of Biology, University of Pennsylvania, 415 S. University Ave., Philadelphia, PA, 19104-6018, USA
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Hepworth SR, Pautot VA. Beyond the Divide: Boundaries for Patterning and Stem Cell Regulation in Plants. FRONTIERS IN PLANT SCIENCE 2015; 6:1052. [PMID: 26697027 PMCID: PMC4673312 DOI: 10.3389/fpls.2015.01052] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 11/12/2015] [Indexed: 05/04/2023]
Abstract
The initiation of plant lateral organs from the shoot apical meristem (SAM) is closely associated with the formation of specialized domains of restricted growth known as the boundaries. These zones are required in separating the meristem from the growing primordia or adjacent organs but play a much broader role in regulating stem cell activity and shoot patterning. Studies have revealed a network of genes and hormone pathways that establish and maintain boundaries between the SAM and leaves. Recruitment of these pathways is shown to underlie a variety of processes during the reproductive phase including axillary meristems production, flower patterning, fruit development, and organ abscission. This review summarizes the role of conserved gene modules in patterning boundaries throughout the life cycle.
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Affiliation(s)
- Shelley R. Hepworth
- Department of Biology, Institute of Biochemistry, Carleton University, OttawaON, Canada
- *Correspondence: Shelley R. Hepworth, ; Véronique A. Pautot,
| | - Véronique A. Pautot
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Université Paris-SaclayVersailles, France
- *Correspondence: Shelley R. Hepworth, ; Véronique A. Pautot,
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50
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Benlloch R, Berbel A, Ali L, Gohari G, Millán T, Madueño F. Genetic control of inflorescence architecture in legumes. FRONTIERS IN PLANT SCIENCE 2015; 6:543. [PMID: 26257753 PMCID: PMC4508509 DOI: 10.3389/fpls.2015.00543] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 07/06/2015] [Indexed: 05/18/2023]
Abstract
The architecture of the inflorescence, the shoot system that bears the flowers, is a main component of the huge diversity of forms found in flowering plants. Inflorescence architecture has also a strong impact on the production of fruits and seeds, and on crop management, two highly relevant agronomical traits. Elucidating the genetic networks that control inflorescence development, and how they vary between different species, is essential to understanding the evolution of plant form and to being able to breed key architectural traits in crop species. Inflorescence architecture depends on the identity and activity of the meristems in the inflorescence apex, which determines when flowers are formed, how many are produced and their relative position in the inflorescence axis. Arabidopsis thaliana, where the genetic control of inflorescence development is best known, has a simple inflorescence, where the primary inflorescence meristem directly produces the flowers, which are thus borne in the main inflorescence axis. In contrast, legumes represent a more complex inflorescence type, the compound inflorescence, where flowers are not directly borne in the main inflorescence axis but, instead, they are formed by secondary or higher order inflorescence meristems. Studies in model legumes such as pea (Pisum sativum) or Medicago truncatula have led to a rather good knowledge of the genetic control of the development of the legume compound inflorescence. In addition, the increasing availability of genetic and genomic tools for legumes is allowing to rapidly extending this knowledge to other grain legume crops. This review aims to describe the current knowledge of the genetic network controlling inflorescence development in legumes. It also discusses how the combination of this knowledge with the use of emerging genomic tools and resources may allow rapid advances in the breeding of grain legume crops.
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Affiliation(s)
- Reyes Benlloch
- Molecular Genetics Department, Center for Research in Agricultural Genomics, Consortium CSIC-IRTA-UAB-UB, Parc de Recerca Universitat Autònoma de BarcelonaBarcelona, Spain
| | - Ana Berbel
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas – Universidad Politécnica de ValenciaValencia, Spain
| | - Latifeh Ali
- Departamento de Genética, Universidad de CórdobaCórdoba, Spain
| | - Gholamreza Gohari
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas – Universidad Politécnica de ValenciaValencia, Spain
| | - Teresa Millán
- Departamento de Genética, Universidad de CórdobaCórdoba, Spain
| | - Francisco Madueño
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas – Universidad Politécnica de ValenciaValencia, Spain
- *Correspondence: Francisco Madueño, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas – Universidad Politécnica de Valencia, Avenida Los Naranjos s/n, Valencia 46022, Spain,
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