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Bhattacharjee S, Bhowmick R, Paul K, Venkat Raman K, Jaiswal S, Tilgam J, Saakre M, Kumari P, Baaniya M, Vijayan J, Sreevathsa R, Pattanayak D. Identification, characterization, and comprehensive expression profiling of floral master regulators in pigeon pea (Cajanus cajan [L.] Millspaugh). Funct Integr Genomics 2023; 23:311. [PMID: 37751043 DOI: 10.1007/s10142-023-01236-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/04/2023] [Accepted: 09/15/2023] [Indexed: 09/27/2023]
Abstract
Pigeon pea is an important protein-rich pulse crop. Identification of flowering master regulators in pigeon pea is highly imperative as indeterminacy and late flowering are impediments towards yield improvement. A genome-wide analysis was performed to explore flowering orthologous groups in pigeon pea. Among the 412 floral orthologs identified in pigeon pea, 148 genes belong to the meristem identity, photoperiod-responsive, and circadian clock-associated ortholog groups. Our comparative genomics study revealed purifying selection pressures (ka/ks) on floral orthologs, and duplication patterns and evolution through synteny with other model species. Phylogenetic analysis of floral genes substantiated a connection between pigeon pea plant architecture and flowering time as all the PEBP domain-containing genes belong to meristem identity floral networks of pigeon pea. Expression profiling of eleven major orthologs in contrasting determinate and indeterminate genotypes indicated that these orthologs might be involved in flowering regulation. Expression of floral inducer, FT, and floral repressor, TFL1, was non-comparable in indeterminate genotypes across all the developmental stages of pigeon pea. However, dynamic FT/TFL1 expression ratio detected in all tissues of both the genotypes suggested their role in floral transition. One TFL1 ortholog having high sequence conserveness across pigeon pea genotypes showed differential expression indicating genotype-dependent regulation of this ortholog. Presence of conserved 6mA-methylation patterns in light-responsive elements and in other cis-regulatory elements of FT and TFL1 across different plant genotypes indicated possible involvement of epigenetic regulation in flowering.
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Affiliation(s)
- Sougata Bhattacharjee
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Rakesh Bhowmick
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata, India
| | - Krishnayan Paul
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - K Venkat Raman
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Sandeep Jaiswal
- ICAR Research Complex for North Eastern Hill Region, Barapani, Meghalaya, India
| | - Jyotsana Tilgam
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Manjesh Saakre
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Priyanka Kumari
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Mahi Baaniya
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Joshitha Vijayan
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Rohini Sreevathsa
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Debasis Pattanayak
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India.
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2
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Weng X, Song H, Sreedasyam A, Haque T, Zhang L, Chen C, Yoshinaga Y, Williams M, O'Malley RC, Grimwood J, Schmutz J, Juenger TE. Transcriptome and DNA methylome divergence of inflorescence development between two ecotypes in Panicum hallii. PLANT PHYSIOLOGY 2023:kiad209. [PMID: 37018475 DOI: 10.1093/plphys/kiad209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 06/19/2023]
Abstract
The morphological diversity of the inflorescence determines flower and seed production, which is critical for plant adaptation. Hall's panicgrass (Panicum hallii, P. hallii) is a wild perennial grass that has been developed as a model to study perennial grass biology and adaptive evolution. Highly divergent inflorescences have evolved between the two major ecotypes in P. hallii, the upland ecotype (P. hallii var hallii, HAL2 genotype) with compact inflorescence and large seed and the lowland ecotype (P. hallii var filipes, FIL2 genotype) with an open inflorescence and small seed. Here we conducted a comparative analysis of the transcriptome and DNA methylome, an epigenetic mark that influences gene expression regulation, across different stages of inflorescence development using genomic references for each ecotype. Global transcriptome analysis of differentially expressed genes (DEGs) and co-expression modules underlying the inflorescence divergence revealed the potential role of cytokinin signaling in heterochronic changes. Comparing DNA methylome profiles revealed a remarkable level of differential DNA methylation associated with the evolution of P. hallii inflorescence. We found that a large proportion of differentially methylated regions (DMRs) were located in the flanking regulatory regions of genes. Intriguingly, we observed a substantial bias of CHH hypermethylation in the promoters of FIL2 genes. The integration of DEGs, DMRs, and Ka/Ks ratio results characterized the evolutionary features of DMRs-associated DEGs that contribute to the divergence of the P. hallii inflorescence. This study provides insights into the transcriptome and epigenetic landscape of inflorescence divergence in P. hallii and a genomic resource for perennial grass biology.
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Affiliation(s)
- Xiaoyu Weng
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Haili Song
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | | | - Taslima Haque
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Li Zhang
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Cindy Chen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yuko Yoshinaga
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Ronan C O'Malley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
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3
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Osnato M, Cota I, Nebhnani P, Cereijo U, Pelaz S. Photoperiod Control of Plant Growth: Flowering Time Genes Beyond Flowering. FRONTIERS IN PLANT SCIENCE 2022; 12:805635. [PMID: 35222453 PMCID: PMC8864088 DOI: 10.3389/fpls.2021.805635] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/23/2021] [Indexed: 05/02/2023]
Abstract
Fluctuations in environmental conditions greatly influence life on earth. Plants, as sessile organisms, have developed molecular mechanisms to adapt their development to changes in daylength, or photoperiod. One of the first plant features that comes to mind as affected by the duration of the day is flowering time; we all bring up a clear image of spring blossom. However, for many plants flowering happens at other times of the year, and many other developmental aspects are also affected by changes in daylength, which range from hypocotyl elongation in Arabidopsis thaliana to tuberization in potato or autumn growth cessation in trees. Strikingly, many of the processes affected by photoperiod employ similar gene networks to respond to changes in the length of light/dark cycles. In this review, we have focused on developmental processes affected by photoperiod that share similar genes and gene regulatory networks.
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Affiliation(s)
- Michela Osnato
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
- Institute of Environmental Science and Technology of the Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ignacio Cota
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Poonam Nebhnani
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Unai Cereijo
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Soraya Pelaz
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
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4
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Liu L, Chai M, Huang Y, Qi J, Zhu W, Xi X, Chen F, Qin Y, Cai H. SDG2 regulates Arabidopsis inflorescence architecture through SWR1-ERECTA signaling pathway. iScience 2021; 24:103236. [PMID: 34746701 PMCID: PMC8551540 DOI: 10.1016/j.isci.2021.103236] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 08/30/2021] [Accepted: 10/04/2021] [Indexed: 12/21/2022] Open
Abstract
Inflorescence architecture is diverse in flowering plants, and two determinants of inflorescence architecture are the inflorescence meristem and pedicel length. Although the ERECTA (ER) signaling pathway, in coordination with the SWR1 chromatin remodeling complex, regulates inflorescence architecture with subsequent effects on pedicel elongation, the mechanism underlying SWR1-ER signaling pathway regulation of inflorescence architecture remains unclear. This study determined that SDG2 genetically interacts with the SWR1-ER signaling pathways in regulating inflorescence architecture. Transcriptome results showed that auxin might potentially influence inflorescence growth mediated by SDG2 and SWR1-ER pathways. SWR1 and ER signaling are required to enrich H2A.Z histone variant and SDG2 regulated SDG2-mediated H3K4me3 histone modification at auxin-related genes and H2A.Z histone variant enrichment. Our study shows how the regulation of inflorescence architecture is mediated by SDG2 and SWR1-ER, which affects auxin hormone signaling pathways.
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Affiliation(s)
- Liping Liu
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mengnan Chai
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Youmei Huang
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jingang Qi
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenhui Zhu
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xinpeng Xi
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Fangqian Chen
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuan Qin
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Hanyang Cai
- College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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5
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Geleta M, Gustafsson C, Glaubitz JC, Ortiz R. High-Density Genetic Linkage Mapping of Lepidium Based on Genotyping-by-Sequencing SNPs and Segregating Contig Tag Haplotypes. FRONTIERS IN PLANT SCIENCE 2020; 11:448. [PMID: 32425961 PMCID: PMC7204607 DOI: 10.3389/fpls.2020.00448] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 03/26/2020] [Indexed: 05/09/2023]
Abstract
Lepidium campestre has been targeted for domestication as future oilseed and catch crop. Three hundred eighty plants comprising genotypes of L. campestre, Lepidium heterophyllum, and their interspecific F2 mapping population were genotyped using genotyping by sequencing (GBS), and the generated polymorphic markers were used for the construction of high-density genetic linkage map. TASSEL-GBS, a reference genome-based pipeline, was used for this analysis using a draft L. campestre whole genome sequence. The analysis resulted in 120,438 biallelic single-nucleotide polymorphisms (SNPs) with minor allele frequency (MAF) above 0.01. The construction of genetic linkage map was conducted using MSTMap based on phased SNPs segregating in 1:2:1 ratio for the F2 individuals, followed by genetic mapping of segregating contig tag haplotypes as dominant markers against the linkage map. The final linkage map consisted of eight linkage groups (LGs) containing 2,330 SNP markers and spanned 881 Kosambi cM. Contigs (10,302) were genetically mapped to the eight LGs, which were assembled into pseudomolecules that covered a total of ∼120.6 Mbp. The final size of the pseudomolecules ranged from 9.4 Mbp (LG-4) to 20.4 Mpb (LG-7). The following major correspondence between the eight Lepidium LGs (LG-1 to LG-8) and the five Arabidopsis thaliana (At) chromosomes (Atx-1-Atx-5) was revealed through comparative genomics analysis: LG-1&2_Atx-1, LG-3_Atx-2&3, LG-4_Atx-2, LG-5_Atx-2&Atx-3, LG-6_Atx-4&5, LG-7_Atx-4, and LG-8_Atx-5. This analysis revealed that at least 66% of the sequences of the LGs showed high collinearity with At chromosomes. The sequence identity between the corresponding regions of the LGs and At chromosomes ranged from 80.6% (LG-6) to 86.4% (LG-8) with overall mean of 82.9%. The map positions on Lepidium LGs of the homologs of 24 genes that regulate various traits in A. thaliana were also identified. The eight LGs revealed in this study confirm the previously reported (1) haploid chromosome number of eight in L. campestre and L. heterophyllum and (2) chromosomal fusion, translocation, and inversion events during the evolution of n = 8 karyotype in ancestral species shared by Lepidium and Arabidopsis to n = 5 karyotype in A. thaliana. This study generated highly useful genomic tools and resources for Lepidium that can be used to accelerate its domestication.
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Affiliation(s)
- Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Cecilia Gustafsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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6
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Asadi Khanouki M, Rezanejad F, Millar AA. Sequence and functional analysis of a TERMINAL FLOWER 1 homolog from Brassica juncea: a putative biotechnological tool for flowering time adjustment. GM CROPS & FOOD 2020; 11:79-92. [PMID: 31876221 DOI: 10.1080/21645698.2019.1707340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Flowering time is an important agricultural trait of the oil crop Brassica juncea (B. juncea), as accelerated flowering enables avoidance of terminal drought leading to increased yields. One gene known to control flowering time is TERMINAL FLOWER 1 (TFL1), which belongs to a family of phosphatidylethanolamine binding proteins, which can either repress or promote flowering time. Here, a TFL1 homolog, named BjTFL1, has been isolated from B. juncea, which shared 95% amino acid identity with TFL1 from Arabidopsis thaliana. Sequence analysis predicts the BjTFL1 protein contains the ligand-binding site, conserved motifs and other amino acid residues that are critical for TFL1 function. Confirming this as a functional TFL1 orthologue, overexpression of BjTFL1 under the control of the constitutive 35S promoter in Arabidopsis delayed flowering time. As a proof-of-concept to investigate its utility to shorten flowering time, an RNAi construct containing a partial sequence of BjTFL1 was transformed into Arabidopsis. Transcript analysis demonstrated the downregulation of endogenous AtTFL1. Moreover, the RNAi BjTFL1 transgenic lines were early flowering and had fewer rosette and cauline leaves compared to wild-type. Therefore, this BjTFL1 RNAi transgene could be used as a biotechnological tool to reduce flowering time in Brassica juncea in a bid to improve agricultural performance.
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Affiliation(s)
- Mohsen Asadi Khanouki
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Farkhondeh Rezanejad
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Anthony A Millar
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, Australia
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7
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Zhu K, Zhang W, Sarwa R, Xu S, Li K, Yang Y, Li Y, Wang Z, Cao J, Li Y, Tan X. Proteomic analysis of a clavata-like phenotype mutant in Brassica napus. Genet Mol Biol 2020; 43:e20190305. [PMID: 32154828 PMCID: PMC7198001 DOI: 10.1590/1678-4685-gmb-2019-0305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 01/08/2020] [Indexed: 12/29/2022] Open
Abstract
Rapeseed is one of important oil crops in China. Better understanding of the
regulation network of main agronomic traits of rapeseed could improve the
yielding of rapeseed. In this study, we obtained an influrescence mutant that
showed a fusion phenotype, similar with the Arabidopsis
clavata-like phenotype, so we named the mutant as
Bnclavata-like (Bnclv-like). Phenotype
analysis illustrated that abnormal development of the inflorescence meristem
(IM) led to the fused-inflorescence phenotype. At the stage of protein
abundance, major regulators in metabolic processes, ROS metabolism, and
cytoskeleton formation were seen to be altered in this mutant. These results not
only revealed the relationship between biological processes and inflorescence
meristem development, but also suggest bioengineering strategies for the
improved breeding and production of Brassica napus.
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Affiliation(s)
- Keming Zhu
- Jiangsu University, Institute of Life Sciences, Zhenjiang, Jiangsu, China.,Ministry of Agriculture, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Wuhan, China
| | - Weiwei Zhang
- Jiangsu University, Institute of Life Sciences, Zhenjiang, Jiangsu, China
| | - Rehman Sarwa
- Jiangsu University, Institute of Life Sciences, Zhenjiang, Jiangsu, China
| | - Shuo Xu
- Jiangsu University, Institute of Life Sciences, Zhenjiang, Jiangsu, China
| | - Kaixia Li
- Jiangsu University, Institute of Life Sciences, Zhenjiang, Jiangsu, China
| | - Yanhua Yang
- Jiangsu University, Institute of Life Sciences, Zhenjiang, Jiangsu, China
| | - Yulong Li
- Jiangsu University, Institute of Life Sciences, Zhenjiang, Jiangsu, China
| | - Zheng Wang
- Jiangsu University, Institute of Life Sciences, Zhenjiang, Jiangsu, China
| | - Jun Cao
- Jiangsu University, Institute of Life Sciences, Zhenjiang, Jiangsu, China
| | - Yaoming Li
- Jiangsu University, Institute of Agricultural Engineering, Zhenjiang, China
| | - Xiaoli Tan
- Jiangsu University, Institute of Life Sciences, Zhenjiang, Jiangsu, China
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8
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System Analysis of MIRNAs in Maize Internode Elongation. Biomolecules 2019; 9:biom9090417. [PMID: 31461907 PMCID: PMC6769733 DOI: 10.3390/biom9090417] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/23/2019] [Accepted: 08/24/2019] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs), the post-transcriptional gene regulators, are known to play an important role in plant development. The identification of differentially expressed miRNAs could better help us understand the post-transcriptional regulation that occurs during maize internode elongation. Accordingly, we compared the expression of MIRNAs between fixed internode and elongation internode samples and classified six differentially expressed MIRNAs as internode elongation-responsive miRNAs including zma-MIR160c, zma-MIR164b, zma-MIR164c, zma-MIR168a, zma-MIR396f, and zma-MIR398b, which target mRNAs supported by transcriptome sequencing. Functional enrichment analysis for predictive target genes showed that these miRNAs were involved in the development of internode elongation by regulating the genes respond to hormone signaling. To further reveal how miRNA affects internode elongation by affecting target genes, the miRNA–mRNA–PPI (protein and protein interaction) network was constructed to summarize the interaction of miRNAs and these target genes. Our results indicate that miRNAs regulate internode elongation in maize by targeting genes related to cell expansion, cell wall synthesis, transcription, and regulatory factors.
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9
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Sun W, Chen D, Xue Y, Zhai L, Zhang D, Cao Z, Liu L, Cheng C, Zhang Y, Zhang Z. Genome-wide identification of AGO18b-bound miRNAs and phasiRNAs in maize by cRIP-seq. BMC Genomics 2019; 20:656. [PMID: 31419938 PMCID: PMC6697968 DOI: 10.1186/s12864-019-6028-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 08/12/2019] [Indexed: 12/20/2022] Open
Abstract
Background Argonaute proteins (AGOs) are important players in the regulation of plant development by directing sRNAs to target mRNAs. In maize (Zea mays), AGO18b is a tassel-enriched and grass-specific AGO. Previous studies have shown that AGO18b is highly expressed in tassels during meiosis and negatively regulates determinacy of spikelet meristems. However, binding profile on RNAs and acting mechanisms of AGO18b remain unknown. Results In this study, we explored the binding profile of AGO18b in maize tassel by UV cross-linking RNA immunoprecipitation, followed by deep sequencing of these cDNA libraries (cRIP-seq), and systematically studied AGO18b-associated small RNAs and mRNAs by bioinformatics analysis. By globally analyzing the phased small-interfering RNA (phasiRNA) and miRNA abundance bound by AGO18b, we found AGO18b primarily binds to 21-nt phasiRNAs/miRNAs with a 5′-uridine and binds less strongly to 24-nt phasiRNAs with a 5′-adenosine in the premeiotic tassels. The abundance profile of AGO18b-associated miRNAs was different from their expression profile. Moreover, AGO18b strongly binds to miR166a-3p. We then obtained the AGO18b-bound mRNA targets of miR166a-3p by cRIP-seq, and confirmed the molecular function of AGO18b in regulating spikelet meristems. Conclusions Our results indicated that AGO18b binds to phasiRNAs with obvious 5 prime end bias under different sRNA length. MiRNAs and their target mRNAs associated with AGO18b indicated the molecular mechanisms of AGO18b as a negative regulator of inflorescence meristem and tassel development through integrating both phasiRNAs and miRNA pathways, which extended our view of sRNA regulation in flower development and provided potential methods to control pollination in the future. Electronic supplementary material The online version of this article (10.1186/s12864-019-6028-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei Sun
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, People's Republic of China.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Dong Chen
- Center for Genome Analysis, ABLife Inc, Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China
| | - Yaqiang Xue
- Laboratory for Genome Regulation and Human Health, ABLife Inc, Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China
| | - Lihong Zhai
- Medical College of Hubei University of Arts and Science, Xiangyang, 441053, People's Republic of China
| | - Dan Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Zheng Cao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Lei Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Chao Cheng
- Center for Genome Analysis, ABLife Inc, Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China
| | - Yi Zhang
- Center for Genome Analysis, ABLife Inc, Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China. .,Laboratory for Genome Regulation and Human Health, ABLife Inc, Optics Valley International Biomedical Park, Building 9-4, East Lake High-Tech Development Zone, 388 Gaoxin 2nd Road, Wuhan, 430075, Hubei, China.
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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10
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Périlleux C, Bouché F, Randoux M, Orman-Ligeza B. Turning Meristems into Fortresses. TRENDS IN PLANT SCIENCE 2019; 24:431-442. [PMID: 30853243 DOI: 10.1016/j.tplants.2019.02.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/25/2019] [Accepted: 02/04/2019] [Indexed: 05/18/2023]
Abstract
TERMINAL FLOWER1 (TFL1) was named from knockout Arabidopsis thaliana mutants in which the inflorescence abnormally terminates into a flower. In wild type plants, the expression of TFL1 in the center of the inflorescence meristem represses the flower meristem identity genes LEAFY (LFY) and APETALA1 (AP1) to maintain indeterminacy. LFY and AP1 are activated by flowering signals that antagonize TFL1. Its characterization in numerous species revealed that the TFL1-mediated regulation of meristem fate has broader impacts on plant development than originally depicted in A. thaliana. By blocking floral transition, TFL1 genes participate in the control of juvenility, shoot growth pattern, inflorescence architecture, and the establishment of life history strategies. Here, we contextualize the role of the TFL1-mediated protection of meristem indeterminacy throughout plant development.
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Affiliation(s)
| | | | - Marie Randoux
- University of Liège, InBioS-PhytoSYSTEMS, Liège, Belgium
| | - Beata Orman-Ligeza
- University of Liège, InBioS-PhytoSYSTEMS, Liège, Belgium; Current address: National Institute of Agricultural Botany, Cambridge, UK
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11
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Liu D, Teng Z, Kong J, Liu X, Wang W, Zhang X, Zhai T, Deng X, Wang J, Zeng J, Xiao Y, Guo K, Zhang J, Liu D, Wang W, Zhang Z. Natural variation in a CENTRORADIALIS homolog contributed to cluster fruiting and early maturity in cotton. BMC PLANT BIOLOGY 2018; 18:286. [PMID: 30458710 PMCID: PMC6245773 DOI: 10.1186/s12870-018-1518-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 11/07/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Plant architecture and the vegetative-reproductive transition have major impacts on the agronomic success of crop plants, but genetic mechanisms underlying these traits in cotton (Gossypium spp.) have not been identified. RESULTS We identify four natural mutations in GoCEN-Dt associated with cluster fruiting (cl) and early maturity. The situ hybridization shows that GhCEN is preferentially expressed in cotton shoot apical meristems (SAM) of the main stem and axillary buds. Constitutive GhCEN-Dt overexpression suppresses the transition of the cotton vegetative apex to a reproductive shoot. Silencing GoCEN leads to early flowering and determinate growth, and in tetraploids causes the main stem to terminate in a floral bud, a novel phenotype that exemplifies co-adaptation of polyploid subgenomes and suggests new research and/or crop improvement approaches. Natural cl variations are enriched in cottons adapted to high latitudes with short frost-free periods, indicating that mutants of GoCEN have been strongly selected for early maturity. CONCLUSION We show that the cotton gene GoCEN-Dt, a homolog of Antirrhinum CENTRORADIALIS, is responsible for determinate growth habit and cluster fruiting. Insight into the genetic control of branch and flower differentiation offers new approaches to develop early maturing cultivars of cotton and other crops with plant architecture appropriate for mechanical harvesting.
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Affiliation(s)
- Dexin Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Zhonghua Teng
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Jie Kong
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, urumqi, Xinjiang 830091 People’s Republic of China
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Xueying Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Wenwen Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Xiao Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Tengfei Zhai
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Xianping Deng
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Jinxia Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Jianyan Zeng
- Biotechnology Research Center, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Yuehua Xiao
- Biotechnology Research Center, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Kai Guo
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Jian Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Dajun Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Weiran Wang
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, urumqi, Xinjiang 830091 People’s Republic of China
| | - Zhengsheng Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
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12
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Genome-Wide Analysis of DCL, AGO, and RDR Gene Families in Pepper (Capsicum Annuum L.). Int J Mol Sci 2018; 19:ijms19041038. [PMID: 29601523 PMCID: PMC5979589 DOI: 10.3390/ijms19041038] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 03/26/2018] [Accepted: 03/27/2018] [Indexed: 12/18/2022] Open
Abstract
RNA silencing is an evolutionarily conserved mechanism that regulates variety of cellular processes in plants. Argonaute protein (AGO), Dicer-like protein (DCL) and RNA-dependent RNA polymerase (RDR) are critical components of RNA silencing. These efficient and indispensable components of the RNAi pathway have not been identified and characterized in pepper. In this study, we identified 12 CaAGO, 4 CaDCL and 6 CaRDR genes in pepper and compared them with those of Arabidopsis, tobacco, potato and tomato. Detailed phylogenetic analyses revealed that each CaAGO, CaDCL and CaRDR protein family were classified into four clades. The tissue specific expression and respond to abiotic or biotic stress were studied. The real-time quantitative polymerase chain reaction (PCR) results demonstrated that CaAGO2, CaAGO10b, CaDCL2 and CaDCL4 were upregulated with cucumber mosaic virus (CMV), potato virus Y (PVY) and tobacco mosaic virus (TMV) infections, whereas they showed difference expression patterns in response to abiotic stress. In addition, we found that many of the candidate genes were induced by phytohormones and H2O2 treatment. Our results provide useful information for further elucidation of gene silencing pathways and RNAi-mediated host immunity in pepper.
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13
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Sun W, Xiang X, Zhai L, Zhang D, Cao Z, Liu L, Zhang Z. AGO18b negatively regulates determinacy of spikelet meristems on the tassel central spike in maize. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:65-78. [PMID: 28875539 DOI: 10.1111/jipb.12596] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 08/31/2017] [Indexed: 05/06/2023]
Abstract
The maize tassel represents an indeterminate male inflorescence. The number of primordia that a given inflorescence meristem produces is related to its determinacy, i.e., capacity for continued meristem activity. Transcription factors (TFs) controlling determinacy in tassel axillary meristems are well studied in maize, and small RNAs are known to influence tassel development by repressing targets, including tassel-related TFs. As core components of the RNA-inducible silence complex (RISC), Argonaute (AGO) proteins are required for small RNA-mediated repression. Here, we characterized the biological function of AGO18b, a tassel-enriched AGO. The abundance of AGO18b transcripts gradually increased during tassel development from inception to gametogenesis and were enriched in the inflorescence meristem and axillary meristems of the tassel. Repressing AGO18b expression resulted in more spikelets, which contributed to a longer central spike of the tassel. Additionally, the transcripts of several HD-ZIP III TFs that were canonical targets of microRNA166 (miR166) accumulated in the AGO18b-repressed lines. We propose that AGO18b is a negative regulator of the determinacy of inflorescence and axillary meristems, and that it acts by interacting with the miR166-HD-ZIP III TF regulatory pathway.
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Affiliation(s)
- Wei Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoli Xiang
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China
| | - Lihong Zhai
- Medical College of Hubei University of Arts and Science, Xiangyang 441053, China
| | - Dan Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Zheng Cao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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14
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Serrano-Mislata A, Fernández-Nohales P, Doménech MJ, Hanzawa Y, Bradley D, Madueño F. Separate elements of the TERMINAL FLOWER 1 cis-regulatory region integrate pathways to control flowering time and shoot meristem identity. Development 2016; 143:3315-27. [DOI: 10.1242/dev.135269] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 06/21/2016] [Indexed: 12/25/2022]
Abstract
TERMINAL FLOWER 1 (TFL1) is a key regulator of Arabidopsis plant architecture, which responds to developmental and environmental signals to control flowering time and the fate of shoot meristems. TFL1 expression pattern is dynamic, being found in all shoot meristems, but not in floral meristems, with its level and distribution changing throughout development. Using a variety of experimental approaches, we have analysed the TFL1 promoter to elucidate its functional structure. TFL1 expression is based on distinct cis-regulatory regions, the most important ones located 3' of the coding sequence. Our results indicate that TFL1 expression in the shoot apical vs. lateral inflorescence meristems is controlled through distinct cis-regulatory elements, suggesting that different signals control expression in these meristem types. Moreover, we identified a cis-regulatory region necessary for TFL1 expression in the vegetative shoot, required for a wild-type flowering time, supporting that TFL1 expression in the vegetative meristem controls flowering time. Our study provides a model for the functional organization of TFL1 cis-regulatory regions, contributing to understanding of how developmental pathways are integrated at the genomic level of a key regulator to control plant architecture.
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Affiliation(s)
- Antonio Serrano-Mislata
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Politécnica de Valencia (UPV), Valencia 46022, Spain
| | - Pedro Fernández-Nohales
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Politécnica de Valencia (UPV), Valencia 46022, Spain
| | - María J. Doménech
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Politécnica de Valencia (UPV), Valencia 46022, Spain
| | - Yoshie Hanzawa
- John Innes Centre, Colney, Norwich NR4 7UH, UK
- Department of Crop Sciences, University of Illinois at Urbana-Champaign. 259 Edward R Madigan Lab, 1201 W Gregory Drive, Urbana, IL 61801, USA
| | | | - Francisco Madueño
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Politécnica de Valencia (UPV), Valencia 46022, Spain
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15
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Sánchez-García AB, Aguilera V, Micol-Ponce R, Jover-Gil S, Ponce MR. Arabidopsis MAS2, an Essential Gene That Encodes a Homolog of Animal NF-κ B Activating Protein, Is Involved in 45S Ribosomal DNA Silencing. THE PLANT CELL 2015; 27:1999-2015. [PMID: 26139346 PMCID: PMC4531349 DOI: 10.1105/tpc.15.00135] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 06/02/2015] [Accepted: 06/12/2015] [Indexed: 05/24/2023]
Abstract
Ribosome biogenesis requires stoichiometric amounts of ribosomal proteins and rRNAs. Synthesis of rRNAs consumes most of the transcriptional activity of eukaryotic cells, but its regulation remains largely unclear in plants. We conducted a screen for ethyl methanesulfonate-induced suppressors of Arabidopsis thaliana ago1-52, a hypomorphic allele of AGO1 (ARGONAUTE1), a key gene in microRNA pathways. We identified nine extragenic suppressors as alleles of MAS2 (MORPHOLOGY OF AGO1-52 SUPPRESSED2). Positional cloning showed that MAS2 encodes the putative ortholog of NKAP (NF-κ B activating protein), a conserved eukaryotic protein involved in transcriptional repression and splicing in animals. The mas2 point mutations behave as informational suppressors of ago1 alleles that cause missplicing. MAS2 is a single-copy gene whose insertional alleles are embryonic lethal. In yeast two-hybrid assays, MAS2 interacted with splicing and ribosome biogenesis proteins, and fluorescence in situ hybridization showed that MAS2 colocalizes with the 45S rDNA at the nucleolar organizer regions (NORs). The artificial microRNA amiR-MAS2 partially repressed MAS2 and caused hypomethylation of 45S rDNA promoters as well as partial NOR decondensation, indicating that MAS2 negatively regulates 45S rDNA expression. Our results thus reveal a key player in the regulation of rRNA synthesis in plants.
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Affiliation(s)
| | - Verónica Aguilera
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain
| | - Rosa Micol-Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain
| | - Sara Jover-Gil
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain
| | - María Rosa Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain
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16
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Scutt CP, Vandenbussche M. Current trends and future directions in flower development research. ANNALS OF BOTANY 2014; 114:1399-406. [PMID: 25335868 PMCID: PMC4204790 DOI: 10.1093/aob/mcu224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 09/24/2014] [Indexed: 05/05/2023]
Abstract
Flowers, the reproductive structures of the approximately 400 000 extant species of flowering plants, exist in a tremendous range of forms and sizes, mainly due to developmental differences involving the number, arrangement, size and form of the floral organs of which they consist. However, this tremendous diversity is underpinned by a surprisingly robust basic floral structure in which a central group of carpels forms on an axis of determinate growth, almost invariably surrounded by two successive zones containing stamens and perianth organs, respectively. Over the last 25 years, remarkable progress has been achieved in describing the molecular mechanisms that control almost all aspects of flower development, from the phase change that initiates flowering to the final production of fruits and seeds. However, this work has been performed almost exclusively in a small number of eudicot model species, chief among which is Arabidopsis thaliana. Studies of flower development must now be extended to a much wider phylogenetic range of flowering plants and, indeed, to their closest living relatives, the gymnosperms. Studies of further, more wide-ranging models should provide insights that, for various reasons, cannot be obtained by studying the major existing models alone. The use of further models should also help to explain how the first flowering plants evolved from an unknown, although presumably gymnosperm-like ancestor, and rapidly diversified to become the largest major plant group and to dominate the terrestrial flora. The benefits for society of a thorough understanding of flower development are self-evident, as human life depends to a large extent on flowering plants and on the fruits and seeds they produce. In this preface to the Special Issue, we introduce eleven articles on flower development, representing work in both established and further models, including gymnosperms. We also present some of our own views on current trends and future directions of the flower development field.
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Affiliation(s)
- Charlie P Scutt
- Laboratoire de Reproduction et Développement des Plantes, (Unité mixte de recherche 5667: CNRS-INRA-Université de Lyon), Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France
| | - Michiel Vandenbussche
- Laboratoire de Reproduction et Développement des Plantes, (Unité mixte de recherche 5667: CNRS-INRA-Université de Lyon), Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France
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