1
|
Sun H, Wang C, Chen X, Liu H, Huang Y, Li S, Dong Z, Zhao X, Tian F, Jin W. dlf1 promotes floral transition by directly activating ZmMADS4 and ZmMADS67 in the maize shoot apex. THE NEW PHYTOLOGIST 2020; 228:1386-1400. [PMID: 32579713 DOI: 10.1111/nph.16772] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/16/2020] [Indexed: 06/11/2023]
Abstract
The floral transition of the maize (Zea mays ssp. mays) shoot apical meristem determines leaf number and flowering time, which are key traits influencing local adaptation and yield potential. dlf1 (delayed flowering1) encodes a basic leucine zipper protein that interacts with the florigen ZCN8 to mediate floral induction in the shoot apex. However, the mechanism of how dlf1 promotes floral transition remains largely unknown. We demonstrate that dlf1 underlies qLB7-1, a quantitative trait locus controlling leaf number and flowering time that was identified in a BC2 S3 population derived from a cross between maize and its wild ancestor, teosinte (Zea mays ssp. parviglumis). Transcriptome sequencing and chromatin immunoprecipitation sequencing demonstrated that DLF1 binds the core promoter of two AP1/FUL subfamily MADS-box genes, ZmMADS4 and ZmMADS67, to activate their expression. Knocking out ZmMADS4 and ZmMADS67 both increased leaf number and delayed flowering, indicating that they promote the floral transition. Nucleotide diversity analysis revealed that dlf1 and ZmMADS67 were targeted by selection, suggesting that they may have played important roles in maize flowering time adaptation. We show that dlf1 promotes maize floral transition by directly activating ZmMADS4 and ZmMADS67 in the shoot apex, providing novel insights into the mechanism of maize floral transition.
Collapse
Affiliation(s)
- Huayue Sun
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Chenglong Wang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Xiaoyang Chen
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Hongbing Liu
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Yumin Huang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Suxing Li
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhaobin Dong
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Xiaoming Zhao
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Feng Tian
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Weiwei Jin
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
2
|
Zhang N, Wang Z, Bao Z, Yang L, Wu D, Shu X, Hua J. MOS1 functions closely with TCP transcription factors to modulate immunity and cell cycle in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:66-78. [PMID: 29086441 DOI: 10.1111/tpj.13757] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 10/03/2017] [Accepted: 10/23/2017] [Indexed: 05/05/2023]
Abstract
Emerging evidence indicates a close connection between cell-cycle progression and the plant immune responses. In Arabidopsis, MODIFIER OF snc1-1 (MOS1) modulates a number of processes including endoreduplication and plant disease resistance, but the molecular mechanism underlying this modulation was not fully understood. Here, we provide biochemical and genetic evidence that TEOSINTE BRANCHED 1, CYCLOIDEA, PCF1 (TCP) transcription factors TCP15 and its homologues are mediators of MOS1 function in the immune response and are likely to be also involved in cell-cycle control. MOS1 and TCP proteins have a direct physical interaction. They both bind to the promoter of the immune receptor gene SUPRESSOR OF npr1-1, CONSTITUTIVE 1 (SNC1) and modulate its expression and consequently immune responses. MOS1 and TCP15 both affect the expression of cell-cycle genes D-type CYCLIN 3;1 (CYCD3;1), which may mediate the MOS1 function in cell-cycle modulation. In addition, CYCD3;1 overexpression upregulates immune responses, and SNC1 expression. This study investigated and revealed a role for MOS1 in transcriptional regulation through TCP15 and its homologues. This finding suggests the coordination of cell-cycle progression and plant immune responses at multiple levels.
Collapse
Affiliation(s)
- Ning Zhang
- State Key Laboratory of Rice Biology, Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, 310029, China
- School of Integrated Plant Science, Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
| | - Zhixue Wang
- State Key Laboratory of Rice Biology, Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, 310029, China
- School of Integrated Plant Science, Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
| | - Zhilong Bao
- School of Integrated Plant Science, Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
| | - Leiyun Yang
- School of Integrated Plant Science, Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
| | - Dianxing Wu
- State Key Laboratory of Rice Biology, Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, 310029, China
| | - Xiaoli Shu
- State Key Laboratory of Rice Biology, Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou, 310029, China
| | - Jian Hua
- School of Integrated Plant Science, Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| |
Collapse
|
3
|
He Y, Wang M, Sun Q, Pawlowski WP. Mapping Recombination Initiation Sites Using Chromatin Immunoprecipitation. Methods Mol Biol 2016; 1429:177-88. [PMID: 27511175 DOI: 10.1007/978-1-4939-3622-9_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Genome-wide maps of recombination sites provide valuable information not only on the recombination pathway itself but also facilitate the understanding of genome dynamics and evolution. Here, we describe a chromatin immunoprecipitation (ChIP) protocol to map the sites of recombination initiation in plants with maize used as an example. ChIP is a method that allows identification of chromosomal sites occupied by specific proteins. Our protocol utilizes RAD51, a protein involved in repair of double-strand breaks (DSBs) that initiate meiotic recombination, to identify DSB formation hotspots. Chromatin is extracted from meiotic flowers, sheared and enriched in fragments bound to RAD51. Genomic location of the protein is then identified by next-generation sequencing. This protocol can also be used in other species of plants, animals, and fungi.
Collapse
Affiliation(s)
- Yan He
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100083, China
| | - Minghui Wang
- Institute of Biotechnology, Biotechnology Resource Center and Section of Plant Biology in School of IntegrativePlant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Qi Sun
- Institute of Biotechnology, Biotechnology Resource Center, Cornell University, Ithaca, NY, 14853, USA
| | - Wojciech P Pawlowski
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
| |
Collapse
|
4
|
Sundararajan A, Dukowic-Schulze S, Kwicklis M, Engstrom K, Garcia N, Oviedo OJ, Ramaraj T, Gonzales MD, He Y, Wang M, Sun Q, Pillardy J, Kianian SF, Pawlowski WP, Chen C, Mudge J. Gene Evolutionary Trajectories and GC Patterns Driven by Recombination in Zea mays. FRONTIERS IN PLANT SCIENCE 2016; 7:1433. [PMID: 27713757 PMCID: PMC5031598 DOI: 10.3389/fpls.2016.01433] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 09/08/2016] [Indexed: 05/20/2023]
Abstract
Recombination occurring during meiosis is critical for creating genetic variation and plays an essential role in plant evolution. In addition to creating novel gene combinations, recombination can affect genome structure through altering GC patterns. In maize (Zea mays) and other grasses, another intriguing GC pattern exists. Maize genes show a bimodal GC content distribution that has been attributed to nucleotide bias in the third, or wobble, position of the codon. Recombination may be an underlying driving force given that recombination sites are often associated with high GC content. Here we explore the relationship between recombination and genomic GC patterns by comparing GC gene content at each of the three codon positions (GC1, GC2, and GC3, collectively termed GCx) to instances of a variable GC-rich motif that underlies double strand break (DSB) hotspots and to meiocyte-specific gene expression. Surprisingly, GCx bimodality in maize cannot be fully explained by the codon wobble hypothesis. High GCx genes show a strong overlap with the DSB hotspot motif, possibly providing a mechanism for the high evolutionary rates seen in these genes. On the other hand, genes that are turned on in meiosis (early prophase I) are biased against both high GCx genes and genes with the DSB hotspot motif, possibly allowing important meiotic genes to avoid DSBs. Our data suggests a strong link between the GC-rich motif underlying DSB hotspots and high GCx genes.
Collapse
Affiliation(s)
| | | | | | | | - Nathan Garcia
- National Center for Genome Resources, Santa FeNM, USA
| | | | | | | | - Yan He
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, IthacaNY, USA
| | - Minghui Wang
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, IthacaNY, USA
- Biotechnology Resource Center Bioinformatics Facility, Cornell University, IthacaNY, USA
| | - Qi Sun
- Biotechnology Resource Center Bioinformatics Facility, Cornell University, IthacaNY, USA
| | - Jaroslaw Pillardy
- Biotechnology Resource Center Bioinformatics Facility, Cornell University, IthacaNY, USA
| | - Shahryar F. Kianian
- Cereal Disease Laboratory, United States Department of Agriculture – Agricultural Research Service, St. PaulMN, USA
| | - Wojciech P. Pawlowski
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, IthacaNY, USA
| | - Changbin Chen
- Department of Horticultural Science, University of Minnesota, St. PaulMN, USA
| | - Joann Mudge
- National Center for Genome Resources, Santa FeNM, USA
- *Correspondence: Joann Mudge,
| |
Collapse
|
5
|
Choi K, Henderson IR. Meiotic recombination hotspots - a comparative view. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:52-61. [PMID: 25925869 DOI: 10.1111/tpj.12870] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 04/15/2015] [Accepted: 04/17/2015] [Indexed: 05/18/2023]
Abstract
During meiosis homologous chromosomes pair and undergo reciprocal genetic exchange, termed crossover. Meiotic recombination has a profound effect on patterns of genetic variation and is an important tool during crop breeding. Crossovers initiate from programmed DNA double-stranded breaks that are processed to form single-stranded DNA, which can invade a homologous chromosome. Strand invasion events mature into double Holliday junctions that can be resolved as crossovers. Extensive variation in the frequency of meiotic recombination occurs along chromosomes and is typically focused in narrow hotspots, observed both at the level of DNA breaks and final crossovers. We review methodologies to profile hotspots at different steps of the meiotic recombination pathway that have been used in different eukaryote species. We then discuss what these studies have revealed concerning specification of hotspot locations and activity and the contributions of both genetic and epigenetic factors. Understanding hotspots is important for interpreting patterns of genetic variation in populations and how eukaryotic genomes evolve. In addition, manipulation of hotspots will allow us to accelerate crop breeding, where meiotic recombination distributions can be limiting.
Collapse
Affiliation(s)
- Kyuha Choi
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| |
Collapse
|
6
|
Xue M, Long J, Jiang Q, Wang M, Chen S, Pang Q, He Y. Distinct patterns of the histone marks associated with recruitment of the methionine chain-elongation pathway from leucine biosynthesis. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:805-12. [PMID: 25428994 PMCID: PMC4321544 DOI: 10.1093/jxb/eru440] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Aliphatic glucosinolates (GLSs) are derived from chain-elongated methionine produced by an iterative three-step process, known to be evolutionarily recruited from leucine biosynthesis. The divergence of homologous genes between two pathways is mainly linked to the alterations in biochemical features. In this study, it was discovered that a distinct pattern of histone modifications is associated with and/or contributes to the divergence of the two pathways. In general, genes involved in leucine biosynthesis were robustly associated with H3k4me2 and H3K4me3. In contrast, despite the considerable abundances of H3K4me2 observed in some of genes involved in methionine chain elongation, H3K4me3 was completely missing. This H3K4m3-depleted pattern had no effect on gene transcription, whereas it seemingly co-evolved with the entire pathway of aliphatic GLS biosynthesis. The results reveal a novel association of the epigenetic marks with plant secondary metabolism, and may help to understand the recruitment of the methionine chain-elongation pathway from leucine biosynthesis.
Collapse
Affiliation(s)
- Ming Xue
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jingcheng Long
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qinlong Jiang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Minghui Wang
- Computational Biology Service Unit, Cornell University, Ithaca, NY14853, USA
| | - Sixue Chen
- Department of Biology, Genetics Institute, and Plant Molecular & Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA
| | - Qiuying Pang
- Alkali Soil Natural Environmental Science Center, Key Laboratory of Saline-alkali Vegetation Ecology Restoration in Oil Field, Northeast Forestry University, Harbin, Heilongjiang 14850, China
| | - Yan He
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| |
Collapse
|
7
|
Endopolyploidization and flowering time are antagonistically regulated by checkpoint component MAD1 and immunity modulator MOS1. Nat Commun 2014; 5:5628. [DOI: 10.1038/ncomms6628] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 10/21/2014] [Indexed: 11/09/2022] Open
|