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Cheng J, Zhang G, Xu L, Liu C, Jiang H. Altered H3K27 trimethylation contributes to flowering time variations in polyploid Arabidopsis thaliana ecotypes. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:1402-1414. [PMID: 34698830 DOI: 10.1093/jxb/erab470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
Polyploidy is a widespread phenomenon in flowering plant species. Polyploid plants frequently exhibit considerable transcriptomic alterations after whole-genome duplication (WGD). It is known that the transcriptomic response to tetraploidization is ecotype-dependent in Arabidopsis; however, the biological significance and the underlying mechanisms are unknown. In this study, we found that 4x Col-0 presents a delayed flowering time whereas 4x Ler does not. The expression of FLOWERING LOCUS C (FLC), the major repressor of flowering, was significantly increased in 4x Col-0 but only a subtle change was present in 4x Ler. Moreover, the level of a repressive epigenetic mark, trimethylation of histone H3 at lysine 27 (H3K27me3), was significantly decreased in 4x Col-0 but not in 4x Ler, potentially leading to the differences in FLC transcription levels and flowering times. Hundreds of other genes in addition to FLC showed H3K27me3 alterations in 4x Col-0 and 4x Ler. LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) and transcription factors required for H3K27me3 deposition presented transcriptional changes between the two ecotypes, potentially accounting for the different H3K27me3 alterations. We also found that the natural 4x Arabidopsis ecotype Wa-1 presented an early flowering time, which was associated with low expression of FLC. Taken together, our results demonstrate a role of H3K27me3 alterations in response to genome duplication in Arabidopsis autopolyploids, and that variation in flowering time potentially functions in autopolyploid speciation.
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Affiliation(s)
- Jinping Cheng
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Guiqian Zhang
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Linhao Xu
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Chang Liu
- Department of Epigenetics, Institute of Biology, University of Hohenheim, Garbenstrasse 30, 70599 Stuttgart, Germany
| | - Hua Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
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2
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Choi B, Jeong S, Kim E. Variation of the seed endophytic bacteria among plant populations and their plant growth-promoting activities in a wild mustard plant species, Capsella bursa-pastoris. Ecol Evol 2022; 12:e8683. [PMID: 35309752 PMCID: PMC8901890 DOI: 10.1002/ece3.8683] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 01/29/2022] [Accepted: 02/10/2022] [Indexed: 12/26/2022] Open
Abstract
Recent studies have revealed that some bacteria can inhabit plant seeds, and they are likely founders of the bacterial community in the rhizosphere of or inside plants at the early developmental stage. Given that the seedling establishment is a critical fitness component of weedy plant species, the effects of seed endophytic bacteria (SEB) on the seedling performance are of particular interest in weed ecology. Here, we characterized the SEB in natural populations of Capsella bursa-pastoris, a model species of weed ecology. The composition of endophytic bacterial community was evaluated using deep sequencing of a 16S rDNA gene fragment. Additionally, we isolated bacterial strains from seeds and examined their plant growth-promoting traits. Actinobacteria, Firmicutes, Alpha-, and Gammaproteobacteria were major bacterial phyla inside seeds. C. bursa-pastoris natural populations exhibited variable seed microbiome such that the proportion of Actinobacteria and Alphaproteobacteria differed among populations, and 60 out of 82 OTUs occurred only in a single population. Thirteen cultivable bacterial species in six genera (Bacillus, Rhodococcus, Streptomyces, Staphylococcus, Paenibacillus, Pseudomonas) were isolated, and none of them except Staphylococcus haemolyticus were previously reported as seed endophytes. Eight isolates exhibited plant growth-promoting traits like phosphate solubilization activity, indole-3-acetic acid, or siderophore production. Despite the differences in the bacterial communities among plant populations, at least one isolated strain from each population stimulated shoot growth of either C. bursa-pastoris or its close relative A. thaliana when grown with plants in the same media. These results suggest that a weedy plant species, C. bursa-pastoris, contains bacterial endophytes inside their seeds, stimulating seedling growth and thereby potentially affecting seedling establishment.
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Affiliation(s)
- Byungwook Choi
- School of Earth Sciences and Environmental EngineeringGwangju Institute of Science and TechnologyGwangjuSouth Korea
| | - Seorin Jeong
- School of Earth Sciences and Environmental EngineeringGwangju Institute of Science and TechnologyGwangjuSouth Korea
| | - Eunsuk Kim
- School of Earth Sciences and Environmental EngineeringGwangju Institute of Science and TechnologyGwangjuSouth Korea
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3
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Zheng Y, Wang N, Zhang Z, Liu W, Xie W. Identification of Flowering Regulatory Networks and Hub Genes Expressed in the Leaves of Elymus sibiricus L. Using Comparative Transcriptome Analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:877908. [PMID: 35651764 PMCID: PMC9150504 DOI: 10.3389/fpls.2022.877908] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/19/2022] [Indexed: 05/10/2023]
Abstract
Flowering is a significant stage from vegetative growth to reproductive growth in higher plants, which impacts the biomass and seed yield. To reveal the flowering time variations and identify the flowering regulatory networks and hub genes in Elymus sibiricus, we measured the booting, heading, and flowering times of 66 E. sibiricus accessions. The booting, heading, and flowering times varied from 136 to 188, 142 to 194, and 148 to 201 days, respectively. The difference in flowering time between the earliest- and the last-flowering accessions was 53 days. Furthermore, transcriptome analyses were performed at the three developmental stages of six accessions with contrasting flowering times. A total of 3,526 differentially expressed genes (DEGs) were predicted and 72 candidate genes were identified, including transcription factors, known flowering genes, and plant hormone-related genes. Among them, four candidate genes (LATE, GA2OX6, FAR3, and MFT1) were significantly upregulated in late-flowering accessions. LIMYB, PEX19, GWD3, BOR7, PMEI28, LRR, and AIRP2 were identified as hub genes in the turquoise and blue modules which were related to the development time of flowering by weighted gene co-expression network analysis (WGCNA). A single-nucleotide polymorphism (SNP) of LIMYB found by multiple sequence alignment may cause late flowering. The expression pattern of flowering candidate genes was verified in eight flowering promoters (CRY, COL, FPF1, Hd3, GID1, FLK, VIN3, and FPA) and four flowering suppressors (CCA1, ELF3, Ghd7, and COL4) under drought and salt stress by qRT-PCR. The results suggested that drought and salt stress activated the flowering regulation pathways to some extent. The findings of the present study lay a foundation for the functional verification of flowering genes and breeding of new varieties of early- and late-flowering E. sibiricus.
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Affiliation(s)
- Yuying Zheng
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Na Wang
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Zongyu Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Wenhui Liu
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Science and Veterinary Medicine, Xining, China
| | - Wengang Xie
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- *Correspondence: Wengang Xie
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4
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An Update to the TraVA Database: Time Series of Capsella bursa-pastoris Shoot Apical Meristems during Transition to Flowering. DATA 2020. [DOI: 10.3390/data5030058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Transition to flowering is a crucial part of plant life directly affecting the fitness of a plant. Time series of transcriptomes is a useful tool for the investigation of process dynamics and can be used for the identification of novel genes and gene networks involved in the process. We present a detailed time series of polyploid Capsella bursa-pastoris shoot apical meristems created with RNA-seq. The time series covers transition to flowering and can be used for thorough analysis of the process. To make the data easy to access, we uploaded them in our database Transcriptome Variation Analysis (TraVA), which provides a convenient depiction of the gene expression profiles, the differential expression analysis between the homeologs and quick data extraction.
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MacQueen AH, White JW, Lee R, Osorno JM, Schmutz J, Miklas PN, Myers J, McClean PE, Juenger TE. Genetic Associations in Four Decades of Multienvironment Trials Reveal Agronomic Trait Evolution in Common Bean. Genetics 2020; 215:267-284. [PMID: 32205398 PMCID: PMC7198278 DOI: 10.1534/genetics.120.303038] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 03/12/2020] [Indexed: 11/18/2022] Open
Abstract
Multienvironment trials (METs) are widely used to assess the performance of promising crop germplasm. Though seldom designed to elucidate genetic mechanisms, MET data sets are often much larger than could be duplicated for genetic research and, given proper interpretation, may offer valuable insights into the genetics of adaptation across time and space. The Cooperative Dry Bean Nursery (CDBN) is a MET for common bean (Phaseolus vulgaris) grown for > 70 years in the United States and Canada, consisting of 20-50 entries each year at 10-20 locations. The CDBN provides a rich source of phenotypic data across entries, years, and locations that is amenable to genetic analysis. To study stable genetic effects segregating in this MET, we conducted genome-wide association studies (GWAS) using best linear unbiased predictions derived across years and locations for 21 CDBN phenotypes and genotypic data (1.2 million SNPs) for 327 CDBN genotypes. The value of this approach was confirmed by the discovery of three candidate genes and genomic regions previously identified in balanced GWAS. Multivariate adaptive shrinkage (mash) analysis, which increased our power to detect significant correlated effects, found significant effects for all phenotypes. Mash found two large genomic regions with effects on multiple phenotypes, supporting a hypothesis of pleiotropic or linked effects that were likely selected on in pursuit of a crop ideotype. Overall, our results demonstrate that statistical genomics approaches can be used on MET phenotypic data to discover significant genetic effects and to define genomic regions associated with crop improvement.
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Affiliation(s)
- Alice H MacQueen
- Integrative Biology, The University of Texas at Austin, Texas 78712
| | - Jeffrey W White
- U.S. Arid Land Agricultural Research Center, U.S. Department of Agriculture-Agricultural Research Service, Maricopa, Arizona 85239
| | - Rian Lee
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, North Dakota 58102
| | - Juan M Osorno
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, North Dakota 58102
| | - Jeremy Schmutz
- Hudson-Alpha Institute for Biotechnology, Huntsville, Alabama 35806
| | - Phillip N Miklas
- Grain Legume Genetics and Physiology Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Prosser, Washington 99350
| | - Jim Myers
- Department of Horticulture, Oregon State University, Corvallis, Oregon 97331
| | - Phillip E McClean
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, North Dakota 58102
| | - Thomas E Juenger
- Integrative Biology, The University of Texas at Austin, Texas 78712
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Spriggs EL, Schlutius C, Eaton DA, Park B, Sweeney PW, Edwards EJ, Donoghue MJ. Differences in flowering time maintain species boundaries in a continental radiation of Viburnum. AMERICAN JOURNAL OF BOTANY 2019; 106:833-849. [PMID: 31124135 DOI: 10.1002/ajb2.1292] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 03/19/2019] [Indexed: 05/21/2023]
Abstract
PREMISE We take an integrative approach in assessing how introgression and Pleistocene climate fluctuations have shaped the diversification of the core Lentago clade of Viburnum, a group of five interfertile species with broad areas of sympatry. We specifically tested whether flowering time plays a role in maintaining species isolation. METHODS RAD-seq data for 103 individuals were used to infer the species relationships and the genetic structure within each species. Flowering times were compared among species on the basis of historical flowering dates documented by herbarium specimens. RESULTS Within each species, we found a strong relationship between flowering date and latitude, such that southern populations flower earlier than northern ones. In areas of sympatry, the species flower in sequence rather than simultaneously, with flowering dates offset by ≥9 d for all species pairs. In two cases it appears that the offset in flowering times is an incidental consequence of adaptation to differing climates, but in the recently diverged sister species V. prunifolium and V. rufidulum, we find evidence that reinforcement led to reproductive character displacement. Long-term trends suggest that the two northern-most species are flowering earlier in response to recent climate change. CONCLUSIONS We argue that speciation in the Lentago clade has primarily occurred through ecological divergence of allopatric populations, but differences in flowering time were essential to maintain separation of incipient species when they came into secondary contact. This combination of factors may underlie diversification in many other plant clades.
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Affiliation(s)
- Elizabeth L Spriggs
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, Connecticut, 06520, USA
| | - Caroline Schlutius
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, Connecticut, 06520, USA
| | - Deren A Eaton
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, New York, 10027, USA
| | - Brian Park
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, Connecticut, 06520, USA
| | - Patrick W Sweeney
- Division of Botany, Peabody Museum of Natural History, Yale University, P.O. Box 208118, New Haven, Connecticut, 06520, USA
| | - Erika J Edwards
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, Connecticut, 06520, USA
- Division of Botany, Peabody Museum of Natural History, Yale University, P.O. Box 208118, New Haven, Connecticut, 06520, USA
| | - Michael J Donoghue
- Department of Ecology and Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, Connecticut, 06520, USA
- Division of Botany, Peabody Museum of Natural History, Yale University, P.O. Box 208118, New Haven, Connecticut, 06520, USA
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7
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Huang HR, Liu JJ, Xu Y, Lascoux M, Ge XJ, Wright SI. Homeologue-specific expression divergence in the recently formed tetraploid Capsella bursa-pastoris (Brassicaceae). THE NEW PHYTOLOGIST 2018; 220:624-635. [PMID: 30028022 DOI: 10.1111/nph.15299] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/31/2018] [Indexed: 06/08/2023]
Abstract
Following allopolyploid formation, extensive genome evolution occurs, with the eventual loss of many homeologous gene copies. Although this process of diploidization has occurred many times independently, the evolutionary forces determining the probability and rate of gene loss remain poorly understood. Here, we conduct genome and transcriptome sequencing in a broad sample of Chinese accessions of Capsella bursa-pastoris, a recently formed allotetraploid. Our whole genome data reveal three groups of these accessions: an Eastern group from low-altitude regions, a Western group from high-altitude regions, and a much more differentiated Northwestern group. Population differentiation in total expression was limited among closely related populations; by contrast, the relative expression of the two homeologous copies closely mirrors the genome-wide SNP divergence. Consistent with this, we observe a negative correlation between expression changes in the two homeologues. However, genes showing population genomic evidence for adaptive evolution do not show an enrichment for expression divergence between homeologues, providing no clear evidence for adaptive shifts in relative gene expression. Overall, these patterns suggest that neutral drift may contribute to the population differentiation in the expression of the homeologues, and drive eventual gene loss over longer periods of time.
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Affiliation(s)
- Hui-Run Huang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Jia-Jia Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Yong Xu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Uppsala, 75236, Sweden
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, the Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, M5S 3B2, ON, Canada
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Feng G, Huang L, Li J, Wang J, Xu L, Pan L, Zhao X, Wang X, Huang T, Zhang X. Comprehensive transcriptome analysis reveals distinct regulatory programs during vernalization and floral bud development of orchardgrass (Dactylis glomerata L.). BMC PLANT BIOLOGY 2017; 17:216. [PMID: 29166861 PMCID: PMC5700690 DOI: 10.1186/s12870-017-1170-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 11/10/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND Vernalization and the transition from vegetative to reproductive growth involve multiple pathways, vital for controlling floral organ formation and flowering time. However, little transcription information is available about the mechanisms behind environmental adaption and growth regulation. Here, we used high-throughput sequencing to analyze the comprehensive transcriptome of Dactylis glomerata L. during six different growth periods. RESULTS During vernalization, 4689 differentially expressed genes (DEGs) significantly increased in abundance, while 3841 decreased. Furthermore, 12,967 DEGs were identified during booting stage and flowering stage, including 7750 up-regulated and 5219 down-regulated DEGs. Pathway analysis indicated that transcripts related to circadian rhythm, photoperiod, photosynthesis, flavonoid biosynthesis, starch, and sucrose metabolism changed significantly at different stages. Coexpression and weighted correlation network analysis (WGCNA) analysis linked different stages to transcriptional changes and provided evidence of inner relation modules associated with signal transduction, stress responses, cell division, and hormonal transport. CONCLUSIONS We found enrichment in transcription factors (TFs) related to WRKY, NAC, AP2/EREBP, AUX/IAA, MADS-BOX, ABI3/VP1, bHLH, and the CCAAT family during vernalization and floral bud development. TFs expression patterns revealed intricate temporal variations, suggesting relatively separate regulatory programs of TF modules. Further study will unlock insights into the ability of the circadian rhythm and photoperiod to regulate vernalization and flowering time in perennial grass.
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Affiliation(s)
- Guangyan Feng
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Linkai Huang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ji Li
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL USA
| | - Lei Xu
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ling Pan
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xinxin Zhao
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xia Wang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ting Huang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xinquan Zhang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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Ewas M, Khames E, Ziaf K, Shahzad R, Nishawy E, Ali F, Subthain H, Amar MH, Ayaad M, Ghaly O, Luo J. The Tomato DOF Daily Fluctuations 1, TDDF1 acts as flowering accelerator and protector against various stresses. Sci Rep 2017; 7:10299. [PMID: 28860556 PMCID: PMC5578996 DOI: 10.1038/s41598-017-10399-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/20/2017] [Indexed: 01/08/2023] Open
Abstract
Adaptation to environmental changes is an important fitness trait for crop development. Photoperiod is an essential factor in seasonal control of flowering time. Sensing of day-length requires an interaction between the Photoperiod and the endogenous rhythms that is controlled by plant circadian clock. Thus, circadian clock is a critical regulator and internal molecular time-keeping mechanism, controlling key agricultural traits in crop plants such as the ability to adjust their growth and physiology to anticipate diurnal environmental changes. Here, we describe the gene Tomato Dof Daily Fluctuations 1 (TDDF1), which is involved in circadian regulation and stress resistance. Large daily oscillations in TDDF1 expression were retained after transferring to continuous dark (DD) or light (LL) conditions. Interestingly, overexpressing TDDF1 induce early flowering in tomato through up-regulation of the flowering-time control genes, moreover, by protein-protein interaction with the floral inducer SFT gene. Notably, overexpressing TDDF1 in tomato was associated with chlorophyll overaccumulation by up-regulating the related biosynthetic genes. TDDF1 expression results in improved drought, salt, various hormones stress tolerance alongwith resistance to late blight caused by Phytophthora infestans. This study can be a distinctive strategy to improve other economically important crops.
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Affiliation(s)
- Mohamed Ewas
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), College of Life Science and Technology, Huazhong Agricultural University, Wuhan Hubei, 430070, China
- Genetic Resources Department, Deserts Research Center (DRC), Cairo, Egypt
| | - Eman Khames
- College of Pharmacy, Tanta University, Tanta, Egypt
| | - Khurram Ziaf
- Institute of Horticultural Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Raheel Shahzad
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), College of Life Science and Technology, Huazhong Agricultural University, Wuhan Hubei, 430070, China
| | - Elsayed Nishawy
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), College of Life Science and Technology, Huazhong Agricultural University, Wuhan Hubei, 430070, China
- Genetic Resources Department, Deserts Research Center (DRC), Cairo, Egypt
| | - Farhan Ali
- Cereal Crops Research Institute (CCRI), Nowshera, Pakistan
| | - Hizar Subthain
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), College of Life Science and Technology, Huazhong Agricultural University, Wuhan Hubei, 430070, China
| | - Mohamed H Amar
- Genetic Resources Department, Deserts Research Center (DRC), Cairo, Egypt
| | - Mohamed Ayaad
- Egyptian Atomic Energy Nuclear Research Center, Inshas, Egypt
| | - Omran Ghaly
- Genetic Resources Department, Deserts Research Center (DRC), Cairo, Egypt
| | - Jie Luo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), College of Life Science and Technology, Huazhong Agricultural University, Wuhan Hubei, 430070, China.
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10
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Kryvokhyzha D, Holm K, Chen J, Cornille A, Glémin S, Wright SI, Lagercrantz U, Lascoux M. The influence of population structure on gene expression and flowering time variation in the ubiquitous weedCapsella bursa-pastoris(Brassicaceae). Mol Ecol 2016; 25:1106-21. [DOI: 10.1111/mec.13537] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 11/18/2015] [Accepted: 12/10/2015] [Indexed: 12/19/2022]
Affiliation(s)
- Dmytro Kryvokhyzha
- Department of Ecology and Genetics; Evolutionary Biology Center and Science for Life Laboratory; Uppsala University; 75236 Uppsala Sweden
| | - Karl Holm
- Department of Ecology and Genetics; Evolutionary Biology Center and Science for Life Laboratory; Uppsala University; 75236 Uppsala Sweden
| | - Jun Chen
- Department of Ecology and Genetics; Evolutionary Biology Center and Science for Life Laboratory; Uppsala University; 75236 Uppsala Sweden
| | - Amandine Cornille
- Department of Ecology and Genetics; Evolutionary Biology Center and Science for Life Laboratory; Uppsala University; 75236 Uppsala Sweden
| | - Sylvain Glémin
- Department of Ecology and Genetics; Evolutionary Biology Center and Science for Life Laboratory; Uppsala University; 75236 Uppsala Sweden
- Institut des Sciences de l'Evolution (ISEM - UMR 5554 Université de Montpellier-CNRS-IRD-EPHE); Place Eugene Bataillon 34075 Montpellier France
| | - Stephen I. Wright
- Department of Ecology and Evolution; University of Toronto; 25 Willcocks St. Toronto ON M5S 3B2 Canada
| | - Ulf Lagercrantz
- Department of Ecology and Genetics; Evolutionary Biology Center and Science for Life Laboratory; Uppsala University; 75236 Uppsala Sweden
| | - Martin Lascoux
- Department of Ecology and Genetics; Evolutionary Biology Center and Science for Life Laboratory; Uppsala University; 75236 Uppsala Sweden
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11
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Zhao Y, Liang H, Li L, Tang S, Han X, Wang C, Xia X, Yin W. Digital gene expression analysis of male and female bud transition in Metasequoia reveals high activity of MADS-box transcription factors and hormone-mediated sugar pathways. FRONTIERS IN PLANT SCIENCE 2015; 6:467. [PMID: 26157452 PMCID: PMC4478380 DOI: 10.3389/fpls.2015.00467] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 06/12/2015] [Indexed: 05/29/2023]
Abstract
Metasequoia glyptostroboides is a famous redwood tree of ecological and economic importance, and requires more than 20 years of juvenile-to-adult transition before producing female and male cones. Previously, we induced reproductive buds using a hormone solution in juvenile Metasequoia trees as young as 5-to-7 years old. In the current study, hormone-treated shoots found in female and male buds were used to identify candidate genes involved in reproductive bud transition in Metasequoia. Samples from hormone-treated cone reproductive shoots and naturally occurring non-cone setting shoots were analyzed using 24 digital gene expression (DGE) tag profiles using Illumina, generating a total of 69,520 putative transcripts. Next, 32 differentially and specifically expressed transcripts were determined using quantitative real-time polymerase chain reaction, including the upregulation of MADS-box transcription factors involved in male bud transition and flowering time control proteins involved in female bud transition. These differentially expressed transcripts were associated with 243 KEGG pathways. Among the significantly changed pathways, sugar pathways were mediated by hormone signals during the vegetative-to-reproductive phase transition, including glycolysis/gluconeogenesis and sucrose and starch metabolism pathways. Key enzymes were identified in these pathways, including alcohol dehydrogenase (NAD) and glutathione dehydrogenase for the glycolysis/gluconeogenesis pathway, and glucanphosphorylase for sucrose and starch metabolism pathways. Our results increase our understanding of the reproductive bud transition in gymnosperms. In addition, these studies on hormone-mediated sugar pathways increase our understanding of the relationship between sugar and hormone signaling during female and male bud initiation in Metasequoia.
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Affiliation(s)
- Ying Zhao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry UniversityBeijing, China
| | - Haiying Liang
- Department of Genetics and Biochemistry, Clemson UniversityClemson, SC, USA
| | - Lan Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry UniversityBeijing, China
| | - Sha Tang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry UniversityBeijing, China
| | - Xiao Han
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry UniversityBeijing, China
| | - Congpeng Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry UniversityBeijing, China
| | - Xinli Xia
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry UniversityBeijing, China
| | - Weilun Yin
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry UniversityBeijing, China
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Van Dijk H, Hautekèete NC. Evidence of genetic change in the flowering phenology of sea beets along a latitudinal cline within two decades. J Evol Biol 2014; 27:1572-81. [PMID: 24835689 DOI: 10.1111/jeb.12410] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 04/08/2014] [Accepted: 04/10/2014] [Indexed: 01/15/2023]
Abstract
Sea beets grown from seeds collected in 1989 and 2009 along the coasts of France and adjacent regions were compared for flowering date under controlled conditions. Seeds from both collection years were sown simultaneously and cultivated under the same glasshouse conditions. Date of flowering onset and year of first flowering were recorded. There was an overall northward shift in flowering time of about 0.35° latitude (i.e. 39 km) over the 20-year period. The southern portion of the latitudinal gradient--that is, from 44.7°N to 47.28°N--flowered significantly later by a mean of 1.78 days, equivalent to a 43.2-km northward shift of phenotypes. In the northern latitudes between 48.6°N and 52°N, flowering date was significantly earlier by a mean of 4.04 days, corresponding to a mean northward shift of 104.9 km, and this shift was apparently due to a diminished requirement of exposure to cold temperatures (i.e. vernalization), for which we found direct and indirect evidence. As all plants were grown from seed under identical conditions, we conclude that genetic changes occurred in the sensitivity to environmental cues that mediate the onset of flowering in both the northern and the southern latitudes of the gradient. Microevolution and gene flow may have contributed to this change. There was no significant change in the frequency of plants that flowered without vernalization. The lack of vernalization requirement may be associated with environmental instability rather than with climate conditions.
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Affiliation(s)
- H Van Dijk
- Laboratoire de Génétique et Evolution des Populations Végétales, UMR CNRS 8198, Université des Sciences et Technologies de Lille - Lille 1, Villeneuve d'Ascq, France
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Lu Q, Zhao L, Li D, Hao D, Zhan Y, Li W. A GmRAV ortholog is involved in photoperiod and sucrose control of flowering time in soybean. PLoS One 2014; 9:e89145. [PMID: 24551235 PMCID: PMC3925180 DOI: 10.1371/journal.pone.0089145] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Accepted: 01/14/2014] [Indexed: 01/02/2023] Open
Abstract
Photoperiod and sucrose levels play a key role in the control of flowering. GmRAV reflected a diurnal rhythm with the highest expression at 4 h after the beginning of a dark period in soybean leaves, and was highly up-regulated under short-day (SD) conditions, despite of not following a diurnal pattern under long-day (LD) conditions. GmRAV-i (GmRAV-inhibition) transgenic soybean exhibited early flowering phenotype. Two of the FT Arabidopsis homologs, GmFT2a and GmFT5a, were highly expressed in the leaves of soybeans with inhibition (-i) of GmRAV under SD conditions. Moreover, the transcript levels of the two FT homologs in GmRAV-i soybeans were more sensitive to SD conditions than LD conditions compared to the WT plant. GmRAV-i soybeans and Arabidopsis rav mutants showed more sensitive hypocotyl elongation responses when compared with wild-type seedlings, and GmRAV-ox overevpressed in tobacco revealed no sensitive changes in hypocotyl length. These indicated that GmRAV was a novel negative regulator of SD-mediated flowering and hypocotyl elongation. Although sucrose has been suggested to promote flowering induction in many plant species, high concentration of sucrose (4% [w/v]) applied into media defer flowering time in Arabidopsis wild-type and rav mutant. This delayed flowering stage might be caused by reduction of LEAFY expression. Furthermore, Arabidopsis rav mutants and GmRAV-i soybean plants were less sensitive to sucrose by the inhibition assays of hypocotyls and roots growth. In contrast, transgenic GmRAV overexpressing (-ox) tobacco plants displayed more sensitivity to sucrose. In conclusion, GmRAV was inferred to have a fundamental function in photoperiod, darkness, and sucrose signaling responses to regulate plant development and flowering induction.
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Affiliation(s)
- Qingyao Lu
- Key Laboratory of Soybean Biology of Chinese Education Ministry (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture), Northeast Agriculture University, Harbin, China
| | - Lin Zhao
- Key Laboratory of Soybean Biology of Chinese Education Ministry (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture), Northeast Agriculture University, Harbin, China
| | - Dongmei Li
- Key Laboratory of Soybean Biology of Chinese Education Ministry (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture), Northeast Agriculture University, Harbin, China
| | - Diqiu Hao
- Key Laboratory of Soybean Biology of Chinese Education Ministry (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture), Northeast Agriculture University, Harbin, China
| | - Yong Zhan
- Agricultural Academy of Shi He Zi, Xinjiang Province, China
| | - Wenbin Li
- Key Laboratory of Soybean Biology of Chinese Education Ministry (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China, Ministry of Agriculture), Northeast Agriculture University, Harbin, China
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Prendeville HR, Barnard-Kubow K, Dai C, Barringer BC, Galloway LF. Clinal variation for only some phenological traits across a species range. Oecologia 2013; 173:421-30. [DOI: 10.1007/s00442-013-2630-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 02/13/2013] [Indexed: 11/30/2022]
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Roschanski AM, Fady B, Ziegenhagen B, Liepelt S. Annotation and re-sequencing of genes from de novo transcriptome assembly of Abies alba (Pinaceae). APPLICATIONS IN PLANT SCIENCES 2013; 1:apps1200179. [PMID: 25202477 PMCID: PMC4105350 DOI: 10.3732/apps.1200179] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 06/30/2012] [Indexed: 06/03/2023]
Abstract
PREMISE OF THE STUDY We present a protocol for the annotation of transcriptome sequence data and the identification of candidate genes therein using the example of the nonmodel conifer Abies alba. • METHODS AND RESULTS A normalized cDNA library was built from an A. alba seedling. The sequencing on a 454 platform yielded more than 1.5 million reads that were de novo assembled into 25149 contigs. Two complementary approaches were applied to annotate gene fragments that code for (1) well-known proteins and (2) proteins that are potentially adaptively relevant. Primer development and testing yielded 88 amplicons that could successfully be resequenced from genomic DNA. • CONCLUSIONS The annotation workflow offers an efficient way to identify potential adaptively relevant genes from the large quantity of transcriptome sequence data. The primer set presented should be prioritized for single-nucleotide polymorphism detection in adaptively relevant genes in A. alba.
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Affiliation(s)
- Anna M. Roschanski
- University of Marburg, Faculty of Biology, Conservation Biology, Karl-von-Frisch-Strasse 35032 Marburg, Germany
| | - Bruno Fady
- INRA, UR629, Ecologie des Forêts Méditerranéennes (URFM), 84914 Avignon, France
| | - Birgit Ziegenhagen
- University of Marburg, Faculty of Biology, Conservation Biology, Karl-von-Frisch-Strasse 35032 Marburg, Germany
| | - Sascha Liepelt
- University of Marburg, Faculty of Biology, Conservation Biology, Karl-von-Frisch-Strasse 35032 Marburg, Germany
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Kemi U, Niittyvuopio A, Toivainen T, Pasanen A, Quilot-Turion B, Holm K, Lagercrantz U, Savolainen O, Kuittinen H. Role of vernalization and of duplicated FLOWERING LOCUS C in the perennial Arabidopsis lyrata. THE NEW PHYTOLOGIST 2013; 197:323-335. [PMID: 23106477 DOI: 10.1111/j.1469-8137.2012.04378.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 09/07/2012] [Indexed: 05/08/2023]
Abstract
FLOWERING LOCUS C (FLC) is one of the main genes influencing the vernalization requirement and natural flowering time variation in the annual Arabidopsis thaliana. Here we studied the effects of vernalization on flowering and its genetic basis in the perennial Arabidopsis lyrata. Two tandemly duplicated FLC genes (FLC1 and FLC2) were compared with respect to expression and DNA sequence. The effect of vernalization on flowering and on the expression of FLC1 was studied in three European populations. The genetic basis of the FLC1 expression difference between two of the populations was further studied by expression quantitative trait locus (eQTL) mapping and sequence analysis. FLC1 was shown to have a likely role in the vernalization requirement for flowering in A. lyrata. Vernalization decreased its expression and the northern study populations showed higher FLC1 expression than the southern one. eQTL mapping between two of the populations revealed one eQTL affecting FLC1 expression in the genomic region containing the FLC genes. Most FLC1 sequence differences between the study populations were found in the promoter region and in the first intron. Variation in the FLC1 sequence may cause differences in FLC1 expression between late- and early-flowering A. lyrata populations.
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Affiliation(s)
- Ulla Kemi
- Department of Biology, University of Oulu, PO Box 3000, FIN-90401, Oulu, Finland
| | - Anne Niittyvuopio
- Department of Biology, University of Oulu, PO Box 3000, FIN-90401, Oulu, Finland
| | - Tuomas Toivainen
- Department of Biology, University of Oulu, PO Box 3000, FIN-90401, Oulu, Finland
- Biocenter Oulu, University of Oulu, 90014, Oulu, Finland
| | - Anu Pasanen
- Department of Biology, University of Oulu, PO Box 3000, FIN-90401, Oulu, Finland
| | - Bénédicte Quilot-Turion
- Department of Biology, University of Oulu, PO Box 3000, FIN-90401, Oulu, Finland
- INRA, UR1052 Génétique et Amélioration des Fruits et Légumes, F-84143, Montfavet, France
| | - Karl Holm
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752, 36 Uppsala, Sweden
| | - Ulf Lagercrantz
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752, 36 Uppsala, Sweden
| | - Outi Savolainen
- Department of Biology, University of Oulu, PO Box 3000, FIN-90401, Oulu, Finland
- Biocenter Oulu, University of Oulu, 90014, Oulu, Finland
| | - Helmi Kuittinen
- Department of Biology, University of Oulu, PO Box 3000, FIN-90401, Oulu, Finland
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