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Shen Y, Mao L, Zhou Y, Sun Y, Lv J, Deng M, Liu Z, Yang B. Transcriptome Analysis Reveals Key Genes Involved in Trichome Formation in Pepper (Capsicum annuum L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:1090. [PMID: 38674502 PMCID: PMC11054266 DOI: 10.3390/plants13081090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/11/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024]
Abstract
Trichomes are specialized organs located in the plant epidermis that play important defense roles against biotic and abiotic stresses. However, the mechanisms regulating the development of pepper epidermal trichomes and the related regulatory genes at the molecular level are not clear. Therefore, we performed transcriptome analyses of A114 (less trichome) and A115 (more trichome) to dig deeper into the genes involved in the regulatory mechanisms of epidermal trichome development in peppers. In this study, the epidermal trichome density of A115 was found to be higher by phenotypic observation and was highest in the leaves at the flowering stage. A total of 39,261 genes were quantified by RNA-Seq, including 11,939 genes not annotated in the previous genome analysis and 18,833 differentially expressed genes. Based on KEGG functional enrichment, it was found that DEGs were mainly concentrated in three pathways: plant-pathogen interaction, MAPK signaling pathway-plant, and plant hormone signal transduction. We further screened the DEGs associated with the development of epidermal trichomes in peppers, and the expression of the plant signaling genes GID1B-like (Capana03g003488) and PR-6 (Capana09g001847), the transcription factors MYB108 (Capana05g002225) and ABR1-like (Capana04g001261), and the plant resistance genes PGIP-like (Capana09g002077) and At5g49770 (Capana08g001721) in the DEGs were higher at A115 compared to A114, and were highly expressed in leaves at the flowering stage. In addition, based on the WGCNA results and the establishment of co-expression networks showed that the above genes were highly positively correlated with each other. The transcriptomic data and analysis of this study provide a basis for the study of the regulatory mechanisms of pepper epidermal trichomes.
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Affiliation(s)
- Yiyu Shen
- Engineering Research Center of Education Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory of Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Y.S.); (L.M.); (Y.Z.); (Y.S.)
| | - Lianzhen Mao
- Engineering Research Center of Education Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory of Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Y.S.); (L.M.); (Y.Z.); (Y.S.)
| | - Yao Zhou
- Engineering Research Center of Education Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory of Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Y.S.); (L.M.); (Y.Z.); (Y.S.)
| | - Ying Sun
- Engineering Research Center of Education Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory of Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Y.S.); (L.M.); (Y.Z.); (Y.S.)
| | - Junheng Lv
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (J.L.); (M.D.)
| | - Minghua Deng
- College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China; (J.L.); (M.D.)
| | - Zhoubin Liu
- Engineering Research Center of Education Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory of Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Y.S.); (L.M.); (Y.Z.); (Y.S.)
| | - Bozhi Yang
- Engineering Research Center of Education Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory of Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Y.S.); (L.M.); (Y.Z.); (Y.S.)
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2
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Ren X, Yang L, Muhammad Y, Xie Y, Lin X, Yu L, Cao Y, Ding M, Jiang Y, Rong J. The GaKAN2, a KANADI transcription factor, modulates stem trichomes in Gossypium arboreum. Mol Genet Genomics 2024; 299:19. [PMID: 38416229 DOI: 10.1007/s00438-024-02098-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 01/11/2024] [Indexed: 02/29/2024]
Abstract
KEY MESSAGE GaKAN2, a member of the KANADI family, was found to be widely expressed in the cotton tissues and regulates trichome development through complex pathways. Cotton trichomes are believed to be the defense barrier against insect pests. Cotton fiber and trichomes are single-cell epidermal extensions with shared regulatory mechanisms. Despite several studies underlying mechanism of trichome development remains elusive. The KANADI is one of the key transcription factors (TFs) family, regulating Arabidopsis trichomes growth. However, the function of KANADI genes in cotton remains unknown. In the current study genome-wide scanning, transcriptomic analysis, gene silencing, subcellular localization, and yeast two-hybrid techniques were employed to decipher the function of KANADI TFs family genes in cotton crop. A total of 7 GaKAN genes were found in the Gossypium arboreum. Transcriptomic data revealed that these genes were significantly expressed in stem and root. Moreover, GaKAN2 was widely expressed in other tissues also. Subsequently, we selected GaKAN2 to validate the function of KANADI genes. Silencing of GaKAN2 resulted in a 24.99% decrease in single-cell trichomes and an 11.33% reduction in internodal distance, indicating its potential role in regulating trichomes and plant growth. RNA-Seq analysis elucidated that GaSuS and GaERS were the downstream genes of GaKAN2. The transcriptional activation and similarity in silencing phenotype between GaKAN2 and GaERS suggested that GaKAN2 regulates trichomes development through GaERS. Moreover, KEGG analysis revealed that a significant number of genes were enriched in the biosynthesis of secondary metabolites and plant hormone signal transduction pathways, thereby suggesting that GaKAN2 regulates the stem trichomes and plant growth. The GFP subcellular localization and yeast transcriptional activation analysis elucidated that GaKAN2 was located in the nucleus and capable of regulating the transcription of downstream genes. This study elucidated the function and characteristics of the KANADI gene family in cotton, providing a fundamental basis for further research on GaKAN2 gene in cotton plant trichomes and plant developmental processes.
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Affiliation(s)
- Xujiao Ren
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Luying Yang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Yasir Muhammad
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Yuxing Xie
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Xinyi Lin
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Li Yu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yuefen Cao
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Mingquan Ding
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Yurong Jiang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Science, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Junkang Rong
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Science, Zhejiang Agriculture and Forestry University, Hangzhou, China.
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3
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Zhu Y, Yang J, Liu X, Sun T, Zhao Y, Xiang F, Chen F, He H. Transcriptome Analysis Reveals Coexpression Networks and Hub Genes Involved in Papillae Development in Lilium auratum. Int J Mol Sci 2024; 25:2436. [PMID: 38397114 PMCID: PMC10889295 DOI: 10.3390/ijms25042436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/12/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024] Open
Abstract
Lilium is a genus of important ornamental plants with many colouring pattern variations. Lilium auratum is the parent of Oriental hybrid lilies. A typical feature of L. auratum is the presence of red-orange special raised spots named papillae on the interior tepals. Unlike the usual raised spots, the papillae are slightly rounded or connected into sheets and usually have hairy tips. To elucidate the potential genes regulating papillae development in L. auratum, we performed high-throughput sequencing of its tepals at different stages. Genes involved in the flavonoid biosynthesis pathway were significantly enriched during the colouration of the papillae, and CHS, F3H, F3'H, FLS, DFR, ANS, and UFGT were significantly upregulated. To identify the key genes involved in the papillae development of L. auratum, we performed weighted gene coexpression network analysis (WGCNA) and further analysed four modules. In total, 51, 24, 1, and 6 hub genes were identified in four WGCNA modules, MEbrown, MEyellow, MEpurple, and MEred, respectively. Then, the coexpression networks were constructed, and important genes involved in trichome development and coexpressed with anthocyanin biosynthesis genes, such as TT8, TTG1, and GEM, were identified. These results indicated that the papillae are essentially trichomes that accumulate anthocyanins. Finally, we randomly selected 12 hub genes for qRT-PCR analysis to verify the accuracy of our RNA-Seq analysis. Our results provide new insights into the papillae development in L. auratum flowers.
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Affiliation(s)
- Yuntao Zhu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; (Y.Z.); (J.Y.); (X.L.); (T.S.); (Y.Z.)
| | - Jie Yang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; (Y.Z.); (J.Y.); (X.L.); (T.S.); (Y.Z.)
- Industrial Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (F.X.); (F.C.)
| | - Xiaolin Liu
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; (Y.Z.); (J.Y.); (X.L.); (T.S.); (Y.Z.)
| | - Tingting Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; (Y.Z.); (J.Y.); (X.L.); (T.S.); (Y.Z.)
| | - Yiran Zhao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; (Y.Z.); (J.Y.); (X.L.); (T.S.); (Y.Z.)
| | - Fayun Xiang
- Industrial Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (F.X.); (F.C.)
| | - Feng Chen
- Industrial Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan 430064, China; (F.X.); (F.C.)
| | - Hengbin He
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; (Y.Z.); (J.Y.); (X.L.); (T.S.); (Y.Z.)
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Pantazopoulou CK, Buti S, Nguyen CT, Oskam L, Weits DA, Farmer EE, Kajala K, Pierik R. Mechanodetection of neighbor plants elicits adaptive leaf movements through calcium dynamics. Nat Commun 2023; 14:5827. [PMID: 37730832 PMCID: PMC10511701 DOI: 10.1038/s41467-023-41530-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 09/07/2023] [Indexed: 09/22/2023] Open
Abstract
Plants detect their neighbors via various cues, including reflected light and touching of leaf tips, which elicit upward leaf movement (hyponasty). It is currently unknown how touch is sensed and how the signal is transferred from the leaf tip to the petiole base that drives hyponasty. Here, we show that touch-induced hyponasty involves a signal transduction pathway that is distinct from light-mediated hyponasty. We found that mechanostimulation of the leaf tip upon touching causes cytosolic calcium ([Ca2+]cyt induction in leaf tip trichomes that spreads towards the petiole. Both perturbation of the calcium response and the absence of trichomes reduce touch-induced hyponasty. Finally, using plant competition assays, we show that touch-induced hyponasty is adaptive in dense stands of Arabidopsis. We thus establish a novel, adaptive mechanism regulating hyponastic leaf movement in response to mechanostimulation by neighbors in dense vegetation.
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Affiliation(s)
- Chrysoula K Pantazopoulou
- Plant-Environment Signaling, Institute of Environment Biology, Utrecht University, Utrecht, The Netherlands.
| | - Sara Buti
- Plant-Environment Signaling, Institute of Environment Biology, Utrecht University, Utrecht, The Netherlands
| | - Chi Tam Nguyen
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Lisa Oskam
- Plant-Environment Signaling, Institute of Environment Biology, Utrecht University, Utrecht, The Netherlands
| | - Daan A Weits
- Plant-Environment Signaling, Institute of Environment Biology, Utrecht University, Utrecht, The Netherlands
| | - Edward E Farmer
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
| | - Kaisa Kajala
- Plant-Environment Signaling, Institute of Environment Biology, Utrecht University, Utrecht, The Netherlands
| | - Ronald Pierik
- Plant-Environment Signaling, Institute of Environment Biology, Utrecht University, Utrecht, The Netherlands.
- Laboratory of Molecular Biology, Wageningen University, Wageningen, The Netherlands.
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5
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Punja ZK, Sutton DB, Kim T. Glandular trichome development, morphology, and maturation are influenced by plant age and genotype in high THC-containing cannabis (Cannabis sativa L.) inflorescences. J Cannabis Res 2023; 5:12. [PMID: 37016398 PMCID: PMC10071647 DOI: 10.1186/s42238-023-00178-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 02/28/2023] [Indexed: 04/06/2023] Open
Abstract
BACKGROUND Glandular capitate trichomes which form on bract tissues of female inflorescences of high THC-containing Cannabis sativa L. plants are important sources of terpenes and cannabinoids. The influence of plant age and cannabis genotype on capitate trichome development, morphology, and maturation has not been extensively studied. Knowledge of the various developmental changes that occur in trichomes over time and the influence of genotype and plant age on distribution, numbers, and morphological features should lead to a better understanding of cannabis quality and consistency. METHODS Bract tissues of two genotypes-"Moby Dick" and "Space Queen"-were examined from 3 weeks to 8 weeks of flower development using light and scanning electron microscopy. Numbers of capitate trichomes on upper and lower bract surfaces were recorded at different positions within the inflorescence. Observations on distribution, extent of stalk formation, glandular head diameter, production of resin, and extent of dehiscence and senescence were made at various time points. The effects of post-harvesting handling and drying on trichome morphology were examined in an additional five genotypes. RESULTS Two glandular trichome types-bulbous and capitate (sessile or stalked)-were observed. Capitate trichome numbers and stalk length were significantly (P = 0.05) greater in "Space Queen" compared to "Moby Dick" at 3 and 6 weeks of flower development. Significantly more stalked-capitate trichomes were present on lower compared to upper bract surfaces at 6 weeks in both genotypes, while sessile-capitate trichomes predominated at 3 weeks. Epidermal and hypodermal cells elongated to different extents during stalk formation, producing significant variation in length (from 20 to 1100 μm). Glandular heads ranged from 40 to 110 μm in diameter. Maturation of stalked-capitate glandular heads was accompanied by a brown color development, reduced UV autofluorescence, and head senescence and dehiscence. Secreted resinous material from glandular heads appeared as droplets on the cuticular surface that caused many heads to stick together or collapse. Trichome morphology was affected by the drying process. CONCLUSION Capitate trichome numbers, development, and degree of maturation were influenced by cannabis genotype and plant age. The observations of trichome development indicate that asynchronous formation leads to different stages of trichome maturity on bracts. Trichome stalk lengths also varied between the two genotypes selected for study as well as over time. The variability in developmental stage and maturation between genotypes can potentially lead to variation in total cannabinoid levels in final product. Post-harvest handling and drying were shown to affect trichome morphology.
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Affiliation(s)
- Zamir K Punja
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada.
| | - Darren B Sutton
- Department of Computing Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Tommy Kim
- Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
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Muto N, Matsumoto T. CRISPR/Cas9-mediated genome editing of RsGL1a and RsGL1b in radish ( Raphanus sativus L.). FRONTIERS IN PLANT SCIENCE 2022; 13:951660. [PMID: 36311091 PMCID: PMC9606758 DOI: 10.3389/fpls.2022.951660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) is a powerful tool widely used for genome editing in various organisms, including plants. It introduces and facilitates the study of rare genetic mutations in a short time and is a potent tool to assist in plant molecular breeding. Radish (Raphanus sativus L.) is an important Brassicaceae vegetable cultivated and consumed worldwide. However, the application of the CRISPR/Cas9 system is limited by the absence of an efficient transformation system in radish. This study aimed to establish a CRISPR/Cas9 system in radish employing the Agrobacterium-mediated genetic transformation system reported recently. For this purpose, we performed genome editing using the CRISPR/Cas9 system targeting the GLABRA1 (GL1) orthologs, RsGL1a and RsGL1b, that induces leaf trichome formation in radish. A Cas9/single guide RNA (sgRNA) vector with a common sgRNA corresponding to RsGL1a and RsGL1b was transferred. A total of eight T0 plants were analyzed, of which six (editing efficiency 75%) had a mutated RsGL1a, five (62.5%) had a mutated RsGL1b, and five showed mutations in both RsGL1a and RsGL1b. Most mutations in T0 plants were short (<3 bp) deletions or insertions, causing frameshift mutations that might produce non-functional proteins. Chimeric mutations were detected in several T0 generation plants. In the T1 generation, the hairless phenotype was observed only in plants with knockout mutations in both RsGL1a and RsGL1b. The majority of mutant alleles in T0 plants, with the exception of the chimeric mutant plants detected, were stably inherited in the T1 generation. In conclusion, we successfully knocked out RsGL1a and RsGL1b using the CRISPR/Cas9 system and demonstrated that both RsGL1a and RsGL1b independently contribute to the induction of leaf trichome formation in radish. In this study, genome-edited plants without T-DNA, which are useful as breeding material, were obtained. The findings prove the feasibility of genome editing in radish using a CRISPR/Cas9 system that could accelerate its molecular breeding to improve agronomically desirable traits.
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Arteaga N, Méndez‐Vigo B, Fuster‐Pons A, Savic M, Murillo‐Sánchez A, Picó FX, Alonso‐Blanco C. Differential environmental and genomic architectures shape the natural diversity for trichome patterning and morphology in different Arabidopsis organs. PLANT, CELL & ENVIRONMENT 2022; 45:3018-3035. [PMID: 35289421 PMCID: PMC9541492 DOI: 10.1111/pce.14308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/21/2022] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
Despite the adaptive and taxonomic relevance of the natural diversity for trichome patterning and morphology, the molecular and evolutionary mechanisms underlying these traits remain mostly unknown, particularly in organs other than leaves. In this study, we address the ecological, genetic and molecular bases of the natural variation for trichome patterning and branching in multiple organs of Arabidopsis (Arabidopsis thaliana). To this end, we characterized a collection of 191 accessions and carried out environmental and genome-wide association (GWA) analyses. Trichome amount in different organs correlated negatively with precipitation in distinct seasons, thus suggesting a precise fit between trichome patterning and climate throughout the Arabidopsis life cycle. In addition, GWA analyses showed small overlapping between the genes associated with different organs, indicating partly independent genetic bases for vegetative and reproductive phases. These analyses identified a complex locus on chromosome 2, where two adjacent MYB genes (ETC2 and TCL1) displayed differential effects on trichome patterning in several organs. Furthermore, analyses of transgenic lines carrying different natural alleles demonstrated that TCL1 accounts for the variation for trichome patterning in all organs, and for stem trichome branching. By contrast, two other MYB genes (TRY and GL1), mainly showed effects on trichome patterning or branching, respectively.
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Affiliation(s)
- Noelia Arteaga
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB)Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
| | - Belén Méndez‐Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB)Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
| | - Alberto Fuster‐Pons
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB)Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
| | - Marija Savic
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB)Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
| | - Alba Murillo‐Sánchez
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB)Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
| | - F. Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD)Consejo Superior de Investigaciones Científicas (CSIC)SevillaSpain
| | - Carlos Alonso‐Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB)Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
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Xin Y, Pan W, Chen X, Liu Y, Zhang M, Chen X, Yang F, Li J, Wu J, Du Y, Zhang X. Transcriptome profiling reveals key genes in regulation of the tepal trichome development in Lilium pumilum D.C. PLANT CELL REPORTS 2021; 40:1889-1906. [PMID: 34259890 DOI: 10.1007/s00299-021-02753-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
A number of potential genes and pathways involved in tepal trichome development were identified in a natural lily mutant by transcriptome analysis and were confirmed with trichome and trichomeless species. Trichome is a specialized structure found on the surface of the plant with an important function in survival against abiotic and biotic stress. It is also an important economic trait in crop breeding. Extensive research has investigated the foliar trichome in model plants (Arabidopsis and tomato). However, the developmental mechanism of tepal trichome remains elusive. Lilium pumilum is an edible ornamental bulb and a good breeding parent possessing cold and salt-alkali resistance. Here, we found a natural mutant of Lilium pumilum grown on a highland whose tepals are covered by trichomes. Our data indicate that trichomes of the mutant are multicellular and branchless. Notably, stomata are also developed on the tepal of the mutant as well, suggesting there may be a correlation between trichome and stomata regulation. Furthermore, we isolated 27 differentially expressed genes (DEGs) by comparing the transcriptome profiling between the natural mutant and the wild type. These 27 genes belong to 4 groups: epidermal cell cycle and division, trichome morphogenesis, stress response, and transcription factors. Quantitative real-time PCR in Lilium pumilum (natural mutant and the wild type) and other lily species (Lilium leichtlinii var. maximowiczii/trichome; Lilium davidii var. willmottiae/, trichomeless) confirmed the validation of RNA-seq data and identified several trichome-related genes.
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Affiliation(s)
- Yin Xin
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Urban Agriculture (North), Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Ministry of Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Wenqiang Pan
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Urban Agriculture (North), Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Ministry of Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xi Chen
- Key Laboratory of Urban Agriculture (North), Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Ministry of Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Yixin Liu
- Key Laboratory of Urban Agriculture (North), Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Ministry of Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Mingfang Zhang
- Key Laboratory of Urban Agriculture (North), Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Ministry of Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xuqing Chen
- Key Laboratory of Urban Agriculture (North), Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Ministry of Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Fengping Yang
- Key Laboratory of Urban Agriculture (North), Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Ministry of Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jingru Li
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing, 100193, China
| | - Jian Wu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture and Landscape Architecture, China Agricultural University, Beijing, 100193, China.
| | - Yunpeng Du
- Key Laboratory of Urban Agriculture (North), Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Ministry of Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Xiuhai Zhang
- Key Laboratory of Urban Agriculture (North), Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Ministry of Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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Wang X, Zhou Y, Xu Y, Wang B, Yuan F. A novel gene LbHLH from the halophyte Limonium bicolor enhances salt tolerance via reducing root hair development and enhancing osmotic resistance. BMC PLANT BIOLOGY 2021; 21:284. [PMID: 34157974 PMCID: PMC8218485 DOI: 10.1186/s12870-021-03094-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/10/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND Identifying genes involved in salt tolerance in the recretohalophyte Limonium bicolor could facilitate the breeding of crops with enhanced salt tolerance. Here we cloned the previously uncharacterized gene LbHLH and explored its role in salt tolerance. RESULTS The 2,067-bp open reading frame of LbHLH encodes a 688-amino-acid protein with a typical helix-loop-helix (HLH) domain. In situ hybridization showed that LbHLH is expressed in salt glands of L. bicolor. LbHLH localizes to the nucleus, and LbHLH is highly expressed during salt gland development and in response to NaCl treatment. To further explore its function, we heterologously expressed LbHLH in Arabidopsis thaliana under the 35S promoter. The overexpression lines showed significantly increased trichome number and reduced root hair number. LbHLH might interact with GLABRA1 to influence trichome and root hair development, as revealed by yeast two-hybrid analysis. The transgenic lines showed higher germination percentages and longer roots than the wild type under NaCl treatment. Analysis of seedlings grown on medium containing sorbitol with the same osmotic pressure as 100 mM NaCl demonstrated that overexpressing LbHLH enhanced osmotic resistance. CONCLUSION These results indicate that LbHLH enhances salt tolerance by reducing root hair development and enhancing osmotic resistance under NaCl stress.
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Affiliation(s)
- Xi Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, P.R. China
| | - Yingli Zhou
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, P.R. China
| | - Yanyu Xu
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, P.R. China
| | - Baoshan Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, P.R. China.
| | - Fang Yuan
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, P.R. China.
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10
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Arteaga N, Savic M, Méndez-Vigo B, Fuster-Pons A, Torres-Pérez R, Oliveros JC, Picó FX, Alonso-Blanco C. MYB transcription factors drive evolutionary innovations in Arabidopsis fruit trichome patterning. THE PLANT CELL 2021; 33:548-565. [PMID: 33955486 PMCID: PMC8136876 DOI: 10.1093/plcell/koaa041] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/24/2020] [Indexed: 05/27/2023]
Abstract
Both inter- and intra-specific diversity has been described for trichome patterning in fruits, which is presumably involved in plant adaptation. However, the mechanisms underlying this developmental trait have been hardly addressed. Here we examined natural populations of Arabidopsis (Arabidopsis thaliana) that develop trichomes in fruits and pedicels, phenotypes previously not reported in the Arabidopsis genus. Genetic analyses identified five loci, MALAMBRUNO 1-5 (MAU1-5), with MAU2, MAU3, and MAU5 showing strong epistatic interactions that are necessary and sufficient to display these traits. Functional characterization of these three loci revealed cis-regulatory mutations in TRICHOMELESS1 and TRIPTYCHON, as well as a structural mutation in GLABRA1. Therefore, the multiple mechanisms controlled by three MYB transcription factors of the core regulatory network for trichome patterning have jointly been modulated to trigger trichome development in fruits. Furthermore, analyses of worldwide accessions showed that these traits and mutations only occur in a highly differentiated relict lineage from the Iberian Peninsula. In addition, these traits and alleles were associated with low spring precipitation, which suggests that trichome development in fruits and pedicels might be involved in climatic adaptation. Thus, we show that the combination of synergistic mutations in a gene regulatory circuit has driven evolutionary innovations in fruit trichome patterning in Arabidopsis.
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Affiliation(s)
- Noelia Arteaga
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28049, Spain
| | - Marija Savic
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28049, Spain
| | - Belén Méndez-Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28049, Spain
| | - Alberto Fuster-Pons
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28049, Spain
| | - Rafael Torres-Pérez
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28049, Spain
| | - Juan Carlos Oliveros
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28049, Spain
| | - F Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas (CSIC), Sevilla 41092, Spain
| | - Carlos Alonso-Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28049, Spain
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11
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Kong L, Li Z, Song Q, Li X, Luo K. Construction of a Full-Length cDNA Over-Expressing Library to Identify Valuable Genes from Populus tomentosa. Int J Mol Sci 2021; 22:ijms22073448. [PMID: 33810585 PMCID: PMC8036549 DOI: 10.3390/ijms22073448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/17/2021] [Accepted: 03/24/2021] [Indexed: 11/16/2022] Open
Abstract
Poplar wood is the main source of renewable biomass energy worldwide, and is also considered to be a model system for studying woody plants. The Full-length cDNA Over-eXpressing (FOX) gene hunting system is an effective method for generating gain-of-function mutants. Large numbers of novel genes have successfully been identified from many herbaceous plants according to the phenotype of gain-of-function mutants under normal or abiotic stress conditions using this system. However, the system has not been used for functional gene identification with high-throughput mutant screening in woody plants. In this study, we constructed a FOX library from the Chinese white poplar, Populus tomentosa. The poplar cDNA library was constructed into the plant expression vector pEarleyGate101 and further transformed into Arabidopsis thaliana (thale cress). We collected 1749 T1 transgenic plants identified by PCR. Of these, 593 single PCR bands from different transgenic lines were randomly selected for sequencing, and 402 diverse sequences of poplar genes were isolated. Most of these genes were involved in photosynthesis, environmental adaptation, and ribosome biogenesis based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation. We characterized in detail two mutant lines carrying PtoCPCa or PtoWRKY13 cDNA insertions. Phenotypic characterization showed that overexpression of these genes in A. thaliana affected trichome development or secondary cell wall (SCW) deposition, respectively. Together, the Populus-FOX-Arabidopsis library generated in our experiments will be helpful for efficient discovery of novel genes in poplar.
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Affiliation(s)
| | | | | | | | - Keming Luo
- Correspondence: ; Tel.: +86-23-6825-3021; Fax: +86-23-6825-2365
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12
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Yuan R, Cao Y, Li T, Yang F, Yu L, Qin Y, Du X, Liu F, Ding M, Jiang Y, Zhang H, Paterson AH, Rong J. Differentiation in the genetic basis of stem trichome development between cultivated tetraploid cotton species. BMC PLANT BIOLOGY 2021; 21:115. [PMID: 33632125 PMCID: PMC7905624 DOI: 10.1186/s12870-021-02871-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/01/2021] [Indexed: 05/14/2023]
Abstract
BACKGROUND Cotton stem trichomes and seed fibers are each single celled structures formed by protrusions of epidermal cells, and were found sharing the overlapping molecular mechanism. Compared with fibers, cotton stem trichomes are more easily observed, but the molecular mechanisms underlying their development are still poorly understood. RESULTS In this study, Gossypium hirsutum (Gh) and G. barbadense (Gb) were found to differ greatly in percentages of varieties/accessions with glabrous stems and in trichome density, length, and number per trichopore. Gh varieties normally had long singular and clustered trichomes, while Gb varieties had short clustered trichomes. Genetic mapping using five F2 populations from crosses between glabrous varieties and those with different types of stem trichomes revealed that much variation among stem trichome phenotypes could be accounted for by different combinations of genes/alleles on Chr. 06 and Chr. 24. The twenty- six F1 generations from crosses between varieties with different types of trichomes had varied phenotypes, further suggesting that the trichomes of tetraploid cotton were controlled by different genes/alleles. Compared to modern varieties, a greater proportion of Gh wild accessions were glabrous or had shorter and denser trichomes; whereas a smaller proportion of Gb primitive accessions had glabrous stems. A close correlation between fuzz fiber number and stem trichome density was observed in both Gh and Gb primitive accessions and modern varieties. CONCLUSION Based on these findings, we hypothesize that stem trichomes evolved in parallel with seed fibers during the domestication of cultivated tetraploid cotton. In addition, the current results illustrated that stem trichome can be used as a morphological index of fiber quality in cotton conventional breeding.
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Affiliation(s)
- Rong Yuan
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Zhejiang, 311300, Hangzhou, China
| | - Yuefen Cao
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Zhejiang, 311300, Hangzhou, China
| | - Tengyu Li
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Zhejiang, 311300, Hangzhou, China
| | - Feng Yang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Zhejiang, 311300, Hangzhou, China
| | - Li Yu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Zhejiang, 311300, Hangzhou, China
| | - Yuan Qin
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China
| | - Xiongming Du
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China
| | - Fang Liu
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China
| | - Mingquan Ding
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Zhejiang, 311300, Hangzhou, China
| | - Yurong Jiang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Zhejiang, 311300, Hangzhou, China
| | - Hua Zhang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Zhejiang, 311300, Hangzhou, China
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Junkang Rong
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Zhejiang, 311300, Hangzhou, China.
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13
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Wang X, Shen C, Meng P, Tan G, Lv L. Analysis and review of trichomes in plants. BMC PLANT BIOLOGY 2021; 21:70. [PMID: 33526015 PMCID: PMC7852143 DOI: 10.1186/s12870-021-02840-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/11/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND Trichomes play a key role in the development of plants and exist in a wide variety of species. RESULTS In this paper, it was reviewed that the structure and morphology characteristics of trichomes, alongside the biological functions and classical regulatory mechanisms of trichome development in plants. The environment factors, hormones, transcription factor, non-coding RNA, etc., play important roles in regulating the initialization, branching, growth, and development of trichomes. In addition, it was further investigated the atypical regulation mechanism in a non-model plant, found that regulating the growth and development of tea (Camellia sinensis) trichome is mainly affected by hormones and the novel regulation factors. CONCLUSIONS This review further displayed the complex and differential regulatory networks in trichome initiation and development, provided a reference for basic and applied research on trichomes in plants.
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Affiliation(s)
- Xiaojing Wang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, People's Republic of China
| | - Chao Shen
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, People's Republic of China
| | - Pinghong Meng
- Institute of Horticulture, Guizhou Province Academy of Agricultural Sciences, Guiyang, Guizhou, People's Republic of China
| | - Guofei Tan
- Institute of Horticulture, Guizhou Province Academy of Agricultural Sciences, Guiyang, Guizhou, People's Republic of China.
| | - Litang Lv
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, People's Republic of China.
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14
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Zhang Y, Xu S, Cheng Y, Wang J, Wang X, Liu R, Han J. Functional identification of PsMYB57 involved in anthocyanin regulation of tree peony. BMC Genet 2020; 21:124. [PMID: 33198624 PMCID: PMC7667756 DOI: 10.1186/s12863-020-00930-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/30/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND R2R3 myeloblastosis (MYB) genes are widely distributed in plants and comprise one of the largest transcription factor gene families. They play important roles in the regulatory networks controlling development, metabolism, and stress responses. Researches on functional genes in tree peony are still in its infancy. To date, few MYB genes have thus far been reported. RESULTS In this study, we constructed a comprehensive reference gene set by transcriptome sequencing to obtain R2R3 MYB genes. The transcriptomes of eight different tissues were sequenced, and 92,837 unigenes were obtained with an N50 of 1662 nt. A total of 48,435 unigenes (77.98%) were functionally annotated in public databases. Based on the assembly, we identified 57 R2R3 MYB genes containing full-length open reading frames, which clustered into 35 clades by phylogenetic analysis. PsMYB57 clustered with anthocyanin regulation genes in Arabidopsis and was mainly transcribed in the buds and young leaves. The overexpression of PsMYB57 induced anthocyanin accumulation in tobacco, and four detected anthocyanin structural genes, including NtCHS, NtF3'H, NtDFR, and NtANS, were upregulated. The two endogenous bHLH genes NtAn1a and NtAn1b were also upregulated and may work in combination with PsMYB57 in regulating anthocyanin structural genes. CONCLUSIONS Our study offers a useful reference to the selection of candidate MYB genes for further functional studies in tree peony. Function analysis of PsMYB57 is helpful to understand the color accumulation in vegetative organs of tree peony. PsMYB57 is also a promising resource to improve plant color in molecular breeding.
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Affiliation(s)
- Yanzhao Zhang
- Life Science Department, Luoyang Normal University, Luoyang, 471022, China.
| | - Shuzhen Xu
- Life Science Department, Luoyang Normal University, Luoyang, 471022, China
| | - Yanwei Cheng
- Life Science Department, Luoyang Normal University, Luoyang, 471022, China
| | - Jing Wang
- Life Science Department, Luoyang Normal University, Luoyang, 471022, China
| | - Xiangxiang Wang
- Life Science Department, Luoyang Normal University, Luoyang, 471022, China
| | - Runxiao Liu
- Life Science Department, Luoyang Normal University, Luoyang, 471022, China
| | - Jianming Han
- Life Science Department, Luoyang Normal University, Luoyang, 471022, China
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15
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Zmienko A, Marszalek-Zenczak M, Wojciechowski P, Samelak-Czajka A, Luczak M, Kozlowski P, Karlowski WM, Figlerowicz M. AthCNV: A Map of DNA Copy Number Variations in the Arabidopsis Genome. THE PLANT CELL 2020; 32:1797-1819. [PMID: 32265262 PMCID: PMC7268809 DOI: 10.1105/tpc.19.00640] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 03/09/2020] [Accepted: 03/30/2020] [Indexed: 05/13/2023]
Abstract
Copy number variations (CNVs) greatly contribute to intraspecies genetic polymorphism and phenotypic diversity. Recent analyses of sequencing data for >1000 Arabidopsis (Arabidopsis thaliana) accessions focused on small variations and did not include CNVs. Here, we performed genome-wide analysis and identified large indels (50 to 499 bp) and CNVs (500 bp and larger) in these accessions. The CNVs fully overlap with 18.3% of protein-coding genes, with enrichment for evolutionarily young genes and genes involved in stress and defense. By combining analysis of both genes and transposable elements (TEs) affected by CNVs, we revealed that the variation statuses of genes and TEs are tightly linked and jointly contribute to the unequal distribution of these elements in the genome. We also determined the gene copy numbers in a set of 1060 accessions and experimentally validated the accuracy of our predictions by multiplex ligation-dependent probe amplification assays. We then successfully used the CNVs as markers to analyze population structure and migration patterns. Finally, we examined the impact of gene dosage variation triggered by a CNV spanning the SEC10 gene on SEC10 expression at both the transcript and protein levels. The catalog of CNVs, CNV-overlapping genes, and their genotypes in a top model dicot will stimulate the exploration of the genetic basis of phenotypic variation.
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Affiliation(s)
- Agnieszka Zmienko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Faculty of Computing Science, Poznan University of Technology, Poznan, Poland
| | | | - Pawel Wojciechowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Faculty of Computing Science, Poznan University of Technology, Poznan, Poland
| | - Anna Samelak-Czajka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Magdalena Luczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Piotr Kozlowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Wojciech M Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
- Institute of Computing Science, Faculty of Computing Science, Poznan University of Technology, Poznan, Poland
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16
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Tan Y, Barnbrook M, Wilson Y, Molnár A, Bukys A, Hudson A. Shared Mutations in a Novel Glutaredoxin Repressor of Multicellular Trichome Fate Underlie Parallel Evolution of Antirrhinum Species. Curr Biol 2020; 30:1357-1366.e4. [DOI: 10.1016/j.cub.2020.01.060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/25/2019] [Accepted: 01/17/2020] [Indexed: 01/24/2023]
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17
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Xuan L, Yan T, Lu L, Zhao X, Wu D, Hua S, Jiang L. Genome-wide association study reveals new genes involved in leaf trichome formation in polyploid oilseed rape (Brassica napus L.). PLANT, CELL & ENVIRONMENT 2020; 43:675-691. [PMID: 31889328 DOI: 10.1111/pce.13694] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 05/18/2023]
Abstract
Leaf trichomes protect against various biotic and abiotic stresses in plants. However, there is little knowledge about this trait in oilseed rape (Brassica napus). Here, we demonstrated that hairy leaves were less attractive to Plutella xylostella larvae than glabrous leaves. We established a core germplasm collection with 290 accessions for a genome-wide association study (GWAS) of the leaf trichome trait in oilseed rape. We compared the transcriptomes of the shoot apical meristem (SAM) between hairy- and glabrous-leaf genotypes to narrow down the candidate genes identified by GWAS. The single nucleotide polymorphisms and the different transcript levels of BnaA.GL1.a, BnaC.SWEET4.a, BnaC.WAT1.a and BnaC.WAT1.b corresponded to the divergence of the hairy- and glabrous-leaf phenotypes, indicating the role of sugar and/or auxin signalling in leaf trichome initiation. The hairy-leaf SAMs had lower glucose and sucrose contents but higher expression of putative auxin responsive factors than the glabrous-leaf SAMs. Spraying of exogenous auxin (8 μm) increased leaf trichome number in certain genotypes, whereas spraying of sucrose (1%) plus glucose (6%) slightly repressed leaf trichome initiation. These data contribute to the existing knowledge about the genetic control of leaf trichomes and would assist breeding towards the desired leaf surface type in oilseed rape.
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Affiliation(s)
- Lijie Xuan
- Provincial Key Laboratory of Crop Gene Resources, Zhejiang University, Hangzhou, China
| | - Tao Yan
- Provincial Key Laboratory of Crop Gene Resources, Zhejiang University, Hangzhou, China
| | - Lingzhi Lu
- Provincial Key Laboratory of Crop Gene Resources, Zhejiang University, Hangzhou, China
| | - Xinze Zhao
- Provincial Key Laboratory of Crop Gene Resources, Zhejiang University, Hangzhou, China
| | - Dezhi Wu
- Provincial Key Laboratory of Crop Gene Resources, Zhejiang University, Hangzhou, China
| | - Shuijin Hua
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Lixi Jiang
- Provincial Key Laboratory of Crop Gene Resources, Zhejiang University, Hangzhou, China
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18
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Sanderson BJ, Park S, Jameel MI, Kraft JC, Thomashow MF, Schemske DW, Oakley CG. Genetic and physiological mechanisms of freezing tolerance in locally adapted populations of a winter annual. AMERICAN JOURNAL OF BOTANY 2020; 107:250-261. [PMID: 31762012 PMCID: PMC7065183 DOI: 10.1002/ajb2.1385] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/14/2019] [Indexed: 05/22/2023]
Abstract
PREMISE Despite myriad examples of local adaptation, the phenotypes and genetic variants underlying such adaptive differentiation are seldom known. Recent work on freezing tolerance and local adaptation in ecotypes of Arabidopsis thaliana from Italy and Sweden provides an essential foundation for uncovering the genotype-phenotype-fitness map for an adaptive response to a key environmental stress. METHODS We examined the consequences of a naturally occurring loss-of-function (LOF) mutation in an Italian allele of the gene that encodes the transcription factor CBF2, which underlies a major freezing-tolerance locus. We used four lines with a Swedish genetic background, each containing a LOF CBF2 allele. Two lines had introgression segments containing the Italian CBF2 allele, and two contained deletions created using CRISPR-Cas9. We used a growth chamber experiment to quantify freezing tolerance and gene expression before and after cold acclimation. RESULTS Freezing tolerance was lower in the Italian (11%) compared to the Swedish (72%) ecotype, and all four experimental CBF2 LOF lines had reduced freezing tolerance compared to the Swedish ecotype. Differential expression analyses identified 10 genes for which all CBF2 LOF lines, and the IT ecotype had similar patterns of reduced cold responsive expression compared to the SW ecotype. CONCLUSIONS We identified 10 genes that are at least partially regulated by CBF2 that may contribute to the differences in cold-acclimated freezing tolerance between the Italian and Swedish ecotypes. These results provide novel insight into the molecular and physiological mechanisms connecting a naturally occurring sequence polymorphism to an adaptive response to freezing conditions.
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Affiliation(s)
- Brian J. Sanderson
- Department of Botany and Plant Pathology and the Purdue Center for Plant BiologyPurdue UniversityWest LafayetteINUSA
| | - Sunchung Park
- MSU‐DOE Plant Research Laboratory and the Plant Resilience InstituteMichigan State UniversityEast LansingMIUSA
- Present address:
USDA ARS SalinasCAUSA
| | - M. Inam Jameel
- Department of Botany and Plant Pathology and the Purdue Center for Plant BiologyPurdue UniversityWest LafayetteINUSA
- Present address:
Department of GeneticsUniversity of GeorgiaAthensGAUSA
| | - Joshua C. Kraft
- Department of Botany and Plant Pathology and the Purdue Center for Plant BiologyPurdue UniversityWest LafayetteINUSA
| | - Michael F. Thomashow
- MSU‐DOE Plant Research Laboratory and the Plant Resilience InstituteMichigan State UniversityEast LansingMIUSA
| | - Douglas W. Schemske
- Department of Plant Biology, and W. K. Kellogg Biological StationMichigan State UniversityEast LansingMIUSA
| | - Christopher G. Oakley
- Department of Botany and Plant Pathology and the Purdue Center for Plant BiologyPurdue UniversityWest LafayetteINUSA
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19
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Sato Y, Tezuka A, Kashima M, Deguchi A, Shimizu-Inatsugi R, Yamazaki M, Shimizu KK, Nagano AJ. Transcriptional Variation in Glucosinolate Biosynthetic Genes and Inducible Responses to Aphid Herbivory on Field-Grown Arabidopsis thaliana. Front Genet 2019; 10:787. [PMID: 31572432 PMCID: PMC6749069 DOI: 10.3389/fgene.2019.00787] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 07/25/2019] [Indexed: 12/20/2022] Open
Abstract
Recently, increasing attempts have been made to understand how plant genes function in natura. In this context, transcriptional profiles represent plant physiological status in response to environmental stimuli. Herein, we combined high-throughput RNA-Seq with insect survey data on 19 accessions of Arabidopsis thaliana grown at a field site in Switzerland. We found that genes with the gene ontology (GO) annotations of "glucosinolate biosynthetic process" and "response to insects" were most significantly enriched, and the expression of these genes was highly variable among plant accessions. Nearly half of the total expression variation in the glucosinolate biosynthetic genes (AOPs, ESM1, ESP, and TGG1) was explained by among-accession variation. Of these genes, the expression level of AOP3 differed among Col-0 accession individuals depending on the abundance of the mustard aphid (Lipaphis erysimi). We also found that the expression of the major cis-jasmone activated gene CYP81D11 was positively correlated with the number of flea beetles (Phyllotreta striolata and Phyllotreta atra). Combined with the field RNA-Seq data, bioassays confirmed that AOP3 was up-regulated in response to attack by mustard aphids. The combined results from RNA-Seq and our ecological survey illustrate the feasibility of using field transcriptomics to detect an inducible defense, providing a first step towards an in natura understanding of biotic interactions involving phenotypic plasticity.
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Affiliation(s)
- Yasuhiro Sato
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
- Research Institute for Food and Agriculture, Ryukoku University, Otsu, Japan
| | - Ayumi Tezuka
- Research Institute for Food and Agriculture, Ryukoku University, Otsu, Japan
| | - Makoto Kashima
- Research Institute for Food and Agriculture, Ryukoku University, Otsu, Japan
| | - Ayumi Deguchi
- Research Institute for Food and Agriculture, Ryukoku University, Otsu, Japan
- Graduate School of Horticulture, Chiba University, Matsudo, Japan
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Misako Yamazaki
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Kentaro K. Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Atsushi J. Nagano
- Department of Plant Life Sciences, Faculty of Agriculture, Ryukoku University, Otsu, Japan
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20
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Sato Y, Shimizu-Inatsugi R, Yamazaki M, Shimizu KK, Nagano AJ. Plant trichomes and a single gene GLABRA1 contribute to insect community composition on field-grown Arabidopsis thaliana. BMC PLANT BIOLOGY 2019; 19:163. [PMID: 31029092 PMCID: PMC6486987 DOI: 10.1186/s12870-019-1705-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 03/11/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND Genetic variation in plants alters insect abundance and community structure in the field; however, little is known about the importance of a single gene among diverse plant genotypes. In this context, Arabidopsis trichomes provide an excellent system to discern the roles of natural variation and a key gene, GLABRA1, in shaping insect communities. In this study, we transplanted two independent glabrous mutants (gl1-1 and gl1-2) and 17 natural accessions of Arabidopsis thaliana to two localities in Switzerland and Japan. RESULTS Fifteen insect species inhabited the plant accessions, with the insect community composition significantly attributed to variations among plant accessions. The total abundance of leaf-chewing herbivores was negatively correlated with trichome density at both field sites, while glucosinolates had variable effects on leaf chewers between the sites. Interestingly, there was a parallel tendency for the abundance of leaf chewers to be higher on gl1-1 and gl1-2 than on their different parental accessions, Ler-1 and Col-0, respectively. Furthermore, the loss of function in the GLABRA1 gene significantly decreased the resistance of plants to the two predominant chewers; flea beetles and turnip sawflies. CONCLUSIONS Overall, our results indicate that insect community composition significantly varies among A. thaliana accessions across two distant field sites, with GLABRA1 playing a key role in altering the abundance of leaf-chewing herbivores. Given that such a trichome variation is widely observed in Brassicaceae plants, the present study exemplifies the community-wide effect of a single plant gene on crucifer-feeding insects in the field.
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Affiliation(s)
- Yasuhiro Sato
- PRESTO, Japan Science and Technology Agency, Kawaguchi, 332-0012 Japan
- Research Institute for Food and Agriculture, Ryukoku University, Yokotani 1-5, Seta Oe-cho, Otsu, Shiga 520-2194 Japan
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Misako Yamazaki
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Kentaro K. Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, 244-0813 Totsuka-ward, Yokohama, Japan
| | - Atsushi J. Nagano
- Department of Plant Life Sciences, Faculty of Agriculture, Ryukoku University, Yokotani 1-5, Seta Oe-cho, Otsu, Shiga 520-2194 Japan
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21
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Wang L, Zhou CM, Mai YX, Li LZ, Gao J, Shang GD, Lian H, Han L, Zhang TQ, Tang HB, Ren H, Wang FX, Wu LY, Liu XL, Wang CS, Chen EW, Zhang XN, Liu C, Wang JW. A spatiotemporally regulated transcriptional complex underlies heteroblastic development of leaf hairs in Arabidopsis thaliana. EMBO J 2019; 38:embj.2018100063. [PMID: 30842098 DOI: 10.15252/embj.2018100063] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 02/08/2019] [Accepted: 02/15/2019] [Indexed: 11/09/2022] Open
Abstract
Heteroblasty refers to a phenomenon that a plant produces morphologically or functionally different lateral organs in an age-dependent manner. In the model plant Arabidopsis thaliana, the production of trichomes (epidermal leaf hairs) on the abaxial (lower) side of leaves is a heteroblastic mark for the juvenile-to-adult transition. Here, we show that the heteroblastic development of abaxial trichomes is regulated by a spatiotemporally regulated complex comprising the leaf abaxial fate determinant (KAN1) and the developmental timer (miR172-targeted AP2-like proteins). We provide evidence that a short-distance chromatin loop brings the downstream enhancer element into close association with the promoter elements of GL1, which encodes a MYB transcription factor essential for trichome initiation. During juvenile phase, the KAN1-AP2 repressive complex binds to the downstream sequence of GL1 and represses its expression through chromatin looping. As plants age, the gradual reduction in AP2-like protein levels leads to decreased amount of the KAN1-AP2 complex, thereby licensing GL1 expression and the abaxial trichome initiation. Our results thus reveal a novel molecular mechanism by which a heteroblastic trait is governed by integrating age and leaf polarity cue in plants.
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Affiliation(s)
- Long Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Chuan-Miao Zhou
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Yan-Xia Mai
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Ling-Zi Li
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China.,University of Chinese Academy of Sciences, Shanghai, China
| | - Jian Gao
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China.,University of Chinese Academy of Sciences, Shanghai, China
| | - Guang-Dong Shang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China.,University of Chinese Academy of Sciences, Shanghai, China
| | - Heng Lian
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Lin Han
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China.,University of Chinese Academy of Sciences, Shanghai, China
| | - Tian-Qi Zhang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China
| | - Hong-Bo Tang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China.,University of Chinese Academy of Sciences, Shanghai, China
| | - Hang Ren
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China.,University of Chinese Academy of Sciences, Shanghai, China
| | - Fu-Xiang Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China.,University of Chinese Academy of Sciences, Shanghai, China
| | - Lian-Yu Wu
- ShanghaiTech University, Shanghai, China
| | | | - Chang-Sheng Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China.,University of Chinese Academy of Sciences, Shanghai, China
| | - Er-Wang Chen
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China.,University of Chinese Academy of Sciences, Shanghai, China
| | - Xue-Ning Zhang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China.,University of Chinese Academy of Sciences, Shanghai, China
| | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), Shanghai, China .,ShanghaiTech University, Shanghai, China
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22
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Monroe JG, Powell T, Price N, Mullen JL, Howard A, Evans K, Lovell JT, McKay JK. Drought adaptation in Arabidopsis thaliana by extensive genetic loss-of-function. eLife 2018; 7:41038. [PMID: 30520727 PMCID: PMC6326724 DOI: 10.7554/elife.41038] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 12/06/2018] [Indexed: 11/26/2022] Open
Abstract
Interdisciplinary syntheses are needed to scale up discovery of the environmental drivers and molecular basis of adaptation in nature. Here we integrated novel approaches using whole genome sequences, satellite remote sensing, and transgenic experiments to study natural loss-of-function alleles associated with drought histories in wild Arabidopsis thaliana. The genes we identified exhibit population genetic signatures of parallel molecular evolution, selection for loss-of-function, and shared associations with flowering time phenotypes in directions consistent with longstanding adaptive hypotheses seven times more often than expected by chance. We then confirmed predicted phenotypes experimentally in transgenic knockout lines. These findings reveal the importance of drought timing to explain the evolution of alternative drought tolerance strategies and further challenge popular assumptions about the adaptive value of genetic loss-of-function in nature. These results also motivate improved species-wide sequencing efforts to better identify loss-of-function variants and inspire new opportunities for engineering climate resilience in crops. Water shortages caused by droughts lead to crop losses that affect billions of people around the world each year. By discovering how wild plants adapt to drought, it may be possible to identify traits and genes that help to improve the growth of crop plants when water is scarce. It has been suggested that plants have adapted to droughts by flowering at times of the year when droughts are less likely to occur. For example, if droughts are more likely to happen in spring, the plants may delay flowering until the summer. Arabidopsis thaliana is a small plant that is found across Eurasia, Africa and North America, including in areas that are prone to drought at different times of the year. Individual plants of the same species may carry different versions of the same gene (known as alleles). Some of these alleles may not work properly and are referred to as loss-of-function alleles. Monroe et al. investigated whether A. thaliana plants carry any loss-of-function alleles that are associated with droughts happening in the spring or summer, and whether they are linked to when those plants will flower. Monroe et al. analyzed satellite images collected over the last 30 years to measure when droughts have occurred. Next, they searched genome sequences of Arabidopsis thaliana for alleles that might help the plants to adapt to droughts in the spring or summer. Combining the two approaches revealed that loss-of-function alleles associated with spring droughts were strongly predicted to be associated with the plants flowering later in the year. Similarly, loss-of-function alleles associated with summer droughts were predicted to be associated with the plants flowering earlier in the year. These findings support the idea that plants can adapt to drought by changing when they produce flowers, and suggest that loss-of-function alleles play a major role in this process. New techniques for editing genes mean it is easier than ever to generate new loss-of-function alleles in specific genes. Therefore, the results presented by Monroe et al. may help researchers to develop new varieties of crop plants that are better adapted to droughts.
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Affiliation(s)
- J Grey Monroe
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, United States.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, United States
| | - Tyler Powell
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, United States.,Department of Biology, Colorado State University, Fort Collins, United States
| | - Nicholas Price
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, United States
| | - Jack L Mullen
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, United States
| | - Anne Howard
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, United States
| | - Kyle Evans
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, United States
| | - John T Lovell
- HudsonAlpha Institute for Biotechnology, Huntsville, United States
| | - John K McKay
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, United States.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, United States
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23
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Tian N, Liu F, Wang P, Zhang X, Li X, Wu G. The molecular basis of glandular trichome development and secondary metabolism in plants. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2017.05.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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24
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Distributions of Mutational Effects and the Estimation of Directional Selection in Divergent Lineages of Arabidopsis thaliana. Genetics 2017; 206:2105-2117. [PMID: 28550014 DOI: 10.1534/genetics.116.199190] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/22/2017] [Indexed: 12/22/2022] Open
Abstract
Mutations are crucial to evolution, providing the ultimate source of variation on which natural selection acts. Due to their key role, the distribution of mutational effects on quantitative traits is a key component to any inference regarding historical selection on phenotypic traits. In this paper, we expand on a previously developed test for selection that could be conducted assuming a Gaussian mutation effect distribution by developing approaches to also incorporate any of a family of heavy-tailed Laplace distributions of mutational effects. We apply the test to detect directional natural selection on five traits along the divergence of Columbia and Landsberg lineages of Arabidopsis thaliana, constituting the first test for natural selection in any organism using quantitative trait locus and mutation accumulation data to quantify the intensity of directional selection on a phenotypic trait. We demonstrate that the results of the test for selection can depend on the mutation effect distribution specified. Using the distributions exhibiting the best fit to mutation accumulation data, we infer that natural directional selection caused divergence in the rosette diameter and trichome density traits of the Columbia and Landsberg lineages.
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25
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Sato Y, Kudoh H. Fine-scale frequency differentiation along a herbivory gradient in the trichome dimorphism of a wild Arabidopsis. Ecol Evol 2017; 7:2133-2141. [PMID: 28405279 PMCID: PMC5383478 DOI: 10.1002/ece3.2830] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 01/28/2017] [Indexed: 12/17/2022] Open
Abstract
Geographic variation is commonly observed in plant resistance traits, where plant species might experience different selection pressure across a heterogeneous landscape. Arabidopsis halleri subsp. gemmifera is dimorphic for trichome production, generating two morphs, trichome-producing (hairy) and trichomeless (glabrous) plants. Trichomes of A. halleri are known to confer resistance against the white butterfly, cabbage sawfly, and brassica leaf beetle, but not against flea beetles. We combined leaf damage, microclimate, and microsatellite loci data of 26 A. halleri populations in central Japan, to explore factors responsible for fine-scale geographic variation in the morph frequency. We found that hairy plants were less damaged than glabrous plants within populations, but the among-site variation was the most significant source of variation in the individual-level damage. Fixation index (Gst″) of a putative trichome locus exhibited a significant divergence along population-level damage with an exception of an outlier population, inferring the local adaptation to herbivory. Notably, this outlier was a population wherein our previous study reported a balancing role of the brassica leaf beetle Phaedon brassicae on the morph frequency. This differentiation of the trichome locus was unrelated to neutral genetic differentiation (evaluated by Gst″ of microsatellite loci) and meteorological factors (including temperature and solar radiation). The present findings, combined with those of our previous work, provide suggestive evidence that herbivore-driven divergence and occasional outbreak of a specific herbivore have jointly contributed to the ecogeographic pattern in the frequency of two morphs.
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Affiliation(s)
- Yasuhiro Sato
- Center for Ecological ResearchKyoto UniversityOtsuShigaJapan
- Present address: Department of Plant Life SciencesFaculty of AgricultureRyukoku UniversityYokotani 1‐5, Seta Oe‐choOtsuShiga520‐2194Japan
| | - Hiroshi Kudoh
- Center for Ecological ResearchKyoto UniversityOtsuShigaJapan
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26
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The genome sequence of Barbarea vulgaris facilitates the study of ecological biochemistry. Sci Rep 2017; 7:40728. [PMID: 28094805 PMCID: PMC5240624 DOI: 10.1038/srep40728] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 12/09/2016] [Indexed: 12/30/2022] Open
Abstract
The genus Barbarea has emerged as a model for evolution and ecology of plant defense compounds, due to its unusual glucosinolate profile and production of saponins, unique to the Brassicaceae. One species, B. vulgaris, includes two ‘types’, G-type and P-type that differ in trichome density, and their glucosinolate and saponin profiles. A key difference is the stereochemistry of hydroxylation of their common phenethylglucosinolate backbone, leading to epimeric glucobarbarins. Here we report a draft genome sequence of the G-type, and re-sequencing of the P-type for comparison. This enables us to identify candidate genes underlying glucosinolate diversity, trichome density, and study the genetics of biochemical variation for glucosinolate and saponins. B. vulgaris is resistant to the diamondback moth, and may be exploited for “dead-end” trap cropping where glucosinolates stimulate oviposition and saponins deter larvae to the extent that they die. The B. vulgaris genome will promote the study of mechanisms in ecological biochemistry to benefit crop resistance breeding.
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27
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Ma J, He X, Bai X, Niu Z, Duan B, Chen N, Shao X, Wan D. Genome-Wide Survey Reveals Transcriptional Differences Underlying the Contrasting Trichome Phenotypes of Two Sister Desert Poplars. Genes (Basel) 2016; 7:genes7120111. [PMID: 27916935 PMCID: PMC5192487 DOI: 10.3390/genes7120111] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 11/24/2016] [Accepted: 11/24/2016] [Indexed: 11/16/2022] Open
Abstract
Trichomes, which are widely used as an important diagnostic characteristic in plant species delimitation, play important roles in plant defense and adaptation to adverse environments. In this study, we used two sister poplar species, Populus pruinosa and Populus euphratica—which have, respectively, dense and sparse trichomes—to examine the genetic differences associated with these contrasting phenotypes. The results showed that 42 and 45 genes could be identified as candidate genes related to trichomes in P. pruinosa and P. euphratica, respectively; most of these genes possessed high degrees of diversification in their coding sequences, but they were similar in intron/exon structure in the two species. We also found that most of the candidate trichome genes were expressed at higher levels in P. pruinosa, which has dense trichomes, than in P. euphratica, where there are few trichomes. Based on analyses of transcriptional profiles, a total of 195 genes, including many transcription factors, were found to show distinct differences in expression. The results of gene function annotation suggested that the genes identified as having contrasting levels of expression level are mainly associated with trichome elongation, ATPase activity, and hormone transduction. Changes in the expression of these and other related genes with high sequence diversification may have contributed to the contrast in the pattern of trichome phenotypes between the two species.
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Affiliation(s)
- Jianchao Ma
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
| | - Xiaodong He
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
| | - Xiaotao Bai
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
| | - Zhimin Niu
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
| | - Bingbing Duan
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
| | - Ningning Chen
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
| | - Xuemin Shao
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
| | - Dongshi Wan
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou 730000, China.
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28
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Hendrick MF, Finseth FR, Mathiasson ME, Palmer KA, Broder EM, Breigenzer P, Fishman L. The genetics of extreme microgeographic adaptation: an integrated approach identifies a major gene underlying leaf trichome divergence in Yellowstone Mimulus guttatus. Mol Ecol 2016; 25:5647-5662. [PMID: 27393073 DOI: 10.1111/mec.13753] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 06/15/2016] [Accepted: 06/22/2016] [Indexed: 12/30/2022]
Abstract
Microgeographic adaptation provides a particularly interesting context for understanding the genetic basis of phenotypic divergence and may also present unique empirical challenges. In particular, plant adaptation to extreme soil mosaics may generate barriers to gene flow or shifts in mating system that confound simple genomic scans for adaptive loci. Here, we combine three approaches - quantitative trait locus (QTL) mapping of candidate intervals in controlled crosses, population resequencing (PoolSeq) and analyses of wild recombinant individuals - to investigate one trait associated with Mimulus guttatus (yellow monkeyflower) adaptation to geothermal soils in Yellowstone National Park. We mapped a major QTL causing dense leaf trichomes in thermally adapted plants to a <50-kb region of linkage Group 14 (Tr14) previously implicated in trichome divergence between independent M. guttatus populations. A PoolSeq scan of Tr14 region revealed a cluster of six genes, coincident with the inferred QTL peak, with high allele frequency differences sufficient to explain observed phenotypic differentiation. One of these, the R2R3 MYB transcription factor Migut.N02661, is a plausible functional candidate and was also strongly associated (r2 = 0.27) with trichome phenotype in analyses of wild-collected admixed individuals. Although functional analyses will be necessary to definitively link molecular variants in Tr14 with trichome divergence, our analyses are a major step in that direction. They point to a simple, and parallel, genetic basis for one axis of Mimulus guttatus adaptation to an extreme habitat, suggest a broadly conserved genetic basis for trichome variation across flowering plants and pave the way for further investigations of this challenging case of microgeographic incipient speciation.
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Affiliation(s)
- Margaret F Hendrick
- Division of Biological Sciences, University of Montana, 32 Campus Dr., Missoula, MT, 59812, USA.,Department of Earth and Environment, Boston University, 685 Commonwealth Ave., Boston, MA, 02215, USA
| | - Findley R Finseth
- Division of Biological Sciences, University of Montana, 32 Campus Dr., Missoula, MT, 59812, USA
| | - Minna E Mathiasson
- School of Biology and Ecology, University of Maine, 5751 Murray Hall, Orono, ME, 04469, USA
| | - Kristen A Palmer
- Department of Biology, Wheaton College, 26 E. Main St., Norton, MA, 02766, USA
| | - Emma M Broder
- Biology Department, Wesleyan University, 45 Wyllys Ave., Middletown, CT, 06259, USA
| | - Peter Breigenzer
- Division of Biological Sciences, University of Montana, 32 Campus Dr., Missoula, MT, 59812, USA
| | - Lila Fishman
- Division of Biological Sciences, University of Montana, 32 Campus Dr., Missoula, MT, 59812, USA
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29
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Onda Y, Mochida K. Exploring Genetic Diversity in Plants Using High-Throughput Sequencing Techniques. Curr Genomics 2016; 17:358-67. [PMID: 27499684 PMCID: PMC4955029 DOI: 10.2174/1389202917666160331202742] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 07/19/2015] [Accepted: 07/21/2015] [Indexed: 12/31/2022] Open
Abstract
Food security has emerged as an urgent concern because of the rising world population. To meet the food demands of the near future, it is required to improve the productivity of various crops, not just of staple food crops. The genetic diversity among plant populations in a given species allows the plants to adapt to various environmental conditions. Such diversity could therefore yield valuable traits that could overcome the food-security challenges. To explore genetic diversity comprehensively and to rapidly identify useful genes and/or allele, advanced high-throughput sequencing techniques, also called next-generation sequencing (NGS) technologies, have been developed. These provide practical solutions to the challenges in crop genomics. Here, we review various sources of genetic diversity in plants, newly developed genetic diversity-mining tools synergized with NGS techniques, and related genetic approaches such as quantitative trait locus analysis and genome-wide association study.
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Affiliation(s)
- Yoshihiko Onda
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa,Japan
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa,Japan
| | - Keiichi Mochida
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa,Japan
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa,Japan
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Kanagawa,Japan
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30
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Zhang H, Wang L, Zheng S, Liu Z, Wu X, Gao Z, Cao C, Li Q, Ren Z. A fragment substitution in the promoter of CsHDZIV11/CsGL3 is responsible for fruit spine density in cucumber (Cucumis sativus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1289-1301. [PMID: 27015676 DOI: 10.1007/s00122-016-2703-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 03/05/2016] [Indexed: 05/25/2023]
Abstract
The indel in the promoter of CsHDZIV11 co-segregates with fruit spine density and could be used for molecular breeding in cucumber. Fruit spine density is an important quality trait for marketing in cucumber (Cucumis sativus L.). However, the molecular basis of fruit spine density in cucumber remains unclear. In this study, we isolated a mutant, few spines 1 (fs1), from CNS2 (wild type, WT), a North China-type cucumber with a high density of fruit spines. Genetic analysis showed that fs1 was controlled by a single recessive Mendelian factor. Bulked segregant analysis combined with genome resequencing were used for mapping fs1 in the F2 population derived from a cross between the fs1 mutant and WT, and it was located on chromosome 6 through association analysis. To develop more polymorphic markers to locate fs1, another F2 population was constructed from the cross between fs1 and 'Chinese long' 9930. Then, fs1 was narrowed down to a 110.4-kb genomic region containing 25 annotated genes. A fragment substitution was identified in the promoter region of Csa6M514870 between fs1 and WT. This fragment in fs1 was also present in wild cucumber. Csa6M514870 encodes a PDF2-related protein, a homeodomain-leucine zipper IV transcription factor (CsHDZIV11/CsGL3) sharing high identity and similarity with proteins related to trichome formation or epidermal cell differentiation. Quantitative reverse-transcription PCR revealed a higher expression level of CsHDZIV11 in young fruits from fs1 compared to WT. A molecular marker based on this indel co-segregated with the spine density. This work provides a solid foundation not only for understanding the molecular mechanism of fruit spine density, but also for molecular breeding in cucumber.
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Affiliation(s)
- Haiyang Zhang
- State Key Laboratory of Corp Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, College of Horticulture Science and Engineering, Shandong Agricultural University, No. 61 Daizong road, Tai'an, 271018, Shandong, China
| | - Lina Wang
- State Key Laboratory of Corp Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, College of Horticulture Science and Engineering, Shandong Agricultural University, No. 61 Daizong road, Tai'an, 271018, Shandong, China
| | - Shuangshuang Zheng
- State Key Laboratory of Corp Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, College of Horticulture Science and Engineering, Shandong Agricultural University, No. 61 Daizong road, Tai'an, 271018, Shandong, China
| | - Zezhou Liu
- State Key Laboratory of Corp Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, College of Horticulture Science and Engineering, Shandong Agricultural University, No. 61 Daizong road, Tai'an, 271018, Shandong, China
| | - Xiaoqin Wu
- State Key Laboratory of Corp Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, College of Horticulture Science and Engineering, Shandong Agricultural University, No. 61 Daizong road, Tai'an, 271018, Shandong, China
| | - Zhihui Gao
- State Key Laboratory of Corp Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, College of Horticulture Science and Engineering, Shandong Agricultural University, No. 61 Daizong road, Tai'an, 271018, Shandong, China
| | - Chenxing Cao
- State Key Laboratory of Corp Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, College of Horticulture Science and Engineering, Shandong Agricultural University, No. 61 Daizong road, Tai'an, 271018, Shandong, China
| | - Qiang Li
- State Key Laboratory of Corp Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, College of Horticulture Science and Engineering, Shandong Agricultural University, No. 61 Daizong road, Tai'an, 271018, Shandong, China
| | - Zhonghai Ren
- State Key Laboratory of Corp Biology, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Huanghuai Region), Ministry of Agriculture, College of Horticulture Science and Engineering, Shandong Agricultural University, No. 61 Daizong road, Tai'an, 271018, Shandong, China.
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Roux F, Bergelson J. The Genetics Underlying Natural Variation in the Biotic Interactions of Arabidopsis thaliana: The Challenges of Linking Evolutionary Genetics and Community Ecology. Curr Top Dev Biol 2016; 119:111-56. [PMID: 27282025 DOI: 10.1016/bs.ctdb.2016.03.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In the context of global change, predicting the responses of plant communities in an ever-changing biotic environment calls for a multipronged approach at the interface of evolutionary genetics and community ecology. However, our understanding of the genetic basis of natural variation involved in mediating biotic interactions, and associated adaptive dynamics of focal plants in their natural communities, is still in its infancy. Here, we review the genetic and molecular bases of natural variation in the response to biotic interactions (viruses, bacteria, fungi, oomycetes, herbivores, and plants) in the model plant Arabidopsis thaliana as well as the adaptive value of these bases. Among the 60 identified genes are a number that encode nucleotide-binding site leucine-rich repeat (NBS-LRR)-type proteins, consistent with early examples of plant defense genes. However, recent studies have revealed an extensive diversity in the molecular mechanisms of defense. Many types of genetic variants associate with phenotypic variation in biotic interactions, even among the genes of large effect that tend to be identified. In general, we found that (i) balancing selection rather than directional selection explains the observed patterns of genetic diversity within A. thaliana and (ii) the cost/benefit tradeoffs of adaptive alleles can be strongly dependent on both genomic and environmental contexts. Finally, because A. thaliana rarely interacts with only one biotic partner in nature, we highlight the benefit of exploring diffuse biotic interactions rather than tightly associated host-enemy pairs. This challenge would help to improve our understanding of coevolutionary quantitative genetics within the context of realistic community complexity.
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Affiliation(s)
- F Roux
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France.
| | - J Bergelson
- University of Chicago, Chicago, IL, United States
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Genome-wide identification and characterization of R2R3MYB family in Solanum lycopersicum. Mol Genet Genomics 2014; 289:1183-207. [PMID: 25005853 DOI: 10.1007/s00438-014-0879-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 06/07/2014] [Indexed: 10/25/2022]
Abstract
The R2R3MYB proteins comprise one of the largest families of transcription factors and play regulatory roles in developmental processes and defense responses in plants. However, there has been relatively little effort to systematically carry out comprehensive genomic and functional analyses of these genes in tomato (Solanum lycopersicum L.), a reference species for Solanaceae plants, and the model plant for fruit development. In this study, a total of 121 R2R3MYB genes were identified in the tomato genome released recently and further classified into 29 subgroups based on the phylogenetic analysis of the complete protein sequences. Phylogenetic comparison of the members of this superfamily among tomato, Arabidopsis, grape, rice, poplar, soybean, cucumber and apple revealed that the putative functions of some tomato R2R3MYB proteins were clustered into the Arabidopsis functional clades. The chromosome distribution pattern revealed that tomato R2R3MYB genes were enriched on several chromosomes and 52 % of the family members were tandemly duplicated genes. Tissue specificity or different expression levels of SlR2R3MYBs in different tissues suggested differential regulation of tissue development as well as metabolic regulation. The transcript abundance level analysis during abiotic conditions identified a group of R2R3MYB genes that responded to one or more treatments suggesting that the SlR2R3MYBs played major roles in the plant response to abiotic conditions and involved in signal transduction pathways. This study not only provides a solid foundation for further functional dissection of tomato R2R3MYB family genes, but may also be profitable for, in the future, the improvement of tomato stress tolerance and fruit quality.
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Hauser MT. Molecular basis of natural variation and environmental control of trichome patterning. FRONTIERS IN PLANT SCIENCE 2014; 5:320. [PMID: 25071803 PMCID: PMC4080826 DOI: 10.3389/fpls.2014.00320] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 06/17/2014] [Indexed: 05/17/2023]
Abstract
Trichomes are differentiated epidermal cells on above ground organs of nearly all land plants. They play important protective roles as structural defenses upon biotic attacks such as herbivory, oviposition and fungal infections, and against abiotic stressors such as drought, heat, freezing, excess of light, and UV radiation. The pattern and density of trichomes is highly variable within natural population suggesting tradeoffs between traits positively affecting fitness such as resistance and the costs of trichome production. The spatial distribution of trichomes is regulated through a combination of endogenous developmental programs and external signals. This review summarizes the current understanding on the molecular basis of the natural variation and the role of phytohormones and environmental stimuli on trichome patterning.
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Affiliation(s)
- Marie-Theres Hauser
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life SciencesVienna, Austria
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Bloomer RH, Lloyd AM, Symonds VV. The genetic architecture of constitutive and induced trichome density in two new recombinant inbred line populations of Arabidopsis thaliana: phenotypic plasticity, epistasis, and bidirectional leaf damage response. BMC PLANT BIOLOGY 2014; 14:119. [PMID: 24885520 PMCID: PMC4108038 DOI: 10.1186/1471-2229-14-119] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 04/25/2014] [Indexed: 05/23/2023]
Abstract
BACKGROUND Herbivory imposes an important selective pressure on plants. In Arabidopsis thaliana leaf trichomes provide a key defense against insect herbivory; however, trichome production incurs a fitness cost in the absence of herbivory. Previous work on A. thaliana has shown an increase in trichome density in response to leaf damage, suggesting a mechanism by which the cost associated with constitutively high trichome density might be mitigated; however, the genetic basis of trichome density induction has not been studied. RESULTS Here, we describe the mapping of quantitative trait loci (QTL) for constitutive and damage induced trichome density in two new recombinant inbred line populations of A. thaliana; mapping for constitutive and induced trichome density also allowed for the investigation of damage response (plasticity) QTL. Both novel and previously identified QTL for constitutive trichome density and the first QTL for induced trichome density and response are identified. Interestingly, two of the four parental accessions and multiple RILs in each population exhibited lower trichome density following leaf damage, a response not previously described in A. thaliana. Importantly, a single QTL was mapped for the response phenotype and allelic variation at this locus appears to determine response trajectory in RILs. The data also show that epistatic interactions are a significant component of the genetic architecture of trichome density. CONCLUSIONS Together, our results provide further insights into the genetic architecture of constitutive trichome density and new insights into induced trichome density in A. thaliana specifically and to our understanding of the genetic underpinnings of natural variation generally.
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Affiliation(s)
- Rebecca H Bloomer
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
| | - Alan M Lloyd
- Institute for Cellular and Molecular Biology, University of Texas, Austin, TX, USA
| | - V Vaughan Symonds
- Institute of Fundamental Sciences, Massey University, Private Bag 11222, Palmerston North 4442, New Zealand
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Nayidu NK, Kagale S, Taheri A, Withana-Gamage TS, Parkin IAP, Sharpe AG, Gruber MY. Comparison of five major trichome regulatory genes in Brassica villosa with orthologues within the Brassicaceae. PLoS One 2014; 9:e95877. [PMID: 24755905 PMCID: PMC3995807 DOI: 10.1371/journal.pone.0095877] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 03/31/2014] [Indexed: 01/21/2023] Open
Abstract
Coding sequences for major trichome regulatory genes, including the positive regulators GLABRA 1(GL1), GLABRA 2 (GL2), ENHANCER OF GLABRA 3 (EGL3), and TRANSPARENT TESTA GLABRA 1 (TTG1) and the negative regulator TRIPTYCHON (TRY), were cloned from wild Brassica villosa, which is characterized by dense trichome coverage over most of the plant. Transcript (FPKM) levels from RNA sequencing indicated much higher expression of the GL2 and TTG1 regulatory genes in B. villosa leaves compared with expression levels of GL1 and EGL3 genes in either B. villosa or the reference genome species, glabrous B. oleracea; however, cotyledon TTG1 expression was high in both species. RNA sequencing and Q-PCR also revealed an unusual expression pattern for the negative regulators TRY and CPC, which were much more highly expressed in trichome-rich B. villosa leaves than in glabrous B. oleracea leaves and in glabrous cotyledons from both species. The B. villosa TRY expression pattern also contrasted with TRY expression patterns in two diploid Brassica species, and with the Arabidopsis model for expression of negative regulators of trichome development. Further unique sequence polymorphisms, protein characteristics, and gene evolution studies highlighted specific amino acids in GL1 and GL2 coding sequences that distinguished glabrous species from hairy species and several variants that were specific for each B. villosa gene. Positive selection was observed for GL1 between hairy and non-hairy plants, and as expected the origin of the four expressed positive trichome regulatory genes in B. villosa was predicted to be from B. oleracea. In particular the unpredicted expression patterns for TRY and CPC in B. villosa suggest additional characterization is needed to determine the function of the expanded families of trichome regulatory genes in more complex polyploid species within the Brassicaceae.
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Affiliation(s)
- Naghabushana K. Nayidu
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, SK, Canada
- Department of Biology, University of Saskatchewan, Saskatoon SK, Canada
| | - Sateesh Kagale
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, SK, Canada
- National Research Council (NRC), Saskatoon SK, Canada
| | - Ali Taheri
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, SK, Canada
| | | | - Isobel A. P. Parkin
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, SK, Canada
| | | | - Margaret Y. Gruber
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, Saskatoon, SK, Canada
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Andrew RL, Bernatchez L, Bonin A, Buerkle CA, Carstens BC, Emerson BC, Garant D, Giraud T, Kane NC, Rogers SM, Slate J, Smith H, Sork VL, Stone GN, Vines TH, Waits L, Widmer A, Rieseberg LH. A road map for molecular ecology. Mol Ecol 2013; 22:2605-26. [DOI: 10.1111/mec.12319] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 03/16/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Rose L. Andrew
- Department of Botany; University of British Columbia; 3529-6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Louis Bernatchez
- DInstitut de Biologie Intégrative et des Systémes; Département de Biologie; 1030, Avenue de la Médecine Université Laval; Québec QC G1V 0A6 Canada
| | - Aurélie Bonin
- Laboratoire d'Ecologie Alpine; CNRS UMR 5553 Université Joseph Fourier; BP 53, 38041 Grenoble Cedex 9 France
| | - C. Alex. Buerkle
- Department of Botany; University of Wyoming; 1000 E. University Ave. Laramie WY 82071 USA
| | - Bryan C. Carstens
- Department of Evolution, Ecology and Organismal Biology; 318 W. 12th Ave. The Ohio State University; Columbus OH 43210 USA
| | - Brent C. Emerson
- Island Ecology and Evolution Research Group; Instituto de Productos Naturales y Agrobiología (IPNA-CSIC) C/Astrofísico Francisco Sánchez 3 La Laguna Tenerife; Canary Islands 38206 Spain
| | - Dany Garant
- Département de Biologie; Université de Sherbrooke; Sherbrooke QC J1K 2R1 Canada
| | - Tatiana Giraud
- Laboratoire Ecologie, Systématique et Evolution; UMR 8079 CNRS-UPS-AgroParisTech, Bâtiment 360 Univ. Paris Sud; 91405 Orsay cedex France
| | - Nolan C. Kane
- Department of Botany; University of British Columbia; 3529-6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Sean M. Rogers
- Department of Biological Sciences; University of Calgary; 2500 University Drive N.W., Calgary AB T2N 1N4 Canada
| | - Jon Slate
- Department of Animal and Plant Sciences; University of Sheffield; Sheffield S10 2TN UK
| | - Harry Smith
- 79 Melton Road Burton-on-the-Wolds Loughborough LE12 5TQ UK
| | - Victoria L. Sork
- Department of Ecology and Evolutionary Biology; University of California Los Angeles; 4139 Terasaki Life Sciences Building, 610 Charles E. Young Drive East Los Angeles CA 90095 USA
| | - Graham N. Stone
- Institute of Evolutionary Biology; University of Edinburgh; The King's Buildings, West Mains Road, Edinburgh EH9 3JT UK
| | - Timothy H. Vines
- Molecular Ecology Editorial Office; 6270 University Blvd Vancouver BC V6T 1Z4 Canada
| | - Lisette Waits
- Department of Fish and Wildlife Sciences; University of Idaho; 875 Perimeter Drive MS 1136 Moscow ID 83844 USA
| | - Alex Widmer
- ETH Zurich; Institute of Integrative Biology; Universitätstrasse 16 Zurich 8092 Switzerland
| | - Loren H. Rieseberg
- Department of Botany; University of British Columbia; 3529-6270 University Blvd Vancouver BC V6T 1Z4 Canada
- Department of Biology; Indiana University; 1001 E. 3 St., Bloomington IN 47405 USA
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Rieseberg L, Vines T, Kane N. Editorial 2013. Mol Ecol 2012; 22:1-14. [PMID: 23252575 DOI: 10.1111/mec.12145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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