1
|
Chen J, Liu L, Chen G, Wang S, Liu Y, Zhang Z, Li H, Wang L, Zhou Z, Zhao J, Zhang X. CsRAXs negatively regulate leaf size and fruiting ability through auxin glycosylation in cucumber. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1024-1037. [PMID: 38578173 DOI: 10.1111/jipb.13655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 03/13/2024] [Indexed: 04/06/2024]
Abstract
Leaves are the main photosynthesis organ that directly determines crop yield and biomass. Dissecting the regulatory mechanism of leaf development is crucial for food security and ecosystem turn-over. Here, we identified the novel function of R2R3-MYB transcription factors CsRAXs in regulating cucumber leaf size and fruiting ability. Csrax5 single mutant exhibited enlarged leaf size and stem diameter, and Csrax1/2/5 triple mutant displayed further enlargement phenotype. Overexpression of CsRAX1 or CsRAX5 gave rise to smaller leaf and thinner stem. The fruiting ability of Csrax1/2/5 plants was significantly enhanced, while that of CsRAX5 overexpression lines was greatly weakened. Similarly, cell number and free auxin level were elevated in mutant plants while decreased in overexpression lines. Biochemical data indicated that CsRAX1/5 directly promoted the expression of auxin glucosyltransferase gene CsUGT74E2. Therefore, our data suggested that CsRAXs function as repressors for leaf size development by promoting auxin glycosylation to decrease free auxin level and cell division in cucumber. Our findings provide new gene targets for cucumber breeding with increased leaf size and crop yield.
Collapse
Affiliation(s)
- Jiacai Chen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Liu Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Guangxin Chen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Shaoyun Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Ye Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Zeqin Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Hongfei Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Liming Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhaoyang Zhou
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Jianyu Zhao
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiaolan Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| |
Collapse
|
2
|
Tang HB, Wang J, Wang L, Shang GD, Xu ZG, Mai YX, Liu YT, Zhang TQ, Wang JW. Anisotropic cell growth at the leaf base promotes age-related changes in leaf shape in Arabidopsis thaliana. THE PLANT CELL 2023; 35:1386-1407. [PMID: 36748203 PMCID: PMC10118278 DOI: 10.1093/plcell/koad031] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 05/17/2023]
Abstract
Plants undergo extended morphogenesis. The shoot apical meristem (SAM) allows for reiterative development and the formation of new structures throughout the life of the plant. Intriguingly, the SAM produces morphologically different leaves in an age-dependent manner, a phenomenon known as heteroblasty. In Arabidopsis thaliana, the SAM produces small orbicular leaves in the juvenile phase, but gives rise to large elliptical leaves in the adult phase. Previous studies have established that a developmental decline of microRNA156 (miR156) is necessary and sufficient to trigger this leaf shape switch, although the underlying mechanism is poorly understood. Here we show that the gradual increase in miR156-targeted SQUAMOSA PROMOTER BINDING PROTEIN-LIKE transcription factors with age promotes cell growth anisotropy in the abaxial epidermis at the base of the leaf blade, evident by the formation of elongated giant cells. Time-lapse imaging and developmental genetics further revealed that the establishment of adult leaf shape is tightly associated with the longitudinal cell expansion of giant cells, accompanied by a prolonged cell proliferation phase in their vicinity. Our results thus provide a plausible cellular mechanism for heteroblasty in Arabidopsis, and contribute to our understanding of anisotropic growth in plants.
Collapse
Affiliation(s)
- Hong-Bo Tang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Shanghai 200032, China
- University of Chinese Academy of Sciences (UCAS), Shanghai 200032, China
| | - Juan Wang
- School of Statistics and Mathematics, Inner Mongolia University of Finance and Economics, Huhehaote 010070, China
| | - Long Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Shanghai 200032, China
| | - Guan-Dong Shang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Shanghai 200032, China
- University of Chinese Academy of Sciences (UCAS), Shanghai 200032, China
| | - Zhou-Geng Xu
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Shanghai 200032, China
- University of Chinese Academy of Sciences (UCAS), Shanghai 200032, China
| | - Yan-Xia Mai
- Core Facility Center of CEMPS, Institute of Plant Physiology and Ecology (SIPPE), Shanghai 200032, China
| | - Ye-Tong Liu
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Shanghai 200032, China
- Shanghai Normal University, College of Life and Environmental Sciences, Shanghai 200234, China
| | - Tian-Qi Zhang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Shanghai 200032, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Institute of Plant Physiology and Ecology (SIPPE), Shanghai 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| |
Collapse
|
3
|
Tabeta H, Gunji S, Kawade K, Ferjani A. Leaf-size control beyond transcription factors: Compensatory mechanisms. FRONTIERS IN PLANT SCIENCE 2023; 13:1024945. [PMID: 36756231 PMCID: PMC9901582 DOI: 10.3389/fpls.2022.1024945] [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: 08/22/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
Plant leaves display abundant morphological richness yet grow to characteristic sizes and shapes. Beginning with a small number of undifferentiated founder cells, leaves evolve via a complex interplay of regulatory factors that ultimately influence cell proliferation and subsequent post-mitotic cell enlargement. During their development, a sequence of key events that shape leaves is both robustly executed spatiotemporally following a genomic molecular network and flexibly tuned by a variety of environmental stimuli. Decades of work on Arabidopsis thaliana have revisited the compensatory phenomena that might reflect a general and primary size-regulatory mechanism in leaves. This review focuses on key molecular and cellular events behind the organ-wide scale regulation of compensatory mechanisms. Lastly, emerging novel mechanisms of metabolic and hormonal regulation are discussed, based on recent advances in the field that have provided insights into, among other phenomena, leaf-size regulation.
Collapse
Affiliation(s)
- Hiromitsu Tabeta
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
- Department of Biology, Tokyo Gakugei University, Tokyo, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Shizuka Gunji
- Department of Biology, Tokyo Gakugei University, Tokyo, Japan
| | - Kensuke Kawade
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- National Institute for Basic Biology, Okazaki, Japan
- Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
| | - Ali Ferjani
- Department of Biology, Tokyo Gakugei University, Tokyo, Japan
| |
Collapse
|
4
|
Wu D, He L. Study on the Mechanism of Elastic Instability Caused by Natural Growth in Orthotropic Material. MATERIALS (BASEL, SWITZERLAND) 2022; 15:7059. [PMID: 36295124 PMCID: PMC9605602 DOI: 10.3390/ma15207059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Compared to synthetic materials, naturally grown biological materials have more specific behavioral patterns and life connotations in their morphological evolution over millions of years of environmental evolution on Earth. In this paper, we investigate the physical mechanisms and manifestations of out-of-plane deformation instability. Firstly, the origin of the instability phenomenon caused by the growth of the leaf is introduced. Leaf instability problems are modeled using rectangular thin plates. Secondly, the variation in the critical intrinsic strain with the principal shear modulus is obtained by numerical solution. The post-buckling behavior of the growth instability is further analyzed by general static analysis, and we obtain the phase diagram of morphogenesis of thin plant organs as functions of the principal shear modulus and off-axis angle. The research results enhance the understanding of the mechanism of elastic instability caused by natural growth in orthotropic materials.
Collapse
|
5
|
Skirycz A, Fernie AR. Past accomplishments and future challenges of the multi-omics characterization of leaf growth. PLANT PHYSIOLOGY 2022; 189:473-489. [PMID: 35325227 PMCID: PMC9157134 DOI: 10.1093/plphys/kiac136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
The advent of omics technologies has revolutionized biology and advanced our understanding of all biological processes, including major developmental transitions in plants and animals. Here, we review the vast knowledge accumulated concerning leaf growth in terms of transcriptional regulation before turning our attention to the historically less well-characterized alterations at the protein and metabolite level. We will then discuss how the advent of biochemical methods coupled with metabolomics and proteomics can provide insight into the protein-protein and protein-metabolite interactome of the growing leaves. We finally highlight the substantial challenges in detection, spatial resolution, integration, and functional validation of the omics results, focusing on metabolomics as a prerequisite for a comprehensive understanding of small-molecule regulation of plant growth.
Collapse
Affiliation(s)
- Aleksandra Skirycz
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
- Boyce Thompson Institute, Ithaca, New York 14853, USA
- Cornell University, Ithaca, New York 14853, USA
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| |
Collapse
|
6
|
Kumar S, Sharma V, Kumari R. Fabaceae leaf morphogenetic evolution: the leaf-lamina architectural variation in the Fabaceae flora of Indian Western Ghats, compared with that genetically characterized in the Fabaceae model species Pisum sativum and Medicago truncatula. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2021. [DOI: 10.1007/s43538-021-00037-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
7
|
Beltramino M, Debernardi JM, Ferela A, Palatnik JF. ARF2 represses expression of plant GRF transcription factors in a complementary mechanism to microRNA miR396. PLANT PHYSIOLOGY 2021; 185:1798-1812. [PMID: 33580700 PMCID: PMC8133599 DOI: 10.1093/plphys/kiab014] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
Members of the GROWTH REGULATING FACTOR (GRF) family of transcription factors play key roles in the promotion of plant growth and development. Many GRFs are post-transcriptionally repressed by microRNA (miRNA) miR396, an evolutionarily conserved small RNA, which restricts their expression to proliferative tissue. We performed a comprehensive analysis of the GRF family in eudicot plants and found that in many species all the GRFs have a miR396-binding site. Yet, we also identified GRFs with mutations in the sequence recognized by miR396, suggesting a partial or complete release of their post-transcriptional repression. Interestingly, Brassicaceae species share a group of GRFs that lack miR396 regulation, including Arabidopsis GRF5 and GRF6. We show that instead of miR396-mediated post-transcriptional regulation, the spatiotemporal control of GRF5 is achieved through evolutionarily conserved promoter sequences, and that AUXIN RESPONSE FACTOR 2 (ARF2) binds to such conserved sequences to repress GRF5 expression. Furthermore, we demonstrate that the unchecked expression of GRF5 in arf2 mutants is responsible for the increased cell number of arf2 leaves. The results describe a switch in the repression mechanisms that control the expression of GRFs and mechanistically link the control of leaf growth by miR396, GRFs, and ARF2 transcription factors.
Collapse
Affiliation(s)
- Matías Beltramino
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET and Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Juan Manuel Debernardi
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET and Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Antonella Ferela
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET and Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Javier F Palatnik
- Instituto de Biología Molecular y Celular de Rosario (IBR), CONICET and Universidad Nacional de Rosario, Rosario 2000, Argentina
- Centro de Estudios Interdisciplinarios, Universidad Nacional de Rosario, Rosario 2000, Argentina
| |
Collapse
|
8
|
Omidbakhshfard MA, Sokolowska EM, Di Vittori V, Perez de Souza L, Kuhalskaya A, Brotman Y, Alseekh S, Fernie AR, Skirycz A. Multi-omics analysis of early leaf development in Arabidopsis thaliana. PATTERNS 2021; 2:100235. [PMID: 33982025 PMCID: PMC8085607 DOI: 10.1016/j.patter.2021.100235] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 03/01/2021] [Accepted: 03/12/2021] [Indexed: 01/15/2023]
Abstract
The growth of plant organs is driven by cell division and subsequent cell expansion. The transition from proliferation to expansion is critical for the final organ size and plant yield. Exit from proliferation and onset of expansion is accompanied by major metabolic reprogramming, and in leaves with the establishment of photosynthesis. To learn more about the molecular mechanisms underlying the developmental and metabolic transitions important for plant growth, we used untargeted proteomics and metabolomics analyses to profile young leaves of a model plant Arabidopsis thaliana representing proliferation, transition, and expansion stages. The dataset presented represents a unique resource comprising approximately 4,000 proteins and 300 annotated small-molecular compounds measured across 6 consecutive days of leaf growth. These can now be mined for novel developmental and metabolic regulators of plant growth and can act as a blueprint for studies aimed at better defining the interface of development and metabolism in other species. Untargeted metabolomics and proteomics characterization of early leaf growth Translation is the primary determiner of protein abundance during early leaf growth 12-OPDA accumulation coincides with meristem arrest
Developmental and metabolic transitions occurring during plant growth are critical for crop yield. The multi-omics dataset presented here was generated to enable the identification of novel molecular players involved in the regulation of plant growth. It comprised approximately 4,000 proteins and 300 annotated small-molecular compounds, measured across early leaf development spanning major developmental transitions. As such, the work provides a blueprint for studies aimed at better defining the interface between metabolism and development, an appreciated yet understudied research frontier across all kingdoms of life.
Collapse
Affiliation(s)
| | | | - Valerio Di Vittori
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | | | - Anastasiya Kuhalskaya
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Yariv Brotman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Aleksandra Skirycz
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Boyce Thompson Institute, Ithaca, NY, USA
| |
Collapse
|
9
|
Moreno S, Canales J, Hong L, Robinson D, Roeder AH, Gutiérrez RA. Nitrate Defines Shoot Size through Compensatory Roles for Endoreplication and Cell Division in Arabidopsis thaliana. Curr Biol 2020; 30:1988-2000.e3. [DOI: 10.1016/j.cub.2020.03.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/29/2020] [Accepted: 03/13/2020] [Indexed: 12/15/2022]
|
10
|
Nelissen H, Gonzalez N. Understanding plant organ growth: a multidisciplinary field. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:7-10. [PMID: 31725876 DOI: 10.1093/jxb/erz448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 09/27/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Gent, Belgium
- Center for Plant Systems Biology, VIB, Technologiepark, Gent, Belgium
| | - Nathalie Gonzalez
- INRA, UMR1332 Biologie du fruit et Pathologie, INRA Bordeaux Aquitaine, CS20032, F-33882, Villenave d'Ornon cedex, France
| |
Collapse
|
11
|
Yang Y, Chen B, Dang X, Zhu L, Rao J, Ren H, Lin C, Qin Y, Lin D. Arabidopsis IPGA1 is a microtubule-associated protein essential for cell expansion during petal morphogenesis. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5231-5243. [PMID: 31198941 PMCID: PMC6793458 DOI: 10.1093/jxb/erz284] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/05/2019] [Indexed: 05/23/2023]
Abstract
Unlike animal cells, plant cells do not possess centrosomes that serve as microtubule organizing centers; how microtubule arrays are organized throughout plant morphogenesis remains poorly understood. We report here that Arabidopsis INCREASED PETAL GROWTH ANISOTROPY 1 (IPGA1), a previously uncharacterized microtubule-associated protein, regulates petal growth and shape by affecting cortical microtubule organization. Through a genetic screen, we showed that IPGA1 loss-of-function mutants displayed a phenotype of longer and narrower petals, as well as increased anisotropic cell expansion of the petal epidermis in the late phases of flower development. Map-based cloning studies revealed that IPGA1 encodes a previously uncharacterized protein that colocalizes with and directly binds to microtubules. IPGA1 plays a negative role in the organization of cortical microtubules into parallel arrays oriented perpendicular to the axis of cell elongation, with the ipga1-1 mutant displaying increased microtubule ordering in petal abaxial epidermal cells. The IPGA1 family is conserved among land plants and its homologs may have evolved to regulate microtubule organization. Taken together, our findings identify IPGA1 as a novel microtubule-associated protein and provide significant insights into IPGA1-mediated microtubule organization and petal growth anisotropy.
Collapse
Affiliation(s)
- Yanqiu Yang
- College of Life Science, Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Binqinq Chen
- College of Life Science, Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xie Dang
- College of Life Science, Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
| | - Lilan Zhu
- College of Life Science, Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jinqiu Rao
- College of Life Science, Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huibo Ren
- College of Life Science, Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chentao Lin
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yuan Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Center for Genomics and Biotechnology, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Deshu Lin
- College of Life Science, Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
- Correspondence:
| |
Collapse
|
12
|
Marchadier E, Hanemian M, Tisné S, Bach L, Bazakos C, Gilbault E, Haddadi P, Virlouvet L, Loudet O. The complex genetic architecture of shoot growth natural variation in Arabidopsis thaliana. PLoS Genet 2019; 15:e1007954. [PMID: 31009456 PMCID: PMC6476473 DOI: 10.1371/journal.pgen.1007954] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 01/11/2019] [Indexed: 12/16/2022] Open
Abstract
One of the main outcomes of quantitative genetics approaches to natural variation is to reveal the genetic architecture underlying the phenotypic space. Complex genetic architectures are described as including numerous loci (or alleles) with small-effect and/or low-frequency in the populations, interactions with the genetic background, environment or age. Linkage or association mapping strategies will be more or less sensitive to this complexity, so that we still have an unclear picture of its extent. By combining high-throughput phenotyping under two environmental conditions with classical QTL mapping approaches in multiple Arabidopsis thaliana segregating populations as well as advanced near isogenic lines construction and survey, we have attempted to improve our understanding of quantitative phenotypic variation. Integrative traits such as those related to vegetative growth used in this work (highlighting either cumulative growth, growth rate or morphology) all showed complex and dynamic genetic architecture with respect to the segregating population and condition. The more resolutive our mapping approach, the more complexity we uncover, with several instances of QTLs visible in near isogenic lines but not detected with the initial QTL mapping, indicating that our phenotyping accuracy was less limiting than the mapping resolution with respect to the underlying genetic architecture. In an ultimate approach to resolve this complexity, we intensified our phenotyping effort to target specifically a 3Mb-region known to segregate for a major quantitative trait gene, using a series of selected lines recombined every 100kb. We discovered that at least 3 other independent QTLs had remained hidden in this region, some with trait- or condition-specific effects, or opposite allelic effects. If we were to extrapolate the figures obtained on this specific region in this particular cross to the genome- and species-scale, we would predict hundreds of causative loci of detectable phenotypic effect controlling these growth-related phenotypes.
Collapse
Affiliation(s)
- Elodie Marchadier
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Mathieu Hanemian
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Sébastien Tisné
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Liên Bach
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Christos Bazakos
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Elodie Gilbault
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Parham Haddadi
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Laetitia Virlouvet
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Olivier Loudet
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
- * E-mail:
| |
Collapse
|
13
|
Zhang Y, Wang B, Qi S, Dong M, Wang Z, Li Y, Chen S, Li B, Zhang J. Ploidy and hybridity effects on leaf size, cell size and related genes expression in triploids, diploids and their parents in Populus. PLANTA 2019; 249:635-646. [PMID: 30327883 DOI: 10.1007/s00425-018-3029-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/05/2018] [Indexed: 05/23/2023]
Abstract
Cell-size enlargement plays a pivotal role in increasing the leaf size of triploid poplar, and polyploidization could change leaf shape. ABP1 was highly expressed in triploid plants and positively related to cell size. In the plant kingdom, the leaf is the most important energy production organ, and polyploidy often exhibits a "Gigas" effect on leaf size, which benefits agriculture and forestry. However, little is known regarding the cellular and molecular mechanisms underlying the leaf size superiority of polyploid woody plants. In the present study, the leaf area and abaxial epidermal cells of diploid and triploid full-sib groups and their parents were measured at three different positions. We measured the expression of several genes related to cell division and cell expansion. The results showed that the leaf area of triploids was significantly larger than that of diploids, and the triploid group showed transgressive variation compared to their full-sib diploid group. Cell size but not cell number was the main reason for leaf size variation. Cell expansion was in accordance with leaf enlargement. In addition, the leaf shape changes in triploids primarily resulted from a significant decrease in the leaf ratio of length to -width. Auxin-binding protein 1 (ABP1) was highly expressed in triploids and positively related to leaf size. These results enhanced the current understanding that giant leaf is affected by polyploidy vigor. However, significant heterosis is not exhibited in diploid offspring. Overall, polyploid breeding is an effective strategy to enhance leaf size, and Populus, as an ideal material, plays an important role in studying the leaf morphological variations of polyploid woody plants.
Collapse
Affiliation(s)
- Yan Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Key Laboratory of Forest Trees and Ornamental Plants Biological Engineering of State Forestry Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Beibei Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Key Laboratory of Forest Trees and Ornamental Plants Biological Engineering of State Forestry Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shuaizheng Qi
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Key Laboratory of Forest Trees and Ornamental Plants Biological Engineering of State Forestry Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Mingliang Dong
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Key Laboratory of Forest Trees and Ornamental Plants Biological Engineering of State Forestry Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Zewei Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Key Laboratory of Forest Trees and Ornamental Plants Biological Engineering of State Forestry Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yixuan Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Key Laboratory of Forest Trees and Ornamental Plants Biological Engineering of State Forestry Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Siyuan Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Key Laboratory of Forest Trees and Ornamental Plants Biological Engineering of State Forestry Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Bailian Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Key Laboratory of Forest Trees and Ornamental Plants Biological Engineering of State Forestry Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| | - Jinfeng Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, Key Laboratory of Forest Trees and Ornamental Plants Biological Engineering of State Forestry Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
| |
Collapse
|
14
|
Huang C, Wang Z, Quinn D, Suresh S, Hsia KJ. Differential growth and shape formation in plant organs. Proc Natl Acad Sci U S A 2018; 115:12359-12364. [PMID: 30455311 PMCID: PMC6298086 DOI: 10.1073/pnas.1811296115] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Morphogenesis is a phenomenon by which a wide variety of functional organs are formed in biological systems. In plants, morphogenesis is primarily driven by differential growth of tissues. Much effort has been devoted to identifying the role of genetic and biomolecular pathways in regulating cell division and cell expansion and in influencing shape formation in plant organs. However, general principles dictating how differential growth controls the formation of complex 3D shapes in plant leaves and flower petals remain largely unknown. Through quantitative measurements on live plant organs and detailed finite-element simulations, we show how the morphology of a growing leaf is determined by both the maximum value and the spatial distribution of growth strain. With this understanding, we develop a broad scientific framework for a morphological phase diagram that is capable of rationalizing four configurations commonly found in plant organs: twisting, helical twisting, saddle bending, and edge waving. We demonstrate the robustness of these findings and analyses by recourse to synthetic reproduction of all four configurations using controlled polymerization of a hydrogel. Our study points to potential approaches to innovative geometrical design and actuation in such applications as building architecture, soft robotics and flexible electronics.
Collapse
Affiliation(s)
- Changjin Huang
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Zilu Wang
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213
| | - David Quinn
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Subra Suresh
- Nanyang Technological University, 639798 Singapore, Republic of Singapore;
| | - K Jimmy Hsia
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213;
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, 639798 Singapore, Republic of Singapore
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 639798 Singapore, Republic of Singapore
| |
Collapse
|
15
|
Kim JH, Kim J, Jun SE, Park S, Timilsina R, Kwon DS, Kim Y, Park SJ, Hwang JY, Nam HG, Kim GT, Woo HR. ORESARA15, a PLATZ transcription factor, mediates leaf growth and senescence in Arabidopsis. THE NEW PHYTOLOGIST 2018; 220:609-623. [PMID: 29949656 DOI: 10.1111/nph.15291] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 05/24/2018] [Indexed: 05/12/2023]
Abstract
Plant leaves undergo a series of developmental changes from leaf primordium initiation through growth and maturation to senescence throughout their life span. Although the mechanisms underlying leaf senescence have been intensively elucidated, our knowledge of the interrelationship between early leaf development and senescence is still fragmentary. We isolated the oresara15-1Dominant (ore15-1D) mutant, which had an extended leaf longevity and an enlarged leaf size, from activation-tagged lines of Arabidopsis. Plasmid rescue identified that ORE15 encodes a PLANT A/T-RICH SEQUENCE- AND ZINC-BINDING PROTEIN family transcription factor. Phenotypes of ore15-1D and ore15-2, a loss-of-function mutant, were evaluated through physiological and anatomical analyses. Microarray, quantitative reverse transcription polymerase chain reaction, and chromatin immunoprecipitation as well as genetic analysis were employed to reveal the molecular mechanism of ORE15 in the regulation of leaf growth and senescence. ORE15 enhanced leaf growth by promoting the rate and duration of cell proliferation in the earlier stage and suppressed leaf senescence in the later stage by modulating the GROWTH-REGULATING FACTOR (GRF)/GRF-INTERACTING FACTOR regulatory pathway. Our study highlighted a molecular conjunction through ORE15 between growth and senescence, which are two temporally separate developmental processes during leaf life span.
Collapse
Affiliation(s)
- Jin Hee Kim
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Korea
| | - Jeongsik Kim
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Korea
| | - Sang Eun Jun
- Department of Molecular Biotechnology, Dong-A University, Busan, 49315, Korea
| | - Sanghoon Park
- Department of New Biology, DGIST, Daegu, 42988, Korea
| | | | - Da Som Kwon
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Korea
| | - Yongmin Kim
- Department of New Biology, DGIST, Daegu, 42988, Korea
- Department of Biology, Chungnam National University, Daejeon, 34134, Korea
| | - Sung-Jin Park
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Korea
| | - Ji Young Hwang
- Department of Molecular Biotechnology, Dong-A University, Busan, 49315, Korea
| | - Hong Gil Nam
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Korea
- Department of New Biology, DGIST, Daegu, 42988, Korea
| | - Gyung-Tae Kim
- Department of Molecular Biotechnology, Dong-A University, Busan, 49315, Korea
| | - Hye Ryun Woo
- Department of New Biology, DGIST, Daegu, 42988, Korea
| |
Collapse
|
16
|
Fujikura U, Jing R, Hanada A, Takebayashi Y, Sakakibara H, Yamaguchi S, Kappel C, Lenhard M. Variation in Splicing Efficiency Underlies Morphological Evolution in Capsella. Dev Cell 2018; 44:192-203.e5. [DOI: 10.1016/j.devcel.2017.11.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 10/10/2017] [Accepted: 11/27/2017] [Indexed: 12/21/2022]
|
17
|
Suzuki M, Shinozuka N, Hirakata T, Nakata MT, Demura T, Tsukaya H, Horiguchi G. OLIGOCELLULA1/ HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES15 Promotes Cell Proliferation With HISTONE DEACETYLASE9 and POWERDRESS During Leaf Development in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2018; 9:580. [PMID: 29774040 PMCID: PMC5943563 DOI: 10.3389/fpls.2018.00580] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 04/13/2018] [Indexed: 05/18/2023]
Abstract
Organ size regulation is dependent on the precise spatial and temporal regulation of cell proliferation and cell expansion. A number of transcription factors have been identified that play a key role in the determination of aerial lateral organ size, but their functional relationship to various chromatin modifiers has not been well understood. To understand how leaf size is regulated, we previously isolated the oligocellula1 (oli1) mutant of Arabidopsis thaliana that develops smaller first leaves than the wild type (WT) mainly due to a reduction in the cell number. In this study, we further characterized oli1 leaf phenotypes and identified the OLI1 gene as well as interaction partners of OLI1. Detailed characterizations of leaf development suggested that the cell proliferation rate in oli1 leaf primordia is lower than that in the WT. In addition, oli1 was associated with a slight delay of the progression from the juvenile to adult phases of leaf traits. A classical map-based approach demonstrated that OLI1 is identical to HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES15 (HOS15). HOS15/OLI1 encodes a homolog of human transducin β-like protein1 (TBL1). TBL1 forms a transcriptional repression complex with the histone deacetylase (HDAC) HDAC3 and either nuclear receptor co-repressor (N-CoR) or silencing mediator for retinoic acid and thyroid receptor (SMRT). We found that mutations in HISTONE DEACETYLASE9 (HDA9) and a switching-defective protein 3, adaptor 2, N-CoR, and transcription factor IIIB-domain protein gene, POWERDRESS (PWR), showed a small-leaf phenotype similar to oli1. In addition, hda9 and pwr did not further enhance the oli1 small-leaf phenotype, suggesting that these three genes act in the same pathway. Yeast two-hybrid assays suggested physical interactions, wherein PWR probably bridges HOS15/OLI1 and HDA9. Earlier studies suggested the roles of HOS15, HDA9, and PWR in transcriptional repression. Consistently, transcriptome analyses showed several genes commonly upregulated in the three mutants. From these findings, we propose a possibility that HOS15/OLI1, PWR, and HDA9 form an evolutionary conserved transcription repression complex that plays a positive role in the regulation of final leaf size.
Collapse
Affiliation(s)
- Marina Suzuki
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Nanae Shinozuka
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Tomohiro Hirakata
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Miyuki T. Nakata
- Research Center for Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Taku Demura
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Hirokazu Tsukaya
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Okazaki Institute for Integrative Bioscience, Okazaki, Japan
| | - Gorou Horiguchi
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
- Research Center for Life Science, College of Science, Rikkyo University, Tokyo, Japan
- *Correspondence: Gorou Horiguchi,
| |
Collapse
|
18
|
Balao F, Paun O, Alonso C. Uncovering the contribution of epigenetics to plant phenotypic variation in Mediterranean ecosystems. PLANT BIOLOGY (STUTTGART, GERMANY) 2018. [PMID: 28637098 DOI: 10.1111/plb.12594] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Epigenetic signals can affect plant phenotype and fitness and be stably inherited across multiple generations. Epigenetic regulation plays a key role in the mechanisms of plant response to the environment, without altering DNA sequence. As plants cannot adapt behaviourally or migrate instantly, such dynamic epigenetic responses may be particularly crucial for survival of plants within changing and challenging environments, such as the Mediterranean-Type Ecosystems (MTEs). These ecosystems suffer recurrent stressful events (warm and dry summers with associated fire regimes) that have selected for plants with similar phenotypic complex traits, resulting in similar vegetation growth forms. However, the potential role of epigenetics in plant adaptation to recurrent stressful environments such as the MTEs has generally been ignored. To understand the full spectrum of adaptive processes in such contexts, it is imperative to prompt study of the causes and consequences of epigenetic variation in natural populations. With this purpose, we review here current knowledge on epigenetic variation in natural populations and the genetic and epigenetic basis of some key traits for plants in the MTEs, namely those traits involved in adaptation to drought, fire and oligotrophic soils. We conclude there is still much to be learned about 'plant epigenetics in the wild' and, thus, we propose future research steps in the study of natural epigenetic variation of key traits in the MTEs at different scales.
Collapse
Affiliation(s)
- F Balao
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | - O Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - C Alonso
- Estación Biológica de Doñana, CSIC, Sevilla, Spain
| |
Collapse
|
19
|
Cattaneo P, Hardtke CS. BIG BROTHER Uncouples Cell Proliferation from Elongation in the Arabidopsis Primary Root. PLANT & CELL PHYSIOLOGY 2017; 58:1519-1527. [PMID: 28922745 PMCID: PMC5914324 DOI: 10.1093/pcp/pcx091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/25/2017] [Indexed: 05/10/2023]
Abstract
Plant organ size is sensitive to environmental conditions, but is also limited by hardwired genetic constraints. In Arabidopsis, a few organ size regulators have been identified. Among them, the BIG BROTHER (BB) gene has a prominent role in the determination of flower organ and leaf size. BB loss-of-function mutations result in a prolonged proliferation phase during leaf(-like) organ formation, and consequently larger leaves, petals and sepals. Whether BB has a similar role in root growth is unknown. Here we describe a novel bb allele which carries a P235L point mutation in the BB RING finger domain. This allele behaves similarly to described bb loss-of-function alleles and displays increased root meristem size due to a higher number of dividing, meristematic cells. In contrast, mature cell length is unaffected. The increased meristematic activity does not, however, translate into overall enhanced root elongation, possibly because bb mutation also results in an increased number of cell files in the vascular cylinder. These extra formative divisions might offset any growth acceleration by extra meristematic divisions. Thus, although BB dampens root cell proliferation, the consequences on macroscopic root growth are minor. However, bb mutation accelerates overall root growth when introduced into sensitized backgrounds. For example, it partially rescues the short root phenotypes of the brevis radix and octopus mutants, but does not complement their phloem differentiation or transport defects. In summary, we provide evidence that BB acts conceptually similarly in leaf(-like) organs and the primary root, and uncouples cell proliferation from elongation in the root meristem.
Collapse
Affiliation(s)
- Pietro Cattaneo
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
| | - Christian S. Hardtke
- Department of Plant Molecular Biology, University of Lausanne, Biophore Building, CH-1015 Lausanne, Switzerland
- Corresponding author: E-mail, ; Fax, +41-21-692-4150
| |
Collapse
|
20
|
Wu Y, Gong W, Yang W. Shade Inhibits Leaf Size by Controlling Cell Proliferation and Enlargement in Soybean. Sci Rep 2017; 7:9259. [PMID: 28835715 PMCID: PMC5569092 DOI: 10.1038/s41598-017-10026-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 08/02/2017] [Indexed: 11/23/2022] Open
Abstract
To gain more insight into the physiological function of shade and how shade affects leaf size, we investigated the growth, leaf anatomical structure, hormones and genes expressions in soybean. Soybean seeds were sown in plastic pots and were allowed to germinate and grow for 30 days under shade or full sunlight conditions. Shade treated plants showed significantly increase on stem length and petiole length, and decrease on stem diameters, shoot biomass and its partition to leaf also were significantly lower than that in full sunlight. Smaller and thinner on shade treated leaves than corresponding leaves on full sunlight plants. The decreased leaf size caused by shade was largely attributable to cell proliferation in young leaves and both cell proliferation and enlargement in old leaves. Shade induced the expression of a set of genes related to cell proliferation and/or enlargement, but depended on the developmental stage of leaf. Shade significantly increased the auxin and gibberellin content, and significantly decreased the cytokinin content in young, middle and old leaves. Taken together, these results indicated that shade inhibited leaf size by controlling cell proliferation and enlargement, auxin, gibberellin and cytokinin may play important roles in this process.
Collapse
Affiliation(s)
- Yushan Wu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, P.R. China
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest, Ministry of Agriculture, Chengdu, 611130, P.R. China
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, 611130, PR China
| | - Wanzhuo Gong
- Characteristic Crops Research Institute, Chongqing Academy of Agricultural Sciences, Chongqing, 402160, P.R. China
| | - Wenyu Yang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, P.R. China.
- Key Laboratory of Crop Ecophysiology and Farming System in Southwest, Ministry of Agriculture, Chengdu, 611130, P.R. China.
- Sichuan Engineering Research Center for Crop Strip Intercropping System, Chengdu, 611130, PR China.
| |
Collapse
|
21
|
Lee KC, Jang YH, Kim SK, Park HY, Thu MP, Lee JH, Kim JK. RRM domain of Arabidopsis splicing factor SF1 is important for pre-mRNA splicing of a specific set of genes. PLANT CELL REPORTS 2017; 36:1083-1095. [PMID: 28401337 DOI: 10.1007/s00299-017-2140-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/04/2017] [Indexed: 05/20/2023]
Abstract
The RNA recognition motif of Arabidopsis splicing factor SF1 affects the alternative splicing of FLOWERING LOCUS M pre-mRNA and a heat shock transcription factor HsfA2 pre-mRNA. Splicing factor 1 (SF1) plays a crucial role in 3' splice site recognition by binding directly to the intron branch point. Although plant SF1 proteins possess an RNA recognition motif (RRM) domain that is absent in its fungal and metazoan counterparts, the role of the RRM domain in SF1 function has not been characterized. Here, we show that the RRM domain differentially affects the full function of the Arabidopsis thaliana AtSF1 protein under different experimental conditions. For example, the deletion of RRM domain influences AtSF1-mediated control of flowering time, but not the abscisic acid sensitivity response during seed germination. The alternative splicing of FLOWERING LOCUS M (FLM) pre-mRNA is involved in flowering time control. We found that the RRM domain of AtSF1 protein alters the production of alternatively spliced FLM-β transcripts. We also found that the RRM domain affects the alternative splicing of a heat shock transcription factor HsfA2 pre-mRNA, thereby mediating the heat stress response. Taken together, our results suggest the importance of RRM domain for AtSF1-mediated alternative splicing of a subset of genes involved in the regulation of flowering and adaptation to heat stress.
Collapse
Affiliation(s)
- Keh Chien Lee
- Division of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Yun Hee Jang
- Division of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Soon-Kap Kim
- Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Hyo-Young Park
- Division of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - May Phyo Thu
- Division of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Jeong Hwan Lee
- Department of Life Sciences, Chonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju, Jeollabuk-do, 54896, Republic of Korea.
| | - Jeong-Kook Kim
- Division of Life Sciences, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea.
| |
Collapse
|
22
|
Musseau C, Just D, Jorly J, Gévaudant F, Moing A, Chevalier C, Lemaire-Chamley M, Rothan C, Fernandez L. Identification of Two New Mechanisms That Regulate Fruit Growth by Cell Expansion in Tomato. FRONTIERS IN PLANT SCIENCE 2017; 8:988. [PMID: 28659942 PMCID: PMC5467581 DOI: 10.3389/fpls.2017.00988] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 05/24/2017] [Indexed: 05/25/2023]
Abstract
Key mechanisms controlling fruit weight and shape at the levels of meristem, ovary or very young fruit have already been identified using natural tomato diversity. We reasoned that new developmental modules prominent at later stages of fruit growth could be discovered by using new genetic and phenotypic diversity generated by saturated mutagenesis. Twelve fruit weight and tissue morphology mutants likely affected in late fruit growth were selected among thousands of fruit size and shape EMS mutants available in our tomato EMS mutant collection. Their thorough characterization at organ, tissue and cellular levels revealed two major clusters controlling fruit growth and tissue morphogenesis either through (i) the growth of all fruit tissues through isotropic cell expansion or (ii) only the growth of the pericarp through anisotropic cell expansion. These likely correspond to new cell expansion modules controlling fruit growth and tissue morphogenesis in tomato. Our study therefore opens the way for the identification of new gene regulatory networks controlling tomato fruit growth and morphology.
Collapse
|
23
|
Baute J, Polyn S, De Block J, Blomme J, Van Lijsebettens M, Inz� D. F-Box Protein FBX92 Affects Leaf Size in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2017; 58:962-975. [PMID: 28340173 PMCID: PMC5429023 DOI: 10.1093/pcp/pcx035] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 03/03/2017] [Indexed: 05/18/2023]
Abstract
F-box proteins are part of one of the largest families of regulatory proteins that play important roles in protein degradation. In plants, F-box proteins are functionally very diverse, and only a small subset has been characterized in detail. Here, we identified a novel F-box protein FBX92 as a repressor of leaf growth in Arabidopsis. Overexpression of AtFBX92 resulted in plants with smaller leaves than the wild type, whereas plants with reduced levels of AtFBX92 showed, in contrast, increased leaf growth by stimulating cell proliferation. Detailed cellular analysis suggested that AtFBX92 specifically affects the rate of cell division during early leaf development. This is supported by the increased expression levels of several cell cycle genes in plants with reduced AtFBX92 levels. Surprisingly, overexpression of the maize homologous gene ZmFBX92 in maize had no effect on plant growth, whereas ectopic expression in Arabidopsis increased leaf growth. Expression of a truncated form of AtFBX92 showed that the contrasting effects of ZmFBX92 and AtFBX92 gain of function in Arabidopsis are due to the absence of the F-box-associated domain in the ZmFBX92 gene. Our work reveals an additional player in the complex network that determines leaf size and lays the foundation for identifying putative substrates.
Collapse
Affiliation(s)
- Joke Baute
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 927, B-9052 Ghent, Belgium
| | - Stefanie Polyn
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 927, B-9052 Ghent, Belgium
| | - Jolien De Block
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 927, B-9052 Ghent, Belgium
| | - Jonas Blomme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 927, B-9052 Ghent, Belgium
| | - Mieke Van Lijsebettens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 927, B-9052 Ghent, Belgium
| | - Dirk Inz�
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 927, B-9052 Ghent, Belgium
- Corresponding author: E-mail, ; Fax, +32-9-3313809
| |
Collapse
|
24
|
Muñoz-Nortes T, Pérez-Pérez JM, Ponce MR, Candela H, Micol JL. The ANGULATA7 gene encodes a DnaJ-like zinc finger-domain protein involved in chloroplast function and leaf development in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:870-884. [PMID: 28008672 DOI: 10.1111/tpj.13466] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 12/16/2016] [Accepted: 12/19/2016] [Indexed: 06/06/2023]
Abstract
The characterization of mutants with altered leaf shape and pigmentation has previously allowed the identification of nuclear genes that encode plastid-localized proteins that perform essential functions in leaf growth and development. A large-scale screen previously allowed us to isolate ethyl methanesulfonate-induced mutants with small rosettes and pale green leaves with prominent marginal teeth, which were assigned to a phenotypic class that we dubbed Angulata. The molecular characterization of the 12 genes assigned to this phenotypic class should help us to advance our understanding of the still poorly understood relationship between chloroplast biogenesis and leaf morphogenesis. In this article, we report the phenotypic and molecular characterization of the angulata7-1 (anu7-1) mutant of Arabidopsis thaliana, which we found to be a hypomorphic allele of the EMB2737 gene, which was previously known only for its embryonic-lethal mutations. ANU7 encodes a plant-specific protein that contains a domain similar to the central cysteine-rich domain of DnaJ proteins. The observed genetic interaction of anu7-1 with a loss-of-function allele of GENOMES UNCOUPLED1 suggests that the anu7-1 mutation triggers a retrograde signal that leads to changes in the expression of many genes that normally function in the chloroplasts. Many such genes are expressed at higher levels in anu7-1 rosettes, with a significant overrepresentation of those required for the expression of plastid genome genes. Like in other mutants with altered expression of plastid-encoded genes, we found that anu7-1 exhibits defects in the arrangement of thylakoidal membranes, which appear locally unappressed.
Collapse
Affiliation(s)
- Tamara Muñoz-Nortes
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, Elche, 03202, Spain
| | - José Manuel Pérez-Pérez
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, Elche, 03202, Spain
| | - María Rosa Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, Elche, 03202, Spain
| | - Héctor Candela
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, Elche, 03202, Spain
| | - José Luis Micol
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, Elche, 03202, Spain
| |
Collapse
|
25
|
Van Dingenen J, Blomme J, Gonzalez N, Inzé D. Plants grow with a little help from their organelle friends. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:6267-6281. [PMID: 27815330 DOI: 10.1093/jxb/erw399] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Chloroplasts and mitochondria are indispensable for plant development. They not only provide energy and carbon sources to cells, but also have evolved to become major players in a variety of processes such as amino acid metabolism, hormone biosynthesis and cellular signalling. As semi-autonomous organelles, they contain a small genome that relies largely on nuclear factors for its maintenance and expression. An intensive crosstalk between the nucleus and the organelles is therefore essential to ensure proper functioning, and the nuclear genes encoding organellar proteins involved in photosynthesis and oxidative phosphorylation are obviously crucial for plant growth. Organ growth is determined by two main cellular processes: cell proliferation and cell expansion. Here, we review how plant growth is affected in mutants of organellar proteins that are differentially expressed during leaf and root development. Our findings indicate a clear role for organellar proteins in plant organ growth, primarily during cell proliferation. However, to date, the role of the nuclear-encoded organellar proteins in the cellular processes driving organ growth has not been investigated in much detail. We therefore encourage researchers to extend their phenotypic characterization beyond macroscopic features in order to get a better view on how chloroplasts and mitochondria regulate the basic processes of cell proliferation and cell expansion, essential to driving growth.
Collapse
Affiliation(s)
- Judith Van Dingenen
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Jonas Blomme
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Nathalie Gonzalez
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| |
Collapse
|
26
|
Mohan V, Gupta S, Thomas S, Mickey H, Charakana C, Chauhan VS, Sharma K, Kumar R, Tyagi K, Sarma S, Gupta SK, Kilambi HV, Nongmaithem S, Kumari A, Gupta P, Sreelakshmi Y, Sharma R. Tomato Fruits Show Wide Phenomic Diversity but Fruit Developmental Genes Show Low Genomic Diversity. PLoS One 2016; 11:e0152907. [PMID: 27077652 PMCID: PMC4831840 DOI: 10.1371/journal.pone.0152907] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 03/21/2016] [Indexed: 01/23/2023] Open
Abstract
Domestication of tomato has resulted in large diversity in fruit phenotypes. An intensive phenotyping of 127 tomato accessions from 20 countries revealed extensive morphological diversity in fruit traits. The diversity in fruit traits clustered the accessions into nine classes and identified certain promising lines having desirable traits pertaining to total soluble salts (TSS), carotenoids, ripening index, weight and shape. Factor analysis of the morphometric data from Tomato Analyzer showed that the fruit shape is a complex trait shared by several factors. The 100% variance between round and flat fruit shapes was explained by one discriminant function having a canonical correlation of 0.874 by stepwise discriminant analysis. A set of 10 genes (ACS2, COP1, CYC-B, RIN, MSH2, NAC-NOR, PHOT1, PHYA, PHYB and PSY1) involved in various plant developmental processes were screened for SNP polymorphism by EcoTILLING. The genetic diversity in these genes revealed a total of 36 non-synonymous and 18 synonymous changes leading to the identification of 28 haplotypes. The average frequency of polymorphism across the genes was 0.038/Kb. Significant negative Tajima’D statistic in two of the genes, ACS2 and PHOT1 indicated the presence of rare alleles in low frequency. Our study indicates that while there is low polymorphic diversity in the genes regulating plant development, the population shows wider phenotype diversity. Nonetheless, morphological and genetic diversity of the present collection can be further exploited as potential resources in future.
Collapse
Affiliation(s)
- Vijee Mohan
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Soni Gupta
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Sherinmol Thomas
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Hanjabam Mickey
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Chaitanya Charakana
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Vineeta Singh Chauhan
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Kapil Sharma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Rakesh Kumar
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Kamal Tyagi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Supriya Sarma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Suresh Kumar Gupta
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Himabindu Vasuki Kilambi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Sapana Nongmaithem
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Alka Kumari
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Prateek Gupta
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Yellamaraju Sreelakshmi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
- * E-mail: (RS); (YS)
| | - Rameshwar Sharma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
- * E-mail: (RS); (YS)
| |
Collapse
|
27
|
Zhu X, Chai M, Li Y, Sun M, Zhang J, Sun G, Jiang C, Shi L. Global Transcriptome Profiling Analysis of Inhibitory Effects of Paclobutrazol on Leaf Growth in Lily (Lilium Longiflorum-Asiatic Hybrid). FRONTIERS IN PLANT SCIENCE 2016; 7:491. [PMID: 27148316 PMCID: PMC4835717 DOI: 10.3389/fpls.2016.00491] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 03/26/2016] [Indexed: 05/23/2023]
Abstract
As a popular ornamental flower, potted lily is an important object of lily breeding. Paclobutrazol, a chemical growth retardation compound, is often used to dwarf plant in producing potted lilies. However, in recent years, the plants with inherited dwarf traits by using genetic engineer breeding technology are being developed. The studies on molecular basis of lily dwarfism will offer some target genes which have profound dwarf effect for genetic engineer breeding. Here, we confirmed that paclobutrazol inhibited plant height and leaf size in Lilium Longiflorum-Asiatic hybrid, and then RNA-Seq technique was employed to analyze gene transcripts of Lilium Longiflorum-Asiatic hybrid leaves by paclobutrazol treatment in order to get a deeper insight into dwarfism mechanism of lily. Approximately 38.6 Gb data was obtained and assemble into 53,681 unigenes. Annotation, pathways, functional classification and phylogenetic classification of these data were analyzed based on Nr, Nt, Swiss-Prot, KEGG, COG, and GO databases. 2704 differentially expressed genes were screened by comparing paclobutrazol-treated samples with untreated samples and quantitative real-time PCR was performed to validate expression profiles. By analyzing dynamic changes of differentially expressed genes, nine metabolic pathways and signal transduction pathways were significantly enriched and many potentially interesting genes were identified that encoded putative regulators or key components of cell division, cell expansion, GA metabolism and signaling transduction and these genes were highlighted to reveal their importance in regulation of plant size. These results will provide a better understanding of the molecular mechanism on lily dwarfism and some potential genes related to lily organ size, which will lay the foundation for molecular breeding of potted lilies. These transcriptome data will also serve as valuable public genomic resources for other genetic research in lily.
Collapse
Affiliation(s)
- Xiaopei Zhu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Min Chai
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of SciencesBeijing, China
- University of Chinese Academy of SciencesBeijing, China
| | - Yang Li
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Meiyu Sun
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Jinzheng Zhang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Guofeng Sun
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Chuangdao Jiang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of SciencesBeijing, China
| | - Lei Shi
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of SciencesBeijing, China
- *Correspondence: Lei Shi
| |
Collapse
|
28
|
Big Data in Plant Science: Resources and Data Mining Tools for Plant Genomics and Proteomics. Methods Mol Biol 2016; 1415:533-47. [PMID: 27115651 DOI: 10.1007/978-1-4939-3572-7_27] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
In modern plant biology, progress is increasingly defined by the scientists' ability to gather and analyze data sets of high volume and complexity, otherwise known as "big data". Arguably, the largest increase in the volume of plant data sets over the last decade is a consequence of the application of the next-generation sequencing and mass-spectrometry technologies to the study of experimental model and crop plants. The increase in quantity and complexity of biological data brings challenges, mostly associated with data acquisition, processing, and sharing within the scientific community. Nonetheless, big data in plant science create unique opportunities in advancing our understanding of complex biological processes at a level of accuracy without precedence, and establish a base for the plant systems biology. In this chapter, we summarize the major drivers of big data in plant science and big data initiatives in life sciences with a focus on the scope and impact of iPlant, a representative cyberinfrastructure platform for plant science.
Collapse
|