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Horsnell R, Leigh FJ, Wright TIC, Burridge AJ, Ligeza A, Przewieslik-Allen AM, Howell P, Uauy C, Edwards KJ, Bentley AR. A wheat chromosome segment substitution line series supports characterization and use of progenitor genetic variation. THE PLANT GENOME 2024; 17:e20288. [PMID: 36718796 DOI: 10.1002/tpg2.20288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/20/2022] [Indexed: 06/18/2023]
Abstract
Genome-wide introgression and substitution lines have been developed in many plant species, enhancing mapping precision, gene discovery, and the identification and exploitation of variation from wild relatives. Created over multiple generations of crossing and/or backcrossing accompanied by marker-assisted selection, the resulting introgression lines are a fixed genetic resource. In this study we report the development of spring wheat (Triticum aestivum L.) chromosome segment substitution lines (CSSLs) generated to systematically capture genetic variation from tetraploid (T. turgidum ssp. dicoccoides) and diploid (Aegilops tauschii) progenitor species. Generated in a common genetic background over four generations of backcrossing, this is a base resource for the mapping and characterization of wheat progenitor variation. To facilitate further exploitation the final population was genetically characterized using a high-density genotyping array and a range of agronomic and grain traits assessed to demonstrate the potential use of the populations for trait localization in wheat.
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Affiliation(s)
- Richard Horsnell
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, UK
| | - Fiona J Leigh
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, UK
| | - Tally I C Wright
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, UK
| | | | - Aleksander Ligeza
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, UK
| | | | - Philip Howell
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, UK
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - Alison R Bentley
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Road, Cambridge, UK
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
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2
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Wei Y, Xu Y, Khan A, Jiang C, Li H, Wu Y, Zhang C, Wang M, Chen J, Zeng L, Zhang M. Analysis of Photosynthetic Characteristics and Screening High Light-Efficiency Germplasm in Sugarcane. PLANTS (BASEL, SWITZERLAND) 2024; 13:587. [PMID: 38475434 DOI: 10.3390/plants13050587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/09/2024] [Accepted: 01/17/2024] [Indexed: 03/14/2024]
Abstract
Sugarcane is a globally significant crop for sugar and energy production, and developing high light-efficiency sugarcane varieties is crucial for enhancing yield and quality. However, limited research is available on the screening of sugarcane germplasm with high photosynthetic efficiency, especially with different leaf positions. The present study, conducted in Guangxi, China, aimed to analyze the photosynthetic characteristics of 258 sugarcane varieties at different leaf positions over three consecutive years in field experiments. The results showed significant differences in photosynthetic characteristics among genotypes, years, and leaf positions. Heritability estimates for various photosynthetic parameters ranged from 0.76 to 0.88. Principal component analysis revealed that the first three principal components accounted for over 99% of the cumulative variance. The first component represented photosynthetic efficiency and light utilization, the second focused on electron transfer and reaction center status, and the third was associated with chlorophyll content. Cluster and discriminant analysis classified sugarcane genotypes into three categories: high photosynthetic efficiency (HPE) with 86 genotypes, medium photosynthetic efficiency (MPE) with 60 genotypes, and low photosynthetic efficiency (LPE) with 112 genotypes. Multi-year trials confirmed that HPE sugarcane genotypes had higher single-stem weight and sucrose content. This study provides valuable insights into the photosynthetic physiological characteristics of different sugarcane varieties, which can contribute to further research regarding high yields and sugar breeding.
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Affiliation(s)
- Yibin Wei
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Yuzhi Xu
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Abdullah Khan
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Chunxiu Jiang
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Huojian Li
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Yuling Wu
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Chi Zhang
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Maoyao Wang
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Jun Chen
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Lifang Zeng
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Muqing Zhang
- College of Agriculture, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
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Barreto Ortiz J, Hirsch CN, Ehlke NJ, Watkins E. SpykProps: an imaging pipeline to quantify architecture in unilateral grass inflorescences. PLANT METHODS 2023; 19:125. [PMID: 37957737 PMCID: PMC10644492 DOI: 10.1186/s13007-023-01104-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/06/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND Inflorescence properties such length, spikelet number, and their spatial distribution across the rachis, are fundamental indicators of seed productivity in grasses and have been a target of selection throughout domestication and crop improvement. However, quantifying such complex morphology is laborious, time-consuming, and commonly limited to human-perceived traits. These limitations can be exacerbated by unfavorable trait correlations between inflorescence architecture and seed yield that can be unconsciously selected for. Computer vision offers an alternative to conventional phenotyping, enabling higher throughput and reducing subjectivity. These approaches provide valuable insights into the determinants of seed yield, and thus, aid breeding decisions. RESULTS Here, we described SpykProps, an inexpensive Python-based imaging system to quantify morphological properties in unilateral inflorescences, that was developed and tested on images of perennial grass (Lolium perenne L.) spikes. SpykProps is able to rapidly and accurately identify spikes (RMSE < 1), estimate their length (R2 = 0.96), and number of spikelets (R2 = 0.61). It also quantifies color and shape from hundreds of interacting descriptors that are accurate predictors of architectural and agronomic traits such as seed yield potential (R2 = 0.94), rachis weight (R2 = 0.83), and seed shattering (R2 = 0.85). CONCLUSIONS SpykProps is an open-source platform to characterize inflorescence architecture in a wide range of grasses. This imaging tool generates conventional and latent traits that can be used to better characterize developmental and agronomic traits associated with inflorescence architecture, and has applications in fields that include breeding, physiology, evolution, and development biology.
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Affiliation(s)
- Joan Barreto Ortiz
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, 55108, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Nancy Jo Ehlke
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Eric Watkins
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, 55108, USA.
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Hartenstein M, Albert M, Krause K. The plant vampire diaries: a historic perspective on Cuscuta research. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:2944-2955. [PMID: 36882965 DOI: 10.1093/jxb/erad082] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/01/2023] [Indexed: 05/21/2023]
Abstract
The angiosperm genus Cuscuta lives as an almost achlorophyllous root- and leafless holoparasite and has therefore occupied scientists for more than a century. The 'evolution' of Cuscuta research started with early studies that established the phylogenetic framework for this unusual genus. It continued to produce groundbreaking cytological, morphological, and physiological insight throughout the second half of the 20th century and culminated in the last two decades in exciting discoveries regarding the molecular basis of Cuscuta parasitism that were facilitated by the modern 'omics' tools and traceable fluorescent marker technologies of the 21st century. This review will show how present activities are inspired by those past breakthroughs. It will describe significant milestones and recurring themes of Cuscuta research and connect these to the remaining as well as newly evolving questions and future directions in this research field that is expected to sustain its strong growth in the future.
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Affiliation(s)
- Maleen Hartenstein
- Department of Biology, Molecular Plant Physiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, D-91058 Erlangen, Germany
| | - Markus Albert
- Department of Biology, Molecular Plant Physiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, D-91058 Erlangen, Germany
| | - Kirsten Krause
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Framstredet 39, 9019 Tromsø, Norway
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Yang Y, You C, Wang N, Wu M, Le Y, Wang M, Zhang X, Yu Y, Lin Z. Gossypium mustelinum genome and an introgression population enrich interspecific genetics and breeding in cotton. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:130. [PMID: 37199762 DOI: 10.1007/s00122-023-04379-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 05/05/2023] [Indexed: 05/19/2023]
Abstract
KEY MESSAGE Genomic and genetic resources of G. mustelinum were effective for identifying genes for qualitative and quantitative traits. Gossypium mustelinum represents the earliest diverging evolutionary lineage of polyploid Gossypium, representing a rich gene pool for numerous desirable traits lost in cotton cultivars. Accurate information of the genomic features and the genetic architecture of objective traits are essential for the discovery and utilization of G. mustelinum genes. Here, we presented a chromosome-level genome assembly of G. mustelinum and developed an introgression population of the G. mustelinum in the background of G. hirsutum that contained 264 lines. We precisely delimited the boundaries of the 1,662 introgression segments with the help of G. mustelinum genome assembly, and 87% of crossover regions (COs) were less than 5 Kb. Genes for fuzzless and green fuzz were discovered, and a total of 14 stable QTLs were identified with 12 novel QTLs across four independent environments. A new fiber length QTL, qUHML/SFC-A11, was confined to a 177-Kb region, and GmOPB4 and GmGUAT11 were considered as the putative candidate genes as potential negative regulator for fiber length. We presented a genomic and genetic resource of G. mustelinum, which we demonstrated that it was efficient for identifying genes for qualitative and quantitative traits. Our study built a valuable foundation for cotton genetics and breeding.
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Affiliation(s)
- Yang Yang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Institute of Nuclear and Biotechnology, Xinjiang Academy of Agricultural Sciences/Xinjiang Key Laboratory of Crop Biotechnology/The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions, Urumqi, 830091, Xinjiang, China
| | - Chunyuan You
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Cotton Research Institute, Shihezi Academy of Agriculture Science, Shihezi, 832000, Xinjiang, China
| | - Nian Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Mi Wu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yu Le
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yu Yu
- Cotton Research Institute, Xinjiang Academy of Agriculture and Reclamation Science, Shihezi, 832000, Xinjiang, China.
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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6
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Zhang M, Liu B, Fei Y, Yang X, Zhao L, Shi C, Zhang Y, Lu N, Wu C, Ma W, Wang J. Genetic architecture of leaf morphology revealed by integrated trait module in Catalpa bungei. HORTICULTURE RESEARCH 2023; 10:uhad032. [PMID: 37090097 PMCID: PMC10120837 DOI: 10.1093/hr/uhad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/14/2023] [Indexed: 05/03/2023]
Abstract
Leaves are crucial for maintaining plant growth and development via photosynthesis, and their function is simultaneously regulated by a suite of phenotypic traits. Although much is known about the genetic architecture of individual leaf traits, unraveling the genetic basis of complex leaf morphology remains a challenge. Based on the functional correlation and coordination of multi-traits, we divided 15 leaf morphological traits into three modules, comprising size (area, length, width, and perimeter), shape (leaf lobes, aspect ratio, circularity, rectangularity, and the relevant ratios), and color (red, green, and blue) for an ornamental tree species, Catalpa bungei. A total of 189 significant single-nucleotide polymorphisms were identified in the leaves of C. bungei: 35, 82, and 76 in the size, shape, and color modules, respectively. Four quantitative trait loci were common between the size and shape modules, which were closely related according to phenotype correlation, genetic mapping, and mRNA analysis. The color module was independent of them. Synergistic changes in the aspect ratio, leaf lobe, and circularity suggest that these traits could be the core indicators of the leaf shape module. The LAS and SRK genes, associated with leaf lobe and circularity, were found to function in plant defense mechanisms and the growth of leaves. The associations between the SRK and CRK2 genes and the leaf lobe and circularity traits were further verified by RT-qPCR. Our findings demonstrate the importance of integrating multi-trait modules to characterize leaf morphology and facilitate a holistic understanding of the genetic architecture of intraspecific leaf morphology diversity.
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Affiliation(s)
| | | | - Yue Fei
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Xiaowei Yang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Linjiao Zhao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Chaozhong Shi
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yueying Zhang
- Academy of Forest and Grassland Inventory and Planning, National Forestry and Grassland Administration, Beijing 100714, China
| | - Nan Lu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Chuangye Wu
- Wenxian Forestry Science Research Institute, Jiaozuo 454850, China
| | - Wenjun Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
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7
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Alizadeh-Moghaddam G, Nasr-Esfahani M, Rezayatmand Z, Khozaei M. Genomic markers analysis associated with resistance to Alternaria alternata (fr.) keissler-tomato pathotype, Solanum lycopersicum L. BREEDING SCIENCE 2022; 72:285-296. [PMID: 36699824 PMCID: PMC9868332 DOI: 10.1270/jsbbs.22003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/09/2022] [Indexed: 05/19/2023]
Abstract
Alternaria alternata, the causal pathogen of early blight (EB) disease, is one of the most important diseases in tomato, and other solanaceae family. We analyzed 35 tomato genotypes for quantitative/qualitative traits and biomass growth parameters, as well as the extent and structure of genetic variation associated with EB resistance. Phenotypic comparisons displayed significant differences in leaf blade width (24.95%), stem thickness (30.28%), foliage density (18.88%), and plant size (18.89%), with significant positive correlations with EB resistance (0.18-0.75). Correlation analysis showed that mature fruit size, thickness of fruit pericarp, and leaf type were significantly and negatively correlated with EB resistance (up to -0.41). The susceptible tomato seedlings represented significant reductions in biomass parameters. According to ISSR analysis, the highest resolving power (≥0.79) and heterozygosity (≥0.24) values revealed the presence of high genetic variability among the tomato genotypes. Bayesian model-based STRUCTURE analysis assembled the genotypes into 4 (best ΔK = 4) genetic groups. Combined phenotypic and molecular markers proved to be significantly useful for genetic diversity assessment associated with EB disease resistance.
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Affiliation(s)
- Giti Alizadeh-Moghaddam
- Department of Biology, Falavarjan Branch, Islamic Azad University, Isfahan, 84517-31167, Iran
- Corresponding author (e-mail: )
| | - Mehdi Nasr-Esfahani
- Department of Plant Protection Research, Isfahan Agricultural and Natural Resources Research and Education Center, AREEO, Isfahan, Iran
| | - Zahra Rezayatmand
- Department of Biology, Falavarjan Branch, Islamic Azad University, Isfahan, 84517-31167, Iran
| | - Mahdi Khozaei
- Plant Biotechnology, Department of Biology, University of Isfahan, Isfahan, Iran
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8
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Moreira JDR, Rosa BL, Lira BS, Lima JE, Correia LNF, Otoni WC, Figueira A, Freschi L, Sakamoto T, Peres LEP, Rossi M, Zsögön A. Auxin-driven ecophysiological diversification of leaves in domesticated tomato. PLANT PHYSIOLOGY 2022; 190:113-126. [PMID: 35639975 PMCID: PMC9434155 DOI: 10.1093/plphys/kiac251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/22/2022] [Indexed: 05/29/2023]
Abstract
Heterobaric leaves have bundle sheath extensions (BSEs) that compartmentalize the parenchyma, whereas homobaric leaves do not. The presence of BSEs affects leaf hydraulics and photosynthetic rate. The tomato (Solanum lycopersicum) obscuravenosa (obv) mutant lacks BSEs. Here, we identify the obv gene and the causative mutation, a nonsynonymous amino acid change that disrupts a C2H2 zinc finger motif in a putative transcription factor. This mutation exists as a polymorphism in the natural range of wild tomatoes but has increased in frequency in domesticated tomatoes, suggesting that the latter diversified into heterobaric and homobaric leaf types. The obv mutant displays reduced vein density, leaf hydraulic conductance and photosynthetic assimilation rate. We show that these and other pleiotropic effects on plant development, including changes in leaf insertion angle, leaf margin serration, minor vein density, and fruit shape, are controlled by OBV via changes in auxin signaling. Loss of function of the transcriptional regulator AUXIN RESPONSE FACTOR 4 (ARF4) also results in defective BSE development, revealing an additional component of a genetic module controlling aspects of leaf development important for ecological adaptation and subject to breeding selection.
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Affiliation(s)
- Juliene d R Moreira
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Bruno L Rosa
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Bruno S Lira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, Brazil
| | - Joni E Lima
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, Minas Gerais, Brazil
| | - Ludmila N F Correia
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Wagner C Otoni
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, Minas Gerais, Brazil
| | - Antonio Figueira
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, 13400-970 Piracicaba, São Paulo, Brazil
| | - Luciano Freschi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, Brazil
| | - Tetsu Sakamoto
- Bioinformatics Multidisciplinary Environment, Instituto Metrópole Digital, Universidade Federal Do Rio Grande Do Norte, 59078-400 Natal, Rio Grande do Norte, Brazil
| | - Lázaro E P Peres
- Laboratory of Hormonal Control of Plant Development, Departamento de Ciências Biológicas (LCB), Escola Superior de Agricultura “Luiz de Queiroz,” Universidade de São Paulo, CP 09, 13418-900 Piracicaba, São Paulo, Brazil
| | - Magdalena Rossi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, 05508-090 São Paulo, Brazil
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9
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Zhu F, Jadhav SS, Tohge T, Salem MA, Lee JM, Giovannoni JJ, Cheng Y, Alseekh S, Fernie AR. A comparative transcriptomics and eQTL approach identifies SlWD40 as a tomato fruit ripening regulator. PLANT PHYSIOLOGY 2022; 190:250-266. [PMID: 35512210 PMCID: PMC9434188 DOI: 10.1093/plphys/kiac200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/28/2022] [Indexed: 05/31/2023]
Abstract
Although multiple vital genes with strong effects on the tomato (Solanum lycopersicum) ripening process have been identified via the positional cloning of ripening mutants and cloning of ripening-related transcription factors (TFs), recent studies suggest that it is unlikely that we have fully characterized the gene regulatory networks underpinning this process. Here, combining comparative transcriptomics and expression QTLs, we identified 16 candidate genes involved in tomato fruit ripening and validated them through virus-induced gene silencing analysis. To further confirm the accuracy of the approach, one potential ripening regulator, SlWD40 (WD-40 repeats), was chosen for in-depth analysis. Co-expression network analysis indicated that master regulators such as RIN (ripening inhibitor) and NOR (nonripening) as well as vital TFs including FUL1 (FRUITFUL1), SlNAC4 (NAM, ATAF1,2, and CUC2 4), and AP2a (Activating enhancer binding Protein 2 alpha) strongly co-expressed with SlWD40. Furthermore, SlWD40 overexpression and RNAi lines exhibited substantially accelerated and delayed ripening phenotypes compared with the wild type, respectively. Moreover, transcriptome analysis of these transgenics revealed that expression patterns of ethylene biosynthesis genes, phytoene synthase, pectate lyase, and branched chain amino transferase 2, in SlWD40-RNAi lines were similar to those of rin and nor fruits, which further demonstrated that SlWD40 may act as an important ripening regulator in conjunction with RIN and NOR. These results are discussed in the context of current models of ripening and in terms of the use of comparative genomics and transcriptomics as an effective route for isolating causal genes underlying differences in genotypes.
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Affiliation(s)
| | | | - Takayuki Tohge
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, Potsdam-Golm 14476, Germany
| | - Mohamed A Salem
- Department of Pharmacognosy and Natural Products, Faculty of Pharmacy, Menoufia University, Menoufia 32511, Egypt
| | | | - James J Giovannoni
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York 14853, USA
- US Department of Agriculture–Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853, USA
| | - Yunjiang Cheng
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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10
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Zhou J, Gali KK, Jha AB, Tar’an B, Warkentin TD. Identification of Quantitative Trait Loci Associated with Seed Protein Concentration in a Pea Recombinant Inbred Line Population. Genes (Basel) 2022; 13:1531. [PMID: 36140699 PMCID: PMC9498679 DOI: 10.3390/genes13091531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/23/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
This research aimed to identify quantitative trait loci (QTLs) associated with seed protein concentration in a recombinant inbred line (RIL) population of pea and aimed to validate the identified QTLs using chromosome segment-introgressed lines developed by recurrent backcrossing. PR-25, an RIL population consisting of 108 F7 bulked lines derived from a cross between CDC Amarillo (yellow cotyledon) and CDC Limerick (green cotyledon), was used in this research. The RIL population was genotyped using an Axiom 90K SNP array. A total of 10,553 polymorphic markers were used for linkage map construction, after filtering for segregation distortion and missing values. The linkage map represents 901 unique loci on 11 linkage groups which covered a map distance of 855.3 Centimorgans. Protein concentration was assessed using near-infrared (NIR) spectroscopy of seeds harvested from field trials in seven station-years in Saskatchewan, Canada, during the 2019-2021 field seasons. Three QTLs located on chromosomes 2, 3 and 5 were identified to be associated with seed protein concentration. These QTLs explained 22%, 11% and 17% of the variation for protein concentration, respectively. The identified QTLs were validated by introgression lines, developed by marker-assisted selection of backcross lines for introgression of corresponding chromosome segments (~1/4 chromosome) harboring the QTL regions. Introgression line PR-28-7, not carrying any protein-related QTLs identified in this study, was 4.7% lower in protein concentration than CDC Amarillo, the lower protein parent of PR-25 which carried one identified protein-related QTL. The SNP markers located at the peak of the three identified QTLs will be converted into breeder-friendly KASP assays, which will be used for the selection of high-protein lines from segregating populations.
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Affiliation(s)
| | | | | | | | - Thomas D. Warkentin
- Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
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11
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Migicovsky Z, Swift JF, Helget Z, Klein LL, Ly A, Maimaitiyiming M, Woodhouse K, Fennell A, Kwasniewski M, Miller AJ, Cousins P, Chitwood DH. Increases in vein length compensate for leaf area lost to lobing in grapevine. AMERICAN JOURNAL OF BOTANY 2022; 109:1063-1073. [PMID: 35851467 PMCID: PMC9545854 DOI: 10.1002/ajb2.16033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/03/2022] [Indexed: 05/19/2023]
Abstract
PREMISE Leaf lobing and leaf size vary considerably across and within species, including among grapevines (Vitis spp.), some of the best-studied leaves. We examined the relationship between leaf lobing and leaf area across grapevine populations that varied in extent of leaf lobing. METHODS We used homologous landmarking techniques to measure 2632 leaves across 2 years in 476 unique, genetically distinct grapevines from five biparental crosses that vary primarily in the extent of lobing. We determined to what extent leaf area explained variation in lobing, vein length, and vein to blade ratio. RESULTS Although lobing was the primary source of variation in shape across the leaves we measured, leaf area varied only slightly as a function of lobing. Rather, leaf area increases as a function of total major vein length, total branching vein length, and vein to blade ratio. These relationships are stronger for more highly lobed leaves, with the residuals for each model differing as a function of distal lobing. CONCLUSIONS For leaves with different extents of lobing but the same area, the more highly lobed leaves have longer veins and higher vein to blade ratios, allowing them to maintain similar leaf areas despite increased lobing. These findings show how more highly lobed leaves may compensate for what would otherwise result in a reduced leaf area, allowing for increased photosynthetic capacity through similar leaf size.
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Affiliation(s)
- Zoë Migicovsky
- Plant, Food, and Environmental Sciences, Faculty of AgricultureDalhousie UniversityTruroNova ScotiaCanada B2N 5E3
| | - Joel F. Swift
- Department of BiologySaint Louis UniversitySt. LouisMO63103‐2010USA
| | - Zachary Helget
- Agronomy, Horticulture, and Plant ScienceSouth Dakota State UniversityBrookingsSD57007USA
| | - Laura L. Klein
- Department of BiologySaint Louis UniversitySt. LouisMO63103‐2010USA
| | - Anh Ly
- Department of Natural and Applied SciencesMissouri State UniversitySpringfieldMO65897USA
| | | | - Karoline Woodhouse
- Agronomy, Horticulture, and Plant ScienceSouth Dakota State UniversityBrookingsSD57007USA
| | - Anne Fennell
- Agronomy, Horticulture, and Plant ScienceSouth Dakota State UniversityBrookingsSD57007USA
| | - Misha Kwasniewski
- Division of Food SciencesUniversity of MissouriColumbiaMO65211USA
- Department of Food SciencesThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | | | | | - Daniel H. Chitwood
- Department of HorticultureMichigan State UniversityEast LansingMI48823USA
- Department of Computational Mathematics, Science & EngineeringMichigan State UniversityEast LansingMI48823USA
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12
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Pennelliiside D, a New Acyl Glucose from Solanum pennellii and Chemical Synthesis of Pennelliisides. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123728. [PMID: 35744854 PMCID: PMC9231340 DOI: 10.3390/molecules27123728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/03/2022] [Accepted: 06/06/2022] [Indexed: 11/25/2022]
Abstract
Acyl glucoses are a group of specialized metabolites produced by Solanaceae. Solanum pennellii, a wild-type tomato plant, produces acyl glucoses in its hair-like epidermal structures known as trichomes. These compounds have been found to be herbicides, microbial growth inhibitors, or allelopathic compounds. However, there are a few reports regarding isolation and investigation of biological activities of acyl glucoses in its pure form due to the difficulty of isolation. Here, we report a new acyl glucose, pennelliiside D, isolated and identified from S. pennellii. Its structure was determined by 1D NMR and 2D NMR, together with FD-MS analysis. To clarify the absolute configuration of the acyl moiety of 2-methylbutyryl in the natural compound, two possible isomers were synthesized starting from β-D-glucose pentaacetate. By comparing the spectroscopic data of natural and synthesized compounds of isomers, the structure of pennelliiside D was confirmed to be 3,4-O-diisobutyryl-2-O-((S)-2-methylbutyryl)-D-glucose. Pennelliiside D and its constituent fatty acid moiety, (S)-2-methylbutanoic acid, did not show root growth-inhibitory activity. Additionally, in this study, chemical synthesis pathways toward pennelliisides A and B were adapted to give 1,6-O-dibenzylpennelliisides A and B.
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13
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Powell AF, Feder A, Li J, Schmidt MHW, Courtney L, Alseekh S, Jobson EM, Vogel A, Xu Y, Lyon D, Dumschott K, McHale M, Sulpice R, Bao K, Lal R, Duhan A, Hallab A, Denton AK, Bolger ME, Fernie AR, Hind SR, Mueller LA, Martin GB, Fei Z, Martin C, Giovannoni JJ, Strickler SR, Usadel B. A Solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1791-1810. [PMID: 35411592 DOI: 10.1111/tpj.15770] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/10/2022] [Accepted: 03/27/2022] [Indexed: 06/14/2023]
Abstract
Wild relatives of tomato are a valuable source of natural variation in tomato breeding, as many can be hybridized to the cultivated species (Solanum lycopersicum). Several, including Solanum lycopersicoides, have been crossed to S. lycopersicum for the development of ordered introgression lines (ILs), facilitating breeding for desirable traits. Despite the utility of these wild relatives and their associated ILs, few finished genome sequences have been produced to aid genetic and genomic studies. Here we report a chromosome-scale genome assembly for S. lycopersicoides LA2951, which contains 37 938 predicted protein-coding genes. With the aid of this genome assembly, we have precisely delimited the boundaries of the S. lycopersicoides introgressions in a set of S. lycopersicum cv. VF36 × LA2951 ILs. We demonstrate the usefulness of the LA2951 genome by identifying several quantitative trait loci for phenolics and carotenoids, including underlying candidate genes, and by investigating the genome organization and immunity-associated function of the clustered Pto gene family. In addition, syntenic analysis of R2R3MYB genes sheds light on the identity of the Aubergine locus underlying anthocyanin production. The genome sequence and IL map provide valuable resources for studying fruit nutrient/quality traits, pathogen resistance, and environmental stress tolerance. We present a new genome resource for the wild species S. lycopersicoides, which we use to shed light on the Aubergine locus responsible for anthocyanin production. We also provide IL boundary mappings, which facilitated identifying novel carotenoid quantitative trait loci of which one was likely driven by an uncharacterized lycopene β-cyclase whose function we demonstrate.
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Affiliation(s)
| | - Ari Feder
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - Jie Li
- Department of Biochemistry and Metabolism, The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Maximilian H-W Schmidt
- Institute for Biology I, BioSC, RWTH Aachen University, 52474, Aachen, Germany
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Lance Courtney
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Saleh Alseekh
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Emma M Jobson
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - Alexander Vogel
- Institute for Biology I, BioSC, RWTH Aachen University, 52474, Aachen, Germany
| | - Yimin Xu
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - David Lyon
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Lab, Berkeley, CA, 94720, USA
| | - Kathryn Dumschott
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Marcus McHale
- Plant Systems Biology Lab, Ryan Institute, National University of Ireland, H91 TK33, Galway, Ireland
| | - Ronan Sulpice
- Plant Systems Biology Lab, Ryan Institute, National University of Ireland, H91 TK33, Galway, Ireland
| | - Kan Bao
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - Rohit Lal
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - Asha Duhan
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - Asis Hallab
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Alisandra K Denton
- Institute for Biology I, BioSC, RWTH Aachen University, 52474, Aachen, Germany
| | - Marie E Bolger
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428, Jülich, Germany
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Sarah R Hind
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | | | - Gregory B Martin
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA, and
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | - Cathie Martin
- Department of Biochemistry and Metabolism, The John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - James J Giovannoni
- Boyce Thompson Institute, Ithaca, New York, 14853, USA
- US Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | | | - Björn Usadel
- Institute for Biology I, BioSC, RWTH Aachen University, 52474, Aachen, Germany
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428, Jülich, Germany
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14
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Jathar V, Saini K, Chauhan A, Rani R, Ichihashi Y, Ranjan A. Spatial control of cell division by GA-OsGRF7/8 module in a leaf explaining the leaf length variation between cultivated and wild rice. THE NEW PHYTOLOGIST 2022; 234:867-883. [PMID: 35152411 DOI: 10.1111/nph.18029] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/05/2022] [Indexed: 06/14/2023]
Abstract
Cellular and genetic understanding of the rice leaf size regulation is limited, despite rice being the staple food of more than half of the global population. We investigated the mechanism controlling the rice leaf length using cultivated and wild rice accessions that remarkably differed for leaf size. Comparative transcriptomics, gibberellic acid (GA) quantification and leaf kinematics of the contrasting accessions suggested the involvement of GA, cell cycle and growth-regulating factors (GRFs) in the rice leaf size regulation. Zone-specific expression analysis and VIGS established the functions of specific GRFs in the process. The leaf length of the selected accessions was strongly correlated with GA levels. Higher GA content in wild rice accessions with longer leaves and GA-induced increase in the leaf length via an increase in cell division confirmed a GA-mediated regulation of division zone in rice. Downstream to GA, OsGRF7 and OsGRF8 function for controlling cell division to determine the rice leaf length. Spatial control of cell division to determine the division zone size mediated by GA and downstream OsGRF7 and OsGRF8 explains the leaf length differences between the cultivated and wild rice. This mechanism to control the rice leaf length might have contributed to optimizing leaf size during domestication.
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Affiliation(s)
- Vikram Jathar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Kumud Saini
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ashish Chauhan
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ruchi Rani
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Yasunori Ichihashi
- RIKEN BioResource Research Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Aashish Ranjan
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
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15
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Sonawane PD, Jozwiak A, Barbole R, Panda S, Abebie B, Kazachkova Y, Gharat SA, Ramot O, Unger T, Wizler G, Meir S, Rogachev I, Doron-Faigenboim A, Petreikov M, Schaffer A, Giri AP, Scherf T, Aharoni A. 2-oxoglutarate-dependent dioxygenases drive expansion of steroidal alkaloid structural diversity in the genus Solanum. THE NEW PHYTOLOGIST 2022; 234:1394-1410. [PMID: 35238413 DOI: 10.1111/nph.18064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 02/01/2022] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Solanum steroidal glycoalkaloids (SGAs) are renowned defence metabolites exhibiting spectacular structural diversity. Genes and enzymes generating the SGA precursor pathway, SGA scaffold and glycosylated forms have been largely identified. Yet, the majority of downstream metabolic steps creating the vast repertoire of SGAs remain untapped. Here, we discovered that members of the 2-OXOGLUTARATE-DEPENDENT DIOXYGENASE (2-ODD) family play a prominent role in SGA metabolism, carrying out three distinct backbone-modifying oxidative steps in addition to the three formerly reported pathway reactions. The GLYCOALKALOID METABOLISM34 (GAME34) enzyme catalyses the conversion of core SGAs to habrochaitosides in wild tomato S. habrochaites. Cultivated tomato plants overexpressing GAME34 ectopically accumulate habrochaitosides. These habrochaitoside enriched plants extracts potently inhibit Puccinia spp. spore germination, a significant Solanaceae crops fungal pathogen. Another 2-ODD enzyme, GAME33, acts as a desaturase (via hydroxylation and E/F ring rearrangement) forming unique, yet unreported SGAs. Conversion of bitter α-tomatine to ripe fruit, nonbitter SGAs (e.g. esculeoside A) requires two hydroxylations; while the known GAME31 2-ODD enzyme catalyses hydroxytomatine formation, we find that GAME40 catalyses the penultimate step in the pathway and generates acetoxy-hydroxytomatine towards esculeosides accumulation. Our results highlight the significant contribution of 2-ODD enzymes to the remarkable structural diversity found in plant steroidal specialized metabolism.
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Affiliation(s)
- Prashant D Sonawane
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
- Department of Natural Products, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
| | - Adam Jozwiak
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ranjit Barbole
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411008, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sayantan Panda
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
- Gilat Research Center, Agricultural Research Organization (ARO), Rural delivery Negev, 85280, Israel
| | - Bekele Abebie
- Department of Plant Pathology and Weed Research, ARO-Volcani Center, Bet Dagan, 50250, Israel
| | - Yana Kazachkova
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Sachin A Gharat
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ofir Ramot
- Metabolic Insights Ltd, Ness Ziona, 7414001, Israel
| | - Tamar Unger
- Israel Structural Proteomics Centre, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Guy Wizler
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Sagit Meir
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Ilana Rogachev
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Adi Doron-Faigenboim
- Institute of Plant Sciences, ARO-Volcani Center, Rishon LeZiyyon, 7505101, Israel
| | - Marina Petreikov
- Institute of Plant Sciences, ARO-Volcani Center, Rishon LeZiyyon, 7505101, Israel
| | - Arthur Schaffer
- Institute of Plant Sciences, ARO-Volcani Center, Rishon LeZiyyon, 7505101, Israel
| | - Ashok P Giri
- Department of Natural Products, Max Planck Institute for Chemical Ecology, Jena, 07745, Germany
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411008, India
| | - Tali Scherf
- NMR unit, Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
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16
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Noshita K, Murata H, Kirie S. Model-based plant phenomics on morphological traits using morphometric descriptors. BREEDING SCIENCE 2022; 72:19-30. [PMID: 36045892 PMCID: PMC8987841 DOI: 10.1270/jsbbs.21078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/20/2021] [Indexed: 06/15/2023]
Abstract
The morphological traits of plants contribute to many important functional features such as radiation interception, lodging tolerance, gas exchange efficiency, spatial competition between individuals and/or species, and disease resistance. Although the importance of plant phenotyping techniques is increasing with advances in molecular breeding strategies, there are barriers to its advancement, including the gap between measured data and phenotypic values, low quantitativity, and low throughput caused by the lack of models for representing morphological traits. In this review, we introduce morphological descriptors that can be used for phenotyping plant morphological traits. Geometric morphometric approaches pave the way to a general-purpose method applicable to single units. Hierarchical structures composed of an indefinite number of multiple elements, which is often observed in plants, can be quantified in terms of their multi-scale topological characteristics using topological data analysis. Theoretical morphological models capture specific anatomical structures, if recognized. These morphological descriptors provide us with the advantages of model-based plant phenotyping, including robust quantification of limited datasets. Moreover, we discuss the future possibilities that a system of model-based measurement and model refinement would solve the lack of morphological models and the difficulties in scaling out the phenotyping processes.
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Affiliation(s)
- Koji Noshita
- Department of Biology, Kyushu University, Fukuoka, Fukuoka 819-0395, Japan
- Plant Frontier Research Center, Kyushu University, Fukuoka, Fukuoka 819-0395, Japan
| | - Hidekazu Murata
- Department of Biology, Kyushu University, Fukuoka, Fukuoka 819-0395, Japan
| | - Shiryu Kirie
- metaPhorest (Bioaesthetics Platform), Department of Electrical Engineering and Bioscience, Waseda University, TWIns, Tokyo 162-8480, Japan
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17
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Jacobs SJ, Grundler MC, Henriquez CL, Zapata F. An integrative genomic and phenomic analysis to investigate the nature of plant species in Escallonia (Escalloniaceae). Sci Rep 2021; 11:24013. [PMID: 34907249 PMCID: PMC8671583 DOI: 10.1038/s41598-021-03419-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 11/26/2021] [Indexed: 12/04/2022] Open
Abstract
What we mean by species and whether they have any biological reality has been debated since the early days of evolutionary biology. Some biologists even suggest that plant species are created by taxonomists as a subjective, artificial division of nature. However, the nature of plant species has been rarely tested critically with data while ignoring taxonomy. We integrate phenomic and genomic data collected across hundreds of individuals at a continental scale to investigate this question in Escallonia (Escalloniaceae), a group of plants which includes 40 taxonomic species (the species proposed by taxonomists). We first show that taxonomic species may be questionable as they match poorly to patterns of phenotypic and genetic variation displayed by individuals collected in nature. We then use explicit statistical methods for species delimitation designed for phenotypic and genomic data, and show that plant species do exist in Escallonia as an objective, discrete property of nature independent of taxonomy. We show that such species correspond poorly to current taxonomic species (\documentclass[12pt]{minimal}
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\begin{document}$$< 20\%$$\end{document}<20%). These discrepancies suggest that evolutionary forces additional to gene flow can maintain the cohesion of species. We propose that phenomic and genomic data analyzed on an equal footing build a broader perspective on the nature of plant species by helping delineate different ‘types of species’. Our results caution studies which take the accuracy of taxonomic species for granted and challenge the notion of plant species without empirical evidence. Note: A version of the complete manuscript in Spanish is available in the Supplemental Materials.
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Affiliation(s)
- Sarah J Jacobs
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA.,Department of Botany, California Academy of Sciences, San Francisco, CA, 94118, USA
| | - Michael C Grundler
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Claudia L Henriquez
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Felipe Zapata
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA.
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18
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Hamilton CA, Winiger N, Rubin JJ, Breinholt J, Rougerie R, Kitching IJ, Barber JR, Kawahara AY. Hidden phylogenomic signal helps elucidate arsenurine silkmoth phylogeny and the evolution of body size and wing shape trade-offs. Syst Biol 2021; 71:859-874. [PMID: 34791485 DOI: 10.1093/sysbio/syab090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 11/13/2022] Open
Abstract
One of the key objectives in biological research is understanding how evolutionary processes have produced Earth's diversity. A critical step towards revealing these processes is an investigation of evolutionary tradeoffs - that is, the opposing pressures of multiple selective forces. For millennia, nocturnal moths have had to balance successful flight, as they search for mates or host plants, with evading bat predators. However, the potential for evolutionary trade-offs between wing shape and body size are poorly understood. In this study, we used phylogenomics and geometric morphometrics to examine the evolution of wing shape in the wild silkmoth subfamily Arsenurinae (Saturniidae) and evaluate potential evolutionary relationships between body size and wing shape. The phylogeny was inferred based on 782 loci from target capture data of 42 arsenurine species representing all 10 recognized genera. After detecting in our data one of the most vexing problems in phylogenetic inference - a region of a tree that possesses short branches and no "support" for relationships (i.e., a polytomy), we looked for hidden phylogenomic signal (i.e., inspecting differing phylogenetic inferences, alternative support values, quartets, and phylogenetic networks) to better illuminate the most probable generic relationships within the subfamily. We found there are putative evolutionary trade-offs between wing shape, body size, and the interaction of fore- and hindwing shape. Namely, body size tends to decrease with increasing hindwing length but increases as forewing shape becomes more complex. Additionally, the type of hindwing (i.e., tail or no tail) a lineage possesses has a significant effect on the complexity of forewing shape. We outline possible selective forces driving the complex hindwing shapes that make Arsenurinae, and silkmoths as a whole, so charismatic.
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Affiliation(s)
- Chris A Hamilton
- Florida Museum of Natural History, McGuire Center for Lepidoptera and Biodiversity, University of Florida, Gainesville, FL 32611 USA.,Department of Entomology, Plant Pathology & Nematology, University of Idaho, Moscow, ID, 83844 USA
| | - Nathalie Winiger
- Florida Museum of Natural History, McGuire Center for Lepidoptera and Biodiversity, University of Florida, Gainesville, FL 32611 USA.,Wildlife Ecology and Management, Albert-Ludwigs-Universität Freiburg, 79106 Freiburg, Germany
| | - Juliette J Rubin
- Florida Museum of Natural History, McGuire Center for Lepidoptera and Biodiversity, University of Florida, Gainesville, FL 32611 USA
| | - Jesse Breinholt
- Florida Museum of Natural History, McGuire Center for Lepidoptera and Biodiversity, University of Florida, Gainesville, FL 32611 USA.,Division of Bioinformatics, Intermountain Healthcare, Precision Genomics, St. George, UT 84790 USA
| | - Rodolphe Rougerie
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Ian J Kitching
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Jesse R Barber
- Department of Biological Sciences, Boise State University, Boise, ID, 83725 USA
| | - Akito Y Kawahara
- Florida Museum of Natural History, McGuire Center for Lepidoptera and Biodiversity, University of Florida, Gainesville, FL 32611 USA
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Xu P, Wang Y, Sun F, Wu R, Du H, Wang Y, Jiang L, Wu X, Wu X, Yang L, Xing N, Hu Y, Wang B, Huang Y, Tao Y, Gao Q, Liang C, Li Y, Lu Z, Li G. Long-read genome assembly and genetic architecture of fruit shape in the bottle gourd. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:956-968. [PMID: 34043857 DOI: 10.1111/tpj.15358] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 06/12/2023]
Abstract
The bottle gourd (Lagenaria siceraria, Cucurbitaceae) is an important horticultural crop exhibiting tremendous diversity in fruit shape. The genetic architecture of fruit shape variation in this species remains unknown. We assembled a long-read-based, high-quality reference genome (ZAAS_Lsic_2.0) with a contig N50 value over 390-fold greater than the existing reference genomes. We then focused on dissection of fruit shape using a one-step geometric morphometrics-based functional mapping approach. We identified 11 quantitative trait loci (QTLs) responsible for fruit shape (fsQTLs), reconstructed their visible effects and revealed syntenic relationships of bottle gourd fsQTLs with 12 fsQTLs previously reported in cucumber, melon or watermelon. Homologs of several well-known and newly identified fruit shape genes, including SUN, OFP, AP2 and auxin transporters, were comapped with bottle gourd QTLs.
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Affiliation(s)
- Pei Xu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Ying Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Fengshuo Sun
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, USA
| | - Huilong Du
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yuhong Wang
- Institute of Vegetables, Ningbo Academy of Agricultural Sciences, Ningbo, China
| | - Libo Jiang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xiaohua Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Xinyi Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Liming Yang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Nailin Xing
- Institute of Vegetables, Ningbo Academy of Agricultural Sciences, Ningbo, China
| | - Yaowen Hu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Baogen Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Yunping Huang
- Institute of Vegetables, Ningbo Academy of Agricultural Sciences, Ningbo, China
| | - Ye Tao
- Biozeron Biotechnology Co., Ltd, Shanghai, China
| | - Qiang Gao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Chengzhi Liang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yanwei Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Zhongfu Lu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Guojing Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
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20
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MacMillan P, Teixeira G, Lopes CM, Monteiro A. The role of grapevine leaf morphoanatomical traits in determining capacity for coping with abiotic stresses: a review. CIÊNCIA E TÉCNICA VITIVINÍCOLA 2021. [DOI: 10.1051/ctv/ctv2021360175] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Worldwide, there are thousands of Vitis vinifera grape cultivars used for wine production, creating a large morphological, anatomical, physiological and molecular diversity that needs to be further characterised and explored, with a focus on their capacity to withstand biotic and abiotic stresses. This knowledge can then be used to select better adapted genotypes in order to help face the challenges of the expected climate changes in the near future. It will also assist grape growers in choosing the most suitable cultivar(s) for each terroir; with adaptation to drought and heat stresses being a fundamental characteristic. The leaf blade of grapevines is the most exposed organ to abiotic stresses, therefore its study regarding the tolerance to water and heat stress is becoming particularly important, mainly in Mediterranean viticulture. This review focuses on grapevine leaf morphoanatomy - leaf blade form, leaf epidermis characteristics (cuticle, indumentum, pavement cells and stomata) and anatomy of mesophyll - and their adaptation to abiotic stresses. V. vinifera xylem architecture and its adaptation capacity when the grapevine is subjected to water stress is also highlighted since grapevines have been observed to exhibit a large variability in responses to water availability. The hydraulic properties of the petiole, shoot and trunk are also reviewed. Summarising, this paper reviews recent advances related to the adaptation of grapevine leaf morphoanatomical features and hydraulic architecture to abiotic stresses, mainly water and heat stress, induced primarily by an ever-changing global climate.
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21
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Qin X, Chetelat RT. Ornithine decarboxylase genes contribute to S-RNase-independent pollen rejection. PLANT PHYSIOLOGY 2021; 186:452-468. [PMID: 33576789 PMCID: PMC8154068 DOI: 10.1093/plphys/kiab062] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/23/2021] [Indexed: 05/14/2023]
Abstract
Unilateral incompatibility (UI) manifests as pollen rejection in the pistil, typically when self-incompatible (SI) species are pollinated by self-compatible (SC) relatives. In the Solanaceae, UI occurs when pollen lack resistance to stylar S-RNases, but other, S-RNase-independent mechanisms exist. Pistils of the wild tomato Solanum pennellii LA0716 (SC) lack S-RNase yet reject cultivated tomato (Solanum lycopersicum, SC) pollen. In this cross, UI results from low pollen expression of a farnesyl pyrophosphate synthase gene (FPS2) in S. lycopersicum. Using pollen from fps2-/- loss-of-function mutants in S. pennellii, we identified a pistil factor locus, ui3.1, required for FPS2-based pollen rejection. We mapped ui3.1 to an interval containing 108 genes situated on the IL 3-3 introgression. This region includes a cluster of ornithine decarboxylase (ODC2) genes, with four copies in S. pennellii, versus one in S. lycopersicum. Expression of ODC2 transcript was 1,034-fold higher in S. pennellii than in S. lycopersicum styles. Pistils of odc2-/- knockout mutants in IL 3-3 or S. pennellii fail to reject fps2 pollen and abolish transmission ratio distortion (TRD) associated with FPS2. Pollen of S. lycopersicum express low levels of FPS2 and are compatible on IL 3-3 pistils, but incompatible on IL 12-3 × IL 3-3 hybrids, which express both ODC2 and ui12.1, a locus thought to encode the SI proteins HT-A and HT-B. TRD observed in F2 IL 12-3 × IL 3-3 points to additional ODC2-interacting pollen factors on both chromosomes. Thus, ODC2 genes contribute to S-RNase independent UI and interact genetically with ui12.1 to strengthen pollen rejection.
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Affiliation(s)
- Xiaoqiong Qin
- Department of Plant Sciences (ms #3), University of California, Davis, One Shields Avenue, Davis, California 95616
| | - Roger T Chetelat
- Department of Plant Sciences (ms #3), University of California, Davis, One Shields Avenue, Davis, California 95616
- Author for communication:
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22
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Albert M, Axtell MJ, Timko MP. Mechanisms of resistance and virulence in parasitic plant-host interactions. PLANT PHYSIOLOGY 2021; 185:1282-1291. [PMID: 33793887 PMCID: PMC8133583 DOI: 10.1093/plphys/kiaa064] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 11/03/2020] [Indexed: 06/12/2023]
Abstract
Parasitic plants pose a major biotic threat to plant growth and development and lead to losses in crop productivity of billions of USD annually. By comparison with "normal" autotrophic plants, parasitic plants live a heterotrophic lifestyle and rely on water, solutes and to a greater (holoparasitic plants) or lesser extent (hemiparasitic plants) on sugars from other host plants. Most hosts are unable to detect an infestation by plant parasites or unable to fend off these parasitic invaders. However, a few hosts have evolved defense strategies to avoid infestation or protect themselves actively post-attack often leading to full or partial resistance. Here, we review the current state of our understanding of the defense strategies to plant parasitism used by host plants with emphasis on the active molecular resistance mechanisms. Furthermore, we outline the perspectives and the potential of future studies that will be indispensable to develop and breed resistant crops.
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Affiliation(s)
- Markus Albert
- Department of Biology, Molecular Plant Physiology, FAU Erlangen-Nuremberg, Staudtstr. 5, 91058 Erlangen, Germany
| | - Michael J Axtell
- Department of Biology and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
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23
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Raduski AR, Igić B. Biosystematic studies on the status of Solanum chilense. AMERICAN JOURNAL OF BOTANY 2021; 108:520-537. [PMID: 33783814 DOI: 10.1002/ajb2.1621] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/19/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Common taxonomic practices, which condition species' descriptions on diagnostic morphological traits, may systematically lump outcrossing species and unduly split selfing species. Specifically, higher effective population sizes and genetic diversity of obligate outcrossers are expected to result less reliable phenotypic diagnoses. Wild tomatoes, members of Solanum sect. Lycopersicum, are commonly used as a source of exotic germplasm for improvement of the cultivated tomato, and are increasingly employed in basic research. Although the section experienced significant early work, which continues presently, the taxonomic status of many wild species has undergone a number of significant revisions and remains uncertain. Species in this section vary in their breeding systems, notably the expression of self-incompatibility, which determines individual propensity for outcrossing METHODS: Here, we examine the taxonomic status of obligately outcrossing Chilean wild tomato (Solanum chilense) using reduced-representation sequencing (RAD-seq), a range of phylogenetic and population genetic analyses, as well as analyses of crossing and morphological data. RESULTS Overall, each of our analyses provides a considerable weight of evidence that the Pacific coastal populations and Andean inland populations of the currently described Solanum chilense represent separately evolving populations, and conceal at least one undescribed cryptic species. CONCLUSIONS Despite its vast economic importance, Solanum sect. Lycopersicon still exhibits considerable taxonomic instability. A pattern of under-recognition of outcrossing species may be common, not only in tomatoes, but across flowering plants. We discuss the possible causes and implications of this observation, with a focus on macroevolutionary inference.
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Affiliation(s)
- Andrew R Raduski
- Dept. of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, 60607, U.S.A
- Dept. of Plant & Microbial Biology, University of Minnesota - Twin Cities, St. Paul, Minnesota, 55108, U.S.A
| | - Boris Igić
- Dept. of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, 60607, U.S.A
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24
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Turner KG, Ostevik KL, Grassa CJ, Rieseberg LH. Genomic Analyses of Phenotypic Differences Between Native and Invasive Populations of Diffuse Knapweed (Centaurea diffusa). Front Ecol Evol 2021. [DOI: 10.3389/fevo.2020.577635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Invasive species represent excellent opportunities to study the evolutionary potential of traits important to success in novel environments. Although some ecologically important traits have been identified in invasive species, little is typically known about the genetic mechanisms that underlie invasion success in non-model species. Here, we use a genome-wide association (GWAS) approach to identify the genetic basis of trait variation in the non-model, invasive, diffuse knapweed [Centaurea diffusa Lam. (Asteraceae)]. To assist with this analysis, we have assembled the first draft genome reference and fully annotated plastome assembly for this species, and one of the first from this large, weedy, genus, which is of major ecological and economic importance. We collected phenotype data from 372 individuals from four native and four invasive populations of C. diffusa grown in a common environment. Using these individuals, we produced reduced-representation genotype-by-sequencing (GBS) libraries and identified 7,058 SNPs. We identify two SNPs associated with leaf width in these populations, a trait which significantly varies between native and invasive populations. In this rosette forming species, increased leaf width is a major component of increased biomass, a common trait in invasive plants correlated with increased fitness. Finally, we use annotations from Arabidopsis thaliana to identify 98 candidate genes that are near the associated SNPs and highlight several good candidates for leaf width variation.
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25
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Mähler N, Schiffthaler B, Robinson KM, Terebieniec BK, Vučak M, Mannapperuma C, Bailey MES, Jansson S, Hvidsten TR, Street NR. Leaf shape in Populus tremula is a complex, omnigenic trait. Ecol Evol 2020; 10:11922-11940. [PMID: 33209260 PMCID: PMC7663049 DOI: 10.1002/ece3.6691] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/26/2020] [Accepted: 07/08/2020] [Indexed: 01/10/2023] Open
Abstract
Leaf shape is a defining feature of how we recognize and classify plant species. Although there is extensive variation in leaf shape within many species, few studies have disentangled the underlying genetic architecture. We characterized the genetic architecture of leaf shape variation in Eurasian aspen (Populus tremula L.) by performing genome-wide association study (GWAS) for physiognomy traits. To ascertain the roles of identified GWAS candidate genes within the leaf development transcriptional program, we generated RNA-Seq data that we used to perform gene co-expression network analyses from a developmental series, which is publicly available within the PlantGenIE resource. We additionally used existing gene expression measurements across the population to analyze GWAS candidate genes in the context of a population-wide co-expression network and to identify genes that were differentially expressed between groups of individuals with contrasting leaf shapes. These data were integrated with expression GWAS (eQTL) results to define a set of candidate genes associated with leaf shape variation. Our results identified no clear adaptive link to leaf shape variation and indicate that leaf shape traits are genetically complex, likely determined by numerous small-effect variations in gene expression. Genes associated with shape variation were peripheral within the population-wide co-expression network, were not highly connected within the leaf development co-expression network, and exhibited signatures of relaxed selection. As such, our results are consistent with the omnigenic model.
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Affiliation(s)
- Niklas Mähler
- Department of Plant PhysiologyUmeå Plant Science CentreUmeå UniversityUmeåSweden
| | - Bastian Schiffthaler
- Department of Plant PhysiologyUmeå Plant Science CentreUmeå UniversityUmeåSweden
| | - Kathryn M. Robinson
- Department of Plant PhysiologyUmeå Plant Science CentreUmeå UniversityUmeåSweden
| | | | - Matej Vučak
- School of Life SciencesCollege of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowScotland
| | - Chanaka Mannapperuma
- Department of Plant PhysiologyUmeå Plant Science CentreUmeå UniversityUmeåSweden
| | - Mark E. S. Bailey
- School of Life SciencesCollege of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowScotland
| | - Stefan Jansson
- Department of Plant PhysiologyUmeå Plant Science CentreUmeå UniversityUmeåSweden
| | - Torgeir R. Hvidsten
- Faculty of Chemistry, Biotechnology and Food ScienceNorwegian University of Life SciencesÅsNorway
| | - Nathaniel R. Street
- Department of Plant PhysiologyUmeå Plant Science CentreUmeå UniversityUmeåSweden
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26
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Li Y, Chen Y, Zhou L, You S, Deng H, Chen Y, Alseekh S, Yuan Y, Fu R, Zhang Z, Su D, Fernie AR, Bouzayen M, Ma T, Liu M, Zhang Y. MicroTom Metabolic Network: Rewiring Tomato Metabolic Regulatory Network throughout the Growth Cycle. MOLECULAR PLANT 2020; 13:1203-1218. [PMID: 32561360 DOI: 10.1016/j.molp.2020.06.005] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/07/2020] [Accepted: 06/10/2020] [Indexed: 05/21/2023]
Abstract
Tomato (Solanum lycopersicum) is a major horticultural crop worldwide and has emerged as a preeminent model for metabolic research. Although many research efforts have focused on the analysis of metabolite differences between varieties and species, the dynamics of metabolic changes during the tomato growth cycle and the regulatory networks that underlie these changes are poorly understood. In this study, we integrated high-resolution spatio-temporal metabolome and transcriptome data to systematically explore the metabolic landscape across 20 major tomato tissues and growth stages. In the resulting MicroTom Metabolic Network, the 540 detected metabolites and their co-expressed genes could be divided into 10 distinct clusters based on their biological functions. Using this dataset, we constructed a global map of the major metabolic changes that occur throughout the tomato growth cycle and dissected the underlying regulatory network. In addition to verifying previously well-established regulatory networks for important metabolites, we identified novel transcription factors that regulate the biosynthesis of important secondary metabolites such as steroidal glycoalkaloids and flavonoids. Our findings provide insights into spatio-temporal changes in tomato metabolism and generate a valuable resource for the study of metabolic regulatory processes in model plants.
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Affiliation(s)
- Yan Li
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
| | - Yang Chen
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
| | - Lu Zhou
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
| | - Shengjie You
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
| | - Heng Deng
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
| | - Ya Chen
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Plant Biotechnology, 4000 Plovdiv, Bulgaria
| | - Yong Yuan
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
| | - Rao Fu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
| | - Zixin Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
| | - Dan Su
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center of Plant Systems Biology and Plant Biotechnology, 4000 Plovdiv, Bulgaria
| | - Mondher Bouzayen
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China; GBF, University of Toulouse, INRA, Castanet-Tolosan, France
| | - Tao Ma
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China
| | - Mingchun Liu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China.
| | - Yang Zhang
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, People's Republic of China.
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Genomic Dissection of a Wild Region in a Superior Solanum pennellii Introgression Sub-Line with High Ascorbic Acid Accumulation in Tomato Fruit. Genes (Basel) 2020; 11:genes11080847. [PMID: 32722275 PMCID: PMC7466095 DOI: 10.3390/genes11080847] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 11/16/2022] Open
Abstract
The Solanum pennellii introgression lines (ILs) have been exploited to map quantitative trait loci (QTLs) and identify favorable alleles that could improve fruit quality traits in tomato varieties. Over the past few years, ILs exhibiting increased content of ascorbic acid in the fruit have been selected, among which the sub-line R182. The aims of this work were to identify the genes of the wild donor S. pennellii harbored by the sub-line and to detect genes controlling ascorbic acid accumulation by using genomics tools. A Genotyping-By-Sequencing (GBS) approach confirmed that no wild introgressions were present in the sub-line besides one region on chromosome 7. By using a dense single nucleotide polymorphism (SNP) map obtained by RNA sequencing (RNA-Seq), the wild region of the sub-line was finely identified; thus, defining 39 wild genes that replaced 33 genes of the ILs genetic background (cv. M82). The differentially expressed genes mapping in the region and the variants detected among the cultivated and the wild alleles evidenced the potential role of the novel genes present in the wild region. Interestingly, one upregulated gene, annotated as a major facilitator superfamily protein, showed a novel structure in R182, with respect to the parental lines. These genes will be further investigated using gene editing strategies.
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28
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Lana-Costa J, de Oliveira Silva FM, Batista-Silva W, Carolino DC, Senra RL, Medeiros DB, Martins SCV, Gago J, Araújo WL, Nunes-Nesi A. High Photosynthetic Rates in a Solanum pennellii Chromosome 2 QTL Is Explained by Biochemical and Photochemical Changes. FRONTIERS IN PLANT SCIENCE 2020; 11:794. [PMID: 32595679 PMCID: PMC7303335 DOI: 10.3389/fpls.2020.00794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/19/2020] [Indexed: 05/09/2023]
Abstract
Enhanced photosynthesis is strictly associated with to productivity and it can be accomplished by genetic approaches through identification of genetic variation. By using a Solanum pennellii introgression lines (ILs) population, it was previously verified that, under normal (CO2), IL 2-5 and 2-6 display increased photosynthetic rates by up to 20% in comparison with their parental background (M82). However, the physiological mechanisms involved in the enhanced CO2 assimilation exhibited by these lines remained unknown, precluding their use for further biotechnological applications. Thereby, here we attempted to uncover the physiological factors involved in the upregulation of photosynthesis in ILs 2-5 and 2-6 under normal (CO2) as well as under elevated (CO2). The results provide evidence for increased biochemical capacity (higher maximum carboxylation velocity and maximum electron transport rate) in plants from IL 2-5 and 2-6, whereas the diffusive components (stomatal and mesophyll conductances) were unaltered in these ILs in comparison to M82. Our analyses revealed that the higher photosynthetic rate observed in these ILs was associated with higher levels of starch as well as total protein levels, specially increased RuBisCO content. Further analyses performed in plants under high (CO2) confirmed that biochemical properties are involved in genetic variation on chromosome 2 related to enhanced photosynthesis.
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Affiliation(s)
- Jaciara Lana-Costa
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | | | - Diego Costa Carolino
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Renato Lima Senra
- Departamento de Bioquímica Aplicada, Universidade Federal de Viçosa, Viçosa, Brazil
| | - David B. Medeiros
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | - Jorge Gago
- Departament de Biologia, Institute of Agro-Environmental Research and Water Economy – INAGEA, Universitat de les Illes Balears, Palma, Spain
| | - Wagner L. Araújo
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
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29
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Galdon-Armero J, Arce-Rodriguez L, Downie M, Li J, Martin C. A Scanning Electron Micrograph-based Resource for Identification of Loci Involved in Epidermal Development in Tomato: Elucidation of a New Function for the Mixta-like Transcription Factor in Leaves. THE PLANT CELL 2020; 32:1414-1433. [PMID: 32169962 PMCID: PMC7203947 DOI: 10.1105/tpc.20.00127] [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: 02/18/2020] [Accepted: 03/09/2020] [Indexed: 05/21/2023]
Abstract
The aerial epidermis of plants plays a major role in environmental interactions, yet the development of the cellular components of the aerial epidermis-trichomes, stomata, and pavement cells-is still not fully understood. We have performed a detailed screen of the leaf epidermis in two generations of the well-established Solanum lycopersicum cv M82 × Solanum pennellii ac. LA716 introgression line (IL) population using a combination of scanning electron microscopy (SEM) techniques. Quantification of trichome and stomatal densities in the ILs revealed four genomic regions with a consistently low trichome density. This study also found ILs with abnormal proportions of different trichome types and aberrant trichome morphologies. This work has led to the identification of new, unexplored genomic regions with roles in trichome formation in tomato. This study investigated one interval in IL2-6 in more detail and identified a new function for the transcription factor SlMixta-like in determining trichome patterning in leaves. This illustrates how these SEM images, publicly available to the research community, provide an important dataset for further studies on epidermal development in tomato and other species of the Solanaceae family.
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Affiliation(s)
- Javier Galdon-Armero
- Department of Metabolic Biology, John Innes Centre, Norwich, NR4 7UH, United Kingdom
| | - Lisette Arce-Rodriguez
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, 36824 Irapuato, Guanajuato, Mexico
| | - Matthew Downie
- Department of Metabolic Biology, John Innes Centre, Norwich, NR4 7UH, United Kingdom
| | - Jie Li
- Department of Metabolic Biology, John Innes Centre, Norwich, NR4 7UH, United Kingdom
| | - Cathie Martin
- Department of Metabolic Biology, John Innes Centre, Norwich, NR4 7UH, United Kingdom
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Affiliation(s)
- Sebastien Andreuzza
- Assistant Features Editor The Plant CellDBT-Cambridge LecturerDepartment of Plant SciencesUniversity of CambridgeUnited KingdomCenter for Cellular and Molecular BiologyHyderabad, India
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Kuhalskaya A, Wijesingha Ahchige M, Perez de Souza L, Vallarino J, Brotman Y, Alseekh S. Network Analysis Provides Insight into Tomato Lipid Metabolism. Metabolites 2020; 10:metabo10040152. [PMID: 32295308 PMCID: PMC7240963 DOI: 10.3390/metabo10040152] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/26/2020] [Accepted: 04/11/2020] [Indexed: 11/16/2022] Open
Abstract
Metabolic correlation networks have been used in several instances to obtain a deeper insight into the complexity of plant metabolism as a whole. In tomato (Solanum lycopersicum), metabolites have a major influence on taste and overall fruit quality traits. Previously a broad spectrum of metabolic and phenotypic traits has been described using a Solanum pennellii introgression-lines (ILs) population. To obtain insights into tomato fruit metabolism, we performed metabolic network analysis from existing data, covering a wide range of metabolic traits, including lipophilic and volatile compounds, for the first time. We provide a comprehensive fruit correlation network and show how primary, secondary, lipophilic, and volatile compounds connect to each other and how the individual metabolic classes are linked to yield-related phenotypic traits. Results revealed a high connectivity within and between different classes of lipophilic compounds, as well as between lipophilic and secondary metabolites. We focused on lipid metabolism and generated a gene-expression network with lipophilic metabolites to identify new putative lipid-related genes. Metabolite–transcript correlation analysis revealed key putative genes involved in lipid biosynthesis pathways. The overall results will help to deepen our understanding of tomato metabolism and provide candidate genes for transgenic approaches toward improving nutritional qualities in tomato.
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Affiliation(s)
- Anastasiya Kuhalskaya
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (A.K.); (M.W.A.); (L.P.d.S.); (J.V.); (Y.B.)
- Department of Life Sciences, Ben Gurion University of the Negev, 84105 Beersheva, Israel
| | - Micha Wijesingha Ahchige
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (A.K.); (M.W.A.); (L.P.d.S.); (J.V.); (Y.B.)
| | - Leonardo Perez de Souza
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (A.K.); (M.W.A.); (L.P.d.S.); (J.V.); (Y.B.)
| | - José Vallarino
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (A.K.); (M.W.A.); (L.P.d.S.); (J.V.); (Y.B.)
| | - Yariv Brotman
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (A.K.); (M.W.A.); (L.P.d.S.); (J.V.); (Y.B.)
- Department of Life Sciences, Ben Gurion University of the Negev, 84105 Beersheva, Israel
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (A.K.); (M.W.A.); (L.P.d.S.); (J.V.); (Y.B.)
- Centre of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Correspondence: ; Tel.: +49-(0)331-567-8211
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Gupta S, Rosenthal DM, Stinchcombe JR, Baucom RS. The remarkable morphological diversity of leaf shape in sweet potato (Ipomoea batatas): the influence of genetics, environment, and G×E. THE NEW PHYTOLOGIST 2020; 225:2183-2195. [PMID: 31652341 DOI: 10.1111/nph.16286] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/19/2019] [Indexed: 06/10/2023]
Abstract
Leaf shape, a spectacularly diverse plant trait, varies across taxonomic levels, geography and in response to environmental differences. However, comprehensive intraspecific analyses of leaf shape variation across variable environments is surprisingly absent. Here, we performed a multilevel analysis of leaf shape using diverse accessions of sweet potato (Ipomoea batatas), and uncovered the role of genetics, environment, and G×E on this important trait. We examined leaf shape using a variety of morphometric analyses, and complement this with a transcriptomic survey to identify gene expression changes associated with shape variation. Additionally, we examined the role of genetics and environment on leaf shape by performing field studies in two geographically separate common gardens. We showed that extensive leaf shape variation exists within I. batatas, and identified promising candidate genes associated with this variation. Interestingly, when considering traditional measures, we found that genetic factors are largely responsible for most of leaf shape variation, but that the environment is highly influential when using more quantitative measures via leaf outlines. This extensive and multilevel examination of leaf shape shows an important role of genetics underlying a potentially important agronomic trait, and highlights that the environment can be a strong influence when using more quantitative measures of leaf shape.
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Affiliation(s)
- Sonal Gupta
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48105, USA
| | - David M Rosenthal
- Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
| | - Regina S Baucom
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48105, USA
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Pathways to defense metabolites and evading fruit bitterness in genus Solanum evolved through 2-oxoglutarate-dependent dioxygenases. Nat Commun 2019; 10:5169. [PMID: 31727889 PMCID: PMC6856131 DOI: 10.1038/s41467-019-13211-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 10/06/2019] [Indexed: 11/09/2022] Open
Abstract
The genus Solanum comprises three food crops (potato, tomato, and eggplant), which are consumed on daily basis worldwide and also producers of notorious anti-nutritional steroidal glycoalkaloids (SGAs). Hydroxylated SGAs (i.e. leptinines) serve as precursors for leptines that act as defenses against Colorado Potato Beetle (Leptinotarsa decemlineata Say), an important pest of potato worldwide. However, SGA hydroxylating enzymes remain unknown. Here, we discover that 2-OXOGLUTARATE-DEPENDENT-DIOXYGENASE (2-ODD) enzymes catalyze SGA-hydroxylation across various Solanum species. In contrast to cultivated potato, Solanum chacoense, a widespread wild potato species, has evolved a 2-ODD enzyme leading to the formation of leptinines. Furthermore, we find a related 2-ODD in tomato that catalyzes the hydroxylation of the bitter α-tomatine to hydroxytomatine, the first committed step in the chemical shift towards downstream ripening-associated non-bitter SGAs (e.g. esculeoside A). This 2-ODD enzyme prevents bitterness in ripe tomato fruit consumed today which otherwise would remain unpleasant in taste and more toxic. Steroidal glycoalkaloids (SGAs) accumulate in Solanum, but their hydroxylating enzymes are unknown. Here, the authors report 2-OXOGLUTARATE DEPENDENT DIOXYGENASE enzymes that catalyze the committed hydroxylation steps in the biosynthesis of leptinine insecticidal compounds in wild potato or non-bitter SGAs in cultivated tomato.
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Li G, Hu S, Hou H, Kimura S. Heterophylly: Phenotypic Plasticity of Leaf Shape in Aquatic and Amphibious Plants. PLANTS (BASEL, SWITZERLAND) 2019; 8:E420. [PMID: 31623228 PMCID: PMC6843204 DOI: 10.3390/plants8100420] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/11/2019] [Accepted: 10/14/2019] [Indexed: 11/17/2022]
Abstract
Leaves show great diversity in shape, size, and color in nature. Interestingly, many plant species have the ability to alter their leaf shape in response to their surrounding environment. This phenomenon is termed heterophylly, and is thought to be an adaptive feature to environmental heterogeneity in many cases. Heterophylly is widespread among land plants, and is especially dominant in aquatic and amphibious plants. Revealing the mechanisms underlying heterophylly would provide valuable insight into the interaction between environmental conditions and plant development. Here, we review the history and recent progress of research on heterophylly in aquatic and amphibious plants.
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Affiliation(s)
- Gaojie Li
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan 430072, Hubei, China.
| | - Shiqi Hu
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan 430072, Hubei, China.
| | - Hongwei Hou
- The State Key Laboratory of Freshwater Ecology and Biotechnology, The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Wuhan 430072, Hubei, China.
| | - Seisuke Kimura
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto-shi, Kyoto 603-8555, Japan.
- Center for Ecological Evolutionary Developmental Biology, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto-shi, Kyoto 603-8555, Japan.
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35
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D'Esposito D, Cappetta E, Andolfo G, Ferriello F, Borgonuovo C, Caruso G, De Natale A, Frusciante L, Ercolano MR. Deciphering the biological processes underlying tomato biomass production and composition. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 143:50-60. [PMID: 31479882 DOI: 10.1016/j.plaphy.2019.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/19/2019] [Accepted: 08/13/2019] [Indexed: 05/20/2023]
Abstract
The huge amounts of biomass residues, remaining in the field after tomato fruits harvesting, can be utilized to produce bioenergy. A multiple level approach aimed to characterize two Solanum pennellii introgression lines (ILs), with contrasting phenotypes for plant architecture and biomass was carried out. The study of gene expression dynamics, microscopy cell traits and qualitative and quantitative cell wall chemical compounds variation enabled the discovery of key genes and cell processes involved biomass accumulation and composition. Enhanced biomass production observed in IL2-6 line is due to a more effective coordination of chloroplasts and mitochondria energy fluxes. Microscopy analysis revealed a higher number of cells and chloroplasts in leaf epidermis in the high biomass line whilst chemical measurements on the two lines pointed out striking differences in the cell wall composition and organization. Taken together, our findings shed light on the mechanisms underlying the tomato biomass production and processability.
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Affiliation(s)
- Daniela D'Esposito
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Elisa Cappetta
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Giuseppe Andolfo
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Francesca Ferriello
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Camilla Borgonuovo
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Gianluca Caruso
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Antonino De Natale
- Department of Biology, University of Naples 'Federico II', Via Cinthia, Monte Sant'Angelo, Building 7, 80126, Naples, Italy.
| | - Luigi Frusciante
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
| | - Maria Raffaella Ercolano
- Department of Agricultural Sciences, University of Naples 'Federico II', Via Università 100, 80055, Portici, Naples, Italy.
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Nunes-Nesi A, Alseekh S, de Oliveira Silva FM, Omranian N, Lichtenstein G, Mirnezhad M, González RRR, Sabio Y Garcia J, Conte M, Leiss KA, Klinkhamer PGL, Nikoloski Z, Carrari F, Fernie AR. Identification and characterization of metabolite quantitative trait loci in tomato leaves and comparison with those reported for fruits and seeds. Metabolomics 2019; 15:46. [PMID: 30874962 PMCID: PMC6420416 DOI: 10.1007/s11306-019-1503-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 01/12/2019] [Indexed: 01/10/2023]
Abstract
INTRODUCTION To date, most studies of natural variation and metabolite quantitative trait loci (mQTL) in tomato have focused on fruit metabolism, leaving aside the identification of genomic regions involved in the regulation of leaf metabolism. OBJECTIVE This study was conducted to identify leaf mQTL in tomato and to assess the association of leaf metabolites and physiological traits with the metabolite levels from other tissues. METHODS The analysis of components of leaf metabolism was performed by phenotypying 76 tomato ILs with chromosome segments of the wild species Solanum pennellii in the genetic background of a cultivated tomato (S. lycopersicum) variety M82. The plants were cultivated in two different environments in independent years and samples were harvested from mature leaves of non-flowering plants at the middle of the light period. The non-targeted metabolite profiling was obtained by gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). With the data set obtained in this study and already published metabolomics data from seed and fruit, we performed QTL mapping, heritability and correlation analyses. RESULTS Changes in metabolite contents were evident in the ILs that are potentially important with respect to stress responses and plant physiology. By analyzing the obtained data, we identified 42 positive and 76 negative mQTL involved in carbon and nitrogen metabolism. CONCLUSIONS Overall, these findings allowed the identification of S. lycopersicum genome regions involved in the regulation of leaf primary carbon and nitrogen metabolism, as well as the association of leaf metabolites with metabolites from seeds and fruits.
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Affiliation(s)
- Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil.
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Golm, OT, Germany.
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Golm, OT, Germany
- Center of Plant System Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
| | | | - Nooshin Omranian
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Golm, OT, Germany
- Center of Plant System Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
| | - Gabriel Lichtenstein
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaría, Consejo Nacional de Investigaciones Científicas y Técnicas, B1712WAA, Castelar, Argentina
| | - Mohammad Mirnezhad
- Plant Ecology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Roman R Romero González
- Plant Ecology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Julia Sabio Y Garcia
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaría, Consejo Nacional de Investigaciones Científicas y Técnicas, B1712WAA, Castelar, Argentina
| | - Mariana Conte
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaría, Consejo Nacional de Investigaciones Científicas y Técnicas, B1712WAA, Castelar, Argentina
| | - Kirsten A Leiss
- Plant Ecology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
- Business Unit Horticulture, Wageningen University & Research, Postbus 20, 2665 ZG, Bleiswijk, The Netherlands
| | - Peter G L Klinkhamer
- Plant Ecology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands
| | - Zoran Nikoloski
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Golm, OT, Germany
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Fernando Carrari
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaría, Consejo Nacional de Investigaciones Científicas y Técnicas, B1712WAA, Castelar, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Universidad de Buenos Aires, Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
- Facultad de Agronomía, Cátedra de Genética, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Golm, OT, Germany
- Center of Plant System Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
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Balakrishnan D, Surapaneni M, Mesapogu S, Neelamraju S. Development and use of chromosome segment substitution lines as a genetic resource for crop improvement. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1-25. [PMID: 30483819 DOI: 10.1007/s00122-018-3219-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 10/24/2018] [Indexed: 05/27/2023]
Abstract
CSSLs are a complete library of introgression lines with chromosomal segments of usually a distant genotype in an adapted background and are valuable genetic resources for basic and applied research on improvement of complex traits. Chromosome segment substitution lines (CSSLs) are genetic stocks representing the complete genome of any genotype in the background of a cultivar as overlapping segments. Ideally, each CSSL has a single chromosome segment from the donor with a maximum recurrent parent genome recovered in the background. CSSL development program requires population-wide backcross breeding and genome-wide marker-assisted selection followed by selfing. Each line in a CSSL library has a specific marker-defined large donor segment. CSSLs are evaluated for any target phenotype to identify lines significantly different from the parental line. These CSSLs are then used to map quantitative trait loci (QTLs) or causal genes. CSSLs are valuable prebreeding tools for broadening the genetic base of existing cultivars and harnessing the genetic diversity from the wild- and distant-related species. These are resources for genetic map construction, mapping QTLs, genes or gene interactions and their functional analysis for crop improvement. In the last two decades, the utility of CSSLs in identification of novel genomic regions and QTL hot spots influencing a wide range of traits has been well demonstrated in food and commercial crops. This review presents an overview of how CSSLs are developed, their status in major crops and their use in genomic studies and gene discovery.
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Affiliation(s)
- Divya Balakrishnan
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Malathi Surapaneni
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Sukumar Mesapogu
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Sarla Neelamraju
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India.
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Abstract
Regulation of plant root angle is critical for obtaining nutrients and water and is an important trait for plant breeding. A plant’s final, long-term root angle is the net result of a complex series of decisions made by a root tip in response to changes in nutrient availability, impediments, the gravity vector and other stimuli. When a root tip is displaced from the gravity vector, the short-term process of gravitropism results in rapid reorientation of the root toward the vertical. Here, we explore both short- and long-term regulation of root growth angle, using natural variation in tomato to identify shared and separate genetic features of the two responses. Mapping of expression quantitative trait loci mapping and leveraging natural variation between and within species including Arabidopsis suggest a role for PURPLE ACID PHOSPHATASE 27 and CELL DIVISION CYCLE 73 in determining root angle.
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Hu L, Zhang H, Yang Q, Meng Q, Han S, Nwafor CC, Khan MHU, Fan C, Zhou Y. Promoter variations in a homeobox gene, BnA10.LMI1, determine lobed leaves in rapeseed (Brassica napus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2699-2708. [PMID: 30219987 DOI: 10.1007/s00122-018-3184-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 09/07/2018] [Indexed: 05/22/2023]
Abstract
BnA10.LMI1 positively regulates the development of leaf lobes in Brassica napus, and cis-regulatory divergences cause the different allele effects. Leaf shape is an important agronomic trait, and large variations in this trait exist within the Brassica germplasm. The lobed leaf is a unique morphological characteristic for Brassica improvement. Nevertheless, the molecular basis of leaf lobing in Brassica is poorly understood. Here, we show that an incompletely dominant locus, BnLLA10, is responsible for the lobed-leaf shape in rapeseed. A LATE MERISTEM IDENTITY1 (LMI1)-like gene (BnA10.LMI1) encoding an HD-Zip I transcription factor is the causal gene underlying the BnLLA10 locus. Sequence analysis of parental alleles revealed no sequence variations in the coding sequences, whereas abundant variations were identified in the regulatory region. Consistent with this finding, the expression levels of BnLMI1 were substantially elevated in the lobed-leaf parent compared with its near-isogenic line. The knockout mutations of BnA10.LMI1 gene were induced using the CRISPR/Cas9 system in both HY (the lobed-leaf parent) and J9707 (serrated leaf) genetic backgrounds. BnA10.LMI1 null mutations in the HY background were sufficient to produce unlobed leaves, whereas null mutations in the J9707 background showed no obvious changes in leaf shape compared with the control. Collectively, our results indicate that BnA10.LMI1 positively regulates the development of leaf lobes in B. napus, with cis-regulatory divergences causing the different allelic effects, providing new insights into the molecular mechanism of leaf lobe formation in Brassica crops.
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Affiliation(s)
- Limin Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hao Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qingyong Yang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Qingwei Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shaoqing Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chinedu Charles Nwafor
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Muhammad Hafeez Ullah Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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40
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Koyama T. A hidden link between leaf development and senescence. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 276:105-110. [PMID: 30348308 DOI: 10.1016/j.plantsci.2018.08.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/04/2018] [Accepted: 08/13/2018] [Indexed: 05/21/2023]
Abstract
Leaf senescence is the final step of leaf development and is usually accompanied by visible color changes from green to yellow or brown. Unlike the senescence of the whole body of animals and unicellular organisms, which is often associated with death, leaf senescence in plants requires highly integrative processes towards cell death with nutrient recycling and storage. Since leaf senescence plays pivotal roles in the production of plant biomass and grain yield, the mechanisms of degradation and relocation of macromolecules as well as the regulation of signaling and biosynthetic pathways have received much attention. The importance of the plant hormone ethylene in the onset of leaf senescence has been clearly documented. However, research has increasingly demonstrated that the function of ethylene in the regulation of leaf senescence is dependent on leaf development. This review raises the issue of how ethylene requires developmental regulators and focuses on the developmental aspect of leaf senescence. It also emphasizes the remarkable impact that developmental regulators have on regulating the onset of leaf senescence.
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Affiliation(s)
- Tomotsugu Koyama
- Bioorganic Research Institute Suntory Foundation for Life Sciences, Japan.
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41
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Galdon‐Armero J, Fullana‐Pericas M, Mulet PA, Conesa MA, Martin C, Galmes J. The ratio of trichomes to stomata is associated with water use efficiency in Solanum lycopersicum (tomato). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:607-619. [PMID: 30066411 PMCID: PMC6321981 DOI: 10.1111/tpj.14055] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 07/03/2018] [Accepted: 07/10/2018] [Indexed: 05/20/2023]
Abstract
Trichomes are specialised structures that originate from the aerial epidermis of plants, and play key roles in the interaction between the plant and the environment. In this study we investigated the trichome phenotypes of four lines selected from the Solanum lycopersicum × Solanum pennellii introgression line (IL) population for differences in trichome density, and their impact on plant performance under water-deficit conditions. We performed comparative analyses at morphological and photosynthetic levels of plants grown under well-watered (WW) and also under water-deficit (WD) conditions in the field. Under WD conditions, we observed higher trichome density in ILs 11-3 and 4-1, and lower stomatal size in IL 4-1 compared with plants grown under WW conditions. The intrinsic water use efficiency (WUEi ) was higher under WD conditions in IL 11-3, and the plant-level water use efficiency (WUEb ) was also higher in IL 11-3 and in M82 for WD plants. The ratio of trichomes to stomata (T/S) was positively correlated with WUEi and WUEb , indicating an important role for both trichomes and stomata in drought tolerance in tomato, and offering a promising way to select for improved water use efficiency of major crops.
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Affiliation(s)
| | - Mateu Fullana‐Pericas
- Research Group on Plant Biology under Mediterranean Conditions – INAGEAUniversitat de les Illes BalearsCarretera de Valldemossa km 7.507122PalmaSpain
| | - Pere A. Mulet
- Research Group on Plant Biology under Mediterranean Conditions – INAGEAUniversitat de les Illes BalearsCarretera de Valldemossa km 7.507122PalmaSpain
| | - Miquel A. Conesa
- Research Group on Plant Biology under Mediterranean Conditions – INAGEAUniversitat de les Illes BalearsCarretera de Valldemossa km 7.507122PalmaSpain
| | - Cathie Martin
- Department of Metabolic BiologyJohn Innes CentreColney LaneNorwichNR4 7UHUK
| | - Jeroni Galmes
- Research Group on Plant Biology under Mediterranean Conditions – INAGEAUniversitat de les Illes BalearsCarretera de Valldemossa km 7.507122PalmaSpain
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42
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Fritz MA, Rosa S, Sicard A. Mechanisms Underlying the Environmentally Induced Plasticity of Leaf Morphology. Front Genet 2018; 9:478. [PMID: 30405690 PMCID: PMC6207588 DOI: 10.3389/fgene.2018.00478] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/26/2018] [Indexed: 01/23/2023] Open
Abstract
The primary function of leaves is to provide an interface between plants and their environment for gas exchange, light exposure and thermoregulation. Leaves have, therefore a central contribution to plant fitness by allowing an efficient absorption of sunlight energy through photosynthesis to ensure an optimal growth. Their final geometry will result from a balance between the need to maximize energy uptake while minimizing the damage caused by environmental stresses. This intimate relationship between leaf and its surroundings has led to an enormous diversification in leaf forms. Leaf shape varies between species, populations, individuals or even within identical genotypes when those are subjected to different environmental conditions. For instance, the extent of leaf margin dissection has, for long, been found to inversely correlate with the mean annual temperature, such that Paleobotanists have used models based on leaf shape to predict the paleoclimate from fossil flora. Leaf growth is not only dependent on temperature but is also regulated by many other environmental factors such as light quality and intensity or ambient humidity. This raises the question of how the different signals can be integrated at the molecular level and converted into clear developmental decisions. Several recent studies have started to shed the light on the molecular mechanisms that connect the environmental sensing with organ-growth and patterning. In this review, we discuss the current knowledge on the influence of different environmental signals on leaf size and shape, their integration as well as their importance for plant adaptation.
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Affiliation(s)
| | - Stefanie Rosa
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Adrien Sicard
- Institut für Biochemie und Biologie, Universität Potsdam, Potsdam, Germany
- Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
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43
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Garbowicz K, Liu Z, Alseekh S, Tieman D, Taylor M, Kuhalskaya A, Ofner I, Zamir D, Klee HJ, Fernie AR, Brotman Y. Quantitative Trait Loci Analysis Identifies a Prominent Gene Involved in the Production of Fatty Acid-Derived Flavor Volatiles in Tomato. MOLECULAR PLANT 2018; 11:1147-1165. [PMID: 29960108 DOI: 10.1016/j.molp.2018.06.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/12/2018] [Accepted: 06/13/2018] [Indexed: 06/08/2023]
Abstract
To gain insight into the genetic regulation of lipid metabolism in tomato, we conducted metabolic trait loci (mQTL) analysis following the lipidomic profiling of fruit pericarp and leaf tissue of the Solanum pennellii introgression lines (IL). To enhance mapping resolution for selected fruit-specific mQTL, we profiled the lipids in a subset of independently derived S. pennellii backcross inbred lines, as well as in a near-isogenic sub-IL population. We identified a putative lecithin:cholesterol acyltransferase that controls the levels of several lipids, and two members of the class III lipase family, LIP1 and LIP2, that were associated with decreased levels of diacylglycerols (DAGs) and triacylglycerols (TAGs). Lipases of this class cleave fatty acids from the glycerol backbone of acylglycerols. The released fatty acids serve as precursors of flavor volatiles. We show that LIP1 expression correlates with fatty acid-derived volatile levels. We further confirm the function of LIP1 in TAG and DAG breakdown and volatile synthesis using transgenic plants. Taken together, our study extensively characterized the genetic architecture of lipophilic compounds in tomato and demonstrated at molecular level that release of free fatty acids from the glycerol backbone can have a major impact on downstream volatile synthesis.
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Affiliation(s)
- Karolina Garbowicz
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Zhongyuan Liu
- Horticultural Sciences, Plant Innovation Center, University of Florida, Gainesville, FL, USA
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany; Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Denise Tieman
- Horticultural Sciences, Plant Innovation Center, University of Florida, Gainesville, FL, USA
| | - Mark Taylor
- Horticultural Sciences, Plant Innovation Center, University of Florida, Gainesville, FL, USA
| | | | - Itai Ofner
- Robert H. Smith Institute of Plant Sciences and Genetics, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Dani Zamir
- Robert H. Smith Institute of Plant Sciences and Genetics, Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Harry J Klee
- Horticultural Sciences, Plant Innovation Center, University of Florida, Gainesville, FL, USA
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany; Center of Plant System Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Yariv Brotman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beersheba, Israel.
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44
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Li M, Frank MH, Coneva V, Mio W, Chitwood DH, Topp CN. The Persistent Homology Mathematical Framework Provides Enhanced Genotype-to-Phenotype Associations for Plant Morphology. PLANT PHYSIOLOGY 2018; 177:1382-1395. [PMID: 29871979 PMCID: PMC6084663 DOI: 10.1104/pp.18.00104] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/21/2018] [Indexed: 05/21/2023]
Abstract
Efforts to understand the genetic and environmental conditioning of plant morphology are hindered by the lack of flexible and effective tools for quantifying morphology. Here, we demonstrate that persistent-homology-based topological methods can improve measurement of variation in leaf shape, serrations, and root architecture. We apply these methods to 2D images of leaves and root systems in field-grown plants of a domesticated introgression line population of tomato (Solanum pennellii). We find that compared with some commonly used conventional traits, (1) persistent-homology-based methods can more comprehensively capture morphological variation; (2) these techniques discriminate between genotypes with a larger normalized effect size and detect a greater number of unique quantitative trait loci (QTLs); (3) multivariate traits, whether statistically derived from univariate or persistent-homology-based traits, improve our ability to understand the genetic basis of phenotype; and (4) persistent-homology-based techniques detect unique QTLs compared to conventional traits or their multivariate derivatives, indicating that previously unmeasured aspects of morphology are now detectable. The QTL results further imply that genetic contributions to morphology can affect both the shoot and root, revealing a pleiotropic basis to natural variation in tomato. Persistent homology is a versatile framework to quantify plant morphology and developmental processes that complements and extends existing methods.
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Affiliation(s)
- Mao Li
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | | | | | - Washington Mio
- Department of Mathematics, Florida State University, Tallahassee, Florida 32306
| | - Daniel H Chitwood
- Independent Scientist, Santa Rosa, California 95409
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, Michigan 48824
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45
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Maugarny-Calès A, Laufs P. Getting leaves into shape: a molecular, cellular, environmental and evolutionary view. Development 2018; 145:145/13/dev161646. [PMID: 29991476 DOI: 10.1242/dev.161646] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Leaves arise from groups of undifferentiated cells as small primordia that go through overlapping phases of morphogenesis, growth and differentiation. These phases are genetically controlled and modulated by environmental cues to generate a stereotyped, yet plastic, mature organ. Over the past couple of decades, studies have revealed that hormonal signals, transcription factors and miRNAs play major roles during leaf development, and more recent findings have highlighted the contribution of mechanical signals to leaf growth. In this Review, we discuss how modulating the activity of some of these regulators can generate diverse leaf shapes during development, in response to a varying environment, or between species during evolution.
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Affiliation(s)
- Aude Maugarny-Calès
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France.,Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
| | - Patrick Laufs
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France
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46
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Zaynab M, Fatima M, Abbas S, Umair M, Sharif Y, Raza MA. Long non-coding RNAs as molecular players in plant defense against pathogens. Microb Pathog 2018; 121:277-282. [PMID: 29859899 DOI: 10.1016/j.micpath.2018.05.050] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/21/2018] [Accepted: 05/29/2018] [Indexed: 12/20/2022]
Abstract
Long non-coding RNAs (lncRNAs) has significant role in of gene expression and silencing pathways for several biological processes in eukaryotes. lncRNAs has been reported as key player in remodeling chromatin and genome architecture, RNA stabilization and transcription regulation, including enhancer-associated activity. Host lncRNAs are reckoned as compulsory elements of plant defense. In response to pathogen attack, plants protect themselves with the help of lncRNAs -dependent immune systems in which lncRNAs regulate pathogen-associated molecular patterns (PAMPs) and other effectors. Role of lncRNAs in plant microbe interaction has been studied extensively but regulations of several lncRNAs still need extensive research. In this study we discussed and provide as overview the topical advancements and findings relevant to pathogen attack and plant defense mediated by lncRNAs. It is hoped that lncRNAs would be exploited as a mainstream player to achieve food security by tackling different plant diseases.
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Affiliation(s)
- Madiha Zaynab
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China.
| | - Mahpara Fatima
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China
| | - Safdar Abbas
- Department of Biochemistry, Quaid-i-Azam University Islamabad, Pakistan
| | - Muhammad Umair
- Department of Biochemistry, Quaid-i-Azam University Islamabad, Pakistan
| | - Yasir Sharif
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, PR China
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47
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Fu G, Huang M, Bo W, Hao H, Wu R. Mapping morphological shape as a high-dimensional functional curve. Brief Bioinform 2018; 19:461-471. [PMID: 28062411 PMCID: PMC5952977 DOI: 10.1093/bib/bbw111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Detecting how genes regulate biological shape has become a multidisciplinary research interest because of its wide application in many disciplines. Despite its fundamental importance, the challenges of accurately extracting information from an image, statistically modeling the high-dimensional shape and meticulously locating shape quantitative trait loci (QTL) affect the progress of this research. In this article, we propose a novel integrated framework that incorporates shape analysis, statistical curve modeling and genetic mapping to detect significant QTLs regulating variation of biological shape traits. After quantifying morphological shape via a radius centroid contour approach, each shape, as a phenotype, was characterized as a high-dimensional curve, varying as angle θ runs clockwise with the first point starting from angle zero. We then modeled the dynamic trajectories of three mean curves and variation patterns as functions of θ. Our framework led to the detection of a few significant QTLs regulating the variation of leaf shape collected from a natural population of poplar, Populus szechuanica var tibetica. This population, distributed at altitudes 2000-4500 m above sea level, is an evolutionarily important plant species. This is the first work in the quantitative genetic shape mapping area that emphasizes a sense of 'function' instead of decomposing the shape into a few discrete principal components, as the majority of shape studies do.
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Affiliation(s)
- Guifang Fu
- Department of Math and Statistics, Utah State University, Logan, Utah, USA
| | - Mian Huang
- Data Engineering Center, Shanghai University of Finance and Economics, Shanghai, China
| | - Wenhao Bo
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Han Hao
- Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA
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48
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Li M, An H, Angelovici R, Bagaza C, Batushansky A, Clark L, Coneva V, Donoghue MJ, Edwards E, Fajardo D, Fang H, Frank MH, Gallaher T, Gebken S, Hill T, Jansky S, Kaur B, Klahs PC, Klein LL, Kuraparthy V, Londo J, Migicovsky Z, Miller A, Mohn R, Myles S, Otoni WC, Pires JC, Rieffer E, Schmerler S, Spriggs E, Topp CN, Van Deynze A, Zhang K, Zhu L, Zink BM, Chitwood DH. Topological Data Analysis as a Morphometric Method: Using Persistent Homology to Demarcate a Leaf Morphospace. FRONTIERS IN PLANT SCIENCE 2018; 9:553. [PMID: 29922307 PMCID: PMC5996898 DOI: 10.3389/fpls.2018.00553] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 04/09/2018] [Indexed: 05/18/2023]
Abstract
Current morphometric methods that comprehensively measure shape cannot compare the disparate leaf shapes found in seed plants and are sensitive to processing artifacts. We explore the use of persistent homology, a topological method applied as a filtration across simplicial complexes (or more simply, a method to measure topological features of spaces across different spatial resolutions), to overcome these limitations. The described method isolates subsets of shape features and measures the spatial relationship of neighboring pixel densities in a shape. We apply the method to the analysis of 182,707 leaves, both published and unpublished, representing 141 plant families collected from 75 sites throughout the world. By measuring leaves from throughout the seed plants using persistent homology, a defined morphospace comparing all leaves is demarcated. Clear differences in shape between major phylogenetic groups are detected and estimates of leaf shape diversity within plant families are made. The approach predicts plant family above chance. The application of a persistent homology method, using topological features, to measure leaf shape allows for a unified morphometric framework to measure plant form, including shapes, textures, patterns, and branching architectures.
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Affiliation(s)
- Mao Li
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Hong An
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Ruthie Angelovici
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Clement Bagaza
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Albert Batushansky
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Lynn Clark
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Viktoriya Coneva
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Michael J. Donoghue
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Erika Edwards
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, United States
| | - Diego Fajardo
- National Center for Genome Resources (NCGR), Santa Fe, NM, United States
| | - Hui Fang
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | | | - Timothy Gallaher
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Sarah Gebken
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Theresa Hill
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Shelley Jansky
- Vegetable Crops Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, United States
| | - Baljinder Kaur
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | - Phillip C. Klahs
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Laura L. Klein
- Department of Biology, Saint Louis University, St. Louis, MO, United States
| | - Vasu Kuraparthy
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | - Jason Londo
- Grape Genetics Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Geneva, NY, United States
| | - Zoë Migicovsky
- Department of Plant, Food, and Environmental Sciences, Dalhousie University, Truro, NS, Canada
| | - Allison Miller
- Department of Biology, Saint Louis University, St. Louis, MO, United States
| | - Rebekah Mohn
- Department of Plant and Microbial Biology, University of Minnesota – Twin Cities, St. Paul, MN, United States
| | - Sean Myles
- Department of Plant, Food, and Environmental Sciences, Dalhousie University, Truro, NS, Canada
| | - Wagner C. Otoni
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
| | - J. C. Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Edmond Rieffer
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Sam Schmerler
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, United States
- American Museum of Natural History, New York, NY, United States
| | - Elizabeth Spriggs
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | | | - Allen Van Deynze
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Kuang Zhang
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | - Linglong Zhu
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | - Braden M. Zink
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Daniel H. Chitwood
- Independent Researcher, Santa Rosa, CA, United States
- Department of Horticulture, Michigan State University, East Lansing, MI, United States
- Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, United States
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49
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Gouil Q, Baulcombe DC. Paramutation-like features of multiple natural epialleles in tomato. BMC Genomics 2018; 19:203. [PMID: 29554868 PMCID: PMC5859443 DOI: 10.1186/s12864-018-4590-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 03/09/2018] [Indexed: 12/05/2022] Open
Abstract
Background Freakish and rare or the tip of the iceberg? Both phrases have been used to refer to paramutation, an epigenetic drive that contravenes Mendel’s first law of segregation. Although its underlying mechanisms are beginning to unravel, its understanding relies only on a few examples that may involve transgenes or artificially generated epialleles. Results By using DNA methylation of introgression lines as an indication of past paramutation, we reveal that the paramutation-like properties of the H06 locus in hybrids of Solanum lycopersicum and a range of tomato relatives and cultivars depend on the timing of sRNA production and conform to an RNA-directed mechanism. In addition, by scanning the methylomes of tomato introgression lines for shared regions of differential methylation that are absent in the S. lycopersicum parent, we identify thousands of candidate regions for paramutation-like behaviour. The methylation patterns for a subset of these regions segregate with non Mendelian ratios, consistent with secondary paramutation-like interactions to variable extents depending on the locus. Conclusion Together these results demonstrate that paramutation-like epigenetic interactions are common for natural epialleles in tomato, but vary in timing and penetrance. Electronic supplementary material The online version of this article (10.1186/s12864-018-4590-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Quentin Gouil
- Present address: Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Australia. .,Department of Plant Sciences, University of Cambridge, Downing Site, Cambridge, CB2 3EA, UK.
| | - David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Downing Site, Cambridge, CB2 3EA, UK.
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50
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Coneva V, Chitwood DH. Genetic and Developmental Basis for Increased Leaf Thickness in the Arabidopsis Cvi Ecotype. FRONTIERS IN PLANT SCIENCE 2018; 9:322. [PMID: 29593772 PMCID: PMC5861201 DOI: 10.3389/fpls.2018.00322] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 02/27/2018] [Indexed: 05/16/2023]
Abstract
Leaf thickness is a quantitative trait that is associated with the ability of plants to occupy dry, high irradiance environments. Despite its importance, leaf thickness has been difficult to measure reproducibly, which has impeded progress in understanding its genetic basis, and the associated anatomical mechanisms that pattern it. Here, we used a custom-built dual confocal profilometer device to measure leaf thickness in the Arabidopsis Ler × Cvi recombinant inbred line population and found statistical support for four quantitative trait loci (QTL) associated with this trait. We used publically available data for a suite of traits relating to flowering time and growth responses to light quality and show that three of the four leaf thickness QTL coincide with QTL for at least one of these traits. Using time course photography, we quantified the relative growth rate and the pace of rosette leaf initiation in the Ler and Cvi ecotypes. We found that Cvi rosettes grow slower than Ler, both in terms of the rate of leaf initiation and the overall rate of biomass accumulation. Collectively, these data suggest that leaf thickness is tightly linked with physiological status and may present a tradeoff between the ability to withstand stress and rapid vegetative growth. To understand the anatomical basis of leaf thickness, we compared cross-sections of Cvi and Ler leaves and show that Cvi palisade mesophyll cells elongate anisotropically contributing to leaf thickness. Flow cytometry of whole leaves show that endopolyploidy accompanies thicker leaves in Cvi. Overall, our data suggest that mechanistically, an altered schedule of cellular events affecting endopolyploidy and increasing palisade mesophyll cell length contribute to increase of leaf thickness in Cvi. Ultimately, knowledge of the genetic basis and developmental trajectory leaf thickness will inform the mechanisms by which natural selection acts to produce variation in this adaptive trait.
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