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Lopes JML, Nascimento LSDQ, Souza VC, de Matos EM, Fortini EA, Grazul RM, Santos MO, Soltis DE, Soltis PS, Otoni WC, Viccini LF. Water stress modulates terpene biosynthesis and morphophysiology at different ploidal levels in Lippia alba (Mill.) N. E. Brown (Verbenaceae). PROTOPLASMA 2024; 261:227-243. [PMID: 37665420 DOI: 10.1007/s00709-023-01890-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 08/18/2023] [Indexed: 09/05/2023]
Abstract
Monoterpenes are the main component in essential oils of Lippia alba. In this species, the chemical composition of essential oils varies with genome size: citral (geraniol and neral) is dominant in diploids and tetraploids, and linalool in triploids. Because environmental stress impacts various metabolic pathways, we hypothesized that stress responses in L. alba could alter the relationship between genome size and essential oil composition. Water stress affects the flowering, production, and reproduction of plants. Here, we evaluated the effect of water stress on morphophysiology, essential oil production, and the expression of genes related to monoterpene synthesis in diploid, triploid, and tetraploid accessions of L. alba cultivated in vitro for 40 days. First, using transcriptome data, we performed de novo gene assembly and identified orthologous genes using phylogenetic and clustering-based approaches. The expression of candidate genes related to terpene biosynthesis was estimated by real-time quantitative PCR. Next, we assessed the expression of these genes under water stress conditions, whereby 1% PEG-4000 was added to MS medium. Water stress modulated L. alba morphophysiology at all ploidal levels. Gene expression and essential oil production were affected in triploid accessions. Polyploid accessions showed greater growth and metabolic tolerance under stress compared to diploids. These results confirm the complex regulation of metabolic pathways such as the production of essential oils in polyploid genomes. In addition, they highlight aspects of genotype and environment interactions, which may be important for the conservation of tropical biodiversity.
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Affiliation(s)
- Juliana Mainenti Leal Lopes
- Department of Biology, Insitute of Biological Science, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
- School of Life Science and Environment, Department of Genetic and Biotechnology, University of Trás-Os-Montes and Alto Douro, 5001-801, Vila Real, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1649-004, Lisbon, Portugal
| | | | - Vinicius Carius Souza
- Department of Biology, Insitute of Biological Science, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Elyabe Monteiro de Matos
- Department of Biology, Insitute of Biological Science, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Evandro Alexandre Fortini
- Laboratory of Plant Tissue Culture (LCTII), Department of Plant Biology/BIOAGRO, Universidade Federal de Viçosa, Av. P.H. Rolfs S/N, Campus Universitário, Viçosa, MG, 36570-000, Brazil
| | | | - Marcelo Oliveira Santos
- Department of Biology, Insitute of Biological Science, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Wagner Campos Otoni
- Laboratory of Plant Tissue Culture (LCTII), Department of Plant Biology/BIOAGRO, Universidade Federal de Viçosa, Av. P.H. Rolfs S/N, Campus Universitário, Viçosa, MG, 36570-000, Brazil
| | - Lyderson Facio Viccini
- Department of Biology, Insitute of Biological Science, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, 36036-900, Brazil.
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Perrella G, Fasano C, Donald NA, Daddiego L, Fang W, Martignago D, Carr C, Conti L, Herzyk P, Amtmann A. Histone Deacetylase Complex 1 and histone 1 epigenetically moderate stress responsiveness of Arabidopsis thaliana seedlings. THE NEW PHYTOLOGIST 2024; 241:166-179. [PMID: 37565540 PMCID: PMC10953426 DOI: 10.1111/nph.19165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/05/2023] [Indexed: 08/12/2023]
Abstract
Early responses of plants to environmental stress factors prevent damage but can delay growth and development in fluctuating conditions. Optimising these trade-offs requires tunability of plant responsiveness to environmental signals. We have previously reported that Histone Deacetylase Complex 1 (HDC1), which interacts with multiple proteins in histone deacetylation complexes, regulates the stress responsiveness of Arabidopsis seedlings, but the underlying mechanism remained elusive. Here, we show that HDC1 attenuates transcriptome re-programming in salt-treated seedlings, and we identify two genes (LEA and MAF5) that inhibit seedling establishment under salt stress downstream of HDC1. HDC1 attenuates their transcriptional induction by salt via a dual mechanism involving H3K9/14 deacetylation and H3K27 trimethylation. The latter, but not the former, was also abolished in a triple knockout mutant of the linker histone H1, which partially mimics the hypersensitivity of the hdc1-1 mutant to salt stress. Although stress-induced H3K27me3 accumulation required both H1 and HDC1, it was not fully recovered by complementing hdc1-1 with a truncated, H1-binding competent HDC1 suggesting other players or independent inputs. The combined findings reveal a dual brake function of HDC1 via regulating both active and repressive epigenetic marks on stress-inducible genes. This natural 'anti-panic' device offers a molecular leaver to tune stress responsiveness in plants.
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Affiliation(s)
- Giorgio Perrella
- Department of BiosciencesUniversità degli Studi di MilanoVia Celoria 26Milan20133Italy
- Plant Science GroupSchool of Molecular Biosciences (SMB), University of GlasgowGlasgowG12 8QQUK
| | - Carlo Fasano
- Italian National Agency for New Technologies, Energy and Sustainable Economic DevelopmentTrisaia Research CentreRotondella (Matera)75026Italy
| | - Naomi A. Donald
- Plant Science GroupSchool of Molecular Biosciences (SMB), University of GlasgowGlasgowG12 8QQUK
| | - Loretta Daddiego
- Italian National Agency for New Technologies, Energy and Sustainable Economic DevelopmentTrisaia Research CentreRotondella (Matera)75026Italy
| | - Weiwei Fang
- Department of BiosciencesUniversità degli Studi di MilanoVia Celoria 26Milan20133Italy
| | - Damiano Martignago
- Department of BiosciencesUniversità degli Studi di MilanoVia Celoria 26Milan20133Italy
| | - Craig Carr
- Plant Science GroupSchool of Molecular Biosciences (SMB), University of GlasgowGlasgowG12 8QQUK
| | - Lucio Conti
- Department of BiosciencesUniversità degli Studi di MilanoVia Celoria 26Milan20133Italy
| | - Pawel Herzyk
- Plant Science GroupSchool of Molecular Biosciences (SMB), University of GlasgowGlasgowG12 8QQUK
- Glasgow Polyomics, Wolfson Wohl Cancer Research CentreUniversity of GlasgowGlasgowG61 1QHUK
| | - Anna Amtmann
- Plant Science GroupSchool of Molecular Biosciences (SMB), University of GlasgowGlasgowG12 8QQUK
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Vazquez‐Vilar M, Fernandez‐del‐Carmen A, Garcia‐Carpintero V, Drapal M, Presa S, Ricci D, Diretto G, Rambla JL, Fernandez‐Muñoz R, Espinosa‐Ruiz A, Fraser PD, Martin C, Granell A, Orzaez D. Dually biofortified cisgenic tomatoes with increased flavonoids and branched-chain amino acids content. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2683-2697. [PMID: 37749961 PMCID: PMC10651156 DOI: 10.1111/pbi.14163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 08/02/2023] [Accepted: 08/07/2023] [Indexed: 09/27/2023]
Abstract
Higher dietary intakes of flavonoids may have a beneficial role in cardiovascular disease prevention. Additionally, supplementation of branched-chain amino acids (BCAAs) in vegan diets can reduce risks associated to their deficiency, particularly in older adults, which can cause loss of skeletal muscle strength and mass. Most plant-derived foods contain only small amounts of BCAAs, and those plants with high levels of flavonoids are not eaten broadly. Here we describe the generation of metabolically engineered cisgenic tomatoes enriched in both flavonoids and BCAAs. In this approach, coding and regulatory DNA elements, all derived from the tomato genome, were combined to obtain a herbicide-resistant version of an acetolactate synthase (mSlALS) gene expressed broadly and a MYB12-like transcription factor (SlMYB12) expressed in a fruit-specific manner. The mSlALS played a dual role, as a selectable marker as well as being key enzyme in BCAA enrichment. The resulting cisgenic tomatoes were highly enriched in Leucine (21-fold compared to wild-type levels), Valine (ninefold) and Isoleucine (threefold) and concomitantly biofortified in several antioxidant flavonoids including kaempferol (64-fold) and quercetin (45-fold). Comprehensive metabolomic and transcriptomic analysis of the biofortified cisgenic tomatoes revealed marked differences to wild type and could serve to evaluate the safety of these biofortified fruits for human consumption.
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Affiliation(s)
- Marta Vazquez‐Vilar
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones CientíficasUniversitat Politècnica de ValénciaValenciaSpain
| | - Asun Fernandez‐del‐Carmen
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones CientíficasUniversitat Politècnica de ValénciaValenciaSpain
| | - Victor Garcia‐Carpintero
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones CientíficasUniversitat Politècnica de ValénciaValenciaSpain
| | | | - Silvia Presa
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones CientíficasUniversitat Politècnica de ValénciaValenciaSpain
| | - Dorotea Ricci
- Biotechnology LaboratoryItalian Agency for New Technologies, Energy and Sustainable Development (ENEA)RomeItaly
| | - Gianfranco Diretto
- Biotechnology LaboratoryItalian Agency for New Technologies, Energy and Sustainable Development (ENEA)RomeItaly
| | - José Luis Rambla
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones CientíficasUniversitat Politècnica de ValénciaValenciaSpain
- Department of Biology, Biochemistry and Natural SciencesUniversitat Jaume ICastellón de la PlanaSpain
| | - Rafael Fernandez‐Muñoz
- Departamento de Mejora Genética y Biotecnología, Estación Experimental La Mayora, Instituto de Hortofruticultura Subtropical y Mediterránea La MayoraUniversidad de Málaga‐Consejo Superior de Investigaciones CientíficasMálagaSpain
| | - Ana Espinosa‐Ruiz
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones CientíficasUniversitat Politècnica de ValénciaValenciaSpain
| | | | | | - Antonio Granell
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones CientíficasUniversitat Politècnica de ValénciaValenciaSpain
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones CientíficasUniversitat Politècnica de ValénciaValenciaSpain
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Guo H, Zhang G, Zhou M, Wan M, Zhu B, Yang Z, Zeng D, Zeng Z. Whole genome doubling-induced the enrichment of H3K27me3 in genes carrying specific TEs in Aegilops tauschii. Front Genet 2023; 14:1241201. [PMID: 37560386 PMCID: PMC10407559 DOI: 10.3389/fgene.2023.1241201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/17/2023] [Indexed: 08/11/2023] Open
Abstract
Polyploidization plays important roles in the evolution and breeding of the common wheat. Aegilops tauschii, the D-genome progenitor of the common wheat, provides a valuable pool of resistance genes to multiple diseases. Extensive studies focus on the exploration of these genes for wheat improvement. However, few studies have unveiled alternations on genome-wide expression pattern and histone modifications induced by whole-genome doubling (WGD) process. In this study, we conducted transcriptome analysis for the diploid and tetraploid Ae. taushcii lines using the leaf and root tissues. Both lines tend to display similar tissue-specific pattern. Interestingly, we found that TEs located in genic regions were depleted of the repressive histone mark H3K27me3, whereas their adjacent chromatin was enriched with H3K27me3. The tetraploid line exhibited higher levels of H3K27me3 in those regions than the diploid line, particularly for genic regions associated with TEs of the long interspersed nuclear elements (LINEs), CACTA, PIF/Harbinger, Tc1/Mariner and unclassed DNA transposon. Surprisingly, the expression levels of these TEs cognate genes were negatively associated with the levels of H3K27me3 between the tetraploid and diploid lines, suggesting the five types of TEs located within genic regions might be involved in the regulation of the ploidy-related gene expression, possibly through differential enrichment of H3K27me3 in the genic regions. These findings will help to understand the potential role of specific types of TEs on transcription in response to WGD.
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Affiliation(s)
- Hongwei Guo
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, China
| | - Guoyan Zhang
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, China
- Horticulture Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Min Zhou
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, China
| | - Min Wan
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, China
| | - Bo Zhu
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, China
- Plant Functional Genomics and Bioinformatics Research Center, Sichuan Normal University, Chengdu, Sichuan, China
| | - Zujun Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Deying Zeng
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, China
- Plant Functional Genomics and Bioinformatics Research Center, Sichuan Normal University, Chengdu, Sichuan, China
| | - Zixian Zeng
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu, Sichuan, China
- Plant Functional Genomics and Bioinformatics Research Center, Sichuan Normal University, Chengdu, Sichuan, China
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Yuan T, Ren W, Wang Z, Fry EL, Tang S, Yin J, Zhang J, Jia Z. How does the pattern of root metabolites regulating beneficial microorganisms change with different grazing pressures? FRONTIERS IN PLANT SCIENCE 2023; 14:1180576. [PMID: 37484473 PMCID: PMC10361787 DOI: 10.3389/fpls.2023.1180576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/08/2023] [Indexed: 07/25/2023]
Abstract
Grazing disturbance can change the structure of plant rhizosphere microbial communities and thereby alter the feedback to promote plant growth or induce plant defenses. However, little is known about how such changes occur and vary under different grazing pressures or the roles of root metabolites in altering the composition of rhizosphere microbial communities. In this study, the effects of different grazing pressures on the composition of microbial communities were investigated, and the mechanisms by which different grazing pressures changed rhizosphere microbiomes were explored with metabolomics. Grazing changed composition, functions, and co-expression networks of microbial communities. Under light grazing (LG), some saprophytic fungi, such as Lentinus sp., Ramichloridium sp., Ascobolus sp. and Hyphoderma sp., were significantly enriched, whereas under heavy grazing (HG), potentially beneficial rhizobacteria, such as Stenotrophomonas sp., Microbacterium sp., and Lysobacter sp., were significantly enriched. The beneficial mycorrhizal fungus Schizothecium sp. was significantly enriched in both LG and HG. Moreover, all enriched beneficial microorganisms were positively correlated with root metabolites, including amino acids (AAs), short-chain organic acids (SCOAs), and alkaloids. This suggests that these significantly enriched rhizosphere microbial changes may be caused by these differential root metabolites. Under LG, it is inferred that root metabolites, especially AAs such as L-Histidine, may regulate specific saprophytic fungi to participate in material transformations and the energy cycle and promote plant growth. Furthermore, to help alleviate the stress of HG and improve plant defenses, it is inferred that the root system actively regulates the synthesis of these root metabolites such as AAs, SCOAs, and alkaloids under grazing interference, and then secretes them to promote the growth of some specific plant growth-promoting rhizobacteria and fungi. To summarize, grasses can regulate beneficial microorganisms by changing root metabolites composition, and the response strategies vary under different grazing pressure in typical grassland ecosystems.
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Affiliation(s)
- Ting Yuan
- Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Weibo Ren
- Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Zhaoming Wang
- Key Laboratory of Forage Breeding and Seed Production of Inner Mongolia, Inner Mongolia M-Grass Ecology and Environment (Group) Co., Ltd., Hohhot, China
| | - Ellen L. Fry
- Department of Biology, Edge Hill University, Ormskirk, United Kingdom
| | - Shiming Tang
- Key Laboratory of Model Innovation in Forage Production Efficiency, Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Jingjing Yin
- Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Jiatao Zhang
- Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, China
| | - Zhenyu Jia
- Key Laboratory of Forage Breeding and Seed Production of Inner Mongolia, Inner Mongolia M-Grass Ecology and Environment (Group) Co., Ltd., Hohhot, China
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Guo H, Zhou M, Zhang G, He L, Yan C, Wan M, Hu J, He W, Zeng D, Zhu B, Zeng Z. Development of homozygous tetraploid potato and whole genome doubling-induced the enrichment of H3K27ac and potentially enhanced resistance to cold-induced sweetening in tubers. HORTICULTURE RESEARCH 2023; 10:uhad017. [PMID: 36968186 PMCID: PMC10031744 DOI: 10.1093/hr/uhad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Polyploid plants typically display advantages on some agronomically important traits over their diploid counterparts. Extensive studies have shown genetic, transcriptomic, and epigenetic dynamics upon polyploidization in multiple plant species. However, few studies have unveiled those alternations imposed only by ploidy level, without any interference from heterozygosity. Cultivated potato is highly heterozygous. Thus, in this study, we developed two homozygous autotetraploid lines and one homozygous diploid line in parallel from a homozygous diploid potato. We confirmed their ploidy levels using chloroplast counting and karyotyping. Oligo-FISH and genome re-sequencing validated that these potato lines are nearly homozygous. We investigated variations in phenotypes, transcription, and histone modifications between two ploidies. Both autotetraploid lines produced larger but fewer tubers than the diploid line. Interestingly, each autotetraploid line displayed ploidy-related differential expression for various genes. We also discovered a genome-wide enrichment of H3K27ac in genic regions upon whole-genome doubling (WGD). However, such enrichment was not associated with the differential gene expression between two ploidies. The tetraploid lines may exhibit better resistance to cold-induced sweetening (CIS) than the diploid line in tubers, potentially regulated through the expression of CIS-related key genes, which seems to be associated with the levels of H3K4me3 in cold-stored tubers. These findings will help to understand the impacts of autotetraploidization on dynamics of phenotypes, transcription, and histone modifications, as well as on CIS-related genes in response to cold storage.
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Affiliation(s)
| | | | | | | | - Caihong Yan
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu 610101, Sichuan, China
| | - Min Wan
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu 610101, Sichuan, China
| | - Jianjun Hu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Wei He
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Deying Zeng
- Department of Biological Science, College of Life Sciences, Sichuan Normal University, Chengdu 610101, Sichuan, China
- Plant Functional Genomics and Bioinformatics Research Center, Sichuan Normal University, Chengdu 610101, Sichuan, China
| | - Bo Zhu
- Corresponding authors. E-mails: ;
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Duan T, Sicard A, Glémin S, Lascoux M. Expression pattern of resynthesized allotetraploid Capsella is determined by hybridization, not whole-genome duplication. THE NEW PHYTOLOGIST 2023; 237:339-353. [PMID: 36254103 PMCID: PMC10099941 DOI: 10.1111/nph.18542] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Polyploidization, the process leading to the increase in chromosome sets, is a major evolutionary transition in plants. Whole-genome duplication (WGD) within the same species gives rise to autopolyploids, whereas allopolyploids result from a compound process with two distinct components: WGD and interspecific hybridization. To dissect the instant effects of WGD and hybridization on gene expression and phenotype, we created a series of synthetic hybrid and polyploid Capsella plants, including diploid hybrids, autotetraploids of both parental species, and two kinds of resynthesized allotetraploids with different orders of WGD and hybridization. Hybridization played a major role in shaping the relative expression pattern of the neo-allopolyploids, whereas WGD had almost no immediate effect on relative gene expression pattern but, nonetheless, still affected phenotypes. No transposable element-mediated genomic shock scenario was observed in either neo-hybrids or neo-polyploids. Finally, WGD and hybridization interacted and the distorting effects of WGD were less strong in hybrids. Whole-genome duplication may even improve hybrid fertility. In summary, while the initial relative gene expression pattern in neo-allotetraploids was almost entirely determined by hybridization, WGD only had trivial effects on relative expression patterns, both processes interacted and had a strong impact on physical attributes and meiotic behaviors.
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Affiliation(s)
- Tianlin Duan
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life LaboratoryUppsala University75236UppsalaSweden
| | - Adrien Sicard
- Department of Plant BiologySwedish University of Agricultural Sciences750 07UppsalaSweden
| | - Sylvain Glémin
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life LaboratoryUppsala University75236UppsalaSweden
- UMR CNRS 6553 ECOBIOCampus Beaulieu, bât 14a, p.118, CS 7420535042RennesFrance
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life LaboratoryUppsala University75236UppsalaSweden
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Shah S, Rastogi S, Vashisth D, Rout PK, Lal RK, Lavania UC, Shasany AK. Altered Developmental and Metabolic Gene Expression in Basil Interspecific Hybrids. PLANTS (BASEL, SWITZERLAND) 2022; 11:1873. [PMID: 35890507 PMCID: PMC9321874 DOI: 10.3390/plants11141873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
To understand the altered developmental changes and associated gene expression in inter-genomic combinations, a study was planned in two diverse yet closely related species of Ocimum, targeting their hybrid F1 and amphidiploids. The existing developmental variations between F1 and amphidiploids was analyzed through phenotypical and anatomical assessments. The absence of 8330 transcripts of F1 in amphidiploids and the exclusive presence of two transcripts related to WNK lysine-deficient protein kinase and geranylgeranyl transferase type-2 subunit beta 1-like proteins in amphidiploids provided a set of genes to compare the suppressed and activated functions between F1 and amphidiploids. The estimation of eugenol and methyleugenol, flavonoid, lignin and chlorophyll content was correlated with the average FPKM and differential gene expression values and further validated through qRT-PCR. Differentially expressed genes of stomatal patterning and development explained the higher density of stomata in F1 and the larger size of stomata in amphidiploids. Gene expression study of several transcription factors putatively involved in the growth and developmental processes of plants clearly amalgamates the transcriptome data linking the phenotypic differences in F1 and amphidiploids. This investigation describes the influence of interspecific hybridization on genes and transcription factors leading to developmental changes and alleviation of intergenomic instability in amphidiploids.
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Affiliation(s)
- Saumya Shah
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India; (S.S.); (S.R.); (D.V.)
| | - Shubhra Rastogi
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India; (S.S.); (S.R.); (D.V.)
| | - Divya Vashisth
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India; (S.S.); (S.R.); (D.V.)
| | - Prashant Kumar Rout
- Department of Phytochemistry, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India;
| | - Raj Kishori Lal
- Department of Genetics and Plant Breeding, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India; (R.K.L.); (U.C.L.)
| | - Umesh Chandra Lavania
- Department of Genetics and Plant Breeding, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India; (R.K.L.); (U.C.L.)
- Department of Botany, University of Lucknow, Lucknow 226007, India
| | - Ajit Kumar Shasany
- Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India; (S.S.); (S.R.); (D.V.)
- ICAR-National Institute for Plant Biotechnology (NIPB), Pusa Campus, New Delhi 110012, India
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9
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Equilibrated evolution of the mixed auto-/allopolyploid haplotype-resolved genome of the invasive hexaploid Prussian carp. Nat Commun 2022; 13:4092. [PMID: 35835759 PMCID: PMC9283417 DOI: 10.1038/s41467-022-31515-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 06/21/2022] [Indexed: 11/08/2022] Open
Abstract
Understanding genome evolution of polyploids requires dissection of their often highly similar subgenomes and haplotypes. Polyploid animal genome assemblies so far restricted homologous chromosomes to a ‘collapsed’ representation. Here, we sequenced the genome of the asexual Prussian carp, which is a close relative of the goldfish, and present a haplotype-resolved chromosome-scale assembly of a hexaploid animal. Genome-wide comparisons of the 150 chromosomes with those of two ancestral diploid cyprinids and the allotetraploid goldfish and common carp revealed the genomic structure, phylogeny and genome duplication history of its genome. It consists of 25 syntenic, homeologous chromosome groups and evolved by a recent autoploid addition to an allotetraploid ancestor. We show that de-polyploidization of the alloploid subgenomes on the individual gene level occurred in an equilibrated fashion. Analysis of the highly conserved actinopterygian gene set uncovered a subgenome dominance in duplicate gene loss of one ancestral chromosome set. The haplotype-resolved assembly of the asexual invasive Prussian carp shows six genome copies (AAABBB), evolved from two ancestral species by a recent self-addition (AB) to its hybrid-tetraploid (AABB) goldfish ancestor. Equilibrated gene loss led to subgenome dominance.
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Liu W, Wang Q, Zhang R, Liu M, Wang C, Liu Z, Xiang C, Lu X, Zhang X, Li X, Wang T, Gao L, Zhang W. Rootstock-scion exchanging mRNAs participate in the pathways of amino acids and fatty acid metabolism in cucumber under early chilling stress. HORTICULTURE RESEARCH 2022; 9:uhac031. [PMID: 35184197 PMCID: PMC9039506 DOI: 10.1093/hr/uhac031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 06/14/2023]
Abstract
Cucumber (Cucumis sativus L.) often experiences chilling stress that limits their growth and productivity. Grafting is widely used to improve abiotic stress resistance by alternating a vigorous root system, suggesting there exists systemic signals communication between distant organs. mRNAs are reported to be evolving in fortification strategies by long-distance signaling when plants suffering from chilling stress. However, the potential function of mobile mRNAs alleviating chilling stress in grafted cucumber is still unknown. Here, the physiological changes, mobile mRNAs profiling, transcriptomic and metabolomic changes in above- and underground tissues of all graft combinations of cucumber and pumpkin responding to chilling stress were established and analyzed comprehensively. The co-relationship between the cluster of chilling-induced pumpkin mobile mRNAs with Differentially Expressed Genes (DEGs) and Differentially Intensive Metabolites (DIMs) revealed that four key chilling-induced pumpkin mobile mRNAs were highly related to glycine, serine and threonine synthesis and fatty acid β-oxidative degradation metabolism in cucumber tissues of heterografts. The verification of mobile mRNAs, potential transport of metabolites and exogenous application of key metabolites of glycerophospholipid metabolism pathway in cucumber seedlings confirmed that the role of mobile mRNAs in regulating chilling responses in grafted cucumber. Our results build a link between the long-distance mRNAs of chilling-tolerant pumpkin and the fatty acid β-oxidative degradation metabolism of chilling-sensitive cucumber. It helps to uncover the mechanism of signaling interaction between scion and stock responding to chilling tolerant in grafted cucumber.
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Affiliation(s)
- Wenqian Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Qing Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Ruoyan Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Mengshuang Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Cuicui Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Zixi Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Chenggang Xiang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
- College of Life Science and Technology, HongHe University, Mengzi, Yunnan 661100, China
| | - Xiaohong Lu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Xiaojing Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Xiaojun Li
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Tao Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Lihong Gao
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
| | - Wenna Zhang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China
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11
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Zhao K, Jin N, Madadi M, Wang Y, Wu L, Xu Z, Wang J, Dong J, Tang SW, Wang Y, Peng L, Xiong Z. Incomplete genome doubling enables to consistently enhance plant growth for maximum biomass production by altering multiple transcript co-expression networks in potato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:461-472. [PMID: 34731273 DOI: 10.1007/s00122-021-03976-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
Cytochimera potato plants, which mixed with diploid and tetraploid cells, could cause the highest and significantly increased biomass yield than the polyploid and diploid potato plants. Polyploidization is an important approach in crop breeding for agronomic trait improvement, especially for biomass production. Cytochimera contains two or more mixed cells with different levels of ploidy, which is considered a failure in whole genome duplication. Using colchicine treatment with diploid (Dip) potato (Solanum chacoense) plantlets, this study generated tetraploid (Tet) and cytochimera (Cyt) lines, which, respectively, contained complete and partial cells with genome duplication. Compared to the Dip potato, we observed remarkably enhanced plant growth and biomass yields in Tet and Cyt lines. Notably, the Cyt potato straw, which was generated from incomplete genome doubling, was of significantly higher biomass yield than that of the Tet with a distinctively altered cell wall composition. Meanwhile, we observed that one layer of the tetraploid cells (about 30%) in Cyt plants was sufficient to trigger a gene expression pattern similar to that of Tet, suggesting that the biomass dominance of Cyt may be related to the proportion of different ploidy cells. Further genome-wide analyses of co-expression networks indicated that down-regulation (against Dip) of spliceosomal-related transcripts might lead to differential alternative splicing for specifically improved agronomic traits such as plant growth, biomass yield, and lignocellulose composition in Tet and Cyt plants. In addition, this work examined that the genome of Cyt line was relatively stable after years of asexual reproduction. Hence, this study has demonstrated that incomplete genome doubling is a promising strategy to maximize biomass production in potatoes and beyond.
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Affiliation(s)
- Kanglu Zhao
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot, 010021, Inner Mongolia, China
| | - Nengzhou Jin
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot, 010021, Inner Mongolia, China
| | - Meysam Madadi
- Biomass and Bioenergy Research Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Laboratory of Biomass Engineering & Nanomaterial Application in Automobiles, College of Food Science & Chemical Engineering, Hubei University of Arts & Science, Xiangyang, China
| | - Youmei Wang
- Biomass and Bioenergy Research Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lei Wu
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot, 010021, Inner Mongolia, China
| | - Zhijun Xu
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot, 010021, Inner Mongolia, China
| | - Jinxuan Wang
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot, 010021, Inner Mongolia, China
| | - Jing Dong
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot, 010021, Inner Mongolia, China
| | - Shang-Wen Tang
- Laboratory of Biomass Engineering & Nanomaterial Application in Automobiles, College of Food Science & Chemical Engineering, Hubei University of Arts & Science, Xiangyang, China
| | - Yanting Wang
- Biomass and Bioenergy Research Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Laboratory of Biomass Engineering & Nanomaterial Application in Automobiles, College of Food Science & Chemical Engineering, Hubei University of Arts & Science, Xiangyang, China
| | - Liangcai Peng
- Biomass and Bioenergy Research Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Laboratory of Biomass Engineering & Nanomaterial Application in Automobiles, College of Food Science & Chemical Engineering, Hubei University of Arts & Science, Xiangyang, China
| | - Zhiyong Xiong
- Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Science, Inner Mongolia University, Hohhot, 010021, Inner Mongolia, China.
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Yin L, Zhu Z, Huang L, Luo X, Li Y, Xiao C, Yang J, Wang J, Zou Q, Tao L, Kang Z, Tang R, Wang M, Fu S. DNA repair- and nucleotide metabolism-related genes exhibit differential CHG methylation patterns in natural and synthetic polyploids (Brassica napus L.). HORTICULTURE RESEARCH 2021; 8:142. [PMID: 34193846 PMCID: PMC8245426 DOI: 10.1038/s41438-021-00576-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 03/29/2021] [Accepted: 04/07/2021] [Indexed: 05/03/2023]
Abstract
Polyploidization plays a crucial role in the evolution of angiosperm species. Almost all newly formed polyploids encounter genetic or epigenetic instabilities. However, the molecular mechanisms contributing to genomic instability in synthetic polyploids have not been clearly elucidated. Here, we performed a comprehensive transcriptomic and methylomic analysis of natural and synthetic polyploid rapeseeds (Brassica napus). Our results showed that the CHG methylation levels of synthetic rapeseed in different genomic contexts (genes, transposon regions, and repeat regions) were significantly lower than those of natural rapeseed. The total number and length of CHG-DMRs between natural and synthetic polyploids were much greater than those of CG-DMRs and CHH-DMRs, and the genes overlapping with these CHG-DMRs were significantly enriched in DNA damage repair and nucleotide metabolism pathways. These results indicated that CHG methylation may be more sensitive than CG and CHH methylation in regulating the stability of the polyploid genome of B. napus. In addition, many genes involved in DNA damage repair, nucleotide metabolism, and cell cycle control were significantly differentially expressed between natural and synthetic rapeseeds. Our results highlight that the genes related to DNA repair and nucleotide metabolism display differential CHG methylation patterns between natural and synthetic polyploids and reveal the potential connection between the genomic instability of polyploid plants with DNA methylation defects and dysregulation of the DNA repair system. In addition, it was found that the maintenance of CHG methylation in B. napus might be partially regulated by MET1. Our study provides novel insights into the establishment and evolution of polyploid plants and offers a potential idea for improving the genomic stability of newly formed Brassica polyploids.
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Affiliation(s)
- Liqin Yin
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China.
- College of Life Sciences, Sichuan University, 29 Wangjiang Road, Chengdu, China.
| | - Zhendong Zhu
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Liangjun Huang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
- Agricultural College, Sichuan Agricultural University, 211 Huimin Road, Chengdu, China
| | - Xuan Luo
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
- Agricultural College, Sichuan Agricultural University, 211 Huimin Road, Chengdu, China
| | - Yun Li
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Chaowen Xiao
- College of Life Sciences, Sichuan University, 29 Wangjiang Road, Chengdu, China
| | - Jin Yang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Jisheng Wang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Qiong Zou
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Lanrong Tao
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Zeming Kang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Rong Tang
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China
| | - Maolin Wang
- College of Life Sciences, Sichuan University, 29 Wangjiang Road, Chengdu, China.
| | - Shaohong Fu
- Institute of Crop Research, Chengdu Academy of Agricultural and Forestry Sciences, 200 Nongke Road, Chengdu, China.
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13
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Esposito S, Aversano R, Tripodi P, Carputo D. Whole-Genome Doubling Affects Pre-miRNA Expression in Plants. PLANTS 2021; 10:plants10051004. [PMID: 34069771 PMCID: PMC8157229 DOI: 10.3390/plants10051004] [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: 01/13/2021] [Revised: 04/09/2021] [Accepted: 05/10/2021] [Indexed: 11/16/2022]
Abstract
Whole-genome doubling (polyploidy) is common in angiosperms. Several studies have indicated that it is often associated with molecular, physiological, and phenotypic changes. Mounting evidence has pointed out that micro-RNAs (miRNAs) may have an important role in whole-genome doubling. However, an integrative approach that compares miRNA expression in polyploids is still lacking. Here, a re-analysis of already published RNAseq datasets was performed to identify microRNAs’ precursors (pre-miRNAs) in diploids (2x) and tetraploids (4x) of five species (Arabidopsis thaliana L., Morus alba L., Brassica rapa L., Isatis indigotica Fort., and Solanum commersonii Dun). We found 3568 pre-miRNAs, three of which (pre-miR414, pre-miR5538, and pre-miR5141) were abundant in all 2x, and were absent/low in their 4x counterparts. They are predicted to target more than one mRNA transcript, many belonging to transcription factors (TFs), DNA repair mechanisms, and related to stress. Sixteen pre-miRNAs were found in common in all 2x and 4x. Among them, pre-miRNA482, pre-miRNA2916, and pre-miRNA167 changed their expression after polyploidization, being induced or repressed in 4x plants. Based on our results, a common ploidy-dependent response was triggered in all species under investigation, which involves DNA repair, ATP-synthesis, terpenoid biosynthesis, and several stress-responsive transcripts. In addition, an ad hoc pre-miRNA expression analysis carried out solely on 2x vs. 4x samples of S. commersonii indicated that ploidy-dependent pre-miRNAs seem to actively regulate the nucleotide metabolism, probably to cope with the increased requirement for DNA building blocks caused by the augmented DNA content. Overall, the results outline the critical role of microRNA-mediated responses following autopolyploidization in plants.
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Affiliation(s)
- Salvatore Esposito
- CREA Research Centre for Cereal and Industrial Crops, 71122 Foggia, Italy;
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy;
| | - Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy;
| | - Pasquale Tripodi
- CREA Research Centre for Vegetable and Ornamental Crops, 84098 Pontecagnano, Italy;
| | - Domenico Carputo
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy;
- Correspondence: ; Tel.: +39-08-1252-9225
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14
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Cara N, Piccoli PN, Bolcato L, Marfil CF, Masuelli RW. Variation in the amino acids, volatile organic compounds and terpenes profiles in induced polyploids and in Solanum tuberosum varieties. PHYTOCHEMISTRY 2020; 180:112516. [PMID: 32949937 DOI: 10.1016/j.phytochem.2020.112516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 07/25/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
Polyploids often display a variety of phenotypic novelties when compared to their diploid progenitors, some of which may represent ecological advantages, especially regarding tolerance to biotic and abiotic factors. Plants cope with environmental factors by producing chemicals such as volatile organic compounds (VOCs) and specific amino acids (AAs). In potato, the third most important food crop in the world, gene introgression from diploid wild relative species into the genetic pool of the cultivated species (tetraploid) would be of great agronomical interest. The consequences of allopolyploidization on the potato VOCs and AAs profiles have not been yet analyzed. In this work, the effects of whole genome duplication on VOCs and AAs contents in leaves of potato allo- and autotetraploids and cultivated varieties were studied. The polyploids were obtained by chromosomal duplication of a genotype of the wild diploid species S. kurtzianum (autopolyploid model), and a diploid interspecific hybrid between the cultivated species S. tuberosum and S. kurtzianum (allopolyploid model). Almost all compounds levels varied greatly among these tetraploid lines; while all tetraploids showed higher contents of non-isoprenoids compounds than diploids, we found either increments or reductions in terpenes and AAs content. The results support the idea that genome duplication is a stochastic source of variability, which might be directly used for introgression in the 4x gene pool of the cultivated potato by sexual hybridization.
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Affiliation(s)
- Nicolás Cara
- Facultad de Ciencias Agrarias, UNCuyo, Almirante Brown 500, M5528AHB, Mendoza, Argentina.
| | - Patricia N Piccoli
- Facultad de Ciencias Agrarias, UNCuyo, Almirante Brown 500, M5528AHB, Mendoza, Argentina; Instituto de Biología Agrícola de Mendoza (IBAM), CONICET-UNCuyo, Almirante Brown 500, M5528AHB, Mendoza, Argentina.
| | - Leonardo Bolcato
- Instituto de Biología Agrícola de Mendoza (IBAM), CONICET-UNCuyo, Almirante Brown 500, M5528AHB, Mendoza, Argentina.
| | - Carlos F Marfil
- Facultad de Ciencias Agrarias, UNCuyo, Almirante Brown 500, M5528AHB, Mendoza, Argentina; Instituto de Biología Agrícola de Mendoza (IBAM), CONICET-UNCuyo, Almirante Brown 500, M5528AHB, Mendoza, Argentina.
| | - Ricardo W Masuelli
- Facultad de Ciencias Agrarias, UNCuyo, Almirante Brown 500, M5528AHB, Mendoza, Argentina; Instituto de Biología Agrícola de Mendoza (IBAM), CONICET-UNCuyo, Almirante Brown 500, M5528AHB, Mendoza, Argentina.
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15
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Correr FH, Hosaka GK, Barreto FZ, Valadão IB, Balsalobre TWA, Furtado A, Henry RJ, Carneiro MS, Margarido GRA. Differential expression in leaves of Saccharum genotypes contrasting in biomass production provides evidence of genes involved in carbon partitioning. BMC Genomics 2020; 21:673. [PMID: 32993494 PMCID: PMC7526157 DOI: 10.1186/s12864-020-07091-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/22/2020] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND The development of biomass crops aims to meet industrial yield demands, in order to optimize profitability and sustainability. Achieving these goals in an energy crop like sugarcane relies on breeding for sucrose accumulation, fiber content and stalk number. To expand the understanding of the biological pathways related to these traits, we evaluated gene expression of two groups of genotypes contrasting in biomass composition. RESULTS First visible dewlap leaves were collected from 12 genotypes, six per group, to perform RNA-Seq. We found a high number of differentially expressed genes, showing how hybridization in a complex polyploid system caused extensive modifications in genome functioning. We found evidence that differences in transposition and defense related genes may arise due to the complex nature of the polyploid Saccharum genomes. Genotypes within both biomass groups showed substantial variability in genes involved in photosynthesis. However, most genes coding for photosystem components or those coding for phosphoenolpyruvate carboxylases (PEPCs) were upregulated in the high biomass group. Sucrose synthase (SuSy) coding genes were upregulated in the low biomass group, showing that this enzyme class can be involved with sucrose synthesis in leaves, similarly to sucrose phosphate synthase (SPS) and sucrose phosphate phosphatase (SPP). Genes in pathways related to biosynthesis of cell wall components and expansins coding genes showed low average expression levels and were mostly upregulated in the high biomass group. CONCLUSIONS Together, these results show differences in carbohydrate synthesis and carbon partitioning in the source tissue of distinct phenotypic groups. Our data from sugarcane leaves revealed how hybridization in a complex polyploid system resulted in noticeably different transcriptomic profiles between contrasting genotypes.
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Affiliation(s)
- Fernando Henrique Correr
- Department of Genetics, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Av Pádua Dias, 11, Piracicaba, 13400-970, Brazil
| | - Guilherme Kenichi Hosaka
- Department of Genetics, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Av Pádua Dias, 11, Piracicaba, 13400-970, Brazil
| | - Fernanda Zatti Barreto
- Department of Biotechnology, Vegetal and Animal Production, Federal University of São Carlos, Center of Agricultural Sciences, Rodovia Anhanguera, km 174, Araras, 13600-970, Brazil
| | - Isabella Barros Valadão
- Department of Biotechnology, Vegetal and Animal Production, Federal University of São Carlos, Center of Agricultural Sciences, Rodovia Anhanguera, km 174, Araras, 13600-970, Brazil
| | - Thiago Willian Almeida Balsalobre
- Department of Biotechnology, Vegetal and Animal Production, Federal University of São Carlos, Center of Agricultural Sciences, Rodovia Anhanguera, km 174, Araras, 13600-970, Brazil
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
| | - Robert James Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
| | - Monalisa Sampaio Carneiro
- Department of Biotechnology, Vegetal and Animal Production, Federal University of São Carlos, Center of Agricultural Sciences, Rodovia Anhanguera, km 174, Araras, 13600-970, Brazil
| | - Gabriel Rodrigues Alves Margarido
- Department of Genetics, University of São Paulo, "Luiz de Queiroz" College of Agriculture, Av Pádua Dias, 11, Piracicaba, 13400-970, Brazil.
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Zhu C, Xiaoyu L, Junlan G, Yun X, Jie R. Integrating transcriptomic and metabolomic analysis of hormone pathways in Acer rubrum during developmental leaf senescence. BMC PLANT BIOLOGY 2020; 20:410. [PMID: 32883206 PMCID: PMC7650285 DOI: 10.1186/s12870-020-02628-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND To fully elucidate the roles and mechanisms of plant hormones in leaf senescence, we adopted an integrated analysis of both non-senescing and senescing leaves from red maple with transcriptome and metabolome data. RESULTS Transcription and metabolite profiles were generated through a combination of deep sequencing, third-generation sequencing data analysis, and ultrahigh-performance liquid chromatograph Q extractive mass spectrometry (UHPLC-QE-MS), respectively. We investigated the accumulation of compounds and the expression of biosynthesis and signaling genes for eight hormones. The results revealed that ethylene and abscisic acid concentrations increased during the leaf senescence process, while the contents of cytokinin, auxin, jasmonic acid, and salicylic acid continued to decrease. Correlation tests between the hormone content and transcriptional changes were analyzed, and in six pathways, genes closely linked with leaf senescence were identified. CONCLUSIONS These results will enrich our understanding of the mechanisms of plant hormones that regulate leaf senescence in red maple, while establishing a foundation for the genetic modification of Acer in the future.
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Affiliation(s)
- Chen Zhu
- Institute of Agricultural Engineering, Anhui Academy of Agricultural Sciences, 40 Nongkenanlu, Hefei, Anhui 230031 P.R. China
| | - Lu Xiaoyu
- College of Forestry and Landscape Architecture, Anhui Agricultural University, 130 Changjiangxilu, Hefei, Anhui 230036 P.R. China
| | - Gao Junlan
- Institute of Agricultural Engineering, Anhui Academy of Agricultural Sciences, 40 Nongkenanlu, Hefei, Anhui 230031 P.R. China
| | - Xuan Yun
- Institute of Agricultural Engineering, Anhui Academy of Agricultural Sciences, 40 Nongkenanlu, Hefei, Anhui 230031 P.R. China
| | - Ren Jie
- Institute of Agricultural Engineering, Anhui Academy of Agricultural Sciences, 40 Nongkenanlu, Hefei, Anhui 230031 P.R. China
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17
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Martí M, Diretto G, Aragonés V, Frusciante S, Ahrazem O, Gómez-Gómez L, Daròs JA. Efficient production of saffron crocins and picrocrocin in Nicotiana benthamiana using a virus-driven system. Metab Eng 2020; 61:238-250. [PMID: 32629020 DOI: 10.1016/j.ymben.2020.06.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/23/2020] [Accepted: 06/21/2020] [Indexed: 02/07/2023]
Abstract
Crocins and picrocrocin are glycosylated apocarotenoids responsible, respectively, for the color and the unique taste of the saffron spice, known as red gold due to its high price. Several studies have also shown the health-promoting properties of these compounds. However, their high costs hamper the wide use of these metabolites in the pharmaceutical sector. We have developed a virus-driven system to produce remarkable amounts of crocins and picrocrocin in adult Nicotiana benthamiana plants in only two weeks. The system consists of viral clones derived from tobacco etch potyvirus that express specific carotenoid cleavage dioxygenase (CCD) enzymes from Crocus sativus and Buddleja davidii. Metabolic analyses of infected tissues demonstrated that the sole virus-driven expression of C. sativus CsCCD2L or B. davidii BdCCD4.1 resulted in the production of crocins, picrocrocin and safranal. Using the recombinant virus that expressed CsCCD2L, accumulations of 0.2% of crocins and 0.8% of picrocrocin in leaf dry weight were reached in only two weeks. In an attempt to improve apocarotenoid content in N. benthamiana, co-expression of CsCCD2L with other carotenogenic enzymes, such as Pantoea ananatis phytoene synthase (PaCrtB) and saffron β-carotene hydroxylase 2 (BCH2), was performed using the same viral system. This combinatorial approach led to an additional crocin increase up to 0.35% in leaves in which CsCCD2L and PaCrtB were co-expressed. Considering that saffron apocarotenoids are costly harvested from flower stigma once a year, and that Buddleja spp. flowers accumulate lower amounts, this system may be an attractive alternative for the sustainable production of these appreciated metabolites.
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Affiliation(s)
- Maricarmen Martí
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València), 46022, Valencia, Spain
| | - Gianfranco Diretto
- Italian National Agency for New Technologies, Energy, and Sustainable Development, Casaccia Research Centre, 00123, Rome, Italy
| | - Verónica Aragonés
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València), 46022, Valencia, Spain
| | - Sarah Frusciante
- Italian National Agency for New Technologies, Energy, and Sustainable Development, Casaccia Research Centre, 00123, Rome, Italy
| | - Oussama Ahrazem
- Instituto Botánico, Departamento de Ciencia y Tecnología Agroforestal y Genética, Facultad de Farmacia, Universidad de Castilla-La Mancha, Campus Universitario S/n, 02071, Albacete, Spain
| | - Lourdes Gómez-Gómez
- Instituto Botánico, Departamento de Ciencia y Tecnología Agroforestal y Genética, Facultad de Farmacia, Universidad de Castilla-La Mancha, Campus Universitario S/n, 02071, Albacete, Spain.
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universitat Politècnica de València), 46022, Valencia, Spain.
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Diretto G, Frusciante S, Fabbri C, Schauer N, Busta L, Wang Z, Matas AJ, Fiore A, K.C. Rose J, Fernie AR, Jetter R, Mattei B, Giovannoni J, Giuliano G. Manipulation of β-carotene levels in tomato fruits results in increased ABA content and extended shelf life. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1185-1199. [PMID: 31646753 PMCID: PMC7152610 DOI: 10.1111/pbi.13283] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 10/09/2019] [Accepted: 10/22/2019] [Indexed: 05/18/2023]
Abstract
Tomato fruit ripening is controlled by the hormone ethylene and by a group of transcription factors, acting upstream of ethylene. During ripening, the linear carotene lycopene accumulates at the expense of cyclic carotenoids. Fruit-specific overexpression of LYCOPENE β-CYCLASE (LCYb) resulted in increased β-carotene (provitamin A) content. Unexpectedly, LCYb-overexpressing fruits also exhibited a diverse array of ripening phenotypes, including delayed softening and extended shelf life. These phenotypes were accompanied, at the biochemical level, by an increase in abscisic acid (ABA) content, decreased ethylene production, increased density of cell wall material containing linear pectins with a low degree of methylation, and a thicker cuticle with a higher content of cutin monomers and triterpenoids. The levels of several primary metabolites and phenylpropanoid compounds were also altered in the transgenic fruits, which could be attributed to delayed fruit ripening and/or to ABA. Network correlation analysis and pharmacological experiments with the ABA biosynthesis inhibitor, abamine, indicated that altered ABA levels were a direct effect of the increased β-carotene content and were in turn responsible for the extended shelf life phenotype. Thus, manipulation of β-carotene levels results in an improvement not only of the nutritional value of tomato fruits, but also of their shelf life.
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Affiliation(s)
- Gianfranco Diretto
- Italian national Agency for New technologies, Energy, and Sustainable Development (ENEA)Casaccia Research CenterRomaItaly
| | - Sarah Frusciante
- Italian national Agency for New technologies, Energy, and Sustainable Development (ENEA)Casaccia Research CenterRomaItaly
| | - Claudia Fabbri
- Department of Biology and BiotechnologySapienza University of RomeRomeItaly
| | - Nicolas Schauer
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
| | - Lucas Busta
- Department of ChemistryUniversity of British ColumbiaVancouverBCCanada
- Center for Plant Science Innovation and Department of BiochemistryUniversity of Nebraska–LincolnLincolnNEUSA
| | - Zhonghua Wang
- Department of BotanyUniversity of British ColumbiaVancouverBCCanada
- College of AgronomyNorthwest A&F UniversityYanglingChina
| | - Antonio J. Matas
- Plant Biology SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
- Department of Plant BiologyInstitute for Mediterranean and Subtropical Horticulture “La Mayora” (IHSM‐UMA‐CSIC)University of MálagaMálagaSpain
| | - Alessia Fiore
- Italian national Agency for New technologies, Energy, and Sustainable Development (ENEA)Casaccia Research CenterRomaItaly
| | - Jocelyn K.C. Rose
- Plant Biology SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
| | - Alisdair R. Fernie
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
| | - Reinhard Jetter
- Department of ChemistryUniversity of British ColumbiaVancouverBCCanada
- Department of BotanyUniversity of British ColumbiaVancouverBCCanada
| | - Benedetta Mattei
- Department of Biology and BiotechnologySapienza University of RomeRomeItaly
- Department of Health, Life and Environmental SciencesUniversity of L'AquilaL'AquilaItaly
| | - Jim Giovannoni
- U.S. Department of Agriculture–Agricultural Research ServiceRobert W. Holley Center for Agriculture and HealthIthacaNYUSA
- Boyce Thompson Institute for Plant ResearchCornell UniversityIthacaNYUSA
| | - Giovanni Giuliano
- Italian national Agency for New technologies, Energy, and Sustainable Development (ENEA)Casaccia Research CenterRomaItaly
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19
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Julião SA, Ribeiro CDV, Lopes JML, de Matos EM, Reis AC, Peixoto PHP, Machado MA, Azevedo ALS, Grazul RM, de Campos JMS, Viccini LF. Induction of Synthetic Polyploids and Assessment of Genomic Stability in Lippia alba. FRONTIERS IN PLANT SCIENCE 2020; 11:292. [PMID: 32273876 PMCID: PMC7113378 DOI: 10.3389/fpls.2020.00292] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/26/2020] [Indexed: 05/14/2023]
Abstract
Polyploidy is widely recognized as a major evolutionary force in plants and has been reported in the genus Lippia (Verbenaceae). Lippia alba, the most studied species, has been documented as a polyploid complex involving at least four ploidal levels. L. alba presents remarkable chemical and genetic variation and represents a model for understanding genome organization. Although the economic and medicinal importance of the species has been widely described, no established polyploid induction protocol has been reported so far. Here, we describe the production of synthetic polyploid plants of L. alba using colchicine. The ploidal levels were estimated by flow cytometry and chromosome counting. In addition, FISH and molecular markers approaches were used to confirm the stability of the synthetic polyploids. The major component of the essential oils was estimated by GCMS to compare with the natural individuals. Tetraploids and triploids were produced providing new opportunities for investigating medicinal, pharmacological, and economic applications as well as addressing intrinsic questions involved in the polyploidization process in tropical plants.
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Affiliation(s)
| | | | | | | | - Aryane Campos Reis
- Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, Brazil
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20
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Dono G, Rambla JL, Frusciante S, Granell A, Diretto G, Mazzucato A. Color Mutations Alter the Biochemical Composition in the San Marzano Tomato Fruit. Metabolites 2020; 10:E110. [PMID: 32183449 PMCID: PMC7143285 DOI: 10.3390/metabo10030110] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/07/2020] [Accepted: 03/12/2020] [Indexed: 01/16/2023] Open
Abstract
San Marzano (SM) is a traditional Italian landrace characterized by red elongated fruits, originating in the province of Naples (Italy) and cultivated worldwide. Three mutations, yellow flesh (r), green flesh (gf) and colorless fruit epidermis (y) were introduced into SM by backcross and the resulting introgression lines (ILs) produced the expected yellow, brown and pink fruit variants. In addition, ILs carrying double combinations of those mutations were obtained. The six ILs plus the SM reference were analyzed for volatile (VOC), non-polar (NP) and polar (P) metabolites. Sixty-eight VOCs were identified, and several differences evidenced in the ILs; overall gf showed epistasis over r and y and r over y. Analysis of the NP component identified 54 metabolites; variation in early carotenoids (up to lycopene) and chlorophylls characterized respectively the ILs containing r and gf. In addition, compounds belonging to the quinone and xanthophyll classes were present in genotypes carrying the r mutation at levels higher than SM. Finally, the analysis of 129 P metabolites evidenced different levels of vitamins, amino acids, lipids and phenylpropanoids in the ILs. A correlation network approach was used to investigate metabolite-metabolite relationships in the mutant lines. Altogether these differences potentially modified the hedonistic and nutritional value of the berry. In summary, single and combined mutations in gf, r and y generated interesting visual and compositional diversity in the SM landrace, while maintaining its original typology.
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Affiliation(s)
- Gabriella Dono
- DAFNE Dept. of Agriculture and Forest Sciences, University of Tuscia, Via S.C. de Lellis snc, 01100 Viterbo, Italy;
| | - Jose Luis Rambla
- IBMCP Institute for Plant Molecular and Cell Biology (CSIC-UPV), Carrer de l’Enginyer Fausto Elio, s/n, 46022 Valencia, Spain; (J.L.R.); (A.G.)
- Department of Agricultural and Environmental Sciences, Jaume I University, Av. Vicent Sos Baynat, s/n. 12071 Castellòn de la Plana, Spain
| | - Sarah Frusciante
- ENEA, Casaccia Research Center, Via Anguillarese 301, S. Maria di Galeria, 00123 Rome, Italy; (S.F.); (G.D.)
| | - Antonio Granell
- IBMCP Institute for Plant Molecular and Cell Biology (CSIC-UPV), Carrer de l’Enginyer Fausto Elio, s/n, 46022 Valencia, Spain; (J.L.R.); (A.G.)
| | - Gianfranco Diretto
- ENEA, Casaccia Research Center, Via Anguillarese 301, S. Maria di Galeria, 00123 Rome, Italy; (S.F.); (G.D.)
| | - Andrea Mazzucato
- DAFNE Dept. of Agriculture and Forest Sciences, University of Tuscia, Via S.C. de Lellis snc, 01100 Viterbo, Italy;
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21
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Wu M, Ge Y, Xu C, Wang J. Metabolome and Transcriptome Analysis of Hexaploid Solidago canadensis Roots Reveals its Invasive Capacity Related to Polyploidy. Genes (Basel) 2020; 11:genes11020187. [PMID: 32050732 PMCID: PMC7074301 DOI: 10.3390/genes11020187] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 02/08/2020] [Accepted: 02/08/2020] [Indexed: 12/29/2022] Open
Abstract
Polyploid plants are more often invasive species than their diploid counterparts. As the invasiveness of a species is often linked to its production of allelopathic compounds, we hypothesize that differences in invasive ability between cytotypes may be due to their different ability to synthesize allelopathic metabolites. We test this using two cytotypes of Solidago canadensis as the model and use integrated metabolome and transcriptome data to resolve the question. Metabolome analysis identified 122 metabolites about flavonoids, phenylpropanoids and terpenoids, of which 57 were differentially accumulated between the two cytotypes. Transcriptome analysis showed that many differentially expressed genes (DEGs) were enriched in ‘biosynthesis of secondary metabolites’, ‘plant hormone signal transduction’, and ‘MAPK signaling’, covering most steps of plant allelopathic metabolite synthesis. Importantly, the differentially accumulated flavonoids, phenylpropanoids and terpenoids were closely correlated with related DEGs. Furthermore, 30 miRNAs were found to be negatively associated with putative targets, and they were thought to be involved in target gene expression regulation. These miRNAs probably play a vital role in the regulation of metabolite synthesis in hexaploid S. canadensis. The two cytotypes of S. canadensis differ in the allelopathic metabolite synthesis and this difference is associated with regulation of expression of a range of genes. These results suggest that changes in gene expression may underlying the increased invasive potential of the polyploidy.
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22
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Wei T, Wang Y, Liu JH. Comparative transcriptome analysis reveals synergistic and disparate defense pathways in the leaves and roots of trifoliate orange ( Poncirus trifoliata) autotetraploids with enhanced salt tolerance. HORTICULTURE RESEARCH 2020; 7:88. [PMID: 32528700 PMCID: PMC7261775 DOI: 10.1038/s41438-020-0311-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 05/06/2023]
Abstract
Polyploid plants often exhibit enhanced stress tolerance relative to their diploid counterparts, but the physiological and molecular mechanisms of this enhanced stress tolerance remain largely unknown. In this study, we showed that autotetraploid trifoliate orange (Poncirus trifoliata (L.) Raf.) exhibited enhanced salt tolerance in comparison with diploid progenitors. Global transcriptome profiling of diploid and tetraploid plants with or without salt stress by RNA-seq revealed that the autotetraploids displayed specific enrichment of differentially expressed genes. Interestingly, the leaves and roots of tetraploids exhibited different expression patterns of a variety of upregulated genes. Genes related to plant hormone signal transduction were enriched in tetraploid leaves, whereas those associated with starch and sucrose metabolism and proline biosynthesis were enriched in roots. In addition, genes encoding different antioxidant enzymes were upregulated in the leaves (POD) and roots (APX) of tetraploids under salt stress. Consistently, the tetraploids accumulated higher levels of soluble sugars and proline but less ROS under salt stress compared to the diploids. Moreover, several genes encoding transcription factors were induced specifically or to higher levels in the tetraploids under salt stress. Collectively, this study demonstrates that the activation of various multifaceted defense systems in leaves and roots contributes to the enhanced salt tolerance of autotetraploids.
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Affiliation(s)
- Tonglu Wei
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yue Wang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
| | - Ji-Hong Liu
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070 China
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23
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Teixeira A, Martins V, Frusciante S, Cruz T, Noronha H, Diretto G, Gerós H. Flavescence Dorée-Derived Leaf Yellowing in Grapevine ( Vitis vinifera L.) Is Associated to a General Repression of Isoprenoid Biosynthetic Pathways. FRONTIERS IN PLANT SCIENCE 2020; 11:896. [PMID: 32625230 PMCID: PMC7311760 DOI: 10.3389/fpls.2020.00896] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/02/2020] [Indexed: 05/03/2023]
Abstract
Flavescence dorée (FD), caused by the phytoplasma Candidatus Phytoplasma vitis, is a major threat to vineyard survival in different European grape-growing areas. It has been recorded in French vineyards since the mid-1950s, and rapidly spread to other countries. In Portugal, the phytoplasma was first detected in the DOC region of 'Vinhos Verdes' in 2006, and reached the central region of the country in 2009. The infection causes strong accumulation of carbohydrates and phenolics in the mesophyll cells and a simultaneous decrease of chlorophylls, events accompanied by a down regulation of genes and proteins involved in the dark and light-dependent reactions and stabilization of the photosystem II (PSII). In the present study, to better elucidate the basis of the leaf chlorosis in infected grapevine cv. Loureiro, we studied the isoprenoid transcript-metabolite correlation in leaves from healthy and FD-infected vines. Specifically, targeted metabolome revealed that twenty-one compounds (out of thirty-two), including chlorophylls, carotenoids, quinones and tocopherols, were reduced in response to FD-infection. Thereafter, and consistently with the biochemical data, qPCR analysis highlighted a severe FD-mediated repression in key genes involved in isoprenoid biosynthetic pathways. A more diverse set of changes, on the contrary, was observed in the case of ABA metabolism. Principal component analysis (PCA) of all identified metabolites clearly separated healthy from FD-infected vines, therefore confirming that the infection strongly alters the biosynthesis of grapevine isoprenoids; additionally, forty-four genes and metabolites were identified as the components mostly explaining the variance between healthy and infected samples. Finally, transcript-metabolite network correlation analyses were exploited to display the main hubs of the infection process, which highlighted a strong role of VvCHLG, VvVTE and VvZEP genes and the chlorophylls intermediates aminolevulunic acid and porphobilinogen in response to FD infection. Overall, results indicated that the FD infection impairs the synthesis of isoprenoids, through the repression of key genes involved in the biosynthesis of chlorophylls, carotenoids, quinones and tocopherols.
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Affiliation(s)
- António Teixeira
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
- *Correspondence: António Teixeira,
| | - Viviana Martins
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - Sarah Frusciante
- Casaccia Research Center, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Telmo Cruz
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
| | - Henrique Noronha
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
| | - Gianfranco Diretto
- Casaccia Research Center, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Hernâni Gerós
- Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Braga, Portugal
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
- Centre of Biological Engineering (CEB), Department of Biological Engineering, University of Minho, Braga, Portugal
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24
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Iannicelli J, Guariniello J, Tossi V, Regalado J, Di Ciaccio L, van Baren C, Pitta Álvarez S, Escandón A. The “polyploid effect” in the breeding of aromatic and medicinal species. SCIENTIA HORTICULTURAE 2020. [PMID: 0 DOI: 10.1016/j.scienta.2019.108854] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
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25
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Ruiz M, Oustric J, Santini J, Morillon R. Synthetic Polyploidy in Grafted Crops. FRONTIERS IN PLANT SCIENCE 2020; 11:540894. [PMID: 33224156 PMCID: PMC7674608 DOI: 10.3389/fpls.2020.540894] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 09/28/2020] [Indexed: 05/05/2023]
Abstract
Synthetic polyploids have been extensively studied for breeding in the last decade. However, the use of such genotypes at the agronomical level is still limited. Polyploidization is known to modify certain plant phenotypes, while leaving most of the fundamental characteristics apparently untouched. For this reason, polyploid breeding can be very useful for improving specific traits of crop varieties, such as quality, yield, or environmental adaptation. Nevertheless, the mechanisms that underlie polyploidy-induced novelty remain poorly understood. Ploidy-induced phenotypes might also include some undesired effects that need to be considered. In the case of grafted or composite crops, benefits can be provided both by the rootstock's adaptation to the soil conditions and by the scion's excellent yield and quality. Thus, grafted crops provide an extraordinary opportunity to exploit artificial polyploidy, as the effects can be independently applied and explored at the root and/or scion level, increasing the chances of finding successful combinations. The use of synthetic tetraploid (4x) rootstocks may enhance adaptation to biotic and abiotic stresses in perennial crops such as apple or citrus. However, their use in commercial production is still very limited. Here, we will review the current and prospective use of artificial polyploidy for rootstock and scion improvement and the implications of their combination. The aim is to provide insight into the methods used to generate and select artificial polyploids and their limitations, the effects of polyploidy on crop phenotype (anatomy, function, quality, yield, and adaptation to stresses) and their potential agronomic relevance as scions or rootstocks in the context of climate change.
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Affiliation(s)
- Marta Ruiz
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias, Moncada, Spain
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Julie Oustric
- Laboratoire Biochimie et Biologie Moléculaire du Végétal, CNRS, UMR 6134 SPE, Université de Corse, Corte, France
| | - Jérémie Santini
- Laboratoire Biochimie et Biologie Moléculaire du Végétal, CNRS, UMR 6134 SPE, Université de Corse, Corte, France
| | - Raphaël Morillon
- CIRAD, UMR AGAP, Equipe SEAPAG, F-97170 Petit-Bourg, Guadeloupe, France - AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
- *Correspondence: Raphaël Morillon,
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26
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Tan FQ, Zhang M, Xie KD, Fan YJ, Song X, Wang R, Wu XM, Zhang HY, Guo WW. Polyploidy remodels fruit metabolism by modifying carbon source utilization and metabolic flux in Ponkan mandarin (Citrus reticulata Blanco). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 289:110276. [PMID: 31623787 DOI: 10.1016/j.plantsci.2019.110276] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 09/13/2019] [Accepted: 09/15/2019] [Indexed: 05/14/2023]
Abstract
The phenotypic variations that follow polyploidization are expected to improve agricultural productivity and efficiency [1]. However, the effect of polyploidization on plant metabolism has rarely been studied. This study evaluated the metabolic alterations that followed autotetraploidization in the fruit of Ponkan mandarin (C. reticulata Blanco) for three consecutive years and explored the underlying changes to the transcriptome. The autotetraploid (4x) Ponkan fruit had higher levels of total acids, ascorbic acid and total phenolic compounds than the diploid (2x). The primary metabolites especially the organic acids tended to accumulate at higher levels in the 4x fruit. Conversely, two major groups of secondary metabolites (i.e. flavonoids and carotenoids) tended to accumulate at lower levels. The expression levels of citric acid biosynthesis-related genes were unaltered in 4x fruit compared to the 2x fruit. Additionally, genes associated with the transport and utilization of citric acid were significantly down-regulated during ripening, which might induce increases in the levels of citric acid in the 4x fruit. Lower levels of flavonoids and carotenoids in the 4x fruit are potentially associated with decreases in the transport and utilization of citric acid, which is an important metabolite. Citric acid contributes to respiration by serving as an intermediated in the tricarboxylic acid cycle (TCA) and also provides carbon for the production of secondary metabolites. This study demonstrates that polyploidization can influence metabolism in plants.
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Affiliation(s)
- Feng-Quan Tan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Miao Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Kai-Dong Xie
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Yan-Jie Fan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin Song
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Rong Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiao-Meng Wu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Hong-Yan Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Wen-Wu Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.
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27
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Wei T, Wang Y, Xie Z, Guo D, Chen C, Fan Q, Deng X, Liu J. Enhanced ROS scavenging and sugar accumulation contribute to drought tolerance of naturally occurring autotetraploids in Poncirus trifoliata. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1394-1407. [PMID: 30578709 PMCID: PMC6576089 DOI: 10.1111/pbi.13064] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 05/20/2023]
Abstract
Tetraploids have been reported to exhibit increased stress tolerance, but the underlying molecular and physiological mechanisms remain poorly understood. In this study, autotetraploid plants were identified by screening natural seedlings of trifoliate orange (Poncirus trifoliata). The tetraploids exhibited different morphology and displayed significantly enhanced drought and dehydration tolerance in comparison with the diploid progenitor. Transcriptome analysis indicated that a number of stress-responsive genes and pathways were differentially influenced and enriched in the tetraploids, in particular those coding for enzymes related to antioxidant process and sugar metabolism. Transcript levels and activities of antioxidant enzymes (peroxidase and superoxide dismutase) and sucrose-hydrolysing enzyme (vacuolar invertase) were increased in the tetraploids upon exposure to the drought, concomitant with greater levels of glucose but lower level of reactive oxygen species (ROS). These data indicate that the tetraploids might undergo extensive transcriptome reprogramming of genes involved in ROS scavenging and sugar metabolism, which contributes, synergistically or independently, to the enhanced stress tolerance of the tetraploid. Our results reveal that the tetraploids take priority over the diploid for stress tolerance by maintaining a more robust system of ROS detoxification and osmotic adjustment via elevating antioxidant capacity and sugar accumulation in comparison with the diploid counterpart.
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Affiliation(s)
- Tonglu Wei
- Key Laboratory of Horticultural Plant Biology (MOE)College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Yue Wang
- Key Laboratory of Horticultural Plant Biology (MOE)College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Zongzhou Xie
- Key Laboratory of Horticultural Plant Biology (MOE)College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Dayong Guo
- Key Laboratory of Horticultural Plant Biology (MOE)College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Chuanwu Chen
- Guangxi Key Laboratory of Citrus BiologyGuangxi Academy of Specialty CropsGuilinChina
| | - Qijun Fan
- Guangxi Key Laboratory of Citrus BiologyGuangxi Academy of Specialty CropsGuilinChina
| | - Xiaodong Deng
- Key Laboratory of Horticultural Plant Biology (MOE)College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
| | - Ji‐Hong Liu
- Key Laboratory of Horticultural Plant Biology (MOE)College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanChina
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28
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Coppola M, Diretto G, Digilio MC, Woo SL, Giuliano G, Molisso D, Pennacchio F, Lorito M, Rao R. Transcriptome and Metabolome Reprogramming in Tomato Plants by Trichoderma harzianum strain T22 Primes and Enhances Defense Responses Against Aphids. Front Physiol 2019; 10:745. [PMID: 31293434 PMCID: PMC6599157 DOI: 10.3389/fphys.2019.00745] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 05/31/2019] [Indexed: 12/02/2022] Open
Abstract
Beneficial fungi in the genus Trichoderma are among the most widespread biocontrol agents of plant pathogens. Their role in triggering plant defenses against pathogens has been intensely investigated, while, in contrast, very limited information is available on induced barriers active against insects. The growing experimental evidence on this latter topic looks promising, and paves the way toward the development of Trichoderma strains and/or consortia active against multiple targets. However, the predictability and reproducibility of the effects that these beneficial fungi is still somewhat limited by the lack of an in-depth understanding of the molecular mechanisms underlying the specificity of their interaction with different crop varieties, and on how the environmental factors modulate this interaction. To fill this research gap, here we studied the transcriptome changes in tomato plants (cultivar "Dwarf San Marzano") induced by Trichoderma harzianum (strain T22) colonization and subsequent infestation by the aphid Macrosiphum euphorbiae. A wide transcriptome reprogramming, related to metabolic processes, regulation of gene expression and defense responses, was induced both by separate experimental treatments, which showed a synergistic interaction when concurrently applied. The most evident expression changes of defense genes were associated with the multitrophic interaction Trichoderma-tomato-aphid. Early and late genes involved in direct defense against insects were induced (i.e., peroxidase, GST, kinases and polyphenol oxidase, miraculin, chitinase), along with indirect defense genes, such as sesquiterpene synthase and geranylgeranyl phosphate synthase. Targeted and untargeted semi-polar metabolome analysis revealed a wide metabolome alteration showing an increased accumulation of isoprenoids in Trichoderma treated plants. The wide array of transcriptomic and metabolomics changes nicely fit with the higher mortality of aphids when feeding on Trichoderma treated plants, herein reported, and with the previously observed attractiveness of these latter toward the aphid parasitoid Aphidius ervi. Moreover, Trichoderma treated plants showed the over-expression of transcripts coding for several families of defense-related transcription factors (bZIP, MYB, NAC, AP2-ERF, WRKY), suggesting that the fungus contributes to the priming of plant responses against pest insects. Collectively, our data indicate that Trichoderma treatment of tomato plants induces transcriptomic and metabolomic changes, which underpin both direct and indirect defense responses.
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Affiliation(s)
| | | | - Maria Cristina Digilio
- Department of Agricultural Sciences, Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Sheridan Lois Woo
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
- National Research Council, Institute for Sustainable Plant Protection, Portici, Italy
| | | | | | - Francesco Pennacchio
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Matteo Lorito
- Department of Agricultural Sciences, Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
- National Research Council, Institute for Sustainable Plant Protection, Portici, Italy
| | - Rosa Rao
- Department of Agricultural Sciences, Portici, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Naples, Italy
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Cara N, Ferrer MS, Masuelli RW, Camadro EL, Marfil CF. Epigenetic consequences of interploidal hybridisation in synthetic and natural interspecific potato hybrids. THE NEW PHYTOLOGIST 2019; 222:1981-1993. [PMID: 30681145 DOI: 10.1111/nph.15706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 01/17/2019] [Indexed: 06/09/2023]
Abstract
Interploidal hybridisation can generate changes in plant chromosome numbers, which might exert effects additional to the expected due to genome merger per se (that is genetic, epigenetic and phenotypic novelties). Wild potatoes are suitable to address this question in an evolutionary context. To this end, we performed genetic (AFLP and single sequence repeart (SSR)), epigenetic (MSAP), and cytological comparisons in: (1) natural populations of the diploid cytotype of the hybrid taxonomic species Solanum × rechei (2n = 2×, 3×) and its parental species, the triploid cytotype of Solanum microdontum (2n = 2×, 3×) and Solanum kurtzianum (2n = 2×); and (2) newly synthesised intraploidal (2× × 2×) and interploidal (3× × 2×) S. microdontum × S. kurtzianum hybrids. Aneuploidy was detected in S. × rechei and the synthetic interploidal progeny; this phenomenon might have originated the significantly higher number of methylation changes observed in the interploidal vs the intraploidal hybrids. The wide epigenetic variability induced by interploidal hybridisation is consistent with the novel epigenetic pattern established in S. × rechei compared to its parental species in nature. These results suggest that aneuploid potato lineages can persist throughout the short term, and possibly medium term, and that differences in parental ploidy resulting in aneuploidy are an additional source of epigenetic variation.
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Affiliation(s)
- Nicolás Cara
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias, U.N.Cuyo, CONICET, Mendoza, Argentina
| | - María Soledad Ferrer
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias, U.N.Cuyo, CONICET, Mendoza, Argentina
| | - Ricardo Williams Masuelli
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias, U.N.Cuyo, CONICET, Mendoza, Argentina
| | - Elsa Lucila Camadro
- Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, CONICET, Mar del Plata, Argentina
| | - Carlos Federico Marfil
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias, U.N.Cuyo, CONICET, Mendoza, Argentina
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30
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Xu C, Ge Y, Wang J. Molecular basis underlying the successful invasion of hexaploid cytotypes of Solidago canadensis L.: Insights from integrated gene and miRNA expression profiling. Ecol Evol 2019; 9:4820-4852. [PMID: 31031947 PMCID: PMC6476842 DOI: 10.1002/ece3.5084] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 02/20/2019] [Accepted: 03/01/2019] [Indexed: 12/04/2022] Open
Abstract
Dissecting complex connections between cytogenetic traits (ploidy levels) and plant invasiveness has emerged as a popular research subject in the field of invasion biology. Although recent work suggests that polyploids are more likely to be invasive than their corresponding diploids, the molecular basis underlying the successful invasion of polyploids remains largely unexplored. To this end, we adopted an RNA-seq and sRNA-seq approach to describe how polyploids mediate invasiveness differences in two contrasting cytotypes of Solidago canadensis L., a widespread wild hexaploid invader with localized cultivated diploid populations. Our analysis of the leaf transcriptome revealed 116,801 unigenes, of which 12,897 unigenes displayed significant differences in expression levels. A substantial number of these differentially expressed unigenes (DEUs) were significantly associated with the biosynthesis of secondary metabolites, carbohydrate metabolism, lipid metabolism, and environmental adaptation pathways. Gene Ontology term enrichment-based categorization of DEU-functions was consistent with this observation, as terms related to single-organism, cellular, and metabolic processes including catalytic, binding, transporter, and enzyme regulator activity were over-represented. Concomitantly, 186 miRNAs belonging to 44 miRNA families were identified in the same leaf tissues, with 59 miRNAs being differentially expressed. Furthermore, we discovered 83 miRNA-target interacting pairs that were oppositely regulated, and a meticulous study of these targets depicted that several unigenes encoding transcription factors, DNA methyltransferase, and leucine-rich repeat receptor-like kinases involved in the stress response were greatly influenced. Collectively, these transcriptional and epigenetic data provide new insights into miRNA-mediated gene expression regulatory mechanisms that may operate in hexaploid cytotypes to favor successful invasion.
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Affiliation(s)
- Chanchan Xu
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Yimeng Ge
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
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Xia J, Ma YJ, Wang Y, Wang JW. Deciphering transcriptome profiles of tetraploid Artemisia annua plants with high artemisinin content. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 130:112-126. [PMID: 29982168 DOI: 10.1016/j.plaphy.2018.06.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/14/2018] [Accepted: 06/15/2018] [Indexed: 06/08/2023]
Abstract
To investigate on the effects of autopolyploidization on growth and artemisinin biosynthesis in Artemisia annua, we performed a comprehensive transcriptomic characterization of diploid and induced autotetraploid A. annua. The polyploidization treatment not only enhanced photosynthetic capacity and endogenous contents of indole-3-acetic acid (IAA), abscisic acid (ABA) and jasmonic acid (JA), oxidative stress, but increased the average level of artemisinin in tetraploids from 42.0 to 63.6%. The obvious phenotypic alterations in tetraploids were observed including shorter stems, larger size of stomata and glandular secretory trichomes (GSTs), larger leaves, more branches and roots. A total of 8763 (8.85%) differentially expressed genes (DEGs) were identified in autotetraploids and mainly involved in carbohydrate metabolic processes, cell wall organization and defense responses. Both the up-regulated expression of DNA methylation unigenes and enhanced level of DNA methylation in autotetraploids indicated a possible role of DNA methylation on transcriptomic remodeling and phenotypic alteration. The up-regulated genes were enriched in response to extracellular protein biosynthesis, photosynthesis and hormone stimulus for cell enlargement and phenotypic alteration. The genomic shock induced by chromosome duplication stimulated the expression of transcripts related to oxidative stress, biosynthesis and signal transduction of ABA and JA, and key enzymes in artemisinin biosynthetic pathway, leading to the increased accumulation of artemisinin. This is the first transcriptomic research that identifies DEGs involved in the polyploidization of A. annua. The results provide novel information for understanding the complexity of polyploidization and for further identification of the factors and genes involve in artemisinin biosynthesis.
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Affiliation(s)
- Jing Xia
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Yan Jun Ma
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Yue Wang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China
| | - Jian Wen Wang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, China.
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Transcriptome analysis in tissue sectors with contrasting crocins accumulation provides novel insights into apocarotenoid biosynthesis and regulation during chromoplast biogenesis. Sci Rep 2018; 8:2843. [PMID: 29434251 PMCID: PMC5809551 DOI: 10.1038/s41598-018-21225-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 02/01/2018] [Indexed: 11/08/2022] Open
Abstract
Crocins, the red soluble apocarotenoids of saffron, accumulate in the flowers of Crocus species in a developmental and tissue-specific manner. In Crocus sieberi, crocins accumulate in stigmas but also in a distinct yellow tepal sector, which we demonstrate contains chromoplast converted from amyloplasts. Secondary metabolites were analysed by LC-DAD-HRMS, revealing the progressive accumulation of crocetin and crocins in the yellow sector, which were also localized in situ by Raman microspectroscopy. To understand the underlying mechanisms of crocin biosynthesis, we sequenced the C. sieberi tepal transcriptome of two differentially pigmented sectors (yellow and white) at two developmental stages (6 and 8) by Illumina sequencing. A total of 154 million high-quality reads were generated and assembled into 248,099 transcripts. Differentially expressed gene analysis resulted in the identification of several potential candidate genes involved in crocin metabolism and regulation. The results provide a first profile of the molecular events related to the dynamics of crocetin and crocin accumulation during tepal development, and present new information concerning apocarotenoid biosynthesis regulators and their accumulation in Crocus. Further, reveals genes that were previously unknown to affect crocin formation, which could be used to improve crocin accumulation in Crocus plants and the commercial quality of saffron spice.
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Sulli M, Mandolino G, Sturaro M, Onofri C, Diretto G, Parisi B, Giuliano G. Molecular and biochemical characterization of a potato collection with contrasting tuber carotenoid content. PLoS One 2017; 12:e0184143. [PMID: 28898255 PMCID: PMC5595298 DOI: 10.1371/journal.pone.0184143] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/18/2017] [Indexed: 12/26/2022] Open
Abstract
After wheat and rice, potato is the third most important staple food worldwide. A collection of ten tetraploid (Solanum tuberosum) and diploid (S. phureja and S. chacoense) genotypes with contrasting carotenoid content was subjected to molecular characterization with respect to candidate carotenoid loci and metabolic profiling using LC-HRMS. Irrespective of ploidy and taxonomy, tubers of these genotypes fell into three groups: yellow-fleshed, characterized by high levels of epoxy-xanthophylls and xanthophyll esters and by the presence of at least one copy of a dominant allele of the β-Carotene Hydroxylase 2 (CHY2) gene; white-fleshed, characterized by low carotenoid levels and by the presence of recessive chy2 alleles; and orange-fleshed, characterized by high levels of zeaxanthin but low levels of xanthophyll esters, and homozygosity for a Zeaxanthin Epoxidase (ZEP) recessive allele. Novel CHY2 and ZEP alleles were identified in the collection. Multivariate analysis identified several groups of co-regulated non-polar compounds, and resulted in the grouping of the genotypes according to flesh color, suggesting that extensive cross-talk exists between the carotenoid pathway and other metabolite pathways in tubers. Postharvest traits like tuber dormancy and weight loss during storage showed little correlation with tuber carotenoid content, with the exception of zeaxanthin and its esters. Other tuber metabolites, such as glucose, monogalactosyldiacyglycerol (a glycolipid), or suberin precursors, showed instead significant correlations with both traits.
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Affiliation(s)
- Maria Sulli
- ENEA, Casaccia Research Center, Via Anguillarese 301, Roma, Italy
- Scuola Superiore S. Anna, Piazza Martiri della Libertà 33, Pisa, Italy
| | - Giuseppe Mandolino
- CREA-Centro Cerealicoltura e Colture Industriali, Sede di Bologna, Via di Corticella 133, Bologna, Italy
| | - Monica Sturaro
- CREA- Centro Cerealicoltura e Colture Industriali, Sede di Bergamo, Via Stezzano 24, Bergamo, Italy
| | - Chiara Onofri
- CREA-Centro Cerealicoltura e Colture Industriali, Sede di Bologna, Via di Corticella 133, Bologna, Italy
| | | | - Bruno Parisi
- CREA-Centro Cerealicoltura e Colture Industriali, Sede di Bologna, Via di Corticella 133, Bologna, Italy
| | - Giovanni Giuliano
- ENEA, Casaccia Research Center, Via Anguillarese 301, Roma, Italy
- * E-mail:
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Diretto G, Rubio-Moraga A, Argandoña J, Castillo P, Gómez-Gómez L, Ahrazem O. Tissue-Specific Accumulation of Sulfur Compounds and Saponins in Different Parts of Garlic Cloves from Purple and White Ecotypes. Molecules 2017; 22:E1359. [PMID: 28825644 PMCID: PMC6152257 DOI: 10.3390/molecules22081359] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/12/2017] [Accepted: 08/14/2017] [Indexed: 11/18/2022] Open
Abstract
This study set out to determine the distribution of sulfur compounds and saponin metabolites in different parts of garlic cloves. Three fractions from purple and white garlic ecotypes were obtained: the tunic (SS), internal (IS) and external (ES) parts of the clove. Liquid Chromatography coupled to High Resolution Mass spectrometry (LC-HRMS), together with bioinformatics including Principal Component Analysis (PCA), Hierarchical Clustering (HCL) and correlation network analyses were carried out. Results showed that the distribution of these metabolites in the different parts of garlic bulbs was different for the purple and the white ecotypes, with the main difference being a slightly higher number of sulfur compounds in purple garlic. The SS fraction in purple garlic had a higher content of sulfur metabolites, while the ES in white garlic was more enriched by these compounds. The correlation network indicated that diallyl disulfide was the most relevant metabolite with regards to sulfur compound metabolism in garlic. The total number of saponins was almost 40-fold higher in purple garlic than in the white variety, with ES having the highest content. Interestingly, five saponins including desgalactotigonin-rhamnose, proto-desgalactotigonin, proto-desgalactotigonin-rhamnose, voghieroside D1, sativoside B1-rhamnose and sativoside R1 were exclusive to the purple variety. Data obtained from saponin analyses revealed a very different network between white and purple garlic, thus suggesting a very robust and tight coregulation of saponin metabolism in garlic. Findings in this study point to the possibility of using tunics from purple garlic in the food and medical industries, since it contains many functional compounds which can be exploited as ingredients.
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Affiliation(s)
- Gianfranco Diretto
- Italian National Agency for New Technologies, Energy and Sustainable Development, Casaccia Research Centre, 00123 Rome, Italy.
| | - Angela Rubio-Moraga
- Instituto Botánico, Departamento de Ciencia y Tecnología Agroforestal y Genética, Facultad de Farmacia, Universidad de Castilla-La Mancha, Campus Universitario, s/n, 02071 Albacete, Spain.
| | - Javier Argandoña
- Instituto Botánico, Departamento de Ciencia y Tecnología Agroforestal y Genética, Facultad de Farmacia, Universidad de Castilla-La Mancha, Campus Universitario, s/n, 02071 Albacete, Spain.
| | - Purificación Castillo
- Coopaman S.C.L., Departamento I+D, Carretera Peñas De San Pedro, km 1.6, 02006 Albacete, Spain.
| | - Lourdes Gómez-Gómez
- Instituto Botánico, Departamento de Ciencia y Tecnología Agroforestal y Genética, Facultad de Farmacia, Universidad de Castilla-La Mancha, Campus Universitario, s/n, 02071 Albacete, Spain.
| | - Oussama Ahrazem
- Instituto Botánico, Departamento de Ciencia y Tecnología Agroforestal y Genética, Facultad de Farmacia, Universidad de Castilla-La Mancha, Campus Universitario, s/n, 02071 Albacete, Spain.
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Campus Tecnológico de la Fábrica de Armas, Avda, Carlos III, s/n, E-45071 Toledo, Spain.
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Aversano R, Contaldi F, Adelfi MG, D'Amelia V, Diretto G, De Tommasi N, Vaccaro C, Vassallo A, Carputo D. Comparative metabolite and genome analysis of tuber-bearing potato species. PHYTOCHEMISTRY 2017; 137:42-51. [PMID: 28215419 DOI: 10.1016/j.phytochem.2017.02.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 02/06/2017] [Accepted: 02/08/2017] [Indexed: 05/20/2023]
Abstract
The cultivated potato Solanum tuberosum is unrivalled among crop plants for its wild relatives, which potentially represent an important source of genetic diversity to improve the nutritional value of potato varieties and understand metabolism regulation. The main aim of this research was to profile human health-related metabolites in a number of clones from 13 Solanum species. Results from HPLC-DAD and LC-ESI-MS analyses highlighted a high interspecific variability in the level of metabolites analysed. Ascorbic acid was confirmed to be the most abundant antioxidant in potato and chlorogenic acid the primary polyphenol. Generally, metabolite-based hierarchical clustering (HCL) and correlation networks did not group clones of identical species in the same cluster. This might be due to various factors, including the outcrossing nature of potato species, gene expression level and metabolic profiling techniques. Access to the genome sequence of S. tuberosum and S. commersonii allowed comparison of the genes involved in ascorbic acid, aromatic amino acid, phenylpropanoid and glycoalkaloid biosynthesis and helped interpret their respective pathways.
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Affiliation(s)
- Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, Portici 80055, Italy
| | - Felice Contaldi
- Department of Agricultural Sciences, University of Naples Federico II, Portici 80055, Italy
| | - Maria Grazia Adelfi
- Department of Agricultural Sciences, University of Naples Federico II, Portici 80055, Italy
| | - Vincenzo D'Amelia
- Department of Agricultural Sciences, University of Naples Federico II, Portici 80055, Italy
| | - Gianfranco Diretto
- Italian National Agency for New Technologies, Energy, and Sustainable Development, Casaccia Research Centre, Rome 00123, Italy
| | - Nunziatina De Tommasi
- Department of Pharmaceutical Sciences, University of Salerno, Via Ponte Don Melillo 1, 84084 Fisciano, Italy
| | - Carmen Vaccaro
- Department of Pharmaceutical Sciences, University of Salerno, Via Ponte Don Melillo 1, 84084 Fisciano, Italy
| | - Antonio Vassallo
- Department of Science, University of Basilicata, Viale dell'Ateneo Lucano 10, 85100 Potenza, Italy
| | - Domenico Carputo
- Department of Agricultural Sciences, University of Naples Federico II, Portici 80055, Italy.
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