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Girija A, Hacham Y, Dvir S, Panda S, Lieberman-Lazarovich M, Amir R. Cystathionine γ-synthase expression in seeds alters metabolic and DNA methylation profiles in Arabidopsis. PLANT PHYSIOLOGY 2023; 193:595-610. [PMID: 37300538 DOI: 10.1093/plphys/kiad330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 06/12/2023]
Abstract
Arabidopsis (Arabidopsis thaliana) seeds expressing the feedback-insensitive form of cystathionine γ-synthase (AtD-CGS), the key gene of methionine (Met) synthesis, under the control of a seed-specific phaseolin promoter (SSE plants) show a significant increase in Met content. This elevation is accompanied by increased levels of other amino acids (AAs), sugars, total protein, and starch, which are important from a nutritional aspect. Here, we investigated the mechanism behind this phenomenon. Gas chromatography-mass spectrometry (GC-MS) analysis of SSE leaves, siliques, and seeds collected at 3 different developmental stages showed high levels of Met, AAs, and sugars compared to the control plants. A feeding experiment with isotope-labeled AAs showed an increased flux of AAs from nonseed tissues toward the developing seeds of SSE. Transcriptome analysis of leaves and seeds displayed changes in the status of methylation-related genes in SSE plants that were further validated by methylation-sensitive enzymes and colorimetric assay. These results suggest that SSE leaves have higher DNA methylation rates than control plants. This occurrence apparently led to accelerated senescence, together with enhanced monomer synthesis, which further resulted in increased transport of monomers from the leaves toward the seeds. The developing seeds of SSE plants, however, show reduced Met levels and methylation rates. The results provide insights into the role of Met in DNA methylation and gene expression and how Met affects the metabolic profile of the plant.
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Affiliation(s)
- Aiswarya Girija
- MIGAL-Galilee Research Institute, Plant Metabolism Lab, Kiryat Shmona 11016, Israel
| | - Yael Hacham
- MIGAL-Galilee Research Institute, Plant Metabolism Lab, Kiryat Shmona 11016, Israel
- Department of Biotechnology, Tel Hai College, Upper Galilee 1220800, Israel
| | - Shachar Dvir
- MIGAL-Galilee Research Institute, Plant Metabolism Lab, Kiryat Shmona 11016, Israel
- Department of Biotechnology, Tel Hai College, Upper Galilee 1220800, Israel
| | - Sayantan Panda
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Michal Lieberman-Lazarovich
- Institute of Plant Sciences, Department of Vegetables and Field Crops, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel
| | - Rachel Amir
- MIGAL-Galilee Research Institute, Plant Metabolism Lab, Kiryat Shmona 11016, Israel
- Department of Biotechnology, Tel Hai College, Upper Galilee 1220800, Israel
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Sunseri F, Aci MM, Mauceri A, Caldiero C, Puccio G, Mercati F, Abenavoli MR. Short-term transcriptomic analysis at organ scale reveals candidate genes involved in low N responses in NUE-contrasting tomato genotypes. FRONTIERS IN PLANT SCIENCE 2023; 14:1125378. [PMID: 36938018 PMCID: PMC10020590 DOI: 10.3389/fpls.2023.1125378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Understanding the complex regulatory network underlying plant nitrogen (N) responses associated with high Nitrogen Use Efficiency (NUE) is one of the main challenges for sustainable cropping systems. Nitrate (NO3 -), acting as both an N source and a signal molecule, provokes very fast transcriptome reprogramming, allowing plants to adapt to its availability. These changes are genotype- and tissue-specific; thus, the comparison between contrasting genotypes is crucial to uncovering high NUE mechanisms. METHODS Here, we compared, for the first time, the spatio-temporal transcriptome changes in both root and shoot of two NUE contrasting tomato genotypes, Regina Ostuni (high-NUE) and UC82 (low-NUE), in response to short-term (within 24 h) low (LN) and high (HN) NO3 - resupply. RESULTS Using time-series transcriptome data (0, 8, and 24 h), we identified 395 and 482 N-responsive genes differentially expressed (DEGs) between RO and UC82 in shoot and root, respectively. Protein kinase signaling plant hormone signal transduction, and phenylpropanoid biosynthesis were the main enriched metabolic pathways in shoot and root, respectively, and were upregulated in RO compared to UC82. Interestingly, several N transporters belonging to NRT and NPF families, such as NRT2.3, NRT2.4, NPF1.2, and NPF8.3, were found differentially expressed between RO and UC82 genotypes, which might explain the contrasting NUE performances. Transcription factors (TFs) belonging to several families, such as ERF, LOB, GLK, NFYB, ARF, Zinc-finger, and MYB, were differentially expressed between genotypes in response to LN. A complementary Weighted Gene Co-expression Network Analysis (WGCNA) allowed the identification of LN-responsive co-expression modules in RO shoot and root. The regulatory network analysis revealed candidate genes that might have key functions in short-term LN regulation. In particular, an asparagine synthetase (ASNS), a CBL-interacting serine/threonine-protein kinase 1 (CIPK1), a cytokinin riboside 5'-monophosphate phosphoribohydrolase (LOG8), a glycosyltransferase (UGT73C4), and an ERF2 were identified in the shoot, while an LRR receptor-like serine/threonine-protein kinase (FEI1) and two TFs NF-YB5 and LOB37 were identified in the root. DISCUSSION Our results revealed potential candidate genes that independently and/or concurrently may regulate short-term low-N response, suggesting a key role played by cytokinin and ROS balancing in early LN regulation mechanisms adopted by the N-use efficient genotype RO.
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Affiliation(s)
- Francesco Sunseri
- Dipartimento Agraria, Università Mediterranea di Reggio Calabria, Reggio Calabria, Italy
- National Research Council of Italy, Institute of Biosciences and Bioresources (CNR-IBBR), Palermo, Italy
| | - Meriem Miyassa Aci
- Dipartimento Agraria, Università Mediterranea di Reggio Calabria, Reggio Calabria, Italy
| | - Antonio Mauceri
- Dipartimento Agraria, Università Mediterranea di Reggio Calabria, Reggio Calabria, Italy
| | - Ciro Caldiero
- Dipartimento Agraria, Università Mediterranea di Reggio Calabria, Reggio Calabria, Italy
| | - Guglielmo Puccio
- National Research Council of Italy, Institute of Biosciences and Bioresources (CNR-IBBR), Palermo, Italy
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, Viale delle Scienze, Palermo, Italy
| | - Francesco Mercati
- National Research Council of Italy, Institute of Biosciences and Bioresources (CNR-IBBR), Palermo, Italy
| | - Maria Rosa Abenavoli
- Dipartimento Agraria, Università Mediterranea di Reggio Calabria, Reggio Calabria, Italy
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Ahouvi Y, Haber Z, Zach YY, Rosental L, Toubiana D, Sharma D, Alseekh S, Tajima H, Fernie AR, Brotman Y, Blumwald E, Sade N. The Alteration of Tomato Chloroplast Vesiculation Positively Affects Whole-Plant Source-Sink Relations and Fruit Metabolism under Stress Conditions. PLANT & CELL PHYSIOLOGY 2023; 63:2008-2026. [PMID: 36161338 DOI: 10.1093/pcp/pcac133] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 09/14/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Changes in climate conditions can negatively affect the productivity of crop plants. They can induce chloroplast degradation (senescence), which leads to decreased source capacity, as well as decreased whole-plant carbon/nitrogen assimilation and allocation. The importance, contribution and mechanisms of action regulating source-tissue capacity under stress conditions in tomato (Solanum lycopersicum) are not well understood. We hypothesized that delaying chloroplast degradation by altering the activity of the tomato chloroplast vesiculation (CV) under stress would lead to more efficient use of carbon and nitrogen and to higher yields. Tomato CV is upregulated under stress conditions. Specific induction of CV in leaves at the fruit development stage resulted in stress-induced senescence and negatively affected fruit yield, without any positive effects on fruit quality. Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (CRISPR/CAS9) knockout CV plants, generated using a near-isogenic tomato line with enhanced sink capacity, exhibited stress tolerance at both the vegetative and the reproductive stages, leading to enhanced fruit quantity, quality and harvest index. Detailed metabolic and transcriptomic network analysis of sink tissue revealed that the l-glutamine and l-arginine biosynthesis pathways are associated with stress-response conditions and also identified putative novel genes involved in tomato fruit quality under stress. Our results are the first to demonstrate the feasibility of delayed stress-induced senescence as a stress-tolerance trait in a fleshy fruit crop, to highlight the involvement of the CV pathway in the regulation of source strength under stress and to identify genes and metabolic pathways involved in increased tomato sink capacity under stress conditions.
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Affiliation(s)
- Yoav Ahouvi
- School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel
| | - Zechariah Haber
- School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel
| | - Yair Yehoshua Zach
- School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel
| | - Leah Rosental
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O.B. 653, 1 David Ben Gurion Blvd., Beer-Sheva 8410501, Israel
| | - David Toubiana
- School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel
| | - Davinder Sharma
- School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel
| | - Saleh Alseekh
- Department of Root Biology and Symbiosis, Max Planck Institute of Molecular Plant Physiology, 1 Am Mühlenberg, Golm, Potsdam 14476, Germany
- Department of Plant Metabolomics, Center for Plant Systems Biology and Biotechnology, 139 Ruski Blvd., Plovdiv 4000, Bulgaria
| | - Hiromi Tajima
- Department of Plant Sciences, University of California, 1 Shields Ave., Davis, CA 95616, USA
| | - Alisdair R Fernie
- Department of Root Biology and Symbiosis, Max Planck Institute of Molecular Plant Physiology, 1 Am Mühlenberg, Golm, Potsdam 14476, Germany
- Department of Plant Metabolomics, Center for Plant Systems Biology and Biotechnology, 139 Ruski Blvd., Plovdiv 4000, Bulgaria
| | - Yariv Brotman
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O.B. 653, 1 David Ben Gurion Blvd., Beer-Sheva 8410501, Israel
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, 1 Shields Ave., Davis, CA 95616, USA
| | - Nir Sade
- School of Plant Sciences and Food Security, Tel Aviv University, P.O.B. 39040, 55 Haim Levanon St., Tel Aviv 6139001, Israel
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Tao T, Hu W, Yang Y, Zou M, Zhou S, Tian S, Wang Y. Transcriptomics reveals the molecular mechanisms of flesh colour differences in eggplant (Solanum melongena). BMC PLANT BIOLOGY 2023; 23:5. [PMID: 36597026 PMCID: PMC9811765 DOI: 10.1186/s12870-022-04002-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Fruit flesh colour is not only an important commodity attribute of eggplant but is also closely related to maturity. However, very little is known about its formation mechanism in eggplant. RESULTS Two inbred lines of eggplant, green 'NC7' and white 'BL', were used in this study to explain the differences in flesh colour. Transcriptome sequencing results revealed a total of 3304 differentially expressed genes (DEGs) in NC7 vs. BL. Of the DEGs obtained, 2050 were higher and 1254 were lower in BL. These DEGs were annotated to 126 pathways, where porphyrin and chlorophyll metabolism, flavonoid biosynthesis, and photosynthesis-antenna proteins play vital roles in the colour formation of eggplant flesh. At the same time, Gene Ontology (GO) enrichment significance analysis showed that a large number of unigenes involved in the formation of chloroplast structure were lower in BL, which indicated that the formation of chloroplasts in white-fleshed eggplant was blocked. This was confirmed by transmission electron microscopy (TEM), which found only leucoplasts but no chloroplasts in the flesh cells of white-fleshed eggplant. Several genes encoding ERF and bHLH transcription factors were predicted to participate in the regulation of chlorophyll biosynthetic genes. CONCLUSIONS The results of this study indicated that differences in the gene expression of the chlorophyll metabolic pathway were the main cause of the different flesh colour formations. These findings will increase our understanding of the genetic basis in eggplant flesh colors formation mechanism.
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Affiliation(s)
- Tao Tao
- Vegetable and Flower Institute of Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China
| | - Wei Hu
- Vegetable and Flower Institute of Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China
| | - Yang Yang
- Vegetable and Flower Institute of Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China
| | - Min Zou
- Vegetable and Flower Institute of Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China
| | - Shanshan Zhou
- Vegetable and Flower Institute of Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China
| | - Shibing Tian
- Vegetable and Flower Institute of Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China.
| | - Yongqing Wang
- Vegetable and Flower Institute of Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China.
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Mauceri A, Aci MM, Toppino L, Panda S, Meir S, Mercati F, Araniti F, Lupini A, Panuccio MR, Rotino GL, Aharoni A, Abenavoli MR, Sunseri F. Uncovering Pathways Highly Correlated to NUE through a Combined Metabolomics and Transcriptomics Approach in Eggplant. PLANTS 2022; 11:plants11050700. [PMID: 35270170 PMCID: PMC8912549 DOI: 10.3390/plants11050700] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 12/01/2022]
Abstract
Nitrogen (N) fertilization is one of the main inputs to increase crop yield and food production. However, crops utilize only 30–40% of N applied; the remainder is leached into the soil, causing environmental and health damage. In this scenario, the improvement of nitrogen-use efficiency (NUE) will be an essential strategy for sustainable agriculture. Here, we compared two pairs of NUE-contrasting eggplant (Solanum melongena L.) genotypes, employing GC-MS and UPLC-qTOF-MS-based technologies to determine the differential profiles of primary and secondary metabolites in root and shoot tissues, under N starvation as well as at short- and long-term N-limiting resupply. Firstly, differences in the primary metabolism pathways of shoots related to alanine, aspartate and glutamate; starch, sucrose and glycine; serine and threonine; and in secondary metabolites biosynthesis were detected. An integrated analysis between differentially accumulated metabolites and expressed transcripts highlighted a key role of glycine accumulation and the related glyA transcript in the N-use-efficient genotypes to cope with N-limiting stress. Interestingly, a correlation between both sucrose synthase (SUS)- and fructokinase (scrK)-transcript abundances, as well as D-glucose and D-fructose accumulation, appeared useful to distinguish the N-use-efficient genotypes. Furthermore, increased levels of L-aspartate and L-asparagine in the N-use-efficient genotypes at short-term low-N exposure were detected. Granule-bound starch synthase (WAXY) and endoglucanase (E3.2.1.4) downregulation at long-term N stress was observed. Therefore, genes and metabolites related to these pathways could be exploited to improve NUE in eggplant.
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Affiliation(s)
- Antonio Mauceri
- Department Agraria, University Mediterranea of Reggio Calabria, 89122 Reggio Calabria, Italy; (M.M.A.); (A.L.); (M.R.P.); (F.S.)
- Correspondence: (A.M.); (M.R.A.)
| | - Meriem Miyassa Aci
- Department Agraria, University Mediterranea of Reggio Calabria, 89122 Reggio Calabria, Italy; (M.M.A.); (A.L.); (M.R.P.); (F.S.)
| | - Laura Toppino
- CREA—Research Centre for Genomics and Bioinformatics, 26836 Montanaso Lombardo, Italy; (L.T.); (G.L.R.)
| | - Sayantan Panda
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel; (S.P.); (S.M.); (A.A.)
| | - Sagit Meir
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel; (S.P.); (S.M.); (A.A.)
| | - Francesco Mercati
- Institute Bioscience and Bioresources—National Research Council CNR, 90129 Palermo, Italy;
| | - Fabrizio Araniti
- Department of Agricultural and Environmental Sciences—Production, Territory, Agroenergy, University of Milano, 20133 Milan, Italy;
| | - Antonio Lupini
- Department Agraria, University Mediterranea of Reggio Calabria, 89122 Reggio Calabria, Italy; (M.M.A.); (A.L.); (M.R.P.); (F.S.)
| | - Maria Rosaria Panuccio
- Department Agraria, University Mediterranea of Reggio Calabria, 89122 Reggio Calabria, Italy; (M.M.A.); (A.L.); (M.R.P.); (F.S.)
| | - Giuseppe Leonardo Rotino
- CREA—Research Centre for Genomics and Bioinformatics, 26836 Montanaso Lombardo, Italy; (L.T.); (G.L.R.)
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel; (S.P.); (S.M.); (A.A.)
| | - Maria Rosa Abenavoli
- Department Agraria, University Mediterranea of Reggio Calabria, 89122 Reggio Calabria, Italy; (M.M.A.); (A.L.); (M.R.P.); (F.S.)
- Correspondence: (A.M.); (M.R.A.)
| | - Francesco Sunseri
- Department Agraria, University Mediterranea of Reggio Calabria, 89122 Reggio Calabria, Italy; (M.M.A.); (A.L.); (M.R.P.); (F.S.)
- Institute Bioscience and Bioresources—National Research Council CNR, 90129 Palermo, Italy;
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Dhakarey R, Yaritz U, Tian L, Amir R. A Myb transcription factor, PgMyb308-like, enhances the level of shikimate, aromatic amino acids, and lignins, but represses the synthesis of flavonoids and hydrolyzable tannins, in pomegranate (Punica granatum L.). HORTICULTURE RESEARCH 2022; 9:uhac008. [PMID: 35147167 PMCID: PMC9113223 DOI: 10.1093/hr/uhac008] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 12/04/2021] [Indexed: 06/14/2023]
Abstract
Pomegranate fruit peels are highly abundant in metabolites derived from the shikimate pathway, such as hydrolyzable tannins (HTs) and flavonoids. These metabolites are beneficial to human health (commercial juice is enriched with peel metabolites), and also protect the fruit from environmental stresses. To understand the transcriptional control of shikimate pathway-related metabolites in pomegranate, we cloned and characterized a subgroup S4 R2R3 Myb transcription factor, PgMyb308-like. Overexpressing PgMyb308-like in pomegranate hairy roots increased the accumulation of shikimate, aromatic amino acids, isoferulic acid, and total lignins, but led to reduced gallic acid and its downstream products HTs, as well as multiple flavonoids. Changes in these metabolites are supported by the increased expression of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase and shikimate dehydrogenase 1 (PgSDH1) (the SDH isoform associated with shikimate biosynthesis), and the reduced expression of PgSDH4 (the SDH isoform suggested to produce gallic acid). Transcriptome analysis of PgMyb308-like-overexpressing hairy roots further revealed reprogramming of cell wall-related genes, while overexpression of PgMyb308-like in Arabidopsis thaliana plants uncovered its distinct role in a different genetic and metabolic background. These results together suggest that PgMyb308-like activates genes in the shikimate pathway and lignin biosynthesis, but suppresses those involved in the production of HTs and flavonoids.
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Affiliation(s)
- Rohit Dhakarey
- Department of Plant Science, Migal – Galilee Technology Center, P.O. Box 831, Kiryat Shmona 1101600, Israel
| | - Uri Yaritz
- Department of Plant Science, Migal – Galilee Technology Center, P.O. Box 831, Kiryat Shmona 1101600, Israel
- Department of Biotechnology, Tel-Hai College, Upper Galilee 1220800, Israel
| | - Li Tian
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Rachel Amir
- Department of Plant Science, Migal – Galilee Technology Center, P.O. Box 831, Kiryat Shmona 1101600, Israel
- Department of Biotechnology, Tel-Hai College, Upper Galilee 1220800, Israel
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7
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Wang J, Xu J, Yang X, Xu S, Zhang M, Lu F. Boosting the power of transcriptomics by developing an efficient gene expression profiling approach. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:201-210. [PMID: 34510693 PMCID: PMC8710826 DOI: 10.1111/pbi.13706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/09/2021] [Accepted: 08/29/2021] [Indexed: 06/13/2023]
Abstract
Recent advances in plant genomics are scaling up gene expression profiling from the individual level to the population level, making transcriptomics a more powerful tool while deciphering the genome function. This study developed an efficient 3'RNA-seq method, Simplified Poly(A) Anchored Sequencing (SiPAS), to perform large-scale experiments of gene expression quantification. Aside from being cost-effective, by conducting a comprehensive performance assessment of SiPAS in hexaploid wheat, we demonstrated that SiPAS is highly sensitive, accurate, and reproducible while quantifying gene expression. Our method is anticipated to boost studies of population transcriptomics in plants and improve our understanding of genome biology.
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Affiliation(s)
- Jing Wang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Jun Xu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaohan Yang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Song Xu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ming Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Fei Lu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
- CAS‐JIC Centre of Excellence for Plant and Microbial Science (CEPAMS)Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
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8
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A High-Throughput 3'-Tag RNA Sequencing for Large-Scale Time-Series Transcriptome Studies. Methods Mol Biol 2021; 2398:151-172. [PMID: 34674175 DOI: 10.1007/978-1-0716-1912-4_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
RNA sequencing (RNA-seq) has proven invaluable for exploring gene expression variation under complex environmental cues. However, the cost of standard RNA-seq (e.g., Illumina TruSeq or NEBNext) remains a barrier for high-throughput applications. 3'-Tag RNA-seq (3'-TagSeq) is a cost-effective solution that permits large-scale experiments. Unlike standard RNA-seq, which generates sequencing libraries for full-length mRNAs, 3'-TagSeq only generates a single fragment from the 3' end of each transcript (a tag read) and quantifies gene expression by tag abundance. Consequently, 3'-TagSeq requires lower sequencing depth (~5 million reads per sample) than standard RNA-seq (~30 million reads per sample), which reduces costs and allows increased technical and biological replication in experiments. Because 3'-TagSeq is considerably cheaper than standard RNA-seq while exhibiting comparable accuracy and reproducibility, researchers focusing on gene expression levels in large or extensive time-series experiments might find 3'-TagSeq to be superior to standard RNA-seq. In this chapter, we describe 3'-TagSeq sequencing library preparation and provide example bioinformatics and statistical analyses of gene expression data.
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9
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Chen J, Zhang X, Yi F, Gao X, Song W, Zhao H, Lai J. MP3RNA-seq: Massively parallel 3' end RNA sequencing for high-throughput gene expression profiling and genotyping. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1227-1239. [PMID: 33559966 DOI: 10.1111/jipb.13077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 02/02/2021] [Indexed: 05/26/2023]
Abstract
Transcriptome deep sequencing (RNA-seq) has become a routine method for global gene expression profiling. However, its application to large-scale experiments remains limited by cost and labor constraints. Here we describe a massively parallel 3' end RNA-seq (MP3RNA-seq) method that introduces unique sample barcodes during reverse transcription to permit sample pooling immediately following this initial step. MP3RNA-seq allows for handling of hundreds of samples in a single experiment, at a cost of about $6 per sample for library construction and sequencing. MP3RNA-seq is effective for not only high-throughput gene expression profiling, but also genotyping. To demonstrate its utility, we applied MP3RNA-seq to 477 double haploid lines of maize. We identified 19,429 genes expressed in at least 50% of the lines and 35,836 high-quality single nucleotide polymorphisms for genotyping analysis. Armed with these data, we performed expression and agronomic trait quantitative trait locus (QTL) mapping and identified 25,797 expression QTLs for 15,335 genes and 21 QTLs for plant height, ear height, and relative ear height. We conclude that MP3RNA-seq is highly reproducible, accurate, and sensitive for high-throughput gene expression profiling and genotyping, and should be generally applicable to most eukaryotic species.
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Affiliation(s)
- Jian Chen
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Xiangbo Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Fei Yi
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Xiang Gao
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Weibin Song
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Haiming Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China
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10
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Mauceri A, Abenavoli MR, Toppino L, Panda S, Mercati F, Aci MM, Aharoni A, Sunseri F, Rotino GL, Lupini A. Transcriptomics reveal new insights into molecular regulation of nitrogen use efficiency in Solanum melongena. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4237-4253. [PMID: 33711100 DOI: 10.1093/jxb/erab121] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
Nitrogen-use efficiency (NUE) is a complex trait of great interest in breeding programs because through its improvement, high crop yields can be maintained whilst N supply is reduced. In this study, we report a transcriptomic analysis of four NUE-contrasting eggplant (Solanum melongena) genotypes following short- and long-term exposure to low N, to identify key genes related to NUE in the roots and shoots. The differentially expressed genes in the high-NUE genotypes are involved in the light-harvesting complex and receptor, a ferredoxin-NADP reductase, a catalase and WRKY33. These genes were then used as bait for a co-expression gene network analysis in order to identify genes with the same trends in expression. This showed that up-regulation of WRKY33 triggered higher expression of a cluster of 21 genes and also of other genes, many of which were related to N-metabolism, that were able to improve both nitrogen uptake efficiency and nitrogen utilization efficiency, the two components of NUE. We also conducted an independent de novo experiment to validate the significantly higher expression of WRKY33 and its gene cluster in the high-NUE genotypes. Finally, examination of an Arabidopsis transgenic 35S::AtWRKY33 overexpression line showed that it had a bigger root system and was more efficient at taking up N from the soil, confirming the pivotal role of WRKY33 for NUE improvement.
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Affiliation(s)
- Antonio Mauceri
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
| | - Maria Rosa Abenavoli
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
| | - Laura Toppino
- CREA - Research Centre for Genomics and Bioinformatics, Via Paullese 28, Montanaso Lombardo, Italy
| | - Sayantan Panda
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Francesco Mercati
- Istituto di Bioscienze e Biorisorse CNR - Consiglio Nazionale Ricerche, Corso Calatafimi 414, Palermo, Italy
| | - Meriem Miyassa Aci
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Francesco Sunseri
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
| | - Giuseppe Leonardo Rotino
- CREA - Research Centre for Genomics and Bioinformatics, Via Paullese 28, Montanaso Lombardo, Italy
| | - Antonio Lupini
- Dipartimento Agraria, Università degli Studi Mediterranea di Reggio Calabria, Loc. Feo di Vito, Reggio Calabria, Italy
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11
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Sudheeran PK, Sela N, Carmeli-Weissberg M, Ovadia R, Panda S, Feygenberg O, Maurer D, Oren-Shamir M, Aharoni A, Alkan N. Induced defense response in red mango fruit against Colletotrichum gloeosporioides. HORTICULTURE RESEARCH 2021; 8:17. [PMID: 33423039 PMCID: PMC7797005 DOI: 10.1038/s41438-020-00452-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 11/22/2020] [Accepted: 12/07/2020] [Indexed: 05/13/2023]
Abstract
Mango fruit exposed to sunlight develops red skin and are more resistant to biotic and abiotic stresses. Here we show that harvested red mango fruit that was exposed to sunlight at the orchard is more resistant than green fruit to Colletotrichum gloeosporioides. LCMS analysis showed high amounts of antifungal compounds, as glycosylated flavonols, glycosylated anthocyanins, and mangiferin in red vs. green mango skin, correlated with higher antioxidant and lower ROS. However, also the green side of red mango fruit that has low levels of flavonoids was resistant, indicated induced resistance. Transcriptomes of red and green fruit inoculated on their red and green sides with C. gloeosporioides were analyzed. Overall, in red fruit skin, 2,187 genes were upregulated in response to C. gloeosporioides. On the green side of red mango, upregulation of 22 transcription factors and 33 signaling-related transcripts indicated induced resistance. The RNA-Seq analysis suggests that resistance of the whole red fruit involved upregulation of ethylene, brassinosteroid, and phenylpropanoid pathways. To conclude, red fruit resistance to fungal pathogen was related to both flavonoid toxicity and primed resistance of fruit that was exposed to light at the orchard.
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Affiliation(s)
- Pradeep Kumar Sudheeran
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, P.O. Box 15159, HaMaccabim Road 68, Rishon LeZion, 7505101, Israel
| | - Noa Sela
- Department of Plant Pathology and Weed Research, ARO, Volcani Center, Rishon LeZion, 7505101, Israel
| | - Mira Carmeli-Weissberg
- Department of Fruit Tree Sciences, Agricultural Research Organization, Volcani Center, PO Box 6, Bet-Dagan, 7505101, Israel
| | - Rinat Ovadia
- Department of Ornamental Plants and Agricultural Biotechnology, ARO, Volcani Center, P.O. Box 15159, HaMaccabim Road 68, Rishon LeZion, 7505101, Israel
| | - Sayantan Panda
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Oleg Feygenberg
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, P.O. Box 15159, HaMaccabim Road 68, Rishon LeZion, 7505101, Israel
| | - Dalia Maurer
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, P.O. Box 15159, HaMaccabim Road 68, Rishon LeZion, 7505101, Israel
| | - Michal Oren-Shamir
- Department of Ornamental Plants and Agricultural Biotechnology, ARO, Volcani Center, P.O. Box 15159, HaMaccabim Road 68, Rishon LeZion, 7505101, Israel
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Noam Alkan
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, P.O. Box 15159, HaMaccabim Road 68, Rishon LeZion, 7505101, Israel.
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12
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Plewiński P, Ćwiek-Kupczyńska H, Rudy E, Bielski W, Rychel-Bielska S, Stawiński S, Barzyk P, Krajewski P, Naganowska B, Wolko B, Książkiewicz M. Innovative transcriptome-based genotyping highlights environmentally responsive genes for phenology, growth and yield in a non-model grain legume. PLANT, CELL & ENVIRONMENT 2020; 43:2680-2698. [PMID: 32885839 DOI: 10.1111/pce.13880] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/21/2020] [Accepted: 08/22/2020] [Indexed: 06/11/2023]
Abstract
The narrow-leafed lupin, Lupinus angustifolius L., is a grain legume crop, cultivated both as a green manure and as a source of protein for animal feed and human food production. During its domestication process, numerous agronomic traits were improved, however, only two trait-related genes were identified hitherto, both by linkage mapping. Genome-wide association studies (GWAS), exploiting genomic sequencing, did not select any novel candidate gene. In the present study, an innovative method of 3'-end reduced representation transcriptomic profiling, a massive analysis of cDNA ends, has been used for genotyping of 126 L. angustifolius lines surveyed by field phenotyping. Significant genotype × environment interactions were identified for all phenology and yield traits analysed. Principal component analysis of population structure evidenced European domestication bottlenecks, visualized by clustering of breeding materials and cultivars. GWAS provided contribution towards deciphering vernalization pathway in legumes, and, apart from highlighting known domestication loci (Ku/Julius and mol), designated novel candidate genes for L. angustifolius traits. Early phenology was associated with genes from vernalization, cold-responsiveness and phosphatidylinositol signalling pathways whereas high yield with genes controlling photosynthesis performance and abiotic stress (drought or heat) tolerance. PCR-based toolbox was developed and validated to enable tracking desired alleles in marker-assisted selection. Narrow-leafed lupin was genotyped with an innovative method of transcriptome profiling and phenotyped for phenology, growth and yield traits in field. Early phenology was found associated with genes from cold-response, vernalization and phosphatidylinositol signalling pathways, whereas high yield with genes running photosystem II and drought or heat stress response. Key loci were supplied with PCR-based toolbox for marker-assisted selection.
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Affiliation(s)
- Piotr Plewiński
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Hanna Ćwiek-Kupczyńska
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Elżbieta Rudy
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Wojciech Bielski
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Sandra Rychel-Bielska
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Stanisław Stawiński
- Department in Przebędowo, Plant Breeding Smolice Ltd., Murowana Goślina, Poland
| | - Paweł Barzyk
- Department in Wiatrowo, Poznań Plant Breeding Ltd., Wiatrowo, Poland
| | - Paweł Krajewski
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Barbara Naganowska
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Bogdan Wolko
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Michał Książkiewicz
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
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13
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Analysis of wild tomato introgression lines elucidates the genetic basis of transcriptome and metabolome variation underlying fruit traits and pathogen response. Nat Genet 2020; 52:1111-1121. [PMID: 32989321 DOI: 10.1038/s41588-020-0690-6] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 08/13/2020] [Indexed: 02/07/2023]
Abstract
Wild tomato species represent a rich gene pool for numerous desirable traits lost during domestication. Here, we exploited an introgression population representing wild desert-adapted species and a domesticated cultivar to establish the genetic basis of gene expression and chemical variation accompanying the transfer of wild-species-associated fruit traits. Transcriptome and metabolome analysis of 580 lines coupled to pathogen sensitivity assays resulted in the identification of genomic loci associated with levels of hundreds of transcripts and metabolites. These associations occurred in hotspots representing coordinated perturbation of metabolic pathways and ripening-related processes. Here, we identify components of the Solanum alkaloid pathway, as well as genes and metabolites involved in pathogen defense and linking fungal resistance with changes in the fruit ripening regulatory network. Our results outline a framework for understanding metabolism and pathogen resistance during tomato fruit ripening and provide insights into key fruit quality traits.
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14
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Duarte-Delgado D, Dadshani S, Schoof H, Oyiga BC, Schneider M, Mathew B, Léon J, Ballvora A. Transcriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes. BMC PLANT BIOLOGY 2020; 20:428. [PMID: 32938380 PMCID: PMC7493341 DOI: 10.1186/s12870-020-02616-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/19/2020] [Indexed: 05/17/2023]
Abstract
BACKGROUND Bread wheat is one of the most important crops for the human diet, but the increasing soil salinization is causing yield reductions worldwide. Improving salt stress tolerance in wheat requires the elucidation of the mechanistic basis of plant response to this abiotic stress factor. Although several studies have been performed to analyze wheat adaptation to salt stress, there are still some gaps to fully understand the molecular mechanisms from initial signal perception to the onset of responsive tolerance pathways. The main objective of this study is to exploit the dynamic salt stress transcriptome in underlying QTL regions to uncover candidate genes controlling salt stress tolerance in bread wheat. The massive analysis of 3'-ends sequencing protocol was used to analyze leave samples at osmotic and ionic phases. Afterward, stress-responsive genes overlapping QTL for salt stress-related traits in two mapping populations were identified. RESULTS Among the over-represented salt-responsive gene categories, the early up-regulation of calcium-binding and cell wall synthesis genes found in the tolerant genotype are presumably strategies to cope with the salt-related osmotic stress. On the other hand, the down-regulation of photosynthesis-related and calcium-binding genes, and the increased oxidative stress response in the susceptible genotype are linked with the greater photosynthesis inhibition at the osmotic phase. The specific up-regulation of some ABC transporters and Na+/Ca2+ exchangers in the tolerant genotype at the ionic stage indicates their involvement in mechanisms of sodium exclusion and homeostasis. Moreover, genes related to protein synthesis and breakdown were identified at both stress phases. Based on the linkage disequilibrium blocks, salt-responsive genes within QTL intervals were identified as potential components operating in pathways leading to salt stress tolerance. Furthermore, this study conferred evidence of novel regions with transcription in bread wheat. CONCLUSION The dynamic transcriptome analysis allowed the comparison of osmotic and ionic phases of the salt stress response and gave insights into key molecular mechanisms involved in the salt stress adaptation of contrasting bread wheat genotypes. The leveraging of the highly contiguous chromosome-level reference genome sequence assembly facilitated the QTL dissection by targeting novel candidate genes for salt tolerance.
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Affiliation(s)
| | - Said Dadshani
- INRES-Plant Breeding, University of Bonn, Bonn, Germany
| | - Heiko Schoof
- INRES-Crop Bioinformatics, University of Bonn, Bonn, Germany
| | | | | | - Boby Mathew
- INRES-Plant Breeding, University of Bonn, Bonn, Germany
| | - Jens Léon
- INRES-Plant Breeding, University of Bonn, Bonn, Germany
| | - Agim Ballvora
- INRES-Plant Breeding, University of Bonn, Bonn, Germany.
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15
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Cohen H, Fedyuk V, Wang C, Wu S, Aharoni A. SUBERMAN regulates developmental suberization of the Arabidopsis root endodermis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:431-447. [PMID: 32027440 DOI: 10.1111/tpj.14711] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 01/12/2020] [Accepted: 01/23/2020] [Indexed: 05/11/2023]
Abstract
Root endodermis, the innermost cortical layer surrounding the root vasculature, serves as the foremost barrier to water, solutes, and nutrients taken up from soil. Endodermis barrier functionality is achieved via its hydrophobic coating of lignified Casparian strips and the suberin lamellae; nonetheless the regulatory mechanisms underlying endodermis suberization are still elusive. Here, we discovered that the Arabidopsis SUBERMAN (SUB) transcription factor controls the establishment of the root suberin lamellae. Transient expression of SUB in Nicotiana benthamiana leaves resulted in the induction of heterologous suberin genes, the accumulation of suberin-type monomers, and consequent deposition of suberin-like lamellae. We demonstrate that SUB exerts its regulatory roles by transactivating promoters of suberin genes. In Arabidopsis, SUB is expressed in patchy and continuous suberization root endodermal cells, and thus roots with higher or lower expression of SUB display altered suberin polymer deposition patterns and modified composition. While these changes did not interfere with Casparian strip formation they had a substantial effect on root uptake capacity, resulting in varied root and leaf ionomic phenotypes. Gene expression profiling revealed that SUB function impacts transcriptional networks associated with suberin, phenylpropanoids, lignin, and cuticular lipid biosynthesis, as well as root transport activities, hormone signalling, and cell wall modification. Our findings highlight SUB as a regulator of root endodermis suberization during normal development, and its characterization is thus a key step towards dissecting the molecular mechanisms partaking in root endodermal barrier functionalities.
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Affiliation(s)
- Hagai Cohen
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Vadim Fedyuk
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Chunhua Wang
- FAFU-UCR Joint Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shuang Wu
- FAFU-UCR Joint Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
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16
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Hu H, Gutierrez‐Gonzalez JJ, Liu X, Yeats TH, Garvin DF, Hoekenga OA, Sorrells ME, Gore MA, Jannink J. Heritable temporal gene expression patterns correlate with metabolomic seed content in developing hexaploid oat seed. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1211-1222. [PMID: 31677224 PMCID: PMC7152608 DOI: 10.1111/pbi.13286] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/24/2019] [Accepted: 10/26/2019] [Indexed: 05/04/2023]
Abstract
Oat ranks sixth in world cereal production and has a higher content of health-promoting compounds compared with other cereals. However, there is neither a robust oat reference genome nor transcriptome. Using deeply sequenced full-length mRNA libraries of oat cultivar Ogle-C, a de novo high-quality and comprehensive oat seed transcriptome was assembled. With this reference transcriptome and QuantSeq 3' mRNA sequencing, gene expression was quantified during seed development from 22 diverse lines across six time points. Transcript expression showed higher correlations between adjacent time points. Based on differentially expressed genes, we identified 22 major temporal co-expression (TCoE) patterns of gene expression and revealed enriched gene ontology biological processes. Within each TCoE set, highly correlated transcripts, putatively commonly affected by genetic background, were clustered and termed genetic co-expression (GCoE) sets. Seventeen of the 22 TCoE sets had GCoE sets with median heritabilities higher than 0.50, and these heritability estimates were much higher than that estimated from permutation analysis, with no divergence observed in cluster sizes between permutation and non-permutation analyses. Linear regression between 634 metabolites from mature seeds and the PC1 score of each of the GCoE sets showed significantly lower p-values than permutation analysis. Temporal expression patterns of oat avenanthramides and lipid biosynthetic genes were concordant with previous studies of avenanthramide biosynthetic enzyme activity and lipid accumulation. This study expands our understanding of physiological processes that occur during oat seed maturation and provides plant breeders the means to change oat seed composition through targeted manipulation of key pathways.
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Affiliation(s)
- Haixiao Hu
- Plant Breeding and Genetics SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
| | | | - Xinfang Liu
- Corn Research InstituteLiaoning Academy of Agricultural SciencesShenyangChina
| | - Trevor H. Yeats
- Plant Breeding and Genetics SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
| | | | | | - Mark E. Sorrells
- Plant Breeding and Genetics SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
| | - Michael A. Gore
- Plant Breeding and Genetics SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
| | - Jean‐Luc Jannink
- Plant Breeding and Genetics SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
- USDA‐ARSRobert W. Holley Center for Agriculture and HealthIthacaNYUSA
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17
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Sudheeran PK, Ovadia R, Galsarker O, Maoz I, Sela N, Maurer D, Feygenberg O, Oren Shamir M, Alkan N. Glycosylated flavonoids: fruit's concealed antifungal arsenal. THE NEW PHYTOLOGIST 2020; 225:1788-1798. [PMID: 31598980 DOI: 10.1111/nph.16251] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 10/04/2019] [Indexed: 05/26/2023]
Abstract
Fruit defense against pathogens relies on induced and preformed mechanisms. The present contribution evaluated performed resistance of red and green mango fruit against the fungal pathogen Colletotrichum gloeosporioides and identified the main active antifungal components. High-performance liquid chromatography analysis of nonhydrolyzed mango peel extracts identified major anthocyanin peaks of glycosylated cyanidin and methylcyanidin, and flavonol peaks of glycosylated quercetin and kaempferol, which were more abundant on the 'red side' of red mango fruit. Organic extracts of red vs green mango peel were more efficient in inhibiting C. gloeosporioides. Transcriptome analysis of the mango-C. gloeosporioides interaction showed increased expression of glucosidase genes related to both fungal pathogenicity and host defense. Glucosidase treatment of organic peel extract increased its antifungal activity. Additionally, quercetin and cyanidin had significantly higher antifungal activity than their glycosylated derivatives. Peel extract volatiles treated with glucosidase had antifungal activity. GCMS analysis identified 15 volatiles after glucosidase hydrolysis, seven of them present only in red fruit. These results suggest that the fruit obtains a concealed arsenal of glycosylated flavonoids in its peel when they are hydrolyzed by β-glucosidase that is induced in both fungus and host during infection process, become more toxic to the fungal pathogen, inhibiting decay development.
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Affiliation(s)
- Pradeep Kumar Sudheeran
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, PO Box 15159, HaMaccabim Road 68, Rishon LeZion 7505101, Israel
| | - Rinat Ovadia
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, Volcani Center, PO Box 15159, HaMaccabim Road 68, Rishon LeZion, 7505101, Israel
| | - Ortal Galsarker
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, PO Box 15159, HaMaccabim Road 68, Rishon LeZion 7505101, Israel
| | - Itay Maoz
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, PO Box 15159, HaMaccabim Road 68, Rishon LeZion 7505101, Israel
| | - Noa Sela
- Department of Plant Pathology, Agricultural Research Organization, Volcani Center, PO Box 15159, HaMaccabim Road 68, Rishon LeZion, 7505101, Israel
| | - Dalia Maurer
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, PO Box 15159, HaMaccabim Road 68, Rishon LeZion 7505101, Israel
| | - Oleg Feygenberg
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, PO Box 15159, HaMaccabim Road 68, Rishon LeZion 7505101, Israel
| | - Michal Oren Shamir
- Department of Ornamental Plants and Agricultural Biotechnology, Agricultural Research Organization, Volcani Center, PO Box 15159, HaMaccabim Road 68, Rishon LeZion, 7505101, Israel
| | - Noam Alkan
- Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Volcani Center, PO Box 15159, HaMaccabim Road 68, Rishon LeZion 7505101, Israel
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18
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Schwacke R, Ponce-Soto GY, Krause K, Bolger AM, Arsova B, Hallab A, Gruden K, Stitt M, Bolger ME, Usadel B. MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis. MOLECULAR PLANT 2019; 12:879-892. [PMID: 30639314 DOI: 10.1016/j.molp.2019.01.003] [Citation(s) in RCA: 239] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 12/14/2018] [Accepted: 01/01/2019] [Indexed: 05/18/2023]
Abstract
Genome sequences from over 200 plant species have already been published, with this number expected to increase rapidly due to advances in sequencing technologies. Once a new genome has been assembled and the genes identified, the functional annotation of their putative translational products, proteins, using ontologies is of key importance as it places the sequencing data in a biological context. Furthermore, to keep pace with rapid production of genome sequences, this functional annotation process must be fully automated. Here we present a redesigned and significantly enhanced MapMan4 framework, together with a revised version of the associated online Mercator annotation tool. Compared with the original MapMan, the new ontology has been expanded almost threefold and enforces stricter assignment rules. This framework was then incorporated into Mercator4, which has been upgraded to reflect current knowledge across the land plant group, providing protein annotations for all embryophytes with a comparably high quality. The annotation process has been optimized to allow a plant genome to be annotated in a matter of minutes. The output results continue to be compatible with the established MapMan desktop application.
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Affiliation(s)
- Rainer Schwacke
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Wilhelm Johnen Straße, Jülich, Germany
| | - Gabriel Y Ponce-Soto
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Wilhelm Johnen Straße, Jülich, Germany
| | - Kirsten Krause
- Department of Arctic and Marine Biology, The Arctic University of Norway, Biology Building, 9037 Tromsø, Norway
| | - Anthony M Bolger
- Institute for Botany and Molecular Genetics, BioEconomy Science Center, Worringer Weg, RWTH Aachen University, 52074 Aachen, Germany
| | - Borjana Arsova
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Wilhelm Johnen Straße, Jülich, Germany
| | - Asis Hallab
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Wilhelm Johnen Straße, Jülich, Germany
| | - Kristina Gruden
- National Institute of Biology, Department of Biotechnology and Systems Biology, Večna Pot 111, 1000 Ljubljana, Slovenia
| | - Mark Stitt
- Max Planck Institute for Molecular Plant Physiology, Department of Systems Regulation, 14476 Potsdam-Golm, Germany
| | - Marie E Bolger
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Wilhelm Johnen Straße, Jülich, Germany.
| | - Björn Usadel
- Institute for Bio- and Geosciences (IBG-2: Plant Sciences), Forschungszentrum Jülich, Wilhelm Johnen Straße, Jülich, Germany; Institute for Botany and Molecular Genetics, BioEconomy Science Center, Worringer Weg, RWTH Aachen University, 52074 Aachen, Germany
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