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Gao P, Qi Y, Li L, Yang S, Guo J, Liu J, Wei H, Huang F, Yu L. Phenylpropane biosynthesis and alkaloid metabolism pathways involved in resistance of Amorphophallus spp. against soft rot disease. FRONTIERS IN PLANT SCIENCE 2024; 15:1334996. [PMID: 38444534 PMCID: PMC10912172 DOI: 10.3389/fpls.2024.1334996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/05/2024] [Indexed: 03/07/2024]
Abstract
Soft rot of konjac (Amorphophallus spp.) is a devastating disease caused by the bacterium Pectobacterium carotovorum subsp. carotovorum (Pcc) with serious adverse effects on plantation development, corm quality and crop yield due to the current lack of effective control measures. The main objective of the present study was to elucidate the mechanisms underlying plant resistance to soft rot disease. A combination of transcriptomic and metabolomic analyses demonstrated significant enrichment of differentially expressed genes (DEG) and differentially accumulated metabolites (DAM) associated with plant hormones, phenylpropanoid biosynthesis and, in particular, alkaloid metabolism, in Amorphophallus muelleri following Pcc infection compared with A. konjac, these data implicate alkaloid metabolism as the dominant mechanism underlying disease resistance of A. muelleri. Quantitative real-time polymerase chain reaction analysis further revealed involvement of PAL, CYP73A16, CCOAOMT1, RBOHD and CDPK20 genes in the response of konjac to Pcc. Analysis of the bacteriostatic activities of total alkaloid from A. muelleri validated the assumption that alkaloid metabolism positively regulates disease resistance of konjac. Our collective results provide a foundation for further research on the resistance mechanisms of konjac against soft rot disease.
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Affiliation(s)
| | | | | | | | | | | | | | - Feiyan Huang
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - Lei Yu
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
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2
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Kushalappa AC, Hegde NG, Yogendra KN. Metabolic pathway genes for editing to enhance multiple disease resistance in plants. JOURNAL OF PLANT RESEARCH 2022; 135:705-722. [PMID: 36036859 DOI: 10.1007/s10265-022-01409-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
Diseases are one of the major constraints in commercial crop production. Genetic diversity in varieties is the best option to manage diseases. Molecular marker-assisted breeding has produced hundreds of varieties with good yields, but the resistance level is not satisfactory. With the advent of whole genome sequencing, genome editing is emerging as an excellent option to improve the inadequate traits in these varieties. Plants produce thousands of antimicrobial secondary metabolites, which as polymers and conjugates are deposited to reinforce the secondary cell walls to contain the pathogen to an initial infection area. The resistance metabolites or the structures produced from them by plants are either constitutive (CR) or induced (IR), following pathogen invasion. The production of each resistance metabolite is controlled by a network of biosynthetic R genes, which are regulated by a hierarchy of R genes. A commercial variety also has most of these R genes, as in resistant, but a few may be mutated (SNPs/InDels). A few mutated genes, in one or more metabolic pathways, depending on the host-pathogen interaction, can be edited, and stacked to increase resistance metabolites or structures produced by them, to achieve required levels of multiple pathogen resistance under field conditions.
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Affiliation(s)
- Ajjamada C Kushalappa
- Plant Science Department, McGill University, Ste.-Anne-de-Bellevue, QC, H9X 3V9, Canada.
| | - Niranjan G Hegde
- Plant Science Department, McGill University, Ste.-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Kalenahalli N Yogendra
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
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3
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Advances in Metabolomics-Driven Diagnostic Breeding and Crop Improvement. Metabolites 2022; 12:metabo12060511. [PMID: 35736444 PMCID: PMC9228725 DOI: 10.3390/metabo12060511] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 02/04/2023] Open
Abstract
Climate change continues to threaten global crop output by reducing annual productivity. As a result, global food security is now considered as one of the most important challenges facing humanity. To address this challenge, modern crop breeding approaches are required to create plants that can cope with increased abiotic/biotic stress. Metabolomics is rapidly gaining traction in plant breeding by predicting the metabolic marker for plant performance under a stressful environment and has emerged as a powerful tool for guiding crop improvement. The advent of more sensitive, automated, and high-throughput analytical tools combined with advanced bioinformatics and other omics techniques has laid the foundation to broadly characterize the genetic traits for crop improvement. Progress in metabolomics allows scientists to rapidly map specific metabolites to the genes that encode their metabolic pathways and offer plant scientists an excellent opportunity to fully explore and rationally harness the wealth of metabolites that plants biosynthesize. Here, we outline the current application of advanced metabolomics tools integrated with other OMICS techniques that can be used to: dissect the details of plant genotype–metabolite–phenotype interactions facilitating metabolomics-assisted plant breeding for probing the stress-responsive metabolic markers, explore the hidden metabolic networks associated with abiotic/biotic stress resistance, facilitate screening and selection of climate-smart crops at the metabolite level, and enable accurate risk-assessment and characterization of gene edited/transgenic plants to assist the regulatory process. The basic concept behind metabolic editing is to identify specific genes that govern the crucial metabolic pathways followed by the editing of one or more genes associated with those pathways. Thus, metabolomics provides a superb platform for not only rapid assessment and commercialization of future genome-edited crops, but also for accelerated metabolomics-assisted plant breeding. Furthermore, metabolomics can be a useful tool to expedite the crop research if integrated with speed breeding in future.
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Abreha KB, Alexandersson E, Resjö S, Lankinen Å, Sueldo D, Kaschani F, Kaiser M, van der Hoorn RAL, Levander F, Andreasson E. Leaf Apoplast of Field-Grown Potato Analyzed by Quantitative Proteomics and Activity-Based Protein Profiling. Int J Mol Sci 2021; 22:12033. [PMID: 34769464 PMCID: PMC8584485 DOI: 10.3390/ijms222112033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 01/11/2023] Open
Abstract
Multiple biotic and abiotic stresses challenge plants growing in agricultural fields. Most molecular studies have aimed to understand plant responses to challenges under controlled conditions. However, studies on field-grown plants are scarce, limiting application of the findings in agricultural conditions. In this study, we investigated the composition of apoplastic proteomes of potato cultivar Bintje grown under field conditions, i.e., two field sites in June-August across two years and fungicide treated and untreated, using quantitative proteomics, as well as its activity using activity-based protein profiling (ABPP). Samples were clustered and some proteins showed significant intensity and activity differences, based on their field site and sampling time (June-August), indicating differential regulation of certain proteins in response to environmental or developmental factors. Peroxidases, class II chitinases, pectinesterases, and osmotins were among the proteins more abundant later in the growing season (July-August) as compared to early in the season (June). We did not detect significant differences between fungicide Shirlan treated and untreated field samples in two growing seasons. Using ABPP, we showed differential activity of serine hydrolases and β-glycosidases under greenhouse and field conditions and across a growing season. Furthermore, the activity of serine hydrolases and β-glycosidases, including proteins related to biotic stress tolerance, decreased as the season progressed. The generated proteomics data would facilitate further studies aiming at understanding mechanisms of molecular plant physiology in agricultural fields and help applying effective strategies to mitigate biotic and abiotic stresses.
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Affiliation(s)
- Kibrom B. Abreha
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
| | - Erik Alexandersson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
| | - Svante Resjö
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
| | - Åsa Lankinen
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
| | - Daniela Sueldo
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; (D.S.); (R.A.L.v.d.H.)
| | - Farnusch Kaschani
- Chemische Biologie, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany; (F.K.); (M.K.)
| | - Markus Kaiser
- Chemische Biologie, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany; (F.K.); (M.K.)
| | - Renier A. L. van der Hoorn
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; (D.S.); (R.A.L.v.d.H.)
| | - Fredrik Levander
- Department of Immunotechnology, Lund University, SE-221 00 Lund, Sweden;
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Lund University, SE-221 00 Lund, Sweden
| | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
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Fukuda A, Hirose T, Hashida Y, Aoki N, Nagano AJ. Selection of transcripts related to low-temperature tolerance using RNA sequencing from F 2 plants between japonica and indica rice (Oryza sativa L.) cultivars. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:984-993. [PMID: 34112311 DOI: 10.1071/fp21088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
At low temperatures (18°C), seedlings of an indica rice (Oryza sativa L.) cultivar Kasalath showed symptoms of chlorosis, although the leaves of a japonica cultivar Arroz da Terra remained green. In this study, transcripts related to the chlorophyll content of rice seedlings grown at 18°C were investigated using RNA-sequencing (RNA-Seq) data for F2 crosses between cultivars Arroz da Terra and Kasalath, as well as their parental cultivars. Differential expression analysis revealed that gene ontology terms related to 'photosynthesis' were significantly enriched in lowly expressed genes at 18°C than at 25°C in Kasalath. However, the gene ontology terms related to 'response to stress' were significantly enriched in highly expressed genes at 18°C than at 25°C in Kasalath. When the F2 plants were grown at 18°C, their chlorophyll contents varied. Transcripts with expression levels related to chlorophyll content were statistically selected using RNA-Seq data from 21 F2 plants. In regression models, frequently selected genes included four photosynthetic and two stress-responsive genes. The expression values of four photosynthetic and two stress-responsive genes in high-frequency selected genes were significantly correlated with chlorophyll content not only in plants analysed using RNA-Seq but also in 95 F2 plants.
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Affiliation(s)
- Akari Fukuda
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan; and Corresponding author.
| | - Tatsuro Hirose
- Faculty of Agriculture, Takasaki University of Health and Welfare, Takasaki, Gunma, Japan
| | - Yoichi Hashida
- Faculty of Agriculture, Takasaki University of Health and Welfare, Takasaki, Gunma, Japan
| | - Naohiro Aoki
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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Roumani M, Besseau S, Gagneul D, Robin C, Larbat R. Phenolamides in plants: an update on their function, regulation, and origin of their biosynthetic enzymes. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2334-2355. [PMID: 33315095 DOI: 10.1093/jxb/eraa582] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
Phenolamides represent a family of specialized metabolites, consisting of the association of hydroxycinnamic acid derivatives with aliphatic or aromatic amines. Since the discovery of the first phenolamide in the late 1940s, decades of phytochemical analyses have revealed a high structural diversity for this family and a wide distribution in the plant kingdom. The occurrence of structurally diverse phenolamides in almost all plant organs has led to early hypotheses on their involvement in floral initiation and fertility, as well as plant defense against biotic and abiotic stress. In the present work, we critically review the literature ascribing functional hypotheses to phenolamides and recent evidence on the control of their biosynthesis in response to biotic stress. We additionally provide a phylogenetic analysis of the numerous N-hydroxycinnamoyltransferases involved in the synthesis of phenolamides and discuss the potential role of other enzyme families in their diversification. The data presented suggest multiple evolutionary events that contributed to the extension of the taxonomic distribution and diversity of phenolamides.
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Affiliation(s)
- Marwa Roumani
- UMR 1121, Laboratoire Agronomie et Environnement (LAE), Université de Lorraine- INRAe, Nancy, France
| | - Sébastien Besseau
- EA 2106, Biomolécules et biotechnologies végétales (BBV), Université de Tours, Tours, France
| | - David Gagneul
- UMR 1158, BioEcoAgro, Université de Lille, INRAe, Université de Liège, UPJV, YNCREA, Université d'Artois, Université Littoral Côte d'Opale, Institut Charles Viollette (ICV), Lille, France
| | - Christophe Robin
- UMR 1121, Laboratoire Agronomie et Environnement (LAE), Université de Lorraine- INRAe, Nancy, France
| | - Romain Larbat
- UMR 1121, Laboratoire Agronomie et Environnement (LAE), Université de Lorraine- INRAe, Nancy, France
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Cao W, Gan L, Wang C, Zhao X, Zhang M, Du J, Zhou S, Zhu C. Genome-Wide Identification and Characterization of Potato Long Non-coding RNAs Associated With Phytophthora infestans Resistance. FRONTIERS IN PLANT SCIENCE 2021; 12:619062. [PMID: 33643350 PMCID: PMC7902931 DOI: 10.3389/fpls.2021.619062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/06/2021] [Indexed: 05/26/2023]
Abstract
Long non-coding RNA (lncRNA) is a crucial regulatory mechanism in the plant response to biotic and abiotic stress. However, their roles in potato (Solanum tuberosum L.) resistance to Phytophthora infestans (P. infestans) largely remain unknown. In this study, we identify 2857 lncRNAs and 33,150 mRNAs of the potato from large-scale published RNA sequencing data. Characteristic analysis indicates a similar distribution pattern of lncRNAs and mRNAs on the potato chromosomes, and the mRNAs were longer and had more exons than lncRNAs. Identification of alternative splicing (AS) shows that there were a total of 2491 lncRNAs generated from AS and the highest frequency (46.49%) of alternative acceptors (AA). We performed R package TCseq to cluster 133 specific differentially expressed lncRNAs from resistance lines and found that the lncRNAs of cluster 2 were upregulated. The lncRNA targets were subject to KEGG pathway enrichment analysis, and the interactive network between lncRNAs and mRNAs was constructed by using GENIE3, a random forest machine learning algorithm. Transient overexpression of StLNC0004 in Nicotiana benthamiana significantly suppresses P. infestans growth compared with a control, and the expression of extensin (NbEXT), the ortholog of the StLNC0004 target gene, was significantly upregulated in the overexpression line. Together, these results suggest that lncRNAs play potential functional roles in the potato response to P. infestans infection.
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Hegde N, Joshi S, Soni N, Kushalappa AC. The caffeoyl-CoA O-methyltransferase gene SNP replacement in Russet Burbank potato variety enhances late blight resistance through cell wall reinforcement. PLANT CELL REPORTS 2021; 40:237-254. [PMID: 33141312 DOI: 10.1007/s00299-020-02629-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/15/2020] [Indexed: 05/28/2023]
Abstract
Metabolic pathway gene editing in tetraploid potato enhanced resistance to late blight. Multiallelic mutation correction of a caffeoyl-CoA O-methyltransferase gene increased accumulation of resistance metabolites in Russet Burbank potato. Late blight of potato is a devastating disease worldwide and requires weekly applications of fungicides to manage. Genetic improvement is the best option, but the self-incompatibility and inter-specific incompatibility makes potato breeding very challenging. Immune receptor gene stacking has increased resistance, but its durability is limited. Quantitative resistance is durable, and it mainly involves secondary cell wall thickening due to several metabolites and their conjugates. Deleterious mutations in biosynthetic genes can hinder resistance metabolite biosynthesis. Here a probable resistance role of the StCCoAOMT gene was first confirmed by an in-planta transient overexpression of the functional StCCoAOMT allele in late blight susceptible Russet Burbank (RB) genotype. Following this, a precise single nucleotide polymorphism (SNP) mutation correction of the StCCoAOMT gene in RB potato was carried out using CRISPR-Cas9 mediated homology directed repair (HDR). The StCCoAOMT gene editing increased the transcript abundance of downstream biosynthetic resistance genes. Following pathogen inoculation, several phenylpropanoid pathway genes were highly expressed in the edited RB plants, as compared to the non-edited. The disease severity (fold change = 3.76) and pathogen biomass in inoculated stems of gene-edited RB significantly reduced (FC = 21.14), relative to non-edited control. The metabolic profiling revealed a significant increase in the accumulation of resistance-related metabolites in StCCoAOMT edited RB plants. Most of these metabolites are involved in suberization and lignification. The StCCoAOMT gene, if mutated, can be edited in other potato cultivars to enhance resistance to late blight, provided it is associated with other functional genes in the metabolic pathway network.
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Affiliation(s)
- Niranjan Hegde
- Plant Science Department, McGill University, Sainte-Anne-de-Bellevue, QC, H9X3V9, Canada
| | - Sripad Joshi
- Plant Science Department, McGill University, Sainte-Anne-de-Bellevue, QC, H9X3V9, Canada
| | - Nancy Soni
- Plant Science Department, McGill University, Sainte-Anne-de-Bellevue, QC, H9X3V9, Canada
| | - Ajjamada C Kushalappa
- Plant Science Department, McGill University, Sainte-Anne-de-Bellevue, QC, H9X3V9, Canada.
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Hegde N, Doddamani D, Kushalappa AC. Identification and functional characterisation of late blight resistance polymorphic genes in Russet Burbank potato cultivar. FUNCTIONAL PLANT BIOLOGY : FPB 2020; 48:88-102. [PMID: 32741427 DOI: 10.1071/fp19327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
In plants, the biosynthesis of the phenylpropanoid, flavonoid and fatty acid pathway monomers, polymers and conjugated metabolites play a vital role in disease resistance. These are generally deposited to reinforce cell walls to contain the pathogen to the site of infection. Identification of sequence variants in genes that biosynthesise these resistance metabolites can explain the mechanisms of disease resistance. The resistant and susceptible genotypes inoculated with Phytophthora infestans were RNA sequenced to identify the single nucleotide polymorphisms (SNPs) and insertion/deletion (InDel) variations. The SNPs/InDels were annotated and classified into different categories based on their effect on gene functions. In the selected 25 biosynthetic genes overlapping 39 transcripts, a total of 52 SNPs/InDels were identified in the protein-coding (CDS) regions. These were categorised as deleterious based on prediction of their effects on protein structure and function. The SNPs/InDels data obtained in this study can be used in genome editing to enhance late blight resistance in Russet Burbank and other potato cultivars.
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Affiliation(s)
- Niranjan Hegde
- Department of Plant Science, McGill University, Ste.-Anne-de-Bellevue, QC, Canada
| | | | - Ajjamada C Kushalappa
- Department of Plant Science, McGill University, Ste.-Anne-de-Bellevue, QC, Canada; and Corresponding author.
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Zhang W, Chen Z, Kang Y, Fan Y, Liu Y, Yang X, Shi M, Yao K, Qin S. Genome-wide analysis of lectin receptor-like kinases family from potato ( Solanum tuberosum L.). PeerJ 2020; 8:e9310. [PMID: 32566405 PMCID: PMC7293193 DOI: 10.7717/peerj.9310] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 05/17/2020] [Indexed: 12/29/2022] Open
Abstract
Lectin receptor-like kinases (LecRLKs) are involved in responses to diverse environmental stresses and pathogenic microbes. A comprehensive acknowledgment of the family members in potato (Solanum tuberosum) genome is largely limited until now. In total, 113 potato LecRLKs (StLecRLKs) were first identified, including 85 G-type, 26 L-type and 2 C-type members. Based on phylogenetic analysis, StLecRLKs were sub-grouped into seven clades, including C-type, L-type, G-I, G-II, G-III G-IV and G-V. Chromosomal distribution and gene duplication analysis revealed the expansion of StLecRLKs occurred majorly through tandem duplication although the whole-genome duplication (WGD)/segmental duplication events were found. Cis-elements in the StLecRLKs promoter region responded mainly to signals of defense and stress, phytohormone, biotic or abiotic stress. Moreover, expressional investigations indicated that the family members of the clades L-type, G-I, G-IV and G-V were responsive to both bacterial and fungal infection. Based on qRT-PCR analysis, the expressions of PGSC0003DMP400055136 and PGSC0003DMP400067047 were strongly induced in all treatments by both Fusarium sulphureum (Fs) and Phytophthora infestans (Pi) inoculation. The present study provides valuable information for LecRLKs gene family in potato genome, and establishes a foundation for further research into the functional analysis.
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Affiliation(s)
- Weina Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Zhongjian Chen
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yichen Kang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Yanling Fan
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Yuhui Liu
- Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
| | - Xinyu Yang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Mingfu Shi
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Kai Yao
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Shuhao Qin
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
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11
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Knollenberg BJ, Li GX, Lambert JD, Maximova SN, Guiltinan MJ. Clovamide, a Hydroxycinnamic Acid Amide, Is a Resistance Factor Against Phytophthora spp. in Theobroma cacao. FRONTIERS IN PLANT SCIENCE 2020; 11:617520. [PMID: 33424909 PMCID: PMC7786005 DOI: 10.3389/fpls.2020.617520] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/04/2020] [Indexed: 05/13/2023]
Abstract
The hydroxycinnamic acid amides (HCAAs) are a diverse group of plant-specialized phenylpropanoid metabolites distributed widely in the plant kingdom and are known to be involved in tolerance to abiotic and biotic stress. The HCAA clovamide is reported in a small number of distantly related species. To explore the contribution of specialized metabolites to disease resistance in cacao (Theobroma cacao L., chocolate tree), we performed untargeted metabolomics using liquid chromatography - tandem mass spectrometry (LC-MS/MS) and compared the basal metabolite profiles in leaves of two cacao genotypes with contrasting levels of susceptibility to Phytophthora spp. Leaves of the tolerant genotype 'Scavina 6' ('Sca6') were found to accumulate dramatically higher levels of clovamide and several other HCAAs compared to the susceptible 'Imperial College Selection 1' ('ICS1'). Clovamide was the most abundant metabolite in 'Sca6' leaf extracts based on MS signal, and was up to 58-fold higher in 'Sca6' than in 'ICS1'. In vitro assays demonstrated that clovamide inhibits growth of three pathogens of cacao in the genus Phytophthora, is a substrate for cacao polyphenol oxidase, and is a contributor to enzymatic browning. Furthermore, clovamide inhibited proteinase and pectinase in vitro, activities associated with defense in plant-pathogen interactions. Fruit epidermal peels from both genotypes contained substantial amounts of clovamide, but two sulfated HCAAs were present at high abundance exclusively in 'Sca6' suggesting a potential functional role of these compounds. The potential to breed cacao with increased HCAAs for improved agricultural performance is discussed.
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Affiliation(s)
- Benjamin J. Knollenberg
- Plant Biology PhD Program ‐ Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
- Department of Plant Sciences, Pennsylvania State University, University Park, PA, United States
| | - Guo-Xing Li
- Department of Chemistry, Pennsylvania State University, University Park, PA, United States
| | - Joshua D. Lambert
- Department of Food Science, Pennsylvania State University, University Park, PA, United States
| | - Siela N. Maximova
- Department of Plant Sciences, Pennsylvania State University, University Park, PA, United States
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Mark J. Guiltinan
- Department of Plant Sciences, Pennsylvania State University, University Park, PA, United States
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
- *Correspondence: Mark J. Guiltinan,
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Nazarian-Firouzabadi F, Joshi S, Xue H, Kushalappa AC. Genome-wide in silico identification of LysM-RLK genes in potato (Solanum tuberosum L.). Mol Biol Rep 2019; 46:5005-5017. [PMID: 31317454 DOI: 10.1007/s11033-019-04951-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/27/2019] [Indexed: 01/22/2023]
Abstract
The receptor like kinases (RLKs) belong to the RLK/Pelle superfamily, one of the largest gene families in plants. RLKs play an important role in plant development, as well as in response to biotic and abiotic stresses. The lysine motif receptor like kinases (LysM-RLKs) are a subfamily of RLKs containing at least one lysine motif (LysM) that are involved in the perception of elicitors or pathogen-associated molecular patterns (PAMPs). In the present study, 77 putative RLKs genes and three receptor like proteins were identified in potato (Solanum tuberosum) genome, following a genome-wide search. The 77 potato RLK proteins are classified into two major phylogenetic groups based on their kinase domain amino acid sequence similarities. Out of 77 RLKs, 10 proteins had at least one LysM. Among them three RLP proteins were found in potato genome with either 2 or three tandem LysM but these lacked a cytoplasmic kinase domain. Expression analyses of a potato LysM-RLKs (StLysM-RLK05) was carried out by a Real time RT-PCR, following inoculation of potato leaves and immature tubers with late blight and common scab pathogens, respectively. The expression was significantly higher in resistant than in susceptible following S. scabies inoculation. The StLysM-RLK05 sequence was verified and it was polymorphic in scab susceptible cultivar. The present study provides an overview of the StLysM-RLKs gene family in potato genome. This information is helpful for future functional analysis of such an important protein family, in Solanaceae species.
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Affiliation(s)
- Farhad Nazarian-Firouzabadi
- Plant Science Department, McGill University, Ste.-Anne-de-Bellevue, QC, H9X3V9, Canada.,Agronomy and Plant Breeding Department, Faculty of Agriculture, Lorestan University, Khorramabad, Iran
| | - Sripad Joshi
- Plant Science Department, McGill University, Ste.-Anne-de-Bellevue, QC, H9X3V9, Canada
| | - Huali Xue
- Plant Science Department, McGill University, Ste.-Anne-de-Bellevue, QC, H9X3V9, Canada.,College of Science, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Ajjamada C Kushalappa
- Plant Science Department, McGill University, Ste.-Anne-de-Bellevue, QC, H9X3V9, Canada.
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Kage U, Yogendra KN, Kushalappa AC. TaWRKY70 transcription factor in wheat QTL-2DL regulates downstream metabolite biosynthetic genes to resist Fusarium graminearum infection spread within spike. Sci Rep 2017; 7:42596. [PMID: 28198421 PMCID: PMC5309853 DOI: 10.1038/srep42596] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/11/2017] [Indexed: 12/15/2022] Open
Abstract
A semi-comprehensive metabolomics was used to identify the candidate metabolites and genes to decipher mechanisms of resistance in wheat near-isogenic lines (NILs) containing QTL-2DL against Fusarium graminearum (Fg). Metabolites, with high fold-change in abundance, belonging to hydroxycinnamic acid amides (HCAAs): such as coumaroylagmatine, coumaroylputrescine and Fatty acids: phosphatidic acids (PAs) were identified as resistance related induced (RRI) metabolites in rachis of resistant NIL (NIL-R), inoculated with Fg. A WRKY like transcription factor (TF) was identified within the QTL-2DL region, along with three resistance genes that biosynthesized RRI metabolites. Sequencing and in-silico analysis of WRKY confirmed it to be wheat TaWRKY70. Quantitative real time-PCR studies showed a higher expression of TaWRKY70 in NIL-R as compared to NIL-S after Fg inoculation. Further, the functional validation of TaWRKY70 based on virus induced gene silencing (VIGS) in NIL-R, not only confirmed an increased fungal biomass but also decreased expressions of downstream resistance genes: TaACT, TaDGK and TaGLI1, along with decreased abundances of RRI metabolites biosynthesized by them. Among more than 200 FHB resistance QTL identified in wheat, this is the first QTL from which a TF was identified, and its downstream target genes as well as the FHB resistance functions were deciphered.
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Affiliation(s)
- Udaykumar Kage
- Plant Science Department, McGill University, 2111 Lakeshore road, Sainte Anne De Bellevue, Quebec, Canada H9X3V9
| | - Kalenahalli N. Yogendra
- Plant Science Department, McGill University, 2111 Lakeshore road, Sainte Anne De Bellevue, Quebec, Canada H9X3V9
| | - Ajjamada C. Kushalappa
- Plant Science Department, McGill University, 2111 Lakeshore road, Sainte Anne De Bellevue, Quebec, Canada H9X3V9
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Babineau M, Mahmood K, Mathiassen SK, Kudsk P, Kristensen M. De novo transcriptome assembly analysis of weed Apera spica-venti from seven tissues and growth stages. BMC Genomics 2017; 18:128. [PMID: 28166737 PMCID: PMC5294808 DOI: 10.1186/s12864-017-3538-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 02/02/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Loose silky bentgrass (Apera spica-venti) is an important weed in Europe with a recent increase in herbicide resistance cases. The lack of genetic information about this noxious weed limits its biological understanding such as growth, reproduction, genetic variation, molecular ecology and metabolic herbicide resistance. This study produced a reference transcriptome for A. spica-venti from different tissues (leaf, root, stem) and various growth stages (seed at phenological stages 05, 07, 08, 09). The de novo assembly was performed on individual and combined dataset followed by functional annotations. Individual transcripts and gene families involved in metabolic based herbicide resistance were identified. RESULTS Eight separate transcriptome assemblies were performed and compared. The combined transcriptome assembly consists of 83,349 contigs with an N50 and average contig length of 762 and 658 bp, respectively. This dataset contains 74,724 transcripts consisting of total 54,846,111 bp. Among them 94% had a homologue to UniProtKB, 73% retrieved a GO mapping, and 50% were functionally annotated. Compared with other grass species, A. spica-venti has 26% proteins in common to Brachypodium distachyon, and 41% to Lolium spp. Glycosyltransferases had the highest number of transcripts in each tissue followed by the cytochrome P450s. The GSTF1 and CYP89A2 transcripts were recovered from the majority of tissues and aligned at a maximum of 66 and 30% to proven herbicide resistant allele from Alopecurus myosuroides and Lolium rigidum, respectively. CONCLUSIONS De novo transcriptome assembly enabled the generation of the first reference transcriptome of A. spica-venti. This can serve as stepping stone for understanding the metabolic herbicide resistance as well as the general biology of this problematic weed. Furthermore, this large-scale sequence data is a valuable scientific resource for comparative transcriptome analysis for Poaceae grasses.
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Affiliation(s)
- Marielle Babineau
- Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse, 4200 Denmark
| | - Khalid Mahmood
- Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse, 4200 Denmark
| | | | - Per Kudsk
- Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse, 4200 Denmark
| | - Michael Kristensen
- Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse, 4200 Denmark
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