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Agho CA, Kaurilind E, Tähtjärv T, Runno-Paurson E, Niinemets Ü. Comparative transcriptome profiling of potato cultivars infected by late blight pathogen Phytophthora infestans: Diversity of quantitative and qualitative responses. Genomics 2023; 115:110678. [PMID: 37406973 PMCID: PMC10548088 DOI: 10.1016/j.ygeno.2023.110678] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 06/30/2023] [Accepted: 07/02/2023] [Indexed: 07/07/2023]
Abstract
The Estonia potato cultivar Ando has shown elevated field resistance to Phytophthora infestans, even after being widely grown for over 40 years. A comprehensive transcriptional analysis was performed using RNA-seq from plant leaf tissues to gain insight into the mechanisms activated for the defense after infection. Pathogen infection in Ando resulted in about 5927 differentially expressed genes (DEGs) compared to 1161 DEGs in the susceptible cultivar Arielle. The expression levels of genes related to plant disease resistance such as serine/threonine kinase activity, signal transduction, plant-pathogen interaction, endocytosis, autophagy, mitogen-activated protein kinase (MAPK), and others were significantly enriched in the upregulated DEGs in Ando, whereas in the susceptible cultivar, only the pathway related to phenylpropanoid biosynthesis was enriched in the upregulated DEGs. However, in response to infection, photosynthesis was deregulated in Ando. Multi-signaling pathways of the salicylic-jasmonic-ethylene biosynthesis pathway were also activated in response to Phytophthora infestans infection.
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Affiliation(s)
- C A Agho
- Chair of Crop Science and Plant Biology, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51006, Estonia.
| | - E Kaurilind
- Chair of Crop Science and Plant Biology, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51006, Estonia
| | - T Tähtjärv
- Centre of Estonian Rural Research and Knowledge, J. Aamisepa 1, 48309 Jõgeva, Estonia
| | - E Runno-Paurson
- Chair of Crop Science and Plant Biology, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51006, Estonia
| | - Ü Niinemets
- Chair of Crop Science and Plant Biology, Estonian University of Life Sciences, Kreutzwaldi 1, Tartu 51006, Estonia; Estonian Academy of Sciences, Kohtu 6, Tallinn 10130, Estonia
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2
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Zoteyeva NM, Evdokimova ZZ. Source material from crosses among Solanum L. spp. for potato breeding. PROCEEDINGS ON APPLIED BOTANY, GENETICS AND BREEDING 2022. [DOI: 10.30901/2227-8834-2022-4-115-121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Background. Late blight (agent: Phytophthora infestans (Mont.) de Bary) is one of the most destructive diseases for potato. The climate conditions in the northwest of Russia are very favorable for annual late blight infestation. Spreading of the pathogen leads to significant harvest losses. A promising breeding strategy is to expand the genetic diversity of resistance sources.Materials and methods. Resistance of experimental hybrid clones to late blight, their ability to form tubers under long daylight conditions, and a number of agronomic traits were studied using standard methods.Results. Long-term evaluation data were obtained for original interspecies potato hybrids concerning their resistance to late blight. The hybrids were also assessed for their yield and agronomic tuber characteristics. Some of the produced interspecies hybrids demonstrated field resistance to late blight, high tuber yield, and good agronomic traits. Clones derived from some cross combinations significantly exceeded both parents in tuber yield per plant and tuber size.Conclusions. Crosses between potato cultivars and various late blight resistance sources made it possible to combine in hybrid clones the genes of wild and cultivated Andean species and Solanum tuberosum L. with different pedigrees. Productive hybrid clones with resistance to late blight and good agronomic characteristics promise to become useful material for potato breeding programs.
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Affiliation(s)
- N. M. Zoteyeva
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources
| | - Z. Z. Evdokimova
- Leningrad Research Agriculture Institute, Branch of Russian Potato Research Center
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3
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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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4
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Fuess LE, Weber JN, den Haan S, Steinel NC, Shim KC, Bolnick DI. Between-population differences in constitutive and infection-induced gene expression in threespine stickleback. Mol Ecol 2021; 30:6791-6805. [PMID: 34582586 PMCID: PMC8796319 DOI: 10.1111/mec.16197] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 09/16/2021] [Accepted: 09/22/2021] [Indexed: 02/06/2023]
Abstract
Vertebrate immunity is a complex system consisting of a mix of constitutive and inducible defences. Furthermore, host immunity is subject to selective pressure from a range of parasites and pathogens which can produce variation in these defences across populations. As populations evolve immune responses to parasites, they may adapt via a combination of (1) constitutive differences, (2) shared inducible responses, or (3) divergent inducible responses. Here, we leverage a powerful natural host‐parasite model system (Gasterosteus aculeatus and Schistochephalus solidus) to tease apart the relative contributions of these three types of adaptations to among‐population divergence in response to parasites. Gene expression analyses revealed limited evidence of significant divergence in constitutive expression of immune defence, and strong signatures of conserved inducible responses to the parasite. Furthermore, our results highlight a handful of immune‐related genes which show divergent inducible responses which may contribute disproportionately to functional differences in infection success or failure. In addition to investigating variation in evolutionary adaptation to parasite selection, we also leverage this unique data set to improve understanding of cellular mechanisms underlying a putative resistance phenotype (fibrosis). Combined, our results provide a case study in evolutionary immunology showing that a very small number of genes may contribute to genotype differences in infection response.
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Affiliation(s)
- Lauren E Fuess
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA.,Department of Biology, Texas State University, San Marcos, Texas, USA
| | - Jesse N Weber
- Department of Integrative Biology, University of Wisconsin - Madison, Madison, Wisconsin, USA
| | - Stijn den Haan
- International Institute for Industrial Environmental Economics (IIIEE), Lund University, Lund, Sweden
| | - Natalie C Steinel
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Kum Chuan Shim
- Department of Ecology, Evolution, and Behavior, University of Texas at Austin, Austin, Texas, USA
| | - Daniel I Bolnick
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, Connecticut, USA
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5
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Xiao C, Huang M, Gao J, Wang Z, Zhang D, Zhang Y, Yan L, Yu X, Li B, Shen Y. Comparative proteomics of three Chinese potato cultivars to improve understanding of potato molecular response to late blight disease. BMC Genomics 2020; 21:880. [PMID: 33297944 PMCID: PMC7727141 DOI: 10.1186/s12864-020-07286-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 11/26/2020] [Indexed: 11/29/2022] Open
Abstract
Background Late blight disease (LBD) caused by the pathogen Phytophthora infestans (PI), is the most devastating disease limiting potato (Solanum tuberosum) production globally. Currently, this disease pathogen is re-emerging and appearing in new areas at a very high intensity. A better understanding of the natural defense mechanisms against PI in different potato cultivars especially at the protein level is still lacking. Therefore, to elucidate potato proteome response to PI, we investigated changes in the proteome and leaf morphology of three potato cultivars, namely; Favorita (FA), Mira (MA), and E-malingshu N0.14 (E14) infected with PI by using the iTRAQ-based quantitative proteomics analysis. Results A total of 3306 proteins were found in the three potato genotypes, and 2044 proteins were quantified. Cluster analysis revealed MA and E14 clustered together separately from FA. The protein profile and related functions revealed that the cultivars shared a typical hypersensitive response to PI, including induction of elicitors, oxidative burst, and suppression of photosynthesis in the potato leaves. Meanwhile, MA and E14 deployed additional specific response mechanism different from FA, involving high induction of protease inhibitors, serine/threonine kinases, terpenoid, hormone signaling, and transport, which contributed to MA tolerance of LBD. Furthermore, inductions of pathogenesis-related proteins, LRR receptor-like kinases, mitogen-activated protein kinase, WRKY transcription factors, jasmonic acid, and phenolic compounds mediate E14 resistance against LBD. These proteins were confirmed at the transcription level by a quantitative polymerase chain reaction and at the translation level by western-blot. Conclusions We found several proteins that were differentially abundant among the cultivars, that includes common and cultivar specific proteins which highlighted similarities and significant differences between FA, MA, and E14 in terms of their defense response to PI. Here the specific accumulation of mitogen-activated protein kinase, Serine/threonine kinases, WRKY transcription played a positive role in E14 immunity against PI. The candidate proteins identified reported in this study will form the basis of future studies and may improve our understanding of the molecular mechanisms of late blight disease resistance in potato. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07286-3.
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Affiliation(s)
- Chunfang Xiao
- State Key Laboratory of Agricultural Microbiology and Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Southern Potato Research Center of China, Enshi, 445000, Hubei, China.,Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi, 445000, Hubei, China
| | - Mengling Huang
- State Key Laboratory of Agricultural Microbiology and Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jianhua Gao
- Southern Potato Research Center of China, Enshi, 445000, Hubei, China.,Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi, 445000, Hubei, China
| | - Zhen Wang
- Southern Potato Research Center of China, Enshi, 445000, Hubei, China.,Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi, 445000, Hubei, China
| | - Denghong Zhang
- Southern Potato Research Center of China, Enshi, 445000, Hubei, China.,Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi, 445000, Hubei, China
| | - Yuanxue Zhang
- Southern Potato Research Center of China, Enshi, 445000, Hubei, China.,Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi, 445000, Hubei, China
| | - Lei Yan
- Southern Potato Research Center of China, Enshi, 445000, Hubei, China.,Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi, 445000, Hubei, China
| | - Xiao Yu
- State Key Laboratory of Agricultural Microbiology and Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Bo Li
- State Key Laboratory of Agricultural Microbiology and Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Yanfen Shen
- Southern Potato Research Center of China, Enshi, 445000, Hubei, China. .,Enshi Tujia and Miao Autonomous Prefecture Academy of Agricultural Sciences, Enshi, 445000, Hubei, China.
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6
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Yang X, Guo X, Chen G, Dong D, Liu F, Yang Y, Yang Y, Li G. Comparison of defense responses of transgenic potato lines expressing three different Rpi genes to specific Phytophthora infestans races based on transcriptome profiling. PeerJ 2020; 8:e9096. [PMID: 32411536 PMCID: PMC7207217 DOI: 10.7717/peerj.9096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 04/09/2020] [Indexed: 12/30/2022] Open
Abstract
Potato late blight, one of the most devastating diseases in potato, is caused by the oomycete Phytophthora infestans. Over 20 resistance genes have been cloned including R1, R3a, and R3b. The distinctions between defense response mechanisms mediated by different resistance genes are still unclear. Here we performed transcriptome profiling in three transgenic lines, R1, R3a, and R3b, and wild-type Desiree under inoculation with two P. infestans isolates, 89148 (race 0) and CN152 (super race), using RNA-seq. Compared with wild type, specific differentially expressed genes (DEGs) were identified in the three transgenic lines. The highest number of DEGs occurred in transgenic R3b, with 779 DEGs in response to isolate 89148 and 864 DEGs in response to infection by CN152, followed by transgenic R1 lines with 408 DEGs for isolate 89148 and 267 DEGs for CN152. Based on gene ontology, the most common GO terms (15 for 89148 and 20 for CN152) were enriched in transgenic R3a and R3b lines. This indicates that the defense pathways mediated by R3a and R3b are more similar than those mediated by R1. Further separate GO analysis of up- or down-regulated DEGs showed that the down-regulated DEGs mainly functioned in mediating the resistance of potato to P. infestans 89148 by response to stress biological process and to CN152 by oxidation reduction biological process. KEGG pathways of DNA replication, plant-pathogen interaction and pentose and glucuronate interconversions are unique for transgenic R1, R3a, and R3b lines in incompatible interactions. Quantitative real-time PCR experimental validation confirmed the induced expression of DEGs in the late blight resistance signaling pathway. Our results will lay a solid foundation for further understanding the mechanisms of plant-pathogen interactions, and provide a theoretical reference for durable resistance in potato.
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Affiliation(s)
- Xiaohui Yang
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Subcenter/ Huang-Huai-Hai Region Scientific Observation and Experimental Station of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Xiao Guo
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Subcenter/ Huang-Huai-Hai Region Scientific Observation and Experimental Station of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Guangxia Chen
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Subcenter/ Huang-Huai-Hai Region Scientific Observation and Experimental Station of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Daofeng Dong
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Subcenter/ Huang-Huai-Hai Region Scientific Observation and Experimental Station of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Fang Liu
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Subcenter/ Huang-Huai-Hai Region Scientific Observation and Experimental Station of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Yuanjun Yang
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Subcenter/ Huang-Huai-Hai Region Scientific Observation and Experimental Station of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Yu Yang
- Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences, Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Subcenter/ Huang-Huai-Hai Region Scientific Observation and Experimental Station of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Jinan, China
| | - Guangcun Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences; Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop, Ministry of Agriculture and Rural Affairs, Beijing, China
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Alexandersson E, Kushwaha S, Subedi A, Weighill D, Climer S, Jacobson D, Andreasson E. Linking crop traits to transcriptome differences in a progeny population of tetraploid potato. BMC PLANT BIOLOGY 2020; 20:120. [PMID: 32183694 PMCID: PMC7079428 DOI: 10.1186/s12870-020-2305-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 02/24/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND Potato is the third most consumed crop in the world. Breeding for traits such as yield, product quality and pathogen resistance are main priorities. Identifying molecular signatures of these and other important traits is important in future breeding efforts. In this study, a progeny population from a cross between a breeding line, SW93-1015, and a cultivar, Désirée, was studied by trait analysis and RNA-seq in order to develop understanding of segregating traits at the molecular level and identify transcripts with expressional correlation to these traits. Transcript markers with predictive value for field performance applicable under controlled environments would be of great value for plant breeding. RESULTS A total of 34 progeny lines from SW93-1015 and Désirée were phenotyped for 17 different traits in a field in Nordic climate conditions and controlled climate settings. A master transcriptome was constructed with all 34 progeny lines and the parents through a de novo assembly of RNA-seq reads. Gene expression data obtained in a controlled environment from the 34 lines was correlated to traits by different similarity indices, including Pearson and Spearman, as well as DUO, which calculates the co-occurrence between high and low values for gene expression and trait. Our study linked transcripts to traits such as yield, growth rate, high laying tubers, late and tuber blight, tuber greening and early flowering. We found several transcripts associated to late blight resistance and transcripts encoding receptors were associated to Dickeya solani susceptibility. Transcript levels of a UBX-domain protein was negatively associated to yield and a GLABRA2 expression modulator was negatively associated to growth rate. CONCLUSION In our study, we identify 100's of transcripts, putatively linked based on expression with 17 traits of potato, representing both well-known and novel associations. This approach can be used to link the transcriptome to traits. We explore the possibility of associating the level of transcript expression from controlled, optimal environments to traits in a progeny population with different methods introducing the application of DUO for the first time on transcriptome data. We verify the expression pattern for five of the putative transcript markers in another progeny population.
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Affiliation(s)
- Erik Alexandersson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Sundsvägen 10, Alnarp, Sweden.
- Present address: Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
| | - Sandeep Kushwaha
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Uppsala, Sweden
- National Institute of Animal Biotechnology, Hyderabad, India
| | - Aastha Subedi
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Sundsvägen 10, Alnarp, Sweden
| | - Deborah Weighill
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Knoxville, TN, USA
| | | | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Knoxville, TN, USA
| | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Sundsvägen 10, Alnarp, Sweden
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Comparative Transcriptome Profiling Reveals Compatible and Incompatible Patterns of Potato Toward Phytophthora infestans. G3-GENES GENOMES GENETICS 2020; 10:623-634. [PMID: 31818876 PMCID: PMC7003068 DOI: 10.1534/g3.119.400818] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Late blight, caused by Phytophthora infestans (P. infestans), is a devastating disease in potato worldwide. Our previous study revealed that the Solanum andigena genotype 03112-233 is resistant to P. infestans isolate 90128, but susceptible to the super race isolate, CN152. In this study, we confirmed by diagnostic resistance gene enrichment sequencing (dRenSeq) that the resistance of 03112-233 toward 90128 is most likely based on a distinct new R gene(s). To gain an insight into the mechanism that governs resistance or susceptibility in 03112-223, comparative transcriptomic profiling analysis based on RNAseq was initiated. Changes in transcription at two time points (24 h and 72 h) after inoculation with isolates 90128 or CN152 were analyzed. A total of 8,881 and 7,209 genes were differentially expressed in response to 90128 and CN152, respectively, and 1,083 differentially expressed genes (DEGs) were common to both time points and isolates. A substantial number of genes were differentially expressed in an isolate-specific manner with 3,837 genes showing induction or suppression following infection with 90128 and 2,165 genes induced or suppressed after colonization by CN152. Hierarchical clustering analysis suggested that isolates with different virulence profiles can induce different defense responses at different time points. Further analysis revealed that the compatible interaction caused higher induction of susceptibility genes such as SWEET compared with the incompatible interaction. The salicylic acid, jasmonic acid, and abscisic acid mediated signaling pathways were involved in the response against both isolates, while ethylene and brassinosteroids mediated defense pathways were suppressed. Our results provide a valuable resource for understanding the interactions between P. infestans and potato.
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Vieira P, Mowery J, Eisenback JD, Shao J, Nemchinov LG. Cellular and Transcriptional Responses of Resistant and Susceptible Cultivars of Alfalfa to the Root Lesion Nematode, Pratylenchus penetrans. FRONTIERS IN PLANT SCIENCE 2019; 10:971. [PMID: 31417588 PMCID: PMC6685140 DOI: 10.3389/fpls.2019.00971] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 07/11/2019] [Indexed: 05/04/2023]
Abstract
The root lesion nematode (RLN), Pratylenchus penetrans, is a migratory species that attacks a broad range of crops, including alfalfa. High levels of infection can reduce alfalfa forage yields and lead to decreased cold tolerance. Currently, there are no commercially certified varieties with RLN resistance. Little information on molecular interactions between alfalfa and P. penetrans, that would shed light on mechanisms of alfalfa resistance to RLN, is available. To advance our understanding of the host-pathogen interactions and to gain biological insights into the genetics and genomics of host resistance to RLN, we performed a comprehensive assessment of resistant and susceptible interactions of alfalfa with P. penetrans that included root penetration studies, ultrastructural observations, and global gene expression profiling of host plants and the nematode. Several gene-candidates associated with alfalfa resistance to P. penetrans and nematode parasitism genes encoding nematode effector proteins were identified for potential use in alfalfa breeding programs or development of new nematicides. We propose that preformed or constitutive defenses, such as significant accumulation of tannin-like deposits in root cells of the resistant cultivar, could be a key to nematode resistance, at least for the specific case of alfalfa-P. penetrans interaction.
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Affiliation(s)
- Paulo Vieira
- Molecular Plant Pathology Laboratory, United States Department of Agriculture – Agricultural Research Service, Beltsville, MD, United States
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, VA, United States
| | - Joseph Mowery
- Electron and Confocal Microscopy Unit, United States Department of Agriculture – Agricultural Research Service, Beltsville, MD, United States
| | - Jonathan D. Eisenback
- School of Plant and Environmental Science, Virginia Tech, Blacksburg, VA, United States
| | - Jonathan Shao
- Molecular Plant Pathology Laboratory, United States Department of Agriculture – Agricultural Research Service, Beltsville, MD, United States
| | - Lev G. Nemchinov
- Molecular Plant Pathology Laboratory, United States Department of Agriculture – Agricultural Research Service, Beltsville, MD, United States
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Masini L, Grenville‐Briggs LJ, Andreasson E, Råberg L, Lankinen Å. Tolerance and overcompensation to infection by Phytophthora infestans in the wild perennial climber Solanum dulcamara. Ecol Evol 2019; 9:4557-4567. [PMID: 31031927 PMCID: PMC6476776 DOI: 10.1002/ece3.5057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 02/16/2019] [Accepted: 02/21/2019] [Indexed: 12/12/2022] Open
Abstract
Studies of infection by Phytophthora infestans-the causal agent of potato late blight-in wild species can provide novel insights into plant defense responses, and indicate how wild plants might be influenced by recurrent epidemics in agricultural fields. In the present study, our aim was to investigate if different clones of Solanum dulcamara (a relative of potato) collected in the wild differ in resistance and tolerance to infection by a common European isolate of P. infestans. We performed infection experiments with six S. dulcamara genotypes (clones) both in the laboratory and in the field and measured the degree of infection and plant performance traits. In the laboratory, the six evaluated genotypes varied from resistant to susceptible, as measured by degree of infection 20 days post infection. Two of the four genotypes susceptible to infection showed a quadratic (concave downward) relationship between the degree of infection and shoot length, with maximum shoot length at intermediate values of infection. This result suggests overcompensation, that is, an increase in growth in infected individuals. The number of leaves decreased with increasing degree of infection, but at different rates in the four susceptible genotypes, indicating genetic variation for tolerance. In the field, the inoculated genotypes did not show any disease symptoms, but plant biomass at the end of the growing season was higher for inoculated plants than for controls, in-line with the overcompensation detected in the laboratory. We conclude that in S. dulcamara there are indications of genetic variation for both resistance and tolerance to P. infestans infection. Moreover, some genotypes displayed overcompensation. Learning about plant tolerance and overcompensation to infection by pathogens can help broaden our understanding of plant defense in natural populations and help develop more sustainable plant protection strategies for economically important crop diseases.
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Affiliation(s)
- Laura Masini
- Plant Protection BiologySwedish University of Agricultural SciencesAlnarpSweden
- Present address:
British American TobaccoPlant Biotechnology DivisionCambridgeUK
| | | | - Erik Andreasson
- Plant Protection BiologySwedish University of Agricultural SciencesAlnarpSweden
| | - Lars Råberg
- Department of BiologyLund UniversityLundSweden
| | - Åsa Lankinen
- Plant Protection BiologySwedish University of Agricultural SciencesAlnarpSweden
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11
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Abreha KB, Lankinen Å, Masini L, Hydbom S, Andreasson E. Late Blight Resistance Screening of Major Wild Swedish Solanum Species: S. dulcamara, S. nigrum, and S. physalifolium. PHYTOPATHOLOGY 2018; 108:847-857. [PMID: 29327646 DOI: 10.1094/phyto-10-17-0355-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
To understand the contribution of wild Solanum species to the epidemiology of potato late blight in Sweden, we characterized the resistance of the three putative alternative hosts: S. physalifolium, S. nigrum, and S. dulcamara to Phytophthora infestans, the causal agent of late blight. The pathogen sporulated in all 10 investigated S. physalifolium genotypes, suggesting susceptibility (S phenotype). Field-grown S. physalifolium was naturally infected but could regrow, though highly infected genotypes were smaller at the end of the season. In 75 S. nigrum genotypes, there were no symptoms (R phenotype) or a lesion restricted to the point of inoculation (RN phenotype), indicating resistance. In 164 S. dulcamara genotypes, most resistance variability was found within sibling groups. In addition to the three resistance phenotypes (R, RN, and S), in S. dulcamara a fourth new resistance phenotype (SL) was identified with lesions larger than the point of inoculation but without visible sporulation of the pathogen. Quantitative PCR confirmed P. infestans growth difference in RN, SL, and S phenotypes. Thus, in Sweden S. physalifolium is susceptible and could be a player in epidemiology. A limited role of S. dulcamara leaves in the epidemiology of late blight was suggested, since no major symptoms have been found in the field.
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Affiliation(s)
- Kibrom B Abreha
- Department of Plant Protection biology, Swedish University of Agricultural Sciences, Box 102, 230 73 Alnarp, Sweden
| | - Åsa Lankinen
- Department of Plant Protection biology, Swedish University of Agricultural Sciences, Box 102, 230 73 Alnarp, Sweden
| | - Laura Masini
- Department of Plant Protection biology, Swedish University of Agricultural Sciences, Box 102, 230 73 Alnarp, Sweden
| | - Sofia Hydbom
- Department of Plant Protection biology, Swedish University of Agricultural Sciences, Box 102, 230 73 Alnarp, Sweden
| | - Erik Andreasson
- Department of Plant Protection biology, Swedish University of Agricultural Sciences, Box 102, 230 73 Alnarp, Sweden
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12
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Chakraborty S, Martínez-García PJ, Dandekar AM. YeATSAM analysis of the walnut and chickpea transcriptome reveals key genes undetected by current annotation tools. F1000Res 2017; 5:2689. [PMID: 28105312 PMCID: PMC5200947 DOI: 10.12688/f1000research.10040.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/15/2016] [Indexed: 11/20/2022] Open
Abstract
Background: The transcriptome, a treasure trove of gene space information, remains severely under-used by current genome annotation methods.
Methods: Here, we present an annotation method in the YeATS suite (YeATSAM), based on information encoded by the transcriptome, that demonstrates artifacts of the assembler, which must be addressed to achieve proper annotation.
Results and Discussion: YeATSAM was applied to the transcriptome obtained from twenty walnut tissues and compared to MAKER-P annotation of the recently published walnut genome sequence (WGS). MAKER-P and YeATSAM both failed to annotate several hundred proteins found by the other. Although many of these unannotated proteins have repetitive sequences (possibly transposable elements), other crucial proteins were excluded by each method. An egg cell-secreted protein and a homer protein were undetected by YeATSAM, although these did not produce any transcripts. Importantly, MAKER-P failed to classify key photosynthesis-related proteins, which we show emanated from Trinity assembly artifacts potentially not handled by MAKER-P. Also, no proteins from the large berberine bridge enzyme (BBE) family were annotated by MAKER-P. BBE is implicated in biosynthesis of several alkaloids metabolites, like anti-microbial berberine. As further validation, YeATSAM identified ~1000 genes that are not annotated in the NCBI database by Gnomon. YeATSAM used a RNA-seq derived chickpea (
Cicer arietinum L.) transcriptome assembled using Newbler v2.3.
Conclusions: Since the current version of YeATSAM does not have an
ab initio module, we suggest a combined annotation scheme using both MAKER-P and YeATSAM to comprehensively and accurately annotate the WGS.
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13
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Lankinen Å, Abreha KB, Alexandersson E, Andersson S, Andreasson E. Nongenetic Inheritance of Induced Resistance in a Wild Annual Plant. PHYTOPATHOLOGY 2016; 106:877-83. [PMID: 27070426 DOI: 10.1094/phyto-10-15-0278-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Nongenetic inheritance (e.g., transgenerational epigenetic effects) has received increasing interest in recent years, particularly in plants. However, most studies have involved a few model species and relatively little is known about wild species in these respects. We investigated transgenerational induced resistance to infection by the devastating oomycete Phytophthora infestans in Solanum physalifolium, a wild relative of cultivated potato. We treated plants with β-aminobutyric acid (BABA), a nontoxic compound acting as an inducing agent, or infected plants with P. infestans. BABA treatment reduced lesion size in detached-leaf assays inoculated by P. infestans in two of three tested genotypes, suggesting that resistance to oomycetes can be induced by BABA within a generation not only in crops or model species but also in wild species directly collected from nature. Both BABA treatment and infection in the parental generation reduced lesions in the subsequent generation in one of two genotypes, indicating a transgenerational influence on resistance that varies among genotypes. We did not detect treatment effects on seed traits, indicating the involvement of a mechanism unrelated to maternal effects. In conclusion, our study provides data on BABA induction and nongenetic inheritance of induced resistance in a wild relative of cultivated potato, implying that this factor might be important in the ecological and agricultural landscape.
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Affiliation(s)
- Åsa Lankinen
- First, second, third, and fifth authors: Swedish University of Agricultural Sciences, Plant Protection Biology, P.O. Box 102, S-230 53 Alnarp, Sweden; and fourth author: Department of Biology, Lund University, Ecology Building, S-223 62 Lund, Sweden
| | - Kibrom B Abreha
- First, second, third, and fifth authors: Swedish University of Agricultural Sciences, Plant Protection Biology, P.O. Box 102, S-230 53 Alnarp, Sweden; and fourth author: Department of Biology, Lund University, Ecology Building, S-223 62 Lund, Sweden
| | - Erik Alexandersson
- First, second, third, and fifth authors: Swedish University of Agricultural Sciences, Plant Protection Biology, P.O. Box 102, S-230 53 Alnarp, Sweden; and fourth author: Department of Biology, Lund University, Ecology Building, S-223 62 Lund, Sweden
| | - Stefan Andersson
- First, second, third, and fifth authors: Swedish University of Agricultural Sciences, Plant Protection Biology, P.O. Box 102, S-230 53 Alnarp, Sweden; and fourth author: Department of Biology, Lund University, Ecology Building, S-223 62 Lund, Sweden
| | - Erik Andreasson
- First, second, third, and fifth authors: Swedish University of Agricultural Sciences, Plant Protection Biology, P.O. Box 102, S-230 53 Alnarp, Sweden; and fourth author: Department of Biology, Lund University, Ecology Building, S-223 62 Lund, Sweden
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Meyer FE, Shuey LS, Naidoo S, Mamni T, Berger DK, Myburg AA, van den Berg N, Naidoo S. Dual RNA-Sequencing of Eucalyptus nitens during Phytophthora cinnamomi Challenge Reveals Pathogen and Host Factors Influencing Compatibility. FRONTIERS IN PLANT SCIENCE 2016; 7:191. [PMID: 26973660 PMCID: PMC4773608 DOI: 10.3389/fpls.2016.00191] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 02/04/2016] [Indexed: 05/18/2023]
Abstract
Damage caused by Phytophthora cinnamomi Rands remains an important concern on forest tree species. The pathogen causes root and collar rot, stem cankers, and dieback of various economically important Eucalyptus spp. In South Africa, susceptible cold tolerant Eucalyptus plantations have been affected by various Phytophthora spp. with P. cinnamomi considered one of the most virulent. The molecular basis of this compatible interaction is poorly understood. In this study, susceptible Eucalyptus nitens plants were stem inoculated with P. cinnamomi and tissue was harvested five days post inoculation. Dual RNA-sequencing, a technique which allows the concurrent detection of both pathogen and host transcripts during infection, was performed. Approximately 1% of the reads mapped to the draft genome of P. cinnamomi while 78% of the reads mapped to the Eucalyptus grandis genome. The highest expressed P. cinnamomi gene in planta was a putative crinkler effector (CRN1). Phylogenetic analysis indicated the high similarity of this P. cinnamomi CRN1 to that of Phytophthora infestans. Some CRN effectors are known to target host nuclei to suppress defense. In the host, over 1400 genes were significantly differentially expressed in comparison to mock inoculated trees, including suites of pathogenesis related (PR) genes. In particular, a PR-9 peroxidase gene with a high similarity to a Carica papaya PR-9 ortholog previously shown to be suppressed upon infection by Phytophthora palmivora was down-regulated two-fold. This PR-9 gene may represent a cross-species effector target during P. cinnamomi infection. This study identified pathogenicity factors, potential manipulation targets, and attempted host defense mechanisms activated by E. nitens that contributed to the susceptible outcome of the interaction.
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Affiliation(s)
- Febé E. Meyer
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Louise S. Shuey
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Sitha Naidoo
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Thandekile Mamni
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Dave K. Berger
- Department of Plant Science, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Alexander A. Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Noëlani van den Berg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Sanushka Naidoo
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
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15
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Chawade A, Alexandersson E, Bengtsson T, Andreasson E, Levander F. Targeted Proteomics Approach for Precision Plant Breeding. J Proteome Res 2016; 15:638-46. [PMID: 26704985 DOI: 10.1021/acs.jproteome.5b01061] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Selected reaction monitoring (SRM) is a targeted mass spectrometry technique that enables precise quantitation of hundreds of peptides in a single run. This technique provides new opportunities for multiplexed protein biomarker measurements. For precision plant breeding, DNA-based markers have been used extensively, but the potential of protein biomarkers has not been exploited. In this work, we developed an SRM marker panel with assays for 104 potato (Solanum tuberosum) peptides selected using univariate and multivariate statistics. Thereafter, using random forest classification, the prediction markers were identified for Phytopthora infestans resistance in leaves, P. infestans resistance in tubers, and plant yield in potato leaf secretome samples. The results suggest that the marker panel has the predictive potential for three traits, two of which have no commercial DNA markers so far. Furthermore, the marker panel was also tested and found to be applicable to potato clones not used during the marker development. The proposed workflow is thus a proof-of-concept for targeted proteomics as an efficient readout in accelerated breeding for complex and agronomically important traits.
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Affiliation(s)
- Aakash Chawade
- Department of Immunotechnology, Lund University , Lund, Scania, Sweden
| | - Erik Alexandersson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences , Alnarp, Sweden
| | - Therese Bengtsson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences , Alnarp, Sweden
| | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences , Alnarp, Sweden
| | - Fredrik Levander
- Department of Immunotechnology, Lund University , Lund, Scania, Sweden.,Bioinformatics Infrastructure for Life Sciences (BILS), Lund University , Lund, Scania, Sweden
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16
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Lenman M, Ali A, Mühlenbock P, Carlson-Nilsson U, Liljeroth E, Champouret N, Vleeshouwers VGAA, Andreasson E. Effector-driven marker development and cloning of resistance genes against Phytophthora infestans in potato breeding clone SW93-1015. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:105-15. [PMID: 26518573 DOI: 10.1007/s00122-015-2613-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/29/2015] [Indexed: 05/03/2023]
Abstract
We show the usefulness of integrating effector screening in a breeding program and in resistance gene cloning, with Phytophthora resistance in the Swedish potato breeding clone SW93-1015 as an example. Phytophthora infestans is one of the most devastating plant pathogens worldwide. We have earlier found that the SW93-1015 potato breeding clone has an efficient resistance against P. infestans under field conditions in Sweden, which has an unusually high local diversity of the pathogen. This potato clone has characteristics that are different from classical R-gene-mediated resistance such as elevated levels of hydrogen peroxide (H2O2) under controlled conditions. Analysis of 76 F1 potato progenies from two individual crosses resulted in nearly 50% resistant clones, from both crosses. This result suggests that the SW93-1015 clone has a simplex genotype for this trait. Screening with over 50 different P. infestans effectors, containing the conserved motif RXLR (for Arg, any amino acid, Leu, Arg), revealed a specific response to Avr2, which suggests that SW93-1015 might contain a functional homolog of the R2 resistance gene. We cloned eight R2 gene homologs from SW93-1015, whereof seven have not been described before and one gene encoded a protein identical to Rpi-ABPT. Expression of this gene in potato cultivar Désirée provided R2-specific resistance, whereas other homologues did not. Using RNAseq analyses we designed a new DNA marker for the R2 resistance in SW93-1015. In summary, we have demonstrated the use of effector screening in practical breeding material and revealed the key resistance mechanism for SW93-1015.
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Affiliation(s)
- Marit Lenman
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden.
| | - Ashfaq Ali
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Per Mühlenbock
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Ulrika Carlson-Nilsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Erland Liljeroth
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Nicolas Champouret
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Wageningen, The Netherlands
| | | | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
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17
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Frades I, Abreha KB, Proux-Wéra E, Lankinen Å, Andreasson E, Alexandersson E. A novel workflow correlating RNA-seq data to Phythophthora infestans resistance levels in wild Solanum species and potato clones. FRONTIERS IN PLANT SCIENCE 2015; 6:718. [PMID: 26442032 PMCID: PMC4585127 DOI: 10.3389/fpls.2015.00718] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 08/27/2015] [Indexed: 05/18/2023]
Abstract
Comparative transcriptomics between species can provide valuable understanding of plant-pathogen interactions. Here, we focus on wild Solanum species and potato clones with varying degree of resistance against Phytophthora infestans, which causes the devastating late blight disease in potato. The transcriptomes of three wild Solanum species native to Southern Sweden, Solanum dulcamara, Solanum nigrum, and Solanum physalifolium were compared to three potato clones, Desiree (cv.), SW93-1015 and Sarpo Mira. Desiree and S. physalifolium are susceptible to P. infestans whereas the other four have different degrees of resistance. By building transcript families based on de novo assembled RNA-seq across species and clones and correlating these to resistance phenotypes, we created a novel workflow to identify families with expanded or depleted number of transcripts in relation to the P. infestans resistance level. Analysis was facilitated by inferring functional annotations based on the family structure and semantic clustering. More transcript families were expanded in the resistant clones and species and the enriched functions of these were associated to expected gene ontology (GO) terms for resistance mechanisms such as hypersensitive response, host programmed cell death and endopeptidase activity. However, a number of unexpected functions and transcripts were also identified, for example transmembrane transport and protein acylation expanded in the susceptible group and a cluster of Zinc knuckle family proteins expanded in the resistant group. Over 400 expressed putative resistance (R-)genes were identified and resistant clones Sarpo Mira and SW93-1015 had ca 25% more expressed putative R-genes than susceptible cultivar Desiree. However, no differences in numbers of susceptibility (S-)gene homologs were seen between species and clones. In addition, we identified P. infestans transcripts including effectors in the early stages of P. infestans-Solanum interactions.
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Affiliation(s)
| | | | | | | | | | - Erik Alexandersson
- Department of Plant Protection Biology, Swedish University of Agricultural SciencesAlnarp, Sweden
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18
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Burra DD, Mühlenbock P, Andreasson E. Salicylic and jasmonic acid pathways are necessary for defence against Dickeya solani as revealed by a novel method for Blackleg disease screening of in vitro grown potato. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:1030-1038. [PMID: 25903921 DOI: 10.1111/plb.12339] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 04/20/2015] [Indexed: 06/04/2023]
Abstract
Potato is major crop ensuring food security in Europe, and blackleg disease is increasingly causing losses in yield and during storage. Recently, one blackleg pathogen, Dickeya solani has been shown to be spreading in Northern Europe that causes aggressive disease development. Currently, identification of tolerant commercial potato varieties has been unsuccessful; this is confounded by the complicated etiology of the disease and a strong environmental influence on disease development. There is currently a lack of efficient testing systems. Here, we describe a system for quantification of blackleg symptoms on shoots of sterile in vitro potato plants, which saves time and space compared to greenhouse and existing field assays. We found no evidence for differences in infection between the described in vitro-based screening method and existing greenhouse assays. This system facilitates efficient screening of blackleg disease response of potato plants independent of other microorganisms and variable environmental conditions. We therefore used the in vitro screening method to increase understanding of plant mechanisms involved in blackleg disease development by analysing disease response of hormone- related (salicylic and jasmonic acid) transgenic potato plants. We show that both jasmonic (JA) and salicylic (SA) acid pathways regulate tolerance to blackleg disease in potato, a result unlike previous findings in Arabidopsis defence response to necrotrophic bacteria. We confirm this by showing induction of a SA marker, pathogenesis-related protein 1 (StPR1), and a JA marker, lipoxygenase (StLOX), in Dickeya solani infected in vitro potato plants. We also observed that tubers of transgenic potato plants were more susceptible to soft rot compared to wild type, suggesting a role for SA and JA pathways in general tolerance to Dickeya.
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Affiliation(s)
- D D Burra
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - P Mühlenbock
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - E Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
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19
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Abreha KB, Alexandersson E, Vossen JH, Anderson P, Andreasson E. Inoculation of Transgenic Resistant Potato by Phytophthora infestans Affects Host Plant Choice of a Generalist Moth. PLoS One 2015; 10:e0129815. [PMID: 26053171 PMCID: PMC4459979 DOI: 10.1371/journal.pone.0129815] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 05/13/2015] [Indexed: 12/29/2022] Open
Abstract
Pathogen attack and the plant's response to this attack affect herbivore oviposition preference and larval performance. Introduction of major resistance genes against Phytophthora infestans (Rpi-genes), the cause of the devastating late blight disease, from wild Solanum species into potato changes the plant-pathogen interaction dynamics completely, but little is known about the effects on non-target organisms. Thus, we examined the effect of P. infestans itself and introduction of an Rpi-gene into the crop on host plant preference of the generalist insect herbivore, Spodoptera littoralis (Lepidoptera: Noctuidae). In two choice bioassays, S. littoralis preferred to oviposit on P. infestans-inoculated plants of both the susceptible potato (cv. Desiree) and an isogenic resistant clone (A01-22: cv. Desiree transformed with Rpi-blb1), when compared to uninoculated plants of the same genotype. Both cv. Desiree and clone A01-22 were equally preferred for oviposition by S. littoralis when uninoculated plants were used, while cv. Desiree received more eggs compared to the resistant clone when both were inoculated with the pathogen. No significant difference in larval and pupal weight was found between S. littoralis larvae reared on leaves of the susceptible potato plants inoculated or uninoculated with P. infestans. Thus, the herbivore's host plant preference in this system was not directly associated with larval performance. The results indicate that the Rpi-blb1 based resistance in itself does not influence insect behavior, but that herbivore oviposition preference is affected by a change in the plant-microbe interaction.
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Affiliation(s)
- Kibrom B. Abreha
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Erik Alexandersson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Jack H. Vossen
- Wageningen UR Plant Breeding, Wageningen University and Research Center, Wageningen, The Netherlands
| | - Peter Anderson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
- * E-mail:
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20
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Xie Z, Si W, Gao R, Zhang X, Yang S. Evolutionary analysis of RB/Rpi-blb1 locus in the Solanaceae family. Mol Genet Genomics 2015; 290:2173-86. [PMID: 26008792 DOI: 10.1007/s00438-015-1068-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 05/12/2015] [Indexed: 11/28/2022]
Abstract
Late blight caused by the oomycete Phytophthora infestans is one of the most severe threats to potato production worldwide. Numerous studies suggest that the most effective protective strategy against the disease would be to provide potato cultivars with durable resistance (R) genes. However, little is known about the origin and evolutional history of these durable R-genes in potato. Addressing this might foster better understanding of the dynamics of these genes in nature and provide clues for identifying potential candidate R-genes. Here, a systematic survey was executed at RB/Rpi-blb1 locus, an exclusive broad-spectrum R-gene locus in potato. As indicated by synteny analysis, RB/Rpi-blb1 homologs were identified in all tested genomes, including potato, tomato, pepper, and Nicotiana, suggesting that the RB/Rpi-blb1 locus has an ancient origin. Two evolutionary patterns, similar to those reported on RGC2 in Lactuca, and Pi2/9 in rice, were detected at this locus. Type I RB/Rpi-blb1 homologs have frequent copy number variations and sequence exchanges, obscured orthologous relationships, considerable nucleotide divergence, and high non-synonymous to synonymous substitutions (Ka/Ks) between or within species, suggesting rapid diversification and balancing selection in response to rapid changes in the oomycete pathogen genomes. These characteristics may serve as signatures for cloning of late blight resistance genes.
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Affiliation(s)
- Zhengqing Xie
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Weina Si
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Rongchao Gao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
| | - Xiaohui Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China.
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China.
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21
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Burra DD, Berkowitz O, Hedley PE, Morris J, Resjö S, Levander F, Liljeroth E, Andreasson E, Alexandersson E. Phosphite-induced changes of the transcriptome and secretome in Solanum tuberosum leading to resistance against Phytophthora infestans. BMC PLANT BIOLOGY 2014; 14:254. [PMID: 25270759 PMCID: PMC4192290 DOI: 10.1186/s12870-014-0254-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 09/20/2014] [Indexed: 05/05/2023]
Abstract
BACKGROUND Potato late blight caused by the oomycete pathogen Phytophthora infestans can lead to immense yield loss. We investigated the transcriptome of Solanum tubersoum (cv. Desiree) and characterized the secretome by quantitative proteomics after foliar application of the protective agent phosphite. We also studied the distribution of phosphite in planta after application and tested transgenic potato lines with impaired in salicylic and jasmonic acid signaling. RESULTS Phosphite had a rapid and transient effect on the transcriptome, with a clear response 3 h after treatment. Strikingly this effect lasted less than 24 h, whereas protection was observed throughout all time points tested. In contrast, 67 secretome proteins predominantly associated with cell-wall processes and defense changed in abundance at 48 h after treatment. Transcripts associated with defense, wounding, and oxidative stress constituted the core of the phosphite response. We also observed changes in primary metabolism and cell wall-related processes. These changes were shown not to be due to phosphate depletion or acidification caused by phosphite treatment. Of the phosphite-regulated transcripts 40% also changed with β-aminobutyric acid (BABA) as an elicitor, while the defence gene PR1 was only up-regulated by BABA. Although phosphite was shown to be distributed in planta to parts not directly exposed to phosphite, no protection in leaves without direct foliar application was observed. Furthermore, the analysis of transgenic potato lines indicated that the phosphite-mediated resistance was independent of the plant hormones salicylic and jasmonic acid. CONCLUSIONS Our study suggests that a rapid phosphite-triggered response is important to confer long-lasting resistance against P. infestans and gives molecular understanding of its successful field applications.
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Affiliation(s)
- Dharani Dhar Burra
- />Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Oliver Berkowitz
- />Centre for Phytophthora Science and Management, School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA 6150 Australia
- />School of Plant Biology, The University of Western Australia, Crawley, WA 6009 Australia
- />Present address: Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, Crawley, WA 6009 Australia
| | - Pete E Hedley
- />Genome Technology, James Hutton Institute, Invergowrie, Dundee, Scotland
| | - Jenny Morris
- />Genome Technology, James Hutton Institute, Invergowrie, Dundee, Scotland
| | - Svante Resjö
- />Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Erland Liljeroth
- />Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Erik Andreasson
- />Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Erik Alexandersson
- />Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
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Ali A, Alexandersson E, Sandin M, Resjö S, Lenman M, Hedley P, Levander F, Andreasson E. Quantitative proteomics and transcriptomics of potato in response to Phytophthora infestans in compatible and incompatible interactions. BMC Genomics 2014; 15:497. [PMID: 24947944 PMCID: PMC4079953 DOI: 10.1186/1471-2164-15-497] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 06/10/2014] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND In order to get global molecular understanding of one of the most important crop diseases worldwide, we investigated compatible and incompatible interactions between Phytophthora infestans and potato (Solanum tuberosum). We used the two most field-resistant potato clones under Swedish growing conditions, which have the greatest known local diversity of P. infestans populations, and a reference compatible cultivar. RESULTS Quantitative label-free proteomics of 51 apoplastic secretome samples (PXD000435) in combination with genome-wide transcript analysis by 42 microarrays (E-MTAB-1515) were used to capture changes in protein abundance and gene expression at 6, 24 and 72 hours after inoculation with P. infestans. To aid mass spectrometry analysis we generated cultivar-specific RNA-seq data (E-MTAB-1712), which increased peptide identifications by 17%. Components induced only during incompatible interactions, which are candidates for hypersensitive response initiation, include a Kunitz-like protease inhibitor, transcription factors and an RCR3-like protein. More secreted proteins had lower abundance in the compatible interaction compared to the incompatible interactions. Based on this observation and because the well-characterized effector-target C14 protease follows this pattern, we suggest 40 putative effector targets. CONCLUSIONS In summary, over 17000 transcripts and 1000 secreted proteins changed in abundance in at least one time point, illustrating the dynamics of plant responses to a hemibiotroph. Half of the differentially abundant proteins showed a corresponding change at the transcript level. Many putative hypersensitive and effector-target proteins were single representatives of large gene families.
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Affiliation(s)
| | | | | | | | | | | | | | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden.
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Chawade A, Alexandersson E, Levander F. Normalyzer: a tool for rapid evaluation of normalization methods for omics data sets. J Proteome Res 2014; 13:3114-20. [PMID: 24766612 PMCID: PMC4053077 DOI: 10.1021/pr401264n] [Citation(s) in RCA: 170] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
High-throughput omics data often contain systematic biases introduced during various steps of sample processing and data generation. As the source of these biases is usually unknown, it is difficult to select an optimal normalization method for a given data set. To facilitate this process, we introduce the open-source tool "Normalyzer". It normalizes the data with 12 different normalization methods and generates a report with several quantitative and qualitative plots for comparative evaluation of different methods. The usefulness of Normalyzer is demonstrated with three different case studies from quantitative proteomics and transcriptomics. The results from these case studies show that the choice of normalization method strongly influences the outcome of downstream quantitative comparisons. Normalyzer is an R package and can be used locally or through the online implementation at http://quantitativeproteomics.org/normalyzer .
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Affiliation(s)
- Aakash Chawade
- Department of Immunotechnology, Lund University , Medicon Village 406, SE 223 81 Lund, Sweden
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24
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Bengtsson T, Weighill D, Proux-Wéra E, Levander F, Resjö S, Burra DD, Moushib LI, Hedley PE, Liljeroth E, Jacobson D, Alexandersson E, Andreasson E. Proteomics and transcriptomics of the BABA-induced resistance response in potato using a novel functional annotation approach. BMC Genomics 2014; 15:315. [PMID: 24773703 PMCID: PMC4234511 DOI: 10.1186/1471-2164-15-315] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 04/16/2014] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Induced resistance (IR) can be part of a sustainable plant protection strategy against important plant diseases. β-aminobutyric acid (BABA) can induce resistance in a wide range of plants against several types of pathogens, including potato infected with Phytophthora infestans. However, the molecular mechanisms behind this are unclear and seem to be dependent on the system studied. To elucidate the defence responses activated by BABA in potato, a genome-wide transcript microarray analysis in combination with label-free quantitative proteomics analysis of the apoplast secretome were performed two days after treatment of the leaf canopy with BABA at two concentrations, 1 and 10 mM. RESULTS Over 5000 transcripts were differentially expressed and over 90 secretome proteins changed in abundance indicating a massive activation of defence mechanisms with 10 mM BABA, the concentration effective against late blight disease. To aid analysis, we present a more comprehensive functional annotation of the microarray probes and gene models by retrieving information from orthologous gene families across 26 sequenced plant genomes. The new annotation provided GO terms to 8616 previously un-annotated probes. CONCLUSIONS BABA at 10 mM affected several processes related to plant hormones and amino acid metabolism. A major accumulation of PR proteins was also evident, and in the mevalonate pathway, genes involved in sterol biosynthesis were down-regulated, whereas several enzymes involved in the sesquiterpene phytoalexin biosynthesis were up-regulated. Interestingly, abscisic acid (ABA) responsive genes were not as clearly regulated by BABA in potato as previously reported in Arabidopsis. Together these findings provide candidates and markers for improved resistance in potato, one of the most important crops in the world.
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Affiliation(s)
- Therese Bengtsson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Box 102, SE-230 53 Alnarp, Sweden
| | - Deborah Weighill
- Institute for Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch University, Stellenbosch, South Africa
| | - Estelle Proux-Wéra
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Box 102, SE-230 53 Alnarp, Sweden
| | | | - Svante Resjö
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Box 102, SE-230 53 Alnarp, Sweden
| | - Dharani Dhar Burra
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Box 102, SE-230 53 Alnarp, Sweden
| | | | - Pete E Hedley
- Genome Technology, James Hutton Institute, Invergowrie, Dundee, Scotland
| | - Erland Liljeroth
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Box 102, SE-230 53 Alnarp, Sweden
| | - Dan Jacobson
- Institute for Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch University, Stellenbosch, South Africa
| | - Erik Alexandersson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Box 102, SE-230 53 Alnarp, Sweden
| | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Box 102, SE-230 53 Alnarp, Sweden
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25
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Tanveer T, Shaheen K, Parveen S, Kazi AG, Ahmad P. Plant secretomics: identification, isolation, and biological significance under environmental stress. PLANT SIGNALING & BEHAVIOR 2014; 9:e29426. [PMID: 25763623 PMCID: PMC4203502 DOI: 10.4161/psb.29426] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 06/01/2014] [Accepted: 06/02/2014] [Indexed: 05/03/2023]
Abstract
Plant secretomes are the proteins secreted by the plant cells and are involved in the maintenance of cell wall structure, relationship between host and pathogen, communication between different cells in the plant, etc. Amalgamation of methodologies like bioinformatics, biochemical, and proteomics are used to separate, classify, and outline secretomes by means of harmonizing in planta systems and in vitro suspension cultured cell system (SSCs). We summed up and explained the meaning of secretome, methods used for the identification and isolation of secreted proteins from extracellular space and methods for the assessment of purity of secretome proteins in this review. Two D PAGE method and HPLC based methods for the analysis together with different bioinformatics tools used for the prediction of secretome proteins are also discussed. Biological significance of secretome proteins under different environmental stresses, i.e., salt stress, drought stress, oxidative stress, etc., defense responses and plant interactions with environment are also explained in detail.
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Affiliation(s)
- Tehreem Tanveer
- Atta-ur-Rahman School of Applied Biosciences; National University of Sciences and Technology; Islamabad, Pakistan
| | - Kanwal Shaheen
- Atta-ur-Rahman School of Applied Biosciences; National University of Sciences and Technology; Islamabad, Pakistan
| | - Sajida Parveen
- Atta-ur-Rahman School of Applied Biosciences; National University of Sciences and Technology; Islamabad, Pakistan
| | - Alvina Gul Kazi
- Atta-ur-Rahman School of Applied Biosciences; National University of Sciences and Technology; Islamabad, Pakistan
| | - Parvaiz Ahmad
- Department of Botany; S.P. College; Jammu and Kashmir, India
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26
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Sandin M, Ali A, Hansson K, Månsson O, Andreasson E, Resjö S, Levander F. An adaptive alignment algorithm for quality-controlled label-free LC-MS. Mol Cell Proteomics 2013; 12:1407-20. [PMID: 23306530 DOI: 10.1074/mcp.o112.021907] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Label-free quantification using precursor-based intensities is a versatile workflow for large-scale proteomics studies. The method however requires extensive computational analysis and is therefore in need of robust quality control during the data mining stage. We present a new label-free data analysis workflow integrated into a multiuser software platform. A novel adaptive alignment algorithm has been developed to minimize the possible systematic bias introduced into the analysis. Parameters are estimated on the fly from the data at hand, producing a user-friendly analysis suite. Quality metrics are output in every step of the analysis as well as actively incorporated into the parameter estimation. We furthermore show the improvement of this system by comprehensive comparison to classical label-free analysis methodology as well as current state-of-the-art software.
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Affiliation(s)
- Marianne Sandin
- Department of Immunotechnology, Lund University, BMC D13, 22184 Lund, Sweden
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27
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Alexandersson E, Ali A, Resjö S, Andreasson E. Plant secretome proteomics. FRONTIERS IN PLANT SCIENCE 2013; 4:9. [PMID: 23378846 PMCID: PMC3561728 DOI: 10.3389/fpls.2013.00009] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 01/11/2013] [Indexed: 05/14/2023]
Abstract
The plant secretome refers to the set of proteins secreted out of the plant cell into the surrounding extracellular space commonly referred to as the apoplast. Secreted proteins maintain cell structure and acts in signaling and are crucial for stress responses where they can interact with pathogen effectors and control the extracellular environment. Typically, secreted proteins contain an N-terminal signal peptide and are directed through the endoplasmic reticulum/Golgi pathway. However, in plants many proteins found in the secretome lack such a signature and might follow alternative ways of secretion. This review covers techniques to isolate plant secretomes and how to identify and quantify their constituent proteins. Furthermore, bioinformatical tools to predict secretion signals and define the putative secretome are presented. Findings from proteomic studies and important protein families of plant secretomes, such as proteases and hydrolases, are highlighted.
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Affiliation(s)
- Erik Alexandersson
- *Correspondence: Erik Alexandersson, Department of Plant Protection Biology, Swedish University of Agricultural Sciences, P.O. Box 102, SE-230 53 Alnarp, Sweden. e-mail:
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