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Zeffa DM, Júnior LP, de Assis R, Delfini J, Marcos AW, Koltun A, Baba VY, Constantino LV, Uhdre RS, Nogueira AF, Moda-Cirino V, Scapim CA, Gonçalves LSA. Multi-locus genome-wide association study for phosphorus use efficiency in a tropical maize germplasm. FRONTIERS IN PLANT SCIENCE 2024; 15:1366173. [PMID: 39246817 PMCID: PMC11380136 DOI: 10.3389/fpls.2024.1366173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 07/10/2024] [Indexed: 09/10/2024]
Abstract
Phosphorus (P) is an essential macronutrient for maize (Zea mays L.) growth and development. Therefore, generating cultivars with upgraded P use efficiency (PUE) represents one of the main strategies to reduce the global agriculture dependence on phosphate fertilizers. In this work, genome-wide association studies (GWAS) were performed to detect quantitative trait nucleotide (QTN) and potential PUE-related candidate genes and associated traits in greenhouse and field trials under contrasting P conditions. The PUE and other agronomy traits of 132 maize inbred lines were assessed in low and normal P supply through the greenhouse and field experiments and Multi-locus GWAS was used to map the associated QTNs. Wide genetic variability was observed among the maize inbred lines under low and normal P supply. In addition, we confirm the complex and quantitative nature of PUE. A total of 306 QTNs were associated with the 24 traits evaluated using different multi-locus GWAS methods. A total of 186 potential candidate genes were identified, mainly involved with transcription regulator, transporter, and transference activity. Further studies are still needed to elucidate the functions and relevance of these genes regarding PUE. Nevertheless, pyramiding the favorable alleles pinpointed in the present study can be considered an efficient strategy for molecular improvement to increase maize PUE.
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Affiliation(s)
- Douglas Mariani Zeffa
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá, Paraná, Brazil
| | - Luiz Perini Júnior
- Departamento de Agronomia, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Rafael de Assis
- Departamento de Biologia, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Jéssica Delfini
- Departamento de Agronomia, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Antoni Wallace Marcos
- Departamento de Agronomia, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | - Alessandra Koltun
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá, Paraná, Brazil
| | - Viviane Yumi Baba
- Departamento de Agronomia, Universidade Estadual de Londrina, Londrina, Paraná, Brazil
| | | | - Renan Santos Uhdre
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá, Paraná, Brazil
| | | | - Vania Moda-Cirino
- Área de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná, Londrina, Paraná, Brazil
| | - Carlos Alberto Scapim
- Departamento de Agronomia, Universidade Estadual de Maringá, Maringá, Paraná, Brazil
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Gandham P, Rajasekaran K, Sickler C, Mohan H, Gilbert M, Baisakh N. MicroRNA (miRNA) profiling of maize genotypes with differential response to Aspergillus flavus implies zma-miR156-squamosa promoter binding protein (SBP) and zma-miR398/zma-miR394-F -box combinations involved in resistance mechanisms. STRESS BIOLOGY 2024; 4:26. [PMID: 38727957 PMCID: PMC11087424 DOI: 10.1007/s44154-024-00158-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 03/05/2024] [Indexed: 05/13/2024]
Abstract
Maize (Zea mays), a major food crop worldwide, is susceptible to infection by the saprophytic fungus Aspergillus flavus that can produce the carcinogenic metabolite aflatoxin (AF) especially under climate change induced abiotic stressors that favor mold growth. Several studies have used "-omics" approaches to identify genetic elements with potential roles in AF resistance, but there is a lack of research identifying the involvement of small RNAs such as microRNAs (miRNAs) in maize-A. flavus interaction. In this study, we compared the miRNA profiles of three maize lines (resistant TZAR102, moderately resistant MI82, and susceptible Va35) at 8 h, 3 d, and 7 d after A. flavus infection to investigate possible regulatory antifungal role of miRNAs. A total of 316 miRNAs (275 known and 41 putative novel) belonging to 115 miRNA families were identified in response to the fungal infection across all three maize lines. Eighty-two unique miRNAs were significantly differentially expressed with 39 miRNAs exhibiting temporal differential regulation irrespective of the maize genotype, which targeted 544 genes (mRNAs) involved in diverse molecular functions. The two most notable biological processes involved in plant immunity, namely cellular responses to oxidative stress (GO:00345990) and reactive oxygen species (GO:0034614) were significantly enriched in the resistant line TZAR102. Coexpression network analysis identified 34 hubs of miRNA-mRNA pairs where nine hubs had a node in the module connected to their target gene with potentially important roles in resistance/susceptible response of maize to A. flavus. The miRNA hubs in resistance modules (TZAR102 and MI82) were mostly connected to transcription factors and protein kinases. Specifically, the module of miRNA zma-miR156b-nb - squamosa promoter binding protein (SBP), zma-miR398a-3p - SKIP5, and zma-miR394a-5p - F-box protein 6 combinations in the resistance-associated modules were considered important candidates for future functional studies.
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Affiliation(s)
- Prasad Gandham
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Kanniah Rajasekaran
- Food and Feed Safety Research Unit, Southern Regional Research Center, USDA-ARS, New Orleans, LA, 70726, USA.
| | - Christine Sickler
- Food and Feed Safety Research Unit, Southern Regional Research Center, USDA-ARS, New Orleans, LA, 70726, USA
| | - Harikrishnan Mohan
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Matthew Gilbert
- Food and Feed Safety Research Unit, Southern Regional Research Center, USDA-ARS, New Orleans, LA, 70726, USA
| | - Niranjan Baisakh
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA.
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Baisakh N, Da Silva EA, Pradhan AK, Rajasekaran K. Comprehensive meta-analysis of QTL and gene expression studies identify candidate genes associated with Aspergillus flavus resistance in maize. FRONTIERS IN PLANT SCIENCE 2023; 14:1214907. [PMID: 37534296 PMCID: PMC10392829 DOI: 10.3389/fpls.2023.1214907] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 06/26/2023] [Indexed: 08/04/2023]
Abstract
Aflatoxin (AF) contamination, caused by Aspergillus flavus, compromises the food safety and marketability of commodities, such as maize, cotton, peanuts, and tree nuts. Multigenic inheritance of AF resistance impedes conventional introgression of resistance traits into high-yielding commercial maize varieties. Several AF resistance-associated quantitative trait loci (QTLs) and markers have been reported from multiple biparental mapping and genome-wide association studies (GWAS) in maize. However, QTLs with large confidence intervals (CI) explaining inconsistent phenotypic variance limit their use in marker-assisted selection. Meta-analysis of published QTLs can identify significant meta-QTLs (MQTLs) with a narrower CI for reliable identification of genes and linked markers for AF resistance. Using 276 out of 356 reported QTLs controlling resistance to A. flavus infection and AF contamination in maize, we identified 58 MQTLs on all 10 chromosomes with a 66.5% reduction in the average CI. Similarly, a meta-analysis of maize genes differentially expressed in response to (a)biotic stresses from the to-date published literature identified 591 genes putatively responding to only A. flavus infection, of which 14 were significantly differentially expressed (-1.0 ≤ Log2Fc ≥ 1.0; p ≤ 0.05). Eight MQTLs were validated by their colocalization with 14 A. flavus resistance-associated SNPs identified from GWAS in maize. A total of 15 genes were physically close between the MQTL intervals and SNPs. Assessment of 12 MQTL-linked SSR markers identified three markers that could discriminate 14 and eight cultivars with resistance and susceptible responses, respectively. A comprehensive meta-analysis of QTLs and differentially expressed genes led to the identification of genes and makers for their potential application in marker-assisted breeding of A. flavus-resistant maize varieties.
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Affiliation(s)
- Niranjan Baisakh
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Eduardo A. Da Silva
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
- Department of Agriculture, Federal University of Lavras, Lavras, Brazil
| | - Anjan K. Pradhan
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
| | - Kanniah Rajasekaran
- Food and Feed Safety Research Unit, Southern Regional Research Center, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), New Orleans, LA, United States
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Lopes NDS, Santos AS, de Novais DPS, Pirovani CP, Micheli F. Pathogenesis-related protein 10 in resistance to biotic stress: progress in elucidating functions, regulation and modes of action. FRONTIERS IN PLANT SCIENCE 2023; 14:1193873. [PMID: 37469770 PMCID: PMC10352611 DOI: 10.3389/fpls.2023.1193873] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 05/08/2023] [Indexed: 07/21/2023]
Abstract
Introduction The Family of pathogenesis-related proteins 10 (PR-10) is widely distributed in the plant kingdom. PR-10 are multifunctional proteins, constitutively expressed in all plant tissues, playing a role in growth and development or being induced in stress situations. Several studies have investigated the preponderant role of PR-10 in plant defense against biotic stresses; however, little is known about the mechanisms of action of these proteins. This is the first systematic review conducted to gather information on the subject and to reveal the possible mechanisms of action that PR-10 perform. Methods Therefore, three databases were used for the article search: PubMed, Web of Science, and Scopus. To avoid bias, a protocol with inclusion and exclusion criteria was prepared. In total, 216 articles related to the proposed objective of this study were selected. Results The participation of PR-10 was revealed in the plant's defense against several stressor agents such as viruses, bacteria, fungi, oomycetes, nematodes and insects, and studies involving fungi and bacteria were predominant in the selected articles. Studies with combined techniques showed a compilation of relevant information about PR-10 in biotic stress that collaborate with the understanding of the mechanisms of action of these molecules. The up-regulation of PR-10 was predominant under different conditions of biotic stress, in addition to being more expressive in resistant varieties both at the transcriptional and translational level. Discussion Biological models that have been proposed reveal an intrinsic network of molecular interactions involving the modes of action of PR-10. These include hormonal pathways, transcription factors, physical interactions with effector proteins or pattern recognition receptors and other molecules involved with the plant's defense system. Conclusion The molecular networks involving PR-10 reveal how the plant's defense response is mediated, either to trigger susceptibility or, based on data systematized in this review, more frequently, to have plant resistance to the disease.
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Affiliation(s)
- Natasha dos Santos Lopes
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus-Bahia, Brazil
| | - Ariana Silva Santos
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus-Bahia, Brazil
| | - Diogo Pereira Silva de Novais
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus-Bahia, Brazil
| | - Carlos Priminho Pirovani
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus-Bahia, Brazil
| | - Fabienne Micheli
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus-Bahia, Brazil
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Meditérranéennes et Tropicales (UMR AGAP Institut), Montpellier, France
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Wang R, Wang Y, Yao W, Ge W, Jiang T, Zhou B. Transcriptome Sequencing and WGCNA Reveal Key Genes in Response to Leaf Blight in Poplar. Int J Mol Sci 2023; 24:10047. [PMID: 37373194 DOI: 10.3390/ijms241210047] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Leaf blight is a fungal disease that mainly affects the growth and development of leaves in plants. To investigate the molecular mechanisms of leaf blight defense in poplar, we performed RNA-Seq and enzyme activity assays on the Populus simonii × Populus nigra leaves inoculated with Alternaria alternate fungus. Through weighted gene co-expression network analysis (WGCNA), we obtained co-expression gene modules significantly associated with SOD and POD activities, containing 183 and 275 genes, respectively. We then constructed a co-expression network of poplar genes related to leaf blight resistance based on weight values. Additionally, we identified hub transcription factors (TFs) and structural genes in the network. The network was dominated by 15 TFs, and four out of them, including ATWRKY75, ANAC062, ATMYB23 and ATEBP, had high connectivity in the network, which might play important functions in leaf blight defense. In addition, GO enrichment analysis revealed a total of 44 structural genes involved in biotic stress, resistance, cell wall and immune-related biological processes in the network. Among them, there were 16 highly linked structural genes in the central part, which may be directly involved in poplar resistance to leaf blight. The study explores key genes associated with leaf blight defense in poplar, which further gains an understanding of the molecular mechanisms of biotic stress response in plants.
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Affiliation(s)
- Ruiqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Yuting Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Wenjing Yao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Wengong Ge
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Boru Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
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Haegeman A, Foucart Y, De Jonghe K, Goedefroit T, Al Rwahnih M, Boonham N, Candresse T, Gaafar YZA, Hurtado-Gonzales OP, Kogej Zwitter Z, Kutnjak D, Lamovšek J, Lefebvre M, Malapi M, Mavrič Pleško I, Önder S, Reynard JS, Salavert Pamblanco F, Schumpp O, Stevens K, Pal C, Tamisier L, Ulubaş Serçe Ç, van Duivenbode I, Waite DW, Hu X, Ziebell H, Massart S. Looking beyond Virus Detection in RNA Sequencing Data: Lessons Learned from a Community-Based Effort to Detect Cellular Plant Pathogens and Pests. PLANTS (BASEL, SWITZERLAND) 2023; 12:2139. [PMID: 37299118 PMCID: PMC10255714 DOI: 10.3390/plants12112139] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 05/26/2023] [Accepted: 05/27/2023] [Indexed: 06/12/2023]
Abstract
High-throughput sequencing (HTS), more specifically RNA sequencing of plant tissues, has become an indispensable tool for plant virologists to detect and identify plant viruses. During the data analysis step, plant virologists typically compare the obtained sequences to reference virus databases. In this way, they are neglecting sequences without homologies to viruses, which usually represent the majority of sequencing reads. We hypothesized that traces of other pathogens might be detected in this unused sequence data. In the present study, our goal was to investigate whether total RNA-seq data, as generated for plant virus detection, is also suitable for the detection of other plant pathogens and pests. As proof of concept, we first analyzed RNA-seq datasets of plant materials with confirmed infections by cellular pathogens in order to check whether these non-viral pathogens could be easily detected in the data. Next, we set up a community effort to re-analyze existing Illumina RNA-seq datasets used for virus detection to check for the potential presence of non-viral pathogens or pests. In total, 101 datasets from 15 participants derived from 51 different plant species were re-analyzed, of which 37 were selected for subsequent in-depth analyses. In 29 of the 37 selected samples (78%), we found convincing traces of non-viral plant pathogens or pests. The organisms most frequently detected in this way were fungi (15/37 datasets), followed by insects (13/37) and mites (9/37). The presence of some of the detected pathogens was confirmed by independent (q)PCRs analyses. After communicating the results, 6 out of the 15 participants indicated that they were unaware of the possible presence of these pathogens in their sample(s). All participants indicated that they would broaden the scope of their bioinformatic analyses in future studies and thus check for the presence of non-viral pathogens. In conclusion, we show that it is possible to detect non-viral pathogens or pests from total RNA-seq datasets, in this case primarily fungi, insects, and mites. With this study, we hope to raise awareness among plant virologists that their data might be useful for fellow plant pathologists in other disciplines (mycology, entomology, bacteriology) as well.
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Affiliation(s)
- Annelies Haegeman
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | - Yoika Foucart
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | - Kris De Jonghe
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | - Thomas Goedefroit
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | - Maher Al Rwahnih
- Foundation Plant Services, Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Neil Boonham
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, UK
| | - Thierry Candresse
- UMR 1332 Biologie du Fruit et Pathologie, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Bordeaux, 33882 Villenave-d’Ornon, France
| | - Yahya Z. A. Gaafar
- Centre for Plant Health, Canadian Food Inspection Agency, 8801 East Saanich Road, North Saanich, BC V8L 1H3, Canada
| | - Oscar P. Hurtado-Gonzales
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture (USDA-APHIS), Beltsville, ML 20705, USA
| | - Zala Kogej Zwitter
- Department of Biotechnology and Systems Biology, National Institute of Biology (NIB), 1000 Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, 1000 Ljubljana, Slovenia
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology (NIB), 1000 Ljubljana, Slovenia
| | - Janja Lamovšek
- Plant Protection Department, Agricultural Institute of Slovenia (KIS), 1000 Ljubljana, Slovenia
| | - Marie Lefebvre
- UMR 1332 Biologie du Fruit et Pathologie, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Bordeaux, 33882 Villenave-d’Ornon, France
| | - Martha Malapi
- Biotechnology Risk Analysis Program, Animal and Plant Health Inspection Service, United States Department of Agriculture (USDA-APHIS), Riverdale, ML 20737, USA
| | - Irena Mavrič Pleško
- Plant Protection Department, Agricultural Institute of Slovenia (KIS), 1000 Ljubljana, Slovenia
| | - Serkan Önder
- Department of Plant Protection, Faculty of Agriculture, Eskişehir Osmangazi University, Odunpazarı, Eskişehir 26160, Turkey
| | | | | | - Olivier Schumpp
- Department of Plant Protection, Agroscope, 1260 Nyon, Switzerland
| | - Kristian Stevens
- Foundation Plant Services, Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Chandan Pal
- Zespri International Limited, 400 Maunganui Road, Mount Maunganui 3116, New Zealand
| | - Lucie Tamisier
- Unités GAFL et Pathologie Végétale, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 84143 Montfavet, France
| | - Çiğdem Ulubaş Serçe
- Department of Plant Production and Technologies, Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, 51240 Niğde, Turkey
| | - Inge van Duivenbode
- Dutch General Inspection Service for Agricultural Seed and Seed Potatoes (NAK), Randweg 14, 8304 AS Emmeloord, The Netherlands
| | - David W. Waite
- Plant Health and Environment Laboratory, Ministry for Primary Industries, Auckland 1140, New Zealand
| | - Xiaojun Hu
- Plant Germplasm Quarantine Program, Animal and Plant Health Inspection Service, United States Department of Agriculture (USDA-APHIS), Beltsville, ML 20705, USA
| | - Heiko Ziebell
- Institute for Epidemiology and Pathogen Diagnostics, Federal Research Centre for Cultivated Plants, Julius Kühn Institute (JKI), Messeweg 11-12, 38104 Braunschweig, Germany
| | - Sébastien Massart
- Plant Pathology Laboratory, University of Liège, Gembloux Agro-Bio Tech, TERRA, 5030 Gembloux, Belgium
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Fang X, Yan P, Luo F, Han S, Lin T, Li S, Li S, Zhu T. Functional Identification of Arthrinium phaeospermum Effectors Related to Bambusa pervariabilis × Dendrocalamopsis grandis Shoot Blight. Biomolecules 2022; 12:biom12091264. [PMID: 36139102 PMCID: PMC9496123 DOI: 10.3390/biom12091264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/02/2022] [Accepted: 09/06/2022] [Indexed: 12/03/2022] Open
Abstract
The shoot blight of Bambusa pervariabilis × Dendrocalamopsis grandis caused by Arthrinium phaeospermum made bamboo die in a large area, resulting in serious ecological and economic losses. Dual RNA-seq was used to sequence and analyze the transcriptome data of A. phaeospermum and B. pervariabilis × D. grandis in the four periods after the pathogen infected the host and to screen the candidate effectors of the pathogen related to the infection. After the identification of the effectors by the tobacco transient expression system, the functions of these effectors were verified by gene knockout. Fifty-three differentially expressed candidate effectors were obtained by differential gene expression analysis and effector prediction. Among them, the effectors ApCE12 and ApCE22 can cause programmed cell death in tobacco. The disease index of B. pervariabilis × D. grandis inoculated with mutant ΔApCE12 and mutant ΔApCE22 strains were 52.5% and 47.5%, respectively, which was significantly lower than that of the wild-type strains (80%), the ApCE12 complementary strain (77.5%), and the ApCE22 complementary strain (75%). The tolerance of the mutant ΔApCE12 and mutant ΔApCE22 strains to H2O2 and NaCl stress was significantly lower than that of the wild-type strain and the ApCE12 complementary and ApCE22 complementary strains, but there was no difference in their tolerance to Congo red. Therefore, this study shows that the effectors ApCE12 and ApCE22 play an important role in A. phaeospermum virulence and response to H2O2 and NaCl stress.
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Affiliation(s)
- Xinmei Fang
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
- Faculty of Mathematics and Natural Sciences, University of Cologne, 50674 Köln, Germany
| | - Peng Yan
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Fengying Luo
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Shan Han
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Tiantian Lin
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Shuying Li
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Shujiang Li
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River, Chengdu 611130, China
- Correspondence: (S.L.); (T.Z.); Tel.: +86-17761264491 (T.Z.)
| | - Tianhui Zhu
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (S.L.); (T.Z.); Tel.: +86-17761264491 (T.Z.)
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Huang Y, Ma H, Yue Y, Zhou T, Zhu Z, Wang C. Integrated transcriptomic and transgenic analyses reveal potential mechanisms of poplar resistance to Alternaria alternata infection. BMC PLANT BIOLOGY 2022; 22:413. [PMID: 36008749 PMCID: PMC9404672 DOI: 10.1186/s12870-022-03793-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Populus davidiana × P. bollena is a species of poplar from northeastern China that is characterized by cold resistance and fast growth but now suffers from pathogen infections. Leaf blight caused by Alternaria alternata has become a common poplar disease that causes serious economic impacts, but the molecular mechanisms of resistance to A. alternata in P. davidiana × P. bollena are still unclear. RESULTS In this study, the transcriptomic response of P. davidiana × P. bollena to A. alternata infection was determined via RNA-Seq. Twelve cDNA libraries were generated from RNA isolated from three biological replicates at four time points (0, 2, 3, and 4 d post inoculation), and a total of 5,930 differentially expressed genes (DEGs) were detected (| log2 fold change |≥ 1 and FDR values < 0.05). Functional analysis revealed that the DEGs were mainly enriched for the "plant hormone signal transduction" pathway, followed by the "phenylpropanoid biosynthesis" pathway. In addition, DEGs that encode defense-related proteins and are related to ROS metabolism were also identified. Numerous transcription factors, such as the bHLH, WRKY and MYB families, were also induced by A. alternata infection. Among these DEGs, those related to JA biosynthesis and JA signal transduction were consistently activated. Therefore, the lipoxygenase gene PdbLOX2, which is involved in JA biosynthesis, was selected for functional characterization. Overexpression of PdbLOX2 enhanced the resistance of P. davidiana × P. bollena to A. alternata, whereas silencing this gene enhanced susceptibility to A. alternata infection. CONCLUSIONS These results provide new insight into the molecular mechanisms of poplar resistance to A. alternata infection and provide candidate genes for breeding resistant cultivars using genetic engineering.
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Affiliation(s)
- Ying Huang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, Harbin, 150040 China
| | - Huijun Ma
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, Harbin, 150040 China
| | - Yuanzhi Yue
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, Harbin, 150040 China
| | - Tianchang Zhou
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, Harbin, 150040 China
| | - Zhenyu Zhu
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, Harbin, 150040 China
| | - Chao Wang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, Harbin, 150040 China
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Liu H, Wu H, Wang Y, Wang H, Chen S, Yin Z. Comparative transcriptome profiling and co-expression network analysis uncover the key genes associated withearly-stage resistance to Aspergillus flavus in maize. BMC PLANT BIOLOGY 2021; 21:216. [PMID: 33985439 PMCID: PMC8117602 DOI: 10.1186/s12870-021-02983-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/13/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND The fungus Aspergillus flavus (A. flavus) is a serious threat to maize (Zea mays) production worldwide. It causes considerable yield and economic losses, and poses a health risk to humans and livestock due to the high toxicity of aflatoxin. However, key genes and regulatory networks conferring maize resistance to A. flavus are not clear, especially at the early stage of infection. Here, we performed a comprehensive transcriptome analysis of two maize inbred lines with contrasting resistance to A. flavus infection. RESULTS The pairwise comparisons between mock and infected kernels in each line during the first 6 h post inoculation (hpi) showed that maize resistance to A. flavus infection was specific to the genotype and infection stage, and defense pathways were strengthened in the resistant line. Further comparison of the two maize lines revealed that the infection-induced up-regulated differentially expressed genes (DEGs) in the resistant line might underlie the enhanced resistance. Gene co-expression network analysis by WGCNA (weighted gene co-expression network analysis) identified 7 modules that were significantly associated with different infection stages, and 110 hub genes of these modules. These key regulators mainly participate in the biosynthesis of fatty acid and antibiotics. In addition, 90 candidate genes for maize resistance to A. flavus infection and/or aflatoxin contamination obtained in previous studies were confirmed to be differentially expressed between the resistant and susceptible lines within the first 6 hpi. CONCLUSION This work unveiled more A. flavus resistance genes and provided a detailed regulatory network of early-stage resistance to A. flavus in maize.
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Affiliation(s)
- Huanhuan Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture & Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Haofeng Wu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture & Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Yan Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture & Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Huan Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture & Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Saihua Chen
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture & Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
| | - Zhitong Yin
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture & Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China.
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Chen Z. Astragaloside iv inhibits salmonella-induced meningitis via modulation of bacterial virulence and host response. Pharmacogn Mag 2021. [DOI: 10.4103/pm.pm_55_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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