1
|
Matuszkiewicz M, Sobczak M. Syncytium Induced by Plant-Parasitic Nematodes. Results Probl Cell Differ 2024; 71:371-403. [PMID: 37996687 DOI: 10.1007/978-3-031-37936-9_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
Plant-parasitic nematodes from the genera Globodera, Heterodera (cyst-forming nematodes), and Meloidogyne (root-knot nematodes) are notorious and serious pests of crops. They cause tremendous economic losses between US $80 and 358 billion a year. Nematodes infect the roots of plants and induce the formation of specialised feeding structures (syncytium and giant cells, respectively) that nourish juveniles and adults of the nematodes. The specialised secretory glands enable nematodes to synthesise and secrete effectors that facilitate migration through root tissues and alter the morphogenetic programme of host cells. The formation of feeding sites is associated with the suppression of plant defence responses and deep reprogramming of the development and metabolism of plant cells.In this chapter, we focus on syncytia induced by the sedentary cyst-forming nematodes and provide an overview of ultrastructural changes that occur in the host roots during syncytium formation in conjunction with the most important molecular changes during compatible and incompatible plant responses to infection with nematodes.
Collapse
Affiliation(s)
- Mateusz Matuszkiewicz
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw University of Life Sciences (WULS-SGGW), Warsaw, Poland.
| | - Mirosław Sobczak
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences (WULS-SGGW), Warsaw, Poland
| |
Collapse
|
2
|
Torabi S, Seifi S, Geddes-McAlister J, Tenuta A, Wally O, Torkamaneh D, Eskandari M. Soybean-SCN Battle: Novel Insight into Soybean's Defense Strategies against Heterodera glycines. Int J Mol Sci 2023; 24:16232. [PMID: 38003422 PMCID: PMC10671692 DOI: 10.3390/ijms242216232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/28/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
Soybean cyst nematode (SCN, Heterodera glycines, Ichinohe) poses a significant threat to global soybean production, necessitating a comprehensive understanding of soybean plants' response to SCN to ensure effective management practices. In this study, we conducted dual RNA-seq analysis on SCN-resistant Plant Introduction (PI) 437654, 548402, and 88788 as well as a susceptible line (Lee 74) under exposure to SCN HG type 1.2.5.7. We aimed to elucidate resistant mechanisms in soybean and identify SCN virulence genes contributing to resistance breakdown. Transcriptomic and pathway analyses identified the phenylpropanoid, MAPK signaling, plant hormone signal transduction, and secondary metabolite pathways as key players in resistance mechanisms. Notably, PI 437654 exhibited complete resistance and displayed distinctive gene expression related to cell wall strengthening, oxidative enzymes, ROS scavengers, and Ca2+ sensors governing salicylic acid biosynthesis. Additionally, host studies with varying immunity levels and a susceptible line shed light on SCN pathogenesis and its modulation of virulence genes to evade host immunity. These novel findings provide insights into the molecular mechanisms underlying soybean-SCN interactions and offer potential targets for nematode disease management.
Collapse
Affiliation(s)
- Sepideh Torabi
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Soren Seifi
- Aurora Cannabis Inc., Comox, BC V9M 4A1, Canada;
| | | | - Albert Tenuta
- Ontario Ministry of Agriculture, Food and Rural Affairs, Ridgetown, ON N0P 2C0, Canada;
| | - Owen Wally
- Harrow Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N0R 1G0, Canada;
| | - Davoud Torkamaneh
- Département de Phytologie, Université Laval, Québec City, QC G1V 0A6, Canada;
| | - Milad Eskandari
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada;
| |
Collapse
|
3
|
Jacquet S, Li S, Mian R, Kassem MA, Rashad L, Viera S, Reta F, Reta J, Yuan J. Evaluating the Response of Glycine soja Accessions to Fungal Pathogen Macrophomina phaseolina during Seedling Growth. PLANTS (BASEL, SWITZERLAND) 2023; 12:3807. [PMID: 38005704 PMCID: PMC10675638 DOI: 10.3390/plants12223807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/27/2023] [Accepted: 10/13/2023] [Indexed: 11/26/2023]
Abstract
Charcoal rot caused by the fungal pathogen Macrophomina phaseolina (Tassi) Goid is one of various devastating soybean (Glycine max (L.) Merr.) diseases, which can severely reduce crop yield. The investigation into the genetic potential for charcoal rot resistance of wild soybean (Glycine soja) accessions will enrich our understanding of the impact of soybean domestication on disease resistance; moreover, the identified charcoal rot-resistant lines can be used to improve soybean resistance to charcoal rot. The objective of this study was to evaluate the resistance of wild soybean accessions to M. phaseolina at the seedling stage and thereby select the disease-resistant lines. The results show that the fungal pathogen infection reduced the growth of the root and hypocotyl in most G. soja accessions. The accession PI 507794 displayed the highest level of resistance response to M. phaseolina infection among the tested wild soybean accessions, while PI 487431 and PI 483660B were susceptible to charcoal rot in terms of the reduction in root and hypocotyl growth. The mean values of the root and hypocotyl parameters in PI 507794 were significantly higher (p < 0.05) than those of PI 487431 and PI 483460B. A analysis of the resistance of wild soybean accessions to M. phaseolina using the root and hypocotyl as the assessment parameters at the early seedling stage provides an alternative way to rapidly identify potential resistant genotypes and facilitate breeding for soybean resistance to charcoal rot.
Collapse
Affiliation(s)
- Shirley Jacquet
- Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (S.J.); (M.A.K.); (L.R.); (S.V.); (F.R.); (J.R.)
| | - Shuxian Li
- Crop Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service (USDA, ARS), 141 Experiment Station Road, P.O. Box 345, Stoneville, MS 38776, USA;
| | - Rouf Mian
- Soybean and Nitrogen Fixation Research Unit, United States Department of Agriculture, Agricultural Research Service (USDA, ARS), 3127 Ligon St., Raleigh, NC 27607, USA;
| | - My Abdelmajid Kassem
- Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (S.J.); (M.A.K.); (L.R.); (S.V.); (F.R.); (J.R.)
| | - Layla Rashad
- Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (S.J.); (M.A.K.); (L.R.); (S.V.); (F.R.); (J.R.)
| | - Sonia Viera
- Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (S.J.); (M.A.K.); (L.R.); (S.V.); (F.R.); (J.R.)
| | - Francisco Reta
- Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (S.J.); (M.A.K.); (L.R.); (S.V.); (F.R.); (J.R.)
| | - Juan Reta
- Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (S.J.); (M.A.K.); (L.R.); (S.V.); (F.R.); (J.R.)
| | - Jiazheng Yuan
- Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (S.J.); (M.A.K.); (L.R.); (S.V.); (F.R.); (J.R.)
| |
Collapse
|
4
|
Mena E, Reboledo G, Stewart S, Montesano M, Ponce de León I. Comparative analysis of soybean transcriptional profiles reveals defense mechanisms involved in resistance against Diaporthe caulivora. Sci Rep 2023; 13:13061. [PMID: 37567886 PMCID: PMC10421924 DOI: 10.1038/s41598-023-39695-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 07/29/2023] [Indexed: 08/13/2023] Open
Abstract
Soybean stem canker (SSC) caused by the fungal pathogen Diaporthe caulivora is an important disease affecting soybean production worldwide. However, limited information related to the molecular mechanisms underlying soybean resistance to Diaporthe species is available. In the present work, we analyzed the defense responses to D. caulivora in the soybean genotypes Williams and Génesis 5601. The results showed that compared to Williams, Génesis 5601 is more resistant to fungal infection evidenced by significantly smaller lesion length, reduced disease severity and pathogen biomass. Transcriptional profiling was performed in untreated plants and in D. caulivora-inoculated and control-treated tissues at 8 and 48 h post inoculation (hpi). In total, 2.322 and 1.855 genes were differentially expressed in Génesis 5601 and Williams, respectively. Interestingly, Génesis 5601 exhibited a significantly higher number of upregulated genes compared to Williams at 8 hpi, 1.028 versus 434 genes. Resistance to D. caulivora was associated with defense activation through transcriptional reprogramming mediating perception of the pathogen by receptors, biosynthesis of phenylpropanoids, hormone signaling, small heat shock proteins and pathogenesis related (PR) genes. These findings provide novel insights into soybean defense mechanisms leading to host resistance against D. caulivora, and generate a foundation for the development of resistant SSC varieties within soybean breeding programs.
Collapse
Affiliation(s)
- Eilyn Mena
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Guillermo Reboledo
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Silvina Stewart
- Programa Nacional de Cultivos de Secano, Instituto Nacional de Investigación Agropecuaria (INIA), La Estanzuela, Colonia, Uruguay
| | - Marcos Montesano
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
- Laboratorio de Fisiología Vegetal, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Inés Ponce de León
- Departamento de Biología Molecular, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay.
| |
Collapse
|
5
|
Malviya D, Singh P, Singh UB, Paul S, Kumar Bisen P, Rai JP, Verma RL, Fiyaz RA, Kumar A, Kumari P, Dei S, Ahmed MR, Bagyaraj DJ, Singh HV. Arbuscular mycorrhizal fungi-mediated activation of plant defense responses in direct seeded rice ( Oryza sativa L.) against root-knot nematode Meloidogyne graminicola. Front Microbiol 2023; 14:1104490. [PMID: 37200920 PMCID: PMC10185796 DOI: 10.3389/fmicb.2023.1104490] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/13/2023] [Indexed: 05/20/2023] Open
Abstract
Rhizosphere is the battlefield of beneficial and harmful (so called phytopathogens) microorganisms. Moreover, these microbial communities are struggling for their existence in the soil and playing key roles in plant growth, mineralization, nutrient cycling and ecosystem functioning. In the last few decades, some consistent pattern have been detected so far that link soil community composition and functions with plant growth and development; however, it has not been studied in detail. AM fungi are model organisms, besides potential role in nutrient cycling; they modulate biochemical pathways directly or indirectly which lead to better plant growth under biotic and abiotic stress conditions. In the present investigations, we have elucidated the AM fungi-mediated activation of plant defense responses against Meloidogyne graminicola causing root-knot disease in direct seeded rice (Oryza sativa L.). The study describes the multifarious effects of Funneliformis mosseae, Rhizophagus fasciculatus, and Rhizophagus intraradices inoculated individually or in combination under glasshouse conditions in rice plants. It was found that F. mosseae, R. fasciculatus and R. intraradices when applied individually or in combination modulated the biochemical and molecular mechanisms in the susceptible and resistant inbred lines of rice. AM inoculation significantly increased various plant growth attributes in plants with simultaneous decrease in the root-knot intensity. Among these, the combined application of F. mosseae, R. fasciculatus, and R. intraradices was found to enhance the accumulation and activities of biomolecules and enzymes related to defense priming as well as antioxidation in the susceptible and resistant inbred lines of rice pre-challenged with M. graminicola. The application of F. mosseae, R. fasciculatus and R. intraradices, induced the key genes involved in plant defense and signaling and it has been demonstrated for the first time. Results of the present investigation advocated that the application of F. mosseae, R. fasciculatus and R. intraradices, particularly a combination of all three, not only helped in the control of root-knot nematodes but also increased plant growth as well as enhances the gene expression in rice. Thus, it proved to be an excellent biocontrol as well as plant growth-promoting agent in rice even when the crop is under biotic stress of the root-knot nematode, M. graminicola.
Collapse
Affiliation(s)
- Deepti Malviya
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
| | - Prakash Singh
- Department of Plant Breeding and Genetics, Veer Kunwar Singh College of Agriculture, Bihar Agricultural University, Dumraon, India
| | - Udai B Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
| | - Surinder Paul
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
| | | | - Jai P Rai
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Ram Lakhan Verma
- Division of Crop Improvement, ICAR-National Rice Research Institute, Cuttack, India
| | - R Abdul Fiyaz
- Division of Crop Improvement, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - A Kumar
- Bihar Agricultural University, Bhagalpur, India
| | - Poonam Kumari
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | | | - Mohd Reyaz Ahmed
- Department of Plant Pathology, Veer Kunwar Singh College of Agriculture, Bihar Agricultural University, Dumraon, India
| | - D J Bagyaraj
- Centre for Natural Biological Resources and Community Development, Bengaluru, India
| | - Harsh V Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms, Maunath Bhanjan, India
| |
Collapse
|
6
|
Tian Y, Li D, Wang X, Zhang H, Wang J, Yu L, Guo C, Luan X, Liu X, Li H, Reif JC, Li YH, Qiu LJ. Deciphering the genetic basis of resistance to soybean cyst nematode combining IBD and association mapping. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:50. [PMID: 36912956 PMCID: PMC10011322 DOI: 10.1007/s00122-023-04268-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 12/07/2022] [Indexed: 06/18/2023]
Abstract
IBD analysis clarified the dynamics of chromosomal recombination during the ZP pedigree breeding process and identified ten genomic regions resistant to SCN race3 combining association mapping. Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is one of the most devastating pathogens for soybean production worldwide. The cultivar Zhongpin03-5373 (ZP), derived from SCN-resistant progenitor parents, Peking, PI 437654 and Huipizhi Heidou, is an elite line with high resistance to SCN race3. In the current study, a pedigree variation map was generated for ZP and its ten progenitors using 3,025,264 high-quality SNPs identified from an average of 16.2 × re-sequencing for each genome. Through identity by decent (IBD) tracking, we showed the dynamic change of genome and detected important IBD fragments, which revealed the comprehensively artificial selection of important traits during ZP breeding process. A total of 2,353 IBD fragments related to SCN resistance including SCN-resistant genes rhg1, rhg4 and NSFRAN07 were identified based on the resistant-related genetic paths. Moreover, 23 genomic regions underlying resistance to SCN race3 were identified by genome-wide association study (GWAS) in 481 re-sequenced cultivated soybeans. Ten common loci were found by both IBD tracking and GWAS analysis. Haplotype analysis of 16 potential candidate genes suggested a causative SNP (C/T, - 1065) located in the promoter of Glyma.08G096500 and encoding a predicted TIFY5b-related protein on chr8 was highly correlated with SCN race3 resistance. Our results more thoroughly elucidated the dynamics of genomic fragments during ZP pedigree breeding and the genetic basis of SCN resistance, which will provide useful information for gene cloning and the development of resistant soybean cultivars using a marker-assisted selection approach.
Collapse
Affiliation(s)
- Yu Tian
- The National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
| | - Delin Li
- The National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
| | - Xueqing Wang
- The National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
| | - Hao Zhang
- The National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
| | - Jiajun Wang
- Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Lijie Yu
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding, College of Life Science and Technology, Harbin Normal University, Heilongjiang Province, Harbin, China
| | - Changhong Guo
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding, College of Life Science and Technology, Harbin Normal University, Heilongjiang Province, Harbin, China
| | - Xiaoyan Luan
- Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Xinlei Liu
- Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Hongjie Li
- The National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
| | - Jochen C Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Ying-Hui Li
- The National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China.
| | - Li-Juan Qiu
- The National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China.
| |
Collapse
|
7
|
Basso MF, Lourenço-Tessutti IT, Moreira-Pinto CE, Mendes RAG, Pereira DG, Grandis A, Macedo LLP, Macedo AF, Gomes ACMM, Arraes FBM, Togawa RC, do Carmo Costa MM, Marcelino-Guimaraes FC, Silva MCM, Floh EIS, Buckeridge MS, de Almeida Engler J, Grossi-de-Sa MF. Overexpression of the GmEXPA1 gene reduces plant susceptibility to Meloidogyne incognita. PLANT CELL REPORTS 2023; 42:137-152. [PMID: 36348064 DOI: 10.1007/s00299-022-02941-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
The overexpression of the soybean GmEXPA1 gene reduces plant susceptibility to M. incognita by the increase of root lignification. Plant expansins are enzymes that act in a pH-dependent manner in the plant cell wall loosening and are associated with improved tolerance or resistance to abiotic or biotic stresses. Plant-parasitic nematodes (PPN) can alter the expression profile of several expansin genes in infected root cells. Studies have shown that overexpression or downregulation of particular expansin genes can reduce plant susceptibility to PPNs. Root-knot nematodes (RKN) are obligate sedentary endoparasites of the genus Meloidogyne spp. of which M. incognita is one of the most reported species. Herein, using a transcriptome dataset and real-time PCR assays were identified an expansin A gene (GmEXPA1; Glyma.02G109100) that is upregulated in the soybean nematode-resistant genotype PI595099 compared to the susceptible cultivar BRS133 during plant parasitism by M. incognita. To understand the role of the GmEXPA1 gene during the interaction between soybean plant and M. incognita were generated stable A. thaliana and N. tabacum transgenic lines. Remarkably, both A. thaliana and N. tabacum transgenic lines overexpressing the GmEXPA1 gene showed reduced susceptibility to M. incognita. Furthermore, plant growth, biomass accumulation, and seed yield were not affected in these transgenic lines. Interestingly, significant upregulation of the NtACC oxidase and NtEFE26 genes, involved in ethylene biosynthesis, and NtCCR and Nt4CL genes, involved in lignin biosynthesis, was observed in roots of the N. tabacum transgenic lines, which also showed higher lignin content. These data suggested a possible link between GmEXPA1 gene expression and increased lignification of the root cell wall. Therefore, these data support that engineering of the GmEXPA1 gene in soybean offers a powerful biotechnology tool to assist in RKN management.
Collapse
Affiliation(s)
- Marcos Fernando Basso
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil
- National Institute of Science and Technology, INCT Plant Stress Biotech, EMBRAPA, Brasília, DF, 70297-400, Brazil
| | - Isabela Tristan Lourenço-Tessutti
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil
- National Institute of Science and Technology, INCT Plant Stress Biotech, EMBRAPA, Brasília, DF, 70297-400, Brazil
| | - Clidia Eduarda Moreira-Pinto
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil
- Federal University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Reneida Aparecida Godinho Mendes
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil
- Federal University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Debora Gonçalves Pereira
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil
- Federal University of Brasília, Brasília, DF, 70910-900, Brazil
| | - Adriana Grandis
- Department of Botany, Biosciences Institute, University of São Paulo, São Paulo, SP, 05508-090, Brazil
| | - Leonardo Lima Pepino Macedo
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil
- National Institute of Science and Technology, INCT Plant Stress Biotech, EMBRAPA, Brasília, DF, 70297-400, Brazil
| | - Amanda Ferreira Macedo
- Department of Botany, Biosciences Institute, University of São Paulo, São Paulo, SP, 05508-090, Brazil
| | | | - Fabrício Barbosa Monteiro Arraes
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil
- National Institute of Science and Technology, INCT Plant Stress Biotech, EMBRAPA, Brasília, DF, 70297-400, Brazil
| | - Roberto Coiti Togawa
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil
- National Institute of Science and Technology, INCT Plant Stress Biotech, EMBRAPA, Brasília, DF, 70297-400, Brazil
| | - Marcos Mota do Carmo Costa
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil
| | - Francismar Corrêa Marcelino-Guimaraes
- National Institute of Science and Technology, INCT Plant Stress Biotech, EMBRAPA, Brasília, DF, 70297-400, Brazil
- Embrapa Soybean, Londrina, PR, 86001-970, Brazil
| | - Maria Cristina Mattar Silva
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil
- National Institute of Science and Technology, INCT Plant Stress Biotech, EMBRAPA, Brasília, DF, 70297-400, Brazil
| | - Eny Iochevet Segal Floh
- Department of Botany, Biosciences Institute, University of São Paulo, São Paulo, SP, 05508-090, Brazil
| | | | - Janice de Almeida Engler
- National Institute of Science and Technology, INCT Plant Stress Biotech, EMBRAPA, Brasília, DF, 70297-400, Brazil
- INRAE, Université Côte d'Azur, CNRS, ISA, 06903, Sophia Antipolis, France
| | - Maria Fatima Grossi-de-Sa
- Embrapa Genetic Resources and Biotechnology, PqEB Final, W5 Norte, PO Box 02372, Brasília, DF, 70770-901, Brazil.
- National Institute of Science and Technology, INCT Plant Stress Biotech, EMBRAPA, Brasília, DF, 70297-400, Brazil.
- Catholic University of Brasília, Brasília, DF, 71966-700, Brazil.
| |
Collapse
|
8
|
Lopes-Caitar VS, Nomura RBG, Hishinuma-Silva SM, de Carvalho MCDCG, Abdelnoor RV, Dias WP, Marcelino-Guimarães FC. Time Course RNA-seq Reveals Soybean Responses against Root-Lesion Nematode and Resistance Players. PLANTS (BASEL, SWITZERLAND) 2022; 11:2983. [PMID: 36365436 PMCID: PMC9655969 DOI: 10.3390/plants11212983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/23/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Pratylenchus brachyurus causes serious damage to soybean production and other crops worldwide. Plant molecular responses to RLN infection remain largely unknown and no resistance genes have been identified in soybean. In this study, we analyzed molecular responses to RLN infection in moderately resistant BRSGO (Chapadões-BRS) and susceptible TMG115 RR (TMG) Glycine max genotypes. Differential expression analysis revealed two stages of response to RLN infection and a set of differentially expressed genes (DEGs) in the first stage suggested a pattern-triggered immunity (PTI) in both genotypes. The divergent time-point of DEGs between genotypes was observed four days post-infection, which included the activation of mitogen-activated protein kinase (MAPK) and plant-pathogen interaction genes in the BRS, suggesting the occurrence of an effector-triggered immunity response (ETI) in BRS. The co-expression analyses combined with single nucleotide polymorphism (SNP) uncovered a key element, a transcription factor phytochrome-interacting factor (PIF7) that is a potential regulator of moderate resistance to RLN infection. Two genes for resistance-related leucine-rich repeat (LRR) proteins were found as BRS-specific expressed genes. In addition, alternative splicing analysis revealed an intron retention in a myo-inositol oxygenase (MIOX) transcript, a gene related to susceptibility, may cause a loss of function in BRS.
Collapse
Affiliation(s)
- Valéria Stefania Lopes-Caitar
- Department of Biological Sciences, Universidade Estadual de Londrina (UEL), Londrina 86057-970, PR, Brazil
- Brazilian Agricultural Research Corporation-Embrapa Soja, Londrina 86001-970, PR, Brazil
| | - Rafael Bruno Guayato Nomura
- Brazilian Agricultural Research Corporation-Embrapa Soja, Londrina 86001-970, PR, Brazil
- Department Biochemistry and Biotechnology, Universidade Estadual de Londrina (UEL), Londrina 86057-970, PR, Brazil
| | - Suellen Mika Hishinuma-Silva
- Brazilian Agricultural Research Corporation-Embrapa Soja, Londrina 86001-970, PR, Brazil
- Department Biochemistry and Biotechnology, Universidade Estadual de Londrina (UEL), Londrina 86057-970, PR, Brazil
| | | | | | - Waldir Pereira Dias
- Brazilian Agricultural Research Corporation-Embrapa Soja, Londrina 86001-970, PR, Brazil
| | | |
Collapse
|
9
|
Arraes FBM, Vasquez DDN, Tahir M, Pinheiro DH, Faheem M, Freitas-Alves NS, Moreira-Pinto CE, Moreira VJV, Paes-de-Melo B, Lisei-de-Sa ME, Morgante CV, Mota APZ, Lourenço-Tessutti IT, Togawa RC, Grynberg P, Fragoso RR, de Almeida-Engler J, Larsen MR, Grossi-de-Sa MF. Integrated Omic Approaches Reveal Molecular Mechanisms of Tolerance during Soybean and Meloidogyne incognita Interactions. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11202744. [PMID: 36297768 PMCID: PMC9612212 DOI: 10.3390/plants11202744] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 05/08/2023]
Abstract
The root-knot nematode (RKN), Meloidogyne incognita, is a devastating soybean pathogen worldwide. The use of resistant cultivars is the most effective method to prevent economic losses caused by RKNs. To elucidate the mechanisms involved in resistance to RKN, we determined the proteome and transcriptome profiles from roots of susceptible (BRS133) and highly tolerant (PI 595099) Glycine max genotypes 4, 12, and 30 days after RKN infestation. After in silico analysis, we described major defense molecules and mechanisms considered constitutive responses to nematode infestation, such as mTOR, PI3K-Akt, relaxin, and thermogenesis. The integrated data allowed us to identify protein families and metabolic pathways exclusively regulated in tolerant soybean genotypes. Among them, we highlighted the phenylpropanoid pathway as an early, robust, and systemic defense process capable of controlling M. incognita reproduction. Associated with this metabolic pathway, 29 differentially expressed genes encoding 11 different enzymes were identified, mainly from the flavonoid and derivative pathways. Based on differential expression in transcriptomic and proteomic data, as well as in the expression profile by RT-qPCR, and previous studies, we selected and overexpressed the GmPR10 gene in transgenic tobacco to assess its protective effect against M. incognita. Transgenic plants of the T2 generation showed up to 58% reduction in the M. incognita reproduction factor. Finally, data suggest that GmPR10 overexpression can be effective against the plant parasitic nematode M. incognita, but its mechanism of action remains unclear. These findings will help develop new engineered soybean genotypes with higher performance in response to RKN infections.
Collapse
Affiliation(s)
- Fabricio B M Arraes
- Postgraduate Program in Cellular and Molecular Biology (PPGBCM), Federal University of Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, RS, Brazil
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT PlantStress Biotech), Brasilia 70770-917, DF, Brazil
| | - Daniel D N Vasquez
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT PlantStress Biotech), Brasilia 70770-917, DF, Brazil
- Postgraduate Program in Genomic Sciences and Biotechnology (PPGCGB), Catholic University of Brasilia (UCB), Brasilia 71966-700, DF, Brazil
| | - Muhammed Tahir
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Daniele H Pinheiro
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT PlantStress Biotech), Brasilia 70770-917, DF, Brazil
| | - Muhammed Faheem
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
- Department of Biological Sciences, National University of Medical Sciences, The Mall, Rawalpindi 46000, Punjab, Pakistan
| | - Nayara S Freitas-Alves
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
- Postgraduate Program in Bioprocess Engineering and Biotechnology (PPGEBB), Federal University of Paraná (UFPR), Curitiba 80060-000, PR, Brazil
| | - Clídia E Moreira-Pinto
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
| | - Valdeir J V Moreira
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT PlantStress Biotech), Brasilia 70770-917, DF, Brazil
- Postgraduate Program in Molecular Biology (PPGBiomol), University of Brasilia (UnB), Brasília 70910-900, DF, Brazil
| | - Bruno Paes-de-Melo
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
| | - Maria E Lisei-de-Sa
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT PlantStress Biotech), Brasilia 70770-917, DF, Brazil
- Minas Gerais Agricultural Research Company (EPAMIG), Uberaba 31170-495, MG, Brazil
| | - Carolina V Morgante
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT PlantStress Biotech), Brasilia 70770-917, DF, Brazil
- Embrapa Semiarid, Petrolina 56302-970, PE, Brazil
| | - Ana P Z Mota
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT PlantStress Biotech), Brasilia 70770-917, DF, Brazil
- INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, 06903 Sophia-Antipolis, France
| | - Isabela T Lourenço-Tessutti
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT PlantStress Biotech), Brasilia 70770-917, DF, Brazil
| | - Roberto C Togawa
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT PlantStress Biotech), Brasilia 70770-917, DF, Brazil
| | - Priscila Grynberg
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT PlantStress Biotech), Brasilia 70770-917, DF, Brazil
| | - Rodrigo R Fragoso
- National Institute of Science and Technology (INCT PlantStress Biotech), Brasilia 70770-917, DF, Brazil
- Embrapa Agroenergy, Brasilia 70770-901, DF, Brazil
| | - Janice de Almeida-Engler
- National Institute of Science and Technology (INCT PlantStress Biotech), Brasilia 70770-917, DF, Brazil
- INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, 06903 Sophia-Antipolis, France
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Maria F Grossi-de-Sa
- Embrapa Genetic Resources and Biotechnology, Plant-Pest Molecular Interaction Laboratory (LIMPP) and Bioinformatics Laboratory, Brasilia 70770-917, DF, Brazil
- National Institute of Science and Technology (INCT PlantStress Biotech), Brasilia 70770-917, DF, Brazil
- Postgraduate Program in Genomic Sciences and Biotechnology (PPGCGB), Catholic University of Brasilia (UCB), Brasilia 71966-700, DF, Brazil
| |
Collapse
|
10
|
Chen L, Song B, Yu C, Zhang J, Zhang J, Bi R, Li X, Ren X, Zhu Y, Yao D, Song Y, Yang S, Zhao R. Identifying Soybean Pod Borer ( Leguminivora glycinivorella) Resistance QTLs and the Mechanism of Induced Defense Using Linkage Mapping and RNA-Seq Analysis. Int J Mol Sci 2022; 23:ijms231810910. [PMID: 36142822 PMCID: PMC9504297 DOI: 10.3390/ijms231810910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/09/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
The soybean pod borer (Leguminivora glycinivorella) (SPB) is a major cause of soybean (Glycine max L.) yield losses in northeast Asia, thus it is desirable to elucidate the resistance mechanisms involved in soybean response to the SPB. However, few studies have mapped SPB-resistant quantitative trait loci (QTLs) and deciphered the response mechanism in soybean. Here, we selected two soybean varieties, JY93 (SPB-resistant) and K6 (SPB-sensitive), to construct F2 and F2:3 populations for QTL mapping and collected pod shells before and after SPB larvae chewed on the two parents to perform RNA-Seq, which can identify stable QTLs and explore the response mechanism of soybean to the SPB. The results show that four QTLs underlying SPB damage to seeds were detected on chromosomes 4, 9, 13, and 15. Among them, qESP-9-1 was scanned in all environments, hence it can be considered a stable QTL. All QTLs explained 0.79 to 6.09% of the phenotypic variation. Meanwhile, 2298 and 3509 DEGs were identified for JY93 and K6, respectively, after the SPB attack, and most of these genes were upregulated. Gene Ontology enrichment results indicated that the SPB-induced and differently expressed genes in both parents are involved in biological processes such as wound response, signal transduction, immune response, and phytohormone pathways. Interestingly, secondary metabolic processes such as flavonoid synthesis were only significantly enriched in the upregulated genes of JY93 after SPB chewing compared with K6. Finally, we identified 18 candidate genes related to soybean pod borer resistance through the integration of QTL mapping and RNA-Seq analysis. Seven of these genes had similar expression patterns to the mapping parents in four additional soybean germplasm after feeding by the SPB. These results provide additional knowledge of the early response and induced defense mechanisms against the SPB in soybean, which could help in breeding SPB-resistant soybean accessions.
Collapse
Affiliation(s)
- Liangyu Chen
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Baixing Song
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Cheng Yu
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Jun Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
- National Crop Variety Approval and Characteristic Identification Station, Jilin Agricultural University, Changchun 130118, China
| | - Jian Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
- Department Biology, University of British Columbia-Okanagan, Kelowna, BC V1V 1V7, Canada
| | - Rui Bi
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Xueying Li
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Xiaobo Ren
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Yanyu Zhu
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Dan Yao
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
| | - Yang Song
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Songnan Yang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (S.Y.); (R.Z.)
| | - Rengui Zhao
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (S.Y.); (R.Z.)
| |
Collapse
|
11
|
Zhang L, Zeng Q, Zhu Q, Tan Y, Guo X. Essential Roles of Cupredoxin Family Proteins in Soybean Cyst Nematode Resistance. PHYTOPATHOLOGY 2022; 112:1545-1558. [PMID: 35050680 DOI: 10.1094/phyto-09-21-0391-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Soybean cyst nematode (SCN, Heterodera glycines), one of the most devastating soybean pathogens, causes a significant yield loss in soybean production. One of the most effective ways to manage SCN is to grow resistant cultivars. Therefore, comparative study using resistant and susceptible soybean cultivars provides a powerful tool to identify new genes involved in soybean SCN resistance. In the present study, a transcriptome analysis was carried out using both the resistant (PI88788) and susceptible (Williams 82) soybean cultivars to characterize the responses to nematode infection. Various defense-related genes and different pathways involved in nematode resistance were recognized as being highly expressed in resistant cultivar. Promoter-GUS analysis was conducted to monitor the spatial expression pattern of the genes highly induced by nematode infection. Two nematode-inducible promoters for Glyma.05g147000 (encoding caffeoyl-CoA O-methyltransferase) and Glyma.06g036700 (encoding cupredoxin superfamily protein) were characterized, and the promoters could efficiently drive the expression of known nematode resistance genes (α-SNAPRhg1HC or GmSHMT) to affect soybean SCN resistance. Interestingly, expression of the cupredoxin family genes was upregulated not only by SCN, but also by jasmonic acid treatment. DNA sequence analysis identified that a conserved motif (GGTGCATG) with high similarity to SCNbox1 and GC-rich element is enriched in their promoter regions, suggesting its potential to serve as a nematode-responsive regulatory element. Overexpression of Glyma.06g036700 significantly enhanced soybean resistance to cyst nematode. Overall, our findings not only highlight the essential role of cupredoxin family genes in SCN resistance, but also offer potential functional tools to develop nematode resistance in crops.
Collapse
Affiliation(s)
- Lei Zhang
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Qian Zeng
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Qun Zhu
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yuanhua Tan
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xiaoli Guo
- State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| |
Collapse
|
12
|
Huang M, Jiang Y, Qin R, Jiang D, Chang D, Tian Z, Li C, Wang C. Full-Length Transcriptional Analysis of the Same Soybean Genotype With Compatible and Incompatible Reactions to Heterodera glycines Reveals Nematode Infection Activating Plant Defense Response. FRONTIERS IN PLANT SCIENCE 2022; 13:866322. [PMID: 35665156 PMCID: PMC9158574 DOI: 10.3389/fpls.2022.866322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/22/2022] [Indexed: 06/04/2023]
Abstract
Full-length transcriptome sequencing with long reads is a powerful tool to analyze transcriptional and post-transcriptional events; however, it has not been applied on soybean (Glycine max). Here, a comparative full-length transcriptome analysis was performed on soybean genotype 09-138 infected with soybean cyst nematode (SCN, Heterodera glycines) race 4 (SCN4, incompatible reaction) and race 5 (SCN5, compatible reaction) using Oxford Nanopore Technology. Each of 9 full-length samples collected 8 days post inoculation with/without nematodes generated an average of 6.1 GB of clean data and a total of 65,038 transcript sequences. After redundant transcripts were removed, 1,117 novel genes and 41,096 novel transcripts were identified. By analyzing the sequence structure of the novel transcripts, a total of 28,759 complete open reading frame (ORF) sequences, 5,337 transcription factors, 288 long non-coding RNAs, and 40,090 novel transcripts with function annotation were predicted. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of differentially expressed genes (DEGs) revealed that growth hormone, auxin-activated signaling pathway and multidimensional cell growth, and phenylpropanoid biosynthesis pathway were enriched by infection with both nematode races. More DEGs associated with stress response elements, plant-hormone signaling transduction pathway, and plant-pathogen interaction pathway with more upregulation were found in the incompatible reaction with SCN4 infection, and more DEGs with more upregulation involved in cell wall modification and carbohydrate bioprocess were detected in the compatible reaction with SCN5 infection when compared with each other. Among them, overlapping DEGs with a quantitative difference was triggered. The combination of protein-protein interaction with DEGs for the first time indicated that nematode infection activated the interactions between transcription factor WRKY and VQ (valine-glutamine motif) to contribute to soybean defense. The knowledge of the SCN-soybean interaction mechanism as a model will present more understanding of other plant-nematode interactions.
Collapse
Affiliation(s)
- Minghui Huang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Ye Jiang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- Heilongjiang Academy of Agricultural Sciences, Daqing, China
| | - Ruifeng Qin
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- Heilongjiang Academy of Agricultural Sciences, Daqing, China
| | - Dan Jiang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- Heilongjiang Academy of Agricultural Sciences, Daqing, China
| | - Doudou Chang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- Heilongjiang Academy of Agricultural Sciences, Daqing, China
| | - Zhongyan Tian
- Heilongjiang Academy of Agricultural Sciences, Daqing, China
| | - Chunjie Li
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Congli Wang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| |
Collapse
|
13
|
Xu P, Li H, Wang X, Zhao G, Lu X, Dai S, Cui X, Yuan M, Liu Z. Integrated analysis of the lncRNA/circRNA-miRNA-mRNA expression profiles reveals novel insights into potential mechanisms in response to root-knot nematodes in peanut. BMC Genomics 2022; 23:239. [PMID: 35346027 PMCID: PMC8962500 DOI: 10.1186/s12864-022-08470-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 03/11/2022] [Indexed: 01/08/2023] Open
Abstract
Background Peanut is the most essential oil and food crop globally due to its high oil and protein content. Root-knot nematode infects peanut roots, causing poor development and severely limiting peanut yields worldwide. The discovery of peanut genome identified a considerable number of genetic loci controlling the peanut root-knot nematode; however, the molecular mechanism of root-knot nematode remains unknown. Results The heterogeneous response to root-knot nematode stress in peanut roots was identified using whole-transcriptome RNA-seq. A total of 430 mRNAs, 111 miRNAs, 4453 lncRNAs, and 123 circRNAs were found to have differential expression between infected and non-infected peanuts. The expression profiles of the lncRNA/circRNA-miRNA-mRNA network were developed to understand the potential pathways that lead to root-knot nematodes in peanut roots. During root-knot nematodes stress, a total of 10 lncRNAs, 4 circRNAs, 5 miRNAs, and 13 mRNAs can create competing endogenous RNA and participate in the oxidation–reduction process as well as other biological metabolism processes in peanuts. The findings will highlight the role of peanut ceRNAs in response to root-knot nematodes. Conclusion The GO classification and KEGG pathway enrichment study of core regulatory networks revealed that ceRNAs are involved in oxidation–reduction, peroxidase activity, lignin synthesis in the xylem, and flavonoid synthesis. Overall, these findings may help researchers better understand the role of non-coding RNAs in response to root-knot nematodes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08470-3.
Collapse
|
14
|
Grunwald DJ, Zapotocny RW, Ozer S, Diers BW, Bent AF. Detection of rare nematode resistance Rhg1 haplotypes in Glycine soja and a novel Rhg1 α-SNAP. THE PLANT GENOME 2022; 15:e20152. [PMID: 34716668 DOI: 10.1002/tpg2.20152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
This study pursued the hypothesis that wild plant germplasm accessions carrying alleles of interest can be identified using available single nucleotide polymorphism (SNP) genotypes for particular alleles of other (unlinked) genes that contribute to the trait of interest. The soybean cyst nematode (SCN, Heterodera glycines [HG]) resistance locus Rhg1 is widely used in farmed soybean [Glycine max (L.) Merr.]. The two known resistance-conferring haplotypes, rhg1-a and rhg1-b, typically contain three or seven to 10 tandemly duplicated Rhg1 segments, respectively. Each Rhg1 repeat carries four genes, including Glyma.18G022500, which encodes unusual isoforms of the vesicle-trafficking chaperone α-SNAP. Using SoySNP50K data for NSFRAN07 allele presence, we discovered a new Rhg1 haplotype, rhg1-ds, in six accessions of wild soybean, Glycine soja Siebold & Zucc. (0.5% of the ∼1,100 G. soja accessions in the USDA collection). The α-SNAP encoded by rhg1-ds is unique at an important site of amino acid variation and shares with the rhg1-a and rhg1-b α-SNAP proteins the traits of cytotoxicity and altered N-ethylmaleimide sensitive factor (NSF) protein interaction. Copy number assays indicate three repeats of rhg1-ds. G. soja PI 507613 and PI 507623 exhibit resistance to HG type 2.5.7 SCN populations, in part because of contributions from other loci. In a segregating F2 population, rhg1-b and rhg1-ds made statistically indistinguishable contributions to resistance to a partially virulent HG type 2.5.7 SCN population. Hence, the unusual multigene copy number variation Rhg1 haplotype was present but rare in ancestral G. soja and was present in accessions that offer multiple traits for SCN resistance breeding. The accessions were initially identified for study based on an unlinked SNP.
Collapse
Affiliation(s)
- Derrick J Grunwald
- Dep. of Plant Pathology, Univ. of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ryan W Zapotocny
- Dep. of Plant Pathology, Univ. of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Seda Ozer
- Dep. of Crop Science, Univ. of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Brian W Diers
- Dep. of Crop Science, Univ. of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Andrew F Bent
- Dep. of Plant Pathology, Univ. of Wisconsin-Madison, Madison, WI, 53706, USA
| |
Collapse
|
15
|
Natukunda MI, Hohenstein JD, McCabe CE, Graham MA, Qi Y, Singh AK, MacIntosh GC. Interaction between Rag genes results in a unique synergistic transcriptional response that enhances soybean resistance to soybean aphids. BMC Genomics 2021; 22:887. [PMID: 34895143 PMCID: PMC8665634 DOI: 10.1186/s12864-021-08147-3] [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: 03/23/2021] [Accepted: 11/03/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Pyramiding different resistance genes into one plant genotype confers enhanced resistance at the phenotypic level, but the molecular mechanisms underlying this effect are not well-understood. In soybean, aphid resistance is conferred by Rag genes. We compared the transcriptional response of four soybean genotypes to aphid feeding to assess how the combination of Rag genes enhanced the soybean resistance to aphid infestation. RESULTS A strong synergistic interaction between Rag1 and Rag2, defined as genes differentially expressed only in the pyramid genotype, was identified. This synergistic effect in the Rag1/2 phenotype was very evident early (6 h after infestation) and involved unique biological processes. However, the response of susceptible and resistant genotypes had a large overlap 12 h after aphid infestation. Transcription factor (TF) analyses identified a network of interacting TF that potentially integrates signaling from Rag1 and Rag2 to produce the unique Rag1/2 response. Pyramiding resulted in rapid induction of phytochemicals production and deposition of lignin to strengthen the secondary cell wall, while repressing photosynthesis. We also identified Glyma.07G063700 as a novel, strong candidate for the Rag1 gene. CONCLUSIONS The synergistic interaction between Rag1 and Rag2 in the Rag1/2 genotype can explain its enhanced resistance phenotype. Understanding molecular mechanisms that support enhanced resistance in pyramid genotypes could facilitate more directed approaches for crop improvement.
Collapse
Affiliation(s)
- Martha I. Natukunda
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011 USA
| | - Jessica D. Hohenstein
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011 USA
| | - Chantal E. McCabe
- Corn Insects and Crop Genetics Research, USDA-ARS, Ames, IA 50011 USA
| | - Michelle A. Graham
- Corn Insects and Crop Genetics Research, USDA-ARS, Ames, IA 50011 USA
- Department of Agronomy, Iowa State University, Ames, IA 50011 USA
| | - Yunhui Qi
- Department of Statistics, Iowa State University, Ames, IA 50011 USA
| | - Asheesh K. Singh
- Department of Agronomy, Iowa State University, Ames, IA 50011 USA
| | - Gustavo C. MacIntosh
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011 USA
| |
Collapse
|
16
|
Khoei MA, Karimi M, Karamian R, Amini S, Soorni A. Identification of the Complex Interplay Between Nematode-Related lncRNAs and Their Target Genes in Glycine max L. FRONTIERS IN PLANT SCIENCE 2021; 12:779597. [PMID: 34956274 PMCID: PMC8705754 DOI: 10.3389/fpls.2021.779597] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 11/08/2021] [Indexed: 05/26/2023]
Abstract
Soybean (Glycine max) is a major plant protein source and oilseed crop. However, plant-parasitic nematodes (PPNs) affect its annual yield. In the current study, in order to better understand the regulation of defense mechanism against PPNs in soybean, we investigated the role of long non-coding RNAs (lncRNAs) in response to two nematode species, Heterodera glycines (SCN: soybean cyst nematode) and Rotylenchulus reniformis (reniform). To this end, two publicly available RNA-seq data sets (SCN data set and RAD: reniform-associated data set) were employed to discover the lncRNAome profile of soybean under SCN and reniform infection, respectively. Upon identification of unannotated transcripts in these data sets, a seven-step pipeline was utilized to sieve these transcripts, which ended up in 384 and 283 potential lncRNAs in SCN data set and RAD, respectively. These transcripts were then used to predict cis and trans nematode-related targets in soybean genome. Computational prediction of target genes function, some of which were also among differentially expressed genes, revealed the involvement of putative nematode-responsive genes as well as enrichment of multiple stress responses in both data sets. Finally, 15 and six lncRNAs were proposed to be involved in microRNA-mediated regulation of gene expression in soybean in response to SNC and reniform infection, respectively. Collectively, this study provides a novel insight into the signaling and regulatory network of soybean-pathogen interactions and opens a new window for further research.
Collapse
Affiliation(s)
| | | | - Roya Karamian
- Department of Biology, Faculty of Sciences, Bu-Ali Sina University, Hamedan, Iran
| | | | - Aboozar Soorni
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| |
Collapse
|
17
|
Zhang H, Hu Z, Yang Y, Liu X, Lv H, Song BH, An YQC, Li Z, Zhang D. Transcriptome profiling reveals the spatial-temporal dynamics of gene expression essential for soybean seed development. BMC Genomics 2021; 22:453. [PMID: 34134624 PMCID: PMC8207594 DOI: 10.1186/s12864-021-07783-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 06/08/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Seeds are the economic basis of oilseed crops, especially soybeans, the most widely cultivated oilseed crop worldwide. Seed development is accompanied by a multitude of diverse cellular processes, and revealing the underlying regulatory activities is critical for seed improvement. RESULTS In this study, we profiled the transcriptomes of developing seeds at 20, 25, 30, and 40 days after flowering (DAF), as these stages represent critical time points of seed development from early to full development. We identified a set of highly abundant genes and highlighted the importance of these genes in supporting nutrient accumulation and transcriptional regulation for seed development. We identified 8925 differentially expressed genes (DEGs) that exhibited temporal expression patterns over the course and expression specificities in distinct tissues, including seeds and nonseed tissues (roots, stems, and leaves). Genes specific to nonseed tissues might have tissue-associated roles, with relatively low transcript abundance in developing seeds, suggesting their spatially supportive roles in seed development. Coexpression network analysis identified several underexplored genes in soybeans that bridge tissue-specific gene modules. CONCLUSIONS Our study provides a global view of gene activities and biological processes critical for seed formation in soybeans and prioritizes a set of genes for further study. The results of this study help to elucidate the mechanism controlling seed development and storage reserves.
Collapse
Affiliation(s)
- Hengyou Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Zhenbin Hu
- Department of Biology, Saint Louis University, St. Louis, MO, USA
| | - Yuming Yang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaoqian Liu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Haiyan Lv
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Bao-Hua Song
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Yong-Qiang Charles An
- US Department of Agriculture, Agricultural Research Service, Midwest Area, Plant Genetics Research Unit at Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Zhimin Li
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
| |
Collapse
|
18
|
Li X, Sun Y, Yang Y, Yang X, Xue W, Wu M, Chen P, Weng Y, Chen S. Transcriptomic and Histological Analysis of the Response of Susceptible and Resistant Cucumber to Meloidogyne incognita Infection Revealing Complex Resistance via Multiple Signaling Pathways. FRONTIERS IN PLANT SCIENCE 2021; 12:675429. [PMID: 34194451 PMCID: PMC8236822 DOI: 10.3389/fpls.2021.675429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/18/2021] [Indexed: 05/24/2023]
Abstract
The root-knot nematode (RKN), Meloidogyne incognita, is a devastating pathogen for cucumber (Cucumis sativus L.) specially in production under protected environments or continuous cropping. High level RKN resistance has been identified in African horned melon Cucumis metuliferus (CM). However, the resistance mechanism remains unclear. In this study, the comparative analysis on phenotypic and transcriptomic responses in the susceptible cucumber inbred line Q24 and the resistant CM, after M. incognita infection, was performed. The results showed that, in comparison with Q24, the CM was able to significantly reduce penetration numbers of second stage juveniles (J2), slow its development in the roots resulting in fewer galls and smaller giant cells suggesting the presence of host resistance in CM. Comparative transcriptomes analysis of Q24 and CM before and after M. incognita infection was conducted and differentially expressed genes (DEGs) associated with host resistance were identified in CM. Enrichment analyses revealed most enriched DEGs in Ca2+ signaling, salicylic acid (SA)/jamonate signaling (JA), as well as auxin (IAA) signaling pathways. In particular, in CM, DEGs in the Ca2+ signaling pathway such as those for the calmodulin and calcium-binding proteins were upregulated at the early stage of M. incognita infection; genes for SA/JA synthesis/signal transduction were markedly activated, whereas the IAA signaling pathway genes were inhibited upon infection suggesting the importance of SA/JA signaling pathways in mediating M. incognita resistance in CM. A model was established to explain the different molecular mechanisms on M. incognita susceptibility in cucumber and resistance to M. incognita infection in CM.
Collapse
Affiliation(s)
- Xvzhen Li
- College of Horticulture, Northwest A&F University/Shaanxi Engineering Research Center for Vegetables, Yangling, China
| | - Yinhui Sun
- College of Horticulture, Northwest A&F University/Shaanxi Engineering Research Center for Vegetables, Yangling, China
| | - Yuting Yang
- College of Horticulture, Northwest A&F University/Shaanxi Engineering Research Center for Vegetables, Yangling, China
| | - Xiaopei Yang
- College of Horticulture, Northwest A&F University/Shaanxi Engineering Research Center for Vegetables, Yangling, China
| | - Wanyu Xue
- College of Horticulture, Northwest A&F University/Shaanxi Engineering Research Center for Vegetables, Yangling, China
| | - Meiqian Wu
- College of Horticulture, Northwest A&F University/Shaanxi Engineering Research Center for Vegetables, Yangling, China
| | - Panpan Chen
- College of Horticulture, Northwest A&F University/Shaanxi Engineering Research Center for Vegetables, Yangling, China
| | - Yiqun Weng
- United States Department of Agriculture, Agriculture Research Service, Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, Madison, WI, United States
| | - Shuxia Chen
- College of Horticulture, Northwest A&F University/Shaanxi Engineering Research Center for Vegetables, Yangling, China
| |
Collapse
|
19
|
Sato K, Uehara T, Holbein J, Sasaki-Sekimoto Y, Gan P, Bino T, Yamaguchi K, Ichihashi Y, Maki N, Shigenobu S, Ohta H, Franke RB, Siddique S, Grundler FMW, Suzuki T, Kadota Y, Shirasu K. Transcriptomic Analysis of Resistant and Susceptible Responses in a New Model Root-Knot Nematode Infection System Using Solanum torvum and Meloidogyne arenaria. FRONTIERS IN PLANT SCIENCE 2021; 12:680151. [PMID: 34122492 PMCID: PMC8194700 DOI: 10.3389/fpls.2021.680151] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 04/30/2021] [Indexed: 06/12/2023]
Abstract
Root-knot nematodes (RKNs) are among the most devastating pests in agriculture. Solanum torvum Sw. (Turkey berry) has been used as a rootstock for eggplant (aubergine) cultivation because of its resistance to RKNs, including Meloidogyne incognita and M. arenaria. We previously found that a pathotype of M. arenaria, A2-J, is able to infect and propagate in S. torvum. In vitro infection assays showed that S. torvum induced the accumulation of brown pigments during avirulent pathotype A2-O infection, but not during virulent A2-J infection. This experimental system is advantageous because resistant and susceptible responses can be distinguished within a few days, and because a single plant genome can yield information about both resistant and susceptible responses. Comparative RNA-sequencing analysis of S. torvum inoculated with A2-J and A2-O at early stages of infection was used to parse the specific resistance and susceptible responses. Infection with A2-J did not induce statistically significant changes in gene expression within one day post-inoculation (DPI), but afterward, A2-J specifically induced the expression of chalcone synthase, spermidine synthase, and genes related to cell wall modification and transmembrane transport. Infection with A2-O rapidly induced the expression of genes encoding class III peroxidases, sesquiterpene synthases, and fatty acid desaturases at 1 DPI, followed by genes involved in defense, hormone signaling, and the biosynthesis of lignin at 3 DPI. Both isolates induced the expression of suberin biosynthetic genes, which may be triggered by wounding during nematode infection. Histochemical analysis revealed that A2-O, but not A2-J, induced lignin accumulation at the root tip, suggesting that physical reinforcement of cell walls with lignin is an important defense response against nematodes. The S. torvum-RKN system can provide a molecular basis for understanding plant-nematode interactions.
Collapse
Affiliation(s)
- Kazuki Sato
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Taketo Uehara
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Julia Holbein
- INRES – Molecular Phytomedicine, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
| | - Yuko Sasaki-Sekimoto
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Pamela Gan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Takahiro Bino
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Japan
| | - Katsushi Yamaguchi
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Japan
| | | | - Noriko Maki
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Shuji Shigenobu
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Japan
| | - Hiroyuki Ohta
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Rochus B. Franke
- Institute of Cellular and Molecular Botany, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
| | - Shahid Siddique
- INRES – Molecular Phytomedicine, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
- Department of Entomology and Nematology, University of California, Davis, Davis, CA, United States
| | - Florian M. W. Grundler
- INRES – Molecular Phytomedicine, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, Germany
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Yasuhiro Kadota
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Ken Shirasu
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Science, The University of Tokyo, Bunkyo, Japan
| |
Collapse
|
20
|
Transcriptome Analysis of Eggplant Root in Response to Root-Knot Nematode Infection. Pathogens 2021; 10:pathogens10040470. [PMID: 33924485 PMCID: PMC8069755 DOI: 10.3390/pathogens10040470] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/31/2021] [Accepted: 04/09/2021] [Indexed: 12/22/2022] Open
Abstract
Eggplant (Solanum melongena L.), which belongs to the Solanaceae family, is an important vegetable crop. However, its production is severely threatened by root-knot nematodes (RKNs) in many countries. Solanum torvum, a wild relative of eggplant, is employed worldwide as rootstock for eggplant cultivation due to its resistance to soil-borne diseases such as RKNs. In this study, to identify the RKN defense mechanisms, the transcriptomic profiles of eggplant and Solanum torvum were compared. A total of 5360 differentially expressed genes (DEGs) were identified for the response to RKN infection. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that these DEGs are mainly involved in the processes of response to stimulus, protein phosphorylation, hormone signal transduction, and plant-pathogen interaction pathways. Many phytohormone-related genes and transcription factors (MYB, WRKY, and NAC) were differentially expressed at the four time points (ck, 7, 14, and 28 days post-infection). The abscisic acid signaling pathway might be involved in plant-nematode interactions. qRT-PCR validated the expression levels of some of the DEGs in eggplant. These findings demonstrate the nematode-induced expression profiles and provide some insights into the nematode resistance mechanism in eggplant.
Collapse
|
21
|
Kofsky J, Zhang H, Song BH. Novel resistance strategies to soybean cyst nematode (SCN) in wild soybean. Sci Rep 2021; 11:7967. [PMID: 33846373 PMCID: PMC8041904 DOI: 10.1038/s41598-021-86793-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 03/15/2021] [Indexed: 02/01/2023] Open
Abstract
Soybean cyst nematode (SCN, Heterodera glycine Ichinohe) is the most damaging soybean pest worldwide and management of SCN remains challenging. The current SCN resistant soybean cultivars, mainly developed from the cultivated soybean gene pool, are losing resistance due to SCN race shifts. The domestication process and modern breeding practices of soybean cultivars often involve strong selection for desired agronomic traits, and thus, decreased genetic variation in modern cultivars, which consequently resulted in limited sources of SCN resistance. Wild soybean (Glycine soja) is the wild ancestor of cultivated soybean (Glycine max) and it's gene pool is indisputably more diverse than G. max. Our aim is to identify novel resistant genetic resources from wild soybean for the development of new SCN resistant cultivars. In this study, resistance response to HG type 2.5.7 (race 5) of SCN was investigated in a newly identified SCN resistant ecotype, NRS100. To understand the resistance mechanism in this ecotype, we compared RNA seq-based transcriptomes of NRS100 with two SCN-susceptible accessions of G. soja and G. max, as well as an extensively studied SCN resistant cultivar, Peking, under both control and nematode J2-treated conditions. The proposed mechanisms of resistance in NRS100 includes the suppression of the jasmonic acid (JA) signaling pathway in order to allow for salicylic acid (SA) signaling-activated resistance response and polyamine synthesis to promote structural integrity of root cell walls. Our study identifies a set of novel candidate genes and associated pathways involved in SCN resistance and the finding provides insight into the mechanism of SCN resistance in wild soybean, advancing the understanding of resistance and the use of wild soybean-sourced resistance for soybean improvement.
Collapse
Affiliation(s)
- Janice Kofsky
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Hengyou Zhang
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
- Donald Danforth Plant Science Center, Saint Louis, MO, 63132, USA
| | - Bao-Hua Song
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
| |
Collapse
|
22
|
Njaci I, Ngugi-Dawit A, Oduor RO, Kago L, Williams B, Hoang LTM, Mundree SG, Ghimire SR. Comparative Analysis Delineates the Transcriptional Resistance Mechanisms for Pod Borer Resistance in the Pigeonpea Wild Relative Cajanus scarabaeoides (L.) Thouars. Int J Mol Sci 2020; 22:ijms22010309. [PMID: 33396747 PMCID: PMC7795875 DOI: 10.3390/ijms22010309] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/15/2020] [Accepted: 12/23/2020] [Indexed: 01/17/2023] Open
Abstract
Insect pests pose a serious threat to global food production. Pod borer (Helicoverpa armigera (Hübner)) is one of the most destructive pests of leguminous crops. The use of host resistance has been an effective, environmentally friendly and sustainable approach for controlling several agricultural pests. The exploitation of natural variations in crop wild relatives could yield pest-resistant crop varieties. In this study, we used a high-throughput transcriptome profiling approach to investigate the defense mechanisms of susceptible cultivated and tolerant wild pigeonpea genotypes against H. armigera infestation. The wild genotype displayed elevated pest-induced gene expression, including the enhanced induction of phytohormone and calcium/calmodulin signaling, transcription factors, plant volatiles and secondary metabolite genes compared to the cultivated control. The biosynthetic and regulatory processes associated with flavonoids, terpenes and glucosinolate secondary metabolites showed higher accumulations in the wild genotype, suggesting the existence of distinct tolerance mechanisms. This study provides insights into the molecular mechanisms underlying insect resistance in the wild pigeonpea genotype. This information highlights the indispensable role of crop wild relatives as a source of crucial genetic resources that could be important in devising strategies for crop improvement with enhanced pest resistance.
Collapse
Affiliation(s)
- Isaac Njaci
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, Nairobi P.O. Box 30709-00100, Kenya; (I.N.); (L.K.)
| | - Abigail Ngugi-Dawit
- Centre for Agriculture and the Bioeconomy (CAB), Queensland University of Technology, Brisbane City, QLD 4000, Australia; (A.N.-D.); (B.W.); (L.T.M.H.)
| | - Richard O. Oduor
- Department of Biochemistry, Microbiology and Biotechnology, Kenyatta University, Nairobi P.O. Box 43844-00100, Kenya;
| | - Leah Kago
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, Nairobi P.O. Box 30709-00100, Kenya; (I.N.); (L.K.)
| | - Brett Williams
- Centre for Agriculture and the Bioeconomy (CAB), Queensland University of Technology, Brisbane City, QLD 4000, Australia; (A.N.-D.); (B.W.); (L.T.M.H.)
| | - Linh Thi My Hoang
- Centre for Agriculture and the Bioeconomy (CAB), Queensland University of Technology, Brisbane City, QLD 4000, Australia; (A.N.-D.); (B.W.); (L.T.M.H.)
| | - Sagadevan G. Mundree
- Centre for Agriculture and the Bioeconomy (CAB), Queensland University of Technology, Brisbane City, QLD 4000, Australia; (A.N.-D.); (B.W.); (L.T.M.H.)
- Correspondence: (S.G.M.); (S.R.G.)
| | - Sita R. Ghimire
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, Nairobi P.O. Box 30709-00100, Kenya; (I.N.); (L.K.)
- Correspondence: (S.G.M.); (S.R.G.)
| |
Collapse
|
23
|
A Comprehensive Transcriptional Profiling of Pepper Responses to Root-Knot Nematode. Genes (Basel) 2020; 11:genes11121507. [PMID: 33333784 PMCID: PMC7765216 DOI: 10.3390/genes11121507] [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: 10/14/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023] Open
Abstract
Genetic resistance remains a key component in integrated pest management systems. The cosmopolitan root-knot nematode (RKN; Meloidogyne spp.) proves a significant management challenge as virulence and pathogenicity vary among and within species. RKN greatly reduces commercial bell pepper yield, and breeding programs continuously develop cultivars to emerging nematode threats. However, there is a lack of knowledge concerning the nature and forms of nematode resistance. Defining how resistant and susceptible pepper cultivars mount defenses against RKN attacks can help inform breeding programs. Here, we characterized the transcriptional responses of the highly related resistant (Charleston Belle) and susceptible (Keystone Resistance Giant) pepper cultivars throughout early nematode infection stages. Comprehensive transcriptomic sequencing of resistant and susceptible cultivar roots with or without Meloidogyneincognita infection over three-time points; covering early penetration (1-day), through feeding site maintenance (7-days post-inoculation), produced > 300 million high quality reads. Close examination of chromosome P9, on which nematode resistance hotspots are located, showed more differentially expressed genes were upregulated in resistant cultivar at day 1 when compared to the susceptible cultivar. Our comprehensive approach to transcriptomic profiling of pepper resistance revealed novel insights into how RKN causes disease and the plant responses mounted to counter nematode attack. This work broadens the definition of resistance from a single loci concept to a more complex array of interrelated pathways. Focus on these pathways in breeding programs may provide more sustainable and enduring forms of resistance.
Collapse
|
24
|
Lakhssassi N, Piya S, Bekal S, Liu S, Zhou Z, Bergounioux C, Miao L, Meksem J, Lakhssassi A, Jones K, Kassem MA, Benhamed M, Bendahmane A, Lambert K, Boualem A, Hewezi T, Meksem K. A pathogenesis-related protein GmPR08-Bet VI promotes a molecular interaction between the GmSHMT08 and GmSNAP18 in resistance to Heterodera glycines. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1810-1829. [PMID: 31960590 PMCID: PMC7336373 DOI: 10.1111/pbi.13343] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/19/2019] [Accepted: 01/03/2020] [Indexed: 05/19/2023]
Abstract
Soybean cyst nematode (SCN, Heterodera glycines) is the most devastating pest affecting soybean production worldwide. SCN resistance requires both the GmSHMT08 and the GmSNAP18 in 'Peking'-type resistance. Here, we describe the molecular interaction between GmSHMT08 and GmSNAP18, which is potentiated by a pathogenesis-related protein GmPR08-Bet VI. Like GmSNAP18 and GmSHMT08, GmPR08-Bet VI expression was induced in response to SCN and its overexpression decreased SCN cysts by 65% in infected transgenic soybean roots. Overexpression of GmPR08-Bet VI did not have an effect on SCN resistance when the two cytokinin-binding sites in GmPR08-Bet VI were mutated, indicating a new role of GmPR08-Bet VI in SCN resistance. GmPR08-Bet VI was mapped to a QTL for resistance to SCN using different mapping populations. GmSHMT08, GmSNAP18 and GmPR08-Bet VI localize to the cytosol and plasma membrane. GmSNAP18 expression and localization hyper-accumulated at the plasma membrane and was specific to the root cells surrounding the nematode in SCN-resistant soybeans. Genes encoding key components of the salicylic acid signalling pathway were induced under SCN infection. GmSNAP18 and GmPR08-Bet VI were also induced under salicylic acid and cytokinin exogenous treatments, while GmSHMT08 was induced only when the resistant GmSNAP18 was present, pointing to the presence of a molecular crosstalk between SCN-resistant genes and defence genes. Expression analysis of GmSHMT08 and GmSNAP18 identified the need of a minimum expression requirement to trigger the SCN resistance reaction. These results provide insight into a new response mechanism towards plant nematode resistance involving haplotype compatibility, gene dosage and hormone signalling.
Collapse
Affiliation(s)
- Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | - Sarbottam Piya
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Sadia Bekal
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | - Shiming Liu
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | - Zhou Zhou
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | - Catherine Bergounioux
- INRAInstitute of Plant Sciences Paris‐Saclay (IPS2)CNRSUniversité Paris‐SudOrsayFrance
| | - Long Miao
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | | | - Aicha Lakhssassi
- Faculty of Sciences and TechnologiesUniversity of LorraineNancyFrance
| | - Karen Jones
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | | | - Moussa Benhamed
- INRAInstitute of Plant Sciences Paris‐Saclay (IPS2)CNRSUniversité Paris‐SudOrsayFrance
| | - Abdelhafid Bendahmane
- INRAInstitute of Plant Sciences Paris‐Saclay (IPS2)CNRSUniversité Paris‐SudOrsayFrance
| | - Kris Lambert
- Department of Crop SciencesUniversity of IllinoisUrbanaILUSA
| | - Adnane Boualem
- INRAInstitute of Plant Sciences Paris‐Saclay (IPS2)CNRSUniversité Paris‐SudOrsayFrance
| | - Tarek Hewezi
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| |
Collapse
|
25
|
Guo W, Chen JS, Zhang F, Li ZY, Chen HF, Zhang CJ, Chen LM, Yuan SL, Li R, Cao D, Hao QN, Chen SL, Shan ZH, Yang ZL, Zhang XJ, Qiu DZ, You QB, Dai WJ, Zhou XA, Shen XJ, Jiao YQ. Characterization of Pingliang xiaoheidou (ZDD 11047), a soybean variety with resistance to soybean cyst nematode Heterodera glycines. PLANT MOLECULAR BIOLOGY 2020; 103:253-267. [PMID: 32152894 DOI: 10.1007/s11103-020-00990-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 03/02/2020] [Indexed: 06/10/2023]
Abstract
KEY MESSAGE A novel QTL (qSCN-PL10) for SCN resistance and related candidate genes were identified in the soybean variety Pingliang xiaoheidou, and plant basal immunity seems to contribute to the SCN resistance. Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is one of the most devastating soybean pests worldwide. The development of host plant resistance represents an effective strategy to control SCN. However, owing to the lack of diversity of resistance genes in soybean varieties, further investigation is necessary to identify new SCN resistance genes. By analyzing the resistance phenotypes of soybean variety Pingliang xiaoheidou (Pingliang, ZDD 11047), we found that it exhibited the different resistance phenotypes from PI 88788 and Peking varieties. Because Pingliang variety contains the Rhg1-a (low copy) haplotype and lacks the resistant Rhg4 haplotype, novel quantitative trait locus might account for their SCN resistance. After sequencing parental lines (Magellan and Pingliang) and 200 F2:3 progenies, a high-density genetic map was constructed using the specific length amplified fragment sequencing method and qSCN-PL10 was identified as a novel locus for SCN resistance. Candidate genes were predicted by RNA sequencing (RNA-seq) in the qSCN-PL10 locus region. The RNA-seq analysis performed also indicated that plant basal immunity plays an important role in the resistance of Pingliang to SCN. These results lay a foundation for the use of marker-assisted breeding to enhance the resistance to SCN.
Collapse
Affiliation(s)
- Wei Guo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China.
| | - Jing S Chen
- Daqing Branch of the Heilongjiang Academy of Agricultural Sciences, Daqing, 163316, Heilongjiang, China
| | - Feng Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Ze Y Li
- Daqing Branch of the Heilongjiang Academy of Agricultural Sciences, Daqing, 163316, Heilongjiang, China
| | - Hai F Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Chan J Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Li M Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Song L Yuan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Rong Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Dong Cao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Qing N Hao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Shui L Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Zhi H Shan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Zhong L Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Xiao J Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - De Z Qiu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Qing B You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Wen J Dai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Xin A Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China
| | - Xin J Shen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, Hubei, China.
| | - Yong Q Jiao
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, Henan, China.
| |
Collapse
|
26
|
Kofsky J, Zhang H, Song BH. Genetic Architecture of Early Vigor Traits in Wild Soybean. Int J Mol Sci 2020; 21:E3105. [PMID: 32354037 PMCID: PMC7247153 DOI: 10.3390/ijms21093105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 04/24/2020] [Indexed: 01/13/2023] Open
Abstract
A worldwide food shortage has been projected as a result of the current increase in global population and climate change. In order to provide sufficient food to feed more people, we must develop crops that can produce higher yields. Plant early vigor traits, early growth rate (EGR), early plant height (EPH), inter-node length, and node count are important traits that are related to crop yield. Glycine soja, the wild counterpart to cultivated soybean, Glycine max, harbors much higher genetic diversity and can grow in diverse environments. It can also cross easily with cultivated soybean. Thus, it holds a great potential in developing soybean cultivars with beneficial agronomic traits. In this study, we used 225 wild soybean accessions originally from diverse environments across its geographic distribution in East Asia. We quantified the natural variation of several early vigor traits, investigated the relationships among them, and dissected the genetic basis of these traits by applying a Genome-Wide Association Study (GWAS) with genome-wide single nucleotide polymorphism (SNP) data. Our results showed positive correlation between all early vigor traits studied. A total of 12 SNPs significantly associated with EPH were identified with 4 shared with EGR. We also identified two candidate genes, Glyma.07G055800.1 and Glyma.07G055900.1, playing important roles in influencing trait variation in both EGR and EPH in G. soja.
Collapse
Affiliation(s)
| | | | - Bao-Hua Song
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; (J.K.); (H.Z.)
| |
Collapse
|
27
|
Pawlowski ML, Vuong TD, Valliyodan B, Nguyen HT, Hartman GL. Whole-genome resequencing identifies quantitative trait loci associated with mycorrhizal colonization of soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:409-417. [PMID: 31707439 DOI: 10.1007/s00122-019-03471-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 11/01/2019] [Indexed: 05/15/2023]
Abstract
KEY MESSAGE A whole-genome resequencing-derived SNP dataset identified six quantitative trait loci (QTL) significantly associated with colonization of soybean by an arbuscular mycorrhizal fungus (Rhizophagus intraradices). Candidate genes identified in these QTL regions include homologs to known nodulin protein families and other symbiosis-specific genes. Arbuscular mycorrhizal fungi (AMF) form associations with over 80% of all terrestrial plant species and assist their host plants by increasing their nutrient uptake, drought tolerance, and resilience against pathogens and pests. Genotypic variation of crop plants to AMF colonization has been identified in crops, including soybean; however, the genetics controlling levels of AMF colonization in soybean are unknown. The overall goal of our study was to identify genomic regions associated with mycorrhizal colonization in soybean using genome-wide association analysis. A diverse panel of 350 exotic soybean genotypes inoculated with Rhizophagus intraradices were microscopically evaluated for root colonization using a modified gridline intersect method. Root colonization differed significantly (P < 0.001) among genotypes and ranged from 11 to 70%. A whole-genome resequencing-derived SNP dataset identified six quantitative trait loci (QTL) significantly associated with R. intraradices colonization that explained 24% of the phenotypic variance. Candidate genes identified in these QTL regions include homologs to known nodulin protein families and other symbiosis-specific genes. The results showed there was a significant genetic component to the level of colonization by R. intraradices in soybean. This information may be useful in the development of AMF-sensitive soybean cultivars to enhance nutrient uptake, drought tolerance, and disease resistance in the crop.
Collapse
Affiliation(s)
- Michelle L Pawlowski
- Department of Crop Science, University of Illinois, 1101 W. Peabody Drive, Urbana, IL, 61801, USA
| | - Tri D Vuong
- Department of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Babu Valliyodan
- Department of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Henry T Nguyen
- Department of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Glen L Hartman
- Department of Crop Science, University of Illinois, 1101 W. Peabody Drive, Urbana, IL, 61801, USA.
- USDA, Agricultural Research Services, University of Illinois, 1101 W. Peabody Dr., Urbana, IL, USA.
| |
Collapse
|
28
|
Zhou Y, Zhao D, Shuang L, Xiao D, Xuan Y, Duan Y, Chen L, Wang Y, Liu X, Fan H, Zhu X. Transcriptome Analysis of Rice Roots in Response to Root-Knot Nematode Infection. Int J Mol Sci 2020; 21:ijms21030848. [PMID: 32013011 PMCID: PMC7037758 DOI: 10.3390/ijms21030848] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/24/2020] [Accepted: 01/27/2020] [Indexed: 12/12/2022] Open
Abstract
Meloidogyne incognita and Meloidogyne graminicola are root-knot nematodes (RKNs) infecting rice (Oryza sativa L.) roots and severely decreasing yield, whose mechanisms of action remain unclear. We investigated RKN invasion and development in rice roots through RNA-seq transcriptome analysis. The results showed that 952 and 647 genes were differently expressed after 6 (invasion stage) and 18 (development stage) days post inoculation, respectively. Gene annotation showed that the differentially expressed genes were classified into diverse metabolic and stress response categories. Furthermore, phytohormone, transcription factor, redox signaling, and defense response pathways were enriched upon RKN infection. RNA-seq validation using qRT-PCR confirmed that CBL-interacting protein kinase (CIPK) genes (CIPK5, 8, 9, 11, 14, 23, 24, and 31) as well as brassinosteroid (BR)-related genes (OsBAK1, OsBRI1, D2, and D11) were altered by RKN infection. Analysis of the CIPK9 mutant and overexpressor indicated that the RKN populations were smaller in cipk9 and larger in CIPK9 OX, while more galls were produced in CIPK9 OX plant roots than the in wild-type roots. Significantly fewer numbers of second-stage infective juveniles (J2s) were observed in the plants expressing the BR biosynthesis gene D2 mutant and the BR receptor BRI1 activation-tagged mutant (bri1-D), and fewer galls were observed in bri1-D roots than in wild-type roots. The roots of plants expressing the regulator of ethylene signaling ERS1 (ethylene response sensor 1) mutant contained higher numbers of J2s and developed more galls compared with wild-type roots, suggesting that these signals function in RKN invasion or development. Our findings broaden our understanding of rice responses to RKN invasion and provide useful information for further research on RKN defense mechanisms.
Collapse
Affiliation(s)
- Yuan Zhou
- College of Plant Protection, Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (Y.Z.); (D.Z.); (D.X.); (Y.X.); (Y.D.); (L.C.); (Y.W.); (X.L.); (H.F.)
| | - Di Zhao
- College of Plant Protection, Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (Y.Z.); (D.Z.); (D.X.); (Y.X.); (Y.D.); (L.C.); (Y.W.); (X.L.); (H.F.)
| | - Li Shuang
- Shaanxi Key Laboratory of Chinese Jujube, College of Life Science, Yan’an University, Yan’an, Shaanxi 716000, China;
| | - Dongxue Xiao
- College of Plant Protection, Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (Y.Z.); (D.Z.); (D.X.); (Y.X.); (Y.D.); (L.C.); (Y.W.); (X.L.); (H.F.)
| | - Yuanhu Xuan
- College of Plant Protection, Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (Y.Z.); (D.Z.); (D.X.); (Y.X.); (Y.D.); (L.C.); (Y.W.); (X.L.); (H.F.)
| | - Yuxi Duan
- College of Plant Protection, Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (Y.Z.); (D.Z.); (D.X.); (Y.X.); (Y.D.); (L.C.); (Y.W.); (X.L.); (H.F.)
| | - Lijie Chen
- College of Plant Protection, Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (Y.Z.); (D.Z.); (D.X.); (Y.X.); (Y.D.); (L.C.); (Y.W.); (X.L.); (H.F.)
| | - Yuanyuan Wang
- College of Plant Protection, Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (Y.Z.); (D.Z.); (D.X.); (Y.X.); (Y.D.); (L.C.); (Y.W.); (X.L.); (H.F.)
| | - Xiaoyu Liu
- College of Plant Protection, Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (Y.Z.); (D.Z.); (D.X.); (Y.X.); (Y.D.); (L.C.); (Y.W.); (X.L.); (H.F.)
| | - Haiyan Fan
- College of Plant Protection, Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (Y.Z.); (D.Z.); (D.X.); (Y.X.); (Y.D.); (L.C.); (Y.W.); (X.L.); (H.F.)
| | - Xiaofeng Zhu
- College of Plant Protection, Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (Y.Z.); (D.Z.); (D.X.); (Y.X.); (Y.D.); (L.C.); (Y.W.); (X.L.); (H.F.)
- Correspondence: ; Tel.: +86-135-1603-9056
| |
Collapse
|
29
|
Miraeiz E, Chaiprom U, Afsharifar A, Karegar A, M Drnevich J, E Hudson M. Early transcriptional responses to soybean cyst nematode HG Type 0 show genetic differences among resistant and susceptible soybeans. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:87-102. [PMID: 31570969 DOI: 10.1007/s00122-019-03442-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 09/18/2019] [Indexed: 05/24/2023]
Abstract
KEY MESSAGE Root transcriptome profiling of three soybean cultivars and a wild relative infected with soybean cyst nematode at migratory phase revealed differential resistance pathway responses between resistant and susceptible genotypes. The soybean cyst nematode (SCN), Heterodera glycines, is the most serious pathogen of soybean production throughout the world. Using resistant cultivars is the primary management strategy against SCN infestation. To gain insight into the still obscure mechanisms of genetic resistance to nematodes in different soybean genotypes, RNA-Seq profiling of the roots of Glycine max cv. Peking, Fayette, Williams 82, and a wild relative (Glycine soja PI 468916) was performed during SCN infection at the migratory phase. The analysis showed statistically significant changes of expression beginning at eight hours after inoculation in genes associated with defense mechanisms and pathways, such as the phenylpropanoid biosynthesis pathway, plant innate immunity and hormone signaling. Our results indicate the importance of the early plant response to migratory phase nematodes in pathogenicity determination. The transcriptome changes occurring during early SCN infection included a number of genes and pathways specific to the different resistant genotypes. We observed the most extensive resistant transcriptome reaction in PI 468916, where the resistant response was qualitatively different from that of commonly used G. max varieties.
Collapse
Affiliation(s)
- Esmaeil Miraeiz
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, Iran
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Usawadee Chaiprom
- PhD Program in Informatics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Alireza Afsharifar
- Plant Virology Research Center, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Akbar Karegar
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Jenny M Drnevich
- High Performance Biological Computing (HPCBio), Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Matthew E Hudson
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| |
Collapse
|
30
|
Yang L, Gao J, Zhang Y, Tian J, Sun Y, Wang C. RNA-Seq identification of candidate defense genes by analyzing Mythimna separata feeding-damage induced systemic resistance in balsas teosinte. PEST MANAGEMENT SCIENCE 2020; 76:333-342. [PMID: 31207043 DOI: 10.1002/ps.5519] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 05/05/2019] [Accepted: 06/11/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Armyworm (Mythimna separata) is a destructive herbivore for maize. Balsas teosinte (Zea mays ssp. parviglumis), the direct wild ancestor of cultivated maize, has shown great potential to defend against herbivory. Here, based on armyworm bioassay, we compared responses of teosinte and B73 maize inbred during armyworm attack in their transcriptome profiles to elucidate the gene expression changes involved in teosinte responses to armyworm attack. The goal of this study was to identify novel resistance alleles that could serve as valuable resources for modern maize breeding. RESULTS Our bioassay revealed that armyworm larvae grew less on teosinte than on maize. A follow-up transcriptomic comparison showed more down-regulated genes in maize B73 and similar numbers of up-regulated genes in both genotypes under armyworm attack. The up-regulated genes in teosinte were markedly enriched in MAPK cascade-mediated signaling pathway and phytohormone pathway. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that phytohormones jasmonic acid, ethylene, salicylic acid and abscisic acid (ABA) were actively involved in armyworm resistance of teosinte plants, and so were transcription factors such as MYBs, WRKYs and TIFYs. Interestingly, teosinte also showed high regulation in three ABA receptor PYLs. Based on differential expression analysis, we identified 30 candidate defense-related genes in teosinte, which belong to 11 gene families and the majority of the genes were up-regulated, while some of them were nonresponsive in maize. CONCLUSION This study demonstrates that teosinte showed more vigorous defense response than maize toward armyworm attack and might be a beneficial genetic resource to improve pest resistance in cultivated maize. © 2019 Society of Chemical Industry.
Collapse
Affiliation(s)
- Liyan Yang
- College of Life Science, Shanxi Normal University, Linfen, China
| | - Jing Gao
- College of Life Science, Shanxi Normal University, Linfen, China
| | - Yurong Zhang
- College of Life Science, Shanxi Normal University, Linfen, China
| | - Jingyun Tian
- College of Life Science, Shanxi Normal University, Linfen, China
| | - Yi Sun
- Biotechnology Research Center, Shanxi Academy of Agricultural Sciences/Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Taiyuan, China
| | - Chuangyun Wang
- Institute of Crop Sciences, Shanxi Academy of Agricultural Sciences, Taiyuan, China
| |
Collapse
|
31
|
Hu Y, You J, Li C, Pan F, Wang C. The Heterodera glycines effector Hg16B09 is required for nematode parasitism and suppresses plant defense response. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 289:110271. [PMID: 31623793 DOI: 10.1016/j.plantsci.2019.110271] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 09/05/2019] [Accepted: 09/12/2019] [Indexed: 06/10/2023]
Abstract
Soybean cyst nematode (Heterodera glycines Ichinohe) is a sedentary root endoparasite that causes serious yield losses on soybean (Glycine max) worldwide. H. glycines secrets effector proteins into host cells to facilitate the success of parasitism. Nowadays, a large number of candidate effectors were identified from the genome sequence of H. glycines. However, the precise functions of these effectors in the nematode-host plant interaction are unknown. Here, an effector gene of dorsal gland protein Hg16B09 from H. glycines was cloned and functionally characterized through generating the transgenic soybean hairy roots. In situ hybridization assay and qRT-PCR analysis indicated Hg16B09 is exclusively expressed in the dorsal esophageal cells and up-regulated in the parasitic-stage juveniles. The constitutive expression of Hg16B09 in soybean hairy roots caused an enhanced susceptibility to H. glycines. In contrast, in planta silencing of Hg16B09 exhibited that nematode reproduction in hairy roots was decreased compared to the empty vector control. In addition, Hg16B09 also suppressed the expression of soybean defense-related genes induced by the pathogen-associated molecular pattern flg22. These data indicate that the effector Hg16B09 might aid H. glycines parasitism through suppressing plant basal defenses in the early parasitic stages.
Collapse
Affiliation(s)
- Yanfeng Hu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, PR China
| | - Jia You
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, PR China; University of Chinese Academy of Science, Beijing, PR China
| | - Chunjie Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, PR China
| | - Fengjuan Pan
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, PR China
| | - Congli Wang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, PR China.
| |
Collapse
|
32
|
Kim JY, Jeong S, Kim KH, Lim WJ, Lee HY, Jeong N, Moon JK, Kim N. Dissection of soybean populations according to selection signatures based on whole-genome sequences. Gigascience 2019; 8:giz151. [PMID: 31869408 PMCID: PMC6927394 DOI: 10.1093/gigascience/giz151] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/21/2019] [Accepted: 12/05/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Domestication and improvement processes, accompanied by selections and adaptations, have generated genome-wide divergence and stratification in soybean populations. Simultaneously, soybean populations, which comprise diverse subpopulations, have developed their own adaptive characteristics enhancing fitness, resistance, agronomic traits, and morphological features. The genetic traits underlying these characteristics play a fundamental role in improving other soybean populations. RESULTS This study focused on identifying the selection signatures and adaptive characteristics in soybean populations. A core set of 245 accessions (112 wild-type, 79 landrace, and 54 improvement soybeans) selected from 4,234 soybean accessions was re-sequenced. Their genomic architectures were examined according to the domestication and improvement, and accessions were then classified into 3 wild-type, 2 landrace, and 2 improvement subgroups based on various population analyses. Selection and gene set enrichment analyses revealed that the landrace subgroups have selection signals for soybean-cyst nematode HG type 0 and seed development with germination, and that the improvement subgroups have selection signals for plant development with viability and seed development with embryo development, respectively. The adaptive characteristic for soybean-cyst nematode was partially underpinned by multiple resistance accessions, and the characteristics related to seed development were supported by our phenotypic findings for seed weights. Furthermore, their adaptive characteristics were also confirmed as genome-based evidence, and unique genomic regions that exhibit distinct selection and selective sweep patterns were revealed for 13 candidate genes. CONCLUSIONS Although our findings require further biological validation, they provide valuable information about soybean breeding strategies and present new options for breeders seeking donor lines to improve soybean populations.
Collapse
Affiliation(s)
- Jae-Yoon Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro 125, Yuseong-gu, Daejeon 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Gajeong-ro 217, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Seongmun Jeong
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro 125, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Kyoung Hyoun Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro 125, Yuseong-gu, Daejeon 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Gajeong-ro 217, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Won-Jun Lim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro 125, Yuseong-gu, Daejeon 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Gajeong-ro 217, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Ho-Yeon Lee
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro 125, Yuseong-gu, Daejeon 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Gajeong-ro 217, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Namhee Jeong
- National Institute of Crop Science, Rural Development Administration, Nongsaengmyeong-ro 370, Deokjin-gu, Jeon-Ju 54874, Republic of Korea
| | - Jung-Kyung Moon
- National Institute of Crop Science, Rural Development Administration, Nongsaengmyeong-ro 370, Deokjin-gu, Jeon-Ju 54874, Republic of Korea
| | - Namshin Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro 125, Yuseong-gu, Daejeon 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Gajeong-ro 217, Yuseong-gu, Daejeon 34141, Republic of Korea
| |
Collapse
|
33
|
Neupane S, Purintun JM, Mathew FM, Varenhorst AJ, Nepal MP. Molecular Basis of Soybean Resistance to Soybean Aphids and Soybean Cyst Nematodes. PLANTS 2019; 8:plants8100374. [PMID: 31561499 PMCID: PMC6843664 DOI: 10.3390/plants8100374] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/05/2019] [Accepted: 09/17/2019] [Indexed: 01/25/2023]
Abstract
Soybean aphid (SBA; Aphis glycines Matsumura) and soybean cyst nematode (SCN; Heterodera glycines Ichninohe) are major pests of the soybean (Glycine max [L.] Merr.). Substantial progress has been made in identifying the genetic basis of limiting these pests in both model and non-model plant systems. Classical linkage mapping and genome-wide association studies (GWAS) have identified major and minor quantitative trait loci (QTLs) in soybean. Studies on interactions of SBA and SCN effectors with host proteins have identified molecular cues in various signaling pathways, including those involved in plant disease resistance and phytohormone regulations. In this paper, we review the molecular basis of soybean resistance to SBA and SCN, and we provide a synthesis of recent studies of soybean QTLs/genes that could mitigate the effects of virulent SBA and SCN populations. We also review relevant studies of aphid–nematode interactions, particularly in the soybean–SBA–SCN system.
Collapse
Affiliation(s)
- Surendra Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Jordan M Purintun
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Febina M Mathew
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57007, USA.
| | - Adam J Varenhorst
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57007, USA.
| | - Madhav P Nepal
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| |
Collapse
|
34
|
Song W, Qi N, Liang C, Duan F, Zhao H. Soybean root transcriptome profiling reveals a nonhost resistant response during Heterodera glycines infection. PLoS One 2019; 14:e0217130. [PMID: 31125369 PMCID: PMC6534303 DOI: 10.1371/journal.pone.0217130] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Accepted: 05/06/2019] [Indexed: 11/19/2022] Open
Abstract
Heterodera glycines (soybean cyst nematode, SCN) is one of the most devastating pathogens of soybean worldwide. The compatible and in compatible interactions between soybean and SCN have well documented. Nevertheless, the molecular mechanism of a nonhost resistant response in soybean against SCN infection remains obscure. Toward this end, a global transcriptional comparison was conducted between susceptible and resistant reactions of soybean roots infected by taking advantage of finding a new pathotype of SCN (SCNT). The soybean cultivar Lee, which exhibits resistant to SCNT and susceptible to HG 1.2.3.4.7 (SCNs) was utilized in the expriments. The results highlighted a nonhost resistant response of soybean. Transcriptome analysis indicated that the number of differentially expressed genes (DEGs) in the resistant interaction (3746) was much larger than that in the susceptible interaction (602). A great number of genes acting as intrinsic component of membrane, integral component of membrane, cell periphery and plasma membrance were remarkably enriched only in the resistant interaction, while the taurine and hypotaurine, phenylpropanoid pathway, plant-pathogen interaction and transcript factors were modulated in both interactions. This is the first study to examine genes expression patterns in a soybean genotype in response to invasion by a virulent and avirulent SCN population at the transcriptional level, which will provide insights into the complicate molecular mechanism of the nonhost resistant interaction.
Collapse
Affiliation(s)
- Wenwen Song
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Nawei Qi
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Chen Liang
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Fangmeng Duan
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Honghai Zhao
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| |
Collapse
|
35
|
Transcriptional profiling of wheat (Triticum aestivum L.) during a compatible interaction with the cereal cyst nematode Heterodera avenae. Sci Rep 2019; 9:2184. [PMID: 30778126 PMCID: PMC6379437 DOI: 10.1038/s41598-018-37824-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 10/26/2018] [Indexed: 12/27/2022] Open
Abstract
Cereal cyst nematode (CCN, Heterodera avenae) presents severe challenges to wheat (Triticum aestivum L.) production worldwide. An investigation of the interaction between wheat and CCN can greatly improve our understanding of how nematodes alter wheat root metabolic pathways for their development and could contribute to new control strategies against CCN. In this study, we conducted transcriptome analyses of wheat cv. Wen 19 (Wen19) by using RNA-Seq during the compatible interaction with CCN at 1, 3 and 8 days past inoculation (dpi). In total, 71,569 transcripts were identified, and 10,929 of them were examined as differentially expressed genes (DEGs) in response to CCN infection. Based on the functional annotation and orthologous findings, the protein phosphorylation, oxidation-reduction process, regulation of transcription, metabolic process, transport, and response process as well as many other pathways previously reported were enriched at the transcriptional level. Plant cell wall hydrolysis and modifying proteins, auxin biosynthesis, signalling and transporter genes were up-regulated by CCN infection to facilitate penetration, migration and syncytium establishment. Genes responding to wounding and jasmonic acid stimuli were enriched at 1 dpi. We found 16 NBS-LRR genes, 12 of which were down-regulated, indicating the repression of resistance. The expression of genes encoding antioxidant enzymes, glutathione S-transferases and UDP-glucosyltransferase was significantly up-regulated during CCN infection, indicating that they may play key roles in the compatible interaction of wheat with CCN. Taken together, the results obtained from the transcriptome analyses indicate that the genes involved in oxidation-reduction processes, induction and suppression of resistance, metabolism, transport and syncytium establishment may be involved in the compatible interaction of Wen 19 with CCN. This study provides new insights into the responses of wheat to CCN infection. These insights could facilitate the elucidation of the potential mechanisms of wheat responses to CCN.
Collapse
|
36
|
Guo W, Zhang F, Bao A, You Q, Li Z, Chen J, Cheng Y, Zhao W, Shen X, Zhou X, Jiao Y. The soybean Rhg1 amino acid transporter gene alters glutamate homeostasis and jasmonic acid-induced resistance to soybean cyst nematode. MOLECULAR PLANT PATHOLOGY 2019; 20:270-286. [PMID: 30264924 PMCID: PMC6637870 DOI: 10.1111/mpp.12753] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Rhg1 (resistance to Heterodera glycines 1) is an important locus that contributes to resistance against soybean cyst nematode (SCN; Heterodera glycines Ichinohe), which is the most economically damaging disease of soybean worldwide. Simultaneous overexpression of three genes encoding a predicted amino acid transporter, an α-soluble N-ethylmaleimide-sensitive factor attachment protein (α-SNAP) and a predicted wound-induced protein resulted in resistance to SCN provided by this locus. However, the roles of two of these genes (excluding α-SNAP) remain unknown. Here, we report the functional characterization of Glyma.18G022400, a gene at the Rhg1 locus that encodes the predicted amino acid transporter Rhg1-GmAAT. Although the direct role of Rhg1-GmAAT in glutamate transport was not demonstrated, multiple lines of evidence showed that Rhg1-GmAAT impacts glutamic acid tolerance and glutamate transportation in soybean. Transcriptomic and metabolite profiling indicated that overexpression of Rhg1-GmAAT activated the jasmonic acid (JA) pathway. Treatment with a JA biosynthesis inhibitor reduced the resistance provided by the Rhg1-containing PI88788 to SCN, which suggested that the JA pathway might play a role in Rhg1-mediated resistance to SCN. Our results could be helpful for the clarification of the mechanism of resistance to SCN provided by Rhg1 in soybean.
Collapse
Affiliation(s)
- Wei Guo
- Key Laboratory of Oil Crop Biology of the Ministry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanHubei430062China
| | - Feng Zhang
- Key Laboratory of Oil Crop Biology of the Ministry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanHubei430062China
| | - Aili Bao
- Key Laboratory of Oil Crop Biology of the Ministry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanHubei430062China
| | - Qingbo You
- Key Laboratory of Oil Crop Biology of the Ministry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanHubei430062China
| | - Zeyu Li
- Daqing Branch of Heilongjiang Academy of Agricultural SciencesDaqingHeilongjiang163316China
| | - Jingsheng Chen
- Daqing Branch of Heilongjiang Academy of Agricultural SciencesDaqingHeilongjiang163316China
| | - Yihui Cheng
- Key Laboratory of Oil Crop Biology of the Ministry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanHubei430062China
| | - Wei Zhao
- Key Laboratory of Oil Crop Biology of the Ministry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanHubei430062China
| | - Xinjie Shen
- Key Laboratory of Oil Crop Biology of the Ministry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanHubei430062China
| | - Xinan Zhou
- Key Laboratory of Oil Crop Biology of the Ministry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanHubei430062China
| | - Yongqing Jiao
- Key Laboratory of Oil Crop Biology of the Ministry of AgricultureOil Crops Research Institute of the Chinese Academy of Agricultural SciencesWuhanHubei430062China
- Collaborative Innovation Center of Henan Grain Crops, College of AgronomyHenan Agricultural UniversityZhengzhouHenan450002China
| |
Collapse
|
37
|
Ali MA, Anjam MS, Nawaz MA, Lam HM, Chung G. Signal Transduction in Plant⁻Nematode Interactions. Int J Mol Sci 2018; 19:ijms19061648. [PMID: 29865232 PMCID: PMC6032140 DOI: 10.3390/ijms19061648] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 05/26/2018] [Accepted: 05/29/2018] [Indexed: 12/26/2022] Open
Abstract
To successfully invade and infect their host plants, plant parasitic nematodes (PPNs) need to evolve molecular mechanisms to overcome the defense responses from the plants. Nematode-associated molecular patterns (NAMPs), including ascarosides and certain proteins, while instrumental in enabling the infection, can be perceived by the host plants, which then initiate a signaling cascade leading to the induction of basal defense responses. To combat host resistance, some nematodes can inject effectors into the cells of susceptible hosts to reprogram the basal resistance signaling and also modulate the hosts’ gene expression patterns to facilitate the establishment of nematode feeding sites (NFSs). In this review, we summarized all the known signaling pathways involved in plant–nematode interactions. Specifically, we placed particular focus on the effector proteins from PPNs that mimic the signaling of the defense responses in host plants. Furthermore, we gave an updated overview of the regulation by PPNs of different host defense pathways such as salicylic acid (SA)/jasmonic acid (JA), auxin, and cytokinin and reactive oxygen species (ROS) signaling to facilitate their parasitic successes in plants. This review will enhance the understanding of the molecular signaling pathways involved in both compatible and incompatible plant–nematode interactions.
Collapse
Affiliation(s)
- Muhammad Amjad Ali
- Department of Plant Pathology, University of Agriculture, Faisalabad 38040, Pakistan.
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad 38040, Pakistan.
| | - Muhammad Shahzad Anjam
- Institute of Molecular Biology & Biotechnology, Bahauddin Zakariya University, Multan 66000, Pakistan.
| | | | - Hon-Ming Lam
- School of Life Sciences and Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu 59626, Korea.
| |
Collapse
|
38
|
Kofsky J, Zhang H, Song BH. The Untapped Genetic Reservoir: The Past, Current, and Future Applications of the Wild Soybean ( Glycine soja). FRONTIERS IN PLANT SCIENCE 2018; 9:949. [PMID: 30038633 PMCID: PMC6046548 DOI: 10.3389/fpls.2018.00949] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/12/2018] [Indexed: 05/20/2023]
Abstract
There is a considerable demand for crop improvement, especially considering the increasing growth of world population, continuing climatic fluctuations, and rapidly evolving plant pests and pathogens. Crop wild relatives hold great potential in providing beneficial alleles for crop improvement. Wild soybean, Glycine soja (Siebold & Zucc.), the wild ancestor to the domesticated soybean (Glycine max (L.) Merr.), harbors a high level of genetic variation. Research on G. soja has been largely devoted to understanding the domestication history of the soybean, while little effort has been made to explore its genetic diversity for crop improvement. High genomic diversity and expanded traits make G. soja populations an excellent source for soybean improvement. This review summarizes recent successful research examples of applying wild soybeans in dissecting the genetic basis of various traits, with a focus on abiotic/biotic stress tolerance and resistance. We also discuss the limitations of using G. soja. Perspective future research is proposed, including the application of advanced biotechnology and emerging genomic data to further utilize the wild soybean to counterbalance the rising demand for superior crops. We proposed there is an urgent need for international collaboration on germplasm collection, resource sharing, and conservation. We hope to use the wild soybean as an example to promote the exploration and use of wild resources for crop improvement in order to meet future food requirements.
Collapse
|