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Hasan MS, Lin CJ, Marhavy P, Kyndt T, Siddique S. Redox signalling in plant-nematode interactions: Insights into molecular crosstalk and defense mechanisms. PLANT, CELL & ENVIRONMENT 2024; 47:2811-2820. [PMID: 38679939 DOI: 10.1111/pce.14925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 04/04/2024] [Accepted: 04/12/2024] [Indexed: 05/01/2024]
Abstract
Plant-parasitic nematodes, specifically cyst nematodes (CNs) and root-knot nematodes (RKNs), pose significant threats to global agriculture, leading to substantial crop losses. Both CNs and RKNs induce permanent feeding sites in the root of their host plants, which then serve as their only source of nutrients throughout their lifecycle. Plants deploy reactive oxygen species (ROS) as a primary defense mechanism against nematode invasion. Notably, both CNs and RKNs have evolved sophisticated strategies to manipulate the host's redox environment to their advantage, with each employing distinct tactics to combat ROS. In this review, we have focused on the role of ROS and its scavenging network in interactions between host plants and CNs and RKNs. Overall, this review emphasizes the complex interplay between plant defense mechanism, redox signalling and nematode survival tactics, suggesting potential avenues for developing innovative nematode management strategies in agriculture.
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Affiliation(s)
- M Shamim Hasan
- Rheinische Friedrich-Wilhelms-University of Bonn, INRES-Molecular Phytomedicine, Bonn, Germany
| | - Ching-Jung Lin
- Department of Plant Pathology, University of California, Davis, California, USA
| | - Peter Marhavy
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre (UPSC), Swedish University of Agricultural Sciences (SLU), Umeå, Sweden
| | - Tina Kyndt
- Department Biotechnology, Research Group Epigenetics & Defence, Gent, Belgium
| | - Shahid Siddique
- Department of Entomology and Nematology, University of California, Davis, Davis, California, USA
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2
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Acharya S, Troell HA, Billingsley RL, Lawrence KS, McKirgan DS, Alkharouf NW, Klink VP. Glycine max polygalacturonase inhibiting protein 11 (GmPGIP11) functions in the root to suppress Heterodera glycines parasitism. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 213:108755. [PMID: 38875777 DOI: 10.1016/j.plaphy.2024.108755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/17/2024] [Accepted: 05/19/2024] [Indexed: 06/16/2024]
Abstract
Pathogen-secreted polygalacturonases (PGs) alter plant cell wall structure by cleaving the α-(1 → 4) linkages between D-galacturonic acid residues in homogalacturonan (HG), macerating the cell wall, facilitating infection. Plant PG inhibiting proteins (PGIPs) disengage pathogen PGs, impairing infection. The soybean cyst nematode, Heterodera glycines, obligate root parasite produces secretions, generating a multinucleate nurse cell called a syncytium, a byproduct of the merged cytoplasm of 200-250 root cells, occurring through cell wall maceration. The common cytoplasmic pool, surrounded by an intact plasma membrane, provides a source from which H. glycines derives nourishment but without killing the parasitized cell during a susceptible reaction. The syncytium is also the site of a naturally-occurring defense response that happens in specific G. max genotypes. Transcriptomic analyses of RNA isolated from the syncytium undergoing the process of defense have identified that one of the 11 G. max PGIPs, GmPGIP11, is expressed during defense. Functional transgenic analyses show roots undergoing GmPGIP11 overexpression (OE) experience an increase in its relative transcript abundance (RTA) as compared to the ribosomal protein 21 (GmRPS21) control, leading to a decrease in H. glycines parasitism as compared to the overexpression control. The GmPGIP11 undergoing RNAi experiences a decrease in its RTA as compared to the GmRPS21 control with transgenic roots experiencing an increase in H. glycines parasitism as compared to the RNAi control. Pathogen associated molecular pattern (PAMP) triggered immunity (PTI) and effector triggered immunity (ETI) components are shown to influence GmPGIP11 expression while numerous agricultural crops are shown to have homologs.
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Affiliation(s)
- Sudha Acharya
- Department of Computer and Information Sciences, Towson University, Towson, MD, 21252, USA; USDA-ARS-NEA-BARC Molecular Plant Pathology Laboratory, Building 004, Room 122, BARC-West, 10300 Baltimore Ave., Beltsville, MD, 20705, USA
| | - Hallie A Troell
- Department of Biological Sciences, Mississippi State University, MS, 39762, USA
| | - Rebecca L Billingsley
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, MS, 39762, USA
| | - Kathy S Lawrence
- Department of Entomology and Plant Pathology, Auburn University, 209 Life Science Building, Auburn, AL, 36849, USA
| | - Daniel S McKirgan
- Department of Computer and Information Sciences, Towson University, Towson, MD, 21252, USA
| | - Nadim W Alkharouf
- Department of Computer and Information Sciences, Towson University, Towson, MD, 21252, USA
| | - Vincent P Klink
- USDA-ARS-NEA-BARC Molecular Plant Pathology Laboratory, Building 004, Room 122, BARC-West, 10300 Baltimore Ave., Beltsville, MD, 20705, USA.
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3
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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.
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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;
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Bisht A, Saini DK, Kaur B, Batra R, Kaur S, Kaur I, Jindal S, Malik P, Sandhu PK, Kaur A, Gill BS, Wani SH, Kaur B, Mir RR, Sandhu KS, Siddique KHM. Multi-omics assisted breeding for biotic stress resistance in soybean. Mol Biol Rep 2023; 50:3787-3814. [PMID: 36692674 DOI: 10.1007/s11033-023-08260-4] [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] [Received: 09/01/2022] [Accepted: 01/09/2023] [Indexed: 01/25/2023]
Abstract
Biotic stress is a critical factor limiting soybean growth and development. Soybean responses to biotic stresses such as insects, nematodes, fungal, bacterial, and viral pathogens are governed by complex regulatory and defense mechanisms. Next-generation sequencing has availed research techniques and strategies in genomics and post-genomics. This review summarizes the available information on marker resources, quantitative trait loci, and marker-trait associations involved in regulating biotic stress responses in soybean. We discuss the differential expression of related genes and proteins reported in different transcriptomics and proteomics studies and the role of signaling pathways and metabolites reported in metabolomic studies. Recent advances in omics technologies offer opportunities to reshape and improve biotic stress resistance in soybean by altering gene regulation and/or other regulatory networks. We suggest using 'integrated omics' to precisely understand how soybean responds to different biotic stresses. We also discuss the potential challenges of integrating multi-omics for the functional analysis of genes and their regulatory networks and the development of biotic stress-resistant cultivars. This review will help direct soybean breeding programs to develop resistance against different biotic stresses.
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Affiliation(s)
- Ashita Bisht
- Department of Plant Breeding and Genetics, Punjab Agricultural University, 141004, Ludhiana, India
- CSK Himachal Pradesh Krishi Vishvavidyalaya, Highland Agricultural Research and Extension Centre, 175142, Kukumseri, Lahaul and Spiti, India
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, 141004, Ludhiana, India.
| | - Baljeet Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, 141004, Ludhiana, India
| | - Ritu Batra
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, 25004, Meerut, India
| | - Sandeep Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, 141004, Ludhiana, India
| | - Ishveen Kaur
- Agriculture, Environmental and Sustainability Sciences, College of sciences, University of Texas Rio Grande Valley, 78539, Edinburg, TX, USA
| | - Suruchi Jindal
- Division of Molecular Biology and Genetic Engineering, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, India
| | - Palvi Malik
- , Gurdev Singh Khush Institute of Genetics, Plant Breeding and Biotechnology, Punjab Agricultural University,, 141004, Ludhiana, India
| | - Pawanjit Kaur Sandhu
- Department of Chemistry, University of British Columbia, V1V 1V7, Okanagan, Kelowna, Canada
| | - Amandeep Kaur
- Division of Molecular Biology and Genetic Engineering, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, India
| | - Balwinder Singh Gill
- Department of Plant Breeding and Genetics, Punjab Agricultural University, 141004, Ludhiana, India
| | - Shabir Hussain Wani
- MRCFC Khudwani, Sher-e-Kashmir University of Agricultural Sciences and Technology, Kashmir, Shalimar, India
| | - Balwinder Kaur
- Department of Entomology, UF/IFAS Research and Education Center, 33430, Belle Glade, Florida, USA
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture, SKUAST-Kashmir, 193201, India
| | - Karansher Singh Sandhu
- Department of Crop and Soil Sciences, Washington State University, 99163, Pullman, WA, USA.
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, 6001, Perth, WA, Australia.
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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.
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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
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Shi X, Chen Q, Liu S, Wang J, Peng D, Kong L. Combining targeted metabolite analyses and transcriptomics to reveal the specific chemical composition and associated genes in the incompatible soybean variety PI437654 infected with soybean cyst nematode HG1.2.3.5.7. BMC PLANT BIOLOGY 2021; 21:217. [PMID: 33990182 PMCID: PMC8120846 DOI: 10.1186/s12870-021-02998-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 04/30/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Soybean cyst nematode, Heterodera glycines, is one of the most devastating pathogens of soybean and causes severe annual yield losses worldwide. Different soybean varieties exhibit different responses to H. glycines infection at various levels, such as the genomic, transcriptional, proteomic and metabolomic levels. However, there have not yet been any reports of the differential responses of incompatible and compatible soybean varieties infected with H. glycines based on combined metabolomic and transcriptomic analyses. RESULTS In this study, the incompatible soybean variety PI437654 and three compatible soybean varieties, Williams 82, Zhonghuang 13 and Hefeng 47, were used to clarify the differences in metabolites and transcriptomics before and after the infection with HG1.2.3.5.7. A local metabolite-calibrated database was used to identify potentially differential metabolites, and the differences in metabolites and metabolic pathways were compared between the incompatible and compatible soybean varieties after inoculation with HG1.2.3.5.7. In total, 37 differential metabolites and 20 KEGG metabolic pathways were identified, which were divided into three categories: metabolites/pathways overlapped in the incompatible and compatible soybeans, and metabolites/pathways specific to either the incompatible or compatible soybean varieties. Twelve differential metabolites were found to be involved in predicted KEGG metabolite pathways. Moreover, 14 specific differential metabolites (such as significantly up-regulated nicotine and down-regulated D-aspartic acid) and their associated KEGG pathways (such as the tropane, piperidine and pyridine alkaloid biosynthesis, alanine, aspartate and glutamate metabolism, sphingolipid metabolism and arginine biosynthesis) were significantly altered and abundantly enriched in the incompatible soybean variety PI437654, and likely played pivotal roles in defending against HG1.2.3.5.7 infection. Three key metabolites (N-acetyltranexamic acid, nicotine and D,L-tryptophan) found to be significantly up-regulated in the incompatible soybean variety PI437654 infected by HG1.2.3.5.7 were classified into two types and used for combined analyses with the transcriptomic expression profiling. Associated genes were predicted, along with the likely corresponding biological processes, cellular components, molecular functions and pathways. CONCLUSIONS Our results not only identified potential novel metabolites and associated genes involved in the incompatible response of PI437654 to soybean cyst nematode HG1.2.3.5.7, but also provided new insights into the interactions between soybeans and soybean cyst nematodes.
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Affiliation(s)
- Xue Shi
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qiansi Chen
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, Henan, China
| | - Shiming Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jiajun Wang
- Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Lingan Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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7
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Kang WS, Chen LJ, Wang YY, Zhu XF, Liu XY, Fan HY, Duan YX. Bacillus simplex treatment promotes soybean defence against soybean cyst nematodes: A metabolomics study using GC-MS. PLoS One 2020; 15:e0237194. [PMID: 32760135 PMCID: PMC7410315 DOI: 10.1371/journal.pone.0237194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/21/2020] [Indexed: 11/19/2022] Open
Abstract
We aimed to profile the metabolism of soybean roots that were infected with soybean cyst nematodes and treated with Bacillus simplex to identify metabolic differences that may explain nematode resistance. Compared with control soybean roots, B. simplex-treated soybean roots contained lower levels of glucose, fructose, sucrose, and trehalose, which reduced the nematodes' food source. Furthermore, treatment with B. simplex led to higher levels of melibiose, gluconic acid, lactic acid, phytosphingosine, and noradrenaline in soybean roots, which promoted nematocidal activity. The levels of oxoproline, maltose, and galactose were lowered after B. simplex treatment, which improved disease resistance. Collectively, this study provides insight into the metabolic alterations induced by B. simplex treatment, which affects the interactions with soybean cyst nematodes.
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Affiliation(s)
- Wen-shu Kang
- College of Environment, Shenyang University, Shenyang, China
| | - Li-jie Chen
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Yuan-yuan Wang
- College of Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Xiao-feng Zhu
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Xiao-yu Liu
- College of Sciences, Shenyang Agricultural University, Shenyang, China
| | - Hai-yan Fan
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Yu-xi Duan
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
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8
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Rahman MS, Linsell KJ, Taylor JD, Hayden MJ, Collins NC, Oldach KH. Fine mapping of root lesion nematode (Pratylenchus thornei) resistance loci on chromosomes 6D and 2B of wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:635-652. [PMID: 31813000 DOI: 10.1007/s00122-019-03495-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 11/26/2019] [Indexed: 05/22/2023]
Abstract
Resistance QTL to root lesion nematode (Pratylenchus thornei) in wheat (Triticum aestivum), QRlnt.sk-6D and QRlnt.sk-2B, were mapped to intervals of 3.5 cM/1.77 Mbp on chromosome 6D and 1.4 cM/2.19 Mbp on chromosome 2B, respectively. Candidate resistance genes were identified in the QTL regions and molecular markers developed for marker-assisted breeding. Two previously known resistance QTL for root lesion nematode (Pratylenchus thornei) in bread wheat (Triticum aestivum), QRlnt.sk-6D and QRlnt.sk-2B, were fine-mapped using a Sokoll (moderately resistant) by Krichauff (susceptible) doubled haploid (DH) population and six newly developed recombinant inbred line populations. Bulked segregation analysis with the 90K wheat SNP array identified linked SNPs which were subsequently converted to KASP assays for mapping in the DH and RIL populations. On chromosome 6D, 60 KASP and five SSR markers spanned a total genetic distance of 23.7 cM. QRlnt.sk-6D was delimited to a 3.5 cM interval, representing 1.77 Mbp in the bread wheat cv. Chinese Spring reference genome sequence and 2.29 Mbp in the Aegilops tauschii genome sequence. These intervals contained 42 and 43 gene models in the respective annotated genome sequences. On chromosome 2B, 41 KASP and 5 SSR markers produced a map spanning 19.9 cM. QRlnt.sk-2B was delimited to 1.4 cM, corresponding 3.14 Mbp in the durum wheat cv. Svevo reference sequence and 2.19 Mbp in Chinese Spring. The interval in Chinese Spring contained 56 high-confidence gene models. Intervals for both QTL contained genes with similarity to those previously reported to be involved in disease resistance, namely genes for phenylpropanoid biosynthetic pathway-related enzymes, NBS-LRR proteins and protein kinases. The potential roles of these candidate genes in P. thornei resistance are discussed. The KASP markers reported in this study could potentially be used for marker-assisted breeding of P. thornei-resistant wheat cultivars.
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Affiliation(s)
- Muhammad Shefatur Rahman
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA, 5064, Australia
- South Australian Research and Development Institute, Glen Osmond, SA, 5064, Australia
| | - Katherine J Linsell
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA, 5064, Australia
- South Australian Research and Development Institute, Glen Osmond, SA, 5064, Australia
| | - Julian D Taylor
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Matthew J Hayden
- Department of Primary Industries, Victorian AgriBiosciences Centre, Bundoora, VIC, 3083, Australia
| | - Nicholas C Collins
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Klaus H Oldach
- School of Agriculture, Food and Wine, The University of Adelaide, Glen Osmond, SA, 5064, Australia.
- South Australian Research and Development Institute, Glen Osmond, SA, 5064, Australia.
- KWS Lochow GmbH, Ferdinand-von-Lochow-Str. 5, 29303, Bergen, Germany.
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9
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Kumar P, Khanal S, Da Silva M, Singh R, Davis RF, Nichols RL, Chee PW. Transcriptome analysis of a nematode resistant and susceptible upland cotton line at two critical stages of Meloidogyne incognita infection and development. PLoS One 2019; 14:e0221328. [PMID: 31504059 PMCID: PMC6736245 DOI: 10.1371/journal.pone.0221328] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 08/06/2019] [Indexed: 11/18/2022] Open
Abstract
Host plant resistance is the most practical approach to control the Southern root-knot nematode (Meloidogyne incognita; RKN), which has emerged as one of the most serious economic pests of Upland cotton (Gossypium hirsutum L.). Previous QTL analyses have identified a resistance locus on chromosome 11 (qMi-C11) affecting galling and another locus on chromosome-14 (qMi-C14) affecting egg production. Although these two QTL regions were fine mapped and candidate genes identified, expression profiling of genes would assist in further narrowing the list of candidate genes in the QTL regions. We applied the comparative transcriptomic approach to compare expression profiles of genes between RKN susceptible and resistance genotypes at an early stage of RKN development that coincides with the establishment of a feeding site and at the late stage of RKN development that coincides with RKN egg production. Sequencing of cDNA libraries produced over 315 million reads of which 240 million reads (76%) were mapped on to the Gossypium hirsutum genome. A total of 3,789 differentially expressed genes (DEGs) were identified which were further grouped into four clusters based on their expression profiles. A large number of DEGs were found to be down regulated in the susceptible genotype at the late stage of RKN development whereas several genes were up regulated in the resistant genotype. Key enriched categories included transcription factor activity, defense response, response to phyto-hormones, cell wall organization, and protein serine/threonine kinase activity. Our results also show that the DEGs in the resistant genotype at qMi-C11 and qMi-C14 loci displayed higher expression of defense response, detoxification and callose deposition genes, than the DEGs in the susceptible genotype.
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Affiliation(s)
- Pawan Kumar
- Dept. of Crop and Soil Sciences and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, United States of America
| | - Sameer Khanal
- Dept. of Crop and Soil Sciences and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, United States of America
| | - Mychele Da Silva
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States of America
| | - Rippy Singh
- Dept. of Crop and Soil Sciences and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, United States of America
| | - Richard F. Davis
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States of America
- USDA-ARS, Crop Protection and Management Research Unit, Tifton, GA, United States of America
- * E-mail: (RFD);(PWC)
| | | | - Peng W. Chee
- Dept. of Crop and Soil Sciences and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, United States of America
- * E-mail: (RFD);(PWC)
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10
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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.
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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
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11
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Li S, Musungu B, Lightfoot D, Ji P. The Interactomic Analysis Reveals Pathogenic Protein Networks in Phomopsis longicolla Underlying Seed Decay of Soybean. Front Genet 2018; 9:104. [PMID: 29666630 PMCID: PMC5891612 DOI: 10.3389/fgene.2018.00104] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 03/15/2018] [Indexed: 12/31/2022] Open
Abstract
Phomopsis longicolla T. W. Hobbs (syn. Diaporthe longicolla) is the primary cause of Phomopsis seed decay (PSD) in soybean, Glycine max (L.) Merrill. This disease results in poor seed quality and is one of the most economically important seed diseases in soybean. The objectives of this study were to infer protein-protein interactions (PPI) and to identify conserved global networks and pathogenicity subnetworks in P. longicolla including orthologous pathways for cell signaling and pathogenesis. The interlog method used in the study identified 215,255 unique PPIs among 3,868 proteins. There were 1,414 pathogenicity related genes in P. longicolla identified using the pathogen host interaction (PHI) database. Additionally, 149 plant cell wall degrading enzymes (PCWDE) were detected. The network captured five different classes of carbohydrate degrading enzymes, including the auxiliary activities, carbohydrate esterases, glycoside hydrolases, glycosyl transferases, and carbohydrate binding molecules. From the PPI analysis, novel interacting partners were determined for each of the PCWDE classes. The most predominant class of PCWDE was a group of 60 glycoside hydrolases proteins. The glycoside hydrolase subnetwork was found to be interacting with 1,442 proteins within the network and was among the largest clusters. The orthologous proteins FUS3, HOG, CYP1, SGE1, and the g5566t.1 gene identified in this study could play an important role in pathogenicity. Therefore, the P. longicolla protein interactome (PiPhom) generated in this study can lead to a better understanding of PPIs in soybean pathogens. Furthermore, the PPI may aid in targeting of genes and proteins for further studies of the pathogenicity mechanisms.
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Affiliation(s)
- Shuxian Li
- Crop Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Stoneville, MS, United States
| | - Bryan Musungu
- Department of Plant Biology, Southern Illinois University, Carbondale, IL, United States
| | - David Lightfoot
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL, United States
| | - Pingsheng Ji
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
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12
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Bohn MO, Marroquin JJ, Flint-Garcia S, Dashiell K, Willmot DB, Hibbard BE. Quantitative Trait Loci Mapping of Western Corn Rootworm (Coleoptera: Chrysomelidae) Host Plant Resistance in Two Populations of Doubled Haploid Lines in Maize (Zea mays L.). JOURNAL OF ECONOMIC ENTOMOLOGY 2018; 111:435-444. [PMID: 29228374 DOI: 10.1093/jee/tox310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Over the last 70 yr, more than 12,000 maize accessions have been screened for their level of resistance to western corn rootworm, Diabrotica virgifera virgifera (LeConte; Coleoptera: Chrysomelidae), larval feeding. Less than 1% of this germplasm was selected for initiating recurrent selection or other breeding programs. Selected genotypes were mostly characterized by large root systems and superior root regrowth after root damage caused by western corn rootworm larvae. However, no hybrids claiming native (i.e., host plant) resistance to western corn rootworm larval feeding are currently commercially available. We investigated the genetic basis of western corn rootworm resistance in maize materials with improved levels of resistance using linkage disequilibrium mapping approaches. Two populations of topcrossed doubled haploid maize lines (DHLs) derived from crosses between resistant and susceptible maize lines were evaluated for their level of resistance in three to four different environments. For each DHL topcross an average root damage score was estimated and used for quantitative trait loci (QTL) analysis. We found genomic regions contributing to western corn rootworm resistance on all maize chromosomes, except for chromosome 4. Models fitting all QTL simultaneously explained about 30 to 50% of the genotypic variance for root damage scores in both mapping populations. Our findings confirm the complex genetic structure of host plant resistance against western corn rootworm larval feeding in maize. Interestingly, three of these QTL regions also carry genes involved in ascorbate biosynthesis, a key compound we hypothesize is involved in the expression of western corn rootworm resistance.
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Affiliation(s)
- Martin O Bohn
- Department of Crop Sciences, University of Illinois, Urbana, IL
| | | | - Sherry Flint-Garcia
- United States Department of Agriculture-Agricultural Research Service Plant Genetics Research Unit, Columbia, MO
| | - Kenton Dashiell
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | | | - Bruce E Hibbard
- United States Department of Agriculture-Agricultural Research Service Plant Genetics Research Unit, Columbia, MO
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13
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Sallam AH, Tyagi P, Brown-Guedira G, Muehlbauer GJ, Hulse A, Steffenson BJ. Genome-Wide Association Mapping of Stem Rust Resistance in Hordeum vulgare subsp. spontaneum. G3 (BETHESDA, MD.) 2017; 7:3491-3507. [PMID: 28855281 PMCID: PMC5633397 DOI: 10.1534/g3.117.300222] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 08/24/2017] [Indexed: 01/06/2023]
Abstract
Stem rust was one of the most devastating diseases of barley in North America. Through the deployment of cultivars with the resistance gene Rpg1, losses to stem rust have been minimal over the past 70 yr. However, there exist both domestic (QCCJB) and foreign (TTKSK aka isolate Ug99) pathotypes with virulence for this important gene. To identify new sources of stem rust resistance for barley, we evaluated the Wild Barley Diversity Collection (WBDC) (314 ecogeographically diverse accessions of Hordeum vulgare subsp. spontaneum) for seedling resistance to four pathotypes (TTKSK, QCCJB, MCCFC, and HKHJC) of the wheat stem rust pathogen (Puccinia graminis f. sp. tritici, Pgt) and one isolate (92-MN-90) of the rye stem rust pathogen (P. graminis f. sp. secalis, Pgs). Based on a coefficient of infection, the frequency of resistance in the WBDC was low ranging from 0.6% with HKHJC to 19.4% with 92-MN-90. None of the accessions was resistant to all five cultures of P. graminis A genome-wide association study (GWAS) was conducted to map stem rust resistance loci using 50,842 single-nucleotide polymorphic markers generated by genotype-by-sequencing and ordered using the new barley reference genome assembly. After proper accounting for genetic relatedness and structure among accessions, 45 quantitative trait loci were identified for resistance to P. graminis across all seven barley chromosomes. Three novel loci associated with resistance to TTKSK, QCCJB, MCCFC, and 92-MN-90 were identified on chromosomes 5H and 7H, and two novel loci associated with resistance to HKHJC were identified on chromosomes 1H and 3H. These novel alleles will enhance the diversity of resistance available for cultivated barley.
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Affiliation(s)
- Ahmad H Sallam
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
| | - Priyanka Tyagi
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, North Carolina 27695
| | - Gina Brown-Guedira
- United States Department of Agriculture-Agricultural Research Service, Raleigh, North Carolina 27695
| | - Gary J Muehlbauer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Alex Hulse
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
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14
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Ali MA, Azeem F, Li H, Bohlmann H. Smart Parasitic Nematodes Use Multifaceted Strategies to Parasitize Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:1699. [PMID: 29046680 PMCID: PMC5632807 DOI: 10.3389/fpls.2017.01699] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Accepted: 09/15/2017] [Indexed: 05/03/2023]
Abstract
Nematodes are omnipresent in nature including many species which are parasitic to plants and cause enormous economic losses in various crops. During the process of parasitism, sedentary phytonematodes use their stylet to secrete effector proteins into the plant cells to induce the development of specialized feeding structures. These effectors are used by the nematodes to develop compatible interactions with plants, partly by mimicking the expression of host genes. Intensive research is going on to investigate the molecular function of these effector proteins in the plants. In this review, we have summarized which physiological and molecular changes occur when endoparasitic nematodes invade the plant roots and how they develop a successful interaction with plants using the effector proteins. We have also mentioned the host genes which are induced by the nematodes for a compatible interaction. Additionally, we discuss how nematodes modulate the reactive oxygen species (ROS) and RNA silencing pathways in addition to post-translational modifications in their own favor for successful parasitism in plants.
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Affiliation(s)
- Muhammad A. Ali
- Department of Plant Pathology, University of Agriculture Faisalabad, Faisalabad, Pakistan
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture Faisalabad, Faisalabad, Pakistan
- *Correspondence: Muhammad A. Ali ;
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Hongjie Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Holger Bohlmann
- Division of Plant Protection, Department of Crop Sciences, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
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15
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Iqbal MJ, Majeed M, Humayun M, Lightfoot DA, Afzal AJ. Proteomic Profiling and the Predicted Interactome of Host Proteins in Compatible and Incompatible Interactions Between Soybean and Fusarium virguliforme. Appl Biochem Biotechnol 2016; 180:1657-1674. [PMID: 27491306 DOI: 10.1007/s12010-016-2194-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 07/13/2016] [Indexed: 12/27/2022]
Abstract
Sudden death syndrome (SDS) is a complex of two diseases of soybean (Glycine max), caused by the soil borne pathogenic fungus Fusarium virguliforme. The root rot and leaf scorch diseases both result in significant yield losses worldwide. Partial SDS resistance has been demonstrated in multiple soybean cultivars. This study aimed to highlight proteomic changes in soybean roots by identifying proteins which are differentially expressed in near isogenic lines (NILs) contrasting at the Rhg1/Rfs2 locus for partial resistance or susceptibility to SDS. Two-dimensional gel electrophoresis resolved approximately 1000 spots on each gel; 12 spots with a significant (P < 0.05) difference in abundance of 1.5-fold or more were picked, trypsin-digested, and analyzed using quadruple time-of-flight tandem mass spectrometry. Several spots contained more than one protein, so that 18 distinct proteins were identified overall. A functional analysis performed to categorize the proteins depicted that the major pathways altered by fungal infection include disease resistance, stress tolerance, and metabolism. This is the first report which identifies proteins whose abundances are altered in response to fungal infection leading to SDS. The results provide valuable information about SDS resistance in soybean plants, and plant partial resistance responses in general. More importantly, several of the identified proteins could be good candidates for the development of SDS-resistant soybean plants.
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Affiliation(s)
- M Javed Iqbal
- Department of Plant Sciences, University of California, Davis, California, 95616, USA
| | - Maryam Majeed
- Department of Biology, SBA School of Science and Engineering, Lahore University of Management Sciences, Lahore, 54792, Pakistan
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Maheen Humayun
- Department of Biology, SBA School of Science and Engineering, Lahore University of Management Sciences, Lahore, 54792, Pakistan
| | - David A Lightfoot
- Department of Molecular Biology, Microbiology, and Biochemistry, Genomics Core Facility and Center for Excellence in Soybean Research, Teaching, and Outreach, and Department of Plant Biology, Southern Illinois University, Carbondale, Illinois, 62901, USA
| | - Ahmed J Afzal
- Department of Biology, SBA School of Science and Engineering, Lahore University of Management Sciences, Lahore, 54792, Pakistan.
- Department of Molecular Biology, Microbiology, and Biochemistry, Genomics Core Facility and Center for Excellence in Soybean Research, Teaching, and Outreach, and Department of Plant Biology, Southern Illinois University, Carbondale, Illinois, 62901, USA.
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16
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Chang HX, Lipka AE, Domier LL, Hartman GL. Characterization of Disease Resistance Loci in the USDA Soybean Germplasm Collection Using Genome-Wide Association Studies. PHYTOPATHOLOGY 2016; 106:1139-1151. [PMID: 27135674 DOI: 10.1094/phyto-01-16-0042-fi] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Genetic resistance is a key strategy for disease management in soybean. Over the last 50 years, soybean germplasm has been phenotyped for resistance to many pathogens, resulting in the development of disease-resistant elite breeding lines and commercial cultivars. While biparental linkage mapping has been used to identify disease resistance loci, genome-wide association studies (GWAS) using high-density and high-quality markers such as single nucleotide polymorphisms (SNPs) has become a powerful tool to associate molecular markers and phenotypes. The objective of our study was to provide a comprehensive understanding of disease resistance in the United States Department of Agriculture Agricultural Research Service Soybean Germplasm Collection by using phenotypic data in the public Germplasm Resources Information Network and public SNP data (SoySNP50K). We identified SNPs significantly associated with disease ratings from one bacterial disease, five fungal diseases, two diseases caused by nematodes, and three viral diseases. We show that leucine-rich repeat (LRR) receptor-like kinases and nucleotide-binding site-LRR candidate resistance genes were enriched within the linkage disequilibrium regions of the significant SNPs. We review and present a global view of soybean resistance loci against multiple diseases and discuss the power and the challenges of using GWAS to discover disease resistance in soybean.
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Affiliation(s)
- Hao-Xun Chang
- All authors: Department of Crop Sciences, University of Illinois, Urbana, IL 61801; and third and fourth authors: USDA-Agricultural Research Services, Urbana
| | - Alexander E Lipka
- All authors: Department of Crop Sciences, University of Illinois, Urbana, IL 61801; and third and fourth authors: USDA-Agricultural Research Services, Urbana
| | - Leslie L Domier
- All authors: Department of Crop Sciences, University of Illinois, Urbana, IL 61801; and third and fourth authors: USDA-Agricultural Research Services, Urbana
| | - Glen L Hartman
- All authors: Department of Crop Sciences, University of Illinois, Urbana, IL 61801; and third and fourth authors: USDA-Agricultural Research Services, Urbana
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17
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Down-regulation of Arabidopsis DND1 orthologs in potato and tomato leads to broad-spectrum resistance to late blight and powdery mildew. Transgenic Res 2015; 25:123-38. [PMID: 26577903 PMCID: PMC4762934 DOI: 10.1007/s11248-015-9921-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 11/07/2015] [Indexed: 11/15/2022]
Abstract
Multiple susceptibility genes (S), identified in Arabidopsis, have been shown to be functionally conserved in crop plants. Mutations in these S genes result in resistance to different pathogens, opening a new way to achieve plant disease resistance. The aim of this study was to investigate the role of Defense No Death1 (DND1) in susceptibility of tomato and potato to late blight (Phytophthora infestans). In Arabidopsis, the dnd1 mutant has broad-spectrum resistance against several fungal, bacterial, and viral pathogens. However this mutation is also associated with a dwarfed phenotype. Using an RNAi approach, we silenced AtDND1 orthologs in potato and tomato. Our results showed that silencing of the DND1 ortholog in both crops resulted in resistance to the pathogenic oomycete P. infestans and to two powdery mildew species, Oidium neolycopersici and Golovinomyces orontii. The resistance to P. infestans in potato was effective to four different isolates although the level of resistance (complete or partial) was dependent on the aggressiveness of the isolate. In tomato, DND1-silenced plants showed a severe dwarf phenotype and autonecrosis, whereas DND1-silenced potato plants were not dwarfed and showed a less pronounced autonecrosis. Our results indicate that S gene function of DND1 is conserved in tomato and potato. We discuss the possibilities of using RNAi silencing or loss-of-function mutations of DND1 orthologs, as well as additional S gene orthologs from Arabidopsis, to breed for resistance to pathogens in crop plants.
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18
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Han Y, Zhao X, Cao G, Wang Y, Li Y, Liu D, Teng W, Zhang Z, Li D, Qiu L, Zheng H, Li W. Genetic characteristics of soybean resistance to HG type 0 and HG type 1.2.3.5.7 of the cyst nematode analyzed by genome-wide association mapping. BMC Genomics 2015; 16:598. [PMID: 26268218 PMCID: PMC4542112 DOI: 10.1186/s12864-015-1800-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 07/27/2015] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is one of the most fatal pests of soybean (Glycine max (L.) Merr.) worldwide and causes huge loss of soybean yield each year. Multiple sources of resistance are urgently needed for effective management of SCN via the development of resistant cultivars. The aim of the present study was to investigate the genetic architecture of resistance to SCN HG Type 0 (race 3) and HG Type 1.2.3.5.7 (race 4) in landraces and released elite soybean cultivars mostly from China. RESULTS A total of 440 diverse soybean landraces and elite cultivars were screened for resistance to SCN HG Type 0 and HG Type 1.2.3.5.7. Exactly 131 new sources of SCN resistance were identified. Lines were genotyped by SNP markers detected by the Specific Locus Amplified Fragment Sequencing (SLAF-seq) approach. A total of 36,976 SNPs were identified with minor allele frequencies (MAF) > 4% that were present in 97% of all the genotypes. Genome-wide association mapping showed that a total of 19 association signals were significantly related to the resistance for the two HG Types. Of the 19 association signals, eight signals overlapped with reported QTL including Rhg1 and Rhg4 genes. Another eight were located in the linked regions encompassing known QTL. Three QTL were found that were not previously reported. The average value of female index (FI) of soybean accessions with resistant alleles was significantly lower than those with susceptible alleles for each peak SNP. Disease resistance proteins with leucine rich regions, cytochrome P450s, protein kinases, zinc finger domain proteins, RING domain proteins, MYB and WRKY transcription activation families were identified. Such proteins may participate in the resistant reaction to SCN and were frequently found in the tightly linked genomic regions of the peak SNPs. CONCLUSIONS GWAS extended understanding of the genetic architecture of SCN resistance in multiple genetic backgrounds. Nineteen association signals were obtained for the resistance to the two Hg Types of SCN. The multiple beneficial alleles from resistant germplasm sources will be useful for the breeding of cultivars with improved resistance to SCN. Analysis of genes near association signals may facilitate the recognition of the causal gene(s) underlying SCN resistances.
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Affiliation(s)
- Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China.
| | - Xue Zhao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China.
| | - Guanglu Cao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China.
| | - Yan Wang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China.
| | - Yinghui Li
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
| | - Dongyuan Liu
- Bioinformatics Division, Biomarker Technologies Corporation, 101300, Beijing, China.
| | - Weili Teng
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China.
| | - Zhiwu Zhang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China.
| | - Dongmei Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China.
| | - Lijuan Qiu
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
| | - Hongkun Zheng
- Bioinformatics Division, Biomarker Technologies Corporation, 101300, Beijing, China.
| | - Wenbin Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030, China.
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19
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Villeth GRC, Carmo LST, Silva LP, Fontes W, Grynberg P, Saraiva M, Brasileiro ACM, Carneiro RMD, Oliveira JTA, Grossi-de-Sá MF, Mehta A. Cowpea-Meloidogyne incognita
interaction: Root proteomic analysis during early stages of nematode infection. Proteomics 2015; 15:1746-59. [DOI: 10.1002/pmic.201400561] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 02/13/2015] [Accepted: 02/26/2015] [Indexed: 11/08/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia; Brasília DF Brazil
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Fang X, Chen J, Dai L, Ma H, Zhang H, Yang J, Wang F, Yan C. Proteomic dissection of plant responses to various pathogens. Proteomics 2015; 15:1525-43. [DOI: 10.1002/pmic.201400384] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Revised: 11/28/2014] [Accepted: 01/12/2015] [Indexed: 01/15/2023]
Affiliation(s)
- Xianping Fang
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and Hunan Provincial Key Laboratory of Biology and Control of Plant Diseases and Insect Pests; Hunan Agricultural University; Changsha Hunan P. R. China
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control; Institute of Virology and Biotechnology; Zhejiang Academy of Agricultural Sciences; Hangzhou P. R. China
- Institute of Biology; Hangzhou Academy of Agricultural Sciences; Hangzhou P. R. China
| | - Jianping Chen
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and Hunan Provincial Key Laboratory of Biology and Control of Plant Diseases and Insect Pests; Hunan Agricultural University; Changsha Hunan P. R. China
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control; Institute of Virology and Biotechnology; Zhejiang Academy of Agricultural Sciences; Hangzhou P. R. China
| | - Liangying Dai
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization and Hunan Provincial Key Laboratory of Biology and Control of Plant Diseases and Insect Pests; Hunan Agricultural University; Changsha Hunan P. R. China
| | - Huasheng Ma
- Institute of Biology; Hangzhou Academy of Agricultural Sciences; Hangzhou P. R. China
| | - Hengmu Zhang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control; Institute of Virology and Biotechnology; Zhejiang Academy of Agricultural Sciences; Hangzhou P. R. China
| | - Jian Yang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control; Institute of Virology and Biotechnology; Zhejiang Academy of Agricultural Sciences; Hangzhou P. R. China
| | - Fang Wang
- Laboratory of Biotechnology; Institute of Biotechnology; Ningbo Academy of Agricultural Sciences; Ningbo P. R. China
| | - Chengqi Yan
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control; Institute of Virology and Biotechnology; Zhejiang Academy of Agricultural Sciences; Hangzhou P. R. China
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21
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Hosseini P, Matthews BF. Regulatory interplay between soybean root and soybean cyst nematode during a resistant and susceptible reaction. BMC PLANT BIOLOGY 2014; 14:300. [PMID: 25421055 PMCID: PMC4262236 DOI: 10.1186/s12870-014-0300-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 10/22/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Plant-parasitic nematodes (PPNs) are obligate parasites that feed on the roots of living host plants. Often, these nematodes can lay hundreds of eggs, each capable of surviving without a host for as long as 12 years. When it comes to wreaking havoc on agricultural yield, few nematodes can compare to the soybean cyst nematode (SCN). Quantifying soybean (Glycine max) transcription factor binding sites (TFBSs) during a late-stage SCN resistant and susceptible reaction can shed light onto the systematic interplay between host and pathogen, thereby elucidating underlying cis-regulatory mechanisms. RESULTS We sequenced the soybean root transcriptome at 6 and 8 days upon independent inoculation with a virulent and avirulent SCN population. Genes such as β-1,4 glucanase, chalcone synthase, superoxide dismutase and various heat shock proteins (HSPs) exhibited reaction-specific expression profiles. Several likely defense-response genes candidates were also identified which are believed to confer SCN resistance. To explore magnitude of TFBS representation during SCN pathogenesis, a multivariate statistical software identified 46 over-represented TFBSs which capture soybean regulatory dynamics across both reactions. CONCLUSIONS Our results reveal a set of soybean TFBSs which are over-represented solely throughout a resistant and susceptible SCN reaction. This set furthers our understanding of soybean cis-regulatory dynamics by providing reaction-specific levels of over-representation at 6 and 8 days after inoculation (dai) with SCN.
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Affiliation(s)
- Parsa Hosseini
- />School of Systems Biology, George Mason University, Manassas, VA USA
- />Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD USA
- />Soybean Genomics and Improvement Laboratory, United States Department of Agriculture, Beltsville, MD USA
| | - Benjamin F Matthews
- />Soybean Genomics and Improvement Laboratory, United States Department of Agriculture, Beltsville, MD USA
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22
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Tschaplinski TJ, Plett JM, Engle NL, Deveau A, Cushman KC, Martin MZ, Doktycz MJ, Tuskan GA, Brun A, Kohler A, Martin F. Populus trichocarpa and Populus deltoides exhibit different metabolomic responses to colonization by the symbiotic fungus Laccaria bicolor. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:546-56. [PMID: 24548064 DOI: 10.1094/mpmi-09-13-0286-r] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Within boreal and temperate forest ecosystems, the majority of trees and shrubs form beneficial relationships with mutualistic ectomycorrhizal (ECM) fungi that support plant health through increased access to nutrients as well as aiding in stress and pest tolerance. The intimate interaction between fungal hyphae and plant roots results in a new symbiotic "organ" called the ECM root tip. Little is understood concerning the metabolic reprogramming that favors the formation of this hybrid tissue in compatible interactions and what prevents the formation of ECM root tips in incompatible interactions. We show here that the metabolic changes during favorable colonization between the ECM fungus Laccaria bicolor and its compatible host, Populus trichocarpa, are characterized by shifts in aromatic acid, organic acid, and fatty acid metabolism. We demonstrate that this extensive metabolic reprogramming is repressed in incompatible interactions and that more defensive compounds are produced or retained. We also demonstrate that L. bicolor can metabolize a number of secreted defensive compounds and that the degradation of some of these compounds produces immune response metabolites (e.g., salicylic acid from salicin). Therefore, our results suggest that the metabolic responsiveness of plant roots to L. bicolor is a determinant factor in fungus-host interactions.
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Xia Z, Zhai H, Lü S, Wu H, Zhang Y. Recent achievement in gene cloning and functional genomics in soybean. ScientificWorldJournal 2013; 2013:281367. [PMID: 24311973 PMCID: PMC3842071 DOI: 10.1155/2013/281367] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 09/18/2013] [Indexed: 11/18/2022] Open
Abstract
Soybean is a model plant for photoperiodism as well as for symbiotic nitrogen fixation. However, a rather low efficiency in soybean transformation hampers functional analysis of genes isolated from soybean. In comparison, rapid development and progress in flowering time and photoperiodic response have been achieved in Arabidopsis and rice. As the soybean genomic information has been released since 2008, gene cloning and functional genomic studies have been revived as indicated by successfully characterizing genes involved in maturity and nematode resistance. Here, we review some major achievements in the cloning of some important genes and some specific features at genetic or genomic levels revealed by the analysis of functional genomics of soybean.
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Affiliation(s)
- Zhengjun Xia
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
- Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Hong Zhai
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Shixiang Lü
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Hongyan Wu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
- Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Yupeng Zhang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
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24
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Li MW, Qi X, Ni M, Lam HM. Silicon era of carbon-based life: application of genomics and bioinformatics in crop stress research. Int J Mol Sci 2013; 14:11444-83. [PMID: 23759993 PMCID: PMC3709742 DOI: 10.3390/ijms140611444] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 05/07/2013] [Accepted: 05/17/2013] [Indexed: 01/25/2023] Open
Abstract
Abiotic and biotic stresses lead to massive reprogramming of different life processes and are the major limiting factors hampering crop productivity. Omics-based research platforms allow for a holistic and comprehensive survey on crop stress responses and hence may bring forth better crop improvement strategies. Since high-throughput approaches generate considerable amounts of data, bioinformatics tools will play an essential role in storing, retrieving, sharing, processing, and analyzing them. Genomic and functional genomic studies in crops still lag far behind similar studies in humans and other animals. In this review, we summarize some useful genomics and bioinformatics resources available to crop scientists. In addition, we also discuss the major challenges and advancements in the "-omics" studies, with an emphasis on their possible impacts on crop stress research and crop improvement.
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Affiliation(s)
- Man-Wah Li
- Center for Soybean Research, State Key Laboratory of Agrobiotechnology and School of Life Sciences, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong; E-Mails: (M.-W.L.); (X.Q.); (M.N.)
| | - Xinpeng Qi
- Center for Soybean Research, State Key Laboratory of Agrobiotechnology and School of Life Sciences, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong; E-Mails: (M.-W.L.); (X.Q.); (M.N.)
| | - Meng Ni
- Center for Soybean Research, State Key Laboratory of Agrobiotechnology and School of Life Sciences, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong; E-Mails: (M.-W.L.); (X.Q.); (M.N.)
| | - Hon-Ming Lam
- Center for Soybean Research, State Key Laboratory of Agrobiotechnology and School of Life Sciences, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong; E-Mails: (M.-W.L.); (X.Q.); (M.N.)
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25
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Characterization of the Pinus massoniana transcriptional response to Bursaphelenchus xylophilus infection using suppression subtractive hybridization. Int J Mol Sci 2013; 14:11356-75. [PMID: 23759987 PMCID: PMC3709736 DOI: 10.3390/ijms140611356] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 05/03/2013] [Accepted: 05/14/2013] [Indexed: 11/17/2022] Open
Abstract
Pine wilt disease (PWD) caused by pine wood nematode (PWN), Bursaphelenchus xylophilus, is the most destructive diseases of pine and poses a threat of serious economic losses worldwide. Although several of the mechanisms involved in disease progression have been discovered, the molecular response of Pinus massoniana to PWN infection has not been explored. We constructed four subtractive suppression hybridization cDNA libraries by taking time-course samples from PWN-inoculated Masson pine trees. One-hundred forty-four significantly differentially expressed sequence tags (ESTs) were identified, and 124 high-quality sequences with transcriptional features were selected for gene ontology (GO) and individual gene analyses. There were marked differences in the types of transcripts, as well as in the timing and levels of transcript expression in the pine trees following PWN inoculation. Genes involved in signal transduction, transcription and translation and secondary metabolism were highly expressed after 24 h and 72 h, while stress response genes were highly expressed only after 72 h. Certain transcripts responding to PWN infection were discriminative; pathogenesis and cell wall-related genes were more abundant, while detoxification or redox process-related genes were less abundant. This study provides new insights into the molecular mechanisms that control the biochemical and physiological responses of pine trees to PWN infection, particularly during the initial stage of infection.
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Matthews BF, Beard H, MacDonald MH, Kabir S, Youssef RM, Hosseini P, Brewer E. Engineered resistance and hypersusceptibility through functional metabolic studies of 100 genes in soybean to its major pathogen, the soybean cyst nematode. PLANTA 2013; 237:1337-57. [PMID: 23389673 PMCID: PMC3634990 DOI: 10.1007/s00425-013-1840-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 01/06/2013] [Indexed: 05/11/2023]
Abstract
During pathogen attack, the host plant induces genes to ward off the pathogen while the pathogen often produces effector proteins to increase susceptibility of the host. Gene expression studies of syncytia formed in soybean root by soybean cyst nematode (Heterodera glycines) identified many genes altered in expression in resistant and susceptible roots. However, it is difficult to assess the role and impact of these genes on resistance using gene expression patterns alone. We selected 100 soybean genes from published microarray studies and individually overexpressed them in soybean roots to determine their impact on cyst nematode development. Nine genes reduced the number of mature females by more than 50 % when overexpressed, including genes encoding ascorbate peroxidase, β-1,4-endoglucanase, short chain dehydrogenase, lipase, DREPP membrane protein, calmodulin, and three proteins of unknown function. One gene encoding a serine hydroxymethyltransferase decreased the number of mature cyst nematode females by 45 % and is located at the Rhg4 locus. Four genes increased the number of mature cyst nematode females by more than 200 %, while thirteen others increased the number of mature cyst nematode females by more than 150 %. Our data support a role for auxin and ethylene in susceptibility of soybean to cyst nematodes. These studies highlight the contrasting gene sets induced by host and nematode during infection and provide new insights into the interactions between host and pathogen at the molecular level. Overexpression of some of these genes result in a greater decrease in the number of cysts formed than recognized soybean cyst nematode resistance loci.
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Affiliation(s)
- Benjamin F Matthews
- Soybean Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, 10300 Baltimore Ave, Bldg 006, Beltsville, MD 20705, USA.
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Afzal AJ, Srour A, Goil A, Vasudaven S, Liu T, Samudrala R, Dogra N, Kohli P, Malakar A, Lightfoot DA. Homo-dimerization and ligand binding by the leucine-rich repeat domain at RHG1/RFS2 underlying resistance to two soybean pathogens. BMC PLANT BIOLOGY 2013; 13:43. [PMID: 23497186 PMCID: PMC3626623 DOI: 10.1186/1471-2229-13-43] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 02/05/2013] [Indexed: 05/26/2023]
Abstract
BACKGROUND The protein encoded by GmRLK18-1 (Glyma_18_02680 on chromosome 18) was a receptor like kinase (RLK) encoded within the soybean (Glycine max L. Merr.) Rhg1/Rfs2 locus. The locus underlies resistance to the soybean cyst nematode (SCN) Heterodera glycines (I.) and causal agent of sudden death syndrome (SDS) Fusarium virguliforme (Aoki). Previously the leucine rich repeat (LRR) domain was expressed in Escherichia coli. RESULTS The aims here were to evaluate the LRRs ability to; homo-dimerize; bind larger proteins; and bind to small peptides. Western analysis suggested homo-dimers could form after protein extraction from roots. The purified LRR domain, from residue 131-485, was seen to form a mixture of monomers and homo-dimers in vitro. Cross-linking experiments in vitro showed the H274N region was close (<11.1 A) to the highly conserved cysteine residue C196 on the second homo-dimer subunit. Binding constants of 20-142 nM for peptides found in plant and nematode secretions were found. Effects on plant phenotypes including wilting, stem bending and resistance to infection by SCN were observed when roots were treated with 50 pM of the peptides. Far-Western analyses followed by MS showed methionine synthase and cyclophilin bound strongly to the LRR domain. A second LRR from GmRLK08-1 (Glyma_08_g11350) did not show these strong interactions. CONCLUSIONS The LRR domain of the GmRLK18-1 protein formed both a monomer and a homo-dimer. The LRR domain bound avidly to 4 different CLE peptides, a cyclophilin and a methionine synthase. The CLE peptides GmTGIF, GmCLE34, GmCLE3 and HgCLE were previously reported to be involved in root growth inhibition but here GmTGIF and HgCLE were shown to alter stem morphology and resistance to SCN. One of several models from homology and ab-initio modeling was partially validated by cross-linking. The effect of the 3 amino acid replacements present among RLK allotypes, A87V, Q115K and H274N were predicted to alter domain stability and function. Therefore, the LRR domain of GmRLK18-1 might underlie both root development and disease resistance in soybean and provide an avenue to develop new variants and ligands that might promote reduced losses to SCN.
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Affiliation(s)
- Ahmed J Afzal
- Department of Molecular Biology, Microbiology and Biochemistry and Center for Excellence the Illinois Soybean Center, Southern Illinois University at Carbondale, IL 62901, USA.
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28
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Zheng ZL, Zhao Y. Transcriptome comparison and gene coexpression network analysis provide a systems view of citrus response to 'Candidatus Liberibacter asiaticus' infection. BMC Genomics 2013; 14:27. [PMID: 23324561 PMCID: PMC3577516 DOI: 10.1186/1471-2164-14-27] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 01/09/2013] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Huanglongbing (HLB) is arguably the most destructive disease for the citrus industry. HLB is caused by infection of the bacterium, Candidatus Liberibacter spp. Several citrus GeneChip studies have revealed thousands of genes that are up- or down-regulated by infection with Ca. Liberibacter asiaticus. However, whether and how these host genes act to protect against HLB remains poorly understood. RESULTS As a first step towards a mechanistic view of citrus in response to the HLB bacterial infection, we performed a comparative transcriptome analysis and found that a total of 21 Probesets are commonly up-regulated by the HLB bacterial infection. In addition, a number of genes are likely regulated specifically at early, late or very late stages of the infection. Furthermore, using Pearson correlation coefficient-based gene coexpression analysis, we constructed a citrus HLB response network consisting of 3,507 Probesets and 56,287 interactions. Genes involved in carbohydrate and nitrogen metabolic processes, transport, defense, signaling and hormone response were overrepresented in the HLB response network and the subnetworks for these processes were constructed. Analysis of the defense and hormone response subnetworks indicates that hormone response is interconnected with defense response. In addition, mapping the commonly up-regulated HLB responsive genes into the HLB response network resulted in a core subnetwork where transport plays a key role in the citrus response to the HLB bacterial infection. Moreover, analysis of a phloem protein subnetwork indicates a role for this protein and zinc transporters or zinc-binding proteins in the citrus HLB defense response. CONCLUSION Through integrating transcriptome comparison and gene coexpression network analysis, we have provided for the first time a systems view of citrus in response to the Ca. Liberibacter spp. infection causing HLB.
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Affiliation(s)
- Zhi-Liang Zheng
- Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, Citrus Research Institute & College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing 400712, China.
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29
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Lodha TD, Hembram P, Basak NTJ. Proteomics: A Successful Approach to Understand the Molecular Mechanism of Plant-Pathogen Interaction. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/ajps.2013.46149] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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30
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Srour A, Afzal AJ, Blahut-Beatty L, Hemmati N, Simmonds DH, Li W, Liu M, Town CD, Sharma H, Arelli P, Lightfoot DA. The receptor like kinase at Rhg1-a/Rfs2 caused pleiotropic resistance to sudden death syndrome and soybean cyst nematode as a transgene by altering signaling responses. BMC Genomics 2012; 13:368. [PMID: 22857610 PMCID: PMC3439264 DOI: 10.1186/1471-2164-13-368] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 06/12/2012] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Soybean (Glycine max (L. Merr.)) resistance to any population of Heterodera glycines (I.), or Fusarium virguliforme (Akoi, O'Donnell, Homma & Lattanzi) required a functional allele at Rhg1/Rfs2. H. glycines, the soybean cyst nematode (SCN) was an ancient, endemic, pest of soybean whereas F. virguliforme causal agent of sudden death syndrome (SDS), was a recent, regional, pest. This study examined the role of a receptor like kinase (RLK) GmRLK18-1 (gene model Glyma_18_02680 at 1,071 kbp on chromosome 18 of the genome sequence) within the Rhg1/Rfs2 locus in causing resistance to SCN and SDS. RESULTS A BAC (B73p06) encompassing the Rhg1/Rfs2 locus was sequenced from a resistant cultivar and compared to the sequences of two susceptible cultivars from which 800 SNPs were found. Sequence alignments inferred that the resistance allele was an introgressed region of about 59 kbp at the center of which the GmRLK18-1 was the most polymorphic gene and encoded protein. Analyses were made of plants that were either heterozygous at, or transgenic (and so hemizygous at a new location) with, the resistance allele of GmRLK18-1. Those plants infested with either H. glycines or F. virguliforme showed that the allele for resistance was dominant. In the absence of Rhg4 the GmRLK18-1 was sufficient to confer nearly complete resistance to both root and leaf symptoms of SDS caused by F. virguliforme and provided partial resistance to three different populations of nematodes (mature female cysts were reduced by 30-50%). In the presence of Rhg4 the plants with the transgene were nearly classed as fully resistant to SCN (females reduced to 11% of the susceptible control) as well as SDS. A reduction in the rate of early seedling root development was also shown to be caused by the resistance allele of the GmRLK18-1. Field trials of transgenic plants showed an increase in foliar susceptibility to insect herbivory. CONCLUSIONS The inference that soybean has adapted part of an existing pathogen recognition and defense cascade (H.glycines; SCN and insect herbivory) to a new pathogen (F. virguliforme; SDS) has broad implications for crop improvement. Stable resistance to many pathogens might be achieved by manipulation the genes encoding a small number of pathogen recognition proteins.
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Affiliation(s)
- Ali Srour
- Department of Molecular Biology, Microbiology and Biochemistry, Southern Illinois University at Carbondale, Carbondale, IL 62901, USA
- Department of Plant Soil and Agricultural Systems, Southern Illinois University at Carbondale, Carbondale, IL 62901-4415, USA
| | - Ahmed J Afzal
- Department of Molecular Biology, Microbiology and Biochemistry, Southern Illinois University at Carbondale, Carbondale, IL 62901, USA
- Department of Plant Soil and Agricultural Systems, Southern Illinois University at Carbondale, Carbondale, IL 62901-4415, USA
- Department of Horticulture and Crop Science, Ohio State University, 2021 Coffey Rd, Columbus, OH 43210, USA
| | - Laureen Blahut-Beatty
- Agriculture and Agri-Food Canada, Building 21, 960 Carling Ave, Ottawa, ON K1A 0C6, USA
| | - Naghmeh Hemmati
- Department of Molecular Biology, Microbiology and Biochemistry, Southern Illinois University at Carbondale, Carbondale, IL 62901, USA
| | - Daina H Simmonds
- Agriculture and Agri-Food Canada, Building 21, 960 Carling Ave, Ottawa, ON K1A 0C6, USA
| | - Wenbin Li
- Key Laboratory of Soybean Biology in the Chinese Ministry of Education, Harbin University, Harbin, China
| | - Miao Liu
- Key Laboratory of Soybean Biology in the Chinese Ministry of Education, Harbin University, Harbin, China
| | | | - Hemlata Sharma
- Department of Molecular Biology, Microbiology and Biochemistry, Southern Illinois University at Carbondale, Carbondale, IL 62901, USA
- Department of Plant Breeding & Genetics, Rajasthan College of Agriculture, MPUAT, Udaipur, India
| | | | - David A Lightfoot
- Department of Molecular Biology, Microbiology and Biochemistry, Southern Illinois University at Carbondale, Carbondale, IL 62901, USA
- Department of Plant Soil and Agricultural Systems, Southern Illinois University at Carbondale, Carbondale, IL 62901-4415, USA
- Key Laboratory of Soybean Biology in the Chinese Ministry of Education, Harbin University, Harbin, China
- Genomics Core Facility; Center for Excellence the Illinois Soybean Center, Southern Illinois University at Carbondale, Carbondale, IL 62901-4415, USA
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Afzal AJ, Srour A, Saini N, Hemmati N, El Shemy HA, Lightfoot DA. Recombination suppression at the dominant Rhg1/Rfs2 locus underlying soybean resistance to the cyst nematode. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:1027-39. [PMID: 22200919 DOI: 10.1007/s00122-011-1766-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 12/04/2011] [Indexed: 05/08/2023]
Abstract
Host resistance to "yellow dwarf" or "moonlight" disease cause by any population (Hg type) of Heterodera glycines I., the soybean cyst nematode (SCN), requires a functional allele at rhg1. The host resistance encoded appears to mimic an apoptotic response in the giant cells formed at the nematode feeding site about 24-48 h after nematode feeding commences. Little is known about how the host response to infection is mediated but a linked set of 3 genes has been identified within the rhg1 locus. This study aimed to identify the role of the genes within the locus that includes a receptor-like kinase (RLK), a laccase and an ion antiporter. Used were near isogeneic lines (NILs) that contrasted at their rhg1 alleles, gene-based markers, and a new Hg type 0 and new recombination events. A syntenic gene cluster on Lg B1 was found. The effectiveness of SNP probes from the RLK for distinguishing homolog sequence variants on LgB1 from alleles at the rhg1 locus on LgG was shown. The resistant allele of the rhg1 locus was shown to be dominant in NILs. None of the recombination events were within the cluster of the three candidate genes. Finally, rhg1 was shown to reduce the plant root development. A model for rhg1 as a dominant multi-gene resistance locus based on the developmental control was inferred.
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Affiliation(s)
- Ahmed J Afzal
- Department of Molecular Biology, Microbiology and Biochemistry, Southern Illinois University at Carbondale, Carbondale, IL 62901, USA
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Alford SR, Rangarajan P, Williams P, Gillaspy GE. myo-Inositol Oxygenase is Required for Responses to Low Energy Conditions in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2012; 3:69. [PMID: 22639659 PMCID: PMC3355591 DOI: 10.3389/fpls.2012.00069] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 03/22/2012] [Indexed: 05/03/2023]
Abstract
myo-Inositol is a precursor for cell wall components, is used as a backbone of myo-inositol trisphosphate (Ins(1,4,5)P(3)) and phosphatidylinositol phosphate signaling molecules, and is debated about whether it is also a precursor in an alternate ascorbic acid synthesis pathway. Plants control inositol homeostasis by regulation of key enzymes involved in myo-inositol synthesis and catabolism. Recent transcriptional profiling data indicate up-regulation of the myo-inositol oxygenase (MIOX) genes under conditions in which energy or nutrients are limited. To test whether the MIOX genes are required for responses to low energy, we first examined MIOX2 and MIOX4 gene expression regulation by energy/nutrient conditions. We found that both MIOX2 and MIOX4 expression are suppressed by exogenous glucose addition in the shoot, but not in the root. Both genes were abundantly expressed during low energy/nutrient conditions. Loss-of-function mutants in MIOX genes contain alterations in myo-inositol levels and growth changes in the root. Miox2 mutants can be complemented with a MIOX2:green fluorescent protein fusion. Further we show here that MIOX2 is a cytoplasmic protein, while MIOX4 is present mostly in the cytoplasm, but also occasionally in the nucleus. Together, these data suggest that MIOX catabolism in the shoot may influence root growth responses during low energy/nutrient conditions.
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Affiliation(s)
| | | | - Phoebe Williams
- Department of Biochemistry, Virginia TechBlacksburg, VA, USA
| | - Glenda E. Gillaspy
- Department of Biochemistry, Virginia TechBlacksburg, VA, USA
- *Correspondence: Glenda E. Gillaspy, Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA. e-mail:
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Zhang Y, Zhao J, Xiang Y, Bian X, Zuo Q, Shen Q, Gai J, Xing H. Proteomics study of changes in soybean lines resistant and sensitive to Phytophthora sojae. Proteome Sci 2011; 9:52. [PMID: 21899734 PMCID: PMC3180303 DOI: 10.1186/1477-5956-9-52] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 09/07/2011] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Phytophthora sojae causes soybean root and stem rot, resulting in an annual loss of 1-2 billion US dollars in soybean production worldwide. A proteomic technique was used to determine the effects on soybean hypocotyls of infection with P. sojae. RESULTS In the present study, 46 differentially expressed proteins were identified in soybean hypocotyls infected with P. sojae, using two-dimensional electrophoresis and matrix-assisted laser desorption/ionization tandem time of flight (MALDI-TOF/TOF). The expression levels of 26 proteins were significantly affected at various time points in the tolerant soybean line, Yudou25, (12 up-regulated and 14 down-regulated). In contrast, in the sensitive soybean line, NG6255, only 20 proteins were significantly affected (11 up-regulated and 9 down-regulated). Among these proteins, 26% were related to energy regulation, 15% to protein destination and storage, 11% to defense against disease, 11% to metabolism, 9% to protein synthesis, 4% to secondary metabolism, and 24% were of unknown function. CONCLUSION Our study provides important information on the use of proteomic methods for studying protein regulation during plant-oomycete interactions.
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Affiliation(s)
- YuMei Zhang
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - JinMing Zhao
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Yang Xiang
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, P.R.China
| | - XiaoChun Bian
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - QiaoMei Zuo
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Qi Shen
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, P.R.China
| | - JunYi Gai
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Han Xing
- National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, P.R. China
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Mathesius U, Djordjevic MA, Oakes M, Goffard N, Haerizadeh F, Weiller GF, Singh MB, Bhalla PL. Comparative proteomic profiles of the soybean (Glycine max) root apex and differentiated root zone. Proteomics 2011; 11:1707-19. [PMID: 21438152 DOI: 10.1002/pmic.201000619] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 12/14/2010] [Accepted: 12/29/2010] [Indexed: 11/06/2022]
Abstract
The root apical meristem (RAM) is responsible for the growth of the plant root system. Because of the importance of root architecture in the performance of crop plants, we established a proteome reference map of the soybean root apex and compared this with the proteome of the differentiated root zone. The root apex samples contained the apical 1 mm of the root, comprising the RAM, quiescent center and root cap. We identified 342 protein spots from 550 excised proteins (∼62%) of root apex samples by MALDI-TOF MS/MS analysis. All these proteins were also present in the differentiated root, but differed in abundance. Functional classification showed that the most numerous protein categories represented in the root were those of stress response, glycolysis, redox homeostasis and protein processing. Using DIGE, we identified 73 differentially accumulated proteins between root apex and differentiated root. Proteins overrepresented in the root apex belonged primarily to the pathways for protein synthesis and processing, cell redox homeostasis and flavonoid biosynthesis. Proteins underrepresented in the root apex were those of glycolysis, tricarboxylic acid metabolism and stress response. Our results highlight the importance of stress and defense response, redox control and flavonoid metabolism in the root apex.
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Affiliation(s)
- Ulrike Mathesius
- ARC Centre of Excellence for Integrative Legume Research, Australia; Division of Plant Science, Research School of Biology, Australian National University, Canberra ACT, Australia.
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Tirumalaraju SV, Jain M, Gallo M. Differential gene expression in roots of nematode-resistant and -susceptible peanut (Arachis hypogaea) cultivars in response to early stages of peanut root-knot nematode (Meloidogyne arenaria) parasitization. JOURNAL OF PLANT PHYSIOLOGY 2011; 168:481-92. [PMID: 20863592 DOI: 10.1016/j.jplph.2010.08.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Revised: 08/17/2010] [Accepted: 08/19/2010] [Indexed: 05/10/2023]
Abstract
The peanut root-knot nematode (RKN, Meloidogyne arenaria) can cause significant yield losses in cultivated peanut (Arachis hypogaea). However, molecular events underlying successful RKN infection and host responses in peanut are sparsely understood. Using suppression subtractive hybridization (SSH), cDNA libraries, enriched with differentially expressed ESTs, were constructed from RKN-challenged root tissues in the pre-penetration and early infection stages from near-isogenic nematode-resistant and -susceptible peanut cultivars NemaTAM and Florunner. Following an initial screen of 960 expressed sequence tags (ESTs) for at least three-fold differential expression between the two libraries, 70 ESTs (36 from the NemaTAM-specific library and 34 from the Florunner-specific library) were identified and annotated into seven functional categories (stress responses, metabolism, transcriptional regulation, protein synthesis and/or modification, transport functions, cellular architecture and proteins with unknown functions). Discreet gene tag clusters primarily including pathogenesis related (PR), patatin-like proteins and universal stress related proteins (USPs), as well as those implicated in alleviation of oxidative stress were primarily represented in RKN-infected NemaTAM roots, reflective of a basal level of resistance operative against invading nematodes. However, significant transcriptional reprogramming and upregulation of genes implicated in modification of cellular architecture, adhesion, and proliferation marked an early onset of compatible host-pathogen interactions discernible in Florunner roots.
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Tran LSP, Mochida K. Functional genomics of soybean for improvement of productivity in adverse conditions. Funct Integr Genomics 2010; 10:447-62. [PMID: 20582712 DOI: 10.1007/s10142-010-0178-z] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 06/01/2010] [Accepted: 06/16/2010] [Indexed: 01/07/2023]
Abstract
Global soybean production is frequently impacted by various stresses, including both abiotic and biotic stresses. To develop soybean plants with enhanced tolerance to different stressors, functional genomics of soybean and a comprehensive understanding of available biotechnological resources and approaches are essential. In this review, we will discuss recent advances in soybean functional genomics which provide unprecedented opportunities to understand global patterns of gene expression, gene regulatory networks, various physiological, biochemical, and metabolic pathways as well as their association with the development of specific phenotypes. Soybean functional genomics, therefore, will ultimately enable us to develop new soybean varieties with improved productivity under adverse conditions by genetic engineering.
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Yesudas CR, Sharma H, Lightfoot DA. Identification of QTL in soybean underlying resistance to herbivory by Japanese beetles (Popillia japonica, Newman). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:353-62. [PMID: 20458460 DOI: 10.1007/s00122-010-1314-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Accepted: 03/02/2010] [Indexed: 05/16/2023]
Abstract
Soybean [Glycine max (L.) Merr.] was one of the most important legume crops in the world in 2010. Japanese beetles (JB; Popillia japonica, Newman) in the US were an introduced and potentially damaging insect pest for soybean. JBs are likely to spread across the US if global warming occurs. Resistance to JB in soybean was previously reported only in plant introductions. The aims here were to identify loci underlying resistance to JB herbivory in recombinant inbred lines (RILs) derived from the cross of Essex x Forrest cultivars (EF94) and to correlate those with loci with factors that confer insect resistance in soybean cultivars. The RIL population was used to map 413 markers, 238 satellite markers and 177 other DNA markers. Field data were from two environments over 2 years. Pest severity (PS) measured defoliation on a 0-9 scale. Pest incidence (PI) was the percentage of plants within each RIL with beetles on them. Antibiosis and antixenosis data were from feeding assays with detached leaves in petri plates. Five QTL were detected for the mean PS field trait (16% < R (2) < 27%). The loci were within the intervals Satt632-A2D8 on linkage group (LG) A2 (chromosome 8); Satt583-Satt415 on LG B1 (11); Satt009-Satt530 on LG N (3); and close to two markers OB02_140 (LG E; 20 cM from Satt572) and OZ15_150 LG (19 cM from Satt291 C2). Two QTL were detected for the mean PI field trait (16% < R (2) < 18%) close to Satt385 on LG A1 and Satt440 on LG I. The no choice feeding studies detected three QTL that were significant; two for antixenosis (22% < R (2) < 24%) between Satt632-A2D8 on LG A2 (8) and Sat_039-Satt160 on LG F (13); and a major locus effect (R (2) = 54%) for antibiosis on LG D2 (17) between Satt464-Satt488. Therefore, loci underlying resistance to JB herbivory were a mixture of major and minor gene effects. Some loci were within regions underlying resistance to soybean cyst nematode (LGs A2 and I) and root knot nematode (LG F) but not other major loci underlying resistance to nematode or insect pests (LGs G, H and M).
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Affiliation(s)
- C R Yesudas
- Plant Biotechnology and Genomics Core-Facility, Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA
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Melito S, Heuberger AL, Cook D, Diers BW, MacGuidwin AE, Bent AF. A nematode demographics assay in transgenic roots reveals no significant impacts of the Rhg1 locus LRR-Kinase on soybean cyst nematode resistance. BMC PLANT BIOLOGY 2010; 10:104. [PMID: 20529370 PMCID: PMC3095272 DOI: 10.1186/1471-2229-10-104] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Accepted: 06/09/2010] [Indexed: 05/17/2023]
Abstract
BACKGROUND Soybean cyst nematode (Heterodera glycines, SCN) is the most economically damaging pathogen of soybean (Glycine max) in the U.S. The Rhg1 locus is repeatedly observed as the quantitative trait locus with the greatest impact on SCN resistance. The Glyma18g02680.1 gene at the Rhg1 locus that encodes an apparent leucine-rich repeat transmembrane receptor-kinase (LRR-kinase) has been proposed to be the SCN resistance gene, but its function has not been confirmed. Generation of fertile transgenic soybean lines is difficult but methods have been published that test SCN resistance in transgenic roots generated with Agrobacterium rhizogenes. RESULTS We report use of artificial microRNA (amiRNA) for gene silencing in soybean, refinements to transgenic root SCN resistance assays, and functional tests of the Rhg1 locus LRR-kinase gene. A nematode demographics assay monitored infecting nematode populations for their progress through developmental stages two weeks after inoculation, as a metric for SCN resistance. Significant differences were observed between resistant and susceptible control genotypes. Introduction of the Rhg1 locus LRR-kinase gene (genomic promoter/coding region/terminator; Peking/PI 437654-derived SCN-resistant source), into rhg1- SCN-susceptible plant lines carrying the resistant-source Rhg4+ locus, provided no significant increases in SCN resistance. Use of amiRNA to reduce expression of the LRR-kinase gene from the Rhg1 locus of Fayette (PI 88788 source of Rhg1) also did not detectably alter resistance to SCN. However, silencing of the LRR-kinase gene did have impacts on root development. CONCLUSION The nematode demographics assay can expedite testing of transgenic roots for SCN resistance. amiRNAs and the pSM103 vector that drives interchangeable amiRNA constructs through a soybean polyubiqutin promoter (Gmubi), with an intron-GFP marker for detection of transgenic roots, may have widespread use in legume biology. Studies in which expression of the Rhg1 locus LRR-kinase gene from different resistance sources was either reduced or complemented did not reveal significant impacts on SCN resistance.
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Affiliation(s)
- Sara Melito
- Department of Plant Pathology, University of Wisconsin - Madison, Madison, WI 53706 USA
| | - Adam L Heuberger
- Department of Plant Pathology, University of Wisconsin - Madison, Madison, WI 53706 USA
| | - David Cook
- Department of Plant Pathology, University of Wisconsin - Madison, Madison, WI 53706 USA
| | - Brian W Diers
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Ann E MacGuidwin
- Department of Plant Pathology, University of Wisconsin - Madison, Madison, WI 53706 USA
| | - Andrew F Bent
- Department of Plant Pathology, University of Wisconsin - Madison, Madison, WI 53706 USA
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Hofmann J, El Ashry AEN, Anwar S, Erban A, Kopka J, Grundler F. Metabolic profiling reveals local and systemic responses of host plants to nematode parasitism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 62:1058-71. [PMID: 20374527 PMCID: PMC2904900 DOI: 10.1111/j.1365-313x.2010.04217.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 03/17/2010] [Accepted: 03/24/2010] [Indexed: 05/18/2023]
Abstract
The plant parasitic beet cyst nematode Heterodera schachtii induces syncytial feeding structures in Arabidopsis roots. The feeding structures form strong sink tissues that have been suggested to be metabolically highly active. In the present study, metabolic profiling and gene targeted expression analyses were performed in order to study the local and systemic effects of nematode infection on the plant host. The results showed increased levels of many amino acids and phosphorylated metabolites in syncytia, as well as high accumulation of specific sugars such as 1-kestose that do not accumulate naturally in Arabidopsis roots. A correlation-based network analysis revealed highly activated and coordinated metabolism in syncytia compared to non-infected control roots. An integrated analysis of the central primary metabolism showed a clear coherence of metabolite and transcript levels, indicating transcriptional regulation of specific pathways. Furthermore, systemic effects of nematode infection were demonstrated by correlation-based network analysis as well as independent component analysis. 1-kestose, raffinose, alpha,alpha-trehalose and three non-identified analytes showed clear systemic accumulation, indicating future potential for diagnostic and detailed metabolic analyses. Our studies open the door towards understanding the complex remodelling of plant metabolism in favour of the parasitizing nematode.
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Affiliation(s)
- Julia Hofmann
- Department of Applied Plant Sciences and Plant Biotechnology, Institute of Plant Protection, BOKU - University of Natural Resources and Applied Life Sciences, Vienna, Peter Jordan-Strasse 82, A-1190 Vienna, Austria.
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Microarray Detection Call Methodology as a Means to Identify and Compare Transcripts Expressed within Syncytial Cells from Soybean (Glycine max) Roots Undergoing Resistant and Susceptible Reactions to the Soybean Cyst Nematode (Heterodera glycines). J Biomed Biotechnol 2010; 2010:491217. [PMID: 20508855 PMCID: PMC2875038 DOI: 10.1155/2010/491217] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2009] [Revised: 09/23/2009] [Accepted: 02/14/2010] [Indexed: 11/27/2022] Open
Abstract
Background. A comparative microarray investigation was done using detection call methodology (DCM) and differential expression analyses. The goal was to identify genes found in specific cell populations that were eliminated by differential expression analysis due to the nature of differential expression methods. Laser capture microdissection (LCM) was used to isolate nearly homogeneous populations of plant root cells. Results. The analyses identified the presence of 13,291 transcripts between the 4 different sample types. The transcripts filtered down into a total of 6,267 that were detected as being present in one or more sample types. A comparative analysis of DCM and differential expression methods showed a group of genes that were not differentially expressed, but were expressed at detectable amounts within specific cell types. Conclusion. The DCM has identified patterns of gene expression not shown by differential expression analyses. DCM has identified genes that are possibly cell-type specific and/or involved in important aspects of plant nematode interactions during the resistance response, revealing the uniqueness of a particular cell population at a particular point during its differentiation process.
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Klink VP, Matthews BF. Emerging approaches to broaden resistance of soybean to soybean cyst nematode as supported by gene expression studies. PLANT PHYSIOLOGY 2009; 151:1017-22. [PMID: 19675146 PMCID: PMC2773110 DOI: 10.1104/pp.109.144006] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Accepted: 08/11/2009] [Indexed: 05/04/2023]
Affiliation(s)
- Vincent P Klink
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi 39762, USA.
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