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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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Wei H, Lian Y, Li J, Li H, Song Q, Wu Y, Lei C, Wang S, Zhang H, Wang J, Lu W. Identification of Candidate Genes Controlling Soybean Cyst Nematode Resistance in "Handou 10" Based on Genome and Transcriptome Analyzes. FRONTIERS IN PLANT SCIENCE 2022; 13:860034. [PMID: 35371127 PMCID: PMC8965568 DOI: 10.3389/fpls.2022.860034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
Soybean cyst nematode (SCN; Heterodera glycines Ichinohe) is a highly destructive pathogen for soybean production worldwide. The use of resistant varieties is the most effective way of preventing yield loss. Handou 10 is a commercial soybean variety with desirable agronomic traits and SCN resistance, however genes underlying the SCN resistance in the variety are unknown. An F2:8 recombinant inbred line (RIL) population derived from a cross between Zheng 9525 (susceptible) and Handou 10 was developed and its resistance to SCN HG type 2.5.7 (race 1) and 1.2.5.7 (race 2) was identified. We identified seven quantitative trait loci (QTLs) with additive effects. Among these, three QTLs on Chromosomes 7, 8, and 18 were resistant to both races. These QTLs could explain 1.91-7.73% of the phenotypic variation of SCN's female index. The QTLs on chromosomes 8 and 18 have already been reported and were most likely overlapped with rhg1 and Rhg4 loci, respectively. However, the QTL on chromosome 7 was novel. Candidate genes for the three QTLs were predicted through genes functional analysis and transcriptome analysis of infected roots of Handou 10 vs. Zheng 9525. Transcriptome analysis performed also indicated that the plant-pathogen interaction played an important role in the SCN resistance for Handou 10. The information will facilitate SCN-resistant gene cloning, and the novel resistant gene will be a source for improving soybeans' resistance to SCN.
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Affiliation(s)
- He Wei
- Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Sciences/National Centre for Plant Breeding/Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of Ministry of Agriculture, Zhengzhou, China
| | - Yun Lian
- Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Sciences/National Centre for Plant Breeding/Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of Ministry of Agriculture, Zhengzhou, China
| | - Jinying Li
- Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Sciences/National Centre for Plant Breeding/Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of Ministry of Agriculture, Zhengzhou, China
| | - Haichao Li
- Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Sciences/National Centre for Plant Breeding/Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of Ministry of Agriculture, Zhengzhou, China
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, United States
| | - Yongkang Wu
- Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Sciences/National Centre for Plant Breeding/Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of Ministry of Agriculture, Zhengzhou, China
| | - Chenfang Lei
- Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Sciences/National Centre for Plant Breeding/Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of Ministry of Agriculture, Zhengzhou, China
| | - Shiwei Wang
- Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Sciences/National Centre for Plant Breeding/Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of Ministry of Agriculture, Zhengzhou, China
| | - Hui Zhang
- Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Sciences/National Centre for Plant Breeding/Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of Ministry of Agriculture, Zhengzhou, China
| | - Jinshe Wang
- Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Sciences/National Centre for Plant Breeding/Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of Ministry of Agriculture, Zhengzhou, China
| | - Weiguo Lu
- Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Sciences/National Centre for Plant Breeding/Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of Ministry of Agriculture, Zhengzhou, China
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Miraeiz E, Chaiprom U, Afsharifar A, Karegar A, M Drnevich J, E Hudson M. Early transcriptional responses to soybean cyst nematode HG Type 0 show genetic differences among resistant and susceptible soybeans. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:87-102. [PMID: 31570969 DOI: 10.1007/s00122-019-03442-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 09/18/2019] [Indexed: 05/24/2023]
Abstract
KEY MESSAGE Root transcriptome profiling of three soybean cultivars and a wild relative infected with soybean cyst nematode at migratory phase revealed differential resistance pathway responses between resistant and susceptible genotypes. The soybean cyst nematode (SCN), Heterodera glycines, is the most serious pathogen of soybean production throughout the world. Using resistant cultivars is the primary management strategy against SCN infestation. To gain insight into the still obscure mechanisms of genetic resistance to nematodes in different soybean genotypes, RNA-Seq profiling of the roots of Glycine max cv. Peking, Fayette, Williams 82, and a wild relative (Glycine soja PI 468916) was performed during SCN infection at the migratory phase. The analysis showed statistically significant changes of expression beginning at eight hours after inoculation in genes associated with defense mechanisms and pathways, such as the phenylpropanoid biosynthesis pathway, plant innate immunity and hormone signaling. Our results indicate the importance of the early plant response to migratory phase nematodes in pathogenicity determination. The transcriptome changes occurring during early SCN infection included a number of genes and pathways specific to the different resistant genotypes. We observed the most extensive resistant transcriptome reaction in PI 468916, where the resistant response was qualitatively different from that of commonly used G. max varieties.
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Affiliation(s)
- Esmaeil Miraeiz
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, Iran
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Usawadee Chaiprom
- PhD Program in Informatics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Alireza Afsharifar
- Plant Virology Research Center, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Akbar Karegar
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Jenny M Drnevich
- High Performance Biological Computing (HPCBio), Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Matthew E Hudson
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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Kankanala P, Nandety RS, Mysore KS. Genomics of Plant Disease Resistance in Legumes. FRONTIERS IN PLANT SCIENCE 2019; 10:1345. [PMID: 31749817 PMCID: PMC6842968 DOI: 10.3389/fpls.2019.01345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/27/2019] [Indexed: 05/15/2023]
Abstract
The constant interactions between plants and pathogens in the environment and the resulting outcomes are of significant importance for agriculture and agricultural scientists. Disease resistance genes in plant cultivars can break down in the field due to the evolution of pathogens under high selection pressure. Thus, the protection of crop plants against pathogens is a continuous arms race. Like any other type of crop plant, legumes are susceptible to many pathogens. The dawn of the genomic era, in which high-throughput and cost-effective genomic tools have become available, has revolutionized our understanding of the complex interactions between legumes and pathogens. Genomic tools have enabled a global view of transcriptome changes during these interactions, from which several key players in both the resistant and susceptible interactions have been identified. This review summarizes some of the large-scale genomic studies that have clarified the host transcriptional changes during interactions between legumes and their plant pathogens while highlighting some of the molecular breeding tools that are available to introgress the traits into breeding programs. These studies provide valuable insights into the molecular basis of different levels of host defenses in resistant and susceptible interactions.
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Transcriptomic profiling of soybean in response to UV-B and Xanthomonas axonopodis treatment reveals shared gene components in stress defense pathways. Genes Genomics 2017. [DOI: 10.1007/s13258-016-0490-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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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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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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Khatoon A, Rehman S, Oh MW, Woo SH, Komatsu S. Analysis of response mechanism in soybean under low oxygen and flooding stresses using gel-base proteomics technique. Mol Biol Rep 2012; 39:10581-94. [PMID: 23053957 DOI: 10.1007/s11033-012-1946-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Accepted: 10/01/2012] [Indexed: 12/20/2022]
Abstract
A proteomics approach was used to analyze the response mechanism in soybean seedlings under low oxygen and flooding stresses. Three-day-old soybean seedlings were subjected to low oxygen and flooding stresses. Growth of root was suppressed in both stresses with more extent of suppression in flooded seedlings at 3 and 6 days following the treatments. Proteins were extracted from roots and separated by two-dimensional polyacrylamide gel electrophoresis. Of total 1,233 protein spots, 27 protein spots were commonly changed under low oxygen and flooding stresses; while the differential change in 4 and 18 protein spots was specific to low oxygen and flooding stresses, respectively. Proteins related to metabolism and energy were increased; while protein destination/storage related proteins were decreased commonly under low oxygen and flooding stresses. Protein specie, TCP domain class transcription factor was decreased specifically under low oxygen stress; while decrease of nine proteins related to metabolism, protein destination/storage and disease/defense was specific in flooded seedlings. The decrease in majority of the proteins related to protein destination/storage specifically in flooded seedlings implies the misfolding of proteins resulting in flooded injuries in an independent way of oxygen deprivation. These results suggest that decrease in proteins related to protein destination/storage and disease/defense causes more growth suppression in soybean seedlings under flooding stress compared to low oxygen stress.
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Affiliation(s)
- Amana Khatoon
- National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, 305-8518, Japan
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de Sá MEL, Conceição Lopes MJ, de Araújo Campos M, Paiva LV, dos Santos RMA, Beneventi MA, Firmino AAP, de Sá MFG. Transcriptome analysis of resistant soybean roots infected by Meloidogyne javanica. Genet Mol Biol 2012; 35:272-82. [PMID: 22802712 PMCID: PMC3392879 DOI: 10.1590/s1415-47572012000200008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Soybean is an important crop for Brazilian agribusiness. However, many factors can limit its production, especially root-knot nematode infection. Studies on the mechanisms employed by the resistant soybean genotypes to prevent infection by these nematodes are of great interest for breeders. For these reasons, the aim of this work is to characterize the transcriptome of soybean line PI 595099-Meloidogyne javanica interaction through expression analysis. Two cDNA libraries were obtained using a pool of RNA from PI 595099 uninfected and M. javanica (J(2)) infected roots, collected at 6, 12, 24, 48, 96, 144 and 192 h after inoculation. Around 800 ESTs (Expressed Sequence Tags) were sequenced and clustered into 195 clusters. In silico subtraction analysis identified eleven differentially expressed genes encoding putative proteins sharing amino acid sequence similarities by using BlastX: metallothionein, SLAH4 (SLAC1 Homologue 4), SLAH1 (SLAC1 Homologue 1), zinc-finger proteins, AN1-type proteins, auxin-repressed proteins, thioredoxin and nuclear transport factor 2 (NTF-2). Other genes were also found exclusively in nematode stressed soybean roots, such as NAC domain-containing proteins, MADS-box proteins, SOC1 (suppressor of overexpression of constans 1) proteins, thioredoxin-like protein 4-Coumarate-CoA ligase and the transcription factor (TF) MYBZ2. Among the genes identified in non-stressed roots only were Ser/Thr protein kinases, wound-induced basic protein, ethylene-responsive family protein, metallothionein-like protein cysteine proteinase inhibitor (cystatin) and Putative Kunitz trypsin protease inhibitor. An understanding of the roles of these differentially expressed genes will provide insights into the resistance mechanisms and candidate genes involved in soybean-M. javanica interaction and contribute to more effective control of this pathogen.
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Affiliation(s)
- Maria Eugênia Lisei de Sá
- Empresa de Pesquisa Agropecuária de Minas Gerais, Uberaba, MG, Brazil
- Laboratório Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
| | - Marcus José Conceição Lopes
- Universidade Federal de Campina Grande, Centro de Educação e Saúde, Cuité, PB, Brazil
- Universidade Federal de Lavras, Lavras, MG, Brazil
| | - Magnólia de Araújo Campos
- Universidade Federal de Campina Grande, Centro de Educação e Saúde, Cuité, PB, Brazil
- Universidade Federal de Lavras, Lavras, MG, Brazil
| | | | | | - Magda Aparecida Beneventi
- Laboratório Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
| | - Alexandre Augusto Pereira Firmino
- Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Laboratório Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
| | - Maria Fátima Grossi de Sá
- Laboratório Interação Molecular Planta-Praga, Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
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Li X, Wang X, Zhang S, Liu D, Duan Y, Dong W. Comparative profiling of the transcriptional response to soybean cyst nematode infection of soybean roots by deep sequencing. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s11434-011-4510-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Simonetti E, Alba E, Montes MJ, Delibes A, López-Braña I. Analysis of ascorbate peroxidase genes expressed in resistant and susceptible wheat lines infected by the cereal cyst nematode, Heterodera avenae. PLANT CELL REPORTS 2010; 29:1169-1178. [PMID: 20690022 DOI: 10.1007/s00299-010-0903-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Revised: 06/28/2010] [Accepted: 07/18/2010] [Indexed: 05/29/2023]
Abstract
Changes in ascorbate peroxidase (APX) enzyme activity in response to nematode (Heterodera avenae) attack were studied in roots of three hexaploid wheat lines carrying Cre2, Cre5, or Cre7 nematode resistance genes and the susceptible Triticum aestivum cv. Anza. A spectrophotometric analysis was carried out with root extracts of infected plants 4, 7, 11, and 14 days after nematode inoculation using uninfected plant as control. APX induction in infected resistant genotypes was similar and higher than in the susceptible control. The introgression wheat/Aegilops ventricosa H-93-8 line, carrying the Cre2 gene, and its parental line H-10-15 as susceptible control were used to analyze whether this increase of activity was correlated with the induction of APX gene expression. Genes encoding cytosolic forms of APX were induced in roots of both lines in response to nematode infection. This induction took place both earlier and with greater intensity in the resistant line than in the susceptible one, and it was also higher in the root area at the site of nematode attachment.
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Affiliation(s)
- Ester Simonetti
- Departamento de Biotecnología, ETS Ing. Agrónomos, UPM, Madrid 28040, Spain
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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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Raju NL, Gnanesh BN, Lekha P, Jayashree B, Pande S, Hiremath PJ, Byregowda M, Singh NK, Varshney RK. The first set of EST resource for gene discovery and marker development in pigeonpea (Cajanus cajan L.). BMC PLANT BIOLOGY 2010; 10:45. [PMID: 20222972 PMCID: PMC2923520 DOI: 10.1186/1471-2229-10-45] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Accepted: 03/11/2010] [Indexed: 05/23/2023]
Abstract
BACKGROUND Pigeonpea (Cajanus cajan (L.) Millsp) is one of the major grain legume crops of the tropics and subtropics, but biotic stresses [Fusarium wilt (FW), sterility mosaic disease (SMD), etc.] are serious challenges for sustainable crop production. Modern genomic tools such as molecular markers and candidate genes associated with resistance to these stresses offer the possibility of facilitating pigeonpea breeding for improving biotic stress resistance. Availability of limited genomic resources, however, is a serious bottleneck to undertake molecular breeding in pigeonpea to develop superior genotypes with enhanced resistance to above mentioned biotic stresses. With an objective of enhancing genomic resources in pigeonpea, this study reports generation and analysis of comprehensive resource of FW- and SMD- responsive expressed sequence tags (ESTs). RESULTS A total of 16 cDNA libraries were constructed from four pigeonpea genotypes that are resistant and susceptible to FW ('ICPL 20102' and 'ICP 2376') and SMD ('ICP 7035' and 'TTB 7') and a total of 9,888 (9,468 high quality) ESTs were generated and deposited in dbEST of GenBank under accession numbers GR463974 to GR473857 and GR958228 to GR958231. Clustering and assembly analyses of these ESTs resulted into 4,557 unique sequences (unigenes) including 697 contigs and 3,860 singletons. BLASTN analysis of 4,557 unigenes showed a significant identity with ESTs of different legumes (23.2-60.3%), rice (28.3%), Arabidopsis (33.7%) and poplar (35.4%). As expected, pigeonpea ESTs are more closely related to soybean (60.3%) and cowpea ESTs (43.6%) than other plant ESTs. Similarly, BLASTX similarity results showed that only 1,603 (35.1%) out of 4,557 total unigenes correspond to known proteins in the UniProt database (or= 5 sequences detected 102 single nucleotide polymorphisms (SNPs) in 37 contigs. As an example, a set of 10 contigs were used for confirming in silico predicted SNPs in a set of four genotypes using wet lab experiments. Occurrence of SNPs were confirmed for all the 6 contigs for which scorable and sequenceable amplicons were generated. PCR amplicons were not obtained in case of 4 contigs. Recognition sites for restriction enzymes were identified for 102 SNPs in 37 contigs that indicates possibility of assaying SNPs in 37 genes using cleaved amplified polymorphic sequences (CAPS) assay. CONCLUSION The pigeonpea EST dataset generated here provides a transcriptomic resource for gene discovery and development of functional markers associated with biotic stress resistance. Sequence analyses of this dataset have showed conservation of a considerable number of pigeonpea transcripts across legume and model plant species analysed as well as some putative pigeonpea specific genes. Validation of identified biotic stress responsive genes should provide candidate genes for allele mining as well as candidate markers for molecular breeding.
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Affiliation(s)
- Nikku L Raju
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad 502 324, Andhra Pradesh, India
| | - Belaghihalli N Gnanesh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad 502 324, Andhra Pradesh, India
- University of Agricultural Sciences, Gandhi Krishi Vignyan Kendra (GKVK), Bangalore, 560 065, Karnataka, India
| | - Pazhamala Lekha
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad 502 324, Andhra Pradesh, India
| | - Balaji Jayashree
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad 502 324, Andhra Pradesh, India
| | - Suresh Pande
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad 502 324, Andhra Pradesh, India
| | - Pavana J Hiremath
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad 502 324, Andhra Pradesh, India
| | - Munishamappa Byregowda
- University of Agricultural Sciences, Gandhi Krishi Vignyan Kendra (GKVK), Bangalore, 560 065, Karnataka, India
| | - Nagendra K Singh
- National Research Centre on Plant Biotechnology (NRCPB), Indian Agricultural Research Institute, New Delhi 110 012, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Greater Hyderabad 502 324, Andhra Pradesh, India
- Genomics towards Gene Discovery Sub Programme, Generation Challenge Programme (GCP) c/o CIMMYT, Int. Apartado Postal 6-641, 06600, Mexico, DF Mexico
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Klink VP, Hosseini P, Matsye PD, Alkharouf NW, Matthews BF. Syncytium gene expression in Glycine max([PI 88788]) roots undergoing a resistant reaction to the parasitic nematode Heterodera glycines. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2010; 48:176-93. [PMID: 20138530 DOI: 10.1016/j.plaphy.2009.12.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Revised: 10/31/2009] [Accepted: 12/15/2009] [Indexed: 05/07/2023]
Abstract
The plant parasitic nematode, Heterodera glycines is the major pathogen of Glycine max (soybean). H. glycines accomplish parasitism by creating a nurse cell known as the syncytium from which it feeds. The syncytium undergoes two developmental phases. The first is a parasitism phase where feeding sites are selected, initiating the development of the syncytium. During this earlier phase (1-4 days post infection), syncytia undergoing resistant and susceptible reactions appear the same. The second phase is when the resistance response becomes evident (between 4 and 6dpi) and is completed by 9dpi. Analysis of the resistant reaction of G. max genotype PI 88788 (G. max([PI 88788])) to H. glycines population NL1-RHg/HG-type 7 (H. glycines([NL1-RHg/HG-type 7])) is accomplished by laser microdissection of syncytia at 3, 6 and 9dpi. Comparative analyses are made to pericycle and their neighboring cells isolated from mock-inoculated roots. These analyses reveal induced levels of the jasmonic acid biosynthesis and 13-lipoxygenase pathways. Direct comparative analyses were also made of syncytia at 6 days post infection to those at 3dpi (base line). The comparative analyses were done to identify localized gene expression that characterizes the resistance phase of the resistant reaction. The most highly induced pathways include components of jasmonic acid biosynthesis, 13-lipoxygenase pathway, S-adenosyl methionine pathway, phenylpropanoid biosynthesis, suberin biosynthesis, adenosylmethionine biosynthesis, ethylene biosynthesis from methionine, flavonoid biosynthesis and the methionine salvage pathway. In comparative analyses of 9dpi to 6dpi (base line), these pathways, along with coumarin biosynthesis, cellulose biosynthesis and homogalacturonan degradation are induced. The experiments presented here strongly implicate the jasmonic acid defense pathway as a factor involved in the localized resistant reaction of G. max([PI 88788]) to H. glycines([NL1-RHg/HG-type 7]).
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Affiliation(s)
- Vincent P Klink
- Department of Biological Sciences, Harned Hall, Mississippi State University, Mississippi State, MS, 39762, USA.
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15
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Klink VP, Hosseini P, Matsye P, Alkharouf NW, Matthews BF. A gene expression analysis of syncytia laser microdissected from the roots of the Glycine max (soybean) genotype PI 548402 (Peking) undergoing a resistant reaction after infection by Heterodera glycines (soybean cyst nematode). PLANT MOLECULAR BIOLOGY 2009; 71:525-67. [PMID: 19787434 DOI: 10.1007/s11103-009-9539-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2009] [Accepted: 08/09/2009] [Indexed: 05/07/2023]
Abstract
The syncytium is a nurse cell formed within the roots of Glycine max by the plant parasitic nematode Heterodera glycines. Its development and maintenance are essential for nematode survival. The syncytium appears to undergo two developmental phases during its maturation into a functional nurse cell. The first phase is a parasitism phase where the nematode establishes the molecular circuitry that during the second phase ensures a compatible interaction with the plant cell. The cytological features of syncytia undergoing susceptible or resistant reactions appear the same during the parasitism phase. Depending on the outcome of any defense response, the second phase is a period of syncytium maintenance (susceptible reaction) or failure (resistant reaction). In the analyses presented here, the localized gene expression occurring at the syncytium during the resistant reaction was studied. This was accomplished by isolating syncytial cells from Glycine max genotype Peking (PI 548402) by laser capture microdissection. Microarray analyses using the Affymetrix soybean GeneChip directly compared Peking syncytia undergoing a resistant reaction to those undergoing a susceptible reaction during the parasitism phase of the resistant reaction. Those analyses revealed lipoxygenase-9 and lipoxygenase-4 as the most highly induced genes in the resistant reaction. The analysis also identified induced levels of components of the phenylpropanoid pathway. These genes included phenylalanine ammonia lyase, chalcone isomerase, isoflavone reductase, cinnamoyl-CoA reductase and caffeic acid O-methyltransferase. The presence of induced levels of these genes implies the importance of jasmonic acid and phenylpropanoid signaling pathways locally at the site of the syncytium during the resistance phase of the resistant reaction. The analysis also identified highly induced levels of four S-adenosylmethionine synthetase genes, the EARLY-RESPONSIVE TO DEHYDRATION 2 gene and the 14-3-3 gene known as GENERAL REGULATORY FACTOR 2. Subsequent analyses studied microdissected syncytial cells at 3, 6 and 9 days post infection (dpi) during the course of the resistant reaction, resulting in the identification of signature gene expression profiles at each time point in a single G. max genotype, Peking.
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Affiliation(s)
- Vincent P Klink
- Department of Biological Sciences, Mississippi State University, Harned Hall, Mississippi State, MS 39762, USA.
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16
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Afzal AJ, Natarajan A, Saini N, Iqbal MJ, Geisler M, El Shemy HA, Mungur R, Willmitzer L, Lightfoot DA. The nematode resistance allele at the rhg1 locus alters the proteome and primary metabolism of soybean roots. PLANT PHYSIOLOGY 2009; 151:1264-80. [PMID: 19429603 PMCID: PMC2773059 DOI: 10.1104/pp.109.138149] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Accepted: 05/03/2009] [Indexed: 05/19/2023]
Abstract
Heterodera glycines, the soybean cyst nematode (SCN), causes the most damaging chronic disease of soybean (Glycine max). Host resistance requires the resistance allele at rhg1. Resistance destroys the giant cells created in the plant's roots by the nematodes about 24 to 48 h after commencement of feeding. In addition, 4 to 8 d later, a systemic acquired resistance develops that discourages later infestations. The molecular mechanisms that control the rhg1-mediated resistance response appear to be multigenic and complex, as judged by transcript abundance changes, even in near isogenic lines (NILs). This study aimed to focus on key posttranscriptional changes by identifying proteins and metabolites that were increased in abundance in both resistant and susceptible NILs. Comparisons were made among NILs 10 d after SCN infestation and without SCN infestation. Two-dimensional gel electrophoresis resolved more than 1,000 protein spots on each gel. Only 30 protein spots with a significant (P < 0.05) difference in abundance of 1.5-fold or more were found among the four treatments. The proteins in these spots were picked, trypsin digested, and analyzed using quadrupole time-of-flight tandem mass spectrometry. Protein identifications could be made for 24 of the 30 spots. Four spots contained two proteins, so that 28 distinct proteins were identified. The proteins were grouped into six functional categories. Metabolite analysis by gas chromatography-mass spectrometry identified 131 metabolites, among which 58 were altered by one or more treatment; 28 were involved in primary metabolism. Taken together, the data showed that 17 pathways were altered by the rhg1 alleles. Pathways altered were associated with systemic acquired resistance-like responses, including xenobiotic, phytoalexin, ascorbate, and inositol metabolism, as well as primary metabolisms like amino acid synthesis and glycolysis. The pathways impacted by the rhg1 allelic state and SCN infestation agreed with transcript abundance analyses but identified a smaller set of key proteins. Six of the proteins lay within the same small region of the interactome identifying a key set of 159 interacting proteins involved in transcriptional control, nuclear localization, and protein degradation. Finally, two proteins (glucose-6-phosphate isomerase [EC 5.3.1.9] and isoflavone reductase [EC 1.3.1.45]) and two metabolites (maltose and an unknown) differed in resistant and susceptible NILs without SCN infestation and may form the basis of a new assay for the selection of resistance to SCN in soybean.
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Affiliation(s)
| | | | | | | | | | | | | | | | - David A. Lightfoot
- Department of Molecular Biology, Microbiology, and Biochemistry (A.J.A., A.N., H.A.E.S., R.M., D.A.L.), Genomics Core Facility and Center for Excellence in Soybean Research, Teaching, and Outreach, Department of Plant Soil and Agricultural Systems (A.J.A., N.S., H.A.E.S., D.A.L.), and Department of Plant Biology (M.G., D.A.L.), Southern Illinois University, Carbondale, Illinois 62901; Institute for Advanced Learning and Research, Institute for Sustainable and Renewable Resources, Danville, Virginia 24540 (M.J.I.); and Max Planck Institute for Molecular Plant Physiology, Potsdam 14476, Germany (R.M., L.W.)
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17
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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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18
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Klink VP, Hosseini P, MacDonald MH, Alkharouf NW, Matthews BF. Population-specific gene expression in the plant pathogenic nematode Heterodera glycines exists prior to infection and during the onset of a resistant or susceptible reaction in the roots of the Glycine max genotype Peking. BMC Genomics 2009; 10:111. [PMID: 19291306 PMCID: PMC2662880 DOI: 10.1186/1471-2164-10-111] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2008] [Accepted: 03/16/2009] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND A single Glycine max (soybean) genotype (Peking) reacts differently to two different populations of Heterodera glycines (soybean cyst nematode) within the first twelve hours of infection during resistant (R) and susceptible (S) reactions. This suggested that H. glycines has population-specific gene expression signatures. A microarray analysis of 7539 probe sets representing 7431 transcripts on the Affymetrix soybean GeneChip were used to identify population-specific gene expression signatures in pre-infective second stage larva (pi-L2) prior to their infection of Peking. Other analyses focused on the infective L2 at 12 hours post infection (i-L2(12h)), and the infective sedentary stages at 3 days post infection (i-L2(3d)) and 8 days post infection (i-L2/L3(8d)). RESULTS Differential expression and false discovery rate (FDR) analyses comparing populations of pi-L2 (i.e., incompatible population, NL1-RHg to compatible population, TN8) identified 71 genes that were induced in NL1-RHg as compared to TN8. These genes included putative gland protein G23G12, putative esophageal gland protein Hgg-20 and arginine kinase. The comparative analysis of pi-L2 identified 44 genes that were suppressed in NL1-RHg as compared to TN8. These genes included a different Hgg-20 gene, an EXPB1 protein and a cuticular collagen. By 12 h, there were 7 induced genes and 0 suppressed genes in NL1-RHg. By 3d, there were 9 induced and 10 suppressed genes in NL1-RHg. Substantial changes in gene expression became evident subsequently. At 8d there were 13 induced genes in NL1-RHg. This included putative gland protein G20E03, ubiquitin extension protein, putative gland protein G30C02 and beta-1,4 endoglucanase. However, 1668 genes were found to be suppressed in NL1-RHg. These genes included steroid alpha reductase, serine proteinase and a collagen protein. CONCLUSION These analyses identify a genetic expression signature for these two populations both prior to and subsequently as they undergo an R or S reaction. The identification of genes like steroid alpha reductase and serine proteinase that are involved in feeding and nutritional uptake as being highly suppressed during the R response at 8d may indicate genes that the plant is targeting. The analyses also identified numerous putative parasitism genes that are differentially expressed. The 1668 genes that are suppressed in NL1-RHg, and hence induced in TN8 may represent genes that are important during the parasitic stages of H. glycines development. The potential for different arrays of putative parasitism genes to be expressed in different nematode populations may indicate how H. glycines evolve mechanisms to overcome resistance.
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Affiliation(s)
- Vincent P Klink
- Department of Biological Sciences, Harned Hall, Mississippi State University, Mississippi State, MS 39762, USA
- United States Department of Agriculture, Plant Sciences Institute, Beltsville, MD 20705, USA
| | - Parsa Hosseini
- Jess and Mildred Fisher College of Science and Mathematics, Department of Computer and Information Sciences, Towson University, 7800 York Road, Towson, Maryland 21252, USA
| | - Margaret H MacDonald
- United States Department of Agriculture, Plant Sciences Institute, Beltsville, MD 20705, USA
| | - Nadim W Alkharouf
- Jess and Mildred Fisher College of Science and Mathematics, Department of Computer and Information Sciences, Towson University, 7800 York Road, Towson, Maryland 21252, USA
| | - Benjamin F Matthews
- United States Department of Agriculture, Plant Sciences Institute, Beltsville, MD 20705, USA
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Choi JJ, Alkharouf NW, Schneider KT, Matthews BF, Frederick RD. Expression patterns in soybean resistant to Phakopsora pachyrhizi reveal the importance of peroxidases and lipoxygenases. Funct Integr Genomics 2008; 8:341-59. [PMID: 18414911 DOI: 10.1007/s10142-008-0080-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2007] [Revised: 03/07/2008] [Accepted: 03/09/2008] [Indexed: 10/22/2022]
Abstract
Soybean rust caused by Phakopsora pachyrhizi Sydow is a devastating foliar disease that has spread to most soybean growing regions throughout the world, including the USA. Four independent rust resistance genes, Rpp1-Rpp4, have been identified in soybean that recognize specific isolates of P. pachyrhizi. A suppressive subtraction hybridization (SSH) complementary DNA (cDNA) library was constructed from the soybean accession PI200492, which contains Rpp1, after inoculation with two different isolates of P. pachyrhizi that result in susceptible or immune reactions. Both forward and reverse SSH were performed using cDNA from messenger RNA pooled from 1, 6, 12, 24, and 48 h post-inoculation. A total of 1,728 SSH clones were sequenced and compared to sequences in GenBank for similarity. Microarray analyses were conducted on a custom 7883 soybean-cDNA clone array encompassing all of the soybean-rust SSH clones and expressed sequence tags from four other soybean cDNA libraries. Results of the microarray revealed 558 cDNA clones differentially expressed in the immune reaction. The majority of the upregulated cDNA clones fell into the functional category of defense. In particular, cDNA clones with similarity to peroxidases and lipoxygenases were prevalent. Downregulated cDNA clones included those with similarity to cell-wall-associated protein, such as extensins, proline-rich proteins, and xyloglucan endotransglycosylases.
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Affiliation(s)
- J J Choi
- Foreign Disease-Weed Science Research Unit, USDA-Agricultural Research Service, 1301 Ditto Avenue, Fort Detrick, MD, 21702, USA.
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20
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A decline in transcript abundance for Heterodera glycines homologs of Caenorhabditis elegans uncoordinated genes accompanies its sedentary parasitic phase. BMC DEVELOPMENTAL BIOLOGY 2007; 7:35. [PMID: 17445261 PMCID: PMC1867819 DOI: 10.1186/1471-213x-7-35] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2006] [Accepted: 04/19/2007] [Indexed: 12/13/2022]
Abstract
Background Heterodera glycines (soybean cyst nematode [SCN]), the major pathogen of Glycine max (soybean), undergoes muscle degradation (sarcopenia) as it becomes sedentary inside the root. Many genes encoding muscular and neuromuscular components belong to the uncoordinated (unc) family of genes originally identified in Caenorhabditis elegans. Previously, we reported a substantial decrease in transcript abundance for Hg-unc-87, the H. glycines homolog of unc-87 (calponin) during the adult sedentary phase of SCN. These observations implied that changes in the expression of specific muscle genes occurred during sarcopenia. Results We developed a bioinformatics database that compares expressed sequence tag (est) and genomic data of C. elegans and H. glycines (CeHg database). We identify H. glycines homologs of C. elegans unc genes whose protein products are involved in muscle composition and regulation. RT-PCR reveals the transcript abundance of H. glycines unc homologs at mobile and sedentary stages of its lifecycle. A prominent reduction in transcript abundance occurs in samples from sedentary nematodes for homologs of actin, unc-60B (cofilin), unc-89, unc-15 (paromyosin), unc-27 (troponin I), unc-54 (myosin), and the potassium channel unc-110 (twk-18). Less reduction is observed for the focal adhesion complex gene Hg-unc-97. Conclusion The CeHg bioinformatics database is shown to be useful in identifying homologs of genes whose protein products perform roles in specific aspects of H. glycines muscle biology. Our bioinformatics comparison of C. elegans and H. glycines genomic data and our Hg-unc-87 expression experiments demonstrate that the transcript abundance of specific H. glycines homologs of muscle gene decreases as the nematode becomes sedentary inside the root during its parasitic feeding stages.
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21
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Alkharouf NW, Klink VP, Matthews BF. Identification of Heterodera glycines (soybean cyst nematode [SCN]) cDNA sequences with high identity to those of Caenorhabditis elegans having lethal mutant or RNAi phenotypes. Exp Parasitol 2007; 115:247-58. [PMID: 17052709 DOI: 10.1016/j.exppara.2006.09.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Revised: 09/05/2006] [Accepted: 09/06/2006] [Indexed: 10/24/2022]
Abstract
The soybean cyst nematode (SCN; Heterodera glycines) is a devastating obligate parasite of Glycine max (soybean) causing one billion dollars in losses to the US economy per year and over ten billion dollars in losses worldwide. While much is understood about the pathology of H. glycines, its genome sequence is not well characterized or fully sequenced. We sought to create bioinformatic tools to mine the H. glycines nucleotide database. One way is to use a comparative genomics approach by anchoring our analysis with an organism, like the free-living nematode Caenorhabditis elegans. Unlike H. glycines, the C. elegans genome is fully sequenced and is well characterized with a number of lethal genes identified through experimental methods. We compared an EST database of H. glycines with the C. elegans genome. Our goal was identifying genes that may be essential for H. glycines survival and would serve as an automated pipeline for RNAi studies to both study and control H. glycines. Our analysis yielded a total of nearly 8334 conserved genes between H. glycines and C. elegans. Of these, 1508 have lethal phenotypes/phenocopies in C. elegans. RNAi of a conserved ribosomal gene from H. glycines (Hg-rps-23) yielded dead and dying worms as shown by positive Sytox fluorescence. Endogenous Hg-rps-23 exhibited typical RNA silencing as shown by RT-PCR. However, an unrelated gene Hg-unc-87 did not exhibit RNA silencing in the Hg-rps-23 dsRNA-treated worms, demonstrating the specificity of the silencing.
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Affiliation(s)
- Nadim W Alkharouf
- United States Department of Agriculture, ARS, Soybean Genomics and Improvement Laboratory, Beltsville, MD 20705-2350, USA
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22
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Klink VP, Overall CC, Matthews BF. Developing a Systems Biology Approach to Study Disease Progression Caused by Heterodera glycinesin Glycine max. GENE REGULATION AND SYSTEMS BIOLOGY 2007. [DOI: 10.1177/117762500700100003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Vincent P. Klink
- United States Department of Agriculture, Soybean Genomics and Improvement Laboratory, Bldg 006, Beltsville, MD 20705
| | - Christopher C. Overall
- Department of Bioinformatics and Computational Biology, George Mason University, Manassas, VA 20110
| | - Benjamin F. Matthews
- United States Department of Agriculture, Soybean Genomics and Improvement Laboratory, Bldg 006, Beltsville, MD 20705
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Elling AA, Mitreva M, Recknor J, Gai X, Martin J, Maier TR, McDermott JP, Hewezi T, McK Bird D, Davis EL, Hussey RS, Nettleton D, McCarter JP, Baum TJ. Divergent evolution of arrested development in the dauer stage of Caenorhabditis elegans and the infective stage of Heterodera glycines. Genome Biol 2007; 8:R211. [PMID: 17919324 PMCID: PMC2246285 DOI: 10.1186/gb-2007-8-10-r211] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2007] [Accepted: 10/05/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The soybean cyst nematode Heterodera glycines is the most important parasite in soybean production worldwide. A comprehensive analysis of large-scale gene expression changes throughout the development of plant-parasitic nematodes has been lacking to date. RESULTS We report an extensive genomic analysis of H. glycines, beginning with the generation of 20,100 expressed sequence tags (ESTs). In-depth analysis of these ESTs plus approximately 1,900 previously published sequences predicted 6,860 unique H. glycines genes and allowed a classification by function using InterProScan. Expression profiling of all 6,860 genes throughout the H. glycines life cycle was undertaken using the Affymetrix Soybean Genome Array GeneChip. Our data sets and results represent a comprehensive resource for molecular studies of H. glycines. Demonstrating the power of this resource, we were able to address whether arrested development in the Caenorhabditis elegans dauer larva and the H. glycines infective second-stage juvenile (J2) exhibits shared gene expression profiles. We determined that the gene expression profiles associated with the C. elegans dauer pathway are not uniformly conserved in H. glycines and that the expression profiles of genes for metabolic enzymes of C. elegans dauer larvae and H. glycines infective J2 are dissimilar. CONCLUSION Our results indicate that hallmark gene expression patterns and metabolism features are not shared in the developmentally arrested life stages of C. elegans and H. glycines, suggesting that developmental arrest in these two nematode species has undergone more divergent evolution than previously thought and pointing to the need for detailed genomic analyses of individual parasite species.
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Affiliation(s)
- Axel A Elling
- Interdepartmental Genetics Program, Iowa State University, Ames, IA 50011, USA
- Department of Plant Pathology, Iowa State University, Ames, IA 50011, USA
- Current address: Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Makedonka Mitreva
- Department of Genetics, Washington University School of Medicine, Genome Sequencing Center, St Louis, MO 63108, USA
| | - Justin Recknor
- Department of Statistics, Iowa State University, Ames, IA 50011, USA
| | - Xiaowu Gai
- LH Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA 50011, USA
- Current address: Center for Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - John Martin
- Department of Genetics, Washington University School of Medicine, Genome Sequencing Center, St Louis, MO 63108, USA
| | - Thomas R Maier
- Department of Plant Pathology, Iowa State University, Ames, IA 50011, USA
| | - Jeffrey P McDermott
- Department of Plant Pathology, Iowa State University, Ames, IA 50011, USA
- Current address: The University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Tarek Hewezi
- Department of Plant Pathology, Iowa State University, Ames, IA 50011, USA
| | - David McK Bird
- Department of Plant Pathology, NC State University, Raleigh, NC 27695, USA
| | - Eric L Davis
- Department of Plant Pathology, NC State University, Raleigh, NC 27695, USA
| | - Richard S Hussey
- Department of Plant Pathology, University of Georgia, Athens, GA 30602, USA
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, IA 50011, USA
| | - James P McCarter
- Department of Genetics, Washington University School of Medicine, Genome Sequencing Center, St Louis, MO 63108, USA
- Divergence Inc., North Warson Road, St Louis, MO 63141, USA
| | - Thomas J Baum
- Interdepartmental Genetics Program, Iowa State University, Ames, IA 50011, USA
- Department of Plant Pathology, Iowa State University, Ames, IA 50011, USA
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Alkharouf NW, Klink VP, Chouikha IB, Beard HS, MacDonald MH, Meyer S, Knap HT, Khan R, Matthews BF. Timecourse microarray analyses reveal global changes in gene expression of susceptible Glycine max (soybean) roots during infection by Heterodera glycines (soybean cyst nematode). PLANTA 2006; 224:838-52. [PMID: 16575592 DOI: 10.1007/s00425-006-0270-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Accepted: 03/11/2006] [Indexed: 05/07/2023]
Abstract
Changes in gene expression within roots of Glycine max (soybean), cv. Kent, susceptible to infection by Heterodera glycines (the soybean cyst nematode [SCN]), at 6, 12, and 24 h, and 2, 4, 6, and 8 days post-inoculation were monitored using microarrays containing more than 6,000 cDNA inserts. Replicate, independent biological samples were examined at each time point. Gene expression was analyzed statistically using T-tests, ANOVA, clustering algorithms, and online analytical processing (OLAP). These analyses allow the user to query the data in several ways without importing the data into third-party software. RT-PCR confirmed that WRKY6 transcription factor, trehalose phosphate synthase, EIF4a, Skp1, and CLB1 were differentially induced across most time-points. Other genes induced across most timepoints included lipoxygenase, calmodulin, phospholipase C, metallothionein-like protein, and chalcone reductase. RT-PCR demonstrated enhanced expression during the first 12 h of infection for Kunitz trypsin inhibitor and sucrose synthase. The stress-related gene, SAM-22, phospholipase D and 12-oxophytodienoate reductase were also induced at the early time-points. At 6 and 8 dpi there was an abundance of transcripts expressed that encoded genes involved in transcription and protein synthesis. Some of those genes included ribosomal proteins, and initiation and elongation factors. Several genes involved in carbon metabolism and transport were also more abundant. Those genes included glyceraldehyde 3-phosphate dehydrogenase, fructose-bisphosphate aldolase and sucrose synthase. These results identified specific changes in gene transcript levels triggered by infection of susceptible soybean roots by SCN.
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Affiliation(s)
- Nadim W Alkharouf
- USDA-ARS-PSI-SGIL, Bldg.006, Rm 118, 10300 Baltimore Avenue, Beltsville, MD 20705, USA
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Klink VP, Alkharouf N, MacDonald M, Matthews B. Laser capture microdissection (LCM) and expression analyses of Glycine max (soybean) syncytium containing root regions formed by the plant pathogen Heterodera glycines (soybean cyst nematode). PLANT MOLECULAR BIOLOGY 2005; 59:965-79. [PMID: 16307369 DOI: 10.1007/s11103-005-2416-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2005] [Accepted: 08/22/2005] [Indexed: 05/05/2023]
Abstract
Roots of soybean, Glycine max cv. Kent L. Merr., plants susceptible to the soybean cyst nematode (SCN), Heterodera glycines Ichinohe, were inoculated and allowed to develop feeding sites (syncytia) for 8 days. Root samples enriched in syncytial cells were collected using laser capture microdissection (LCM). RNA was extracted and used to make a cDNA library and expressed sequence tags (ESTs) were produced and used for a Gene Ontology (GO) analysis. RT-PCR results indicated enhanced expression of an aquaporin (GmPIP2,2), alpha-tubulin (GmTubA1), beta-tubulin (GmTubB4) and several other genes in syncytium-enriched samples as compared to samples extracted from whole roots. While RT-PCR data showed increased transcript levels of GmPIP2,2 from LCM tissue enriched in syncytial cells, in situ hybridization showed prominent GmPIP2,2 hybridization to RNA in the parenchymal cells tightly juxtaposed to the syncytium. Immunolocalization indicated stronger alpha-tubulin signal within the syncytium as compared to surrounding tissue. However, alpha-tubulin labeling appeared diffuse or clumped. Thus, LCM allowed for the isolation of tissue enriched for syncytial cells, providing material suitable for a variety of molecular analyses.
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Affiliation(s)
- Vincent P Klink
- United States Department of Agriculture, 10300, Baltimore Ave., Bldg. 006, Rm. 118, Beltsville, MD, 20705-2350, USA.
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Alkharouf NW, Matthews BF. SGMD: the Soybean Genomics and Microarray Database. Nucleic Acids Res 2004; 32:D398-400. [PMID: 14681442 PMCID: PMC308860 DOI: 10.1093/nar/gkh126] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2003] [Revised: 10/15/2003] [Accepted: 10/23/2003] [Indexed: 11/14/2022] Open
Abstract
The Soybean Genomics and Microarray Database (SGMD) attempts to provide an integrated view of the interaction of soybean with the soybean cyst nematode and contains genomic, EST and microarray data with embedded analytical tools allowing correlation of soybean ESTs with their gene expression profiles. SGMD provides analytical tools to mine the microarray data quickly by integrating many analysis methods within the database itself. The expression profiles of genes at time intervals during the first 8 days of nematode invasion is searchable by gene name or GenBank accession number. Recent developments include the addition of a searchable database for soybean cyst nematode ESTs and photographs of the invasion process at time points examined using microarrays. SGMD is completely accessible from the web at: http://psi081.ba.ars.usda.gov/SGMD/default.htm.
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Affiliation(s)
- Nadim W Alkharouf
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Building 006, Room 118, 10300 Baltimore Avenue, Beltsville, MD 20705-2350, USA
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2004. [PMCID: PMC2447475 DOI: 10.1002/cfg.357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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