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      Glycine max Homologs of DOESN'T MAKE INFECTIONS 1, 2, and 3 Function to Impair Heterodera glycines Parasitism While Also Regulating Mitogen Activated Protein Kinase Expression

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          Abstract

          Glycine max root cells developing into syncytia through the parasitic activities of the pathogenic nematode Heterodera glycines underwent isolation by laser microdissection (LM). Microarray analyses have identified the expression of a G. max DOESN'T MAKE INFECTIONS3 ( DMI3) homolog in syncytia undergoing parasitism but during a defense response. DMI3 encodes part of the common symbiosis pathway (CSP) involving DMI1, DMI2, and other CSP genes. The identified DMI gene expression, and symbiosis role, suggests the possible existence of commonalities between symbiosis and defense. G. max has 3 DMI1, 12 DMI2, and 2 DMI3 paralogs. LM-assisted gene expression experiments of isolated syncytia under further examination here show G. max DMI1-3, DMI2-7, and DMI3-2 expression occurring during the defense response in the H. glycines-resistant genotypes G. max [Peking/PI548402] and G. max [PI88788] indicating a broad and consistent level of expression of the genes. Transgenic overexpression (OE) of G. max DMI1-3, DMI2-7, and DMI3-2 impairs H. glycines parasitism. RNA interference (RNAi) of G. max DMI1-3, DMI2-7, and DMI3-2 increases H. glycines parasitism. The combined opposite outcomes reveal a defense function for these genes. Prior functional transgenic analyses of the 32-member G. max mitogen activated protein kinase ( MAPK) gene family has determined that 9 of them act in the defense response to H. glycines parasitism, referred to as defense MAPKs. RNA-seq analyses of root RNA isolated from the 9 G. max defense MAPKs undergoing OE or RNAi reveal they alter the relative transcript abundances (RTAs) of specific DMI1, DMI2, and DMI3 paralogs. In contrast, transgenically-manipulated DMI1-3, DMI2-7, and DMI3-2 expression influences MAPK3-1 and MAPK3-2 RTAs under certain circumstances. The results show G. max homologs of the CSP, and defense pathway are linked, apparently involving co-regulated gene expression.

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          Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

          The two most commonly used methods to analyze data from real-time, quantitative PCR experiments are absolute quantification and relative quantification. Absolute quantification determines the input copy number, usually by relating the PCR signal to a standard curve. Relative quantification relates the PCR signal of the target transcript in a treatment group to that of another sample such as an untreated control. The 2(-Delta Delta C(T)) method is a convenient way to analyze the relative changes in gene expression from real-time quantitative PCR experiments. The purpose of this report is to present the derivation, assumptions, and applications of the 2(-Delta Delta C(T)) method. In addition, we present the derivation and applications of two variations of the 2(-Delta Delta C(T)) method that may be useful in the analysis of real-time, quantitative PCR data. Copyright 2001 Elsevier Science (USA).
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            A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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              A Revised Medium for Rapid Growth and Bio Assays with Tobacco Tissue Cultures

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                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                04 May 2022
                2022
                : 13
                : 842597
                Affiliations
                [1] 1Department of Biological Sciences, Mississippi State University , Starkville, MS, United States
                [2] 2Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University , Starkville, MS, United States
                [3] 3Department of Entomology and Plant Pathology, Auburn University , Auburn, AL, United States
                [4] 4Department of Computer and Information Sciences, Towson University , Towson, MD, United States
                [5] 5USDA ARS NEA BARC Molecular Plant Pathology Laboratory , Beltsville, MD, United States
                [6] 6Center for Computational Sciences High Performance Computing Collaboratory, Mississippi State University , Starkville, MS, United States
                Author notes

                Edited by: Marc Libault, University of Nebraska-Lincoln, United States

                Reviewed by: Senjuti Sinharoy, National Institute of Plant Genome Research (NIPGR), India; Pingchuan Deng, Northwest A&F University, China

                *Correspondence: Vincent P. Klink vincent.klink@ 123456usda.gov

                This article was submitted to Plant Cell Biology, a section of the journal Frontiers in Plant Science

                †ORCID: Rishi Khatri orcid.org/0000-0003-4985-0607

                Prakash M. Niraula orcid.org/0000-0002-3145-6364

                ‡Present address: Shankar R. Pant, Pebble Labs, Los Alamos, NM, United States

                Keshav Sharma, Cereal Disease Laboratory, Saint Paul, MN, United States

                Prakash M. Niraula, Department of Biological Sciences, Delaware State University, Dover, DE, United States

                Bisho R. Lawaju, Department of Plant Pathology, North Dakota State University, Fargo, ND, United States

                Article
                10.3389/fpls.2022.842597
                9114929
                e079e03a-9863-4145-81b8-e5ff572f585b
                Copyright © 2022 Khatri, Pant, Sharma, Niraula, Lawaju, Lawrence, Alkharouf and Klink.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 23 December 2021
                : 21 March 2022
                Page count
                Figures: 7, Tables: 3, Equations: 0, References: 171, Pages: 26, Words: 22758
                Funding
                Funded by: Mississippi State University, doi 10.13039/100007250;
                Award ID: College or Arts and Sciences SR! 2018-01
                Funded by: Cotton Incorporated, doi 10.13039/100006481;
                Categories
                Plant Science
                Original Research

                Plant science & Botany
                plant parasitic nematode,pathogen recognition receptor (prr),effector triggered immunity (eti),pathogen associated molecular pattern (pamp),pamp triggered immunity (pti),glycine max,common symbiosis pathway (csp),doesn't make infections (dmi)

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