Glossary

ABC transporters A large family of proteins embedded in plasma membranecharacterized by a highly conserved ATP-binding domain; they constitute a class ofmembrane transporter proteins capable of transferring sugar molecules, inorganicions, polypeptides, certain anticancer drugs and antibiotics

Acquired resistance Enhancement of resistance of plants following infection ortreatment with biotic or abiotic resistance inducers

Actin Structural proteins are present abundantly in eukaryotic cells that can interactwith many other proteins; these proteins polymerize to form cytoskeletal filaments

Activator Transcription factor that stimulates transcription

Active site The region of an enzyme that binds substrate molecules and catalyzesan enzymatic reaction

Active transport Export of an ion or small molecule across a membrane againstits concentration gradient driven by the hydrolysis of ATP

Alarm signal In response to pathogenic infection, chemical(s) produced, may sendsignal to host cell proteins/genes leading to synthesis of compounds inhibitory to theinvading pathogen

Algorithm A logical description of the manner in which a problem can be solvedand that can be used as a specification for how to write a computer program; a com-putational procedure that employs a combination of simple operations to process,analyze and present pictorially data about sequences of DNA, RNA, proteins orother molecules

Alignment This is an arrangement of two or more molecular sequences one belowthe other in such a way that regions that are identical or similar are placed immedi-ately below one another

Allele It is an alternate form of a gene occupying a given locus on the samechromosome which controls expression (of product) in different ways

Allozyme An allele of the gene may be involved in the production of an enzymewith properties slightly different from that of the enzyme produced by the geneconcerned

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298 Glossary

Amino acid profile Quantitative delineation of how much of each amino acid ispresent in a particular protein

Aminoacyl-tRNA synthetase Enzyme that catalyzes the linkage of an amino acidto a specific tRNA to be used for protein synthesis

Amplicon A specific sequence of DNA that is produced from the template frag-ment by reactions such as polymerase chain reaction assay

Amplification Synthesis of additional copies of a DNA sequence found either aschromosomal or extrachromosomal DNA

Analog A compound or molecule that is a structural derivative of a ‘parent’ com-pound; this term also refers to a molecule that may be structurally similar, but notidentical to another, and may exhibit many or some of the biological functions ofthe other

Ankyrin a protein capable of binding spectrin and links the actin cytoskeleton tothe plasma membrane

Annealing The process by which the complementary base pairs in the strands ofDNA combine

Annotated gene A gene is said to be annotated when it has been recognized froma large segment of genome sequence and if its cellular role is known to someextent

Antibody A protein (immunoglobulin) formed in an animal circulatory system inresponse to introduction of an antigen (usually a protein or nucleoprotein)

Anticodon The sequence of three bases on tRNA that combines with the comple-mentary triplet codon on mRNA

Antigen A protein or live or inactivated microbe capable of inducing the productionof a specific antibody in an animal system and capable of reacting with that antibodyin a specific manner

Antisense technology A molecular technique that uses a nucleic acid sequencecomplementary to mRNA so that the two bind and the mRNA is effectivelyneutralized

Apoplast Space outside of the plasma membrane of cells constituted by cell wallsand conducting cells of the xylem in which aqueous phase of intercellular solutes ispresent

Apoptosis It is a natural phenomenon encountered in animal cells for the elimina-tion of cells involving a highly regulated, energy-dependent process by which a cellbrings about its own death (programmed cell death in plants)

Attacins These proteins constitute a class of antimicrobial peptides produced in theinsect hemolymph; synthesis of outer membrane proteins of Gram negative bacteriais inhibited by attacins

Glossary 299

Avidin A protein found in egg white and bacteria like Streptomyces that binds withvery high affinity to the vitamin biotin (vitamin H)

Avirulence Opposite of virulence indicating the inability of a pathogen to infecta particular species or cultivar of a plant, presumably because of the presence ofavirulence gene(s) whose product(s) alerts the host resistance mechanism

Avirulence conferring enzyme (ACE) The avirulence gene of the fungal pathogencoding for the enzyme that is recognized by the resistant cultivar carrying corre-sponding resistance gene. The rice resistance gene Pi33 recognizes Magnaporthegrisea isolates carrying ACE 1 gene

Avr gene Pathogen gene that is responsible for the inability to infect a given plantspecies or cultivar

Avr protein The protein coded for by the avr gene, capable of functioning as anelicitor of defense responses in plants

Bacterial artificial chromosome (BAC) DNA molecules that are used as cloningvectors, derived from plasmids. This type of vector can be employed for cloninglarge inserts (of about 150,000 bp) of DNA in bacteria

Base pair (bp) Association of two complementary nucleotides in a DNA or RNAmolecule stabilized by hydrogen bonding between their base components adeninepairing with thymine or uracil and guanine pairing with cytosine

Biofilm Bacteria or fungi may be embedded in polysaccharide matrix that plays arole in attachment to host surface, colonization and invasion

Bioinformatics Computer based analysis of data on biological sequencing of thegenome of an organism to predict gene function, protein and RNA structure, genomeorganization and molecular bases in relation to responses of plants to microbialpathogens

Biolistic This term has been coined from the words ‘biologic’ and ‘ballistic’; refersto process involving the use of pellets coated with the desired genes that are fired froma gun into seeds or plant tissues in order to get plants expressing these transgenes

Bioluminescence Emission of light from a living organism

BLAST (Basic Local Alignment Search Tool) This program is used widely forsearching sequence databases for entries that are similar to a specified sequence inquestion

Bootstrapping A statistics protocol used to estimate the reliability of a result (suchas construction of phylogenetic tree) that involves sampling data with replacementfrom the original set of data

Calmodulin A small cytosolic regulatory protein that binds four Ca2+ ions; theCa2+/calmodulin complex can interact with many proteins resulting in inhibition oractivation of those proteins

Capsid Protein coat of viruses that encloses the viral genome

300 Glossary

Cauliflower mosaic virus 35S promoter (CaMV 35S) This promoter consisting ofDNA sequences of the virus is employed very frequently in genetic engineering tocontrol expression of an inserted gene (synthesis of desired protein in a plant)

cDNA A complementary DNA strand to an RNA strand and synthesized from RNAstrand using reverse transcriptase enzyme. It is also known as copy DNA

cDNA clone A DNA molecule synthesized from a mRNA sequence via sequentialuse of reverse transcription and DNA polymerase

cDNA library A collection of cDNA clones which represent all the genetic informa-tion expressed by a given cell or by a given tissue type is known as a cDNA library

Cecropins Antimicrobial proteins isolated from insects capable of forming pores inand causing lysis of bacterial cell membrane (see humoral immunity)

Chaperon protein A protein molecule attached to and to facilitate the export ofan effector protein secreted through a type III secretion system of bacteria. It mayprotect theeffectorprotein fromcoming incontactwithotherproteins.Thechaperonesmay also assist with correct folding as the protein molecule emerges from the cell’sribosome

Chemotaxis Capacity of a cell or organism to move toward or away from certainchemicals

Chromosome walking A technique employed for determining the location of andsequencing a given gene within the genome of the organism, by sequencing specificDNA fragments that overlap and span collectively

cis-acting protein This protein has the exceptional property of acting only on themolecule of DNA from which it was expressed

Cistron Viral sequences of nucleotides of DNA/RNA that code for particular proteinand are considered to be analogous to genes of other organisms

Clade A clade consists of all the species descending from an internal node ofgenealogical tree

Clone Genetically identical individuals produced asexually from one individual

Cloning of DNA Introduction of a segment of DNA from one species into the DNAof another species leading to the formation of many copies of the hybrid DNA byreplication

Codon A sequence of three nucleotide (triplet) bases on mRNA that interacts withthe anticodon on tRNA and specifies the incorporation of a specific amino acid into apolypeptide during translation process

Codon usage The frequency of occurrence of each codon in a gene or genome,especially the relative frequencies with which synonymous codons are used

Colony hybridization A technique used in situ hybridization to identify bacterialcolonies carrying inserted DNA that is homologous with some particular sequence(used as probe)

Glossary 301

Complementary sequences Two nucleic acid sequences that may form an exactlymatching double strand as a result of A-T and G-C pairing. Complementary sequencesrun in opposite directions

Constitutive genes These genes code for certain protein products that are required atall times for general cell maintenance and metabolism. These genes are expressed asa function of the interaction of RNA polymerase with the promoter without additionalregulation. They are also known as household genes

Contigs Overlapping DNA segments that as a collection, form a longer and gaplesssegment of DNA

Cosmid It is a larger insert cloning vector, useful for analysis of highly complexgenomes; forms an important component of many genome mapping projects; cosmidvectors are constructed by incorporating the cos sites from the phage λ

Cross-protection Enhancement of resistance in plants following infection by onevirus or its strain(s) to reinfection by the same virus or its strains/related viruses

Cytoplasmic resistance Resistance attributed to the genetic material present in thecell cytoplasm

Cytoskeleton A three-dimensional network of fibrous elements comprising primar-ily of microtubules, actin microfilaments and intermediate filaments found in thecytoplasm of eukaryotic cells; the cytoskeleton offers structural support for the celland permits directed movement of organelles, chromosomes and even the cell

Cytosol Unstructured aqueous phase of cytoplasm excluding organelles, membranesand insoluble cytoskeletal components

Dalton A mass unit used to indicate the size of a biomolecule; one dalton is equivalentto molecular mass of a hydrogen atom

Data mining A computerized program used to search for relationships between andoverall patterns among the data available within a database

Defensins Defense-related,cysteinerich,antimicrobialpeptidespresent in theplasmamembrane of host plant species; they constitute a group designated defensins capableof providing resistance against microbial plant pathogens

Denaturation The conformation of a protein or nucleic acid may be drasticallyaltered because of disruption of various bonds due to heating or exposure to chemicals;this may result in loss of biological function(s)

Dendrogram A branching diagram that shows the relative sequence similaritybetween many different proteins or genes to indicate the phylogenetic relationships;typicallyhorizontal lines indicate thedegreeofdifferences insequences,whileverticallines are used for clarity to separate branches

DNA fingerprinting/ DNA profiling This technique involves the use of restrictionenzymes and electrophoresis to determine the differences and similarities in the DNAof individual organisms

302 Glossary

DNA library This represents a collection of cloned DNA molecules/fragments ofentire genome or DNA copies of all mRNAs produced by a cell type (cDNA library)inserted into suitable cloning vector

DNA ligase The enzyme that seals breaks in DNA strand and also catalyzes theformation of the final phosphoester bond in DNA replication

DNA microarray Oligonucleotides or fragments of cDNAs are printed on a glassslide or membrane filter at a high density, permitting simultaneous analysis of thou-sands of genes by hybridization of the microarray with fluorescent probes

Domain A portion of polypeptide chain that folds into a compact globular units ofthe protein forming the basic unit of the tertiary structure and remains distinct evenwithin the tertiary structure of the protein; a discrete part of a protein with its owndistinct function

Downstream A relative direction of DNA sequence, as the DNA is usually writtenwith 5’ end to the left; downstream would be to the right of a reference point – eg. thestart codon is downstream of the protmoter

Ectopic A gene inserted in an unnatural location

Effectors These molecules can manipulate host cell structure and function, therebyfacilitating infection (virulence factors/toxins) and /or triggering defense responses(avirulence factors/elicitors)

Effector proteins Bacterial virulence determinants injected into host cells via typeIII secretion system (TTSS) of the bacterial pathogen

Elongation factor A group of nonribosomal proteins required for continued transla-tion of mRNA (protein synthesis) following initiation; guiding the elongation phaseof transcription or translation, during protein synthesis

Endoplasmic reticulum (ER) An extensive network of membrane-enclosed tubulesand sacs involved in protein sorting and processing as well as in lipid synthesis

Epitope A specific group of atoms on an antigen molecule that is recognized by thespecific antibody produced against the antigen concerned; it is also called as antigenicdeterminant

Episome An independent genetic element (DNA) that is present inside the bacterialspecies in addition to the normal bacterial cell genome. The episome can replicateeither as an autonomous unit or as one integrated into host genome

Exon A segment of an eukaryotic gene that contains a coding sequence and this partof gene sequence is transcribed into an mRNA and translated to give rise to a specificdomain of the protein

Expressed sequence tags (ESTs) These are partial sequences of cDNA clones inan expressed cDNA library; useful for identifying all unique sequences (genes) todetermine their functions; a profile of mRNAs allowing cloning of a large number ofgenes being expressed in a cell population

Glossary 303

Expression vector A modified plasmid or virus that carries a gene or cDNA intosuitable host cell in which it directs synthesis of the encoded protein; expressionvector can be used to screen DNA libraries for a gene of interest or to produce largeamounts of a protein from its cloned gene

Expressivity The intensity of realization of the effect of a gene in a phenotype; thedegree to which a particular effect is expressed by individuals

Extracellular matrix Secreted proteins and polysaccharides that fill the spacesbetween cells and bind cells and tissues together

Flagellin These proteins associated with flagella of bacteria, are capable of function-ing as a receptor system for general elicitors

Flanking sequence A segment of DNA molecule that either precedes or follows theregion of interest on the molecule

Flux The flow of intermediates in metabolism; the rate at which substrates enter andexit a pathway

Footprinting This is a technique employed for identifying protein-binding regionsof DNA or RNA based on the ability of a protein bound to a region of DNA or RNAto protect that region from digestion

Free radical A molecule that has one or more unpaired electrons

Functional genomics Functions and interactions of genes or groups of genesbelonging to host plants, pathogens or both are genetically examined

Gene cloning Characterization of gene functions by isolating and multiplying indi-vidual gene or sequences by insertion into bacteria (Escherichia coli); the sequencesare duplicated as the bacteria multiplies by fission

Gene expression Conversion of genetic information within a gene into an actualprotein or cell process; an overall process applied to assess the information encodedin a gene that can be converted into an observable phenotype (production of a protein)

Gene expression profiling Identification of specific genes that are ‘switched on’in a cell at particular point of time or process, enabling the precise definition of thephenotypic condition of that cell

Gene flow Movement of genes (under examination) through specific process, fromone population to another population geographically separated apart

Gene knockouts Genetically modified individuals containing either a defective geneor lacking a gene

Gene silencing Interrupting or suppressing the activity of desired gene(s), resultingin the loss of coordination for production of specific proteins

Gene targeting Insertion of antisense DNA molecules into selected cells of theorganism in order to block the activity of undesirable genes such as oncogenes

304 Glossary

Genetic code The correspondence between nucleotide triplets and amino acids inproteins; the sequence of bases in mRNA specify the amino acid sequence of apolypeptide, read in triplets (codons), based on a set of rules

Genome sequencing Reading of all nucleotides present in the entire genomic DNAof the organism in an orderly way

Genomic library Contains a collection of recombinant DNA clones that collectivelyconstitute the genome of the organism (see DNA library)

Gprotein Afamilyofmembrane–boundcell-signalingproteinsregulatedbyguaninenucleotide binding

Green fluorescent protein (GFP) A protein from jellyfish possessing the propertyof fluorescing; useful as a marker in fluorescence microscopy

GUS gene Production of β- glucuronidase (GUS protein) in certain organisms suchas Escherichia coli is controlled by this gene; it is commonly used as a marker genefor genetically engineered plants

Haplotype Acollectionofalleles inanindividual thatare locatedononechromosome;alleles within a haplotype are, often, inherited as a single unit from one generation toanother; it also refers to a group of genomic variations found repeatedly in manyindividuals within a population

Harpins Proteins coded by hrp genes present in the type III secretion system (TTSS)of phytobacterial pathogens; these proteins can induce resistance in susceptible plants

HeterotrimericGprotein Aguaninenucleotide-bindingconsistingof threesubunits

High-throughput methods Large number of genes or gene products can be studiedusing these partially automated protocols

Homologs The individuals considered to have sequences that are evolutionarilyrelated by descent from a common ancestor; proteins or genes exhibiting similarity(homology)

Homology A sequence of amino acid in two or more proteins that are identical toeach other; nucleic acid homology indicates the presence of complementary strandsthat can hybridize with each other

Horizontal gene transfer Incorporation of a ‘foreign’ gene acquired from an unre-lated species into the genome of another organism

Host-specific toxins (HSTs) Some pathogens elaborate toxins that can induce allprimary symptoms as the pathogen itself; production of HSTs is governed by specificgenes which are expressed in susceptible plants

Hot spots Events such as mutations with unusual high frequency may occur in certainsites in genes, termed as hot spots

Humoral immune response In response to infection, rapid production and secretionof soluble blood serum components occurs in the animal body

Glossary 305

Humoral immunity By injecting viable nonpathogenic or inactivated phytopatho-genic bacteria into insects, formation of new proteins in the hemolymph of theseinsects is induced leading to the development of humoral immunity; these proteinshave antibacterial properties; cecropins and attacins are formed in the hemolymph ofHyalophora cecropia

Hybridization probes DNA or RNA molecules that are complementary to a regionin DNA; useful for detecting specific gene(s) in fingerprinting

Hybridoma Ahybridcell lineproducedbyfusingamyeloma(capableofmultiplyingindefinitely) with a lymphocyte (capable of producing antibodies); the hybridomaprovides continuous supply of specific immunoglobulins (antibodies)

Hypersensitive response (HR) A protective or defense response of plants to infec-tion or inoculation with pathogen in which the initially infected cells and the adja-cent ones express the phenomenon of programmed cell death (PCD) resulting in selfdestruction to cordon off the infected area and to restrict the spread of pathogen toother cells/tissues (see programmed cell death)

Idiotype The specific site of antibody molecule capable of combining with the spe-cific site in the antigen (epitope) is said to have an idiotype (for that epitope), servingas an identifying characteristic of an epitope

Indel An insertion or deletion occurring in a protein or nucleic acid sequence;frequently it may be difficult to find out whether a change in a sequence is due toa deletion in that sequence or an insertion of a related sequence

Indexing Testing the plants or seeds or propagative plant materials for the presenceof microbial pathogens by biological and/ molecular techniques

Induced systemic resistance (ISR) Colonization of roots of plants by plant growthpromoting rhizobacteria (PGPRs) induces systemic resistance to pathogens infectingtissues/organs far away from the roots of plants; this type of resistance to disease isreferred to as induced systemic resistance

Inducible promoter The promoter in which start or increase of promotion occursusually in the presence of a pathogen or toxin or toxic metabolites of the pathogenleading to initiation of defense-related activity

in silico Experimental process performed on a computer and not by bench research

Intergenic sequence DNA sequence between two genes; sometimes called as‘junk DNA’

Intron The sequence for protein synthesis is absent in the intron; this noncodingsequence of the gene interrupting exons is cut out of the mRNA (splicing) prior totranslation

Isoforms Different forms of the same protein whose amino acid sequences differslightly and whose general activities are similar; isoforms may be encoded by differentgenes or by a single gene whose primary transcript undergoes alternative splicing

306 Glossary

Isozymes Different forms of an enzyme involved in the same or similar reactions,but need different optima for their activity

Karyopherin A family of nuclear transport proteins that function as an importin,exportin or occasionally both; each karyopherin binds to a specific signal sequence ina protein (cargoprotein) to be imported or exported

Killer toxin (KT) A proteinaceous toxin isolated from microorganisms like yeasthas antimicrobial properties

Knockout gene Selective inactivation of a desired gene by replacing it with a non-functional (disrupted) allele in an otherwise normal organism

Lectins Plant proteins capable of binding to specific carbohydrates; they can be usedto detect the carbohydrates in situ

Leucine-rich repeats (LRR) Segments of amino acids containing multiple copiesof leucine present repeatedly in a protein; these proteins are known as LRR proteins

Ligand A molecule other than an enzyme substrate that binds tightly and specificallyto a macromolecule, usually a protein forming a macromolecule-ligand complex

Linkage On the same chromosome two different loci governing two different traitsmay be inherited together; closer the loci greater are the chances of linkage

Linker A short segment of ds-DNA that can be ligated onto a second fragment ofDNA to facilitate the cloning of that fragment. Linkers contain a restriction site so thatthey can be ligated to produce the desired sticky ends for ligation

Locus The locatable position of a gene on a chromosome; all alleles of a particulargene occupy the same locus

Marker-assisted selection (MAS) A known resistance gene or chromosomal se-quence closely linked to a gene that is used as a genetic marker to select the progeniesof crosses or genotypes containing the selected marker by DNA testing; this procedureis very useful in hastening the development of cultivars with built-in resistance to cropdiseases

Messenger RNA (mRNA) An RNA molecule serving as a template for protein syn-thesis

Metabolome It represents the entire metabolic content of a cell or organism; the com-plete set/complement of all metabolites and other molecules involved in or producedduring a cell’s metabolism

Microarray A glass slide or silicon chip onto which several DNA probes are de-posited for simultaneous determination of gene expression levels of many genes inthe same tissue sample

MicroRNA (miRNA) A naturally occurring short non-coding RNA that can act toregulate gene expression

MicRNAs (messenger-RNA-interfering complementary RNAs) These complemen-taryRNAmoleculesbind to theRNAtranscriptsof specificgenes resulting inblockageof their translation; they are also called antisense RNAs

Glossary 307

Molecular cloning Insertion of a desired DNA fragment into a DNA molecule(vector) that can replicate independently in a host cell

Molecular markers DNA sequence (s) that is characteristic of the DNA seg-ment/gene is used for comparing or detecting the similarities of related organismsor genotypes (see marker assisted selection)

Monocistronic Messenger RNAs encoding a single polypeptide chain

Monoclonal antibody An antibody secreted by a clonal line of B lymphocytes

Monophyletic A group of species on a phylogenetic tree sharing a common ancestorthat is not shared by species outside the group; a clade is a monophyletic group

Motif A sequence of amino acids or nucleotides that perform a particular role and isoften conserved in other species or molecules

Movementproteins Viruscoded-specificproteins involved in themovementofplantviruses in the host plants

Mutagen A chemical capable of inducing a high frequency of mutations

Nonhost resistance Resistance exhibited by a plant species on which the pathogenin question is unable to establish infection; the plant species is termed as a nonhostand the interaction is called as incompatible

Ontogenic resistance The level of resistance of plants may vary with the growthstages of host plant species; plants are highly susceptible to viruses in the early growthstages (seedling), but they develop resistance progressively as the plants become older

Open reading frame (ORF) Region of a gene which contains a series of tripletcoding foraminoacidswithout any terminationcodon isknownasORF; thesequencescontained in the ORF may be potentially translatable into a protein

Operon Oneormoregenesmaybepresent in thisgeneunit; theyspecifyapolypeptideand an operator regulates the structural gene

Orthologs Sequences from different organisms (species) that are evolutionarily re-lated by descent from a common ancestral sequence and later diverged from oneanother as a result of speciation

Pathogenicity factors The factors (genes) of pathogen origin, are essential for initi-ation of infection and further colonization of plants

Pathogenesis-related (PR) proteins PR proteins are coded for by the host plant, butinducedonly inpathologicalor relatedconditions.Theyareproducedpostinfectionallyduring plant-pathogen interactions; they have different roles in the development ofresistance to the diseases caused by pathogens; these proteins are classified into 14families; PR genes/PR proteins are widely used as marker genes/ proteins to study thedefense mechanisms of plants

Peptide mapping Following partial hydrolysis of a protein, a characteristic two di-mensional pattern may be recognized (on paper or agar gel) due to the separation of amixture of peptides

308 Glossary

Phytoalexins These are low-molecular antimicrobial compounds that accumulateat the site of infection by incompatible pathogens. Several biosynthetic enzymes areinvolved in the production of phytoalexins and hence highly coordinated signal trans-duction events are required

Phytoanticipins Toxic compounds naturally present in the plants that can affect thedevelopment of pathogens adversely

Plasmid Represents an independent, stable, self-replicating piece of extrachromo-somal DNA in bacterial cells; it does form a component of normal cell genome, butdoes not get integrated into the host chromosome

Point mutation A mutation resulting in a change in only one nucleotide in a DNAmolecule

Polycistronic Coding region representing more than one gene may be present in themRNA; it codes for two or more polypeptide chains; RNA genomes of plant viruses(such as Tobacco mosaic virus) are polycistronic

Posttranscriptional modification A set of reactions that occur to change the struc-ture of newly synthesized polypeptides

Primer A short nucleic acid sequence containing free 3’-hydroxyl group that formsbase pair with a complementary template strand and functions as the starting point foraddition of nucleotides to copy the template strand

Probe Defined RNA or DNA fragment radioactively or chemically labeled that isused to detect specific nucleic acid sequences by hybridization

Programmed cell death (PCD) Death of cells at the site of initiation of infection bythepathogenas theearlyresponseof thehost; thesecellshaveapredeterminedfunctionamounting to suicide to prevent further spread of the pathogen to other cells/tisssues(see hypersensitive response)

Promoter A region of DNA upstream of a gene that can act as a binding site for atranscription factor and ensure the transcription of the gene concerned

Proteasome A large protease complex that degrades proteins tagged by ubiquitin

Proteome The entire range of proteins expressed in a specified cell

Proteomics Comprehensive analysis of all cell proteins

Pseudogene It is the nonfunctional copy of the gene

Quorum sensing The ability of bacterial or fungal propagules to sense the concen-tration of certain signal molecules in their environment prior to activation of infectionprocess

Reactive oxygen species (ROS) Intermediate and radical species generated fromoxygen such as superoxide or hydrogen peroxide as resistance response in plants

Recognition factors Specific receptor molecules or structures on the host plant sur-face useful for recognizing the presence of a pathogen

Glossary 309

Recombinant DNA A hybrid DNA formed by incorporation of DNA segment fromone species into another species

Recombinant protein A polypeptide synthesized by transcription of the hybridDNA and translation of the mRNA

Regulatory proteins These proteins can bind to DNA and influence the action ofRNA polymerase thereby acquire the ability to control the rate of protein synthesis

Reporter gene It is a gene inserted into the DNA of a cell capable of reporting theoccurrence of signal transduction or gene expression

Repression of gene function Inhibition of transcription or translation by binding ofa product of a gene (repressor protein) to a specific site in the DNA or RNA molecule

Restriction endonucleases Hydrolytic enzymes capable of catalyzing the cleavageof phosphoester bonds at specific nucleotide sequences in DNA

Restriction site This is a specific nucleotide segment of (base pairs) in a DNAmolecule that can be recognized and cleaved by the restriction endonuclease enzymeemployed

Reverse genetics A method of analysis of gene function by introducing mutationsinto a cloned gene

Reverse transcription Synthesis of DNA from an RNA template using appropriatereverse transcriptase

RNA-induced silencing complex (RISC) Large multiprotein complex associatedwith a short ss-RNA that mediates degradation or translational repression of a com-plementary or near complementary mRNA

RNA interference (RNAi) Degradation of mRNAs by short complementary double-stranded RNA molecules

RNA processing Refers to various modifications that are made in RNAs within thenucleus

RNA splicing A process that results in removal of introns and joining exons inpre-mRNA

Sequencing The process used to determine the sequential arrangement of aminoacids/nucleotides in protein /nucleic acid molecule

Serotypes Groups of an organism differentiated based on the variations in the sero-logical reactions with different antibodies; monoclonal antibodies are frequently usedfor characterization of serotypes of plant pathogens

Signaling Communication established between and within cells of an organism

Signal molecules Host factors (molecules) that respond to the presence or initiationof infection by a pathogen and transmit the signal to and activate proteins or genesin the tissues away from the site of pathogen entry leading to restriction of pathogenspread/disease development

310 Glossary

Signal transduction Reception, conversion and transmission of ‘chemical message’by a cell

Singlenucleotidepolymorphism(SNP) Variationdetected in individualnucleotideswithin a DNA molecule; SNPs usually occur in the same genomic location in differentindividuals

siRNAs Specific short sequences of dsRNA of less than 30-bp in length that cantrigger degradation of mRNA containing the same sequence (present in siRNA) withinthe cell as part of process known as RNA interference (RNAi)

Site-directed mutagenesis A laboratory protocol employed to modify the aminoacid sequence of a protein

Somaclonal variation Variability detected in different calli for various characteris-tics, including disease resistance; the calli exhibiting resistance to disease(s) may beregenerated into whole plants that are tested for the level of resistance to disease(s)

Sticky ends Exposed complementary single strands of DNA can bind (stick) to com-plementary single strands in another DNA molecule, producing a hybrid piece of DNA

Synteny Two genetic loci are presumed to be linked to the same chromosome,whether or not linkage has been demonstrated, as against the asyntenic loci that arelinked to different chromosomes

Systemic acquired resistance (SAR) Resistance to diseases caused by microbialpathogens can be induced by biotic and abiotic inducers of resistance in treated plants;a set of genes referred to as ‘SAR genes’ is activated by the inducers resulting in thesystemic resistance in various organs/parts of plants

Tat pathway The twin-arginine translocation (Tat) system is involved in physiolog-ical functions of bacterial pathogens; the Tat pathway operates in the inner membraneof Gram negative bacteria

TATA box A conserved sequence in the promoter of several eukaryotic protein-coding genes where the tranascription initiation complex assembles

Transactivating protein A protein that ‘switches on’ a cascade of genes /generegulation

Transactivation Activation of transcription by binding a transcription factor to theDNA regulatory sequence in question

Transcripts During transcription of a gene, various segments of mRNA, known astranscripts, are formed

Transcription The genetic information contained in one strand of DNA is used asa template and transcribed through the enzyme-catalyzed process to specify and pro-duce a complementary mRNA strand; the genetic information in the DNA is rewritteninto mRNA

Transcription factor A protein that binds to a regulatory region of DNA, often up-stream of the coding region and influences the rate of gene transcription

Glossary 311

Transcriptome The entire set of all gene transcripts (mRNA segments derived fromtranscription process) in a specified organism; provides the knowledge of their rolesin the growth, structure, health and disease of the organism concerned

Transduction Bacterial genes may be transferred from one bacterium to another bymeans of bacterial virus (bacteriophage)

Transformation This a process by which free DNA may be transferred directly intoa competent recipient cell; plant cells may be transformed with genes from differentkinds of organism to enhance the level of resistance to microbial pathogen(s)

Transgenic An organism carrying in its genome one or more DNA sequences (trans-gene) from another organism

Translation Synthesis of a polypeptide chain from an mRNA template

Transposon A DNA sequence (segment or molecule) capable of replicating andinserting one copy (of itself) at a new location in the genome

Trypsin inhibitor (TI) protein This protein is constitutively expressed in maturemaize kernels of resistant maize genotype at higher levels compared to susceptibleleaves

Tubulin A family of globular cytoskeletal proteins that polymerize to formmicrotubules

Two-hybrid system The yeast or bacterial system that is employed for detectingspecificprotein- protein interaction; theproteinof interest isusedasa ‘bait’ to ‘fishout’proteins that may bind to it (referred to as ‘prey’)

Ubiquitin A small protein present in all eukaryotic cells that has an important rolein ‘tagging’ other protein molecules; the tagged protein molecules are said to be‘ubiquitinated’

Upstream A relative direction of nucleic acids often used to describe the location ofa protmoter relative to the start transcription site; the start codon is upstream of thestop codon

Vector An agent used to carry foreign DNA in recombinant DNA technology; naturalcarrier of microbial pathogens, commonly viruses from infected plant to healthy plantresulting in the spread of the pathogen/disease under natural conditions

Virulence factors Genes or factors essential for and contribute to the virulence ofthe pathogen; may not be required for the growth and reproduction of the pathogen

Yeast two-hybrid system An experimental technique of detecting the protein-protein interactions in yeast cells

Zinc finger domain A kind of DNA- binding domain consisting of loops containingcysteine and histidine residues that bind zinc ions

Index

AAbiotic inducers of resistance to

bacterial diseases, 243–244fungal diseases, 232–233viral diseases, 245–246

Abscisic acid (ABA) signalingpathway, 100

Accumulation of phytoalexins, 87, 225Accumulation of PR-1 in plants, 224, 228Accumulation of salicylic acid (SA), 245Acibenzolar-S-methyl (ASM), 223, 238, 240Acquired immunity, 220Acquired resistance, 111ACRE genes, 53Actin, 28Actin-dependent resistance pathway, 59Actin-independent resistance pathway, 59Activator of SA-dependent defense genes, 84Active defense mechanisms, 25, 50Active resistance response, 119Adult plant resistance, 24Agroinfection, 63Agroinfiltration of VIGS vector, 129Agrobacterium tumefaciens-mediated

transformation, 3AK-toxin, 73Alien genes of plants, 200Allele-specific amplification of gene

segments, 280Allele-specific PCR (ASPCR), 282Allelic forms for resistance, 49Allelism tests, 48All-stage resistance to all races of pathogen, 37Amplifiable markers for BCAs, 263Amplified fragment length polymorphism

(AFLP) markers, 40, 42, 43, 229,264, 284

Antagonistic mechanisms, 264

Analysis of β-tubulin genes TUB1 andTUB2, 282

Antibiosis, 263Antibiotic production by BCAs, 265Antibody engineering, 186Antibody expression, 16Antibody fusion proteins, 199Antifungal protein (AFP) from Aspergillus

giganteus, 197Antifungal viral genes, 199Antigen concentration, 26Antimicrobial compounds, 50Antisense/micRNAs (mRNA-interfering

complementary RNAs), 180Appoplastic antioxidant system, 122Apoplastic effectors, 61Arbitrarily primed (AP)-PCR, 260, 282Area under disease progress curve (AUDPC),

39, 40Asymptomatic infection, 117ATB-binding cassette (ABC) transporters,

273, 282Attacin genes, 204Autofluorescence in epidermal cells, 236Avirulence conferring enzyme 1 (ACE1), 57Avirulence determinants, 104, 122Avirulence factors, 104, 122Avirulence genes, 31, 43, 51, 122Avirulence gene candidates, 55Avirulence gene products, 42Avirulence-mediated recognition of fungal

pathogen, 61Avirulence signal, 52Avr/Cf that rapidly elicited (ACRE) genes,

53, 97Avr9/Cf-9 induced kinase1 (AICK1), 53Avr proteins, 2, 51, 62Avr 4-responsive tomato (ART) fragments, 54

313

314 Index

BBacillus subtilis, an inducer of resistance in

tomato, 229Bacteria as biocontrol agents (BCAs), 261–263Bacterial effector proteins, 104Bacterial flagellins, 94Bacterial harpin proteins, 107Bacteriocin genes, 261, 267, 268Bacterio-ospin, 206Bacteriophage lysozymes, 203Basal host defense mechanisms, 100Bean chitinase gene, 190Benign variant of CMV sat-RNA, 182Benza (1,2,3)-thiadiazole-7-carbothioic

acid-S-methyl ether (BTH), 223,238, 243

Binary PVX expression, 32Binary PVX vector, 66Bioassay technique for fungicide resistance,

280Biochemical markers, 122Biocontrol agents as inducers of resistance, 1Biocontrol active strains, 258Biocontrol agents as inducers of resistance,

225Biocontrol potential, 264, 267, 270Biofungicide AQ-10, 258Bioinformatics analysis, 62Biomarkers, 271Bio-risks, 13BIO-PCR, 9Biotic agents, 220Biotic inducers of resistance, 224, 242, 246Biotin/avidin (BA)-ELISA, 26Blast resistance genes, 44Blocking vascular movement of virus, 122Bulked segregant analysis (BSA), 43, 93, 116

Cδ-cadinene synthase (CDNS) gene, 109Calmodulin, 28Callose deposition, 71Cauliflower mosaic virus (CaMV) 35S

promoter, 173cDNA microarrays, 77cDNA-AFLP analysis, 32cDNA library, 76Cell-based genetic screen for virulence

factors, 103Cell-death inducers (elicitors), 62Cell-death suppressor (CDS), 103Cell-to-cell movement of viruses, 114, 121Cellular redox, 100

Cellular redox stage, 221Cellular level resistance, 119Cellulose-binding elicitor and lectin-like

(CBEL) protein, 66Cell wall appositions, 229, 232Cell wall degrading enzymes (CWDE), 263Cell wall fragments, 230Cell wall proteins, 230Certification programs, 1, 16Certification of seeds, 19C f -mediated defense responses, 53Characterization of disease resistance

genes, 102Chemical inducers of resistance, 234Chimeric attenuated virus strains, 183Chimeric gene, 173Chitin deposition, 88Chitin-binding proteins, 52Chitinase, induction of, 87Chitinase, localization of, 86Chitosan, 228Chromosome-located genes for copper

resistance, 291Cistron encoding Potato virus Y protease, 179Citrus tristeza virus-specific antibodies, 14Cloned genes, 44Cloning copper resistance genes, 290, 291Cloning of resistance genes, 3, 36Clusters of resistance genes, 50CMV-associated RNA5 (CARNA5), 182Coat protein (CP) gene, 4, 112, 173Coat protein (CP) gene, as an elicitor of

resistance, 173Codominant SSR, 44Collection of Avr9/Cf-9 that rapidly elicited

(ACRE) genes, 53Combination of sequences of satellite and CP

genes, 182Complete resistance, 110Components of cell death machinery, 103Components of signaling pathway, 3Conserved signaling pathway, 79Constitutive expression of afp in rice, 198Convergence of signal cascades, 98Copper resistant strains, 290, 291Coregulating molecular switch, 103Coronatine, 96CP gene in sense and antisense orientation, 174CP transgene insertion sites, 175CP-mediated resistance, 173-175Crop management systems, 7Cross-protection, 183, 220Cross-resistance to chemicals, 288

Index 315

Cryptogein, an elicitor of resistance, 206, 231CUTE plants, 65Cysteine-rich antimicrobial proteins of onion

Ace-AMP1, 194Cysteine-rich small proteins, 62Cytotoxic genes against bacterial pathogens,

206

D‘Defeated’ resistance genes, 39Defense-activating signaling molecules, 76Defense gene suppression, 90Defense-related antioxidants, 104Defense-related enzymes, 70Defensins, 70Degenerate oligonucleotide primers

for PCR, 36Degradation of sat-RNA sequences, 182Denaturing gradient gel electrophoresis

(DGGE), 267Detection of bacteria by ELISA, 13Detection of gene induction, 77Detection limit, 10, 15Detection of latent infection, 31Detection of pathogens by ELISA, 13Detection of pathogens in seed tubers, 10Detection of resistance development in

pathogens, 280Detection of transgene-specific small-

interfering RNAs, 186Detection of tri5 gene in Trichoderma spp.,

258Dicarboximide resistance, 283Differentially expressed genes, 54Differentially expressed transcription-derived

fragments (TDFs), 32Differentially regulated genes, 32Differentiation of BCAs by molecular

techniques, 257Differentiation of plant pathogens, 2Differentiation of self and non-self, 51Diffusible signal molecules from pathogens,

50, 69Direct R-Avr protein interaction, 56Direct tissue blot immunoassay (DTBIA), 14Disease complex, 25Disease diagnosis centers (DDCs), 16Disease resistance, 23Disease rating scale, 110Disease risk assessment, 10Disease-effector proteins, 61Disease-free planting materials, 1, 15Disease suppressive microflora, 271

Disease suppressiveness, 262DMI resistance of pathogens, 287DNA-based markers, 114DNeasy Plant Minikit, 11DNA markers for authentication of BCA

strains, 259DNA microarray technology, 3, 38, 76DNA virus-derived siRNAs, 128Double-stranded (ds)-RNAs, 180Domestic plant quarantines, 1Dominant resistance genes, 114, 119Dot-blot test, 110, 117Double antibody sandwich (DAS)-ELISA, 10,

18, 92Drosophila Toll protein and interleukin-1-

receptor (TIR), 51, 112ds-RNA-mediated interference, 123ds-RNA-mediated resistance, 181ds-RNA transcripts, 184Durable resistance, 39, 62

EEarly basal resistance (EBR), 94, 97Early defense gene transcription suppression,

103EBR-related chitinases, 97EBR-related proteins, 97Ecological fitness of PGPRs, 268Ectopic expression of bacterial elicitor, 201Effect of AC1 gene on viral DNA, 177Effector-induced genes, 100Effector proteins, 24Electrolyte leakage, 64Elicitation of ISR, 222, 228Elicitin-like (inf ) genes, 63Elicitins, 62Elicitins of Oomycetes, 230Elicitor gene, 4Elicitor molecules, 31Elicitor perception, 31Elicitor-active epitope of flagellin, 94Elicitors, 53, 230Endochitinase gene ech42, 269Engineered mild strains of viruses, 183Enzyme-linked immunosorbent assay

(ELISA), 26, 119, 125, 185Enzyme-linked oligosorbent assay

(ELOSA), 261Epifluorescence microscopy, 271ERF genes, 78, 97ERF target genes, 97Ethylene responsive factor (ERF), 96Ethylene (ET) responsive transcriptional

factor, 239

316 Index

Ethylene emission, 80ET-dependent defense mechanism, 107ET-dependent signaling, 122Exo-β-1,3-glucanase for protection of apple

fruits, 261Exogenous DNA, 172Exotic plant pathogens, 2Expressed gene tagging, 3Expressed sequence tags (ESTs), 38, 69, 76Expression analyses, 66Expression of defense-related genes, 87Expression of genes simultaneously, 3Expression of resistant genes, 41Expression of scFV in plant cytosol, 187Expression of synthetic antimicrobial

peptides, 199Expression of tabtoxin resistance gene, 202Expression profile of plants, 54Expressomes of BCAs, 273Extrahaustorial matrix, 56

FField resistance, 29, 47Flagellin gene flic, 95Flagellin-induced defenses, 95Flagellin perception, 95Flagellin receptor gene, 95Flagellin Rapidly Elicited (FLARE) genes, 96Flagellin signaling, 95Fluorescent in situ hybridization, 49Forms of induced resistance, 221Foundation source plants, 15Fungal antagonists, 259Fungal DNA estimates, 28, 29Fungal resistance alleles, 280Fungi, as biocontrol agents (BCAs), 258Fungicide resistance management, 5Fungicide resistance monitoring, 292Fungicide resistant strains, 4, 279, 289Fusarium cell wall protein, inducer of

resistance, 230

GGain-and loss-of-function mutants, 97Gene disruption, 264Gene pyramiding, 40, 43, 93Gene-for-gene hypothesis, 50Gene-for-gene interaction, 31, 99Gene-for-gene specificities, 51Gene replacement mutants, 268, 269Genes encoding for PR proteins, 188Genes for modification of host metabolism,

195Genes interfering bacterial virulence, 202

General elicitors, 31Genetic basis of BCA activity, 262Genetic basis of resistance, 44, 91, 109Genetic determinants of systemic infection,

129Genetic diversity of pathogen population for

fungicide resistance, 293Genetic engineering methods, 171Genetic fingerprinting, 282Genotypic diversity of BCAs, 267Genetic variability of pathogens, 47, 49Genomic location of genes, 92Genotyping for resistance, 48Germin, 68GFP-based transient expression assay, 130GFP-encoding gene (gfp), 271GFP reporter expression, 61GFP tagging, 121Glucanase inhibitors, 62, 67β-glucuronidase (GUS) activity, 30Grading resistance, 111Grapevine stilbene genes, 87, 195Green fluorescent protein (GFP) reporter gene,

57, 116, 121, 197Guard hypothesis, 53gus reporter gene, 63

HHairpin RNAs, 180Hairpin RNA from Potato spindle tuber viroid

(PSTVd), 131Harpin of Erwinia amylovora, 232Harpin, as primary elicitors, 106Harpin, inducer of SAR, 201Harpins, 106Haustorially expressed secreted proteins

(HESPs), 56Haustorium-specific cDNA, 56HC-Pro, as a suppressor of PTGS, 130, 176Helminthosporoside, 33Helper component (HC-Pro) protein, 122, 129Hm1 gene product inactivating HC-toxin, 35HMT-toxin, 34Homologs, 58Host cell wall appositions, 85Host resistance genes, 111Host responses, 25Host-specific toxins (HSTs), 33, 35, 73House keeping genes, 265HR-assisting proteins (HRAP), 106HR lesions (HRLs), 80HR – localized PCD, 102hpa (HR-associated) genes, 107

Index 317

hrp-encoded protein translocation complex,106

hrp regulating system, 107Human interferon-induced ds-RNA-dependent

protein kinase, 188Human lactoferin cDNA, 205Human lysozyme protein, 205Humoral immunity, 203Hybridoma technology, 186Hydrogen peroxide in plant defense, 71Hydroxyproline–rich glycoprotein

(HRGP), 229Hypersensitive response (HR), 51, 109

IIdentification of biocontrol agents (BCA) using

molecular techniques, 255Identification of resistance genes, 35Immunity-associated PCD, 103Immunoassays, 25, 26Immunoblotting, 89Immunocapture (IC)-RT-PCR method, 18Immunogold labeling, 85Immunolocalization tests, 88, 195Immuno-magnetic separation (IMS), 10Improvement of biocontrol potential, 269Indexing, 15Indicator plants, 17Indirect ELISA, 18, 26Induced resistance-mediated HR, 56Induced systemic resistance (ISR), 4, 75,

219, 272Inducers of RNA-mediated HR, 56Induction of chitinase, 86Induction of resistance to bacterial

diseases, 240Induction of resistance to diseases, 120, 219Induction of resistance to fungal diseases, 224Induction of resistance to viral diseases, 244Induction of SAR, 244Induction of systemic resistance, 221Infectible plants, 109INF elicitin, 32INF1-mediated HR, 54INF recognition, 32INF-responsive plants, 32Inhibitor of virus accumulation, 119Inhibitor of virus infection, 111Innate immunity, 51Innate immunity gates, 95Insertional mutagenesis, 269Integrated disease management system, 1Intercellular fluid, 64

Intercellular washing fluid (IWF), 86Internal transcribed spacer (ITS), 28International plant quarantines, 1International Seed Health Initiative (ISHI), 9Introduced biocontrol agents, 1Introduction of plant pathogens, 7Invasive pathogens, 8Isozyme genotypes, 31

JJasmonic acid (JA) pathway, 80, 81, 101JA-dependent PR-proteins, 81JA insensitive mutants, 81JA-mediated defense, 84JA-responsive genes, 84JA synthesis genes, 81

KKazal-like inhibitors, 67Killer toxin (KT) from Pichia anomala, 204Knockout mutants, 223, 241

LLate basal resistance (LBR), 97Leucine-rich repeats (LRR), 52, 69Levels of resistance, 2, 23, 111Liginification in disease resistance, 224Linkage of disease resistance, 47Lipid transfer protein (LTP) gene, 65, 70, 194Lipopolysaccharides, 98Localization of CBEL, 66Localization of chitinase, 85Localized acquired immunity, 220Long-distance information transmission, 100Loss-of-function mutants, 88LPS-induced gene expression, 98Luciferase reporter transgene, 127Lysozymes, 203

MMagainin against bacterial pathogens, 205Map-based cloning strategy, 44, 93, 196MAPK cascades, 82MAPK genes, 83Marker-assisted selection (MAS), 2, 13, 36,

37, 40, 41, 47, 93, 110, 114Mechanisms of biocontrol activities, 258Melanin biosynthesis inhibitors (MBIs), 289Membrane-associated receptors, 79Messenger RNA-interfering complementary

RNAs (micRNAs), 180Microarray, 76Macroarray-based expression patterns, 115

318 Index

Microarray-based expression profilingmethods, 37, 75, 88

Microbe-associated molecular patterns(MAMPs), 70, 71

Microbial plant pathogens, 23MicroRNAs (miRNAs), 3, 105Microsatellite allele data, 41Microsatellite loci, 46Microsatellite markers, 41, 43, 443′-Minor Groove Binding (MGB) probe, 261Mismatch amplification mutation assay

(MAMA)-PCR, 292Mitogen-activated protein kinase (MAPK)

cascade, 64, 82Mobile silencing signals, 124Molecular basis of biocontrol potential, 263Molecular basis of resistance specificity, 105Molecular detection methods, 8Molecular mapping, 42Molecular markers, 37, 44, 115, 259, 281Molecular markers for BCA strain

differentiation, 259, 262Molecular markers linked to disease

resistance, 37Molecular mechanisms of disease resis-

tance, 37Molecular mechanisms of PTGS, 40, 123Molecular parasites, 124Molecular techniques for pathogen

detection, 1differentiation, 1identification, 1quantification, 1

Monitoring of BCA gene expression, 272Monitoring resistance to chemicals, 279Monoclonal antibodies, 10, 12Monogenic resistance, 36, 47, 91Movement protein (MP) gene, 113, 127Multiple copies of transgene, 175Multiplex PCR, 16, 36, 117Multiplex real-time PCR assay, 115Mutation at codon 198 of TUB2, 281Mutations in pathogen DNA, 284Mycoparasitism, 263, 269Mycotoxins, 42

NN gene, 111Natural disease resistance (NDR) genes, 227Natural disease resistance system, 4Natural disease suppression, 262NBS-LRR class of resistance genes, 45NBS-LRR domain, 45

NBS-LRR resistance gene analogues, 47NBS-LRR type proteins, 54, 120Necrosis-and ethylene-inducing proteins

(NEPs), 73Necrosis-inducing peptides, 52Necrosis-inducing proteins, 52, 66Nectarin proteins, 72Negative upregulation of basal resistance, 102Nitric oxide (NO) as signal in disease

resistance, 74Nonexpressor of PR genes (NPR1), 80, 221Nonhost resistance, 62, 95Nonhost-specific elicitors, 70Nonspecific resistance, 47Northern blots, 32, 33, 76, 90NPR1 as regulator of SA-mediated

resistance, 245NPR1 gene-mediated resistance, 80NPR1 homolog genes, 101NPR1-mediated resistance pathway, 223Nucellar source plants, 15Nuclear import and export of viruses, 120Nuclear localization signals, 62Nuclear targeted Avr proteins, 105Nucleic acid (NA)-based techniques, 25Nucleocapsid (N) protein N gene, 179Nucleoprotein of tospoviruses, 178Nucleotide-binding site (NBS)-leucine-rich-

repeat (LRR) type, 36Nucleotide-binding sites (NBSs), 36, 49,

112, 120

OOligandrin, an elicitor of resistance, 4, 231Oligogenic resistance, 92Oligonucleotide-based arrays, 37One-tube nested PCR-RFLP technique, 14Organic compounds as inducers of

resistance, 233Oxidative burst, 88

PPAMP-responsive genes, 101Pathogen-associated molecular patterns

(PAMPs), 2, 70, 94, 99, 127Papilla-based resistance, 59Passive (preformed) resistance, 50Pathogen biomass, 55Pathogen DNA, 9, 27Pathogen-induced cell wall appositions, 60Pathogen of quarantine significance, 8Pathogen-derived elicitors, 59, 120Pathogen-derived genes, 172Pathogen-derived resistance, 172

Index 319

Pathogenesis-related (PR)-proteins, 58, 70,85, 220

Pathogenesis-related genes, 37, 76Pathogenicity assays, 27Pathosystems, 36, 50, 58, 119Pathotoxin, 33Pathotypes, 57, 73PCR-based assays, 263PCR-based RGAP mapping, 49PCR-based screening method for BCAs, 266PCR-denaturing gradient gel electrophoresis

(DGGE), 262PCR Luminex system, 289PENETRATION1 (PEN1) gene, 60Penetration resistance, 60Permatins, 220Phage display technology, 186Phosphate-mediated resistance, 235Phospholipases, 239Phospholipid signaling, 98Physiological acquired resistance, 220Phytoalexins, 73, 81, 90, 189, 195, 220Phytoalexins biosynthesis genes, 77Phytoanticipins, 90Phytophthora Inhibited Protease 1 (PIP, 1), 68Phytosanitary testing, 10Phytotoxins, 33, 73Plant biosecurity system, 8Plant genetic transformation, 3Plant growth-promoting rhizobacteria

(PGPRs), 4, 75, 261Plant quarantines

domestic, 1, 8international, 1, 8

Plate-trapped antibody (PTA)-ELISA, 12Polyclonal antibodies, 10Polygalacturonase-inhibiting proteins (PGIPs),

87, 193Polygenic resistance, 47Polyketide synthase (PKS), 57Polymorphism information contents, 41Posttranscriptional gene silencing (PTGS), 3,

53, 123, 128, 175Posttranscriptional modifications (PTMs), 100Potato spindle tuber viroid (PSTVd)-specific

siRNAs, 131Pr -1-regulon genes, 220P R-1 gene as marker for SAR, 220Prereaction step in DTBIA, 14PR gene expression, 80PR gene induction, 80PR gene transcription, 80Primary responses of plants, 50

Primary sources of infection, 8Principal types of resistance to virus

diseases, 114Principles of disease management, 1Production of disease-free seeds, 9Programmed cell death (PCD), 50, 60, 69, 73,

98, 112Protease inhibitors, 119Proteinase inhibitor (PI) gene, 65, 89Protein phosphorylation, 82Protein polymorphisms, 51Protein (poly) ubiquitinization pathways, 58Protein secretory pathway genes, 221Proteinase inhibitors, 65Proteomic analysis, 75, 79PTGS-associated antiviral response, 124PTGS-mediated resistance, 184Pyramiding of resistance genes, 40, 43, 93

QQuantitative ELISA, 92Quantitative ELISA estimates of bacteria, 92Quantitative loci (QTLs), 38, 47, 92, 116Quantitative resistance, 43, 48, 91, 110Quantitative-competitive PCR (QC-PCR), 261

RR gene as receptor of avr product, 2R gene analogs (RGAs), 36R genes, 24Race-specific immune responses, 59Race-specific RAPD bands, 31Random amplified satellite primers, 13Random amplified polymorphic DNA (RAPD),

30, 38, 171, 261RAPD markers, 40, 43, 116Rapid systemic response (RSR), 127R-Avr protein interaction, 56Reactive oxygen species (ROS), 64, 70Real-time fluorescent PCR, 27Real-time PCR, 9, 27, 29, 30, 76Real-time polymerase chain reaction (PCR)

assay, 11, 45, 184, 232, 261Real-time quantitative PCR, 27Receptor-elicitor mode, 53Receptor-like genes, 46Receptor-like kinases (RLKs), 36, 44Recessive gene conferring virus resistance,

114, 121Recognition of elicitins, 63Recognition specificity, 41Recombinant antibodies (rAbs) expression,

186, 198Recombinant inbred lines (RIL), 37, 42

320 Index

Redox balance, 80Replicase gene, 181Repetitive (rep) PCR, 292Replication-associated viral genes, 177Resistance gene analog (RGA) polymorphism,

37, 44, 49, 77Resistance gene candidates (RGCs), 50Resistance gene specificities, 46, 50Resistance genes from plant sources, 196Resistance mechanisms, 25Resistance proteins signaling networks, 75Resistance to benzimidazoles, 280, 281Resistance to carbendazim, 279Resistance to chemicals due to amino acid

substitution, 281Resistance to chemicals in bacterial pathogens,

290Resistance conferring fragments, 283Resistance specificities, 41Resistance to demethylation inhibitors (DMIs),

285Resistance to QoI fungicides, 284Resistance to RNA silencing-mediated

degradation, 131Resistance to toxins, 33Resistance to virus vectors, 111Resistance wheat lines expressing KP4, 199Resistant isolate identification by PCR, 222Restriction enzyme-mediated integration

(REMI) transformation, 269Restriction fragment length polymorphism

(RFLP), 43, 116, 259Reverse transcription (RT)-PCR, 10, 11, 175RFLP mapping, 49RFLP markers, 43RGA assay, 44Ribosome-inhibiting proteins (RIPs), 187,

192, 225Ribozymes, 188Rice chitinase genes, 189Rice transformed with Xa21 gene, 200RISC complex for RNA degradation, 123RNA degradation mechanism, 123RNA expression level of transgenes, 124RNA hybridization, 119RNA interference, 88, 123, 200RNA profiles, 115RNA silencing, 68, 128RNA silencing-mediated resistance, 181RNA-dependent RNA polymerase (RdRp),

126, 187RNA-dependent RNA polymerase involved in

PTGS, 123, 126

RNAi suppression mechanism, 130RNA-induced silencing complex (RISC),

125, 131RNA-mediated defense response, 3RNA-mediated gene silencing, 105RNA-mediated transcriptional gene silencing

(TGS), 123RNA-mediated transgenic resistance, 173RPM1-interacting protein (RIN, 4), 104RPM1-mediated resistance, 104RT-PCR assay, 11, 125, 175, 232

SSA-mediated defense, 84SA-induced protein kinase (SIPK), 83, 112SA signaling mutations, 60SA signaling pathway, 81Salicylic acid (SA), 228, 235, 236, 244, 270Salicylic acid (SA)-dependent PR-proteins, 80Same-day test, 11SAR genes, 75, 220SAR long-distance signaling, 221SAR marker, 89SAR-regulated PATHOGENESIS-RELATED 1

expression, 85SAR transcriptional signature, 100Satellite RNAs, 182Sat-RNA sequence degradation, 182SCAR markers, 115Scorable marker of resistance, 115Secondary responses, 50Seed health testing, 9Sequence characterized amplified region

(SCAR) primers, 13, 115, 261Sequence diversity, 117Sick plots, 30Signal transduction pathways components,

35, 112Signal transduction networks, 2Silicon-mediated resistance, 235Simple sequence repeat (SSR) markers, 37,

40, 93Single multiplex RT-PCR technique, 11Single nucleotide polymorphism markers, 44Single-site mode of action of fungicides, 285Single-point mutation in β-tubulin, 280Single-strand conformation polymorphism

(SSCP) analysis, 282siRNA-mediated gene silencing, 105Site-directed mutagenesis, 57, 186Slow-rusting resistance, 39Small cysteine-rich proteins, 194Small interfering RNAs (siRNAs), 3, 105, 123

Index 321

SNAKIN 2 peptides, 78SNARE protein-dependent defense

reactions, 59Sodium dodecyl sulfate-polyacrylamide gel

electrophoresis (SDS-PAGE), 86Somaclones, 32Sources of resistance, 28, 122Southern blot analysis, 175Southern hybridization, 291Species-specific PCR primers, 281Specific receptor sites, 51Specific signal molecules, 50ss-DNA satellite, 117Stilbene synthesis, 87Stomatal defense, 96Strobilurin resistance, 284Structural barriers, 50Subliminal infection by plant viruses, 109Superoxide dismutase (SOD) activity, 68, 69Suppression of basal defense, 59Suppression subtraction hybridization (SSH),

32, 115, 239, 262Suppressor gene, 117Suppressor of JA-dependent pathway, 84Suppressor proteins of viruses, 84Surveillance systems for detecting effectors, 51Synthetic antimicrobial peptides, 199Systemic acquired immunity, 220Systemic acquired resistance (SAR), 4, 51, 75,

85, 219Systemic host responses, 75

TTaqMan R© chemistry, 11Targeted gene disruption, 264T-DNA, 97, 172Thaumatin-like proteins (TLPs), 86, 220α-Thionin gene expression, 203Thionins in transgenic tomato, 203TIR-NBS-LRR class of R genes, 51, 112Tolerance limits for pathogens, 8Toll interleukin-1-receptor homology-

nucleotide-binding site-leucine-richrepeat (TIR-NBS-LRR) class proteins,51

Tomatinase gene, 91Toxins, 52Transcriptional reprogramming, 102Transcription-derived fragments (TDFs), 32Transformants with defective replicase, 177Transformation of plants, 2, 172Transgenic expression of chitinases/

Transgenic expression of viral genes, 178Transgenic pear expressing harpin gene, 201Transgenic plants expressing CP genes,

173–176Transgenic plants expressing MP genes, 178Transgenic plants expressing antimicrobial

compounds, 181Transgenic resistance, 171Transgenic resistance to virus diseases, 172Transgenic strain of T. atroviride, 270Transgenic strain of T. harzianum, 273Transient induced gene silencing (TIGS), 59Translation elongation factor-1α (EF-1α), 28Transposon mutagenesis, 268T richoderma atroviride endo- and exochitinase

genes, 191T richoderma hamatum, as resistance inducer

in cucumber, 225, 242Trichodermin, 263TRV-based VIGS, 129Trypsin inhibitor (TI) proteins, 89T-toxin, 33TTSS-secreted effectors, 24TUB2-conferred resistance, 282β-tubulin sequencing, 281, 282β – tubulin, 280β-tubulin gene, 281Type I secretion system, 99

UUbiquitin ligase (E3), 53Uneven PCR, 44Unigenes, 56, 77Universally-primed PCR (UP-PCR), 260Up-regulated genes, 76

VVacuolar processing enzyme (VPE), 67Victorin, 33, 34VIGS vectors, 129Viral CP as avirulence determinant, 122Viral DNA estimated by dot-blot hybridization,

110Viral elicitor, 121Viral MP as avirulence determinant, 122Viral RNA polymerase as avirulence

determinant, 122Viral silencing suppressor protein, 127Viroid-induced RNA silencing (VdIRS), 131Virulence determinants, 24, 106Virulence factors, 52Virus movement-based form of resistance, 114,

116, 120Virus-coded functions, 111PR-proteins, 189, 191

322 Index

Virus-free potato seed tubers, 11Viruses as inducers of PTGS, 124Viruses as targets of PTGS, 124Virus-derived siRNA generation, 124Virus-induced gene silencing (VIGS), 3, 53,

64, 124, 129Virus-specific ds-RNA forms, 124Visual assessment of resistance, 25

WWestern blotting, 79, 88WIPK of tobacco MAPK, 83

Wound-induced protein kinase (WIPK), 112WRKY genes, 84WRKY proteins, 84, 220WRKY transcription factor family, 84WRKY transcription factors, 102

XXa21-mediated bacterial pathogen

recognition, 99

YYeast two-hybrid system, 56