International Research Journal of Biological Sciences ___________________________________ ISSN 2278-3202Vol. 3(1), 73-88, January (2014) Int. Res. J. Biological Sci. International Science Congress Association 73 Review Paper Involvement of Disease Resistant Quantitative trait loci (QTLs) and resistant (R) Genes in key Signaling pathways of Arabidopsis thaliana during pathogen infection: An OverviewBarik Sushanta Kumar National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001 Uttarpradesh, INDIAAvailable online at: www.isca.in, www.isca.me Received 30th July 2013, revised 11th August 2013, accepted 12th September 2013Abstract Plant must continuously defend themselves against attack from fungi, bacteria, viruses, invertebrates etc. The regulating mechanism of any plant pathogen interaction is complex and dynamic. Plants possess both preformed and an inducible defense mechanism. Many resistant genes (R) are present within the chromosome of Arabidopsis thaliana which help in resistance activity against pathogens .In A. thaliana, the disease resistant genes (R) are extremely polymorphic confer parasite recognition and are found at several loci. Quantitative trait loci study in A. thaliana will provide knowledge on number of quantitative resistant loci involved in complex disease resistance, interactions between pathogen biology, plant development and biochemistry .The main QTL approach in A. thaliana is based on rapid developments in marker technology, statistical methodology will help in identifying the same kind of complex disease resistant loci in other crop plants. The A. thaliana genome carries diverse resistant genes are found in several loci linked with salicylic acid, jasmonic acid and ethylene signaling pathways. The present review focus on presence of disease resistant QTLs and genes linked in signaling pathways in A. thaliana during pathogen invasion as well as interaction.Keywords:Arabidopsis thaliana, QTLs, SA, JA, ET, Resistant gene (R), Avirulence gene(Avr) IntroductionArabidopsis thaliana belongs from family Brassicaceae is a preferred model plant for genomic studies due to its short life cycle, small size as well as a known genome sequence. The entire reported 25,496 genes of A.thaliana with a genome size of 125 megabases are distributed over five chromosomes. The incorporation of disease resistant genes of A. thaliana in to agronomically important crops will be one of the most economically effective method for controlling plant diseases. In this context, the present study on the identification of resistant genes of A.thaliana and its positions on different chromosomes loci are enumerated in this review. The hypothesis mentioning on “gene for gene resistance” aptly defines “The pathogen avirulent (avr) gene and the plant resistant genes(R) are fully interacted during pathogen interaction’’Another type of defense mechanism in A. thalianaon innate immunity is the receptor mediated due to pathogen associated molecular patterns and leucine rich repeat receptor kinasesIn A. thaliana, disease resistant genes (R) were interconnected with salicylate, jasmonate and ethylene signaling molecules. Mutation in disease resistant genes activate or suppress any one of three signaling pathways in Arabidopsis.The three main signaling pathways of salicylate, jasmonate and ethylene dependent resistance responses are mutually inhibitory in case of A. thaliana. A. thaliana is under a constant threat of infection with many biotrophic and necrotrophic pathogens as well as viruses such as Pseudomonas syringae , Peronospora parasitica, Ralstonia solanacearum, Xanthomonas campestris, Albugo candida, Alternaria brassicicola, Fusarium oxysporum, Tobacco etch virus, Cucumber mosaic virus, Cauliflower mosaic virus, Heterodera schachtii and Pythium species etc.Brief idea on Arabidopsis thaliana disease resistant genes In A. thaliana, Based on structural motif and interacting domain, seven distinct classes of resistant genes (R) are acting against specific pathogen. Short description of this disease resistant genes of A. thaliana are given below in table 1. A. thalianacontain a large number of disease resistant genes are characterized structurally with nucleotide binding sites, leucine rich repeat region, tir-domain, a putative coiled coil domain. The A. thaliana contains the total eighty five number of tir-nbs-lrr genes at sixty four loci, thirty six numbers of cc-nbs-lrr genes at thirty loci. The nbs-lrr classes are without tir or cc domain at their N -terminus present seven times at six loci, fifteen truncated tir -nbs-lrr genes lack lrr at ten loci, six numbers of cc-nbs genes at five loci. In Arabidopsis genome fourty six numbers of disease resistant genes are single tons and fifty are in pairs in given below in table 2. International Research Journal of Biological Sciences ________________________________________________ ISSN 2278-3202 Vol. 3(1), 73-88, January (2014) Int. Res. J. Biological Sci. International Science Congress Association 74 Table-1 Seven distinct classes of disease resistant genes in Arabidopsis thaliana are given belowClass Gene Structure References IRE1/bZIP60 Defining myrostilation motif / serine/threonine kinase catalytic domain 159 ADR1,RPS2Leucine rich repeat domain(LRR)/RPS2 binding site domain(NBS)/ N-TerminaLeucin Zippedomain/Coiledcoildomain160,161 RLM3,WRR4,RPP5,RPP2A,RPP2B, TAO1 Similar to Class 2 but instead of an LZ or CC domain contains a domain that is Toll like / Interleukin1 domain/ TIR domain 80,162,70,163 RPP27 LRR domain in extracellular, transmemembrane domain in single and a small cytoplasmic tail proteins are called RLPs. 121 RLK1/RLK4/RLK5, FLS2/RLK3/ ERECTA Cytoplasmic Serine/Threonine kinase domain/Extracellular LRR domain/and a Transmembrane domain(TM) . These genes are called receptor like kinases 164165166 RPW8 Small cytoplasmic proteins and contain a coiled colied domain 17 Small cytoplasmic protein not anchored in Plasmamembrane/ contains two tandem protein kinase domains. A few proteins in Arabidopsis thaliana are not categorized in to one of these seven classes Table-2 Resistant genes are distributed between chromosomes ofArabidopsis thaliana are given below Chromosome Number of disease resistant genes 49 2 2 16 28 55 The Arabidopsis genome initiative (2000)Brief idea on Arabidopsis thaliana pathosystem The eighteenth century is the beginning of the scientific emergence of plant pathology. In A. thaliana, the defense mechanism is guided by a complex signaling network. In plant species, a relatively small proportion of pathogens successfully invade it as well as spread diseases. The hypersensitive response generated by invading phyto-pathogen. Then the hypersensitive response leads to triggers nonspecific resistance known as systemic acquired resistance. Both the response work each other during different pathogen infection. The name of diseases caused by different pathogens in A. thaliana are given below in table-3. Quantitative trait loci and disease resistant genes in Arabidopsis thaliana with different pathogens: Here, we focus many number of disease resistant gene loci present in five different chromosomes of A. thaliana against different pathogens and the resistant loci was given the name of pathogen. The disease resistant genes and quantitative trait loci of A. thalianaare mapped in to five chromosomes .The map was given below in figure-1. (contain gene ID from TAIR, www.arabidopsis.org).Table-3 Arabidopsis thaliana pathosystems167Disease Pathogen Fungal 1 Downy mildewHyaloperonospora parasitica 2 White blister Albugo candida 3 Damping Off Pythium Species 4 Dark leaf spot Alternariabrassicicola 5 Powdery mildew E. cruciferarum, E.cichoracearum 6 Vascular wiltF. oxysporum 7 Leaf mold and Leaf spotCladosporium 8 Damping off or wire stemThanatephorus cucumeris Bacterial 9 Black rot on crucifers Xanthomonas campestris 10.Bacterial speck on crucifersPseudomonas syringae Viral 11.Mild stunting Tobacco mosaic virus 12. Mild stunting and desiccation Turnip crinkle virus 13 Vein clearing and chlorotic spots Cauliflower mosaic virus Nematode 14 Cyst nematodeHeterodera schachtii International Research Journal of Biological Sciences ________________________________________________ ISSN 2278-3202 Vol. 3(1), 73-88, January (2014) Int. Res. J. Biological Sci. International Science Congress Association 75 Resistant towards Erysiphe species The powdery mildew diseases are common plant diseases on agricultural and horticultural crops. A. thaliana found to be infected with three powdery mildews called as Erysiphe cichoracearum(UCSC isolate), Erysiphe cruciferarum(UEA isolate) and Erysiphe orontiiThe resistance reaction phenotypes of A. thaliana was characterized and resistant loci were mapped. A.thaliana disease resistant genes shown resistance to few pathogenic strains of a particular type of pathogen. A. thaliana six accessions Wa-1,Kas-1,Stw-0,Su-0,Sl-o and Te-0 were shown resistant to a wild isolate of the powdery mildew pathogen Erysiphe cichoracearum .A.thaliana contains five semi dominant powdery mildew disease resistant loci RPW1,RPW2,RPW4,RPW5. The name of loci are designed as RPW (recognition to powdery mildew ). The loci are map to chromosomes 2, 3, 4 and 5 respectively and RPW3 was a recessive resistant locus located on chromosome 3. A. thaliana accessions La-er and Ms-o infected by two Erysiphe strains Erysiphe cruciferarum UEA1 and Erysiphe cichoracearumUCSC1 .The three dominant loci RPW6, RPW7, RPW8 were identified in A. thaliana and mapped to chromosome 5, 3 and 3. RPW7 and RPW8 were found to be complex resistant loci with dual specificity .A. thaliana RPW8 locus contains two naturally polymorphic, dominant RPW8.1 and RPW8.2, individually control resistance through salicylic acid dependent defenses In A. thaliana, RPW8 mediated resistance causes an oxidative burst, a hypersensitive reaction and induction of pathogenesis related gene-1 expression10. A. thaliana RPW8 loci determines the frequency of powdery mildew disease in a heterogenous environments and potentially maintains genetic variation for resistance in natural populations11. RPW8.2 played the main role in post penetration resistance against Golovinomyces cichoracearum UMSG112,13. A.thaliana RPW8 functions as a broad spectrum mildew disease resistance by targeting the extra haustorial membrane (EHM) of the invading pathogen14RPW8 may serve a “guardess” for RAR1 and EDS115. The nucleotide diversities were high at RPW8.1 and RPW8.2 in fifty one A.thaliana accessions as well as the identified mutations confer phenotypic variations. The presence of RPW8 giving fitness benefits and costs effects in the presence and absence of the pathogens16. However, the origin of the powdery mildew disease locus obtained through sequence analysis of RPW8 from A. lyrata, Brassica rapa and Brassica oleraceae17In further experimental studies of A.thalianaMs -0accession against Golovinomyces species indicates that RPW8 loci contain two paralogus genes RPW8.1 and RPW8.2 confers resistance through salicylic acid signaling pathways. The 14-3-3 lambda is a positive regulator for RPW818. A.thaliana Col-0 accessions, RPW8.2 interacts with phytochrome-associated protein phosphatase type 2C negatively regulates basal defense against powdery mildew19. The quantitative trait loci RPW10, RPW11 and RPW12 were confer resistant against powdery mildew disease in A. thaliana Col-gl1xKas-1. The QTL of RPW -10 was mapped on chromosome-3, RPW-11 occurred on chromosome -5 and RPW-12 was mapped on the chromosome- 2 in A. thaliana20A well developed pathosystem in between A. thaliana accessions col-0 and E. orontii were observed. A.thaliana accession columbia infection with E orontii leads to expression of defense related genes PR1, BGL2(PR2), PR5 and GST1. A. thaliana mutants containing Pad4-1, npr1-1, eds5-1 and a double npr1-1 eds5-1 shows susceptibility to E. orontii. 21. A.thaliana mutants are displays enhanced disease resistance-1 to the fungus E. cichoracearum. The enhanced disease resistant mutant does not constitutively express the pathogenesis related genes of PR-1, BGL2 or PR5. The edr-1 was mapped to chromosome- 122 In other way, A. thaliana mutant that shown enhanced disease resistance-2 to the E. cichoracearum. A. thaliana mutant in edr-2 mediated resistance inhibits salicylic acid defense signaling in npr1, pad4 and sid-2. Edr2 gene locus was mapped on chromosome - 423. A. thaliana mutants constitutively express a vegetative storage protein-1(VSP-1) now called Cev-1 were produced very smaller quantity that mediate jasmonate and ethylene signaling pathways and was mapped on chromosome-524. A. thaliana four mutant loci designated as powdery mildew resistant -1,-2,-3,-4 ( pmr- 1, pmr-2, pmr-3, pmr-4) were identified as susceptible to E. cichoracearum. Pmr1 and pmr2 were mapped to chromosome -1, Pmr-4 was mapped to chromosome 4 and Pmr-3 was mapped to chromosome 525. Pmr-5 gene mutation rendered in A. thaliana resistance to the E. cichoracearum and E.orontii . Resistance in this mutant may be due to the loss of a susceptibility factor or to the activation of a novel form of defense26Pmr-6 encodes a pectate lyase like protein is a susceptibility locus in A.thaliana. salicylic acid, jasmonic acid and ethylene signaling pathways are not involved in the Pmr-6 gene mechanism27. A. thaliana three mutants called eds14,eds15,eds16 found to be highly disease susceptibility to Erysiphe orontii. Eds16 was mapped to chromosome 1.28..Pen-3 mutants of A.thaliana were resistant to Erysiphe cichoracearum.Pen-3 loci was mapped to chromosome-1 29..Resistant towards Pseudomonas syringae The genetic tractability of both A. thaliana and Pseudomonas syringae shown a remarkable model for research on plant pathogen interactions. Tremendous progress had been made in understanding how plant A.thaliana recognizes Pseudomonas syringae Avr proteins and mounts effective defense against A. thaliana resistant loci RPS2 shown significant defense against RPM130.. In a map based cloning approach many A. thalianaRPS2, RPM1, RPS4, RPS5 and PBS1 were isolated where PBS1 belongs to the nucleotide binding site leucine rich repeat class and RPS2, RPM1 and RPS5 proteins have coiled –coiled structures at their N termini and are classified in the CC subclass of NBS-LRR31-36. In A. thaliana RPS2 leucine-rich repeat domain determine very well interaction with Pseudomonas syringae37. RPS4 had a Toll Interleukin-1 receptor like homology along with other NBS-LRR proteins. The Avr gene products AvrRpt2, AvrRpm1, AvrB, AvrRps4 and AvrPphB were believed to be delivered from bacteria in to plant cell.38.. Avr genes expression in the plant cell leads to International Research Journal of Biological Sciences ________________________________________________ ISSN 2278-3202 Vol. 3(1), 73-88, January (2014) Int. Res. J. Biological Sci. International Science Congress Association 76 the HR dependent on the corresponding resistant genes39NDR1 mutation strongly affects resistance by a class of CC-NBS-LRR genes40NDR1 mutation affected Pseudomonas syringae, resistance by CC-NBS-LRRs class of gene name RPS2, RPM1 and RPS5 resistant genes where as resistance mediated RPS4. TIR-NBS-LRR was affected by EDS1 mutation but not by NDR141. RPS2 was required for elicitation of hypersensitive (HR) response when Pseudomonas syringaewas mounted . RPS2 was a quantative trait loci mapped on the chromosome- 442Five classes of mutants of A.thaliana were identified including mutations at RPS2 , dnd mutations causing a “defense, no death” loss of HR phenotype, a lesion mimic mutant that also exhibited an hypersensitive response phenotype43 A. thaliana was four hyper induced reaction gene family known as HIR1-HIR4. A. thaliana HIR1 and HIR2 form complexes with RPS2 reduced the growth of Pseudomonas syringae Pto Dc3000 by effector triggered immunity(ETI)44. Mutational analysis of RPS2 gene encodes a 105kd protein revealed that the NBS and an N-terminal leucine zipper (LZ) motif were critical for RPS2 function45A. thaliana WIN3gene requires PAD4 in the resistance pathways towards Pseudomonas syringae effector AvrRpt2. WIN3 gene accumulates salicylic acid during infection with Pseudomonas syringae46. RPS4 was a disease resistant locus identified in Arabidopsis on chromosome-5.47. RPS3 was a disease resistance locus mapped on chromosome-3 using a previously cloned avirulence gene AvrB from a non-Arabidopsis soybean pathogen . Pseudomonassyringae pv glycine and RPG1 and RPS3 both confer AvrB-specific disease resistance ,suggesting that these genes are homologous48. EDS1 require a resistant gene loci for RPS4 against Pseudomonas bacteria expressing the avirulence gene AvrRps449. A.thaliana PAD4 gene mapped to chromosome-350. RPS5 was a disease resistance gene in A.thaliana with specificity AvrPph3and was mapped to chromosome-151RPS6 was a disease resistant gene in A. thaliana against Pseudomonas syringae. RPS6 loci was mapped on chromosome 552. In another experiment, Enhanced Disease Susceptibility-1 (EDS1) regulated by RPS4 and RPS6 provide basal resistance in A.thaliana53RPS6 belongs to TIR-NBS-LRR class of gene.54..A defense gene ELI3 expresses mRNA in A. thaliana leaves in response to Pseudomonas syringae strains . and this loci was mapped on chromosome-355Fitness cost of RPM1 locus in A. thaliana fight the pathogen Pseudomonas syringae carrying AvrRPM1 or AvrB56. AGO4 gene exert an effective resistance in A. thaliana against Pseudomonas syringae. AGO4 was one of the critical components in the transcriptional gene silencing pathway associated with siRNA that directs DNA methylation at specific loci57. NHO1 was a gene in A.thaliana required for resistant against pseudomonassyringae58A. thaliana six ACBP3 genes ACBP1 to ACBP6 mediate defense to the bacterial pathogen Pseudomonas syringae pv tomato DC 300059. A.thaliana contains higher nicotinamide adenine dinucleotide play an important role in plant immunity by stimulating salicylic acid60Resistant towards Peronospora parasitica A. thaliana accession Wassilewskija, the RPP1 was a complex loci contains four genetically linked recognition specificities and was mapped on chromosome 361In different accessions of A.thaliana , so many number of disease resistant loci RPP1 to RPP28 were mapped in presence of major recognition gene complexes on five chromosomes which were resistant to Peronospora parasitica62. RPP5 was a complex loci in A. thaliana Ler and Col-O haplotypes exhibits intra specific polymorphism play an important role in innate immunity.The RPP5 gene complex exhibit high level polymorphism by extensive recombination between LRRs encode different numbers of LRRs63. The A. thaliana different accessions interact with Peronospora parasiticaNoco2 isolate and four RPP loci were identified such as RPP14.1, RPP14.2 RPP14.3 and RPP 5.2. RPP14.1, RPP14.2. RPP14.3 resistant loci were mapped on chromosome 3 and RPP5.2 loci was mapped on chromosome 464. RPP5 locus was respond to pathogens that disturb RNA silencing65. Using gene chip A.thaliana genome array ,three RPP genes called RPP4, RPP7 and RPP8 directed towards the pathogenic oomycete Peronospora parasitica. These common set of target genes controls the regulation of all three signaling pathways . Many defense genes predominantly encode putative signaling protein molecules that play an important role in defense66In A. thaliana , RPP1, RPP10, RPP14 loci were mapped to the same locus on the chromosome- 3 which were resistant towards P. parasitica isolates Emoy2, Cala2 and Noco2. RPP1, RPP10, RPP14 were complex locus encodes Toll-Interleukin-1-Resistance –Nucleotide binding site to detect the four Peronospora parasitica isolates. The RPP13 loci was mapped to chromosome-367. Another two RPP resistance loci called as RPP7 and RPP8 in A.thaliana against Peronospora parasitica was mapped on chromosome-1 and chromosome-5. RPP7 and RPP8 loci resistant activity was not suppressed by mutations in either EDS1or NDR168. RPP4 was mapped on chromosome- 469EDS1 require a subset of RPP2, RPP4, RPP5, RPP21 conferring resistance to the Peronospora parasitica70. In A. thaliana ,Ssi-1(suppressor of salicylic acid insensitivity1)dominant gene restores pathogenesis related gene like PR1, PR2, PR5 genes to pseudomonassyringae pv tomato and Ssi was mapped to chromosome 471. A. thaliana mutants reduced susceptibility to the downy mildew pathogen Hyaloperonospora parasitica was studied and six dmr (downy mildew resistance) loci called as dmr1, dmr2, dmr3, dmr4, dmr5, dmr6 were identified72In A. thaliana , recessive downy mildew resistant -1 allele (Dmr1) encodes homoserine kinase that was involved in resistance73. Hyaloperonospora Arabidopsis ATR1 was interact with RPP1 leading to activation of plant disease resistance in A. thaliana74 International Research Journal of Biological Sciences ________________________________________________ ISSN 2278-3202 Vol. 3(1), 73-88, January (2014) Int. Res. J. Biological Sci. International Science Congress Association 77 Resistant towards Botrytis cinerea. Botrytis cinerea is a necrotrophic fungi interact very well with A.thaliana..When Botrytis cinerea interact with A thaliana , antimicrobial compound camalexin accumulated which provides defense response. 75 .A. thaliana three loci BOS2, BOS3 and BOS4 were identified as resistant loci against Botrytis cinerea. BOS2 BOS3 loci were mapped to chromosomes- 4 and -1 ..The BOS2, BOS3 and BOS4 loci influence camalexin levels and activate the ethylene and jasmonate signaling pathways76Resistant towards Albugo candida Biotrophic oomycete pathogen Albugo candida infects A. thaliana .The disease caused by Albugo candida bears its name white rust for the production of white sori77Three resistant loci called RAC-1(Recognition of Albugo candida), RAC-2 and RAC-3 were used to map and identify in accessions of A.thaliana accessions Ksk1 and Ksk-2 . 78. .RAC -1 is a dominant loci of Arabidopsis accession Ksk-1 mapped to chromosome 1 ,RAC-3 is closely linked to the RPP8/HRT on chromosome- 5, RAC-2 is a recessive resistant loci of A. thaliana accession Ksk-2 mapped on chromosome- 3. The resistant gene WRR4 (White rust resistance) encodes a cytoplasmic toll interleukin receptor like nucleotide binding leucine rich repeat receptor like protein(TIR-NB-LRR) that confers a dominant, broad -spectrum, white rust resistance in A. thaliana accession columbia. This gene was mapped in chromosome 1. The WRR4 protein requires functional expression of the lipase like protein EDS179,80Resistant towards Ralstonia solanacearumRalstonia solanacearum is the causal agent of bacterial wilt of many important agricultural crops such as potato, tomato, banana, pepper and even trees such as eucalyptus etc.81.. Two A.thaliana genes RRS1-S and RRS1-R involved in resistant towards the Ralstonia solanacearum82. RRS1 was mapped on chromosome- 583.Arabidopsis thaliana accessions Ler ×Col-O accessions recombinant inbreed lines showed that resistance was governed by at least three loci named as QRS1 (Quantitative resistance to Ralstonia solanacearum) and QRS2 on chromosome-2, QRS3 on chromosome- 5. ERECTA gene lies close to QRS1 mapped on chromosome 284. A.thalianaaccessions Ws-O RRS1 and RPS4 function as resistant to Ralstonia solanacearum, C. higginsianum and Pseudomonas syringae pv tomato strainDC300085Resistant towards Xanthomonas campestris Xanthomonas campestrisPV campestris the causal agent of black rot crucifers85Four Quantitative resistant trait loci called RXC1, RXC2, RXC3, RXC4 (Reaction to Xanthomonas campestris) were identified through genetic analysis of A. thaliana Col-O×Ler recombinant inbreed lines. RXC1 loci was mapped on chromosome 2, a gene conferring tolerance to Xanthomonas campestris 2D520, RXC2 loci was mapped on chromosome 5, RXC3 loci was mapped on chromosome 5 and RXC4 loci was mapped on chromosome 2 of A. thaliana in above inbreed accessions86. Another gene loci was identified in Arabidopsis against Xanthomonas i.e. RXC587Resistant towards Trichoplusia ni The quantitative trait loci in Trichoplusia ni is strongly correlate with higher glucosinolate levels .88..TASTY locus was found to discover in A.thaliana on a chromosome-1 to know about susceptibility status of recombinant inbreed lines89. A myrosinase associated protein ESM1 loci was identified through map based cloning on chromosome -3 in A. thaliana landesberg erecta xcolumbia accessions inbreed lines and found to be insect resistance90Resistant towards Leptosphaeria maculans A blackleg disease of Brassica oilcrops was caused by Leptosphaeria maculans is a hemi biotrophic fungi91 RLM1 (Resistance against Leptosphaeria maculans) and RLM2 were two A. thaliana TIR-NBS-LRR resistant genes effective against Leptosphaeria maculans92. RLM1 resistant loci in Arabidopsis accessions Col-O, Ws-O and Cvi-1 was mapped on chromosome 1 and RLM2 resistant loci in Col-0 ×Ler-O, and Ler-2×Cvi-1 was mapped on chromosome - 4. Loss of two RLM1 and RLM2 resistance loci in A. thaliana Col-O x Ler-Oinbreed lines showed susceptibility for Leptosphaeria maculans93Resistant towards Tobacco etch virus The Tobacco etch virus (TEV)-Arabidopsis model system for identification of host genes. From the model observation two points are identified i.e. first virus unable to encountered due to presence of resistant allele and second is the resistant genes act against a known viral genotype but not for polymorphic viral genotypes94Three complex resistance loci RTM1 (Restricted to Tobacco etch virus movement) RTM2, RTM3 were observed through mutational analysis in Arabidopsis accession Col-O ecotype. RTM2 resistant loci was mapped on chromosome-5 of A. thalianaCol-O ecotype.RTM2 was a multi domain configuration which was homologus to thermal shock proteins .RTM1 loci was mapped on chromosome-1. RTM3 gene loci was mapped on chromosome 3 that encodes a new type of protein95-98.Resistant towards Cucumber mosaic virus Mutation in ssi2 gene conferred enhanced resistant to cucumber mosaic virus in A. thaliana and is salicylic acid independent pathway99. The RCY1 in the A. thaliana ecotype C24 was associated with the hypersensitive response and mapped on chromosome- 5100 International Research Journal of Biological Sciences ________________________________________________ ISSN 2278-3202 Vol. 3(1), 73-88, January (2014) Int. Res. J. Biological Sci. International Science Congress Association 78 Rresistant towards Turnip Crinkle VirusA dominant HRT gene confers a hypersensitive response to Turnip crinkle virus (TCV) had been cloned from Arabidopsisecotype Dijon(Di17) and was a LZ-NBS-LRR class resistant gene .HRT signaling pathway in A. thaliana is dependent on salicylic acid and is independent of NPR1, NDR1, ETR1, COI1 and perhaps of EDS1 and PAD4101. A locus in A. thaliana Di17×Col-0 accession inbreed lines designated HRTmapped on chromosome 5 which confers the ability to develop a hypersensitive response after TCV inoculation102A. thaliana cryptochrome (CRY-2) and Phototropin (PHOT -2) gave stability during TCV infection103. Arabidopsis ecotype DijonDi17) was regulated by presence of two host genes HRTand RRT results development of hypersensitive response and was salicylic acid dependent104. CRT1 was a GHKL ATPase resistance to turnip crinkle virus in A.thaliana mediated through the HRT by developing HR failed to control virus replication105Resistant towards cauliflower mosaic virusGenetic variants of Cauliflower mosaic virus (Camv) and A. thaliana were characterized to identify mild and severe symptoms. Infections of a glabrous mutant (gl1) of A. thaliana ecotype columbia (Col-Ogl1)by 30 Camv isolates. Thirteen isolates failed to cause symptoms and a greater variety of symptom type was observed in a single. A.thaliana ecotype infected with a typical Camv isolate Cabb B-JI105. Two A. thaliana ecotype Enkheim -2(En -2) and Bla -14 were resistant to systemic infection by cauliflower mosaic virus. Cauliflower mosaic virus resistance by a single semi dominant gene called cauliflower mosaicvirus resistance -1 located at chromosome-106Resistant towards Tobacco ring spot nepo virus: Tobacco ring spot virus resistance is display by many Arabidopsis ecotypes. TTR-1 (Tolerance to Tobacco ring spot virus -1 gene) encoding a TIR-NBS-LRR protein..TTR1 gene involved in SGT-dependent defense responses107TTR1 was mapped to chromosome 5108Resistant towards Plum pox poty virus and Spring beauty latent virus infection A. thaliana accession cvi-1 restrict to plum pox poty virus long distance movement controlled by a single recessive gene designated as rpv1 which was mapped to chromosome -1109. In several accessions of A. thaliana ,symptom development in spring beauty latent virus (SBLV) were to designed a loci SSB1(Symtom development by SBLV infection) which shown resistant activity .This semi dominant loci SSB1 was mapped to chromosome -5110Resistant towards Fusarium oxysporum Many QTLs which were genetically complex control natural variation in A.thaliana accessions Bay-0 and Shahdara resiatnce to Botrytis cinerea. In A.thaliana Ty-O x Col-O six dominant RFO (resistance to Fusarium oxysporum) loci shows resistant activity towards Fusarium oxysporum..The name of six loci are RFO1 to RFO6 and might be represent more than one gene. The A.thaliana RFO loci were mapped on five chromosomes such as RFO1, RFO2 mapped on chromosome-1, chromosome -3 contain RFO3 loci, chromosome -4 contain RFO4 loci ,chromosome- 5 contain RFO5 and RFO6 loci.RFO1 loci was the largest contributor resistant to fusarium races identical with a previously known gene called as WAKL 22111. A. thaliana Thionin Thi2.1 gene over expression involved in resistance to Fusarium oxysporum112Resistant towards Heterodera schachtii Heterodera are obligate sedentary endoparasites of agricultural crops. The relationship between nematodes and their host were well established. Seventy four different ecotypes of Arabidopsiswere screened for their susceptibility towards Heterodera schachtii and consider Arabidopsis as a host for plant parasitic nematodes will provide a model system for the molecular genetic analysis of this interaction113. Heterodera schachtii and root knot Meloidogyne incognitaexpression levels of pathogenesis related genes PR-1 to PR5 were examined in the roots and leaves of A.thaliana. .The PR3 and PR4 are expressed in jasmonic acid (JA)-dependent SAR.. The PR-1,PR-2 and PR-5 were highly induced in roots as well as PR-3 is to a lesser114. The use of Arabidopsis as a susceptible host in which to study the induction and formation of syncytia by cyst nematodes will benefit greatly from the established expertise in Arabidopsis research .Arabidopsis provides a genetically tractable model system for the study of nematode CLE signaling. as well as role in defense. HsCLE-1 and HsCLE- 2 were CLE like genes from Heterodera schachtii sharing highest similarity to Arabidopsis thaliana CLEs 1-7115116Resistant towards Pythium irregulareThe resistance to pythium does not directly involve to the hypersensitive response but by jasmonate and ethylene signaling pathways117. A. thaliana mutant plants fad3-2, fad 7-2 ,fad8 were deficient in jasomonate synthesis to demonstrate that jasmonate signaling was essential for protection against the Pythium mastophorum118. Six member genes of propep1-6 was well studied in A. thaliana. Over expression of two family members propep-1and propep-2 enhances resistance of A. thaliana plants against the pathogen oomycete Pythiumirregulare119. The 23aa peptide activates the transcription of defensin gene PDF1.2 and synthesis H and over expression of Propep-1 confer resistance against a root pathogen Pythium irregulare120 International Research Journal of Biological Sciences ________________________________________________ ISSN 2278-3202 Vol. 3(1), 73-88, January (2014) Int. Res. J. Biological Sci. International Science Congress Association 79 Resistant towards Cladosporium fulvumReceptor like proteins were leucine rich repeat proteins.In A.thaliana genome contains approximately 59 RLP family genes. The 17 genes of this family were present on chromosome -1 including CLV2, TMM, RPP27 and other 12 genes were present on chromosome 2,16 number of genes on chromosome 3,8 number of genes on chromosome- 4, 6 number of genes on chromosome -5121Resistant towards Alternaria brassicicolaAlternaria brassicicola with A.thaliana interaction helps to identify genes play an important role in resistance. Microarray experiment revealed that 168 genes are up regulated yet to be determined in resistance during an interaction between the A. thaliana ecotype col-0 and Alternaria brassicicola122..A.thaliana RESURRECTION -1(RST1) gene which was mapped on chromosome- 3 play a major role in defense. The RST1 gene of A.thaliana act asa negative regulator in jasmonic acid signaling123 Figure-1 AT3G50450-RPW8.1 ; AT3G50460-RPW8.2; AT3G50470-RPW8.3; AT3G50480-RPW8.4; AT4G19040- EDR2; AT2G14610- PR1; AT3G54920- PMR6; AT4G03550-PMR4; AT5G44420 PDF1.2; AT1G11310 PMR2; AT4G39030 EDS5; AT1G64280 NPR1; AT1G74710 EDS16 AT5G45250 RPS4; AT4G26090 RPS2; AT1G59870 PEN3; AT3G07040 RPS3/RPM1; AT1G12220 RPS5; AT5G46470 RPS6; AT3G52430 PAD4; AT3G44480 RPP1;AT3G46530 RPP13;AT5G43470 RPP8/HRT/RCY1; AT4G16950 RPP5; AT4G16860 RPP4; AT1G54470 RPP27; AT3G26470 RPW8 ; AT5G45260 RRS1; AT1G05760 RTM1; AT5G04890 RTM2; AT3G58350 RTM3; AT1G54040 TASTY/ESP; AT3G14210 ESM-1; AT1G64070 RLM1;AT5G44870 TTR1; AT1G79670 RFO1; AT3G57260 PR2; AT3G12500 PR3; AT3G04720 PR4; AT1G75040 PR; AT1G08720 EDR1 [The QTLs and Genes are distributed in five chromosomes of Arabidopsis thaliana. The Gene ID of diisease resistant genes from TAIR.(www.arabidopsis.org).The QTL map was based on gene ID. International Research Journal of Biological Sciences ________________________________________________ ISSN 2278-3202 Vol. 3(1), 73-88, January (2014) Int. Res. J. Biological Sci. International Science Congress Association 80 Arabidopsis thaliana Salicylic acid, Jasmonic acid and Ethylene response genes during pathogen infection: A.thaliana contains signaling molecules like salicylic acid, jasmonic acid and ethylene function in different ways. A.thaliana contains salicylic acid is a critical mediator in innate immunity and plays an important role in limiting the growth and reproduction of the virulent powdery mildew Golovinomyces orontii in A. thaliana124. In A.thaliana, salicylic acid accumulates in pathogen challenged tissues and expression of pathogenesis related PR1,PR2 and PR5 genes. The A. thaliana containing NahG were low level of salicylic acid contents compared to the sid (salicylic acid induction deficient) mutants125. A.thaliana Sid mutants express PR2, PR5 genes and accumulates camalexin during pathogen interaction126. Salicylic acid signaling require NPR1 which was a nuclear transported protein involved in defense gene activation during systemic acquired resistance 127..The A. thaliana NIM1/NPR1 mutant was isolated that unavailed the network to establish systemic acquired resistance against Peronospora parasitica due to downstream signaling of salicylic acid 128.129..A.thaliana contains a number of genes such as PAD4 ,EDS5,NPR1,SGTb1,EDR1 in salicylic acid signaling pathways contribute resistance to powdery mildews. A. thaliana atg2-2 mutant required salicylic acid activating defense related genes resistance to Golovinomyces cichoracearum13. NPR1/NIM1 acting as a positive regulator of defense responses during pathogen interaction.PAD4 involved in salicylic acid signaling 131,132..Two separate signaling branches are EDS1 and PAD4 proteins with limited homology to lipases and other requires NDR1133.The EDS1 and PAD4 pathway is associated with TIR-NBS-LRR proteins and the NDR1 pathway was typically associated with CC-NBS-LRR proteins. Snc1 was fully dependent on PAD4 but point mutation in Snc1 block the synthesis of salicylic acid134. .PR1, PR2, PR5 were set of genes activated in response to salicylic acid signaling and PDF1.2, PR3, PR4 were activated in response to jasmonic acid signaling pathway135. .A. thaliana Coi1 or Pad3 mutants requires phytoalexin camalexin and jasmonic acid for resistance against Alternaria brassicicola136. In A. thaliana, the molecular cloning of genes involved in ethylene signaling had revealed a variety of signaling modules in the ethylene response pathways. Ethylene signaling in molecular and cellular details in A. thaliana will provide innovative tools for improving plant adaptability against pathogens. Ethylene receptors were membrane proteins and related to receptor proteins found in bacteria, algae and plants namely two component regulatory systems that initiates a series of phosphorylation reactions in response to external stimuli. In A. thaliana, ethylene was perceived by ETR1, ETR2,ERS1,ERS2 and EIN4 five family 137..CTR1, a Raf like kinase suppresses downstream ethylene responses in the absence of ethylene and vice versa in presence of ethylene. Signal transduction and subsequent gene expression continue by EIN2 and EIN3. The first Arabidopsis ethylene mutant was etr1-138..Ethylene insensitive A. thaliana reacted similarly to infection by pythium species and was identified by the ein2-1 mutants which were enhanced susceptibility. The etr1-1 mutants appeared to be as resistant as wild type Arabidopsis139. Ethylene insensitive ein 2-1 mutants showed reduced disease severity after inoculation with bacterial leaf pathogens Pseudomonas syringae or Xanthomonas campestris in A. thaliana140but Arabidopsis etr1 and etr2 mutants indicates enhanced susceptibility141. EIN2 was required the systemic induction of genes PDF1.2, PR3 and PR4 in the ethylene insensitive Arabidopsis mutant ein2-1. A.thaliana mutant ein2-1 shown enhanced susceptibility towards Botrytis cinerea than wild type142. Ethylene response factor-1(erf1) is a regulator of ethylene after pathogen attack in Arabidopsis and drives the activation of defense related genes such as pr4 and pdf1.2 and its over expression positively confers resistant to Fusarium oxysporum, Plectosphaerella cucumerina and several necrotrophic fungi143Pdf1.2 regulated by apetala 2/ethylene response factor transcription factor ora59144. The Arabidopsis ein2-1 an ethylene insensitive mutant shown delay in wilt disease development caused by the Ralstoinia solanacearum145. During ethylene signaling, A. thaliana increases susceptibility to the Egyptian cotton worm Spodoptera literallis but not against diamond back moth Plutella xylostella. The Arabidopsishookless1 (hls1) and ein2 mutant affects ethylene signaling conferred resistance to Egyptian cotton worm Spodoptera littoralis146. ISR1 locus on chromosome 3 controlling Rhizobacteria such as Pseudomonas fluorescens WCS417r involved in ethylene signaling in A. thaliana147. In A. thalianamutant etr1-1 shown enhanced resistant activity against Verticillium dahlia due to increased accumulation of the PR1, PR2, PR5, GSTF1 (Glutathiones transferase), GSTU16, CHI-1, (Chitinase),CHI-2 and Myb 75 genes 148. .Jasmonic acid control defense gene expression through large scale transcriptional reprogramming. Jasmonic acid was necessary for defense gene expression in response to various microbial pathogens and arthropod herbivores. Arabidopsis plants were showed expression of the jasmonic acid responsive genes lox2, pdf1.2 and vsp by Pseudomonas syringae pv tomato dc3000. Npr1 found to be essential for salicylic acid mediated defense gene expression.149. Npr1 was a key regulatory pathogen in the systemic acquired resistance. In Arabidopsis systemic acquired resistance were effective through parallel activation of npr1 dependent defense response against Pseudomonas syringae pv tomato 150.The interaction between npr1 and ethylene modulate in defense response upon pathogen. Ethylene and jasmonic acid signaling in the A.thaliana ssi 1 mutants affect the npr1 independent expression of pdf1.2 and pr1 leads to susceptibility towards Pseudomonas syringae and Peronospora parasitica151. Two jasmonate signaling mutants Jin1 and Jin4 (Jasmonate -insensitive) shown increased in resistant activity in Arabidopsisupon treatment with biotrophic pathogen Pseudomonas syringaeand necrotrophic pathogen Botrytis cinerae152. Due to lack in the production of jasmonic acid A. thaliana several fatty acid desaturase (fad3/fad7/fad8), coronatine insensitive 1. Coi1 and jasmonic acid resistant-1(jar1), jin- 1 (jasmonate insensitive -1 gene) mutants shown high susceptibility to a variety of pathogens Botrytis cinerae, Fusarium oxysporum International Research Journal of Biological Sciences ________________________________________________ ISSN 2278-3202 Vol. 3(1), 73-88, January (2014) Int. Res. J. Biological Sci. International Science Congress Association 81 ,Pythium species ,Alternaria brassicicola and the bacterial pathogen Erwinia carotovora ,Pseudomonas syringae pv tomato .,154...Jasmonic acid dependent genes like plant defensin 1.2 (pdf1.2); thionin 2.1 (thi2.1), hevein like protein (hel) and chitinase b(chi-b) were involved in Jasmonic acid pathway dependent defense responses for resistant against biotrophic fungus E.cichoracearum,Pseudomonas syringae pv maucicola.155.The Arabidopsis gene coi -1 required for jasmonic acid signaling pathways.156.. Ein2gene act as a defense response in Arabidopsis against Botrytis cinerea A subset of pathogen resistant genes in Arabidopsis comprising pr-3,pr-4 and pr-12(pdf1.2) genes coregulate the jasmonate and ethylene signaling pathways. These genes were encode antimicrobial proteins .Additional study on EIN2 and COI1 mutants confirm at least two separate signal transduction pathways is essential for resistance against different pathogens , one that is salicylic acid dependent and other one was jasmonic acid or ethylene –dependent. Fumonisin, is a toxin produced by the fungus Fusarium moniliforme interplay between different signaling components in the control of hypersensitive response157. Bos2, bos3 and bos4 (Botrytis cinerea susceptibility) mutants accumulate reduced levels of camalexin than wild type and responsiveness to ethylene and jasmonate.Genetic evidence found that cev1(vsp1) stimulates both the jasmonic acid and ethylene signal pathways through coi1(Coronatine insensitive -1), an essential component of the jasmonic acid signaling pathways and etr1 encodes the ethylene receptor . The A.thaliana mutants npr1,eds5,ein2 and jar1 disrupt the salicylic acid, jasmonic acid and ethylene and cpr1, cpr5, cpr6 mutants constitutively activate these pathways identified by epistasis analysis158Conclusion The identification of disease resistant genes and gene loci in A. thaliana is an input knowledge to built agriculture .The Resistance genes from Arabidopsis are introduced in to different crop species and these varities of crop species are used in agriculture farming. In other way, our environment should clean from pesticides ,herbicides and different poisonous chemicals used for pathogen killing in crop varieties. The disease resistant genes which were identified in Arabidopsis can help to study of different protein classes related to other crop resistant gene loci encoding protein classes. The A.thaliana resistant genes involved in signaling pathways is a source of finding for this same link in other crop varieties. 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