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Plant immune system: plant disease resistance genes and its applications.

Resistance Gene (R genes)

Plants have developed immune systems to combat the pathogens attacks. The immune systems involve two modes to destroy the invading pathogens. The first one includes transmembrane pattern recognition receptors (PRRs) mode. The PRRs belong to the family of receptor like proteins (RLPs) and recognize conserved microbial patterns (1). RRRs act in response to slowly evolving microbial associated molecular patterns (MAMPS) or pathogen associated molecular patterns (PAMPs) such as flagellin (2). Flagellin is the structural protein of bacteria that forms the major component of flagellar filaments. The flagellin has PAMPs that can be predicted by plant, leading to activation of defence response. The second mode uses the polymorphic Nucleotide Binding (NB) and Leucine-Rich Repeats (NB-LRR) protein products encoded by R genes. Resistance proteins (R-proteins) are the second line of defence system present in all the plants. These proteins provide the resistance against different pathogens by recognizing the effector molecules of pathogens. Specific effectors molecules produced by pathogens are directly recognized by different R proteins. The mechanism of defence is mediated by the disease resistance proteins that function is identification of pathogen effectors.

Flor, 1971 performed inherent analyses of plants and pathogens and defined a model known as gene for gene model. In this model it has been predicted that R gene may function as receptor to recognize the pathogen derived elicitor encoded by Avr genes. Flor, 1971) studied the interaction between flax and the fungal pathogen (Melampsora lini) and reported that flax genes for resistance were dominant and rust genes for virulence were recessive and finally concluded that pathogens contain a mixture of molecules encoded by dominant avirulence (Avr) genes that generate defence responses in plants carrying the corresponding R gene (3). This model predicted that plant resistance will occur only when a plant possesses a dominant resistance gene (R) and the pathogen expresses the complementary functional avirulence gene (Avr). The pathogen avirulence genes are referred to as effector genes and have disease causing ability (4). Different bacterial and fungal pathogens contain diverse sets of effectors molecules and Avr genes (5).

The most important class of R genes consist of a nucleotide binding domain (NB) and leucine rich repeat (LRR) domains and are referred to as NB-LRR R genes. The NB domain binds either GTP/GDP or ATP/ADP and the LRR domain is involved in protein-protein interactions. The most important function of LRR domain is disease resistant. Large number NBS of coding sequence have been isolated from different plant species by genome wide analysis methods. In papaya and Cucumis sativus 50 NBS coding sequence (6,7) and in Oryza sativa 653 NBS coding sequence have been isolated (8).

Applications of R genes in major plants

Mildew resistance locus (MLO) genes are present as small family in the genomes of all higher plants. MLO genes family exists in plants and exhibits resistance against the wide variety of pathogens. Various members of MLO gene family may play an essential role against phytopathogenic fungus in dicots. Presently, 15 MLO genes in Arabidopsis, 9 in maize, 12 in rice and 17 in grapes have been reported (9-12). The details of major R genes reported in important plants are summarized below:

R genes in Arabidopsis (Arabidopsis thaliana)

Meyer et al., (2003) identified over 149 resistance genes encoding NBS-LRR class in Arabidopsis using in silico analysis (13). NBS-LRR locus contains different allelic forms that can confer resistance to different class of pathogens. Disease resistance gene RPS6 was identified in Arabidopsis (14) and locus has been mapped on chromosome 5. RPS6 gene exhibits disease resistant against the Pseudomonas syringae (15). Various members of MLO gene families in Arabidopsis include AtMLO2, AtMLO6 and AtMLO12 play essential role in resistance to disease. The AtMLO2 gene reduced susceptibility to Golovinomyces orontii. Two other Arabidopsis genes such as AtMLO12 and AtMLO6 were mutated withAtMLO2 and which showed resistance to the powdery mildew (10). Apart from MLO gene family, other resistance gene RPW8 works against the powdery mildew disease inArabidopsis which has an amino terminal transmembrane domain and CC domain. In Arabidopsis thaliana locus contains two dominant R genes are RPW8.1 and RPW8.2. RPW8.1 and RPW8.2 genes confer resistance to powdery mildew disease caused by fungi Erysiphe cruciferarum (16).

Ashfield et al., (2003) cloned Rpg1-b resistance gene from soybean and compared this gene with RPM1 resistance gene from Arabidopsis and found that Rpg1-b gene of soybean and RPM1 gene of Arabiodpsis thalina mediate recognition of same effector protein from Pseudomonas syringae. Both the genes RPM1 and Rpg1-b belong to the coiled-coil NBS-LRR class of R genes (17). The three PEN1, PEN2 and PEN3 proteins encoded by genes and acts as essential components in cell wall-based defence against powdery mildew Blumeria graminis fsp. Hordei (18).

R genes in rice (Oryza sativa)

Bacterial blight is one of the most serious disease of rice worldwide caused by Xanthomonas oryzae pv. oryzae (Xoo) which causes loss of productivity upto 81%19. Resistance to bacterial blight regulated by disease R genes and defence responsive genes. Thirty eight resistance genes for bacterial blight have been identified and utilized in rice breeding programs (20). Five of them includes Xa1 (21), Xa21 (22), Xa5 (23), Xa26 (24) and Xa7 (25) have been cloned. The gene Xa 5 have been widely used globally for gene pyramiding to develop rice resistance varieties (26,27,20).

Blast disease of rice is another disease caused by Magnaporthe grisea fungus (28). Till date 96 genes for blast resistance have been identified and mapped (29). Several R genes are clustered in specifically on chromosome 6, 9, 11 and 12 in rice genome (30,31). Rirlb gene belongs to defence related gene family that has been identified in cereals (32). Many blast resistance genes have been successfully introgressed into elite breeding lines using gene pyramiding approach. For example, the variety Pusa1602 (PRR78+Piz5) and Pusa1603 (PRR78+Pi54) lines were developed by incorporating the blast resistance genes Piz-5 and Pi54, using a marker assisted backcrossing (MABC) breeding (33). The Rongfeng B hybrid rice line was also developed through MABC breeding (34). The blast resistance Pi genes (Pi-7(t), Pi-d(t)1 and Pir2-3(t) and qLN2 QTL) from the Pongsu Seribu 1 rice variety was introduced into popular Malaysian mega rice variety MR263 (29).

R gene in tomato (Solanum lycopersicum)

Tomato is one of the important vegetable crops worldwide .The tomato Pto gene is resistance gene encoding a serine/threonine protein kinase (PK) and shows resistance to Pseudomonas syringae. pv. tomato that express by the avirulence gene Avr Pto. Many family of MLO genes have been cloned in Arabidopsis, tomato and pea (9-35) Whole genome of tomato have available and provides all the information which are related to structural features and phylogenetic relationship of the MLO gene family. In tomato 17 MLO genes are identified by bioinformatics methods (36).

By the biotechnological methods transgenic tomato has produced that shows resistance to wide varieties of pathogens. Mi gene has introduced into the cultivated Lycopesicon esculentum tomato from its natural relative L. peravianum cultivar (37). Mi-1 encodes a cytoplasmic NBS-LRR-CC protein. The Mi locus localized at chromosome 6. Mi locus contains two highly homologous genes such as Mi-1.1 and Mi1.2 or Mi-1 genes. These genes effective against nematodes, oomycetes and fungi (38). In the pepper Bs2 R gene shows resistance against the bacterial spot disease caused by the bacterium Xanthomonas campestris. X. campestris is also pathogen of tomato. This Bs2 R gene has been cloned from pepper into tomato that encodes a NB-LRR protein of R genes. Transgenic tomato carries Bs2 and effective against X. campestris.

The tomato I-3 gene is a novel gene for resistance to Fusarium wilt disease caused by Fusarium oxysporum f. sp. lycopersici (Fol) races 3. I-3 encodes an SRLK (S-receptor-like kinase) reveals a new pathway for Fol resistance and confer Avr3-dependent resistance to Fol race 3 (39). Tomato yellow leaf curl virus causes disease in tomato worldwide. Ty-2 resistance gene shows resistance against virus. By bioinformatics techniques, 22 disease-resistance candidate genes of Ty-2 were recognized. These genes involve not only in of in tomato growth and development but also responses to various stresses (40).

R gene in barley (Hordeum vulgare L.)

Mildew resistance locus o (MLO) is a novel class of plant integral membrane proteins Mlo gene is control element of plant pathogene resistant. MLO gene family may play an important role in defence system resistance against the variety of plant pathogens. Tucker et al., (2013) found many R genes such as Mla-9, Ml-ra, Mla-6 and the combinations of Mla-1 plus Mla-A12 and Mla-6 plus Mla-14 and Mla-13 plus MlRu3 together with the recessive resistance gene mlo-5 in barley against powdery mildew caused by the fungus Blumeria graminis f. sp. hordei (Bgh) in Western Australia (41).

Many diseases are mostly seen in barley likes leaf rust, stem rust and loose smut diseases. Leaf rust disease is caused by Puccinia hordei (fungus) in barley. Rph23 additive adult plant resistance gene is a new resistance gene to leaf rust in barley. This gene was identified from a doubled haploid population resulting from an intercross between and Australian barley varieties Franklin (F) and Yerong (Y). Rph23 leaf rust gene has been mapped on 7HS chromosome (42). Stem rust disease caused by Puccinia graminis f. sp. tritici. Rpg1 gene provides durable protection against stem rust that loss in widely grown barley cultivars. An Rpg1 gene encodes a receptor kinase like protein with two tandem protein kinase domains (A novel class of plant resistance genes) (43). Rpg5 is another stem rust resistance gene shows dominant resistance against rye stem rust in barley (44). Zhou et al., (2014) studied on association mapping of stem rust race TTKSK resistance in US barley breeding germplasm. They used 3000 cultivars for resistance at seedling stage as well as adult plant stage. In seedling stage two SNP markers on chromosome 7 H (11_21491 and 12_30528) were found which linked with resistance and resistance QTL was Rpg-qtl-7H-12_30528. In adult stage two SNP markers on chromosome 5H (11_11355 and 12_31427) were found which linked with resistance and resistance QTL was Rpg-qtl5H-11_11355 (45). Zang et al., (2015) identified smut resistance gene Un8 and was mapped on long arm of chromosome 5 (1HL) (46).

R gene in wheat (Triticum aestivum L.)

Various types of diseases are found in wheat such as leaf rust, stem rust and stripe rust caused by different types of microorganisms. Leaf rust disease is caused by the fungus Puccinia triticina Eriks. is widespread diseases of bread wheat (Triticum aestivum L.) worldwide (47,48). Charpe et al., (2012) work on marker assisted gene pyramiding of leaf rust resistance genes Lr9, Lr24 and Lr28 in a bread wheat cultivar HD 2329 against virulent pathotypes of leaf rust 77-5 (121R63-1) and achieved that all genes showed a high degree of seedling and adult plant resistance (49). Wang et al., (2014) studied on genetic analysis and molecular mapping of leaf rust resistance genes in the wheat line 5R618 bred at china. In this study they crossed between wheat line 5R618 (resistance) and Zhengzhou5389 (susceptible) with Chinese P. triticina pathotype THJP and found that Lr5R gene showed resistance to P. triticina and Lr5R gene was located on the 3DL chromosome. They concluded that Lr5R is novel leaf rust resistance gene (50). Shahin et al., (2015) performed research on relationship between partial resistance and heritage of adult plant leaf rust resistance gene Lr46 in six bread wheat varieties such as Gemmeiza 9, Giza 168 and Gemmeiza 7, Gemmeiza 1, Sakha 93 and Sids 1 and found two varieties like Giza 168 and Gemmeiza 9 have three leaf rust genes i.e. Lr45, Lr46 and Lr47 and other four varieties do not contain any leaf rust gene after segregation of [F.sub.2] plant (51).

Stem rust, another rust disease caused by Puccinia graminis f. sp. tritici (Pgt) is serious diseases of wheat (Triticum aestivum L.) worldwide. Yadav et al., (2015) applied marker assisted backcrossing method and transferred the three stem rust resistant genes Sr25, SrWeb and Sr50 from the CIMMYT breeding line PMBWIR4 into the wheat cv. HUW234 (popular Indian wheat cultivar) and found that improved version of wheat cv. HUW234 showed superior resistance as compared to source cultivar against stem rust (52).

Stripe rust is caused by Puccinia striiformis f. sp. tritici (Pst) is one of the most damaging diseases of wheat. Various stripe rust resistance genes have been mapped on chromosome 2B such as Yr5, Yr7, Yr27, Yr31, YrSp, YrV23, YrQz, YrTp1 and YrCN19 (53-55). These genes show resistance to all or to a few races of P. striiformis f. sp. tritici.. Stripe rust resistance gene Yr51 has been mapped on 4AL chromosome and showed resistance against Australian pathotypes of Puccinia striiformis f. sp. tritici (56). Zhou et al., (2014) studied on identification of stripe rust gene Yr59 to stripe rust in wheat germplasm PI 178759 of Washington state, USA. In this research they crossed between wheat germplasm PI 178759 and Avocet susceptible with P striiformis f. sp. tritici. They identified that wheat germplasm PI 178759 was high temperature adult resistance (HTAP) and has been mapped on long arm of 7B chromosome (57).

R gene in Maize (Zea mays)

Various types of diseases are found in maize such as Aspergillus ear rot, Gibberella ear rot and Diplodia ear rot caused by different types of microorganisms. Aspergillus ear rot is caused by fungus Aspergillus flavus which produces a mycotoxin called as aflatoxin. Several researches have reported that QTLs show resistance to aflatoxin accumulation (58-60) and to Aspergillus ear rot (59). Gibberella ear rot is caused by the fungus Gibberella zeae and Fusraium graminearum. Ali et al., (2005) studied and identified 11 QTLs shows resistance to Gibberella ear rot disease (61). Diplodia ear rot disease is caused by Stenocarpella maydis. Olatinwo et al., (1998) suggested that non additive gene play an important role for resistant to diplodia ear rot disease (62) and Dorrance et al., (1998) suggested that general and specific additive gene play an important role in resistant against this disease (63).

R gene in Linseed (Linum usitatissimum)

L6 resistance gene encodes NBS-LRR class ofR gene that confers race specific resistance to strains of flax rust (Melampsora lini) that carry avirulence alleles of the AvrL567 gene (64). The resistance genes L5, L6, L7, M, P and P2 and the corresponding avirulence gene have been cloned and currently avirulence/virulence genes at four loci, AvrL567, AvrM, AvrP4 andAvrP/AvrP123 have been cloned. (65). Genes at the M locus in flax (Linum usitatissimum) that confer resistance to flax rust (Melampsora lini). Two other functional resistance genes M1 and M3 have cloned at this locus by candidate gene approaches and transposon tagging methods. M1 and M3 belongs to family of the nucleotide binding site, leucine-rich repeat (NBS-LRR) of R gene (66). 147 NBS-LRR genes identified that encode R gene to detect pathogens and to induce defense responses (67).

Various diseases are found in linseed which causes loss in its productivity includes rust caused by Melomsora lini, powdery mildew caused by Oidium lini, Alternaria blight caused by Alternaria lini and wilt caused by Fusarium oxysporum. Some disease resistance varieties of linseed have been developed and they show resistance to rust, powdery mildew, Alternaria blight, wilt and budfly diseases. LCK-9216 and LMH-16-5 varieties show resistance to powdery mildew and rust and moderate resistance to Alternaria blight and budfly but LMH-16-5 variety also shows moderate resistance to wilt. Jawahar Linseed-9 variety shows resistance to powdery mildew, rust and wilt and are tolerant to Alternaria blight. LMH-62 variety shows resistance to powdery mildew, rust and wilt (68). PKV NL-260 variety shows moderate resistance to powdery mildew, Alternaria and budfly. NL-142 variety is moderate susceptible to Alternaria blight, wilt and rust and moderate resistance to bud fly and powdery mildew. NL-165 variety is moderate susceptible to Alternaria blight and resistance to leaf minor and moderate resistance to powdery mildew, wilt and budfly (69). Surbhi (Kl-1) and Nagarkot (KL-31) varieties show resistance to rust, drought and powdery mildew. Jeevan (DPL-21) and Janaki (KL-43) varieties show resistance to rust, wilt and powdery mildew. Himalini variety shows fairly resistance to powdery mildew, wilt and resistance to rust. Him Alsi-I (KL-187) variety shows resistance to blight rust and wilt (70).


The main focus of the research is to manage the yield loss caused by diseases of plant at global level. Chemical management of plant diseases is simple and effective option. The most important difficulty associated with chemical management is environmental pollution and health hazards caused by toxic chemicals released during disease management. Chemical management gives good results for a few pathogens only, but bad results against other beneficial pathogens. Thus in order to recognize a sustainable agriculture and obtain high value products in terms of health safe, the use of resistance (tolerant) varieties have become a most important tool to reduce or decreases caused by various pathogens. Many varieties that are resistant to various pathogens are available for various plants.

Biotechnological tools are being used to make easy the existing disease management planning. The various molecular biology techniques are being used to assist the conventional breeding programme and to help in shorten the period required to grow resistance cultivar in various plants. In molecular biology techniques, molecular marker offer enormous scope for improving the efficiency of traditional plant breeding programme in which gene pyramiding and marker assisted backcrossing method are applied for obtaining disease resistance plants. Gene pyramiding with marker technology can combine into existing plant breeding programme to permit researchers to access, transmit and unite genes at a rate and with precision not before possible. Gene pyramiding is the method of combining more than one gene for resistance in a common genetic background through the repeated back crossing and selection with the virulence races of the pathogen. This technique is very effective in obtaining durable resistance to the pathogens. Molecular markers are used to detect the presence of desire character which is significantly important. Marker assisted backcrossing (MABC) is a specific and an efficient method to introgress a single locus controlling a trait of interest while retaining the important characteristics of the recurrent parent. MABC is superior to conventional backcrossing in accuracy and efficiency. MABC involves subsequent backcrossing to eliminate the genetic background of the donor while getting better genetic properties of recurrent parent as much as possible.


The authors are thankful to U. P. Council of Agricultural Research, Lucknow for giving the opportunity to this study.


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Shashi Prabha [1], Ashwani Yadav [1], Akanksha Sharma [1], Hemant Kumar Yadav [2], Sujit Kumar [1] and Rajendra Kumar [1] *

[1] U.P. Council of Agricultural Research, Lucknow, Uttar Pradesh, India.

[2] National Botanical Research Institute, Lucknow, Uttar Pradesh, India.

(Received: 30 January 2016; accepted: 06 March 2016)

* To whom all correspondence should be addressed.

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Author:Prabha, Shashi; Yadav, Ashwani; Sharma, Akanksha; Yadav, Hemant Kumar; Kumar, Sujit; Kumar, Rajendra
Publication:Journal of Pure and Applied Microbiology
Article Type:Report
Date:Jun 1, 2016
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