Os05g0107700

Os05g0107700, named as xa5, is a recessive gene associated with resistance to rice bacterial leaf blight.

Annotated Information

Function

The gene xa5 provides racespecific resistance to X. oryzae pv. oryzae, and encodes the small subunit of transcription factor IIA(TFIIAγ). This recessive gene provides race-specific resistance to X. oryzae pv. oryzae, and is structurally unlike the more than 40 plant R genes previously cloned. xa5 is inherited in a completely recessive manner and the susceptible allele Xa5 is fully dominant. xa5-mediated recessive resistance is the result of restricted bacterial movement, but not restricted multiplication.

Plants with lesions less than 4 cm are resistant, while those greater than 4 cm are susceptible. The susceptible indica isoline IR24 and the resistant indica isoline IRBB5 were referred to as IS and IR respectively. No significant difference in lesion length between IS and heterozygous F2s 14 dpi was observed. In addition, bacterial populations over time in heterozygous plants were similar to those in homozygous susceptible IS individuals. These results demonstrate that the Xa5 allele is not dose-dependent in the indica IR24 background.

Although X. oryzae pv. oryzae multiplied extensively in resistant IR lines, lesion lengths were consistently less than 4 cm. Genetic background may play a role in resistance mediated by specific Xa genes. X. oryzae pv. oryzae -xa5 dynamics appear to differ in the indica and japonica NILs. Bacterial movement is restricted in both indica and japonica resistant plants. In both indica and japonica NILs, X. oryzae pv. oryzae movement down the leaf was dramatically faster in susceptible than in resistant leaves. Movement in resistant leaves appeared to be more restricted in JR than IR.

No significant difference between untransformed susceptible japonicas(JS) and Xa5 transformed previously resistant japonicas (JR::Xa5) was observed. In the japonica subspecies as in the indica, xa5 operates as a recessive gene and genetic background does not affect its gene action. Since the transgenic JR::Xa5 plants contain two copies of the recessive resistant xa5 allele, one allele of Xa5 is sufficient for disease even in plants with two copies of xa5. Additional insertions of Xa5 do not result in increased disease severity in previously resistant genotypes，suggesting that Xa5 may be a susceptibility allele（Iyer-Pascuzzi et al., 2008).

Using several key experimental observations, we have shown that xa5 encodes TFIIAγ. First, a collection of individuals recombinant between resistant and susceptible parents allowed us to narrow the region to an approximately 8.1-kb interval containing the gamma subunit of TFIIA. This region was located 1.5 kb upstream of the gene encoding the hypothetical protein Q94HL4. Sequencing and expression analysis eliminated Q94HL4 from further consideration but identified a single amino acid change within the coding region of TFIIAγ that distinguished the resistant and susceptible isolines and would not affect the expression TFIIAγ. Third, sequencing of 27 resistant and nine susceptible cultivars in the Aus-Boro group demonstrated a perfect association between the haplotype of E39 and resistance to race 2 of X. oryzae pv. oryzae. Together, these lines of evidence demonstrate that TFIIAγ encodes the xa5 resistance gene.

TFIIA is one of a set of general transcription factors required for transcription by RNA polymerase II (Orphanides et al. 1996). The functional molecule is composed of two subunits in yeast and three in plants and humans. TFIIA is essential to cell growth and has been shown to have several roles in transcription, including stimulation and stabilization of the interaction between the TATA-box binding protein and the general transcription factor TFIID, promoter selection, gene-specific regulation, and activator-dependent transcription (Hampsey et al. 1998; Orphanides et al. 1996).

Expression

The rice xa5 gene for disease resistance to Xanthomonas oryzae pv. oryzae has been positionally cloned and encodes the gamma subunit of transcription factor IIA (TFIIAγ). TFIIAγis a general eukaryotic transcription factor with no previously known role in disease resistance. xa5 is unusual in that it is recessive and does not conform to one of the typical resistance gene structural classes. Sequencing of TFIIAγ in resistant and susceptible isolines revealed two nucleotide substitutions resulting in an amino acid change between resistant and susceptible cultivars. This association was conserved across 27 resistant and nine susceptible rice lines in the Aus-Boro group.

Positional cloning identifies xa5 in an 8.1-kb region containing TFIIAγ in the subtelomeric region of chromosome 5. The start codon, splice junctions, and 3′UTR of the TFIIγgene were defined by aligning a Nipponbare TFIIAγ cDNA (GI 32975200) to the IR24 (susceptible) BAC. This identified two nucleotide substitutions resulting in an amino acid substitution from valine to glutamic acid at position 39 in the resistant cultivar, a significant change from a hydrophobic to hydrophilic amino acid. Examination of the structure of TFIIAγ further showed that the variable amino acid at position 39 resided in a solvent-exposed surface, suggesting that it may play a role in protein-protein interactions (Bleichenbacher et al., 2003).This single amino acid change in TFIIAγ is consistent with the stable expression of this gene in both susceptible and resistant plants and leads to the hypothesis that it functions both as general transcription factor and as xa5.

A single resistant haplotype conserved across all 27 resistant lines was found. There were two haplotypes among the 11 susceptible accessions, each of which carried nucleotides that would result in a valine at position 39. The japonica Nipponbare as well as four of the Aus-Boro lines contained the same susceptible haplotype as IR24, while five Aus-Boro lines had a silent mutation within the coding region（Iyer and McCouch, 2004）.

Xa5,this novel disease R gene provides adult plant resistance and encodes the gamma subunit of transcription factor IIA (TFIIAγ), one of several general transcription factors responsible for accurate transcription by RNA polymerase II.

Previous results had narrowed xa5 to an approximately 100-kb segment in the subtelomeric region of chromosome 5.

Evolution

xa5 is a recessive, race-specific R gene that provides immunity to races of Xanthomonas oryzae pv. oryzae expressing avrxa5, the cognate avirulence gene to xa5. X. oryzae pv. oryzae causes rice bacterial blight, a severe disease in South and Southeast Asia. Avrxa5 is likely to be a member of the AvrBs3 family of proteins (Bai et al., 2000; Hopkins et al., 1992), which are usually characterized by nuclear localization signals and transcriptional activation domains (Bonas and Lahaye, 2002).

xa5 is a naturally occurring mutation that is most commonly found in the Aus-Boro group of rice (Oryzae sativa L.) varieties from the Bangladeshi region of Asia (Garris et al., 2003).There are over 20 resistance genes to X. oryzae pv. oryzae, three of which have been cloned (Xa21,Xa1, and Xa26) and fall into one of the five typical R gene classes (Song et al., 1995; Sun et al., 2004; Yoshimura et al., 1998). Xa21 and Xa26 both encode NBS-LRR proteins containing a kinase domain, while Xa1 encodes a member of the NBS-LRR class.

xa5 does not resemble either of the two cloned recessive resistance genes in plants, mlo or RRS1-R. In contrast to xa5, resistance governed by barley mlois not race-specific (Buschges et al., 1997). Mutations in Mlo result in immunity to nearly all isolates of the fungal pathogen Erysiphe graminis f. sp. hordei. The RRS1-R gene from Arabidopsis provides resistance to several strains of Ralstonia solanacearum and encodes an NBSLRR protein with a WRKY motif characteristic of some plant transcription factors (Deslandes et al., 2002). The RRS1-R gene product physically interacts with its cognate protein PopP2 (Deslandes et al., 2003). Unlike xa5, RRS1-R shares many characteristics with dominant R genes (Deslandes et al., 2003). For example, while genetically defined as recessive, RRS1-R behaves as a dominant gene in transgenic plants and is a member of the NBS-LRR R gene class.

Labs working on this gene

Plant Genome Mapping Laboratory, University of Georgia,Riverbend Research Laboratory, Room 162, Athens,GA 30602, USA

Institute of Genomic Diversity, Plant Breeding Department,130 Biotechnology Building, Cornell University, USA

CIAT - International Center for Tropical Agriculture,A. A. 6713, Cali, Colombia, South America

Central Rice Research Institute (CRRI), Cuttack 753 006, India

International Rice Research Institute (IRRI), Los Banos, Philippines

College of Life Sciences, Wuhan University,Wuhan, 430072, P.R. China

Department of Plant Breeding and Genetics, 240 Emerson Hall, Cornell University, Ithaca NY 14853, USA

References

(1)A. S. Iyer-Pascuzzi;H. Jiang;L. Huang;and S. R. McCouch. Genetic and Functional Characterization of the Rice Bacterial Blight Disease Resistance Gene xa5. Phytopathology, 2008, 98(3): 289-295

(2)Anjali S. Iyer;and Susan R. McCouch. The Rice Bacterial Blight Resistance Gene xa5 Encodes a Novel Form of Disease Resistance. Molecular Plant-Microbe Interactions, 2004, 17(12): 1348-1354

(3)Matthew W. Blair;Amanda J. Garris;Anjali S. Iyer;Brad Chapman;Stephen Kresovich;Susan R. McCouch. High resolution genetic mapping and candidate gene identification at the xa5 locus for bacterial blight resistance in rice (Oryza sativa L.). Theoretical and Applied Genetics, 2003, 107(1): 62-73

(4)Marella Lalitha Shanti; M. L. C. George; C. M. Vera Cruz; M. A. Bernardo; R. J. Nelson; H. Leung; J. N. Reddy and R. Sridhar. Identification of Resistance Genes Effective Against Rice Bacterial Blight Pathogen in Eastern India. Phytopathology, 2001, 85(5): 506-512

(5)D. Yang;A. Sanchez;G. S. Khush;Y. Zhu and N. Huang. Construction of a BAC contig containing the xa5 locus in rice. Theoretical and Applied Genetics, 1998, 97(7): 1120-1124

(6)M. W. Blair and S. R. McCouch. Microsatellite and sequence-tagged site markers diagnostic for the rice bacterial leaf blight resistance gene xa-5. Theoretical and Applied Genetics, 1997, 95(1-2): 174-184

(7)V. Petpisit;Gurdev S. Khush and H. E. Kauffman. Inheritance of Resistance to Bacterial Blight in Rice. Crop Science, 1977, 17(4): 551-554

(8)Identification and gene prediction of a 24 kbregion containing xa5,a recessive bacterial blight resistance gene in rice(Oryza sativa L.)[J]. Chinese Science Bulletin,2003,24:2725-2729.

(9)Comparative physical mapping of rice BAC clones linked to resistance genes Glh,Bph-3 and xa-5 in Oryza sativa L. and O. granulata Nees et Arn.ex Watt.[J]. Chinese Science Bulletin,2004,06:591-596.

(10)Virulence of Xanthomonas oryzae pv. oryzae on Rice Near-Isogenic Lines with Single Resistance Gene and Pyramiding Lines in China[J]. Agricultural Sciences in China,2004,10:45-50.

(11)Application of Functional Markers to Identify Genes for Bacterial Blight Resistance in Oryza rufipogon[J]. Rice Science,2010,01:73-76.

(12)Identification of an avirulence gene,avrxa5,from the rice pathogen Xanthomonas oryzae pv.oryzae[J]. Science China(Life Sciences),2010,12:1440-1449.

(13)Evaluation of the Pathotypes of Xanthomonas oryzae pv. oryzae and Preliminary Analysis of the Resistant Reactions of Main Japonica Rice in the Yunnan Plateau, China[J]. Agricultural Sciences in China,2006,04:299-306.