Abstract
Bacterial blight (BB) of rice (Oryza sativa L.) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a destructive disease in rice worldwide. Xa3, a gene conferring resistance to BB at the booting stage of the rice plant, has been characterized previously using map-based cloning. We cloned and sequenced the Xa3/xa3 gene in the Korean cultivars Hwayeong, Ilmi, and Goun and conferred resistance or susceptibility to BB. We detected polymorphisms, and polymerase chain reaction-based functional markers were developed based on the single nucleotide polymorphism from the Xa3 and xa3 nucleotide sequence. Susceptible or resistant individuals from an F2 population developed from a cross between Milyang 244 and Ilmi, near-isogenic lines carrying BB resistance genes, were screened with functional markers. The BB3-RF and BB3-RR primers consistently amplified a resistance-specific fragment of 255 bp only in resistant plants, whereas the BB3-SF and BB3-SR primers were specific to susceptible plants. Genoty** results were co-segregated with phenotype by conducting the BB resistance test with the K3 race. These markers could be effective for marker-assisted selection of the Xa3 gene in rice breeding programs.
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References
Andersen JR, Lübberstedt T (2003) Functional markers in plants. Trends Plant Sci 8(11):554–560
Bhasin H, Bhatia D, Raghuvanshi S, Lore JS, Sahi GK, Kaur B, Vikal Y, Singh K (2011) New PCR-based sequence-tagged site marker for bacterial blight resistance gene Xa38 of rice. Mol Breed 30(1):607–611
Cao Y, Ding X, Cai M, Zhao J, Lin Y, Li X, Xu C, Wang S (2007) The expression pattern of a rice disease resistance gene xa3/xa26 is differentially regulated by the genetic backgrounds and developmental stages that influence its function. Genetics 177(1):523–533
Chen DH, Ronald PC (1999) A rapid DNA minipreparation method suitable for AFLP and other PCR applications. Plant Mol Biol Rep 17:53–57
Dangle JL, Jones JDG (2001) Plant pathogens and integrated defence response to infection. Nature 411:826–833
Gnanamanickam SS, Brindha Priyadarisini V, Narayanan NN, Vasudevan P, Kavitha S (1999) An overview of bacterial blight disease of rice and strategies for its management. Current Sci 77(11):1435–1443
Iyer-Pascuzzi AS, McCouch SR (2007) Functional markers for xa5-mediated resistance in rice (Oryza sativa, L.). Mol Breed 19(4):291–296
Kauffman HE, Reddy APD, Ksiek SPV, Marca SD (1973) An improved technique for evaluating resistance of race varieties to Xanthomonas oryzae. Plant Dis Rep 57:537–541
Lee KS, Rasabandith S, Angeles ER, Khush GS (2003) Inheritance of resistance to bacterial blight in 21 cultivars of rice. Phytopathology 93(2):147–152
Liu J, Liu D, Tao W, Li W, Wang S, Chen P, Cheng S, Gao D (2000) Molecular marker-facilitated pyramiding of different genes for powdery mildew resistance in wheat. Plant Breed 119(1):21–24
Perumalsamy S, Bharani M, Sudha M, Nagarajan, Arul L, Saraswathi R, Balasubramanian P, Ramalingam J (2010) Functional marker-assisted selection for bacterial leaf blight resistance genes in rice (Oryza sativa L.). Plant Breed 129(4):400–406
Richard I, Beckmann JS (1995) How neutral are synonymous codon mutations? Nat Genet 10:259
Sanchez AC, Brar DS, Huang N, Li Z, Khush GS (2000) Sequence tagged site marker-assisted selection for three bacterial blight resistance genes in rice. Crop Sci 40:792–797
Sun X, Cao Y, Yang Z, Xu C, Li X, Wang S, Zhang Q (2004) Xa26, a gene conferring resistance to Xanthomonas oryzae pv. oryzae in rice, encodes an LRR receptor kinase-like protein. Plant J 37(4):517–527
Sunyaev S, Hanke J, Aydin A, Wirkner U, Zastrow I, Reich J, Bork P (1999) Prediction of nonsynonymous single nucleotide polymorphisms in human disease-associated genes. J Mol Med (Berl) 77(11):754–760
**ang Y, Cao Y, Xu C, Li X, Wang S (2006) Xa3, conferring resistance for rice bacterial blight and encoding a receptor kinase-like protein, is the same as Xa26. Theor Appl Genet 113(7):1347–1355
Yoshimura S, Yoshimura A, Iwata N, McCouch SR, Abenes ML, Baraoidan MR, Wah Mew T, Nelson RJ (1995) Tagging and combining bacterial blight resistance genes in rice using RAPD and RFLP markers. Mol Breed 1(4):375–387
Zhou Y, Cao Y, Huang Y, **e W, Xu C, Li X, Wang S (2009) Multiple gene loci affecting genetic background-controlled disease resistance conferred by R gene Xa3/Xa26 in rice. Theor Appl Genet 120(1):127–138
Acknowledgments
This work was supported by a grant from the Next-Generation BioGreen 21 Program (Plant Molecular Breeding Center No. PJ008062), Rural Development Administration, Republic of Korea.
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Hur, Y.J., Jeung, JU., Kim, S.Y. et al. Functional markers for bacterial blight resistance gene Xa3 in rice. Mol Breeding 31, 981–985 (2013). https://doi.org/10.1007/s11032-012-9831-7
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DOI: https://doi.org/10.1007/s11032-012-9831-7