Abstract
Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae, is a major disease of rice managed largely through the deployment of resistance genes. Xa38, a BB resistance gene identified from Oryza nivara acc. IRGC 81825, was mapped on chromosome 4L in a 38.4-kb region. The closely linked markers for this gene, identified earlier, were simple sequence repeat marker RM17499 and sequence-tagged site markers developed from loci Os04g53060 and Os04g53120. Marker Os04g53060 is dominant while the other two markers show smaller size differences difficult to resolve accurately on agarose gel. Based on gene annotation, three nucleotide binding site–leucine-rich repeat genes present in the target region were cloned from O. nivara and sequenced. One of the loci, LOC_Os04g53050, had a 48-base-pair deletion in O. nivara acc. IRGC 81825 compared to the cultivated rice. Primers were designed around the deletion and the resulting marker is codominant and easy to score in agarose gel. The newly designed marker co-segregated with Xa38, amplifying products of 269 bp in O. nivara and 317 bp in cultivated rice. This marker could be more useful for marker-assisted selection than ones reported earlier.
References
Andersen JR, Lubberstedt T (2003) Functional markers in plants. Trends Plant Sci 8:554–560
Cheema KK, Grewal NK, Vikal Y, Sharma R, Lore JS, Das A, Bhatia D, Mahajan R, Gupta V, Bharaj TS, Singh K (2008) A novel bacterial blight resistance gene from Oryza nivara mapped to 38 kb region on chromosome 4L and transferred to Oryza sativa L. Genet Res Camb 90:397–407
Chu Z, Fu B, Yang H, Xu C, Li Z, Sanchez A, Park YZ, Bennetzen JL, Zhang Q, Wang S (2006) Targeting xa13, a recessive gene for bacterial blight resistance in rice. Theor Appl Genet 112:455–461
Huang N, Angeles ER, Domingo J, Magpantay G, Singh S, Zhang G, Kumaravadivel N, Bennett J, Khush GS (1997) Pyramiding of bacterial blight resistance genes in rice: marker-assisted selection using RFLP and PCR. Theor Appl Genet 95:313–320
Iyer-Pascuzzi AS, McCouch SR (2007) Functional markers for xa5-mediated resistance in rice (Oryza sativa L.). Mol Breed 19:291–296
Khush GS (2001) Green revolution: the way forward. Nat Rev Genet 2:815–822
Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181
Sun X, Yang Z, Wang S, Zhang Q (2003) Identification of a 47-kb DNA fragment containing Xa4, a locus for bacterial blight resistance in rice. Theor Appl Genet 106:683–687
Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:1441–1452
Vikal Y, Das A, Patra B, Goel RK, Sidhu JS, Singh K (2007) Identification of new sources of bacterial blight (Xanthomonas oryzae pv. oryzae) resistance in wild Oryza species and O. glaberrima. Plant Genet Resourc 5:108–112
Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78
Acknowledgments
The authors gratefully acknowledge financial support from the Department of Biotechnology, Ministry of Science and Technology, Government of India vide grant no. BT/AB/03/FG-2/2003. We are grateful to Delhi University South Campus, New Delhi for extending facilities for sequencing.
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Bhasin, H., Bhatia, D., Raghuvanshi, S. et al. New PCR-based sequence-tagged site marker for bacterial blight resistance gene Xa38 of rice. Mol Breeding 30, 607–611 (2012). https://doi.org/10.1007/s11032-011-9646-y
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DOI: https://doi.org/10.1007/s11032-011-9646-y