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Fine mapping of rice blast QTLl from Oryza rufipogon and IR644 by SNP markers

Utami D., Moeljopawiro S., Hanarida I., Tharreau D.. 2008. SABRAO Journal of Breeding and Genetics, 40 (2) : p. 105-115.

Oryza rufipogon is one of the wild rice species that may be used as source of gene/s for rice improvement. A backcross (BC5) population had been developed from a cross between IR64 and O. rufipogon to exploit the blast resistance genes from wild rice. The blast resistance genes Pir4, originating from O. rufipogon, and Pir7, originating from IR64, were mapped on chromosome 2 using a BC2 population. The tentative map indicated that Pir 4 and Pir 7 were between the two SSR markers RM263 and RM250 and were 28.5 cM apart from each other. Fine mapping was conducted to detect the exact positions of the target genes by selecting two lines from the BC5 population, namely, 317-25-1-6 and 317-25-1-3. In silico analysis was applied at the target peak region between RM263 and RM250 markers, which resulted in a consecutive order of 25 putative resistance genes. These putative resistance genes were further analyzed by sequencing to design Single Nucleotide Polymorphism (SNP) primers. The interval mapping analysis (CIM) showed the highest LOD value obtained to be 17.1. Results of GLM analysis for the association test indicated significance at the PiSNP4 primer, at 110.9 cM position for blast isolate ID31 having the CM28 avr gene, while PiSNP7 was at 122.8 cM with LOD value 7.3 that was significant for ID9 which has the PH14 avr gene. The progeny contrast for the two target genes showed IR64 to be resistant to PH14 but recessive to CM28, whereas O. rufipogon was opposite in performance. The resistance of the two NILs, 317-25-1-6 (Pir7) and 317-25-1-3 (Pir4), were similar to IR64 and O. rufipogon, respectively, and these lines were selected for multilocation testing. (Résumé d'auteur)

Mots-clés : résistance aux maladies; magnaporthe grisea; marqueur génétique; locus des caractères quantitatifs; gène; carte génétique; oryza rufipogon; qtl

Thématique : Génétique et amélioration des plantes; Maladies des plantes

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