Identification of Microsatellite (SSR) and RAPD Markers Linked to Rice Blast Disease Resistance gene in Rice (Oryza sativa L.)

A mapping population comprising 220 F-2 individuals was developed by raising the selfed F-1 seed of a single hybrid plant, White Ponni x Moroberekan. Two hundred and twenty two F-3 families were phenotyped for blast resistance under artificial condition. Fifty random amplified polymorphic (RAPD) primers were used to identify parental polymorphism. Twelve RAPD markers which showed clear polymorphism were scored in the F-2 mapping population. Out of 12 markers, 11 loci (91.97 %) fitted into the expected segregation ratio of 3:1 based on chi(2) - test at 0.05% probability value. Four hundred microsatellite primer pairs were used in the parental survey, Out of which 52 simple sequence repeats (SSR) primers were polymorphic. Out of 52 marker loci, 44 marker loci (84.61%) fitted into the expected Mendelian segregation ratio of 1:2:1 based on chi(2) - test at 0.05% probability value. The multipoint analysis resulted in the construction of preliminary genetic linkage map with 40 loci. One way analysis of variance (ANOVA) was performed to identify the marker phenotype association which resulted in the identification of 23 SSR markers putatively associated for the six traits studied. Three SSR markers (RM 5757, RM 451 and RM 492 from chromosomes four and two) were linked for leaf blast resistance, six markers for days to flowering, nine markers for pigmentation trait, two markers for plant height, four markers for panicle length and seven markers linked for grain yield per plant. Out of 12 RAPD markers studied, 7 were found to be linked to three traits viz., leaf blast resistance (OPBB 5(258), OPBB 5(194), OPAL 16(940) and OPBD 12(680)), five markers for glume purple tip (GPT) and one marker for grain yield per plant based on single marker analysis.