Development of cytoplasmic male sterile (CMS) lines with elongated uppermost internode (EUI) trait is a desirable alternative to eliminate the use of GA3 in hybrid rice production. In this study, a simple and reliable PCR based, simple sequence repeats (SSR) markers was identified, for the eui gene to facilitate marker assisted selection (MAS). A total of 28 SSR markers, mapped in the vicinity of the genomic clone AC130605 (PD0010D04), were chosen for assessing the polymorphism between IR58025B and IR91-1591-3. A set of 151 F2 plants derived from the cross IR58025B/IR91-1591-3 were surveyed using 15 polymorphic SSR markers. Analysis using MAPMAKER 3.0 revealed that seven SSR markers viz., RM6054, RM3870, RM3476, RM5970, RM7801, RM7446 and RM3620 were linked with euilocus at the genetic distance ranging from 1.0 to 7.1 cM with EUI phenotype. Furthermore, these markers were validated in – F2 (IR58025A/IR91-1591-3) and backcross (IR58025B/IR91-1591-2//IR58025B) population segregating for euigene. The SSR markers reported in this study might be useful for the incorporation of eui gene into CMS lines of rice through marker-assisted backcrossing.
Key words: Rice, cytoplasmic male sterility, elongated uppermost internode, microsatellites, marker assisted selection, panicle exsertion.
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