Development of STS marker linked to elongated uppermost internode (eui-1) gene in rice (Oryza sativa L.)

The elongated uppermost internode (eui) gene provides a genetic alternative for GA₃ application in hybrid rice seed production by overcoming incomplete panicle exertion of cytoplasmic male sterile (CMS) lines. In the present study, a random amplified polymorphic DNA (RAPD) marker, OPAG01₁₀₀₀ previously found linked to eui gene, was converted into a sequenced tagged site (STS) marker, SAG01₁₀₅₁ by molecular cloning and nucleotide sequencing. Sequence homology search of the RAPD fragment against rice genomic nucleotide database showed 98.0% homology with a portion of nucleotide sequence in the clone P0010D04 (AC130605) on chromosome 5. Based on the consensus results obtained from this study and earlier reports we infer that the internode elongation trait in IR91-1591-3 is controlled by eui-1 locus located within or near the genomic clone P0010D04 on chromosome 5. The STS marker pair amplifies 1051bp and 1100bp fragment in the EUI parent IR91-1591-3 and only 1100bp in the non-EUI parent, which indicated the dominant nature of the marker. Linkage analysis of the STS marker with EUI phenotype showed it to be linked at genetic distance of 3.4 cM. With an objective to identify co-dominant STS marker 23 EST based primers representing five clones were synthesized and used for parental polymorphism. Results indicated only one marker sMRF19 to be polymorphic between the parents. Linkage analysis showed the marker to be located at a genetic distance of 2.4cM from the eui-1 gene. We propose that the co-dominant marker sMRF19 identified in the present study can be used effectively to introgress the eui-1 gene into desired CMS lines for overcoming incomplete panicle exertion problem.