Genome Analysis And Development Of DNA Marker For The Detection Of Restorer Lines Of Wild Abortive Cytoplasmic Male Sterile Source In Rice (Oryza Sativa L.)

The aim of the present study was to develop candidate gene specific polymorphic DNA marker(s) to detect the restorer lines of wild abortive cytoplasmic male sterility source in rice. To suppress the male sterility inducing components of mitochondria, nuclear genome encoded proteins need to be targeted to mitochondria with the help of signal peptide. Fertility restoration in crop species is governed by the pentatricopeptide proteins and proteins involved in the cellular oxidoreductase processes. Therefore, the present study was focused on (i) identifying the genomic regions code for these genes using rice genome database, (ii) listing the number of genes possess mitochondrial targeting signal peptide sequence, (iii) develop primer pairs to amplify the region of signal peptide sequence regions, (iv) assess the polymorphism if any, and (v) validate the polymorphic markers among germplasm lines known for their fertility restoration ability. Earlier reports on molecular mapping of fertility restorer genes (Rfs) in rice indicated Rf genes are located on chromosome 1 and 10 and therefore these two chromosomes were chosen for the genome analysis. A set of 132 loci out of 393 clones from chromosome 1 and 84 loci out of 202 clones from chromosome 10 were found to possess the select genes of interest. Using Mitoprot software, genes containing the mitochondrial signal sequences were identified and their sequences were retrieved. A set of 59 sequence tagged site (STS) markers to amplify at and around the region of mitochondrial signal sequence were developed. Amplification check of these primers was performed initially with two cytoplasmic male sterile lines namely IR58025A and Pusa6A and two restorer lines KMR3 and PRR78. Out of 59 markers analyzed, two markers namely CGS2 and CGS36 were polymorphic among CMS and restorer lines. Therefore, these markers were analyzed further among a set of 30 CMS lines, 34 maintainer lines, 54 restorer lines and two F2 segregating populations for the validation. The efficiency of the marker to detect the restore lines was found to be 87.5%. Marker-trait association analysis revealed STS marker CGS36 was associated with the restoration trait at the significance level of p <0.001 and its phenotypic variance was 71.74%. This result indicated the STS marker CGS36 as informative to detect the restorer lines.