Studies on some major yield responsive genes in selected rice (Oryza species) cultivars grown in Nigeria using candidate gene SSR-based markers approach

Abstract

This study was aimed at determining the presence of five major yield responsive genes shown to be among key determinants of rice yield in ten rice cultivars grown in Nigeria using candidate gene SSRs markers (Cg-SSRs). DNAs were extracted from young leaf samples using optimized cetyltrimethylammonium bromide (CTAB)-extraction method. An established gene sequences for high yielding rice Nipponbare cultivar for the five genes were retrieved from NCBI database and used to mine for SSRS using SSR identification tool. A pair of primer were designed manually from the nucleotide sequences flanking the selected SSRS for each gene. The designed primers were used to screen for the presence of the genes. Three pair of primers (for Gif1, Gn1a and Gw2) were able to amplify the targeted regions. The remaining two (for Gs3 and Dep1) did not amplify even the positive control. Two representative polymerase chain reaction (PCR)-products for the PCR-positive genes were sequenced and compared with established gene sequences of high yielding cultivars on NCBI database and their percentage sequence identities were determined. Phylogenetic trees (dendrograms) were generated using neighbor joining method. Overall, all the ten cultivars have both Gif1 and Gn1a genes while only eight cultivars have Gw2 gene. Gs3 and Dep1 need further optimization of PCR-conditions.