Assessment of a PCR-based SNP marker system related to grain size in rice (Oryza sativa L.) germplasm

Grain size is one of the most effective characters in rice (Oryza sativa L.) yield; meanwhile it is a highly important quality trait as well. It is problematic for breeders to improve grain size in early stage of growth. Marker assisted selection (MAS) has an essential role in improvement of quantitative and qualitative traits in crops. Functional markers based on polymorphic loci within genes that directly affecting phenotypic variation improves the quality of MAS process. GS3 is a quantitative trait loci (QTL) in pericentromeric region of chromosome 3 is reported to be responsible for 80–90% of the variation in grain length and weight and the minor QTL for grain width and thickness in rice. In this investigation, the usefulness of a PCR-based SNP marker as a functional SNP in grain size was evaluated. A collection of 100 diverse rice genotypes were planted in 3 replicated lattice design and grain size characters (grain length, width and thickness) were measured. By Analysis of this SNP marker two alleles were detected. ANOVA shows a significant difference in grain size characters between these two groups of alleles. Results indicate that PCR-based SNP marker could discriminate the long and short grain; hence it could be an appropriate, simple and commodious approach for improvement of rice grain size via MAS of GS3 QTL.