Assessment of Parental Polymorphism between Swarna / Oryza rufipogon IC309814 Derived Mapping Population

Detection of molecular markers with parental polymorphism is a pre-requisite for QTL mapping and further identification of genomic regions. PCR based InDel markers tend to have a greater degree to show polymorphism among the parental genotypes for any specific cross. Polymorphic studies were carried out between the two parents Swarna (Cultivated rice variety) and Oryza rufipogon IC309814 (Wild rice accession) using 192 randomly selected InDel markers and 40 gene specific markers for Iron and Zinc covering the entire 12 chromosomes. Results revealed that InDel markers were polymorphic between both the parents and highest percentage of polymorphism observed on chromosome 10 (75%) followed by chromosome 5 (60%) and chromosome 9 (55.6%) and lowest polymorphism percentage was shown in chromosome 3 (8.3%) with an overall 22.4 % polymorphism percentage among all the markers used in this study. Detected polymorphic (SSR) markers were for genotyping the mapping population derived from the cross between Swarna cultivar and Oryza rufipogon to map Quantitative Trait Loci (QTLs) associated with yield and grain quality traits.