Source and Inheritance of the Within Cultivar Residual Variation Detected in an indica Variety IR64

The phenotypically uniform indica variety IR64 was chosen for study of the source and inheritance of within cultivar residual variation using a set of SSR markers. Residual heterogeneity in IR64 was identified on the short arm of chromosome 2 involving at least 5 SSR loci spanning nearly 30 cM. The SSR variations originated from the parental lines of IR64 (IR5657-33-2/IR2061-465-1-5-5) and were segregating in the selfed bulk seed stock in a Mendelian manner for more than 20 years. This study verified that the within cultivar variations of SSR in a morphologically uniform variety IR64 of a selfing crop came from its parental lines, which has immediate and commercial applications including test of hybrid seed purity, varietal fingerprinting, and curation and propagation of germplasm collections.