Identification and mapping of an AFLP marker linked to GM7, a gall midge resistance gene and its conversion to a SCAR marker for its utility in marker aided selection in rice

We have identified an AFLP marker SA598 that is linked to Gm7, a gene conferring resistance to biotypes 1, 2 and 4 of the gall midge (Orseolia oryzae), a major dipteran pest of rice. A set of PCR primers specific to an RFLP marker, previously identified to be linked to another gall midge resistance gene Gm2, also amplified a 1.5-kb (F8LB) fragment that is linked to Gm7. Gm7 is a dominant gene and non-allelic to Gm2. Hybridization experiments with clones from a YAC library of Nipponbare, a japonica variety, a BAC library of IR-BB21, an indica variety, and cosmid clones encompassing Gm2 from Phalguna, an indica variety, with F8LB and SA598 as probes, revealed that Gm7 is tightly linked to Gm2 and is located on chromosome 4 of rice. SA598 was sequenced and the sequence information was used to design sequence-characterized amplified region (SCAR) primers. The potential use of these SCAR primers in marker-aided selection of Gm7 in a rice breeding program has been demonstrated.