Flanking SSR markers for allelism test for the Asian rice gall midge (Orseolia oryzae) resistance genes

Screening of rice germplasm against Asian rice gall midge, Orseolia oryzae (Wood-Mason), biotypes in India has led to identification of over 300 resistant rice genotypes. However, only ten resistance genes have been characterized so far. Identification of new genes through classical allelism test is tedious and time consuming. We propose to use closely linked flanking Simple Sequence Repeat (SSR) markers in allelism tests for identification of resistance genes. Of the ten known gall midge resistance genes, eight have been tagged and mapped. The Gm1 and Gm2 genes have closely linked flanking markers. Hence SSR markers RM219 and RM444, flanking the gene Gm1, and RM317, RM241 along with the SCAR marker F8, flanking the gene Gm2, were selected for this study. Tests with one set of 13 genotypes likely to carry Gm1 and another set of 17 genotypes suspected to contain Gm2 suggested the presence of the respective allele in all the 13 and 15 genotypes from these sets, respectively. Classical allelism test perfectly matched with the markers test. There were two exceptions involving amplification with RM444 in cultivar Kavya and with RM241 in genotype AE20, suggesting a single recombination which could have resulted in the mismatch. All the three markers in the genotype Bhumansan and the two flanking markers RM317 and F8 in AE20 indicated the absence of the Gm2 allele. This was validated through a classical test, revealing a segregation ratio of 15 resistant: 1 susceptible F-2 progeny of both the crosses between the Gm2 source Phalguna and these genotypes. We performed the allelism test with the markers on another set of 56 randomly selected gall midge resistant genotypes to discover possible sources of new resistance genes.