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

Abstract

Screening of rice germplasm against Asian rice gall midge, Orseolia oryzae (WoodMason), 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.

Putting Plant Genetic Diversity and Variability at Work for Breeding: Hybrid Rice Suitability in West Africa

“…Recently the major QTL of AfRGM were located and validated [11], being the QTL with major effect (qAfRGM4) on chromosome 4. They could be easily incorporated into the parental lines of the promising hybrids through marker-aided backcrossing [33]. Knowledge on the distribution of virulent RYMV populations across different target sites will also help to deploy safely rice hybrids in sub-Saharan Africa.…”

Flanking Microsatellite Markers for Breeding Varieties Against Asian Rice Gall Midge

“…But their benefit in molecular breeding programs is yet to be realised because the markers were either genotype specific or dominant in nature or not very tightly linked. Codominant SSR markers are most suitable in marker-assisted breeding and have already been developed for Gm1 and Gm2 (Himabindu et al 2007) and their success in breeding programs has been demonstrated. But both the genes lack resistance to rice gall midge biotype4.…”

“…in different crop species. Many disease and insect pests resistance genes in rice have been tagged and mapped using microsatellite markers (Chen et al 2006;Fujita et al 2006;Gu et al 2004;Jena et al 2006;Sirithunya et al 2002;Xi-ming et al 2004) Tightly linked co-dominant SSR markers for Gm1 and Gm2 gall midge resistance genes have been developed (Himabindu et al 2007). Gm1 is resistant to biotypes 1, 3, 5, and 6 while Gm2 is resistant to biotypes 1, 2, and 5.…”

A new rice gall midge resistance gene in the breeding line CR57-MR1523, mapping with flanking markers and development of NILs

“…Classical allelism tests could not establish the identity of resistance genes in this breeding line. However, the novel molecular allelism test (Himabindu et al 2007) using linked markers revealed that the gene(s) in CR57-MR1523 is(are) nonallelic to the Gm1, Gm2 and Gm4. Further the single dominant gene in CR57-MR1523 conferring resistance to GMB4 may not be allelic to gall midge recessive gene gm3 and it may not be allelic to Gm8, which exhibits HR-type of reaction, conferring resistance to both GMB4 and GMB4M.…”

“…Once the tentative chromosome location was known, all the SSR markers on that particular chromosome were further analyzed in the selected 158 F 10 population showing clear 'R' and 'S' phenotype. The linked SSR markers for the genes Gm1, Gm2 and Gm4 were used for allelism test with the markers (Himabindu et al 2007) to predict the corresponding allele in CR57-MR1523.…”