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 (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 F2 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.
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ABSTRACT: The world's oldest and largest Medicago truncatula collection is housed at the South Australian Research and Development Institute (SARDI). We used six simple sequence repeat (SSR) loci to analyse the genetic diversity and relationships between randomly selected individuals from 192 accessions in the core collection. M. truncatula is composed of three subspecies (ssp.): ssp. truncatula, ssp. longeaculeata, and ssp. tricycla. Analysis at the level of six SSR loci supports the concept of ssp. tricycla, all the samples of which showed unique alleles at two loci. Contingency Chi-squared tests were significant between ssp. tricycla and ssp. truncatula at four loci, suggesting a barrier to gene flow between these subspecies. In accessions defined as ssp. longeaculeata, no unique allelic distribution or diagnostic sizes were observed, suggesting this apparent ssp. is a morphological variant of ssp. truncatula. The data also suggest M. truncatula that exhibits unusually wide genotype dispersal throughout its native Mediterranean region, possibly due to animal and trade-related movements. Our results showed the collection to be highly diverse, exhibiting an average of 25 SSR alleles per locus, with over 90% of individuals showing discrete genotypes. The rich diversity of the SARDI collection provides an invaluable resource for studying natural allelic variation of M. truncatula. To efficiently exploit the variation in the SARDI collection, we have defined a subset of accessions (n = 61) that maximises the diversity.Theoretical and Applied Genetics 04/2006; 112(5):977-83. · 3.66 Impact Factor
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ABSTRACT: Pi-z is a disease resistance gene that has been effectively used to combat a broad-spectrum of races of the rice blast fungus Magnaporthe grisea. Although DNA markers have been reported for selection of the Pi2(t) and Pi-z resistance genes at the Pi-z locus, markers that are more tightly linked to the Pi-z locus would benefit rapid and effective cultivar development. Analysis of the publicly available genome sequence of Nipponbare near the Pi-z locus revealed numerous SSRs that could be converted into markers. Three SSRs on rice PAC AP005659 were found to be very tightly linked to the Pi-z locus, with one marker, AP5659-3, co-segregating with the Pi-z resistance reaction. The Pi-z factor conferring resistance to two races of blast was mapped to a 57kb region on the physical map of Nipponbare in a location where the Pi2(t) gene was physically mapped. Two SSR marker haplotypes were unique for cultivars carrying the Pi-z gene, which indicates these markers are useful for selection of resistance genes at the Pi-z locus in rice germplasm.Molecular Breeding 01/2006; 17(2):149-157. · 3.25 Impact Factor
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ABSTRACT: Three major genes (Pi1, Piz-5 and Pita) for blast resistance on chromosomes 11, 6 and 12, respectively, were fine-mapped and closely linked RFLP markers identified. New markers for Pi1 and Pita were found that were flanking the genes. The three genes were pyramided using RFLP markers. A PCR-based SAP (sequence amplified polymorphism) marker was used to identify Piz-5 in the segregating population. The plants carrying the two- and three-gene combinations that were tested for resistance to leaf blast in the Philippines and India indicated that combinations including Piz-5 have enhanced resistance than when it is present alone. The genes from the pyramided lines are at present being deployed into agronomically superior ricevarieties by marker-aided selection (MAS).Theoretical and Applied Genetics 04/2000; 100(7):1121-1128. · 3.66 Impact Factor