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Thirty polymorphic Oryza sativa microsatellite loci (SSRs) were used to study population genetic structure of O. rufipogon Griff. natural populations in Malaysia. A total of 445 alleles were detected with an average of 14.8 alleles per locus in 176 individuals of O. rufipogon sampled from the states of Penang, Kedah, Kelantan and Terengganu where the natural populations are still found. The Kelantan population in the northeast of Peninsular Malaysia had the highest level of genetic diversity as measured by the mean number of alleles per locus, A a =7.67, average number of effective alleles, A e =5.50, percentage of polymorphic loci, P=100%, observed heterozygosity, H o =0.631 and expected heterozygosity, H e =0.798. In contrast, the Terengganu population in the east showed the lowest level of genetic diversity measured by the same criteria (A a =4.23, A e =2.10, P= 100%, H o =0.549 and H e =0.449).Model-based clustering analysis using the STRUCTURE 2.2 program placed all the individuals into 12 clusters that corresponded to the geographic sampling locations. Neighbour-joining tree was constructed based on Nei's genetic distance to further assess the genetic structure of the O. rufipogon individuals, showed good agreement (93.8%) with the model-based cluster analysis. However, the neighbour-joining tree identified subpopulations that STRUCTURE could not identify. The classification of individuals from the same populations under the same cluster supported the population differentiation. These two analyses seemed to indicate expansion of populations from the northeast of Peninsular Malaysia (Tumpat, Pasir Mas and Kota Bahru, Kelantan) not only to the immediate south of the region i.e. Terengganu but also into the northwest (i.e. Penang and Kedah) with the former being more recent. Oryza rufipogon accession IRGC105491 and O. sativa ssp. indica cultivar MR219, which were included in this study for comparisons with the local wild rice accessions, indicated that introgression of cultivated rice could change genetic composition and affect the population genetic structure of wild rice. This possibility should be carefully considered in plans to conserve this wild rice. AbbreviationsRAPD Randomly amplified polymorphic DNA RFLP Restriction fragment length polymorphism SSR Microsatellite or simple sequence repeat QTL Quantitative trait locus DNA Deoxyribonucleic acid PCR Polymerase chain reaction Communicated by: Hongwei Cai Electronic supplementary material The online version of this article (

ABSTRACT. Advanced backcross families derived from Oryza sativa cv MR219/O. rufipogon IRGC105491 were utilized for identification of quantitative trait loci (QTL) for blast resistance using simple sequence repeat markers. Two hundred and sixty-one BC 2 F 3 families were used to construct a linkage map, using 87 markers, which covered 2375.2 cM of 12 rice chromosomes, with a mean density of 27.3 cM. The families were evaluated in a greenhouse for resistance to blast disease caused by pathotypes P7.2 and P5.0 of Magnaporthe oryzae. Five QTLs (qBL5.1, qBL5.2, qBL6.1, qBL8.1, and qBL10.1) for pathotype P5.0 and four QTLs (qBL5.3, qBL5.4, qBL7.1, and qBL8.2) for pathotype P7.2 were identified using the BC 2 F 3 families. Another linkage map was also constructed based on 31 BC 2 F 5 families, using 63 SSR markers, which covered 474.9 cM of 9 rice chromosomes, with a mean density of 8.01 cM. Five suggestive QTLs (qBL11.2, qBL11.3, qBL12.1, qBL12.2, qBL12.3) and one putative QTL (qBL2.1) were identified for pathotype P7.2. Also, seven suggestive QTLs (qBL1.1, qBL2.2, qBL4.1, qBL4.2, qBL5.3, qBL8.3, and qBL11.1) were detected for pathotype P5.0. We conclude that there is a non-race-specific resistance spectrum of O. rufipogon against M. oryzae pathotypes.