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Identification of microsatellite markers linked to the blast resistance gene Pi-1(t) in rice

Abstract

The present work was conducted to identify microsatellite markers linked to the rice blast resistance gene Pi-1(t) for a marker-assisted selection program. Twenty-four primer pairs corresponding to 19 microsatellite loci were selected from the Gramene database (www. gramene.org) considering their relative proximity to Pi-1(t) gene in the current rice genetic map. Progenitors and DNA bulks of resistant and susceptible families from F3 segregating populations of a cross between the near-isogenic lines C101LAC (resistant) and C101A51 (susceptible) were used to identify polymorphic microsatellite markers associated to this gene through bulked segregant analysis. Putative molecular markers linked to the blast resistance gene Pi-1(t) were then used on the whole progeny for linkage analysis. Additionally, the diagnostic potential of the microsatellite markers associated to the resistance gene was also evaluated on 17 rice varieties planted in Latin America by amplification of the specific resistant alleles for the gene in each genotype. Comparing with greenhouse phenotypic evaluations for blast resistance, the usefulness of the highly linked microsatellite markers to identify resistant rice genotypes was evaluated. As expected, the phenotypic segregation in the F3 generation agreed to the expected segregation ratio for a single gene model. Of the 24 microsatellite sequences tested, six resulted polymorphic and linked to the gene. Two markers (RM1233*I and RM224) mapped in the same position (0.0 cM) with the Pi-1(t) gene. Other three markers corresponding to the same genetic locus were located at 18.5 cM above the resistance gene, while another marker was positioned at 23.8 cM below the gene. Microsatellite analysis on elite rice varieties with different genetic background showed that all known sources of blast resistance included in this study carry the specific Pi-1(t) allele. Results are discussed considering the potential utility of the microsatellite markers found, for MAS in rice breeding programs aiming at developing rice varieties with durable blast resistance based on a combination of resistance genes.

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Acknowledgments

The Rice program of the International Centre for Tropical Agriculture (CIAT) and the International Atomic Energy Agency from Vienna, Austria (Research Contract 12816/R0) supported this research. The authors would like to thank Hector Fabio Buendia from CIAT for his help in the use of MAPMAKER software. We appreciate the fruitful discussions with Dr Daniel G. Debouck from Genetic Resources Unit from CIAT. We also want to express our acknowledgment to anonymous Reviewers because their comments greatly helped to improve the quality of the manuscript.

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Correspondence to Jorge Luis Fuentes.

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Centro Internactional de Agricultura Tropical (CIAT) institute where the research was carried out

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Fuentes, J.L., Correa-Victoria, F.J., Escobar, F. et al. Identification of microsatellite markers linked to the blast resistance gene Pi-1(t) in rice. Euphytica 160, 295–304 (2008). https://doi.org/10.1007/s10681-007-9497-0

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Keywords

  • Blast (Pyricularia grisea Sacc)
  • Marker-assisted selection
  • Microsatellite
  • Resistance gene
  • Rice (Oryza sativa L)