Identification and fine mapping of two blast resistance genes in rice cultivar 93-11

Rice blast, caused by Magnaporthe oryzae, is a major disease of rice almost worldwide. The Chinese indica cultivar 93-11 is resistant to numerous isolates of the blast fungus in China, and can be used as broad-spectrum resistance resource, particularly in japonica rice breeding programs. In this study, we identified and mapped two blast resistance genes, Pi60(t) and Pi61(t), in cv. 93-11 using F2 and F3 populations derived from a cross between the susceptible cv. Lijiangxintuanheigu (LTH) and resistant cv. 93-11 and inoculated with M. oryzae isolates from different geographic origins. Pi60(t) was delimited to a 274 kb region on the short arm of chromosome 11, flanked by InDel markers K1-4 and E12 and cosegregated with InDel markers B1 and Y10. Pi61(t) was mapped to a 200 kb region on the short arm (near the centromere) of chromosome 12, flanked by InDel markers M2 and S29 and cosegregating with InDel marker M9. In the 274 kb region of Pi60(t), 93-11 contains six NBS-LRR genes including the two Pia/PiCO39 alleles (BGIOSGA034263 and BGIOSGA035032) which are quite close to the two Pia/PiCO39 alleles (SasRGA4 and SasRGA5) in Sasanishiki and CO39, with only nine amino acids differing in the protein sequences of BGIOSGA035032 and SasRGA5. In the 200 kb region of Pi61(t), 93-11 contains four NBS-LRR genes, all of which show high identities in protein sequence with their corresponding NBS-LRR alleles in susceptible cv. Nipponbare. Comparison of the response spectra and physical positions between the target genes and other R genes in the same chromosome regions indicated that Pi60(t) could be Pia/PiCO39 or its allele, whereas Pi61(t) appears to be different from Pita, Pita-2, Pi19(t), Pi39(t) and Pi42(t) in the same R gene cluster. DNA markers tightly linked to Pi60(t) and Pi61(t) will enable marker-assisted breeding and map-based cloning.