1-c). The F3 progenies derived from these five recombinants showed the expected segregating or homozygous resistant responses after challenge with isolate 001-99-1, completely corresponding to their genotypes at the two marker loci ( Fig. 1-c). Thus Pi60(t) was delimited to a 274 kb region flanked by InDel markers K1-4 and E12. For fine mapping of the Pi61(t) locus, a total of 2102 99-26-2-susceptible F2 individuals were genotyped with 14 InDel and SSR markers, viz. G2, G7, RM101, E4, T7, M1, M2, M9, G8, 12-5, P1, RRS63, RM27990 and 12-6 ( Table 3). As a result, Pi61(t) was located to a 0.15 cM interval (200 kb) on the short arm of chromosome 12, flanked by

markers M2 (0.10 cM) and find more S29 (0.05 cM) and co-segregating with marker M9 ( Fig. 2-b). For Pi60(t), the target 274 kb Protein Tyrosine Kinase inhibitor region (6,374,147–6,648,601 bp) was covered by four PAC/BAC clones, including 48 putative genes annotated in the Gramene and

TIGR databases ( Fig. 1-d); these included 8 intact NBS-LRR genes (Os11g11550, Os11g11580, Os11g11770, Os11g11790, Os11g11810, Os11g11940, Os11g11950 and Os11g11960), 12 expressed proteins, 16 hypothetical proteins and 12 retrotransposons. Sequence alignment of the NBS-LRR genes showed that 93-11 contained only six NBS-LRR genes, viz. BGIOSGA034264, BGIOSGA034263, BGIOSGA035032, BGIOSGA035036, BGIOSGA034259 and BGIOSGA034258, corresponding to Os11g11770, Os11g11790 (SasRGA4 allele of Pia), Os11g11810 (SasRGA5 allele of Pia), Os11g11940, Os11g11950 and Os11g11960 at identity levels of 79.1%, 89.5%, 45.7%, 96.4%, 84.5% and 89.2% in

protein sequence, respectively. For Pi61(t), the target 200 kb region (9,924,675–10,124,186) in the Nipponbare sequence was covered by Mannose-binding protein-associated serine protease six PAC/BAC clones, including 44 putative genes annotated in the Gramene and TIGR database ( Fig. 2-c), viz. 5 tandem NBS-LRR type genes, Os12g17410, Os12g17420, Os12g17430, Os12g17480 and Os12g17490 in a 40 kb cluster, 21 retrotransposons, 1 transposon, 11 hypothetical proteins and 6 expressed proteins. However, only four NBS-LRR genes can be amplified in cv. 93-11 using the specific primers ( Table 4), viz. BGIOSGA018510, BGIOSGA018508, BGIOSGA018507 and BGIOSGA018506, corresponding to Os12g17410, Os12g17430, Os12g17480 and Os12g17490 at identity levels of 68.7%, 99.3% (2-amino acid differences), 99.7% (3-amino acid differences) and 99.7% (3-amino acid differences) in protein sequences, respectively. Two other major blast R genes, Pi30(t) and cloned Pia/PiCO39, were previously mapped in the vicinity of Pi60(t) (6,374,147–6,648,601 bp) on chromosome 11 [11], [37] and [38]. Pi30(t) was roughly located within an interval of 6.1 Mb (441,392–6,578,785), and presumed to be Pia [59]. Sequencing of the two Pia/PiCO39 alleles in 93-11 showed that the two alleles, viz.