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Bacterial leaf steak (BLS) is one of the most destructive diseases in rice. Studies have shown that BLS resistance in rice is quantitatively inherited, controlled by multiple quantitative trait loci (QTLs). A QTL with relatively large effect,  qBlsr5a , was previously mapped in a region of ∼380 kb on chromosome 5. To fine map  qBlsr5a  further, a set of overlapping sub-chromosome segment substitution lines (sub-CSSLs) were developed from a large secondary F 2  population (containing more than 7000 plants), in which only the chromosomal region harboring  qBlsr5a  was segregated. By genotyping the sub-CSSLs with molecular markers covering the target region and phenotyping the sub-CSSLs with artificial inoculation,  qBlsr5a  was delimited to a 30.0-kb interval, in which only three genes were predicted. qRT-PCR analysis indicated that the three putative genes did not show significant response to the infection of BLS pathogen in both resistant and susceptible parental lines. However, two nucleotide substitutions were found in the coding sequence of gene LOC_Os05g01710, which encodes the gamma chain of transcription initiation factor IIA (TFIIAγ). The nucleotide substitutions resulted in a change of the 39 th  amino acid from valine (in the susceptible parent) to glutamic acid (in the resistant parent). Interestingly, the resistant parent allele of LOC_Os05g01710 is identical to  xa5 , a major gene resistant to bacterial leaf blight (another bacterial disease of rice). These results suggest that LOC_Os05g01710 is very possibly the candidate gene of  qBlsr5a .

Toward the Positional Cloning of qBlsr5a, a QTL Underlying Resistance to Bacterial Leaf Streak, Using Overlapping Sub-CSSLs in Rice