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Yellow stem borer (YSB; Scirpophaga incertulas ) is a major constraint on rice production in Asia. To dissect the genetic basis of YSB resistance, we developed 265 F 9 recombinant inbred lines (RILs) from the resistant parent A232 and the susceptible parent G46B and performed whole-genome resequencing for bin mapping and linkage analysis, generating 3,327 bins. Resistance was evaluated as dead heart index in two field trials under natural infestation. Composite interval mapping consistently detected a reproducible QTL, qTir04 , on chromosome 4, with a peak LOD of 15.14 and 21.8% phenotypic variance explained. Local mapping with nine InDel markers resolved qTir04 into two linked sub-loci, qTir04 . 1 (~300 kb) and qTir04 . 2 (~1.14 Mb). Validation in a BC 3 F 2 -derived NIL population confirmed the effect of qTir04 , prioritized qTir04 . 1 as the primary and most reproducible resistance interval, and indicated that the effect of qTir04 . 2 was conditional or less stable under our validation conditions. Transcriptome profiling and qRT-PCR in NILs, together with parental fixed SNPs/InDels and structural variants, identified five genes within qTir04 . 1 showing genotype- and/or infestation-associated expression divergence and prioritized receptor-like kinases and subtilisin-like proteases as leading candidates. These results provide a genetically validated QTL interval and closely linked markers for future marker-assisted breeding, and establish a foundation for functional validation and cloning of the prioritized qTir04 . 1 candidate genes.
Dai et al. (Fri,) studied this question.