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A doubled haploid (DH) population consisting of 125 DHLs derived from the popular rice hybrid, KRH-2 (IR58025A/KMR3R) was utilized for Quantitative Trait Loci (QTL) mapping to identify novel genomic regions associated with yield related traits. A genetic map was constructed with 126 polymorphic SSR and EST derived markers, which were distributed across rice genome. QTL analysis using inclusive composite interval mapping (ICIM) method identified a total of 24 major and minor effect QTLs. Among them, twelve major effect QTLs were identified for days to fifty percent flowering ( qDFF12-1 ), total grain yield/plant ( qYLD3-1 and qYLD6-1 ), test (1,000) grain weight ( qTGW6-1 and qTGW7-1 ), panicle weight ( qPW9-1 ), plant height ( qPH12-1 ), flag leaf length ( qFLL6-1 ), flag leaf width ( qFLW4-1 ), panicle length ( qPL3-1 and qPL6-1 ) and biomass ( qBM4-1 ), explaining 29.95–56.75% of the phenotypic variability with LOD scores range of 2.72–16.51. Chromosomal regions with gene clusters were identified on chromosome 3 for total grain yield/plant ( qYLD3-1 ) and panicle length ( qPL3-1 ) and on chromosome 6 for total grain yield/plant ( qYLD6-1 ), flag leaf length ( qFLL6-1 ) and panicle length ( qPL6-1 ). Majority of the QTLs identified were observed to be co-localized with the previously reported QTL regions. Five novel, major effect QTLs associated with panicle weight ( qPW9-1 ), plant height ( qPH12-1 ), flag leaf width ( qFLW4-1 ), panicle length ( qPL3-1 ) and biomass ( qBM4-1 ) and three novel minor effect QTLs for panicle weight ( qPW3-1 and qPW8-1 ) and fertile grains per panicle ( qFGP5-1 ) were identified. These QTLs can be used in breeding programs aimed to yield improvement after their validation in alternative populations.
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