Panicle exertion, the distance between the leaf cushion of flag and the neck-panicle node, is an important morphological trait, which has significant impact on hybrid seed production of rice. In this study, 94 chromosome segment substitution lines (CSSL), derived from 9311/Nipponbare with 9311 as the recurrent parent, were used to analyze quantitative trait loci (QTL) controlling the panicle exertion. The results showed that 17 CSSL contained QTL for the panicle exertion. Using substitution mapping, 8 QTLs were mapped on rice chromosomes 2, 3, 7, 8, 9, and 11, respectively. The QTL additive effect ranged from 0.10 to 3.20, and the additive effects of qPE-9 and qPE-11 were 3.15 and 2.95, respectively, showing the feature of a major gene. In addition, qPE-2-2, qPE-3-1, qPE-3-2, qPE-7, and qPE-8 were mapped in a marker interval less than 10.0 cM. Mapping of the QTL has laid a foundation for improving the panicle exertion with marker-assisted selection and cloning of the QTL in rice.
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