Detection of a quantitative trait locus controlling carbon isotope discrimination and its contribution to stomatal conductance in japonica rice

Increasing leaf photosynthesis offers a possible way to improve yield potential in rice (Oryza sativa L.). Carbon isotope discrimination (Δ¹³C) has potential as an indirect selection criterion. In this study, we searched for quantitative trait loci (QTLs) controlling Δ¹³C, and assessed their association with leaf photosynthesis. Substitution mapping by using chromosome segment substitution lines (CSSLs), that carry segments from the indica cultivar Kasalath in the genetic background of the japonica cultivar Koshihikari, identified genomic regions affecting Δ¹³C on chromosomes (Chr.) 2, 3, 6, 7, and 12. One of the CSSLs, SL208, in which most regions on Chr. 3 were substituted with Kasalath segments, showed higher leaf stomatal conductance for CO₂ (g _s) and Δ¹³C than Koshihikari during the vegetative stage although leaf photosynthetic rate did not differ between them. These results suggest an association between Δ¹³C and g _s. To test this association, we performed a QTL analysis for Δ¹³C at vegetative and heading stages in an F₂ population derived from a cross between SL208 and Koshihikari. The results confirmed a QTL controlling Δ¹³C on the long arm of Chr. 3. By using a near-isogenic line specific to Hd6, we ruled out the possibility that variation in Δ¹³C was generated through the pleiotropic effect of heading date.