Genetic architecture of leaf photosynthesis in rice revealed by different types of reciprocal mapping populations

The improvement of leaf net photosynthetic rate (A(n)) is a major challenge in enhancing crop productivity. However, the genetic control of A(n) among natural genetic accessions is still poorly understood. The high-yielding indica cultivar Takanari has the highest A(n) of all rice cultivars, 20–30% higher than that of the high-quality japonica cultivar Koshihikari. By using reciprocal backcross inbred lines and chromosome segment substitution lines derived from a cross between Takanari and Koshihikari, we identified three quantitative trait loci (QTLs) where the Takanari alleles enhanced A(n) in plants with a Koshihikari genetic background and five QTLs where the Koshihikari alleles enhanced A(n) in plants with a Takanari genetic background. Two QTLs were expressed in plants with both backgrounds (type I QTL). The expression of other QTLs depended strongly on genetic background (type II QTL). These beneficial alleles increased stomatal conductance, the initial slope of A(n) versus intercellular CO(2) concentration, or A(n) at CO(2) saturation. Pyramiding of these alleles consistently increased A(n). Some alleles positively affected biomass production and grain yield. These alleles associated with photosynthesis and yield can be a valuable tool in rice breeding programs via DNA marker-assisted selection.