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 CO₂ concentration, or A_n at CO₂ 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.