In order to explore the genetic basis for photosynthesis and its related physiological traits, sixty-five chromosome segment substitution lines (CSSLs), derived from a cross between an indica cultivar IR24 and a japonica cultivar Asominori of rice (Oryza sativa L.), were utilized for mapping quantitative trait loci (QTL) for photosynthetic and its related physiological traits. Net photosynthesis (Pn), stomatal conductance (Gs), transpiration rate (Tr), intercellular CO2 concentration (Ci), leaf chlorophyll (CHL), and total leaf nitrogen content (TLN) in flag leaves were measured at heading stage. The CSSLs showed transgressive segregation for many of the traits, and significant correlations were observed for most of the traits. In total, ten QTLs were detected on chromosomes 1, 3, 4, 5, 7, 8, and 10 with a range of percentages of variance explained (PVE) from 9.5% to 46.5%. LOD scores of these QTLs ranged from 2.77 to 8.42. A consistent location was mapped for a QTL controlling stomatal conductance (qGs-8) and leaf chlorophyll concentration (qCHL-8) in the vicinity of R727 on chromosome 8 and for a QTL controlling stomatal conductance (qGs-10) and intercellular CO2 concentration (qCi-10) in the vicinity of C1166 on chromosome 10. No other overlapping loci associated with different traits were detected. These results indicated that the genetic mechanism of photosynthesis was complex in rice.
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