Chlorophyll a fluorescence parameters can provide qualitative and quantitative information about photosynthetic processes in chloroplasts. JIP-test and modulated fluorescence (MF) parameters are commonly used chlorophyll a fluorescence parameters. This study was conducted to identify quantitative trait loci (QTLs) associated with JIP-test parameters, MF parameters, and photosynthetic rate (P(N)), and to examine the relationships among them in soybean (Glycine max (L.) Merr.). Pot and field experiments were performed to evaluate 184 recombinant inbred lines (RILs) for five JIP-test parameters (ABS/RC, TR(O)/ABS, ET(O)/TR(O), RE(O)/ET(O), and PI(ABS)), four MF parameters (Fv/Fm, Fv'/Fm', PhiPSII, and qP), and P(N).Significant correlations were commonly observed among JIP-test parameters, MF parameters, and P(N). QTL mapping analysis identified 13, 9, and 4 QTLs for JIP-test parameters, MF parameters, and P(N), respectively, of which 13 were stable. Four major genomic regions were detected: LG A2 (19.81 cM) for JIP-test parameters, LG C1 (94.31 and 97.61 cM) for P(N) and MF parameters, LG M (100.51 cM) for JIP-test and MF parameters, and LG O (30.61-49.91 cM) for P(N), JIP-test, and MF parameters. These results indicate that chlorophyll fluorescence parameters, especially PHIPSII and qP, could play an important role in regulating P(N), and that JIP-test and MF parameters could be controlled by the same or different genes. The QTLs identified in this study will help in the understanding of the genetic basis of photosynthetic processes in plants. They will also contribute to the development of marker-assisted selection breeding programs for photosynthetic capacity in soybean.
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