Genome-wide association analysis detecting significant single nucleotide polymorphisms for chlorophyll and chlorophyll fluorescence parameters in soybean (Glycine max) landraces

Chlorophyll fluorescence parameters are generally used to characterize the intrinsic action of photosystem II (PSII), which is interrelated with the photosynthetic capacity. Mapping of quantitative trait loci for chlorophyll fluorescence parameters and associated traits is important for genetic improvement in soybean. In this study, a genome-wide association analysis was conducted to detect key single-nucleotide polymorphisms (SNPs) associated with chlorophyll content (chl) and chlorophyll fluorescence using 1,536 SNPs in a soybean landraces panel. The analysis revealed significant correlations among chl and five chlorophyll fluorescence parameters, including maximum quantum yield of PSII primary photochemistry in the dark-adapted state (Fv/Fm), light energy absorbed per reaction center (ABS/RC), quantum yield for electron transport (ETo/ABS), probability that a trapped exciton moves an electron into the electron transport chain beyond QA(-) (ETo/TRo), and performance index on absorption basis (PIABS). Genome-wide association analysis using a mixed linear model detected 51 SNPs associated with chl and chlorophyll fluorescence parameters. Among these identified SNPs, 14 SNPs were co-associated with two or more different traits in this study, and 8 SNPs were co-associated with soybean yield and yield components in our previous study. These significant SNPs will help to better understand the genetic basis of photosynthesis-related physiological traits, and facilitate the pyramiding of favorable alleles for photosynthetic traits in soybean marker assisted selection schemes for high photosynthetic efficiency.