Additive main effect and digenic epistatic quantitative trait loci for chlorophyll fluorescence traits influencing salt tolerance at seedling stage in rice

Abstract

In this investigation, an attempt was made to identify quantitative trait locus (QTL)/gene associated with JIP-test parameters in rice. Thirty main effect additive QTLs (M-QTLs) along with more than 500 digenic epistatic QTLs were detected using a backcross-derived population from tolerant genotype Pokkali (AC41585) and the susceptible counterpart IR64. These M-QTLs were located in almost all the chromosomes except chromosome number 6 and 8. Most of the M-QTLs showed pleiotropic effects. Positional similarity of all these overlapping additive and additive × additive interaction, QTLs indicated the substantial resemblance of the genetic basis of many JIP-test parameters which imparted salinity tolerance in rice at the seedling stage. Twenty-three potential functional genes were also delineated inside these additive QTLs regions. The identified putative QTLs for JIP-test parameters and probable functional genes lying therein are useful for imparting greater photosynthetic potential in rice under salt stress.