Additive and Epistatic QTL on Cadmium (Cd) Tolerance Associated with Seed Germinating Ability in Rice

To understand the mechanisms of cadmium (Cd) tolerance during seed germination in rice, quantitative trait loci (QTLs) and epistasis were analyzed using 124 rice backcross recombinant inbred lines (BRILs) derived from a cross between indica CH891 and japonica 02428, and six additive QTLs along with 16 pairs of epistatic QTLs involving 17 loci were identified for germination rate (GR) under Cd and control conditions. The expression of these QTLs and their epistasis under Cd stress and control conditions were not the same, and more pairs of epistatic QTLs were detected under Cd stress than under control conditions, suggesting that Cd stress could induce a different gene expression network and that Cd tolerance with respect to GR is controlled by additive effects and gene interactions. To our knowledge, this is the first study of rice seed germination ability under Cd stress in a typical indica/japonica cross. Notably, all the major additive QTLs for GR were mapped to a small chromosomal region (60–980 kb). These QTLs could be highly valuable genetic factors for cadmium tolerance improvement in rice lines. Moreover, the BRILs developed in this study will serve as an appropriate choice for mapping and studying the genetic basis of complex traits in rice.