A Pseudo-near isogenic F₂ population strategy for rapid QTL cloning

Near isogenic F₂ (NIF₂) population frequently developed by conventional backcross has dramatically contributed to QTL identification in plants. Developing such a NIF₂ population is time-consuming. Thus, it is urgent to rapidly produce a NIF₂ population for QTL cloning. Here, we proposed a rapid QTL cloning strategy by generating a Pseudo-near isogenic F₂ population (Pseudo-NIF₂), which segregates at the target QTL but is fixed at other QTLs for the target trait. Nineteen QTLs for GL, GW, and TGW were detected in the F₂ population from the cross between Zhenshan 97 and Egy316. To verify the efficiency of Pseudo-NIF₂ in QTL quick cloning, the novel moderate QTL qGL10.1 which explained 9.1% and 5.6% of grain length variation in F₂ and F_2:3 populations was taken as an example. An F₂ plant (F₂-120), which segregated at qGL10.1 but fixed at other 8 QTLs for grain length, was screened to generate a Pseudo-NIF₂ population by selfing cross. In the Pseudo-NIF₂ population, the segregation ratio of plants with long grains to short grains fits 3:1, indicating that one gene controlled the variation of grain length. Based on the Pseudo-NIF₂ and its progeny, qGL10.1 was fine mapped to a 19.3-kb region, where a gene OsMADS56 was verified as the candidate by functional polymorphism between parental alleles. Pseudo-NIF₂ strategy is a rapid way for QTL cloning, which saves 3 to 4 cropping seasons compared to the conventional way. Applying the method for cloning QTL with moderate or major effects is promising.

The online version contains supplementary material available at 10.1007/s11032-023-01408-x.