A Pseudo-near isogenic F population strategy for rapid QTL cloning.

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Near isogenic F (NIF) population frequently developed by conventional backcross has dramatically contributed to QTL identification in plants. Developing such a NIF population is time-consuming. Thus, it is urgent to rapidly produce a NIF population for QTL cloning. Here, we proposed a rapid QTL cloning strategy by generating a Pseudo-near isogenic F population (Pseudo-NIF), 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 F population from the cross between Zhenshan 97 and Egy316. To verify the efficiency of Pseudo-NIF in QTL quick cloning, the novel moderate QTL which explained 9.1% and 5.6% of grain length variation in F and F populations was taken as an example. An F plant (F-120), which segregated at but fixed at other 8 QTLs for grain length, was screened to generate a Pseudo-NIF population by selfing cross. In the Pseudo-NIF 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-NIF and its progeny, was fine mapped to a 19.3-kb region, where a gene was verified as the candidate by functional polymorphism between parental alleles. Pseudo-NIF 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.

SUPPLEMENTARY INFORMATION

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