Duplicated Genes on Homologous Chromosomes Decipher the Dominant Epistasis of the Fiberless Mutant in Cotton.

Cotton fiber initiation determines the fiber yield, yet the genetic basis underlying lint and fuzz initiation has still not been fully uncovered. Here, map-based cloning was carried out to identify the fiberless mutant genes derived from a cross between acc. WT and a natural fiberless mutant, . The 12:3:1 segregation ratio in F populations (including 1848 and 3100 individuals that were developed in 2016 and 2018, respectively) revealed dominant epistasis, with the fuzz gene exerting dominance over the lint gene. Genetic linkage analysis revealed that controls fuzz fiber initiation, while both and regulate lint fiber development. Sequencing analyses showed that the mutant exhibited a K104M mutation in the R2R3 domain of and a transposable element insertion in , leading to fiberless seeds. Knockout of produced fuzzless seeds, knockout of led to no obvious change in seeds, and knockout of both (&) resulted in fiberless seeds. The 12:3:1 ratio reappeared in the F population developed from the & mutated plants as female and Jin668 as the male, which further confirmed the genetic interaction observed in . RNA-seq analysis revealed that regulates cotton fiber initiation through multiple pathways, especially fatty acid metabolism. This study elucidates the key genes and their genetic interaction mechanisms governing cotton fiber initiation, providing a theoretical foundation for genetic improvement of cotton fiber traits.