As an allotetraploid, most genes have multiple copies that belong to At and Dt subgenomes in cotton.

Different types of gene editing tools are desirable for the functional genomic research in cotton: a plant species with very complex genome (AADD, 2n=4x=52; genome size of 2.5 Gb). CRISPR/Cpf1 (Cas12a) is a novel member of CRISPR Cas system from Alicyclobacillus acidoterrestris, and currently, there have three kinds of Cpf1 commonly used for genome editing, namely AsCpf1, LbCpf1 and FnCpf1. Recently, several groups have successfully applied the CRISPR/Cpf1 system in plant species such as rice, soybean, tobacco and maize. Here, we established an efficient CRISPR/Cpf1 system to expand the scope of genome editing in cotton. To my knowledge, this is the first report of the application of CRISPR/Cpf1 system for cotton genome editing with a very high efficiency (87%) and no off‐target effects were detected in the most potential off‐target sites. More importantly, the mutated phenotype and genotype in T0 generation were faithfully inherited to their progeny and some homozygous mutants were obtained in T1 generation. These results further support the finding that the CRISPR/Cpf1 system is highly specific and efficient system in plant genome editing, which will be a very promising alternative of CRISPR/Cas9 system for the genome editing in cotton.