Abstract

Background Herbicide tolerance in crops enables them to survive when lethal doses of herbicides are applied to surrounding weeds. Herbicide-tolerant crops can be developed through transgenic approaches or traditional mutagenesis approaches. At present, no transgenic herbicide tolerant cotton have been commercialized in China due to the genetically-modified organism (GMO) regulation law. We aim to develop a non-transgenic herbicide-tolerant cotton through ethyl methanesulfonate (EMS) mutagenesis, offering an alternative choice for weed management. Results Seeds of an elite cotton cultivar Lumianyan 37 (Lu37) were treated with EMS, and a mutant Lu37-1 showed strong tolerance to imidazolinone (IMI) herbicides was identified. A novel nonsynonymous substitution mutation Ser642Asn at acetolactate synthase (ALS) ( Gh_D10G1253 ) in Lu37-1 mutant line was found to be the potential cause to the IMI herbicides tolerance in cotton. The Ser642Asn mutation in ALS did not present among the genomes of natural Gossypium species. Cleaved amplified polymorphic sequence (CAPS) markers were developed to identify the ALS mutant allele. The  Arabidopsis overexpressing the mutanted ALS also showed high tolerance to IMI herbicides. Conclusion The nonsynonymous substitution mutation Ser642Asn of the ALS gene Gh_D10G1253 is a novel identified mutation in cotton. This substitution mutation has also been identified in the orthologous ALS genes in other crops. This mutant ALS allele can be used to develop IMI herbicide-tolerant crops via a non-transgenic or transgenic approach. Graphical abstract