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The sustainability of rice cropping systems is jeopardized by the large number and variety of populations of polyploid  Echinochloa  spp. resistant to ALS inhibitors. Better knowledge of the  Echinochloa  species present in Italian rice fields and the study of  ALS  genes involved in target-site resistance could significantly contribute to a better understanding of resistance evolution and management. Using a CAPS- rbcL  molecular marker, two species,  E. crus-galli  (L.) P. Beauv. and  E. oryzicola  (Vasinger) Vasing., were identified as the most common species in rice in Italy. Mutations involved in ALS inhibitor resistance in the different species were identified and associated with the  ALS  homoeologs. The relative expression of the  ALS  gene copies was evaluated. Molecular characterization led to the identification of three  ALS  genes in  E. crus-galli  and two in  E. oryzicola . The two species also carried different point mutations conferring resistance: Ala122Asn in  E. crus-galli  and Trp574Leu in  E. oryzicola . Mutations were carried in the same gene copy ( ALS1 ), which was significantly more expressed than the other copies ( ALS2  and  ALS3 ) in both species. These results explain the high resistance level of these populations and why mutations in the other  ALS  copies are not involved in herbicide resistance.

Target-Site Mutations and Expression of ALS Gene Copies Vary According to Echinochloa Species