Sequences of ACCase gene of three herbicide-resistant weeds threatening paddy rice: Digitaria sanguinalis, Panicum dichotomiflorum and Echinochloa oryzicola
Description
The objectives of this study were: a) to confirm the ACCase resistance in two grass weeds, Digitaria sanguinalis (DIGSA) ans Panicum dichotomiflorum (PANDI) and the shifting to higher levels of resistance of known cases of ACCase resistance in Echinochloa oryzicola (ECHCR); b) to investigate the ACCase target-site resistance mechanism of these three resistant biotypes; c) to provide a quick molecular tool for their detection and d) to discuss the sustainability of the actual agronomic practices in relation to these resistance cases. In this dataset three series of data are included: Folder 1: The sequences of ACCase (acetil-CoA carboxylase) gene of the three monocot rice weeds, DIGSA, PANDI and ECHCR. All of them proved to be highly resistant to the inhibitors of ACCase herbicides, with some diversification as regards resistance to cycloxydim. The genotyping of ACCase gene of the different species revealed that two different mutations were responsible for resistance. In all three grass weeds, the most common ACCase mutation associated with broad-spectrum resistance to ACCase inhibitors detected was the ATA/TTA point mutation in position 1781. This led to an amino acid substitution Ile to Leu in all populations with resistance level to cycloxydim from moderate (i.e., to dose 1x) to high (i.e., also to dose 3x). In a population of DIGSA, the same amino acid substitution (Ile/Leu), but involving a different allelic variant (ATA/CTA) was identified. In ECHCR, the cross-resistant to the two ACCase inhibitors cyhalofop and profoxydim, but not to cycloxydim , was associated with a mutation in position 2027 of the ACCase gene. Folder 2: The cloning of part of the ACCase gene of ECHCR plants carrying the mutation 2027 led to the identification of the different allelic variants present. Three different allelic variants were identified in expressed ACCase gene copies of E. oryzicola (cDNA data). The phylogenetic analysis that was conducted to identify specific motifs in the sequences of this tetraploid species to distinguish the homologous gene copies led to the identification of four ACCase copies, and the blast analysis led to give a correspondence of these four copies with the previously identified in Echinochloa phyllopogon. The study showed that the most frequent variant (Trp/Ser) was associated with the ACC1 gene copy, whereas less frequent variants (Trp/Cys, with two allelic forms) were associated with ACC3. Folder 3: Alongside the sequencing experiments, a quicker and less expensive molecular marker working on all three grass species was set up to detect plants carrying the most common mutation detected, a mutation in codon 1781 of the ACCase gene. A validation step testing a series of plants belonging to the different species and populations was performed to prove the ability of the marker to detect the 1781 mutation and the cross-check by sequencing the PCR product produced in the first step was performed and sequences are reported in this folder
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Institutions
- Institute for Sustainable Plant ProtectionPiedmont, Turin