Rapid identification of the Leptosphaeria maculans avirulence gene AvrLm2 using an intraspecific comparative genomics approach
2015
Ghanbarnia, Kaveh | Fudal, Isabelle | Larkan, Nicholas J. | Links, Matthew G. | Balesdent, Marie-Helene | Profotova, Bronislava | Fernando, W. G. Dilantha | Rouxel, Thierry | Borhan, M. Hossein | Dept Plant Sci ; University of Manitoba [Winnipeg] | Agriculture and Agri-Food (AAFC) | BIOlogie et GEstion des Risques en agriculture (BIOGER) ; Institut National de la Recherche Agronomique (INRA)-AgroParisTech | Dept Comp Sci, ; University of Saskatchewan [Saskatoon, Canada] (U of S) | Government of Saskatchewan Agricultural Development Fund (ADF); Growing Forward 2 (SaskCanola); Growing Forward 2 (AAFC); Marie Curie Training Site FunGene [HPMT-CT-2001-00395]; FunGene project
Five avirulence genes from Leptosphaeria maculans, the causal agent of blackleg of canola (Brassica napus), have been identified previously through map-based cloning. In this study, a comparative genomic approach was used to clone the previously mapped AvrLm2. Given the lack of a presence-absence gene polymorphism coincident with the AvrLm2 phenotype, 36 L.maculans isolates were resequenced and analysed for single-nucleotide polymorphisms (SNPs) in predicted small secreted protein-encoding genes present within the map interval. Three SNPs coincident with the AvrLm2 phenotype were identified within LmCys1, previously identified as a putative effector-coding gene. Complementation of a virulent isolate with LmCys1, as the candidate AvrLm2 allele, restored the avirulent phenotype on Rlm2-containing B.napus lines. AvrLm2 encodes a small cysteine-rich protein with low similarity to other proteins in the public databases. Unlike other avirulence genes, AvrLm2 resides in a small GC island within an AT-rich isochore of the genome, and was never found to be deleted completely in virulent isolates.
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