One-step, codominant detection of imidazolinone resistance mutations in weedy rice (Oryza sativa L.)

Abstract

Background: Weedy rice (Oryza sativa L.) is a noxious form of cultivated rice (O. sativa L.) associated with intensive rice production and dry seeding. A cost-efficient strategy to control this weed is the Clearfield rice production system, which combines imidazolinone herbicides with mutant imidazolinone-resistant rice varieties. However, imidazolinone resistance mutations can be introgressed in weedy rice populations by natural outcrossing, reducing the lifespan of the Clearfield technology. Timely and accurate detection of imidazolinone resistance mutations in weedy rice may contribute to avoid the multiplication and dispersion of resistant weeds and to protect the Clearfield system. Thus, highly sensitive and specific methods with high throughput and low cost are needed. KBioscience's Allele Specific PCR (KASP) is a codominant, competitive allele-specific PCR based genotyping method. KASP enables both alleles to be detected in a single reaction in a closed-tube format. The aim of this work was to assess the suitability and validity of the KASP method for detection in weedy rice of the three imidazolinone resistance mutations reported to date in rice.

Results: Validation was carried out by determining the analytical performance of the new method and comparing it with conventional allele specific PCR, when genotyping sets of cultivated and weedy rice samples. The conventional technique had a specificity of 0.97 and a sensibility of 0.95, while for KASP method both parameters were 1.00.

Conclusions: The new method had equal accuracy while was more informative and saved time and resources compared to conventional methods, which make it suitable for monitoring imidazolinone resistant weedy rice in Clearfield rice fields.