Abstract
article i nfo 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 mutationscan beintrogressed inweedy rice populations bynatural outcrossing, reducing the life span of the Clearfield technology. Timely and accurate detection of imidazolinone resistance mutations in weedy rice may contribute to avoiding 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 is 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 wascarriedoutbydetermining the analyticalperformance of thenew method andcomparing 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, whereas for the KASP method, both parameters were 1.00. Conclusions: The new method has equal accuracy while being more informative and saving time and resources compared with conventional methods, which make it suitable for monitoring imidazolinone-resistant weedy rice in Clearfield rice fields.
Highlights
Weedy rice (WR, Oryza sativa L, known as “red rice”) is a troublesome weed of paddy rice worldwide, compromising crop productivity and quality [1]
Validation was achieved through three approaches: I) determination of the sensitivity and specificity of the KBioscience’s Allele Specific PCR (KASP) method when analyzing three panels of 96 known genotypes, one for each mutation; II) comparison of KASP and allele-specific PCR (AS-PCR) results when analyzing for mutation S653D, a set of 96 samples of known genotypes; and III) comparison of KASP and AS-PCR results when applying both methods for analyzing for mutation S653D, a set of 270 Uruguayan WR accessions of unknown genotype
INTA PuitáCL: cultivars resistant to IMI (CL) variety, homozygous for A122T mutation; CL161: CL variety, homozygous for S653D mutation; IRGA 422CL: CL variety, homozygous for G564E mutation; AvaxíCL: CL hybrid cultivar, heterozygous for S653D mutation; INIA Olimar: conventional cultivar (IMI susceptible); SWR: imidazolinone herbicides (IMI) susceptible WR; WR: WR of unknown genotype; 1:1 DNA mixes: 1:1 vol/vol mixes of 100 ng/μL DNA extracted from INIA Olimar and from CL cultivars homozygous for each interrogated mutation
Summary
Weedy rice (Oryza sativa L.) is a noxious form of cultivated rice (O. sativa L.) associated with intensive rice production and dry seeding. And accurate detection of imidazolinone resistance mutations in weedy rice may contribute to avoiding the multiplication and dispersion of resistant weeds and to protect the Clearfield system. The aim of this work is 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. Conclusions: The new method has equal accuracy while being more informative and saving time and resources compared with conventional methods, which make it suitable for monitoring imidazolinone-resistant weedy rice in Clearfield rice fields
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
