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

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 imidazol...

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Autores principales:	Rosas,Juan E, Bonnecarrère,Victoria, Pérez de Vida,Fernando
Lenguaje:	English
Publicado:	Pontificia Universidad Católica de Valparaíso 2014
Materias:	Clearfield rice DNA-based resistance diagnosis Herbicide resistance KASP Red rice SNP
Acceso en línea:	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582014000200007
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spelling	oai:scielo:S0717-345820140002000072014-09-02One-step, codominant detection of imidazolinone resistance mutations in weedy rice (Oryza sativa L.)Rosas,Juan EBonnecarrère,VictoriaPérez de Vida,Fernando Clearfield rice DNA-based resistance diagnosis Herbicide resistance KASP Red rice SNP 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 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 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, 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.info:eu-repo/semantics/openAccessPontificia Universidad Católica de ValparaísoElectronic Journal of Biotechnology v.17 n.2 20142014-03-01text/htmlhttp://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582014000200007en10.1016/j.ejbt.2014.02.003
institution	Scielo Chile
collection	Scielo Chile
language	English
topic	Clearfield rice DNA-based resistance diagnosis Herbicide resistance KASP Red rice SNP
spellingShingle	Clearfield rice DNA-based resistance diagnosis Herbicide resistance KASP Red rice SNP Rosas,Juan E Bonnecarrère,Victoria Pérez de Vida,Fernando One-step, codominant detection of imidazolinone resistance mutations in weedy rice (Oryza sativa L.)
description	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 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 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, 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.
author	Rosas,Juan E Bonnecarrère,Victoria Pérez de Vida,Fernando
author_facet	Rosas,Juan E Bonnecarrère,Victoria Pérez de Vida,Fernando
author_sort	Rosas,Juan E
title	One-step, codominant detection of imidazolinone resistance mutations in weedy rice (Oryza sativa L.)
title_short	One-step, codominant detection of imidazolinone resistance mutations in weedy rice (Oryza sativa L.)
title_full	One-step, codominant detection of imidazolinone resistance mutations in weedy rice (Oryza sativa L.)
title_fullStr	One-step, codominant detection of imidazolinone resistance mutations in weedy rice (Oryza sativa L.)
title_full_unstemmed	One-step, codominant detection of imidazolinone resistance mutations in weedy rice (Oryza sativa L.)
title_sort	one-step, codominant detection of imidazolinone resistance mutations in weedy rice (oryza sativa l.)
publisher	Pontificia Universidad Católica de Valparaíso
publishDate	2014
url	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582014000200007
work_keys_str_mv	AT rosasjuane onestepcodominantdetectionofimidazolinoneresistancemutationsinweedyriceoryzasatival AT bonnecarrerevictoria onestepcodominantdetectionofimidazolinoneresistancemutationsinweedyriceoryzasatival AT perezdevidafernando onestepcodominantdetectionofimidazolinoneresistancemutationsinweedyriceoryzasatival
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One-step, codominant detection of imidazolinone resistance mutations in weedy rice (Oryza sativa L.)

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