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Title: Development and validation of a quantitative PCR assay method of assessing relative resistance of oat ( Avena sativa ) to crown rust ( Puccinia coronata f. sp. avenae )

Abstract

Evaluation of oat crown rust resistance is usually based on visual assessment of disease severity or infection types. Visual assessment is subjective, prone to rater bias and requires expert knowledge. PCR‐based quantitative assays can overcome challenges associated with visual assessment. New TaqMan primers and probes were designed from Puccinia coronata f. sp. avenae (Pca) sequences. The primer–probe sets were specific to Pca, amplified using as little as 0.5 pg fungal DNA (fDNA) and allowed for scaling to variation in sample total DNA quantity. The quantitative PCR (qPCR) assay was validated using oat recombinant inbred lines (RILs) from the Provena × 94197A1‐9‐2‐2‐2‐5 cross evaluated under a controlled environment. For comparison with fDNA load, inoculation with the Pca race LCBB provided segregation data on the hypersensitive response, while Pca race LSLG provided data on segregation for reduced pustule number. fDNA content was positively correlated with both pustule number and infection type (IT). Composite interval mapping identified two quantitative trait loci (QTLs) on oat linkage groups Mrg12 and Mrg20 using visual and qPCR assessments (pustule number, IT and fDNA). In this study a qPCR assay method that can be used to assess the relative resistance of oat to crown rust was refined and validated, and singlemore » nucleotide polymorphisms (SNPs) closely linked with two QTLs derived from the crown rust resistant line 94197A1‐9‐2‐2‐2‐5 were identified.« less

Authors:
ORCiD logo [1];  [2];  [2];  [2]
  1. Oak Ridge Institute for Science and Education (ORISE) Research Participant 100 Orau Way Oak Ridge TN 37831 USA
  2. United States Department of Agriculture Agricultural Research Service Small Grains and Potato Germplasm Research 1691 S. 2700 W. Aberdeen ID 83210 USA
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1497738
Alternate Identifier(s):
OSTI ID: 1497739
Resource Type:
Published Article
Journal Name:
Plant Pathology
Additional Journal Information:
Journal Name: Plant Pathology Journal Volume: 68 Journal Issue: 4; Journal ID: ISSN 0032-0862
Publisher:
Wiley-Blackwell
Country of Publication:
United Kingdom
Language:
English

Citation Formats

Admassu‐Yimer, B., Gordon, T., Bonman, J. M., and Esvelt Klos, K. Development and validation of a quantitative PCR assay method of assessing relative resistance of oat ( Avena sativa ) to crown rust ( Puccinia coronata f. sp. avenae ). United Kingdom: N. p., 2019. Web. doi:10.1111/ppa.12988.
Admassu‐Yimer, B., Gordon, T., Bonman, J. M., & Esvelt Klos, K. Development and validation of a quantitative PCR assay method of assessing relative resistance of oat ( Avena sativa ) to crown rust ( Puccinia coronata f. sp. avenae ). United Kingdom. https://doi.org/10.1111/ppa.12988
Admassu‐Yimer, B., Gordon, T., Bonman, J. M., and Esvelt Klos, K. Sun . "Development and validation of a quantitative PCR assay method of assessing relative resistance of oat ( Avena sativa ) to crown rust ( Puccinia coronata f. sp. avenae )". United Kingdom. https://doi.org/10.1111/ppa.12988.
@article{osti_1497738,
title = {Development and validation of a quantitative PCR assay method of assessing relative resistance of oat ( Avena sativa ) to crown rust ( Puccinia coronata f. sp. avenae )},
author = {Admassu‐Yimer, B. and Gordon, T. and Bonman, J. M. and Esvelt Klos, K.},
abstractNote = {Evaluation of oat crown rust resistance is usually based on visual assessment of disease severity or infection types. Visual assessment is subjective, prone to rater bias and requires expert knowledge. PCR‐based quantitative assays can overcome challenges associated with visual assessment. New TaqMan primers and probes were designed from Puccinia coronata f. sp. avenae (Pca) sequences. The primer–probe sets were specific to Pca, amplified using as little as 0.5 pg fungal DNA (fDNA) and allowed for scaling to variation in sample total DNA quantity. The quantitative PCR (qPCR) assay was validated using oat recombinant inbred lines (RILs) from the Provena × 94197A1‐9‐2‐2‐2‐5 cross evaluated under a controlled environment. For comparison with fDNA load, inoculation with the Pca race LCBB provided segregation data on the hypersensitive response, while Pca race LSLG provided data on segregation for reduced pustule number. fDNA content was positively correlated with both pustule number and infection type (IT). Composite interval mapping identified two quantitative trait loci (QTLs) on oat linkage groups Mrg12 and Mrg20 using visual and qPCR assessments (pustule number, IT and fDNA). In this study a qPCR assay method that can be used to assess the relative resistance of oat to crown rust was refined and validated, and single nucleotide polymorphisms (SNPs) closely linked with two QTLs derived from the crown rust resistant line 94197A1‐9‐2‐2‐2‐5 were identified.},
doi = {10.1111/ppa.12988},
journal = {Plant Pathology},
number = 4,
volume = 68,
place = {United Kingdom},
year = {Sun Mar 03 00:00:00 EST 2019},
month = {Sun Mar 03 00:00:00 EST 2019}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1111/ppa.12988

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Cited by: 3 works
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