hagis, an R Package Resource for Pathotype Analysis of Phytophthora sojae Populations Causing Stem and Root Rot of Soybean

Article

McCoy, Austin G., Noel, Zachary, Sparks, Adam H. and Chilvers, Martin. 2019. "hagis, an R Package Resource for Pathotype Analysis of Phytophthora sojae Populations Causing Stem and Root Rot of Soybean." Molecular Plant-Microbe Interactions. 32 (12), pp. 1574-1576. https://doi.org/10.1094/MPMI-07-19-0180-A
Article Title

hagis, an R Package Resource for Pathotype Analysis of Phytophthora sojae Populations Causing Stem and Root Rot of Soybean

ERA Journal ID2766
Article CategoryArticle
AuthorsMcCoy, Austin G. (Author), Noel, Zachary (Author), Sparks, Adam H. (Author) and Chilvers, Martin (Author)
Journal TitleMolecular Plant-Microbe Interactions
Journal Citation32 (12), pp. 1574-1576
Number of Pages3
Year2019
PublisherAmerican Phytopathological Society
Place of PublicationUnited States
ISSN0894-0282
1943-7706
Digital Object Identifier (DOI)https://doi.org/10.1094/MPMI-07-19-0180-A
Web Address (URL)https://apsjournals.apsnet.org/doi/10.1094/MPMI-07-19-0180-A
Abstract

Phytophthora sojae is a significant pathogen of soybean worldwide. Pathotype surveys for Phytophthora sojae are conducted to monitor resistance gene efficacy and determine if new resistance genes are needed. Valuable measurements for pathotype analysis include the distribution of susceptible reactions, pathotype complexity, pathotype frequency, and diversity indices for pathotype distributions. Previously the Habgood-Gilmour Spreadsheet (HaGiS), written in Microsoft Excel, was used for data analysis. However, the growing popularity of the R programming language in plant pathology and desire for reproducible research made HaGiS a prime candidate for conversion into an R package. Here we report on the development and use of an R package, hagis, that can be used to produce all outputs from the HaGiS Excel sheet for P. sojae or other gene-for-gene pathosystem studies.

KeywordsPhytophthora sojae; soybean; pathogen; pathotype analysis; Habgood-Gilmour Spreadsheet
ANZSRC Field of Research 2020461299. Software engineering not elsewhere classified
300409. Crop and pasture protection (incl. pests, diseases and weeds)
Byline AffiliationsMichigan State University, United States
Centre for Crop Health
Institution of OriginUniversity of Southern Queensland
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