hagis, an R Package Resource for Pathotype Analysis of Phytophthora sojae Populations Causing Stem and Root Rot of Soybean
Article
Article Title | hagis, an R Package Resource for Pathotype Analysis of Phytophthora sojae Populations Causing Stem and Root Rot of Soybean |
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ERA Journal ID | 2766 |
Article Category | Article |
Authors | McCoy, Austin G. (Author), Noel, Zachary (Author), Sparks, Adam H. (Author) and Chilvers, Martin (Author) |
Journal Title | Molecular Plant-Microbe Interactions |
Journal Citation | 32 (12), pp. 1574-1576 |
Number of Pages | 3 |
Year | 2019 |
Publisher | American Phytopathological Society |
Place of Publication | United States |
ISSN | 0894-0282 |
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. |
Keywords | Phytophthora sojae; soybean; pathogen; pathotype analysis; Habgood-Gilmour Spreadsheet |
ANZSRC Field of Research 2020 | 461299. Software engineering not elsewhere classified |
300409. Crop and pasture protection (incl. pests, diseases and weeds) | |
Byline Affiliations | Michigan State University, United States |
Centre for Crop Health | |
Institution of Origin | University of Southern Queensland |
https://research.usq.edu.au/item/q572z/hagis-an-r-package-resource-for-pathotype-analysis-of-phytophthora-sojae-populations-causing-stem-and-root-rot-of-soybean
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