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

McCoy, Austin G. and Noel, Zachary and Sparks, Adam H. ORCID: https://orcid.org/0000-0002-0061-8359 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. ISSN 0894-0282

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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.


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Item Type: Article (Commonwealth Reporting Category C)
Refereed: Yes
Item Status: Live Archive
Faculty/School / Institute/Centre: Current - Institute for Life Sciences and the Environment - Centre for Crop Health (24 Mar 2014 -)
Faculty/School / Institute/Centre: Current - Institute for Life Sciences and the Environment - Centre for Crop Health (24 Mar 2014 -)
Date Deposited: 22 Jan 2020 06:55
Last Modified: 29 Jan 2020 05:42
Uncontrolled Keywords: Phytophthora sojae; soybean; pathogen; pathotype analysis; Habgood-Gilmour Spreadsheet
Fields of Research : 08 Information and Computing Sciences > 0803 Computer Software > 080306 Open Software
07 Agricultural and Veterinary Sciences > 0703 Crop and Pasture Production > 070308 Crop and Pasture Protection (Pests, Diseases and Weeds)
Socio-Economic Objective: D Environment > 96 Environment > 9604 Control of Pests, Diseases and Exotic Species > 960403 Control of Animal Pests, Diseases and Exotic Species in Farmland, Arable Cropland and Permanent Cropland Environments
Identification Number or DOI: 10.1094/MPMI-07-19-0180-A
URI: http://eprints.usq.edu.au/id/eprint/37379

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