New resource for breeding better soybeans

PSM post-doc researcher Austin McCoy  (Chilvers) has created a large, free, publicly available data repository that allows plant breeders to see trends in resistance gene efficacy in different regions. ″I made the repository while I was putting together a study looking at the decline of soybean resistance gene efficacy to Phytopthora sojae,″ Austin said. (https://www.nature.com/articles/s41467-023-41321-7)

Soybean plants with characteristic Phytophthora root and stem rot lesions that initiate at or below the soil line, typically up one side or girdling the stem. Austin McCoy and Martin Chilvers

Austin has collected all the known phenotypic data from standard soybean resistance gene carrying varieties ("differentials") in response to inoculation with collected P. sojae isolates (resistance/effective gene, and susceptible/ineffective gene) occurring from 1977-2021 worldwide. ″Even going so far as using google translate for the old surveys from China and South America that were not in English.″

He then entered the data from publications into excel during COVID lockdown, and curated and built the repository using an R package, also made for the analysis, called 'hagis.'  ″Even if we didn’t plan on using it in our study—we just wanted to make sure the data was available in the future. I then used the repository for the study that I had originally wanted to do before building the database.″

Faculty may find the data helpful to use in a class/lab as an example for students, or may be able to use the data in research, Austin said. ″There aren’t really any similar repositories for this type of data that I'm aware of, and it may be pretty niche for uses.″

Austin would like to make sure people know that it’s available. ″Right now it’s in raw code and data in R that users will have to download and use. And the more user feedback we get, the better it will become.″