Oryza CLIMtools Unveiled at the NSF Plant Genome Research Program 26 th Annual Awardee Meeting

The 26th awardee meeting of the Plant Genome Research Program (PGRP) was held at the U.S. National Science Foundation (NSF) in Alexandria, Virginia on September 7th and 8th, 2023. Over 100 awardees met to exchange research progress and ideas. The program featured selected talks and posters from all participants. During an “open mic” session, Sally Assmann, a Professor in the Biology Department at Penn State University, introduced Oryza CLIMtools, a web-based tool that was developed under PGRP funding and is hosted at Gramene. Oryza CLIMtools provides pan-genome prediction of climate-associated genetic variants in rice (Oryza sativa). The resource is based on 658 geo-referenced Indica landraces and 283 geo-referenced Japonica landraces in the 3K Rice Genomes Project, as well as 400+ climate parameters that define each of the geo-referenced sites, extracted from weather station, NASA remote sensing, and soil composition datasets. The interactive databases of Oryza CLIMtools allow the user to: i) query any rice gene of interest and identify climate parameters for which genic variation and environmental variation co-associate; ii) conversely, query any of the climate parameters of interest, to identify genes that co-vary with it. In landraces, such associations are indicative that the gene is involved in adaptation to the local climate. Oryza CLIMtools thus fosters identification of candidate genes involved in environmental response in rice.

Dr. Sally Assmann (Penn State University) presenting Oryza CLIMtools, an interactive webtool hosted at Gramene that associates climate variation with genetic variants in rice.