OryzaCLIM V1.0 is a component of Oryza CLIMtools, hosted by Gramene, which describes the local environment of rice providing an interactive spatial analysis web platform. Data points represent the sites of collection of sequenced rice landraces in an interactive world map. This tool allows the user to explore the local environmental conditions at the collection site of 658 Indica and 283 Japonica rice landrace accessions sequenced as part of the 3K rice Genomes Project. The user can choose among the more than 400 geo-environmental variables to be displayed on the map, using a color gradient within the ranges and units detailed in the color palette within the map. Clicking on any of the data points on the map provides information on the selected accession, including its curation details, and the value of the chosen environmental variable for the selected location.
OryzaCLIM V1.0 allows the inspection of two environment variables simultaneously. The more than 400 environmental variables that can be selected on the map can be compared with a second environmental variable that is user-specified; the two variables are displayed with a linear correlation provided based on data for the local environments of landraces grown in South-Eastern Asia. We also provide an interactive tabulated database describing the environmental variables available at OryzaCLIM V1.0, including their source, units, and period of data collection.
The environmental dataset compiled in our study is available using the download buttom. Within the data folder as well as in the app itself, there is information on the descriptors and the source of each of the environmental parameters used.
-Ángel Ferrero-Serrano, David Chakravorty, Kobie J Kirven & Sarah M Assmann (2022). Oryza CLIMtools: An Online Portal for Investigating Genome-Environment Associations in Rice. bioRxiv 2023.05.10.540241; doi: https://doi.org/10.1101/2023.05.10.540241
