Oryza CLIMtools: An Online Portal for Investigating Genome-Environment Associations in Rice

Elite crop varieties display an evident mismatch between their current distributions and the suitability of the local climate for their productivity. To this end, we present Oryza CLIMtools, (https://gramene.org/CLIMtools/oryza_v1.0/) the first pan-genome prediction of climate-associated genetic variants in a crop species. This resource consists of interactive web-based databases that allow the user to: i) explore the local environment and its interaction with natural existing genetic variation in local rice varieties (landraces) in South-Eastern Asia, and; ii) investigate the environment × genome associations for 658 Indica and 283 Japonica rice landrace accessions included in the 3K Rice Genomes Project and previously collected from their geo-referenced local environments. We exemplify the value of these resources, identifying an interplay between flowering time and temperature in the local environment that is facilitated by adaptive natural variation in OsHD2 and disrupted by maladaptive variation in OsSOC1. Prior QTL analysis has suggested the importance of heterotrimeric G proteins in the control of agronomic traits. Accordingly, we analyzed the climate associations of the different heterotrimeric G protein subunits. We identified a coordinated role of G proteins in adaptation to the prevailing Potential Evapotranspiration gradient and their regulation of key agronomic traits including plant height, seed, and panicle length. We conclude by highlighting the prospect of targeting heterotrimeric G proteins to produce crops that are climate-change-ready.

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