Oryza CLIMtools:A genome–environment association resource reveals adaptive roles for heterotrimeric G proteins in the regulation of rice agronomic traits

Modern crop varieties display a degree of mismatch between their current distributions and the suitability of the local climate for their productivity.To address this issue,we present Oryza CLIMtools(https://gramene.org/CLIMtools/oryza_v1.0/),thefirst resource for pan-genome prediction of climate-associated genetic variants in a crop species.Oryza CLIMtools consists of interactive web-based databases that enable the user to(1)explore the local environments of traditional rice varieties(landraces)in South-East Asia and(2)investigate the environment by genome associations for 658 Indica and 283 Japonica rice landrace accessions collected from georeferenced local environments and included in the 3K Rice Ge-nomes Project.We demonstrate the value of these resources by identifying an interplay betweenflowering time and temperature in the local environment that is facilitated by adaptive natural variation in OsHD2 and disrupted by a natural variant in OsSOC1.Prior quantitative trait locus analysis has suggested the impor-tance of heterotrimeric G proteins in the control of agronomic traits.Accordingly,we analyzed the climate associations of natural variants in the different heterotrimeric G protein subunits.We identified a coordi-nated role of G proteins in adaptation to the prevailing potential evapotranspiration gradient and revealed their regulation of key agronomic traits,including plant height and seed and panicle length.We conclude by highlighting the prospect of targeting heterotrimeric G proteins to produce climate-resilient crops.

Plants and heterotrimeric G proteins:Expect the unexpected

The United Nations estimates that by 2050 the world population will reach 9.7 billion(United Nations Department of Economic and Social Affairs,Population Division,2022),which will increase food demand.Meanwhile,predictions anticipate global crop yield declines of 5.6%–18.2%as a result of climate change(Zhao et al.,2017).Climate change will result in extreme weather events that are already occurring and that will become more frequent and variable in the future.Now,more than ever,we need plants that can cope with unpredictable weather events such as drought or heat waves.Therefore,understanding and controlling plant stress responses is likely to be one of several fundamental advances crucial to meeting increased crop production requirements.There is an urgent necessity to develop crops that tolerate multiple stresses without a deleterious reduction in fitness under optimal conditions.However,efforts to release such varieties have often failed because of an unacceptable trade-off between growth and stress tolerance.