Integrated environmental and genomic analysis reveals the drivers of fine‐scale divergence and local adaptation in northern populations of two wild rice species in China

Abstract

Societal Impact StatementCrop wild relatives represent precious genetic resources for crop improvement. Investigating their local adaptation to marginal environments is important for the utilization of wild genetic resources. Oryza officinalis and Oryza granulata are wild relatives of cultivated rice and possess genes that convey resistance to insects, disease, and tolerance to shade and drought. The northern edge for the distribution of these two lies in China where populations are facing habitat destruction. This study found that the northern marginal populations of both species have adapted to local conditions, with specific implications for the conservation and utilization of wild rice.Summary O. officinalis and O. granulata, wild relatives of cultivated rice, represent important gene reservoirs with the potential to improve rice with respect to insect resistance and stress tolerance. However, the northern marginal populations of these two species in China are facing habitat destruction. Here, we investigated the genetic diversity and divergence of northern marginal populations of O. officinalis and O. granulata. The genomic variation of two species was examined by whole‐genome sequencing on 357 individuals. Generalized dissimilarity modeling was applied to investigate the effects of geographic and environmental isolation on population differentiation. Genetic‐environment association analysis and genome‐wide FST outlier scans were used to identify environmentally driven signals of selection. The marginal populations of both species exhibited low genetic diversity and obvious genetic differentiation stemmed from the joint effects of isolation by geographic distance and the environment. Both genomes exhibited specific signals of adaptation to cold environments in the north. Investigation of the divergence and adaptation of marginal populations of O. officinalis and O. granulata will help us to determine how wild rice can adapt to local environments, thus allowing for the development of scientific conservation policies and the identification of new genetic resources for rice with improved resistance.