Where the wild things are: Genetic associations of environmental adaptation in the oryza rufipogon species complex

Authors: WANG, DIANE - Purdue University; KANTAR, MICHAEL - University Of Hawaii; MURUGAIYAN, VARUN - International Rice Research Institute; Neyhart, Jeffrey

Submitted to: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/22/2023
Publication Date: 6/9/2023
Citation: Wang, D.R., Kantar, M.B., Murugaiyan, V., Neyhart, J.L. 2023. Where the wild things are: Genetic associations of environmental adaptation in the oryza rufipogon species complex. Genes, Genomes, Genetics. https://doi.org/10.1093/g3journal/jkad128.
DOI: https://doi.org/10.1093/g3journal/jkad128

Interpretive Summary: Natural selection has shaped the adaptation of crop wild relatives to a wide range of habitats. As climate change increases the occurrence of extreme weather events and other abiotic stresses, a more complete understanding of the genetic variation that underlies this adaptation could enable fuller utilization of wild relatives for crop improvement. Our study examined environmental associations in Oryza rufipogon, the wild progenitor of cultivated Asian rice. We used genomic data and local climate information to determine genomic regions that may be responsible for local environmental adaptation in this crop wild relative. We discovered many genomic regions associated with one or more environmental variables (precipitation, temperature, or soil), some of which contained genes with a suggested role in climate adaptation. Potentially beneficial variants at these genomic regions were also present in cultivated rice populations. These variants may be targets for selection in rice breeding programs to improve abiotic stress tolerance.

Technical Abstract: Crop wild relatives host unique adaptation strategies that enable them to thrive across a wide range of habitats. As pressures from a changing climate mount, a more complete understanding of the genetic variation that underlies this adaptation could enable fuller utilization of wild materials for crop improvement. Here, we carry out environmental association analyses (EAA) in the Oryza rufipogon species complex (ORSC), the wild progenitor of cultivated Asian rice, to identify genomic regions associated with environmental adaptation characterized by variation in bioclimatic and soil variables. We further examine regions for colocalizations with phenotypic associations within the same collection. EAA results indicate that Quantitative Trait Loci (QTL) tend to associate with single environmental variables, although two significant loci on chromosomes three and five are detected that are common across multiple variable types (i.e., precipitation, temperature, and/or soil). Distributions of allele frequencies at significant loci across subpopulations of cultivated O. sativa indicate that, in some cases, adaptive variation may already be present among cultivars. This work has implications for the potential utility of wild genetic resources in pre-breeding efforts for rice improvement.