Detection of locally adapted genomic regions in wild rice (Oryza rufipogon) using environmental association analysis

Abstract

Oryza rufipogon is the wild progenitor of cultivated rice Oryza sativa and exhibits high levels of genetic diversity across its distribution, making it a useful resource for the identification of abiotic stress-tolerant varieties and genes that could limit future climate-changed-induced yield losses. To investigate local adaptation in O. rufipogon, we analyzed single nucleotide polymorphism (SNP) data from a panel of 286 samples located across a diverse range of climates. Environmental association analysis (EAA), a genome-wide association study (GWAS)-based method, was used and revealed 15 regions of the genome significantly associated with various climate factors. Genes within these environmentally associated regions have putative functions in abiotic stress response, phytohormone signaling, and the control of flowering time. This provides an insight into potential local adaptation in O. rufipogon and reveals possible locally adaptive genes that may provide opportunities for breeding novel rice varieties with climate change-resilient phenotypes.

Keywords: Oryza rufipogon; Plant Genetics and Genomics; abiotic stress; climate; domestication; environmental association analysis; genomics; local adaptation; wild rice.

Fig. 1.

a) Mean annual temperature (°C; BIO1) and b) mean annual precipitation (mm; BIO12) across the 286 O. rufipogon sample locations.

Fig. 2.

Accession distribution based on primary and secondary principal components derived from the environmental data. Points correspond to individual rice accessions, and arrows are the variable loadings, annotated with the variable name. Percentages represent the amount of variation explained by each axis.

Fig. 3.

a) Distribution of SNPs across the diversity panel. Points represent the approximate locations of accessions (overlapping points offset for clarity), separated by the SNP ORRUF07_09153554T:C in the region R7.1, which is associated with BIO5 and contains 26 genes including the flowering time gene Ghd7. b) Association between the SNP and BIO5 maximum temperature of the warmest month (°C). Each point represents an individual accession, with mean ± 1 SD overlayed.