Global climate change has threatened world crop production and food security. Decoding the adaptive genetic basis of wild relatives provides an invaluable genomic resource for climate-smart crop breedinG. Here, we performed whole-genome sequencing of 185 diverse wild soybean (Glycine soja) accessions collected from three major agro-ecological zones in China to parse the genomic basis of local adaptation in wild soybean. The population genomic diversity pattern exhibited clear agro-ecological zone-based population structure, and multiple environmental factors were observed to contribute to the genetic divergence. Demographic analysis shows that wild soybeans from the three ecological zones diverged about 1 × 105 years ago, and then the effective population sizes have undergone different degrees of expansions. Genome-environment association identified multiple genes involved in the local adaptation, such as flowering time and temperature-related genes. A locus containing two adjacent MADS-box transcription factors on chromosome 19 was identified for multiple environmental factors, and it experienced positive selection that enables the adaptation to high-latitude environment. This study provides insights into the genetic mechanism of ecological adaptation in wild soybean that may facilitate climate-resilient soybean breeding.
Keywords: genome‐environment association; local adaptation; population divergence; wild soybean.
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