| Summary: | Abstract Salvia hispanica L. (chia) is a source of abundant ω‐3 polyunsaturated fatty acids (ω‐3‐PUFAs) that are highly beneficial to human health. The genomic basis for this accrued ω‐3‐PUFA content in this emerging crop was investigated through the assembly and comparative analysis of a chromosome‐level reference genome for S. hispanica. The highly contiguous 321.5‐Mbp genome assembly covering all six chromosomes enabled the identification of 32,922 protein‐coding genes. Two whole‐genome duplications (WGD) events were identified in the S. hispanica lineage. However, these WGD events could not be linked to the high α‐linolenic acid (ALA, ω‐3) accumulation in S. hispanica seeds based on phylogenomics. Instead, our analysis supports the hypothesis that evolutionary expansion through tandem duplications of specific lipid gene families, particularly the stearoyl‐acyl carrier protein desaturase (ShSAD) gene family, is the main driver of the abundance of ω‐3‐PUFAs in S. hispanica seeds. The insights gained from the genomic analysis of S. hispanica will help establish a molecular breeding target that can be leveraged through genome editing techniques to increase ω‐3 content in oil crops.
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