Comparative genomics points to tandem duplications of SAD gene clusters as drivers of increased -linolenic (-3) content in S. hispanica seeds

Salvia hispanica L. (chia) is a source of abundant omega-3 polyunsaturated fatty acids (omega-3-PUFAs) that are highly beneficial to human health. The genomic basis for this accrued omega-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 alpha-linolenic acid (ALA, omega-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 omega-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 omega-3 content in oil crops.