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

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. Core Ideas A high‐quality chromosome‐level reference genome of S. hispanica was assembled and analyzed. Ancestral whole‐genome duplication events have not promoted high α‐linolenic acid content in S. hispanica seeds. Tandem duplication of six stearoyl‐ACP desaturase genes is a plausible cause for high ω‐3 content in chia seeds. Plain Language Summary Chia is an emerging crop that has been qualified as “superfood” because of it is a rich source of omega 3 fatty acids which have benefits for human nutrition and health. To understand the genetic make‐up underlying this abundant production of fatty acids, we sequence the genome of a black commercial variety of chia and compare the gene content against other plant species. We found that the number of genes of a specific family producing stearoyl‐ACP desaturase enzymes has been expanded in this particular plant species. This expansion in number of genes from this family was shown to have ocurred through tandem duplication, which is the doubling of a genome chunk occurring during the multiplication of the reproductive cells. We also found that these enzyme are being put under Natural Selection to remain efficient and this, with their larger that expected number, might explain why chia produces so much omega 3s.