Identification of a new GmSACPD-C allele in high stearic acid mutant Hfa180 derived from gamma-ray irradiation

Stearic acid is the most important saturated fatty acid compound in soybean oil. A typical soybean cultivar has 2–3% stearic acid content of total oil. Recently, a new high stearic acid mutant Hfa180 was developed from gamma-ray irradiation with “Ilmikong.” The objectives of this study were to identify the mutant gene associated with high stearic acid content in Hfa180 and to develop a Kompetitive Allele-Specific PCR (KASP) assay for selection of soybeans with elevated levels of stearic acid in seeds. Target sequencing of the whole GmSACPD-C gene encoding D9-stearoyl-ACP-desaturase revealed that Hfa180 contained a three-base-pair deletion (GAG) at genomic positions 190 to 192 of the 1st exon of GmSACPD-C. The three-base deletion caused a variant with a single amino acid (glutamine) deletion at position 64 in the predicted GmSACPD-C amino acid in Hfa180, as well as an average 60% reduction in GmSACPD-C gene expression in Hfa180 compared to that of the wild type. Genetic linkage analysis using the F₂ population derived from a crossing between Hfa180 and the wild-type “Deapung” confirmed that the mutation allele of GmSACPD-C was perfectly correlated with elevation of seed stearic acid content. In addition, a KASP marker was developed to identify the mutation allele on the GmSACPD-C gene, which was successfully applied to select high stearic acid soybean lines. The identification of the mutant gene of the high stearic acid mutant Hfa180 and development of the KASP marker could be useful for improving stearic acid content in soybean oil.