A new low linolenic acid allele of GmFAD3A gene in soybean PE1690

Relative fatty acid content of soybean oil is about 12 % palmitic acid, 4 % stearic acid, 23 % oleic acid, 54 % linoleic acid, and 8 % linolenic acid. To improve oxidative stability and quality of oil, breeding programs have mainly focused on reducing saturated fatty acids, increasing oleic acid, and reducing linolenic acid in soybean oil. The objective of this study was to characterize the low linolenic acid trait in seed oil of PE1690, which was derived from an ethyl methanesulfonated-mediated mutagenesis. PE1690 DNA was used to examine the genomic sequence of a candidate gene, and we found a point mutation which substituted guanine to adenine in the second intron splice site of the GmFAD3A gene. Mutation of PE1690 at the first base of the second intron caused missplicing which led to the inclusion of 334 bp of the second intron into the coding sequence. The amino acid sequence of the mutant was analyzed based on cDNA sequence of GmFAD3A in PE1690. The position 128 amino acid, which codes for tryptophan (TGG) in PE1690, was changed to a premature stop codon (TGA). Therefore, the single base mutation in the PE1690 GmFAD3A gene renders the desaturase enzyme nonfunctional. Based on a genetic marker that we developed, the association of the PE1690 derived GmFAD3A allele with linolenic acid level was tested in 89 F₂ progeny of a cross between Pungsannamul (wild type) × PE1690. The results showed that the mutation of GmFAD3A in PE1690 was associated with reduced linolenic acid content in the soybean seed oil. A newly developed low linolenic acid soybean PE1690 provides a good genetic resource to improve the quality of soybean oil.