A mutation in a 3-keto-acyl-ACP synthase II gene is associated with elevated palmitic acid levels in soybean seeds

Palmitic acid is the major saturated fatty acid component of soybean [Glycine max (L.) Merr.] oil, typically accounting for approximately 11% of total seed oil content. Several genetic loci have been shown to control the seed palmitate content of soybean. One such locus, fap(2), mediates an elevated seed palmitate phenotype. Previous biochemical studies indicated that the fap2 locus is associated with a reduction in the activity of 3-keto-acyl-ACP synthase II (KAS II), an enzyme that initiates the elongation of palmitoyl-ACP to stearoyl-ACP in the plastid. The objective of the present research was to define the molecular basis by which the fap2 locus increases seed palmitate levels. We isolated two closely related, yet unique KAS II cDNAs, designated GmKAS IIA and GmKAS IIB, from soybean cultivar Century (Fap(2), Fap(2)) and its derivative high palmitate germplasm C1727 (fap(2), fap(2)). The GmKAS IIB cDNAs recovered from Century and C1727 were identical. In contrast, a single base-pair substitution was found in the GmKAS IIA gene from C1727 versus Century which converted a tryptophan codon into a premature stop codon, a mutation that would be predicted to render the encoded enzyme nonfunctional. Knowledge of the DNA sequence polymorphism led to the development a facile, robust cleavage amplified polymorphic sequence (CAPS) marker that readily distinguishes the mutant GmKAS IIA gene. This marker faithfully associated with a second independent germplasm line bearing the fap2 locus, and thus may be useful in breeding programs that target the development of high palmitate soybean cultivars.