Palmitic acid is the major saturated fatty acid found in soybean [Glycine max (L.) Merr.] oil, accounting for approximately 11% of the seed oil content. Reducing the palmitic acid levels of the oil is desirable because of the negative health effects specifically associated with this fatty acid. One of the genetic loci known to reduce the seed palmitate content in soybean is fapnc. Previous studies indicated that fapnc is associated with a deletion in a gene (designated FATB) encoding 16:0‐ACP thioesterase activity. In this report, we isolated full length cDNAs of three of the four unique FATB genes expressed in soybean and show that the isoform designated GmFATB1a represents the specific gene deleted in lines possessing the fapnc locus. Allele specific primers corresponding to GmFATB1a were used to genotype plants from two F4‐derived populations that were segregating for fapnc The GmFATB1a‐specific markers were effective in accounting for 62 to 70% of the genotypic variation in palmitate content in the two populations studied. Because the markers developed in this study are 100% linked to the locus of interest, they should be particularly useful in marker‐assisted selection programs designed to lower the palmitic acid levels of soybean oil.

Soybeans [Glycine max (L.) Merr.] have undesirable levels of polyunsaturated fatty acids in their oil that result in oxidative instability and poor flavor. The process of hydrogénation improves the stability but creates undesirable trans fats. Lines carrying fan genes have decreased linolenic acid (18:3) content. Changes in transcription or activity of the desaturase encoded by the GmFAD3 gene cause a reduction in 18:3 content in certain lines.