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It is important to study target genes that control de§novo fatty acid biosynthesis and triacylglycerol in§soybean (Glycine max L. Merr.). At least 5 recessive§alleles condition the low palmitic acid (16:0)§contents of soybean seeds: fap1, fap3, fap , fapnc§and sop1. The fapnc mutation affects the normal§function of the enzyme 16:0-ACP thioesterase encoded§by the gene FATB1. There are four FATB1 isoforms in§soybean: GmFATB1a, GmFATB1b, GmFATB2a, and GmFATB2b. §At least three major loci are responsible for low§linolenic acid (18:3) content in soybean seed oil§(fan, fan2 and fan3). The FAD3 gene encodes an§omega-3 desaturase that converts 18:2 to 18:3. It has§four highly similar microsomal isoforms: GmFAD3A and§GmFAD3B, FAD3-2a and FAD3-2b.§The root and leaf tissue fatty acid composition of§two lines carrying the fapnc, fap1, the fan(PI123440)§(a SNP in intron 2 of GmFAD3A) alleles and Brim a§high yielding line, was examined. It was concluded§that fapnc or fap1 or both mutations have pleiotropic§effects on the leaf fatty acid composition. The fan§mutation has a pleiotropic effects on the leaf and§root fatty acid composition but has not been§negatively correlated with yield.