In order to keep the quality of vegetable oil stable, it is important to reduce the a.-linolenic acid content. Previously, we developed three low-alpha-linonenic acid soybean mutants, 'J18', 'M5', and 'M24'. In this study, we obtained and characterized four cDNAs, GmFAD3-1a, GmFAD3-1b, GmFAD3-2a, and GniFAD3-2b, encoding microsomal omega-3 fatty acid desaturase from soybean developing seeds. The GmFAD3-1b transcript does not accumulate in the J18' mutant, whereas 'M5' and 'M24' contain a 19-base pair and a single-base pair deletion in the coding region of the GmFAD3-1b and GmFAD3-1a genes, respectively. Furthermore, heterologous expression of these two mutant genes in Saccharomyces cerevisiae revealed that the COOH-terminal region of both mutant gene products is essential for their enzymatic activity. In this report, we also discuss the contribution of each microsomal omega-3 fatty acid desaturase gene for a-linolenic acid biosynthesis in soybean seeds. (c) 2005 Elsevier Ireland Ltd. All rights reserved.