The FAD2 Gene Family of Soybean: Insights into the Structural and Functional Divergence of a Paleopolyploid Genome

The ω‐6 fatty acid desaturase (FAD2) gene family in soybean Glycine max (L.) Merr. consists of at least five members in four regions of the genome and are responsible for the conversion of oleic acid to linoleic acid. Here we report the identification of two new ω‐6 fatty acid desaturase (FAD2) gene copies from soybean expressed sequence tags (ESTs). Four bacterial artificial chromosomes (BACs) containing five FAD2 genes were sequenced to investigate structural and functional conservation between duplicate loci. Sequence comparisons show that the soybean genome is a mosaic, with some duplicate regions retaining high sequence conservation in both genic and intergenic regions, while others have only the FAD2 genes in common. Genetic mapping using SSRs from within the BAC sequences showed that two BACs with high sequence homeology mapped to linkage groups I and O; these groups share syntenic markers. Another BAC mapped to linkage group L. The fourth BAC could not be mapped. Reverse transcriptase–polymerase chain reaction (RT–PCR) analysis of the five FAD2 genes showed that the FAD2‐2B and FAD2‐2C copies were the best candidates for temperature‐dependent expression changes in developing pod tissue. Semiquantitative RT‐PCR confirmed these results, with FAD2‐2C showing upward of an eightfold increase in expression in developing pods grown in cooler conditions relative to those grown in warm conditions. The implications of these results suggest a candidate gene for controlling the levels of linoleic acid in developing pods grown in cooler climates.