Identifying FATB1a Deletion That Causes Reduced Palmitic Acid Content in Soybean N87-2122-4 to Develop a Diagnostic Marker for a High Throughput Marker-Assisted Selection

Palmitic acid is the major saturated fatty acid in soybean oil, which accounted for more than half of the vegetable oil consumption in the U.S. in 2013.  Consumption of saturated fat is linked to a risk of coronary diseases and several cancers.  Development of soybean cultivars with reduced palmitic fatty acid content is one of the important goals of soybean breeding. The FATB1a gene was found to be responsible for reduced palmitic acid in soybean line N87-2122-4. The objective of this research was to characterize the FATB1a gene in N87-2122-4 and develop a breeder-friendly, diagnostic marker to facilitate marker-assisted selection and improve breeding efficiency for low palmitic soybean.  With the availability of FATB1a gene sequence, we have designed specific primers to target the intervals up and down stream of the gene for PCR and sequencing using the DNA from N87-2122-4 and a control variety Benning. Sequencing result revealed a 254 kbp deletion at FATB1a locus on chromosome 5 that caused disfunction of the gene.  Based on the gene deletion information, we have designed an TaqMan marker and tested it with an F₃ population consisting of 140 individuals derived from Cook x N87-2122-4. The marker had great performance and accounted for 55% of phenotypic variation. The TaqMan marker has also been validated using a panel of 88 diverse soybean lines with known phenotype.  This marker has become an efficient tool in marker-assisted breeding for early generation selection or backcrossing of low palmitic acid trait in soybean.