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Title: High-throughput and functional SNP detection assays for oleic and linolenic acids in soybean

Author
item SHI, ZI - University Of Georgia
item BACHLEDA, NICOLE - University Of Georgia
item PHAM, ANH - University Of Georgia
item Bilyeu, Kristin
item SHANNON, GROVER - University Of Missouri
item NGUYEN, HENRY - University Of Missouri
item LI, ZENGLU - University Of Georgia

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/4/2015
Publication Date: 8/12/2015
Publication URL: http://handle.nal.usda.gov/10113/62189
Citation: Shi, Z., Bachleda, N., Pham, A.T., Bilyeu, K.D., Shannon, G.J., Nguyen, H., Li, Z. 2015. High-throughput and functional SNP detection assays for oleic and linolenic acids in soybean. Molecular Breeding. 35(8):176.

Interpretive Summary: Soybean oil is an important global commodity. The functionality of soybean oil can be improved by breeding for multiple variant alleles (forms) of soybean fatty acid desaturases, the enzymes that control the fatty acid profile of the oil. The objective of this work was to develop high throughput molecular marker assay (DNA based gene tracking technology) resources that can be applied to a breeding program aimed at high oleic acid and low linolenic acid oil traits. Existing knowledge on the molecular basis of these traits formed the basis to develop improved diagnostic assays that would fit into high throughput molecular selection programs. Six allele specific assays were developed and validated that will allow for perfect selection of the traits. These assays can be used to speed breeding efforts and to develop new high oleic and low linolenic acid soybean varieties with improved oil functionality.

Technical Abstract: Soybean is a primary source of vegetable oil, accounting for 53% of the total vegetable oil consumption in the USA in 2013. Soybean oil with high oleic acid and low linolenic acid content is desired, because it not only improves the oxidative stability of the oil, but also reduces the amount of undesirable trans-fat production by the hydrogenation processing. The mutant FAD2-1A and FAD2-1B alleles contribute to an elevated oleic acid level, while mutations in FAD3A and FAD3C lead to a reduction in linolenic acid levels of soybean seed oil. Although SNP (Single Nucleotide Polymorphism) SimpleProbe assays have been developed for these genes, breeder friendly and high-throughput marker systems are needed for large scale selection in soybean breeding programs. TaqMan or Kompetitive Allele Specific PCR (KASP) assays were successfully developed to detect and discriminate mutant alleles of FAD2-1A (17D and PI 603452 sources) and FAD2-1B (PI 283327 source) for the high oleic acid trait, as well as those of FAD3A (CX1512-44 and C1640 sources) and FAD3C (CX1512-44 source) for low linolenic acid content soybean. All of the assays have been proven to be robust in distinguishing different genotypes in a high-throughput setting. The accuracy of the assays was validated using multiple populations as well as a panel of diverse soybean lines and a significant correlation was observed between the SNP alleles and their corresponding fatty acid phenotypes. These marker assays appear to be very reliable for detecting mutant and wild type alleles, and thus will assist forward and backcrossing breeding of soybean lines with desired oil profiles in an accurate and efficient manner.