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Title: Characterization of the fan1 locus in soybean line A5 and development of molecular assays for high-throughput genotyping of FAD3 genes

Author
item PHAM, ANH-TUNG - University Of Georgia
item Bilyeu, Kristin
item CHEN, PENGYIN - University Of Arkansas
item BOERMA, ROGER - University Of Georgia
item LI, ZENGLU - University Of Georgia

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/3/2013
Publication Date: 12/27/2013
Citation: Pham, A., Bilyeu, K.D., Chen, P., Boerma, R.H., Li, Z. 2013. Characterization of the fan1 locus in soybean line A5 and development of molecular assays for high-throughput genotyping of FAD3 genes. Molecular Breeding. 33:895-907.

Interpretive Summary: Soybean is one of the world’s most important oilseed crops. The oil quality can now be improved by accelerated breeding strategies utilizing molecular gene marker assays. The development of soybean cultivars with the ultra-low linolenic acid soybean oil quality trait has been slowed because the lack of characterization of a critical gene donor (parental line) that has prevented the deployment of the most efficient molecular marker-based selection strategies. The objective of this research was to characterize the gene donor and develop functional molecular marker assays to be utilized in the development of soybean cultivars with an important oil quality trait. The results of the research were successful, and the new assays should enhance the speed with which soybean varieties with improved oil quality can be released.

Technical Abstract: Soybean is one of the most important oil crops in the world, and reduced linolenic acid content of soybean oil will provide increased stability of the oil to consumers and food manufacturers and limit the amount of trans-fat to be used in the processed foods. The linolenic content in soybean seeds is controlled by three fatty acid desaturase (FAD) 3 enzymes, including FAD3A, B and C, with the FAD3A enzyme having the major effect on the final linolenic acid content in soybean seeds. The widely used soybean lines for breeding in the U.S.with 1% linolenic acid content have mutations in each of the three FAD genes derived from A5 (deletion of FAD3A), A26 and A23 (missense mutations in FAD3B and C, respectively). Although soybean line A5 has been released for 30 years, the extent and definition of the deletion of the FAD3A gene has not been characterized which prevented us from designing robust molecular markers for effective marker-assisted selection. Using a PCR-based genomic strategy, we have identified a 6.5 kbp deletion of the FAD3A gene in A5 and developed a TaqMan detection assay by targeting the deletion junction in A5 which could be used to distinguish the homozygotes and heterozygotes of the gene. In addition, based on mutant SNPs in FAD3B and FAD3C identified in A26 and A23, respectively, we have also developed TaqMan assays for high throughput marker-assisted selection (MAS). The TaqMan assays have proven to be a very effective platform to detect the mutant FAD3 alleles and thus will greatly facilitate the high-throughput MAS for development of soybean lines with reduced linolenic acid content.