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Molecular Breeding

, Volume 33, Issue 4, pp 895–907 | Cite as

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

  • Anh-Tung Pham
  • Kristin Bilyeu
  • Pengyin Chen
  • H. Roger Boerma
  • Zenglu LiEmail author
Article

Abstract

Soybean is one of the most important oil crops worldwide, and reducing the linolenic acid content of soybean oil will provide increased stability of the oil to consumers and limit the amount of trans fat in processed foods. The linolenic content in soybean seed is controlled by three fatty acid desaturase (FAD) three enzymes, FAD3A, B, and C. The soybean lines with 1 % linolenic acid content which are widely used in breeding for reduced linolenic acid in the USA have mutations in each of the three FAD genes derived from lines 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 has prevented researchers from designing robust molecular markers for effective marker-assisted selection (MAS). Using a PCR-based genomic strategy, we have identified a 6.4-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 single nucleotide polymorphisms in FAD3B and FAD3C identified in A26 and A23, respectively, we have also developed TaqMan assays for high-throughput MAS. The TaqMan assays have proven to be a very effective platform for detecting the mutant FAD3 alleles and thus will greatly facilitate high-throughput MAS for development of soybean lines with reduced linolenic acid content.

Keywords

FAD3 Low linolenic TaqMan assay genotyping Marker-assisted selection 

Notes

Acknowledgments

The authors wish to acknowledge the excellent technical assistance provided by Christine Cole, and two undergraduate helpers Jonathan Serrano and Bryan Grommersch. Funding for this research was provided by the United Soybean Board.

Supplementary material

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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Anh-Tung Pham
    • 1
  • Kristin Bilyeu
    • 2
  • Pengyin Chen
    • 3
  • H. Roger Boerma
    • 1
    • 4
  • Zenglu Li
    • 1
    Email author
  1. 1.Department of Crop and Soil Sciences, Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensUSA
  2. 2.Plant Genetics Research UnitUSDA-ARSColumbiaUSA
  3. 3.Department of Crop, Soil, and Environmental SciencesUniversity of ArkansasFayettevilleUSA
  4. 4.Georgia Seed Development CommissionAthensUSA

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