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

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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 single nucleotide polymorphism (SNP) SimpleProbe assays have been developed for these genes, breeder-friendly and high-throughput marker systems are needed for large-scale selections in soybean breeding programs. TaqMan or Kompetitive Allele Specific PCR 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. The accuracy of the assays was validated using multiple populations as well as a panel of diverse soybean lines, and a perfect association was observed between the SNP alleles and their corresponding fatty acid phenotypes. These marker assays have been proven to be robust and 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.

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Acknowledgments

We would like to acknowledge Dr. H. Roger Boerma at the University of Georgia for developing some of populations which were used in this research and Dale Wood and Steve Finnerty for their technical assistance in field/greenhouse planting. We also thank Colleen Wu and Tatyana Nienow for their assistance with sampling and genotyping. We appreciate the funding support from the United Soybean Board to this research.

Author contribution

ZS drafted the manuscript with edits from ZL, KB, and HN. ZS and NB involved in the data acquisition and marker validation and performed association analysis for all the markers in the study. AP designed all the TaqMan primers and probes. KB involved in the fatty acid profiling and initial SNP discovery. GS and KB contributed to the development of lines used to create populations and assay implementation. ZL provided oversight of the experiment and interpreted the results.

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Author notes

  1. Anh T. Pham

    Present address: School of Agriculture, Food, and Wine, University of Adelaide, Urrbrae, SA, Australia

Authors and Affiliations

  1. Department of Crop and Soil Science, Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA

    Zi Shi, Nicole Bachleda, Anh T. Pham & Zenglu Li

  2. Plant Genetics Research Unit, USDA-ARS, Columbia, MO, 65211, USA

    Kristin Bilyeu

  3. Division of Plant Sciences, National Center for Soybean Biotechnology (NCSB), University of Missouri, Portageville, MO, 63873, USA

    Grover Shannon

  4. Division of Plant Sciences, National Center for Soybean Biotechnology (NCSB), University of Missouri, Columbia, MO, 65211, USA

    Henry Nguyen

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  1. Zi Shi
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  2. Nicole Bachleda
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Correspondence to Zenglu Li.

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Shi, Z., Bachleda, N., Pham, A.T. et al. High-throughput and functional SNP detection assays for oleic and linolenic acids in soybean. Mol Breeding 35, 176 (2015). https://doi.org/10.1007/s11032-015-0368-4

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  • DOI: https://doi.org/10.1007/s11032-015-0368-4

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