Skip to main content
SpringerLink
Log in

Identifying FATB1a deletion that causes reduced palmitic acid content in soybean N87-2122-4 to develop a functional marker for marker-assisted selection

  • Published:
Molecular Breeding Aims and scope Submit manuscript

Abstract

Palmitic acid is a major saturated fatty acid in soybean oil, and consumption of saturated fat is linked to a risk of coronary diseases. Development of soybean (Glycine max) cultivars with reduced palmitic acid content is an important goal of soybean breeding. The FATB1a gene was previously found to be responsible for reduced palmitic acid in the soybean line N87-2122-4. The objective of this research was to characterize the FATB1a gene identified in N87-2122-4 and develop a breeder-friendly, functional marker to facilitate marker-assisted selection and improve breeding efficiency for reduced palmitic soybeans. With the availability of soybean genetic maps, reference genome, and gene annotations, an approximate 254 kb deleted genomic region, including the FATB1a gene, was identified. Based on the gene deletion information, we developed a TaqMan marker and tested it with a segregating F 2 population that consisted of 140 individual plants derived from ‘Cook’ × N87-2122-4. The marker performed well and accounted for 57 % of the phenotypic variation. The marker was also validated using a panel of 121 diverse soybean lines with known fatty acid profiles. The result indicated that the marker can be used effectively in marker-assisted breeding for reduced palmitic acid in soybean.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Anai T, Hoshino T, Imai N, Takagi Y (2012) Molecular characterization of two high-palmitic-acid mutant loci induced by X-ray irradiation in soybean. Breed Sci 61:631–638

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Beuselinck PR, Sleper DA, Bilyeu KD (2006) An assessment of phenotype selection for linolenic acid using genetic markers. Crop Sci 46:747–750

    Article  CAS  Google Scholar 

  • Boerma HR, Hussey RS, Phillips DV, Wood ED, Finnerty SL (1992) Registration of ‘Cook’ soybean. Crop Sci 32:497

    Article  Google Scholar 

  • Boerma HR, Hussey RS, Phillips DV, Wood ED, Rowan GB, Finnerty SL (1997) Registration of ‘Benning’ soybean. Crop Sci 37:6

    Article  Google Scholar 

  • Bubeck DM, Fehr WR, Hammond EG (1989) Inheritance of palmitic and stearic acid mutants of soybean. Crop Sci 29:652–656

    Article  Google Scholar 

  • Burton JW, Wilson RF, Brim CA (1983) Recurrent selection in soybeans. IV. Selection for increased oleic acid percentage in seed oil. Crop Sci 23:744–747

    Article  CAS  Google Scholar 

  • Burton JW, Wilson RF, Brim CA (1994) Registration of N79-2077-12 and N87-2122-4, two soybean germplasm lines with reduced palmitic acid in seed oil. Crop Sci 34:313

    Google Scholar 

  • Burton JW, Wilcox JR, Wilson RF, Novitzky WP, Rebetzke GJ (1998) Registration of low palmitic acid soybean germplasm lines N94-2575 and C1943. Crop Sci 38:1407

    Article  Google Scholar 

  • Cardinal AJ, Burton JW, Camacho-Roger AM, Yang JH, Wilson RF, Dewey RE (2007) Molecular analysis of soybean lines with low palmitic acid content in the seed oil. Crop Sci 47:304–311

    Article  CAS  Google Scholar 

  • Erickson EA, Wilcox JR, Cavins JF (1988) Inheritance of altered palmitic acid percentages in two soybean mutants. J Hered 79:465–468

    CAS  Google Scholar 

  • Fedick A, Su J, Treff NR (2012) Development of TaqMan allelic discrimination based genotyping of large DNA deletions. Genomics 99:127–131

    Article  CAS  PubMed  Google Scholar 

  • Fehr WR (2007) Breeding for modified fatty acid composition in soybean. Crop Sci 47:S72–S87

    Article  Google Scholar 

  • Fehr WR, Welke GA, Cianzio SR, Duvick DN, Hammond EG (1991) Inheritance of reduced palmitic acid content in seed oil of soybean. Crop Sci 31:88–89

    Article  CAS  Google Scholar 

  • Giancola S, McKhann HI, Berard A, Camilleri C, Durand S, Libeau P, Roux F, Reboud X, Gut IG, Brunel D (2006) Utilization of the three high-throughput SNP genotyping methods, the GOOD assay, Amplifluor, and TaqMan, in diploid and polyploid plants. Theor Appl Genet 112:1115–1124

    Article  CAS  PubMed  Google Scholar 

  • Gillman J, Tetlow A, Hagely K, Boersma J, Cardinal A, Rajcan I, Bilyeu K (2014) Identification of the molecular genetic basis of the low palmitic acid seed oil trait in soybean mutant line RG3 and association analysis of molecular markers with elevated seed stearic acid and reduced seed palmitic acid. Mol Breed 34:447–455

    Article  CAS  Google Scholar 

  • Gizlice Z, Carter TE, Burton JW (1994) Genetic base for North-American public soybean cultivars released between 1947 and 1988. Crop Sci 34:1143–1151

    Article  Google Scholar 

  • Hunter JE, Zhang J, Kris-Etherton PM (2010) Cardiovascular disease risk of dietary stearic acid compared with trans, other saturated, and unsaturated fatty acids: a systematic review. Am J Clin Nutr 91:46–63

    Article  CAS  PubMed  Google Scholar 

  • Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, Buxton S, Cooper A, Markowitz S, Duran C, Thierer T, Ashton B, Mentjies P, Drummond A (2012) Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–1649

    Article  PubMed  PubMed Central  Google Scholar 

  • Keim P, Olson TC, Shoemaker RC (1988) A rapid protocol for isolating soybean DNA. Soybean Genet Newsl 15:150–152

    Google Scholar 

  • Lawrence GD (2013) Dietary fats and health: dietary recommendations in the context of scientific evidence. Adv Nutr 4:294–302

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li Z, Wilson RF, Rayford WE, Boerma HR (2002) Molecular mapping genes conditioning reduced palmitic acid content in N87-2122-4 soybean. Crop Sci 42:373–378

    Article  CAS  Google Scholar 

  • Pham AT, Bilyeu K, Chen P, Boerma R, Li Z (2014) Characterization of the fan1 locus in soybean line A5 and development of molecular assays for high-throughput genotyping of FAD3 genes. Mol Breed 33:895–907

    Article  CAS  Google Scholar 

  • Primomo VS, Falk DE, Ablett GR, Tanner JW, Rajcan I (2002) Inheritance and interaction of low palmitic and low linolenic soybean. Crop Sci 42:31–36

    Article  CAS  PubMed  Google Scholar 

  • Shen GQ, Abdullah KG, Wang QK (2009) The TaqMan method for SNP genotyping. Methods Mol Biol 578:293–306

    Article  CAS  PubMed  Google Scholar 

  • Shi Z, Bachleda N, Pham A, Bilyeu K, Nguyen H, Li Z (2015) High-throughput and functional SNP detection assays for fatty acid in soybean. Mol Breed 35:176. doi:10.1007/s11032-015-0368-4

    Article  Google Scholar 

  • Steinberg D (2005) Thematic review series: the pathogenesis of atherosclerosis. An interpretive history of the cholesterol controversy: Part II: the early evidence linking hypercholesterolemia to coronary disease in humans. J Lipid Res 46:179–190

    Article  CAS  PubMed  Google Scholar 

  • Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG (2012) Primer3-new capabilities and interfaces. Nucleic Acids Res 40(15):e115

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wilcox JR, Cavins JF (1990) Registration of C1726 and C1727 soybean germplasm with altered levels of palmitic acid. Crop Sci 30:240

    Article  Google Scholar 

  • Wilson RF, Marquardt TC, Novitzky WP, Burton JW, Wilcox JR, Kinney AJ, Dewey RE (2001) Metabolic mechanisms associated with alleles governing the 16:0 concentration of soybean oil. J Am Oil Chem Soc 78:335–340

    Article  CAS  Google Scholar 

Download references

Acknowledgments

The authors would like to thank Dr. Kristen Bilyeu from USDA-ARS, Columbia, MO, for fatty acid analyses of soybean ancestral lines and Dr. Donna Harris, Dale Wood, Tatyana Nienow and Colleen Wu for their technical assistance. This research was funded by the United Soybean Board and the USDA Agriculture and Food Research Initiative (AFRI) grant.

Author information

Author notes

  1. Anh Pham

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

Authors and Affiliations

  1. Institute of Plant Breeding, Genetics, and Genomics and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA

    Nicole Bachleda, Anh Pham & Zenglu Li

Authors
  1. Nicole Bachleda
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Anh Pham
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Zenglu Li
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Zenglu Li.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Bachleda, N., Pham, A. & Li, Z. Identifying FATB1a deletion that causes reduced palmitic acid content in soybean N87-2122-4 to develop a functional marker for marker-assisted selection. Mol Breeding 36, 45 (2016). https://doi.org/10.1007/s11032-016-0468-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s11032-016-0468-9

Keywords

Search

Navigation