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Mapping the low palmitate fap1 mutation and validation of its effects in soybean oil and agronomic traits in three soybean populations

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Abstract

Key message

fap 1 mutation is caused by a G174A change in GmKASIIIA that disrupts a donor splice site recognition and creates a GATCTG motif that enhanced its expression.

Abstract

Soybean oil with reduced palmitic acid content is desirable to reduce the health risks associated with consumption of this fatty acid. The objectives of this study were: to identify the genomic location of the reduced palmitate fap1 mutation, determine its molecular basis, estimate the amount of phenotypic variation in fatty acid composition explained by this locus, determine if there are epistatic interactions between the fap1 and fap nc loci and, determine if the fap1 mutation has pleiotropic effects on seed yield, oil and protein content in three soybean populations. This study detected two major QTL for 16:0 content located in chromosome 5 (GmFATB1a, fap nc) and chromosome 9 near BARCSOYSSR_09_1707 that explained, with their interaction, 66–94 % of the variation in 16:0 content in the three populations. Sequencing results of a putative candidate gene, GmKASIIIA, revealed a single unique polymorphism in the germplasm line C1726, which was predicted to disrupt the donor splice site recognition between exon one and intron one and produce a truncated KASIIIA protein. This G to A change also created the GATCTG motif that enhanced gene expression of the mutated GmKASIIIA gene. Lines homozygous for the GmKASIIIA mutation (fap1) had a significant reduction in 16:0, 18:0, and oil content; and an increase in unsaturated fatty acids content. There were significant epistatic interactions between GmKASIIIA (fap1) and fap nc for 16:0 and oil contents, and seed yield in two populations. In conclusion, the fap1 phenotype is caused by a single unique SNP in the GmKASIIIA gene.

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Abbreviations

16:0:

Palmitic acid

18:0:

Stearic acid

18:1:

Oleic acid

18:2:

Linoleic acid

18:3:

Linolenic acid

BLUP:

Best linear unbiased predictor

DAP:

Days after planting

FATB:

16:0-ACP thioesterase

KASIII:

3-Ketoacyl-ACP synthase enzyme III

R2:

Flowering date

R8:

Maturity date

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Acknowledgments

The authors would like to thank William Novitzky at the USDA-ARS Soybean and Nitrogen Fixation Research Unit, Raleigh, NC, for providing training and equipment for the fatty acid analysis; James B. Holland for providing technical expertise in QTL analysis and discussion of results; Martha Ramirez for isolating RNA; and Carol Griffin for performing Northern analysis. This project was funded by the United Soybean Board (Grant # 59-.6645-2-071).

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical Standards

The experiments performed for this publication comply with the current laws of the United States of America.

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Authors and Affiliations

  1. Department of Crop Science, North Carolina State University, Raleigh, NC, 27695-7620, USA

    Andrea J. Cardinal, Rebecca Whetten, Sanbao Wang & Ralph Dewey

  2. La Coop fédérée, Montreal, QC, Canada

    Jérôme Auclair

  3. Soybean Genomics and Improvement Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD, 20705, USA

    David Hyten & Perry Cregan

  4. DuPont Pioneer, P.O. Box 1000, Johnston, IA, 50131-0184, USA

    David Hyten

  5. Monsanto Vegetable Seeds, 37437 State Hwy 16, Woodland, CA, 95695, USA

    Eleni Bachlava

  6. Plant Genetics Research Unit, USDA-ARS, University of Missouri, Room 204, Curtis Hall, Columbia, MO, 65211, USA

    Jason Gillman

  7. Soybean and Nitrogen Fixation Research Unit, USDA-ARS, Raleigh, NC, 27607, USA

    Martha Ramirez, Greg Upchurch, Lilian Miranda & Joseph W. Burton

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  1. Andrea J. Cardinal
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  2. Rebecca Whetten
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  3. Sanbao Wang
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  9. Martha Ramirez
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  10. Ralph Dewey
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  12. Lilian Miranda
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  13. Joseph W. Burton
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Corresponding author

Correspondence to Andrea J. Cardinal.

Additional information

Communicated by I. Rajcan.

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Cardinal, A.J., Whetten, R., Wang, S. et al. Mapping the low palmitate fap1 mutation and validation of its effects in soybean oil and agronomic traits in three soybean populations. Theor Appl Genet 127, 97–111 (2014). https://doi.org/10.1007/s00122-013-2204-8

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