Theoretical and Applied Genetics

, Volume 127, Issue 1, pp 97–111 | Cite as

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

  • Andrea J. CardinalEmail author
  • Rebecca Whetten
  • Sanbao Wang
  • Jérôme Auclair
  • David Hyten
  • Perry Cregan
  • Eleni Bachlava
  • Jason Gillman
  • Martha Ramirez
  • Ralph Dewey
  • Greg Upchurch
  • Lilian Miranda
  • Joseph W. Burton
Original Paper


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.


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.


Simple Sequence Repeat Marker Agronomic Trait Segregation Distortion Maturity Group Palmitic Acid Content 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



Palmitic acid


Stearic acid


Oleic acid


Linoleic acid


Linolenic acid


Best linear unbiased predictor


Days after planting


16:0-ACP thioesterase


3-Ketoacyl-ACP synthase enzyme III


Flowering date


Maturity date



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.

Supplementary material

122_2013_2204_MOESM1_ESM.xlsx (55 kb)
Supplementary material 1 (XLSX 54 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Andrea J. Cardinal
    • 1
    Email author
  • Rebecca Whetten
    • 1
  • Sanbao Wang
    • 1
  • Jérôme Auclair
    • 2
  • David Hyten
    • 3
    • 4
  • Perry Cregan
    • 3
  • Eleni Bachlava
    • 5
  • Jason Gillman
    • 6
  • Martha Ramirez
    • 7
  • Ralph Dewey
    • 1
  • Greg Upchurch
    • 7
  • Lilian Miranda
    • 7
  • Joseph W. Burton
    • 7
  1. 1.Department of Crop ScienceNorth Carolina State UniversityRaleighUSA
  2. 2.La Coop fédéréeMontrealCanada
  3. 3.Soybean Genomics and Improvement LaboratoryU.S. Department of Agriculture, Agricultural Research ServiceBeltsvilleUSA
  4. 4.DuPont PioneerJohnstonUSA
  5. 5.Monsanto Vegetable SeedsWoodlandUSA
  6. 6.Plant Genetics Research UnitUSDA-ARS, University of MissouriColumbiaUSA
  7. 7.Soybean and Nitrogen Fixation Research UnitUSDA-ARSRaleighUSA

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