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Theoretical and Applied Genetics

, Volume 131, Issue 5, pp 1099–1110 | Cite as

Characterization of a new GmFAD3A allele in Brazilian CS303TNKCA soybean cultivar

  • Luiz Claudio Costa Silva
  • Rafael Delmond Bueno
  • Loreta Buuda da Matta
  • Pedro Henrique Scarpelli Pereira
  • Danyelle Barbosa Mayrink
  • Newton Deniz Piovesan
  • Carlos Sigueyuki Sediyama
  • Elizabeth Pacheco Batista Fontes
  • Andrea J. Cardinal
  • Maximiller Dal-Bianco
Original Article

Abstract

Key Message

We molecularly characterized a new mutation in the GmFAD3A gene associated with low linolenic content in the Brazilian soybean cultivar CS303TNKCA and developed a molecular marker to select this mutation.

Abstract

Soybean is one of the most important crops cultivated worldwide. Soybean oil has 13% palmitic acid, 4% stearic acid, 20% oleic acid, 55% linoleic acid and 8% linolenic acid. Breeding programs are developing varieties with high oleic and low polyunsaturated fatty acids (linoleic and linolenic) to improve the oil oxidative stability and make the varieties more attractive for the soy industry. The main goal of this study was to characterize the low linoleic acid trait in CS303TNKCA cultivar. We sequenced CS303TNKCA GmFAD3A, GmFAD3B and GmFAD3C genes and identified an adenine point deletion in the GmFAD3A exon 5 (delA). This alteration creates a premature stop codon, leading to a truncated protein with just 207 residues that result in a non-functional enzyme. Analysis of enzymatic activity by heterologous expression in yeast support delA as the cause of low linolenic acid content in CS303TNKCA. Thus, we developed a TaqMan genotyping assay to associate delA with low linolenic acid content in segregating populations. Lines homozygous for delA had a linolenic acid content of 3.3 to 4.4%, and the variation at this locus accounted for 50.83 to 73.70% of the phenotypic variation. This molecular marker is a new tool to introgress the low linolenic acid trait into elite soybean cultivars and can be used to combine with high oleic trait markers to produce soybean with enhanced economic value. The advantage of using CS303TNKCA compared to other lines available in the literature is that this cultivar has good agronomic characteristics and is adapted to Brazilian conditions.

Notes

Acknowledgements

This work was funded by the CNPq (Grant 455812/2014-4), graduate fellowships (L.C.C.S. and L.B.M), post-doctoral fellowships (R.D.B) and a science initiation scholarship (D.B.M. and P.H.S.P.); FAPEMIG (Grant APQ-00077-13 and in part by APQ-01416-16). In memoriam professor Maurilio Alves Moreira.

Compliance with ethical standards

Conflict of interest

On behalf of all authors, the corresponding author declares that there is no conflict of interest.

Supplementary material

122_2018_3061_MOESM1_ESM.docx (19 kb)
Supplementary material 1 (DOCX 19 kb)
122_2018_3061_MOESM2_ESM.pdf (53 kb)
Supplementary material 2 (PDF 52 kb)
122_2018_3061_MOESM3_ESM.pdf (36 kb)
Supplementary material 3 (PDF 36 kb)

References

  1. ABIOVE (2017) Estatística Mensal do Complexo SojaGoogle Scholar
  2. Alt JL, Fehr WR, Welke GA, Shannon JG (2005) Transgressive segregation for oleate content in three soybean populations. Crop Sci 45:2005–2007CrossRefGoogle Scholar
  3. Anai T, Yamada T, Kinoshita T, Rahman SM, Takagi Y (2005) Identification of corresponding genes for three low-α-linolenic acid mutants and elucidation of their contribution to fatty acid biosynthesis in soybean seed. Plant Sci 168:1615–1623CrossRefGoogle Scholar
  4. Andersen CL, Jensen JL, Orntoft TF (2004) Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res 64:5245–5250CrossRefPubMedGoogle Scholar
  5. Artimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, de Castro E, Duvaud S, Flegel V, Fortier A, Gasteiger E, Grosdidier A, Hernandez C, Ioannidis V, Kuznetsov D, Liechti R, Moretti S, Mostaguir K, Redaschi N, Rossier G, Xenarios I, Stockinger H (2012) ExPASy: SIB bioinformatics resource portal. Nucl Acids Res 40:W597–603CrossRefPubMedPubMedCentralGoogle Scholar
  6. Bachleda N, Pham AT, Li Z (2016) Identifying FATB1a deletion that causes reduced palmitic acid content in soybean N87-2122-4 to develop a functional marker for marker-assisted selection. Mol Breed 36(4):45CrossRefGoogle Scholar
  7. Baud S, Lepiniec L (2010) Physiological and developmental regulation of seed oil production. Prog Lipid Res 49:235–249CrossRefPubMedGoogle Scholar
  8. Bilyeu KD, Palavalli L, Sleper DA, Beuselinck PR (2003) Three microsomal omega-3 fatty-acid dessaturase genes contribute to soybean linolenic acid levels. Crop Sci 43:1833–1838CrossRefGoogle Scholar
  9. Bilyeu KD, Palavalli L, Sleper DA, Beuselinck PR (2005) Mutations in soybean microsomal omega-3 fatty acid dessaturase genes reduce linolenic acid concentration in soybean seeds. Crop Sci 45(5):1830–1836CrossRefGoogle Scholar
  10. Bilyeu KD, Palavalli L, Sleper DA, Beuselinck PR (2006) Molecular genetic resources for development of 1% linolenic acid soybeans. Crop Sci 46:1913–1918CrossRefGoogle Scholar
  11. Bilyeu KD, Gillman JD, Leroy AR (2011) Novel FAD3 mutant allele combinations produce soybeans containing 1% linolenic acid in the seed oil. Crop Sci 52:259–264CrossRefGoogle Scholar
  12. Brazil (2017) Lei nº 13.263, de março de 2016Google Scholar
  13. Bruner AC, Jung S, Abbott AG, Powell GL (2001) The naturally occurring high oleate oil character in some peanut varieties results from reduced oleoyl-PC desaturase activity from mutation of aspartate 150 to asparagine. This work was partially supported by grants from the South Carolina Exp. Stn., Clemson Univ., and by a grant from AgraTech Seeds Inc., Ashburn, GA. Crop Sci 41:522–526Google Scholar
  14. Bubeck DM, Fehr WR, Hammond EG (1989) Inheritance of palmitic and stearic acid mutants of soybean. Crop Sci 29:562–656CrossRefGoogle Scholar
  15. Burkey KO, Booker FL, Pursley WA, Heagle AS (2007) Elevated carbon dioxide and ozone effects on peanut: II. Seed Yield and Quality. Crop Sci 47:1488–1497CrossRefGoogle Scholar
  16. Byrum JR, Kinney AJ, Stecca KL, Grace DJ, Diers BW (1997) Alteration of the omega-3 fatty acid desaturase gene is associated with reduced linolenic acid in the A5 soybean genotype. Theor Appl Genet 94:4CrossRefGoogle Scholar
  17. Cardinal A, Burton JW, Camacho-Roger AM, Whetter R, Chappell AS, Bilyeu KD, Auclair J, Dewey RE (2011) Molecular analysis of GmFAD3A in two soybean populations segregating for the fan, fap1, and fapnc loci. Crop Sci 51(5):2104–2112CrossRefGoogle Scholar
  18. Chapell AS, Bilyeu KD (2006) A GmFAD3A mutation in the low linolenic acid soybean line C1640. Plant Breed 125:535–536CrossRefGoogle Scholar
  19. CONAB (2017) Acompanhamento da Safra Brasileira. SAFRA, p 164Google Scholar
  20. Cruz CD (2013) Genes—a software package for analysis in experimental statistics and quantitative genetics. Acta Sci Agron 35:5CrossRefGoogle Scholar
  21. Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15Google Scholar
  22. Dunton HJ, Lancaster CR, Evans CD, Cowan JC (1951) The flavor problem of soybean oil VII. Linolenic acid. J Am Oil Chem 28:115–118CrossRefGoogle Scholar
  23. FDA (2015) Final determination regarding partially hydrogenated oils (removing trans fat)Google Scholar
  24. FDA (2016) Constituent update: FDA takes step to remove artificial trans fats from processed foodsGoogle Scholar
  25. Fehr WR (2007) Breeding for modified fatty acid composition in soybean. Crop Sci 47:72–87CrossRefGoogle Scholar
  26. Fehr WR, Hammond EG (2000) Reduced linolenic acid production in soybeans. U. S. Patent 6,133,509Google Scholar
  27. Flores T, Karpova O, Su X, Zeng P, Bilyeu K, Sleper DA, Nguyen HT, Zhang ZJ (2008) Silencing of GmFAD3 gene by siRNA leads to low alpha-linolenic acids (18:3) of fad3-mutant phenotype in soybean [Glycine max (Merr.)]. Trans Res 17(5):839–850CrossRefGoogle Scholar
  28. Gietz RD, Schiestl RH (2007) High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method. Nat Protoc 2(1):31CrossRefPubMedGoogle Scholar
  29. Goettel W, Xia E, Upchurch R, Wang ML, Chen P, An YQ (2014) Identification and characterization of transcript polymorphisms in soybean lines varying in oil composition and content. BMC Genom 15:299CrossRefGoogle Scholar
  30. Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar DS (2012) Phytozome: a comparative platform for green plant genomics. Nucl Acids Res Database Issue 40:D1178–1186CrossRefGoogle Scholar
  31. Hammond EG, Fehr WR (1983) Registration of A5 germplasm line of soybean (Reg. No. GP44). Crop Sci 23:192–193Google Scholar
  32. Hellemans J, Mortier G, De Paepe A, Speleman F, Vandesompele J (2007) qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol 8:R19CrossRefPubMedPubMedCentralGoogle Scholar
  33. Hu FB, Stampfer MJ, Manson JE, Rimm E, Colditz GA, Rosner BA, Hennekens CH, Willett WC (1997) Dietary fat intake and the risk of coronary heart disease in women. N Engl J Med 337:1491–1499CrossRefPubMedGoogle Scholar
  34. Hu R, Fan C, Li H, Zhang Q, Fu YF (2009) Evaluation of putative reference genes for gene expression normalization in soybean by quantitative real-time RT-PCR. BMC Mol Biol 10:93CrossRefPubMedPubMedCentralGoogle Scholar
  35. Le DT, Aldrich DL, Valliyodan B, Watanabe Y, Ha CV, Nishiyama R, Guttikonda SK, Quach TN, Gutierrez-Gonzalez JJ, Tran LS, Nguyen HT (2012) Evaluation of candidate reference genes for normalization of quantitative RT-PCR in soybean tissues under various abiotic stress conditions. PLoS ONE 7:e46487CrossRefPubMedPubMedCentralGoogle Scholar
  36. Leffel RC (1994a) Registration of BARC-12 a low linolenic acid soybean germplasm line. Crop Sci 34:1426–1427CrossRefGoogle Scholar
  37. Leffel RC (1994b) Registration of BARC-12 a low linolenic acid soybean germplasm line. Crop Sci 34:1426–1427CrossRefGoogle Scholar
  38. Li L, Wang X, Gai J, Yu D (2007) Molecular cloning and characterization of a novel microsomal oleate desaturase gene from soybean. J Plant Physiol 164:1516–1526CrossRefPubMedGoogle Scholar
  39. Li Q, Fan CM, Zhang XM, Fu YF (2012) Validation of reference genes for real-time quantitative PCR normalization in soybean developmental and germinating seeds. Plant Cell Rep 31:1789–1798CrossRefPubMedGoogle Scholar
  40. Libault M, Thibivilliers S, Bilgin DD, Radwan O, Benitez M, Clough SJ, Stacey G (2008) Identification of four soybean reference genes for gene expression normalization. Plant Genome 1:44–54CrossRefGoogle Scholar
  41. Lozinsky S, Yang H, Forseille L, Cook GR, Ramirez-Erosa I, Smith MA (2014) Characterization of an oleate 12-desaturase from Physaria fendleri and identification of 5′UTR introns in divergent FAD2 family genes. Plant Physiol Biochem 75:114–122CrossRefPubMedGoogle Scholar
  42. Miranda Vde J, Coelho RR, Viana AA, de Oliveira Neto OB, Carneiro RM, Rocha TL, de Sa MF, Fragoso RR (2013) Validation of reference genes aiming accurate normalization of qPCR data in soybean upon nematode parasitism and insect attack. BMC Res Notes 6:196CrossRefPubMedGoogle Scholar
  43. Mozaffarian D, Katan MB, Ascherio A, Stampfer MJ, Willett WC (2006) Trans fatty acids and cardiovascular disease. N Engl J Med 354:1601–1613CrossRefPubMedGoogle Scholar
  44. Pfaffl MW, Tichopad A, Prgomet C, Neuvians TP (2004) Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper–Excel-based tool using pair-wise correlations. Biotechnol Lett 26:509–515CrossRefPubMedGoogle Scholar
  45. Pham AT, Lee JD, Shannon JG, Bilyeu KD (2010) Mutant alleles of FAD2-1A and FAD2-1B combine to produce soybeans with the high oleic acid seed oil trait. BMC Plant Biol 10:195CrossRefPubMedPubMedCentralGoogle Scholar
  46. Pham AT, Lee JD, Shannon JG, Bilyeu KD (2011) A novel FAD2-1 A allele in a soybean plant introduction offers an alternate means to produce soybean seed oil with 85% oleic acid content. Theor Appl Genet 123:793–802CrossRefPubMedGoogle Scholar
  47. Pham AT, Shannon JG, Bilyeu KD (2012) Combinations of mutant FAD2 and FAD3 genes to produce high oleic acid and low linolenic acid soybean oil. Theor Appl Genet 125:503–515CrossRefPubMedGoogle Scholar
  48. Pham AT, Bilyeu KD, Chen P, Boerma HR, 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 33:895–907CrossRefGoogle Scholar
  49. Pinto MO, Good-God PIV, Moreira MA, Barros EG (2013) Association of SNP markers with the linolenic acid content in soybean seeds. Pesqui Agropecu Bras 48:263–269CrossRefGoogle Scholar
  50. Rahman SM, Takagi Y, Kinoshita T (1996) Genetic control of high oleic acid content in the seed oil of two soybean mutants. Crop Sci 36:1125–1128CrossRefGoogle Scholar
  51. Reinprecht Y, Pauls KP (2016) Microsomal omega-3 fatty acid desaturase genes in low linolenic acid soybean line RG10 and validation of major linolenic acid QTL. Front Genet 7:38CrossRefPubMedPubMedCentralGoogle Scholar
  52. Reinprecht Y, Luk-Labey SY, Larsen J, Poysa VW, Yu K, Rajcan I, Ablett GR, Pauls KP (2009) Molecular basis of the low linolenic acid trait in soybean EMS mutant line RG10. Plant Breed 128:253–258CrossRefGoogle Scholar
  53. Ross AJ, Fehr WR, Welke GA, Hammond EG, Cianzio SR (2000) Agronomic and seed traits of 1%—linolenate soybean genotypes. Crop Sci 40:383–386CrossRefGoogle Scholar
  54. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:365–386PubMedGoogle Scholar
  55. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–183CrossRefPubMedGoogle Scholar
  56. Shanklin J, Whittle E, Fox BG (1994) Eight histidine residues are catalytically essential in a membrane-associated iron enzyme, stearoyl-CoA desaturase, and are conserved in alkane hydroxylase and xylene monooxygenase. Biochemistry 33:12787–12794CrossRefPubMedGoogle Scholar
  57. Shi Z, Bachleda N, Pham AT, Bilyeu KD, Shannon G, Nguyen H, Li Z (2015) High-throughput and functional SNP detection assays for oleic and linolenic acids in soybean. Mol Breed 35:176CrossRefGoogle Scholar
  58. Stojsin D, LuzziI BM, Ablett GR, Tanner JW (1998) Inheritance of low linolenic acid level in the soybean line RG10. Crop Sci 38:1441–1444CrossRefGoogle Scholar
  59. Sun R, Gao L, Yu X, Zheng Y, Li D, Wang X (2016) Identification of a Delta12 fatty acid desaturase from oil palm (Elaeis guineensis Jacq.) involved in the biosynthesis of linoleic acid by heterologous expression in Saccharomyces cerevisiae. Gene 591:21–26CrossRefPubMedGoogle Scholar
  60. Thompson JD, Gibson TJ, Higgins DG (2002) Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinform. Chapter 2: Unit 2–3Google Scholar
  61. USDA (2017a) Foreign agricultural service: table 03: major vegetable oils: world supply and distribution (commodity view)Google Scholar
  62. USDA (2017b) Foreign agricultural service: world agricultural productionGoogle Scholar
  63. van de Mortel M, Recknor JC, Graham MA, Nettleton D, Dittman JD, Nelson RT, Godoy CV, Abdelnoor RV, Almeida AM, Baum TJ, Whitham SA (2007) Distinct biphasic mRNA changes in response to Asian soybean rust infection. Mol Plant Microbe Interact 20:887–899CrossRefPubMedGoogle Scholar
  64. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3:RESEARCH0034CrossRefPubMedPubMedCentralGoogle Scholar
  65. Waltz E (2010) Food firms test fry Pioneer’s trans fat-free soybean oil. Nat Biotechnol 28:769–770CrossRefPubMedGoogle Scholar
  66. Warner K, Fehr W (2008) Mid-oleic/ultra low linolenic acid soybean oil: a healthful new alternative to hydrogenated oil for frying. J Am Oil Chem Soc 95:945–951CrossRefGoogle Scholar
  67. White HB, Quakenbush FW, Probst AH (1961) Occurrence and inheritance of linolenic and linoleic acids in soybean seeds. J Am Oil Chem 38:113–117CrossRefGoogle Scholar
  68. Wilcox JR, Cavins JF, Nielsen NC (1984) Genetic alteration of soybean oil compositon by a chemical mutagen. J Am Oil Chem 61:97–100CrossRefGoogle Scholar
  69. Wilson RF, Burton JW, Brim CA (1981) Progress in the selection for altered fatty acid composition in soybeans. Crop Sci 21:788–791CrossRefGoogle Scholar
  70. Yadav NS (1996) Soybean genetics, molecular biology and biotechnology. Biotechnology in Agriculture Series. CAB InternationalGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Luiz Claudio Costa Silva
    • 1
  • Rafael Delmond Bueno
    • 1
  • Loreta Buuda da Matta
    • 2
  • Pedro Henrique Scarpelli Pereira
    • 3
  • Danyelle Barbosa Mayrink
    • 1
  • Newton Deniz Piovesan
    • 1
  • Carlos Sigueyuki Sediyama
    • 4
  • Elizabeth Pacheco Batista Fontes
    • 5
  • Andrea J. Cardinal
    • 6
    • 7
  • Maximiller Dal-Bianco
    • 8
  1. 1.Laboratório de Bioquímica Genética de Plantas, 212, BIOAGROUniversidade Federal de ViçosaViçosaBrazil
  2. 2.Seeds Bayer Crop ScienceRio VerdeBrazil
  3. 3.Laboratório de Biologia Celular e Molecular de PlasmódioUniversidade de São PauloSão PauloBrazil
  4. 4.Departamento de Fitotecnia, sala 205Universidade Federal de ViçosaViçosaBrazil
  5. 5.Laboratório de Biologia Molecular de Plantas, Sala 214, BIOAGROUniversidade Federal de ViçosaViçosaBrazil
  6. 6.Crop Science DepartmentNorth Carollina State UniversityRaleighUSA
  7. 7.Syngenta Biotechnology, IncResearch Triangle ParkUSA
  8. 8.Laboratório de Bioquímica Genética de Plantas, 212, BIOAGRO and Departamento de Bioquímica e Biologia MolecularUniversidade Federal de ViçosaViçosaBrazil

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