TILLING-by-Sequencing Reveals the Role of Novel Fatty Acid Desaturases (GmFAD2-2s) in Increasing Soybean Seed Oleic Acid Content

Overview

Journal Cells

Publisher MDPI

Specialties Biochemistry
Biophysics
Cell Biology
Molecular Biology

Date 2021 Jun 2

PMID 34069320

Citations 11

Authors

Naoufal Lakhssassi

Valeria Stefania Lopes-Caitar

Dounya Knizia

Mallory A Cullen

Oussama Badad

Abdelhalim El Baze

Zhou Zhou

Mohamed G Embaby

Jonas Meksem

Aicha Lakhssassi

Pengyin Chen

Amer AbuGhazaleh

Tri D Vuong

Henry T Nguyen

Tarek Hewezi

Khalid Meksem

Affiliations

Soon will be listed here.

Abstract

Soybean is the second largest source of oil worldwide. Developing soybean varieties with high levels of oleic acid is a primary goal of the soybean breeders and industry. Edible oils containing high level of oleic acid and low level of linoleic acid are considered with higher oxidative stability and can be used as a natural antioxidant in food stability. All developed high oleic acid soybeans carry two alleles; and . However, when planted in cold soil, a possible reduction in seed germination was reported when high seed oleic acid derived from alleles were used. Besides the soybean fatty acid desaturase () subfamily, the subfamily is composed of five members, including , , , , and . Segmental duplication of /, , , and have occurred about 10.65, 27.04, 100.81, and 106.55 Mya, respectively. Using TILLING-by-Sequencing+ technology, we successfully identified 12, 8, 10, 9, and 19 EMS mutants at the , , , , and genes, respectively. Functional analyses of newly identified mutants revealed unprecedented role of the five , , , , and members in controlling the seed oleic acid content. Most importantly, unlike members, subcellular localization revealed that members of the subfamily showed a cytoplasmic localization, which may suggest the presence of an alternative fatty acid desaturase pathway in soybean for converting oleic acid content without substantially altering the traditional plastidial/ER fatty acid production.

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References

Lakhssassi N, Zhou Z, Cullen M, Badad O, El Baze A, Chetto O . TILLING-by-Sequencing to Decipher Oil Biosynthesis Pathway in Soybeans: A New and Effective Platform for High-Throughput Gene Functional Analysis. Int J Mol Sci. 2021; 22(8). PMC: 8073088. DOI: 10.3390/ijms22084219. View

Li W, Gojobori T, Nei M . Pseudogenes as a paradigm of neutral evolution. Nature. 1981; 292(5820):237-9. DOI: 10.1038/292237a0. View

Buhr T, Sato S, Ebrahim F, Xing A, Zhou Y, Mathiesen M . Ribozyme termination of RNA transcripts down-regulate seed fatty acid genes in transgenic soybean. Plant J. 2002; 30(2):155-63. DOI: 10.1046/j.1365-313x.2002.01283.x. View

Robinson J, Thorvaldsdottir H, Winckler W, Guttman M, Lander E, Getz G . Integrative genomics viewer. Nat Biotechnol. 2011; 29(1):24-6. PMC: 3346182. DOI: 10.1038/nbt.1754. View

Javelle M, Vernoud V, Depege-Fargeix N, Arnould C, Oursel D, Domergue F . Overexpression of the epidermis-specific homeodomain-leucine zipper IV transcription factor Outer Cell Layer1 in maize identifies target genes involved in lipid metabolism and cuticle biosynthesis. Plant Physiol. 2010; 154(1):273-86. PMC: 2938141. DOI: 10.1104/pp.109.150540. View

Anders S, Pyl P, Huber W . HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics. 2014; 31(2):166-9. PMC: 4287950. DOI: 10.1093/bioinformatics/btu638. View

Liu J, Chen N, Grant J, Cheng Z, Stewart Jr C, Hewezi T . Soybean kinome: functional classification and gene expression patterns. J Exp Bot. 2015; 66(7):1919-34. PMC: 4378628. DOI: 10.1093/jxb/eru537. View

Pham A, Shannon J, Bilyeu K . Combinations of mutant FAD2 and FAD3 genes to produce high oleic acid and low linolenic acid soybean oil. Theor Appl Genet. 2012; 125(3):503-15. DOI: 10.1007/s00122-012-1849-z. View

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

10.

Dyer J, Mullen R . Immunocytological localization of two plant fatty acid desaturases in the endoplasmic reticulum. FEBS Lett. 2001; 494(1-2):44-7. DOI: 10.1016/s0014-5793(01)02315-8. View

11.

Cooper J, Till B, Laport R, Darlow M, Kleffner J, Jamai A . TILLING to detect induced mutations in soybean. BMC Plant Biol. 2008; 8:9. PMC: 2266751. DOI: 10.1186/1471-2229-8-9. View

12.

Pham A, Lee J, Shannon J, Bilyeu K . Mutant alleles of FAD2-1A and FAD2-1B combine to produce soybeans with the high oleic acid seed oil trait. BMC Plant Biol. 2010; 10:195. PMC: 2956544. DOI: 10.1186/1471-2229-10-195. View

13.

Clark K, Makrides M, Neumann M, Gibson R . Determination of the optimal ratio of linoleic acid to alpha-linolenic acid in infant formulas. J Pediatr. 1992; 120(4 Pt 2):S151-8. DOI: 10.1016/s0022-3476(05)81250-8. View

14.

Juretic N, Hoen D, Huynh M, Harrison P, Bureau T . The evolutionary fate of MULE-mediated duplications of host gene fragments in rice. Genome Res. 2005; 15(9):1292-7. PMC: 1199544. DOI: 10.1101/gr.4064205. View

15.

Kelley L, Mezulis S, Yates C, Wass M, Sternberg M . The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc. 2015; 10(6):845-58. PMC: 5298202. DOI: 10.1038/nprot.2015.053. View

16.

Pettersen E, Goddard T, Huang C, Couch G, Greenblatt D, Meng E . UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004; 25(13):1605-12. DOI: 10.1002/jcc.20084. View

17.

Schmutz J, Cannon S, Schlueter J, Ma J, Mitros T, Nelson W . Genome sequence of the palaeopolyploid soybean. Nature. 2010; 463(7278):178-83. DOI: 10.1038/nature08670. View

18.

Alfonso M . Improving soybean seed oil without poor agronomics. J Exp Bot. 2020; 71(22):6857-6860. PMC: 7906773. DOI: 10.1093/jxb/eraa407. View

19.

Roman A, Andreu V, Hernandez M, Lagunas B, Picorel R, Martinez-Rivas J . Contribution of the different omega-3 fatty acid desaturase genes to the cold response in soybean. J Exp Bot. 2012; 63(13):4973-82. PMC: 3427996. DOI: 10.1093/jxb/ers174. View

20.

Marchler-Bauer A, Derbyshire M, Gonzales N, Lu S, Chitsaz F, Geer L . CDD: NCBI's conserved domain database. Nucleic Acids Res. 2014; 43(Database issue):D222-6. PMC: 4383992. DOI: 10.1093/nar/gku1221. View