The FAD2 Gene Family of Soybean: Insights into the Structural and Functional Divergence of a Paleopolyploid Genome

Schlueter, Jessica A.; Vasylenko-Sanders, Iryna F; Deshpande, Shweta; Yi, Jing; Siegfried, Majesta; Roe, Bruce A.; Schlueter, Shannon D.; Scheffler, Brian E.; Shoemaker, Randy C.

doi:10.2135/cropsci2006.06.0382tpg

Cited by 122 publications

(124 citation statements)

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“…According to the reference soybean genome sequence, 20 annotated genes are predicted within the chromosome 10 deletion (Supplemental Table S2), including FAD2-1A (Glyma10g42470). No CNV was detected in the other characterized soybean v-6 fatty acid desaturase genes FAD2-1B, FAD2-2A, FAD2-B, and FAD2-C (Schlueter et al, 2007;Pham et al, 2010; data not shown).…”

Section: Fn Mutants With Visual Phenotypesmentioning

confidence: 87%

Phenotypic and Genomic Analyses of a Fast Neutron Mutant Population Resource in Soybean

et al. 2011

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Mutagenized populations have become indispensable resources for introducing variation and studying gene function in plant genomics research. In this study, fast neutron (FN) radiation was used to induce deletion mutations in the soybean (Glycine max) genome. Approximately 120,000 soybean seeds were exposed to FN radiation doses of up to 32 Gray units to develop over 23,000 independent M2 lines. Here, we demonstrate the utility of this population for phenotypic screening and associated genomic characterization of striking and agronomically important traits. Plant variation was cataloged for seed composition, maturity, morphology, pigmentation, and nodulation traits. Mutants that showed significant increases or decreases in seed protein and oil content across multiple generations and environments were identified. The application of comparative genomic hybridization (CGH) to lesion-induced mutants for deletion mapping was validated on a midoleate x-ray mutant, M23, with a known FAD2-1A (for fatty acid desaturase) gene deletion. Using CGH, a subset of mutants was characterized, revealing deletion regions and candidate genes associated with phenotypes of interest. Exome resequencing and sequencing of PCR products confirmed FN-induced deletions detected by CGH. Beyond characterization of soybean FN mutants, this study demonstrates the utility of CGH, exome sequence capture, and next-generation sequencing approaches for analyses of mutant plant genomes. We present this FN mutant soybean population as a valuable public resource for future genetic screens and functional genomics research.

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Section: Fn Mutants With Visual Phenotypesmentioning

confidence: 87%

Phenotypic and Genomic Analyses of a Fast Neutron Mutant Population Resource in Soybean

et al. 2011

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“…Fad2a ’s highest allelic diversity of 21 alleles contrasted with the conservation of fad2b with only 5. The fad2b gene plays a major role in producing LIO and remains a housekeeping microsomal Δ12 oleate desaturase with constitutive expression throughout the plant (Cao et al 2013; Schlueter et al 2007). In soybean, fad2 - 2 , the ortholog of fad2b , was shown to be the most important gene for increasing LIO content (Schlueter et al 2007).…”

Section: Discussionmentioning

confidence: 99%

“…The fad2b gene plays a major role in producing LIO and remains a housekeeping microsomal Δ12 oleate desaturase with constitutive expression throughout the plant (Cao et al 2013; Schlueter et al 2007). In soybean, fad2 - 2 , the ortholog of fad2b , was shown to be the most important gene for increasing LIO content (Schlueter et al 2007). Site-directed mutagenesis of fad2 , altering a few amino acid residues, modified the enzymatic activity of the encoded FAD2 in Lesquerella fendleri and Synechocystis sp.…”

Section: Discussionmentioning

confidence: 99%

Genetic variation of six desaturase genes in flax and their impact on fatty acid composition

et al. 2013

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Flax (Linum usitatissimum L.) is one of the richest plant sources of omega-3 fatty acids praised for their health benefits. In this study, the extent of the genetic variability of genes encoding stearoyl-ACP desaturase (SAD), and fatty acid desaturase 2 (FAD2) and 3 (FAD3) was determined by sequencing the six paralogous genes from 120 flax accessions representing a broad range of germplasm including some EMS mutant lines. A total of 6 alleles for sad1 and sad2, 21 for fad2a, 5 for fad2b, 15 for fad3a and 18 for fad3b were identified. Deduced amino acid sequences of the alleles predicted 4, 2, 3, 4, 6 and 7 isoforms, respectively. Allele frequencies varied greatly across genes. Fad3a, with 110 SNPs and 19 indels, and fad3b, with 50 SNPs and 5 indels, showed the highest levels of genetic variations. While most of the SNPs and all the indels were silent mutations, both genes carried nonsense SNP mutations resulting in premature stop codons, a feature not observed in sad and fad2 genes. Some alleles and isoforms discovered in induced mutant lines were absent in the natural germplasm. Correlation of these genotypic data with fatty acid composition data of 120 flax accessions phenotyped in six field experiments revealed statistically significant effects of some of the SAD and FAD isoforms on fatty acid composition, oil content and iodine value. The novel allelic variants and isoforms identified for the six desaturases will be a resource for the development of oilseed flax with unique and useful fatty acid profiles.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-013-2161-2) contains supplementary material, which is available to authorized users.

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“…Characterization of the expression of the individual soybean FAD2 genes confirmed the importance of FAD2-1A and FAD2-1B with expression of these genes during peak oil synthesis; a possible role was also revealed for FAD2-2C under cool temperature conditions [5]. Differential response to temperature was also demonstrated for the soybean FAD2-1A and FAD2-1B enzymes expressed in yeast [7].…”

Section: Introductionmentioning

confidence: 96%

“…While in Arabidopsis and maize only one single copy of a FAD2 gene was identified [4,6], soybean appears to possess multiple copies of the gene due to the consequence of repeated rounds of genome duplication followed by limited sequence loss [5]. The soybean FAD2 gene family has been previously characterized at the genome level for structure and expression [5].…”

Section: Introductionmentioning

confidence: 99%

Mutant alleles of FAD2-1A and FAD2-1Bcombine to produce soybeans with the high oleic acid seed oil trait

et al. 2010

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BackgroundThe alteration of fatty acid profiles in soybean [Glycine max (L.) Merr.] to improve soybean oil quality is an important and evolving theme in soybean research to meet nutritional needs and industrial criteria in the modern market. Soybean oil with elevated oleic acid is desirable because this monounsaturated fatty acid improves the nutrition and oxidative stability of the oil. Commodity soybean oil typically contains 20% oleic acid and the target for high oleic acid soybean oil is approximately 80% of the oil; previous conventional plant breeding research to raise the oleic acid level to just 50-60% of the oil was hindered by the genetic complexity and environmental instability of the trait. The objective of this work was to create the high oleic acid trait in soybeans by identifying and combining mutations in two delta-twelve fatty acid desaturase genes, FAD2-1A and FAD2-1B.ResultsThree polymorphisms found in the FAD2-1B alleles of two soybean lines resulted in missense mutations. For each of the two soybean lines, there was one unique amino acid change within a highly conserved region of the protein. The mutant FAD2-1B alleles were associated with an increase in oleic acid levels, although the FAD2-1B mutant alleles alone were not capable of producing a high oleic acid phenotype. When existing FAD2-1A mutations were combined with the novel mutant FAD2-1B alleles, a high oleic acid phenotype was recovered only for those lines which were homozygous for both of the mutant alleles.ConclusionsWe were able to produce conventional soybean lines with 80% oleic acid in the oil in two different ways, each requiring the contribution of only two genes. The high oleic acid soybean germplasm developed contained a desirable fatty acid profile, and it was stable in two production environments. The presumed causative sequence polymorphisms in the FAD2-1B alleles were developed into highly efficient molecular markers for tracking the mutant alleles. The resources described here for the creation of high oleic acid soybeans provide a framework to efficiently develop soybean varieties to meet changing market demands.

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The FAD2 Gene Family of Soybean: Insights into the Structural and Functional Divergence of a Paleopolyploid Genome

Cited by 122 publications

References 62 publications

Phenotypic and Genomic Analyses of a Fast Neutron Mutant Population Resource in Soybean

Phenotypic and Genomic Analyses of a Fast Neutron Mutant Population Resource in Soybean

Genetic variation of six desaturase genes in flax and their impact on fatty acid composition

Mutant alleles of FAD2-1A and FAD2-1Bcombine to produce soybeans with the high oleic acid seed oil trait

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