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Article

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

by
Naoufal Lakhssassi
1,
Valéria Stefania Lopes-Caitar
2,†,
Dounya Knizia
1,†,
Mallory A. Cullen
1,†,
Oussama Badad
1,
Abdelhalim El Baze
1,
Zhou Zhou
1,
Mohamed G. Embaby
3,
Jonas Meksem
4,
Aicha Lakhssassi
5,
Pengyin Chen
6,
Amer AbuGhazaleh
3,
Tri D. Vuong
6,
Henry T. Nguyen
6,
Tarek Hewezi
2 and
Khalid Meksem
1,*
1
Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA
2
Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
3
Department of Animal Science, Food, and Nutrition, Southern Illinois University, Carbondale, IL 62901, USA
4
Trinity College of Arts and Sciences, Duke University, Durham, NC 27708, USA
5
Faculty of Sciences and Technologies, University of Lorraine, 54506 Nancy, France
6
Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to the work.
Cells 2021, 10(5), 1245; https://0-doi-org.brum.beds.ac.uk/10.3390/cells10051245
Submission received: 26 April 2021 / Revised: 15 May 2021 / Accepted: 16 May 2021 / Published: 19 May 2021
(This article belongs to the Section Cellular Metabolism)
Browse Figures
Versions Notes

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; GmFAD2-1A and GmFAD2-1B. However, when planted in cold soil, a possible reduction in seed germination was reported when high seed oleic acid derived from GmFAD2-1 alleles were used. Besides the soybean fatty acid desaturase (GmFAD2-1) subfamily, the GmFAD2-2 subfamily is composed of five members, including GmFAD2-2A, GmFAD2-2B, GmFAD2-2C, GmFAD2-2D, and GmFAD2-2E. Segmental duplication of GmFAD2-1A/GmFAD2-1B, GmFAD2-2A/GmFAD2-2C, GmFAD2-2A/GmFAD2-2D, and GmFAD2-2D/GmFAD2-2C 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 GmFAD2-2A, GmFAD2-2B, GmFAD2-2C, GmFAD2-2D, and GmFAD2-2E genes, respectively. Functional analyses of newly identified mutants revealed unprecedented role of the five GmFAD2-2A, GmFAD2-2B, GmFAD2-2C, GmFAD2-2D, and GmFAD2-2E members in controlling the seed oleic acid content. Most importantly, unlike GmFAD2-1 members, subcellular localization revealed that members of the GmFAD2-2 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.

1. Introduction

Soybean oil is the one of the most consumed vegetable oils worldwide. Soybean oil’s utilization is determined by its fatty acid composition. Usually, the content of oleic acid (18:1, ω-9) in soybean oil is about 18–20% [1]. Consumption of oil with high oleic acid content is desirable because this monounsaturated fatty acid improves shelf life and reduces the need for hydrogenation [2]. Additionally, oil high in oleic acid and low in saturated fatty acids are desired by the biodiesel industry, in order to improve the oxidative stability while increasing cold flow [3].
In plants, mutations can be artificially induced by mutagenic agents and their utilization for production of new superior varieties of species from the traditional variety [4]. Genetic modification of the fatty acid composition of soybean oil is an important goal to improving soybean breeding for better oil traits [5,6,7,8]. While traditional breeding may take several years to achieve traits of interest, mutation breeding is the most useful and vital technology for soybean production. Selection of effective and efficient mutagens is very essential for recovering a high frequency of desirable mutants [9].
Mutations within the GmFAD2-1A and GmFAD2-1B genes encoding fatty acid desaturases (omega-6 FAD; EC 1.3.1.35) in soybeans was used to produce high oleic acid soybean germplasm [8,10]. However, it has been reported that high seed oleic acid derived from GmFAD2-1 may have a possible reduction in seed germination when planted in cold soil [5,11,12,13]. The soybean community and industry are making tremendous efforts to determine the optimum allele combinations to produce environmentally stable high oleic/low linolenic acid soybean varieties for US soybean production environments (USB# 1720-162-0109). Therefore, looking for new alternatives to increase soybean seed oleic acid content while maintaining good yield is considered as high priority for the soybean industry. The fatty acid desaturase-2 enzyme (FAD2) is responsible for the conversion of oleic acid to linoleic acid in the developing soybean seeds by introducing a double bond at the Δ12 position of oleic acid [14,15,16]. This mono-unsaturated fatty acid contains only one double bond in its carbon chain. The high polyunsaturated fatty acid content in soybean oil exhibits low oxidative stability and must be hydrogenated for many applications, but such process introduces trans fats that cause a number of health problems in humans [17]. Elevated oleic acid content in soybean oil improves oxidative stability and shelf life to avoid hydrogenation and is considered healthier for human consumption [2]. 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 [18,19,20,21]. The traditional GmFAD2-1A and GmFAD2-B genes were well characterized for their role in unsaturated fatty acid biosynthesis. However, members of the GmFAD2-2 subfamily reported earlier [8] were not characterized yet. Initially, the expression of the two microsomal GmFAD2-1 desaturases has been mainly detected in developing soybean seeds, therefore, GmFAD2-1A and GmFAD2-1B were regarded as the best candidate genes to develop soybean lines with elevated oleic acid content [22]. However, members of the other GmFAD2-2 gene subfamily were poorly characterized for their role in the fatty acid pathway. The GmFAD2-2 gene family in soybean is composed of five members including GmFAD2-2A (Glyma.19G147300), GmFAD2-2B (Glyma.19G147400), and GmFAD2-2C (Glyma.03G144500), GmFAD2-2D (Glyma.09G111900) and GmFAD2-2E (Glyma.15G195200) [8]. Using CRISPR/Cas9, it has been shown recently that GmFAD2-1A and GmFAD2-2A mutants accumulate high levels of soybean seed oleic acid [23,24].
Conventional breeding and genetic engineering have been widely applied to produce soybeans with oleic acid content > 80% of the total oil. Although downregulation of GmFAD2-1 genes can achieve the elevated levels of oleate through ribozyme-terminated antisense, restrictive regulations from foreign destinations hindered the potentials in exportation of these transgenic soybean [25]. Identification of mutations in GmFAD2-1 genes via reverse genetic approaches appears to be a sustainable strategy to develop non-transgenic soybean with high oleic acid content [8,10]. Several soybean lines with more than 80% seed oleic acid content have been produced through combining GmFAD2-1A and GmFAD2-1B alleles (soybean diversity) [5,26,27]. Additionally, using targeted mutagenesis with transcription activator-like effector nucleases (TALENs) in GmFAD2-1 genes, nontransgenic high oleic acid content (80%) can be obtained [28].
The use of silencing and/or CRISPR techniques is another strategy that could be used to produce high oleic acid soybean lines [23,24]. However, although it has been accepted in the U.S. as nontransgenic approach, there is still a worldwide debate about the technology and concerns of the vectors used and transgenesis approach to produce and study the desired traits. Therefore, the characterization and availability of TILLING (Targeting Induced Local Lesions IN Genomes) mutants within the GmFAD2-2 gene family members will not only elucidate and attribute a new function of these genes but will definitely speed up the use of these genes in breeding process.
Ethyl-methanesulfonate (EMS) mutagenesis alkylates DNA and can cause significant changes to the DNA bases of genes underlying agronomic traits such us oil biosynthesis. Producing EMS mutants with a single base pair mutation has shown to be a better strategy for developing lines with agronomically important traits without unintended poor agronomic characteristics [29,30]. Using EMS mutagenesis effects on DNA, significant changes to the genes and gene network underlying the oil profile in soybean can be achieved [7,8,10]. These changes are difficult to achieve using standard breeding techniques. In the current study, we developed a population of soybean EMS mutagenized lines and used TILLING by sequencing+ [29,30], to functionally characterize the five members of the GmFAD2-2 subfamily in soybean.

2. Material and Methods

2.1. Development of an EMS Mutagenized Forrest Population

Forrest is a soybean cultivar that belongs to the Maturity Group V with resistance to several soybean pathogens including Soybean Cyst Nematode (SCN), Sudden Death Syndrome (SDS), and Reniform nematode, reasons why it was used originally as background to develop the EMS mutants. As it is a cultivar, Forrest could be easily used for breeding purposes to introgress the high oleic acid content trait into high-yielding lines without compromising their agronomic performance while transferring its package of resistance.
The soybean cv. “Forrest” seed was used to develop an EMS mutagenized population (at 0.6% EMS) as shown earlier [29], and planted to harvest 4032 M2 families and then advanced to the M3 generation at the Horticulture Research Center at Southern Illinois University Carbondale, IL, USA. DNA from all 4032 M2 families has been used in the TILLING-by-sequencing+ platform to make the corresponding DNA pools.

2.2. FAD2 Sequences and Phylogenetic Analysis

GmFAD2 sequences used in the phylogenetic analyses were retrieved from different databases including UniProt, NCBI, Soybase (W82.a2.v1), and Phytozome (v12.1). Sequences were identified by querying sequences from the seven members belonging to the two GmFAD2 subfamilies against sequences from these databases using tblastn default parameters. Sequences from monocots, eudictos, and basal angiosperm with 90% identity/similarity and above were selected, in addition to other GmFAD2 homologs from plant primitive species including, algae, moss, and a lycophyte. The retrieved GmFAD2 sequences belong to sets of plants (48 in total) with fully sequenced genomes representing key positions in the angiosperm phylogenetic tree. Sequences were carefully inspected and corrected for annotation errors before use. Multiple sequence alignments of the retrieved GmFAD2s were performed using the MEGA4 software package [31] and the ClustalW sequence alignment tools. An unrooted phylogenetic tree was calculated with the neighbor-joining method [32]. Next, tree topology robustness was tested through bootstrap analysis of 1000 replicates.

2.3. Chromosomal Distribution and Synteny Analysis

The locations of the two fatty acid desaturase GmFAD2-1 members and the five GmFAD2-2 members in soybean and their corresponding chromosomes were obtained from the soybean genome annotation a2.v1 assembly (Williams 82 reference genome) available on the soybean database (SoyBase.org). Nonsynonymous (Ka) versus synonymous substitution (Ks) rates were calculated based on their values retrieved from the Plant Genome Duplication Database (PGDD). Based on the Ks values and the rate of 6.1 × 10−9 substitutions/site/year, the divergence time (T) was estimated using the following formula: Ks/(2 × 6.1 × 10−9) × 10−6 Mya [33].

2.4. Library Preparation, Probe Design and TILLING-by-Sequencing+

Genomic DNA samples from 42 “96-well plates” were pooled using a bidimensional scheme as shown recently [29]. Forty-four probes were constructed to amplify the whole gene region of GmFAD2-1A with up to 99.6% coverage, 77 probes were constructed to amplify the whole gene region of GmFAD2-1B with up to 98.4% coverage, 18 probes were constructed to amplify the whole gene region of GmFAD2-2A with up to 99.7% coverage, 58 probes were constructed to amplify the whole gene region of GmFAD2-2B with up to 98.8% coverage, 47 probes were constructed to amplify the whole gene region of GmFAD2-2C with up to 99.8% coverage, 37 probes were constructed to amplify the whole gene region of GmFAD2-2D with up to 98.9% coverage, and the GmFAD2-2E gene was covered by 20 probes with up to 99.8% coverage (Table S1). Probe synthesis, DNA library preparation, capture enrichment (using magnetic beads), and next generation sequencing (Illumina HiSeqX 2 × 150 bp) were carried out by Rapid Genomics LLC. (Gainesville, FL, USA) as described recently [30].

2.5. Variant Calling for Mutation Detection

The FASTQ raw reads were subjected to quality control using FastQC v0.11.9, trimming, and filtering of low-quality reads was performed using Trimmomatic V0.39 [34]. BWA v0.7.17 [35] was used to map clean reads to the Williams 82 reference genome. SAM tools v1.10 [36] were used to filter and sort the bam files to serve as an input for variant calling using Freebayes v1.0.0 [37] and CRISP v1.18.0 [38] The VCF files were filtered by VCF tools v0.1.16 [39] and visualized in IGV v 2.9.2 [40].

2.6. Mutation Density Evaluation

The mutation density is estimated using the formula as the total number of mutations divided by the total number of base pairs (amplicon size × individuals screened) as described earlier [41].

2.7. Analysis of Seed Fatty Acids

For EMS mutant lines, a five-seed sample taken from each M3 mutant line was placed in an envelope and manually crushed with a hammer. Fatty acid extraction procedure was carried out as previously described [42]. Five major fatty acid contents were measured from selected according to the two-step methylation procedure as described earlier [43].

2.8. Confirmation of the Mutants by SANGER Sequencing

The specific primers (Table S2) were designed to amplify the 7 fatty acid desaturases using the extracted DNAs as the templates with 38 cycles of PCR amplification at 94 °C for 30 s, 51 °C for 30 s, and 72 °C for 1 min. The PCR products were purified as shown earlier [8]. The purified PCR fragments were sequenced by GENEWIZ, LLC.

2.9. Homology Modeling of GmFAD2-2 Proteins and Mutational Analysis

Homology modeling of putative GmFAD2-2A, GmFAD2-2B, GmFAD2-2C, GmFAD2-2D, and GmFAD2-2E protein structures was retrieved from bar.utoronto.ca database. The PDB template used to model these structures was 4zyo and the confidence value was 99.2. The 3D molecule data used in this study come from [44], Pfam domain data come from [45], and CDD feature hits come from [46]. Homology modeling shows an amino acid modeling rate of 43.98%, 77.28%, 78.32%, 78.75%, and 92.07% for GmFAD2-2A, GmFAD2-2B, GmFAD2-2C, GmFAD2-2D, and GmFAD2-2E proteins, respectively. Mutation mapping and visualizations were performed using the UCSF Chimera package as shown earlier [47].

2.10. GmFAD2-1 and GmFAD2-2 Subcellular Localization and Cloning

The GmFAD2-1A, GmFAD2-1B, GmFAD2-2A, GmFAD2-2B, GmFAD2-2C, GmFAD2-2D, and GmFAD2-2E coding sequences were amplified from “Forrest” cDNA using gene specific forward and reverse primers containing EcoRI and SalI restriction enzyme sites, respectively. The amplified PCR products were fused to the N-terminus of the yellow fluorescent protein (YFP) reporter gene in the pSAT6-EYFP-N1 vector. The fusion constructs were then verified by sequencing. Three micrograms of DNA for each plasmid were bombarded into onion epidermal cells as previously described [48]. The pSAT6-EYFP-N1 empty vector was used as a cytoplasmic control. Onion epidermal peels were incubated at 26 °C in the dark for at least 20 h. The subcellular localization of the fused proteins was visualized using the EVOS® FL Auto Cell Imaging System (Life Technologies, Carlsbad, CA, USA). The subcellular localization experiment was repeated twice.

2.11. Analysis of Putative Cis-Elements at the GmFAD2-1 and GmFAD2-2 Promoters

Putative cis-elements in the upstream region (-2Kb upstream) of all 7 GmFAD2-1 and GmFAD2-2 gene members were searched using the programs PLACE, Plant PAN 2.0 and MatInspector [49,50,51]. Additional filtering was carried out based on motif score and redundant repeated motifs. Next, significant motifs were searched manually using PLACE for the putative role in plant development [49].

2.12. Statistical Analysis

All presented results were performed using JMP Pro 14 using the Student’s t-test for comparisons of means.

2.13. RNA-seq Library Preparation and Analysis

Four plant soybean tissues were used for RNA-seq including seed, leaf, root, flower and pods. Total RNA of each sample was extracted from 100 mg of frozen grounded samples using RNeasy QIAGEN KIT (Cat. No./ID: 74004). Total RNA was treated with DNase I (Invitrogen, Carlsbad, CA, USA). RNA-seq libraries preparation and sequencing were performed at Novogene INC. using Illumina NovaSeq 6000. The four libraries were multiplexed and sequenced in two different lanes generating 20 million raw pair end reads per sample (150bp). Quality assessment of sequenced reads was performed using fastqc, version 0.11.9 [34]. After removing the low-quality reads and adapters with trimmomatic, version V0.39 [34], the remaining high-quality reads were mapped to the soybean reference genome Wm82.a2.v1 using STAR, version v2.7.9 [52,53]. Uniquely mapped reads were counted using Python package HTseq v0.13.5 [54]. Read count normalization and differential gene expression analysis were conducted using the Deseq2 package v1.30.1 [55] integrated in the OmicsBox platform from BioBam (Valencia, Spain).

3. Results

3.1. FAD2 Duplication within the Soybean Genome

In soybeans, two GmFAD2 subfamilies were previously reported [8]. Two members constitute the GmFAD2-1 subfamily and five members belong to the GmFAD2-2 subfamily. GmFAD2-1A and GmFAD2-1B are located on chromosomes Chrs.10 and 20, respectively. GmFAD2-2A and GmFAD2-2B are located in Tandem in Chr.19, whereas GmFAD2-2C, GmFAD2-2D, and GmFAD2-2E are located in Chr.03, 09, and 15, respectively (Figure S1). The four independent segmental duplicated blocks containing the genomic pairs GmFAD2-2A/GmFAD2-2C, GmFAD2-2A/GmFAD2-2D, GmFAD2-2D/GmFAD2-2C, and GmFAD2-1A/GmFAD2-1B were previously identified in ±100 kb duplicated regions centered around the GmFAD2 genes [8]. However, GmFAD2-2B was not found to be a result of a segmental duplication. Synteny analysis from the current study suggests that GmFAD2-2B may be the result of a tandem duplication involving GmFAD2-2A.
The calculated ratios of nonsynonymous to synonymous substitutions (Ka/Ks) of the four GmFAD2-2A/GmFAD2-2C (Ka/Ks = 0.18), GmFAD2-2A/GmFAD2-2D (Ka/Ks = 0.12), GmFAD2-2D/GmFAD2-2C (Ka/Ks = 0.1), and GmFAD2-1A/GmFAD2-1B (Ka/Ks = 0.23) gene-pairs (chromosomal duplications) were less than 1, suggesting that their evolution may follow a purifying natural selection that could act on their coding sequences [56,57]. The duplication time of the five GmFAD2 members was estimated to match the recent (GmFAD2-1A/GmFAD2-1B and GmFAD2-2A/GmFAD2-2C), and old (GmFAD2-2A/GmFAD2-2D and GmFAD2-2D/GmFAD2-2C) duplication events. The segmental duplication of GmFAD2-1A/GmFAD2-1B and GmFAD2-2A/GmFAD2-2C was calculated to have occurred about 10.65 and 27.04 Mya, while the segmental duplications of GmFAD2-2A/GmFAD2-2D and GmFAD2-2D/GmFAD2-2C may have occurred 100.81 and 106.55 Mya. These data suggest that the calculated duplication time of GmFAD2-1A/GmFAD2-1B and GmFAD2-2A/GmFAD2-2C was close to the suggested recent duplication event (~13 mya). The calculated duplication time of GmFAD2-1A/GmFAD2-1B and GmFAD2-2A/GmFAD2-2C may belong to the old duplication event (~59 mya) [58], which is consistent with the obtained soybean GmFAD2 intragenome syntenic relationships calculated earlier using the Plant Genome Duplication Database [8].

3.2. Evolution of the GmFAD2 Gene Family

To understand the evolutionary relationships within the GmFAD2 gene family, the seven GmFAD2 protein members were aligned with orthologous protein sequences from 48 plant species, 7 monocots, 37 eudicots, and the most primitive plants including a basal angiosperm (Amborella trichopoda), a lycophyte (Selaginella moellendorff), a moss (Physcomitrella patens), and a chlorophyte (Chlamydomonas reinhardtii) (Figure 1).
Phylogenetic analysis separately grouped FAD2s from monocot, eudicot, a basal angiosperm, and the two primitive land species (mosses and lycophytes). The analysis shows that the ancestral FAD2 from the chlorophytic algae was outgrouped. These results demonstrate clearly that the fatty acid desaturase-2 followed the typical path of evolution, from aquatic to land plant species, being essential for plant survival.
Within the eudicot clade, the analysis revealed the presence of three different subclades containing the seven FAD2 members. While the two GmFAD2-1A and GmFAD2-1B were found in the subclade (C) containing FAD2s from different tree species (Apple, Crab apple, Chinese pear, and English walnut), the other five GmFAD2-2 members were imbedded in two other different subclades containing FAD2s from several other leguminous. GmFAD2-2A, GmFAD2-2B, GmFAD2-2C, and GmFAD2-2E were grouped together in the subclade (A) and phylogenetically close to FAD2 leguminous including velvet bean, cowpea, mung bean, pigeon pea, common bean, and red mung beans (Figure 1). The GmFAD2-2D member was separately grouped in another subclade (B) containing other FAD2s from cacao tree, an endemic woody shrub, and FAD2 from other three leguminous (red mung bean, common bean, and mung bean).

3.3. Expression Analysis of GmFAD2 Gene Family

First, publicly available RNA-seq data of developing Williams 82 soybean seeds were examined. The expression pattern of all seven GmFAD2 gene family members in the soybean reference genome Williams 82 was carried out in different tissues in order to investigate their specific evolutionary path. The two traditional GmFAD2-1A and GmFAF2-1B members showed the highest gene expression in seeds (at 35–42 DAF) (Figure 2). When comparing members of the GmFAD2-2 gene family, both GmFAD2-2B and GmFAD2-2C transcripts were highly expressed in pod shell (at 10–14 DAF). GmFAD2-2A, GmFAD2-2D, and GmFAD2-2E showed the lowest expression.
To gain more insight into the expression of the seven GmFAD2 members in soybean cv. Forrest (MG V), used to develop the mutagenized soybean population in this study, RNA-Seq analysis was carried out to check the expression levels of the GmFAD2 members. RNA-Seq analysis showed that GmFAD2-2B and GmFAD2-2C transcripts were highly expressed than the traditional GmFAD2-1 members in root and leaves (Figure 2). In seeds, flower, and pods, GmFAD2-2B and GmFAD2-2C together with GmFAD2-1B transcripts were more abundant than GmFAD2-1A. GmFAD2-2A, GmFAD2-2D, and GmFAD2-2E showed the lowest expression like in Williams 82 cultivar.

3.4. TILLING by Target Capture Sequencing

To identify novel allelic variation within the GmFAD2 gene family, a population of 4,032 EMS mutagenized soybeans was developed using the “Forrest” cultivar. Next, TILLING-by-Sequencing+ was used to identify several mutants from GmFAD2-2A, GmFAD2-2B, GmFAD2-2C, GmFAD2-2D, and GmFAD2-2E. Using this reverse genetic approach, we successfully identified 12 GmFAD2-2A, 8 GmFAD2-2B, 10 GmFAD2-2C, 9 GmFAD2-2D, and 19 GmFAD2-2E missense mutants (Figure 3).

3.5. Mutation Density of the “Forrest” EMS Mutagenized Soybean Population

The first soybean TILLING mutagenized populations were produced with a mutation density corresponding to ~1/140 kb and ~1/550 kb using EMS or N-nitroso-N-methylurea (NMU), respectively [41]. TILLING-by-Sequencing+ analysis of the seven fatty acid desaturase genes resulted in the identification of 441 SNP mutations and 16 InDels (Table 1). About 74% of mutations were the typical EMS mutations (G to A and C to T), while the other type of mutations account for about 26% of the total mutations. The mutation density is estimated to be ~1/155 kb, ~1/154 kb, ~1/128 kb, ~1/138, ~1/102, ~1/121, and ~1/67 kb for the GmFAD2-1A, GmFAD2-1B, GmFAD2-2A, GmFAD2-2B, GmFAD2-2C, GmFAD2-2D, and GmFAD2-2E genes, respectively. Within the coding regions, 50–70% of missense mutations, 1–8% of nonsense mutations, and 22–26% of silent mutations were obtained (Figure S1).

3.6. All Five GmFAD2-2s Are Involved in High Oleic Acid Content

The identified EMS mutants were mapped on the five GmFAD2-2 protein models (Figure 3). The results showed that most of the mutations were mapped on key protein domains including the catalytic activity of the enzyme (di-iron center), homodimer interface, and/or substrate binding, suggesting that the isolated mutations may have a negative impact on protein activity and/or dimerization.
Most importantly, all isolated missense and nonsense Gmfad2-2a, Gmfad2-2b, Gmfad2-2c, Gmfad2-2d, and Gmfad2-2e mutants showed a significant increase in their seed oleic acid content when compared to the wild-type “Forrest” (Table 2). Mutations on GmFAD2-2A, GmFAD2-2B, GmFAD2-2C, GmFAD2-2D, and GmFAD2-2E resulted in an oleic acid increase with up to 31.9%, 28.1%, 29.6%, 32.7, and 35.7%, respectively. Our results showed that GmFAD2-2A, GmFAD2-2B, GmFAD2-2C, GmFAD2-2D, and GmFAD2-2E play an unprecedented role in unsaturated fatty acid biosynthesis in soybeans, suggesting that members of the GmFAD2-2 subfamily may have been subfunctionalized in soybeans during the two whole genome duplication events.

3.7. Subcellular Localization of GmFAD2-1 and GmFAD2-2 Subfamily Members

Although FAD2 genes were involved in converting oleic acid into linoleic acid, several subcellular localization patents of the FAD2 genes have been reported in different plant species. It has been shown that the fatty acid desaturase-2 from other plant species like Arabidopsis thaliana [59], Artemisia sphaerocephala [60], cucumber [61], and spinach [62] are located in the endoplasmic reticulum. Several studies have predicted the endoplasmic reticulum localization of the GmFAD2-1A and GmFAD2-1B proteins. However, up to date, no study has shown the subcellular localization of the two GmFAD2-1 and/or the five GmFAD2-2 subfamily members in soybean. In order to gain more insight into the function of the fatty acid desaturases-2 in soybeans, their subcellular localization was examined using YFP fusion in onion epidermal cells using biolistic bombardment. Onion epidermal cells expressing GmFAD2-1s:YFP fusion confirmed their localization in the endoplasmic reticulum, but also showed an interesting expression pattern in the chloroplasts (Figure 4). The accumulation of GmFAD2-1A and GmFAD2-1B in the endoplasmic reticulum and chloroplast is consistent with the role of this class of proteins in fatty acid desaturation reported earlier. GmFAD2-2s:YFP fusion showed a distinct pattern localization from GmFAD2-1s:YFP (Figure 4). While GmFAD2-2C signal was found only in the cytosol, GmFAD2-2B signal was located mainly in the vacuole, in addition to the cytosol. The other three members, GmFAD2-2A, GmFAD2-2D, and GmFAD2-2E showed a reticulum endoplasmic localization in addition to the presence of a cytosolic signal.

3.8. Analysis of Putative Cis-Elements in the Promoter Region of GmFAD2-1 and GmFAD2-2 Gene Members

The analysis of putative cis-elements in the promoter region (−2 Kb upstream) of the translation start codon of GmFAD2-1 and GmFAD2-2 gene members showed an enrichment of a cis-binding motifs for the Arabidopsis homeobox protein domain (Figure 5). The frequency of this cis-element was significantly higher (459) when compared to the other cis-elements that are present in the GmFAD2s promoter region (2.65–459 times higher) (Table S3). The promoter analysis shows that GmFAD2-1A, GmFAD2-1B, GmFAD2-2A, GmFAD2-2B, GmFAD2-2C, GmFAD2-2D, and GmFAD2-2E promoters contain 59, 64, 81, 34, 67, 102, and 52 Arabidopsis homeobox protein binding elements, respectively. An extremely high presence of the Arabidopsis homeobox protein binding element was also observed in GmFAD2-1A and GmFAD2-1B promoter regions (81 and 102, respectively). These data may suggest an involvement of Arabidopsis homeobox protein in the oleic acid biosynthesis. This is coherent with a previous study showing the involvement of a homeodomain transcription factor in lipid metabolism. In fact, 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 [63].
Additionally, the promoter analysis revealed the absence of the DNA-binding proteins with the plant specific TCP-domain in the GmFAD2-1 subfamily that was shared only between the five members of the GmFAD2-2 subfamily (Table S3). The presence of this cis-element within the GmFAD2-2 subfamily only may be linked to specific mode of regulation taking into consideration the subcellular localization pattern that was different from the GmFAD2-1 subfamily.

4. Discussion

4.1. Involvement of the Five GmFAD2-2 Members in the Unsaturated Fatty Acid Pathway

Several studies have investigated the role and function of the FAD2 genes in several plant species. FAD2s were well studied and known for their roles in unsaturated fatty acid biosynthesis by converting oleic acid to linoleic acid. Traditionally, fatty acids are synthesized in plastid/endoplasmic reticulum [64]. In soybeans, members of the GmFAD2-1 subfamily have been reported to increase seed oleic acid [5,8]. The endoplasmic reticulum subcellular localization of the traditional GmFAD2-1A and GmFAD2-1B subfamily members is consistent with the subcellular localization reported earlier in other plant species including shrub [60] and Arabidopsis [59]. In cucumber, while the retention signal of some fatty acid desaturases like CsFAD2 and CsFAD3 was found to target the endoplasmic reticulum, other fatty acid desaturases like CsFAD4, CsFAD5, CsFAD6, CsFAD7 and three CsFAB2s contained a predicted chloroplast signal peptide [61]. This is consistent with the chloroplastic localization of the GmFAD2-1A and GmFAD2-1B proteins shown in this study. EMS induced and spontaneous occurring mutations at the GmFAD2-1A and GmFAD2-1B genes were widely used in the soybean breeding programs to increase seed oleic acid content up to 85% after combining the two alleles to generate double GmFAD2-1A/GmFAD2-1B mutants [26,27]. However, very little is known about the role of the other members of the GmFAD2-2 subfamily. Using TILLING-by-Sequencing+, we successfully identified several mutations within the five members of the GmFAD2-2 subfamily and showed for the first time their involvement in increasing seed oleic acid content (Figure 6). Interestingly, in addition to their subcellular cytoplasmic localization, GmFAD2-2A, GmFAD2-2D, and GmFAD2-2E members have shown an endoplasmic reticulum localization, while GmFAD2-2B showed a clear vacuole localization (Figure 6). Although fatty acids were shown to be synthesized in Plastid/endoplasmic reticulum (ER), it has been reported that this synthesis can also happen directly from malonyl-CoA in the cytoplasm without substantially altering plastidial/ER fatty acid production, known as “de novo pathway” [64]. Therefore, the presence of such pathway in soybean involving members of the GmFAD2-2 subfamily may have a positive impact on developing soybean lines with increased fatty acid and/or high very long chain polyunsaturated fatty acids that present several benefits for human health (Figure 6).
Protein homology modeling analysis revealed that most of the mutations were mapped on key protein domains including the catalytic activity of the enzyme (di-iron center), homodimer interface, and/or substrate binding, suggesting that the isolated mutations may have a negative impact on the protein activity and/or dimerization. This could be explained by the fact that mutations at the fatty acid desaturase2-2 proteins (GmFAD2-2) failed to convert seed oleic acid into linoleic acid or possess very low enzymatic activity. Since enzymatic reactions are commonly reversible, is it possible that mutated desaturases are capable of converting linoleic acid (generated by normal desaturases) into oleic acid. This may suggest that it is possible that mutated desaturases not only lose original enzymatic activity, but also may catalyze the reverse reaction impacting positively the seed oleic acid content as seen in all the isolated GmFAD2-2 TILLING mutants.
Moreover, the accumulation of GmFAD2-2B in the cytosol and vacuole may suggest another role in controlling fatty acid desaturation at the plasma membrane and controlling ion exchange activity impacting the fluidization of membrane lipids, being essential for abiotic stress tolerance and early seedling growth [65] (Figure 6). In fact, the Arabidopsis fatty acid desaturase AtFAD2 was shown to play an essential role in plant resistance to salt stress by controlling the Na+/H+ exchange activity. The Arabidopsis AtFAD2 mediates a high-level of vacuolar and plasma membrane fatty acid desaturation. Plants maintaining a high Na+/H+ ratio in the cytosol show a high tolerance to soil salinity, a major abiotic stress that results in considerable crop yield losses worldwide [68]. Additionally, it is also essential for the proper function of membrane attached Na+/H+ exchangers to maintain a low cytosolic Na+ concentration for salt tolerance during seed germination and early seedling growth in Arabidopsis. The observed differences in subcellular localization may suggest that the GmFAD2-2B member underwent a process of neofunctionalization within the soybean genome, unlike the rest of the GmFAD2-2 members. Our subcellular localization data of the two GmFAD2 subfamily members is congruent with the evolution pattern shown earlier, which suggests that their evolution pattern may dictate their subcellular localization.
Up to date, soybean geneticists and breeders have heavily used induced mutations (EMS and fast neutron), natural variations and/or genetic engineering approaches to increase oleic acid content up to 85%. TALEN and CRISPR technologies were recently used to create targeted mutations based on GmFAD2-1A/GmFAD2-1B genes. The available high oleic acid soybeans based on GmFAD2-1A/GmFAD2-1B alleles (plastidial/ER fatty acid production) present affected germination in cold soil [13]. Loss of function of the GmFAD2-1A and GmFAD2-1B may affect the incorporation of fatty acids into phospholipids in the endoplasmic reticulum impacting membrane lipids and membrane fluidity; therefore, affecting cold stress tolerance and fatty acid stability of these lines [66]. Thus, the discovery of new fatty acid desaturases impacting positively the seed oleic acid content without disturbing the plastid/ER pathway and subsequent incorporation to phospholipids is extremely beneficial to develop an alternate strategy to improve seed oleic acid in soybean and their commercialization (Figure 6).

4.2. Subfunctionalization of GmFAD2-2 Gene Family during Whole Genome Duplication

The soybean genome has been diversified due to the presence of two different large-scale duplication events (~13 and 59 million years ago) [58], resulting in a paleopolyploid genome where three quarters of the genes are present in multiple copies [69], impacting the development of important agronomic traits [70,71]. As a consequence of these two duplication events, the two GmFAD2-1 and GmFAD2-2 subfamilies resulted in seven GmFAD2 members that derived from three independent syntenic duplicated genomic regions and one tandem duplication. These data may suggest the existence of a common FAD2 ancestor. The identification of a single FAD2 gene in C. reinhardtii in addition to the evolutionary conservation of the FAD2 proteins among soybeans from phylogenetically separated species further support this feature. Additionally, the fact that all five members of the GmFAD2-2 subfamily are involved in the unsaturated fatty acid biosynthesis, similar to the GmFAD2-1 subfamily, points to the presence of a subfunctionalization event of the GmFAD2 gene family, which may be most probably the result of successive duplications of an ancestral FAD2, leading to the enhancement of soybean oil biosynthesis. Like the GmFAD2-1 subfamily, stacking more GmFAD2-2 members is expected to provide additive effect leading to increasing the seed oleic acid content in soybean without the alteration of the plastidial/ER fatty acid production. The presence of subfunctionalization event has been reported earlier in soybeans. Two members of the Soluble NSF attachment proteins, the GmSNAP18 and GmSNAP11, have subfunctionalized to play a role in resistance to soybean cyst nematode [72], in addition to the four members of the Stearoyl-acyl carrier protein desaturases, which have been subfunctionalized to play a role in the fatty acid unsaturation by converting seed stearic acid to seed oleic acid. Furthermore, the observed substantial changes in GmFAD2 gene expression may be most probably due to gene duplication and selection pressure imposed by environmental conditions. This may explain functional differences of the oleic acid and linoleic acid contents observed within the two GmFAD2 gene subfamilies. Although the current study showed the potential of using members of the GmFAD2-2 gene subfamily to develop soybean lines with increased seed oleic acid content, their specific role in the cytoplasm/plasma membrane needs to be further investigated.

5. Conclusions

Using a novel technology, TILLING-by-Sequencing+, we functionally characterized the five members of the GmFAD2-2 subfamily. The identified mutations showed the presence of a positive impact on increasing soybean seed oleic acid content. Subcellular localization indicated that members of the two GmFAD2-2 subfamilies are located in cellular compartments different from those previously reported for the traditional GmFAD2-1s, suggesting the presence of an alternative pathway to convert oleic acid to linoleic acid in soybeans without substantially altering the traditional plastidial/ER fatty acid production. The isolated soybean TILLING mutants from this study can be used in soybean breeding programs to improve seed fatty acid composition trait.

Supplementary Materials

The following are available online at https://0-www-mdpi-com.brum.beds.ac.uk/article/10.3390/cells10051245/s1, Figure S1. Physical positions and gene structures corresponding to the seven GmFAD2s are shown. (A) Six chromosomes carry the GmFAD2 gene family. Glyma.10G278000 (Chr10: 50,013,484–50,015,460); Glyma.20G111000 (Chr20: 35,315,629–35,319,062); Glyma.19G147300 (Chr19: 40,814,864–40,815,855); Glyma.19G147400 (Chr19: 40,819,961–40,824,925); Glyma.03G144500 (Chr03: 36,014,623–36,020,910), Glyma.09G111900 (Chr09: 22,174,486–22,179,275), Glyma.15G195200 (Chr15: 22,308,021–22,308,902). (B) Gene structures of soybean fatty acid desaturases from three gene families. The structures of 19 soybean fatty acid desaturases genes were plotted with yellow boxes representing exons (coding DNA sequence, CDS), black lines illustrating introns, and blue boxes indicating 5′-UTR and 3′-UTR regions. The size of gene structures could be measured by the scale in the unit of base pair (bp) at the bottom. The gene structure was drawn using the Gene Structure Display Server. Table S1. Designed GmFAD2-1A, GmFAD2-1B, GmFAD2-2A, GmFAD2-2B, GmFAD2-2C, GmFAD2-2D, and GmFAD2-2E probes used for TILLING by Target Capture Sequencing. Table S2. Primers used for target Sanger sequencing. Table S3. Summary of the identified cis-elements at the promoter region (−2 Kb upstream) of the translation start codon of GmFAD2-1 and GmFAD2-2 gene members showing an enrichment of the Arabidopsis homeobox protein domain within the seven GmFAD2 members.

Author Contributions

N.L. writing—original draft, conceptualization, formal analysis, validation, and investigation, performed in silico, syntenic, phylogenetic analysis, homology modeling, mutational analysis, data analysis and interpretation, and TILLING by sequencing+ analysis. N.L. and Z.Z. developed the EMS soybean mutagenized population and performed high-throughput DNA extractions. N.L. and O.B. developed TILLING-by-sequencing+ pipeline. V.S.L.-C. and T.H. did subcellular localization. A.A., T.D.V., P.C. and H.T.N. performed fatty acid analysis and edited the manuscript. N.L., Z.Z., D.K., M.A.C. and A.E.B. performed TILLING-by-sequencing+ analyses and characterized induced mutations. M.G.E., J.M. and A.L., did data analysis and edited the manuscript. K.M. conceptualization, funding acquisition, project administration, supervision, writing—review and editing. All authors have read and agreed to the published version of the manuscript.

Funding

This research was supported in part from the United Soybean Board, project USB#2020-162-0127 to (1) K.M. and N.L., and (2) was partially supported by funds from the Tennessee Soybean Promotion Board to T.H.

Institutional Review Board Statement

This study did not involve humans or animals.

Informed Consent Statement

Not applicable.

Acknowledgments

The authors thank Stewart Selves, The Delta Research Center, The University of Missouri, for his technical assistance.

Conflicts of Interest

The authors declare no conflict of interest.

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Figure 1. Phylogenetic tree of the fatty acid desaturase-2 from 48 sequenced plant species. FAD2 proteins identified in five model plants; C. reinhardtii (algae; green box), P. patens (moss), S. moellendorfii (lycophyte), O. sativa (monocot), and M. truncatula (eudicot leguminous), in addition to G. max (soybean) and other monocots and eudicots FAD2s were included in the analysis. The phylogenetic tree was generated using MEGA4 software package and the ClustalW algorithm and calculated using the neighbor-joining method. The tree bootstrap values are indicated at the nodes (n = 1000).
Figure 1. Phylogenetic tree of the fatty acid desaturase-2 from 48 sequenced plant species. FAD2 proteins identified in five model plants; C. reinhardtii (algae; green box), P. patens (moss), S. moellendorfii (lycophyte), O. sativa (monocot), and M. truncatula (eudicot leguminous), in addition to G. max (soybean) and other monocots and eudicots FAD2s were included in the analysis. The phylogenetic tree was generated using MEGA4 software package and the ClustalW algorithm and calculated using the neighbor-joining method. The tree bootstrap values are indicated at the nodes (n = 1000).
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Figure 2. Expression pattern of soybean GmFAD2-1 and GmFAD2-2 gene members. (A) Expression of the seven GmFAD2 members in Williams 82 were retrieved from publicly available RNA-seq data from the SoyBase (http://www.soybase.org/soyseq), in addition to (B) the RNAseq data from the cultivar “Forrest”.
Figure 2. Expression pattern of soybean GmFAD2-1 and GmFAD2-2 gene members. (A) Expression of the seven GmFAD2 members in Williams 82 were retrieved from publicly available RNA-seq data from the SoyBase (http://www.soybase.org/soyseq), in addition to (B) the RNAseq data from the cultivar “Forrest”.
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Figure 3. Homology modeling of the five GmFAD2-2 proteins and corresponding identified EMS mutations. Mutated residues on the five GmFAD2-2 proteins identified by Tilling-by-Sequencing+ were mapped on the five GmFAD2-2 protein homology models. Homology modeling of the GmFAD2-2A (A), GmFAD2-2B (B), GmFAD2-2C (C), GmFAD2-2D (D), and GmFAD2-2E (E) predicted proteins. The identified mutations and corresponding amino acid changes are shown on blue. Putative di-iron binding sites residues and substrate-binding pocket are shown in green.
Figure 3. Homology modeling of the five GmFAD2-2 proteins and corresponding identified EMS mutations. Mutated residues on the five GmFAD2-2 proteins identified by Tilling-by-Sequencing+ were mapped on the five GmFAD2-2 protein homology models. Homology modeling of the GmFAD2-2A (A), GmFAD2-2B (B), GmFAD2-2C (C), GmFAD2-2D (D), and GmFAD2-2E (E) predicted proteins. The identified mutations and corresponding amino acid changes are shown on blue. Putative di-iron binding sites residues and substrate-binding pocket are shown in green.
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Figure 4. Subcellular localization of soybean GmFAD2-1 and GmFAD2-2 proteins. The GmFAD2 coding sequences from all seven members were fused to eYFP and delivered into onion epidermal cells using biolistic bombardment. GmFAD2-1A and GmFAD2-1B showed an endoplasmic reticulum (ER) and chloroplastic (P) localization pattern. GmFAD2-2A, GmFAD2-2D, and GmFAD2-2E showed a reticulum endoplasmic and cytosol (C) localization. GmFAD2-2C signal was found in the cytosol only. GmFAD2-2B shows a vacuole (VC) and cytoplasmic localization. The chloroplast-targeted GmSACPD-D was used as positive control [29]. Bar = 100 µM.
Figure 4. Subcellular localization of soybean GmFAD2-1 and GmFAD2-2 proteins. The GmFAD2 coding sequences from all seven members were fused to eYFP and delivered into onion epidermal cells using biolistic bombardment. GmFAD2-1A and GmFAD2-1B showed an endoplasmic reticulum (ER) and chloroplastic (P) localization pattern. GmFAD2-2A, GmFAD2-2D, and GmFAD2-2E showed a reticulum endoplasmic and cytosol (C) localization. GmFAD2-2C signal was found in the cytosol only. GmFAD2-2B shows a vacuole (VC) and cytoplasmic localization. The chloroplast-targeted GmSACPD-D was used as positive control [29]. Bar = 100 µM.
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Figure 5. Analysis of putative cis-elements in the promoter region of the GmFAD2-1 and GmFAD2-2 gene members. (A) All identified cis-elements at the GmFAD2-1 and GmFAD2-2 promoter region (−2 Kb upstream). (B) Shows the conserved Arabidopsis homeobox protein domain (P$AHBP) that was shared between all GmFAD2-1 and GmFAD2-2 subfamily members with a total match that was significantly higher (459) when compared to the other cis-elements shown in (A).
Figure 5. Analysis of putative cis-elements in the promoter region of the GmFAD2-1 and GmFAD2-2 gene members. (A) All identified cis-elements at the GmFAD2-1 and GmFAD2-2 promoter region (−2 Kb upstream). (B) Shows the conserved Arabidopsis homeobox protein domain (P$AHBP) that was shared between all GmFAD2-1 and GmFAD2-2 subfamily members with a total match that was significantly higher (459) when compared to the other cis-elements shown in (A).
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Figure 6. Cartoon deciphering the soybean seed fatty acid biosynthesis pathway. The seven GmFAD2-1 and GmFAD2-2 members are responsible for converting oleic acid (C18:0-ACP) to linoleic acid (C18:1Δ9-ACP) in the plastid (GmFAD2-1A and GmFAD2-1B), ER (GmFAD2-1A, GmFAD2-1B, GmFAD2-2A, GmFAD2-2D, and GmFAD2-2E), and cytoplasm (GmFAD2-2A, GmFAD2-2B, GmFAD2-2C, GmFAD2-2D, and GmFAD2-2E). GmFAD2-2B is located in the vacuole and is likely to play a role during seed germination and early seed growth by maintaining low cytosolic Na+ as described in Arabidopsis [65]. In bold are the five newly identified fatty acid desaturases involved in the unsaturated fatty acid biosynthesis. GmFAD2-2A, GmFAD2-2B, GmFAD2-2C, GmFAD2-2D, and GmFAD2-2E members present a good alternative for converting oleic acid content without substantially altering the traditional plastidial/ER fatty acid production pathway in soybean. The flux of fatty acids between the plastid and the ER occurs among different plant species [66]. A portion of C16:0-ACP, C18:0-ACP, and C18:1-ACP pool can be incorporated into phosphatidylglycerol (PG) and galactolipids in the plastid. A portion of the acyl-CoA moieties can be incorporated into triacylglycerol (TAG, the major lipid fraction in plant seed oils) biosynthesis in the seed via the Kennedy pathway. GmFAD3 genes are differentially expressed during seed development or cold temperature exposure [67]. The GmFAD7/8 promote C18:3 biosynthesis in the plastid, acting as precursors for the biosynthesis of Jasmonate and are expected to be involved in defense responses and biotic stress signaling [67]. GmSACPD-C is the nodule specific isoforms as shown earlier [29].
Figure 6. Cartoon deciphering the soybean seed fatty acid biosynthesis pathway. The seven GmFAD2-1 and GmFAD2-2 members are responsible for converting oleic acid (C18:0-ACP) to linoleic acid (C18:1Δ9-ACP) in the plastid (GmFAD2-1A and GmFAD2-1B), ER (GmFAD2-1A, GmFAD2-1B, GmFAD2-2A, GmFAD2-2D, and GmFAD2-2E), and cytoplasm (GmFAD2-2A, GmFAD2-2B, GmFAD2-2C, GmFAD2-2D, and GmFAD2-2E). GmFAD2-2B is located in the vacuole and is likely to play a role during seed germination and early seed growth by maintaining low cytosolic Na+ as described in Arabidopsis [65]. In bold are the five newly identified fatty acid desaturases involved in the unsaturated fatty acid biosynthesis. GmFAD2-2A, GmFAD2-2B, GmFAD2-2C, GmFAD2-2D, and GmFAD2-2E members present a good alternative for converting oleic acid content without substantially altering the traditional plastidial/ER fatty acid production pathway in soybean. The flux of fatty acids between the plastid and the ER occurs among different plant species [66]. A portion of C16:0-ACP, C18:0-ACP, and C18:1-ACP pool can be incorporated into phosphatidylglycerol (PG) and galactolipids in the plastid. A portion of the acyl-CoA moieties can be incorporated into triacylglycerol (TAG, the major lipid fraction in plant seed oils) biosynthesis in the seed via the Kennedy pathway. GmFAD3 genes are differentially expressed during seed development or cold temperature exposure [67]. The GmFAD7/8 promote C18:3 biosynthesis in the plastid, acting as precursors for the biosynthesis of Jasmonate and are expected to be involved in defense responses and biotic stress signaling [67]. GmSACPD-C is the nodule specific isoforms as shown earlier [29].
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Table
Table 1. SNP mutations, InDels, and mutation density for the GmFAD2-1A, GmFAD2-1B, GmFAD2-2A, GmFAD2-2B, GmFAD2-2C, GmFAD2-2D, and GmFAD2-2E genes.
Table 1. SNP mutations, InDels, and mutation density for the GmFAD2-1A, GmFAD2-1B, GmFAD2-2A, GmFAD2-2B, GmFAD2-2C, GmFAD2-2D, and GmFAD2-2E genes.
Gene IDAmplicon Size (bp)Base ChangesType of Base ChangesInDelMutation Density (Kb)AA ChangesMissense MutationsNonsense MutationsSilent Mutations
G > AC > TOthers
Glyma.10G2780001928501329801/1552817011
Glyma.20G11100034038922293831/1542511113
Glyma.19G147300889281312311/12813913
Glyma.19G14740027117926391451/138392829
Glyma.03G14450022108729352331/1022815112
Glyma.09G11190016635518231421/121332526
Glyma.15G1952008815316241321/67302505
Total44113719111316 196130759
Table
Table 2. All 58 isolated EMS Gmfad2-2 TILLING mutants showing increase in the seed oleic acid content.
Table 2. All 58 isolated EMS Gmfad2-2 TILLING mutants showing increase in the seed oleic acid content.
Gene IDPlant IDNucleotide ChangeAmino Acid SubstitutionC16:0C18:0C18:1C18:2C18:3
GmFAD2-2A
Glyma.19g147300		F490G410TR137L10.43.529.650.16.4
F601G283AA95T9.64.824.854.36.4
F300C134TT45I10.74.125.154.06.1
F1410C38AP13H10.65.127.850.95.6
F960C91TR31C10.23.624.254.37.6
F935C103TR35C10.33.725.153.47.5
F239C211TP71S11.14.226.853.34.6
F1044C245TA82V10.05.226.154.14.6
F1202C331TH11Y9.44.131.949.05.5
F141G346AV116I10.85.127.950.35.8
F1581C376TR126C10.54.528.651.25.2
F1493C379TR127C9.73.425.854.56.6
GmFAD2-2B
Glyma.19g147400		F211G994AA332T10.73.925.152.08.4
F185C277TQ93 *9.63.525.650.610.7
F45G1118AS373N10.83.726.352.17.1
F1103G284AC95Y10.33.528.151.36.9
F1496G460AD154N9.74.827.851.36.4
F1562G466AV156I9.94.227.352.26.4
F253A672TQ224H10.14.227.452.75.6
F921C1049TP350L10.23.724.153.58.5
GmFAD2-2C
Glyma.03G144500		496C625TH209Y9.93.128.350.58.3
1106G1114AE372K10.24.229.650.85.3
468C88TP30S9.95.628.250.06.2
595G781AV261M10.45.125.753.55.3
F408G49AE17K10.34.328.951.35.2
F1222G175AD59N10.44.025.252.77.7
F1748C259TP87S10.34.726.151.07.9
F1111C313AH105N10.55.325.552.76.0
F58A672TQ224H10.24.924.453.76.9
F1165G799AV267M9.33.227.950.29.4
GmFAD2-2D
Glyma.09G111900		313C643TP215S11.04.926.948.88.4
81A622TR208 *10.35.232.746.55.2
369C751TL251F10.75.025.353.15.9
1436G1094TC365F10.45.227.750.06.7
F1381A1020TK340N10.14.128.950.26.7
F275G905AR302K10.56.429.247.76.2
F1117G579AW193 *10.64.427.750.66.7
F470G510AW170 *9.74.730.548.16.9
F1268C439TH147Y9.84.026.052.57.6
GmFAD2-2E
Glyma.15g195200		F1087G329AG110E10.33.821.355.78.9
F380C502TP168S9.94.224.653.57.7
F9C829TP277S10.94.324.053.67.3
F1215A803TE268V10.64.929.948.46.2
F602G754AE252K10.44.225.254.06.2
F1328G751AG251R10.24.727.252.45.5
F1285G721AE241K10.43.924.452.58.8
F1065C706TH236Y11.34.829.847.66.5
F226G628AD210N11.35.033.744.95.1
F69G626AR209k10.54.525.952.17.0
F1803G605AG202E12.35.032.045.55.2
F480T595AW199R10.94.526.451.66.6
F372C397TL133F10.53.625.753.96.3
F1180C350TA117V10.54.224.054.56.9
F123C334TP112S10.45.328.650.45.3
F238G328AG110R10.26.327.250.55.8
F1480C167TS56F9.84.225.753.07.3
F1711T166AS56T9.45.135.743.56.3
F1462G61AA21T9.73.833.347.85.4
FWT 11.63.321854.56.19
* TILLING Gmfad2-2 nonsense mutants resulting in stop codons. Fatty acid content in bold shows the increased seed oleic acid and decreased linoleic acid content due to the presence of deleterious mutations affecting the GmFAD2-2 protein activity. Underline oleic acid content shows the highest seed oleic acid content that was obtained in each one of the five GmFAD2-2 members. Some Gmfad2-2 mutants showed a significant increase in their seed stearic acid content (bold).
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Lakhssassi, N.; Lopes-Caitar, V.S.; Knizia, D.; Cullen, M.A.; Badad, O.; El Baze, A.; Zhou, Z.; Embaby, M.G.; Meksem, J.; Lakhssassi, A.; et al. TILLING-by-Sequencing+ Reveals the Role of Novel Fatty Acid Desaturases (GmFAD2-2s) in Increasing Soybean Seed Oleic Acid Content. Cells 2021, 10, 1245. https://0-doi-org.brum.beds.ac.uk/10.3390/cells10051245

AMA Style

Lakhssassi N, Lopes-Caitar VS, Knizia D, Cullen MA, Badad O, El Baze A, Zhou Z, Embaby MG, Meksem J, Lakhssassi A, et al. TILLING-by-Sequencing+ Reveals the Role of Novel Fatty Acid Desaturases (GmFAD2-2s) in Increasing Soybean Seed Oleic Acid Content. Cells. 2021; 10(5):1245. https://0-doi-org.brum.beds.ac.uk/10.3390/cells10051245

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Lakhssassi, Naoufal, Valéria Stefania Lopes-Caitar, Dounya Knizia, Mallory A. Cullen, Oussama Badad, Abdelhalim El Baze, Zhou Zhou, Mohamed G. Embaby, Jonas Meksem, Aicha Lakhssassi, and et al. 2021. "TILLING-by-Sequencing+ Reveals the Role of Novel Fatty Acid Desaturases (GmFAD2-2s) in Increasing Soybean Seed Oleic Acid Content" Cells 10, no. 5: 1245. https://0-doi-org.brum.beds.ac.uk/10.3390/cells10051245

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