Genome-wide identification and analysis of soybean acyl-ACP thioesterase gene family reveals the role of GmFAT to improve fatty acid composition in soybean seed

Zhou, Zhou; Lakhssassi, Naoufal; Knizia, Dounya; Cullen, Mallory A; Baz, Abdelhalim El; Embaby, Mohamed G.; Liu, Shiming; Badad, Oussama; Vuong, Tri D.; AbuGhazaleh, A.A.; Nguyen, Henry T.; Meksem, Khalid

doi:10.1007/s00122-021-03917-9

Cited by 22 publications

(23 citation statements)

References 59 publications

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“…FATB1B encodes acyl-acyl carrier protein, which terminates the intraplastidial fatty acid synthesis in plants by hydrolyzing the acyl-ACP intermediates and releasing free fatty acids to be incorporated into glycerolipids ( Sanchez-Garcia et al, 2010 ). The mutations at GmFATB presented low PA and high OA phenotypes ( Zhou et al, 2021 ). SACPD encodes stearoyl-acyl carrier protein, which is essential for the production of the major UFAs in plant lipids.…”

Section: Discussionmentioning

confidence: 99%

Transcriptomic Analysis Reveals the Regulatory Networks and Hub Genes Controlling the Unsaturated Fatty Acid Contents of Developing Seed in Soybean

et al. 2022

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Soybean [Glycine max (L.) Merr.] is one of the most important crops, which produces about 25% of the world’s edible oil. The nutritional value of soybean oil depends mostly on the relative contents of three unsaturated fatty acids (UFAs), i.e., oleic acid, linoleic acid (LA), and linolenic acid. However, the biosynthetic mechanism of UFAs remains largely unknown, and there are few studies on RNA-seq analysis of developing seeds. To identify the candidate genes and related pathways involved in the regulation of UFA contents during seed development in soybean, two soybean lines with different UFA profiles were selected from 314 cultivars and landraces originated from Southern China, and RNA-seq analysis was performed in soybean seeds at three developmental stages. Using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, a series of genes and pathways related to fatty acid metabolism were identified, and 40 days after flowering (DAF) was found to be the crucial period in the formation of UFA profiles. Further, weighted gene co-expression network analysis identified three modules with six genes whose functions were highly associated with the contents of oleic and LA. The detailed functional investigation of the networks and hub genes could further improve the understanding of the underlying molecular mechanism of UFA contents and might provide some ideas for the improvement in fatty acids profiles in soybean.

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Section: Discussionmentioning

confidence: 99%

Transcriptomic Analysis Reveals the Regulatory Networks and Hub Genes Controlling the Unsaturated Fatty Acid Contents of Developing Seed in Soybean

et al. 2022

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“…Finally, according to the annotations described in Liu et al [55], along with Arabidopsis homologous information in ARALIP and soybean pathway annotation in SFGD, 70 candidate genes were mined (Additional file 1: Table S8). Among these genes, 9 soybean genes were confirmed by transgenic experiments in soybean (Table 2), i.e., GmLEC1-b [56], GmFAB2 [9], GmFatA and GmFatB1a [57], GmPLDα1 [13], GmABI3b [56], GmDGAT1a [10], GmPDAT1 [12], and GmSEI [17]. 14 genes are homologs to those in Arabidopsis, which are confirmed by transgenic experiments, e.g., Atα-PDHC [58], AtPLDζ [59], AtFAX1 [60], and AtPDCT [14]; 32 genes or their homologs in Arabidopsis have been predicted to participate in oil biosynthesis and lipid metabolism; and 15 genes were newly found in this study (Additional file 1: Table S8).…”

Section: Detection Of Qtls and Their Candidate Genes For Oil-related ...mentioning

confidence: 97%

4D genetic networks reveal the genetic basis of metabolites and seed oil-related traits in 398 soybean RILs

Han

Zhang

Liu

et al. 2022

Biotechnol Biofuels

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Background The yield and quality of soybean oil are determined by seed oil-related traits, and metabolites/lipids act as bridges between genes and traits. Although there are many studies on the mode of inheritance of metabolites or traits, studies on multi-dimensional genetic network (MDGN) are limited. Results In this study, six seed oil-related traits, 59 metabolites, and 107 lipids in 398 recombinant inbred lines, along with their candidate genes and miRNAs, were used to construct an MDGN in soybean. Around 175 quantitative trait loci (QTLs), 36 QTL-by-environment interactions, and 302 metabolic QTL clusters, 70 and 181 candidate genes, including 46 and 70 known homologs, were previously reported to be associated with the traits and metabolites, respectively. Gene regulatory networks were constructed using co-expression, protein–protein interaction, and transcription factor binding site and miRNA target predictions between candidate genes and 26 key miRNAs. Using modern statistical methods, 463 metabolite–lipid, 62 trait–metabolite, and 89 trait–lipid associations were found to be significant. Integrating these associations into the above networks, an MDGN was constructed, and 128 sub-networks were extracted. Among these sub-networks, the gene–trait or gene–metabolite relationships in 38 sub-networks were in agreement with previous studies, e.g., oleic acid (trait)–GmSEI–GmDGAT1a–triacylglycerol (16:0/18:2/18:3), gene and metabolite in each of 64 sub-networks were predicted to be in the same pathway, e.g., oleic acid (trait)–GmPHS–d-glucose, and others were new, e.g., triacylglycerol (16:0/18:1/18:2)–GmbZIP123–GmHD-ZIPIII-10–miR166s–oil content. Conclusions This study showed the advantages of MGDN in dissecting the genetic relationships between complex traits and metabolites. Using sub-networks in MGDN, 3D genetic sub-networks including pyruvate/threonine/citric acid revealed genetic relationships between carbohydrates, oil, and protein content, and 4D genetic sub-networks including PLDs revealed the relationships between oil-related traits and phospholipid metabolism likely influenced by the environment. This study will be helpful in soybean quality improvement and molecular biological research.

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“…Palmitic acid (16:0) is one of two primary saturated fatty acids in soybeans, accounting for about 11% of soybean oil [ 9 ]. Increased palmitic acid content can improve the stability of soybean oil, whereas lower palmitic acid content can reduce the risk of cardiovascular diseases in humans [ 10 ]. Traditional breeding and recent advances in genetic engineering have been used to obtain soybean cultivars with low polyunsaturated fatty acid content and improved oxidative stability without chemical hydrogenation [ 11 , 12 ].…”

Section: Introductionmentioning

confidence: 99%

“…Traditional breeding and recent advances in genetic engineering have been used to obtain soybean cultivars with low polyunsaturated fatty acid content and improved oxidative stability without chemical hydrogenation [ 11 , 12 ]. Modification of genes related to palmitic acid content has been reported to develop a suitable germplasm with palmitic acid content (>4 to <40%) that can meet health requirements [ 10 ]. In recent years, near-infrared spectroscopy has been used to detect fatty acid components in seeds without damage, especially in agriculture, industrial production, and scientific research [ 13 , 14 , 15 , 16 ].…”

Section: Introductionmentioning

confidence: 99%

“…Five genes affecting palmitic acid content have been identified, fap1 , fap3 , fapx , sop1 , and fapnc , but their allelic relationship is not entirely known. There is molecular evidence that fapnc and fap3 are located at the same locus [ 10 , 19 ]. A disrupted splicing mutation in an allele gene of fap1 , 3-ketoacyl-ACP synthase enzyme III ( GmKASIIIA , Glyma09g41380 ), has been associated with the reduced palmitic acid phenotype [ 20 ].…”

Section: Introductionmentioning

confidence: 99%

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QTL Mapping of Palmitic Acid Content Using Specific-Locus Amplified Fragment Sequencing (SLAF-Seq) Genotyping in Soybeans (Glycine max L.)

Xue

Gao

Liu

et al. 2022

IJMS

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Soybeans are essential crops that supply protein and oil. The composition and contents of soybean fatty acids are relevant to human health and have a significant relationship with soybean oil processing and applications. Identifying quantitative trait locus (QTL) genes related to palmitic acid could facilitate the development of a range of nutritive soybean cultivars using molecular marker-assisted selection. In this study, we used a cultivar with higher palmitic acid content, ‘Dongnong42’, and a lower palmitic acid content cultivar, ‘Hobbit’, to establish F2:6 recombinant inbred lines. A high-density genetic map containing 9980 SLAF markers was constructed and distributed across 20 soybean chromosomes. The genetic map contained a total genetic distance of 2602.58 cM and an average genetic distance of 0.39 cM between adjacent markers. Two QTLs related to palmitic acid content were mapped using inclusive composite interval mapping, explaining 4.2–10.1% of the phenotypic variance in three different years and environments, including the QTL included in seed palmitic 7-3, which was validated by developing SSR markers. Based on the SNP/Indel and significant differential expression analyses of Dongnong42 and Hobbit, two genes, Glyma.15g119700 and Glyma.15g119800, were selected as candidate genes. The high-density genetic map, QTLs, and molecular markers will be helpful for the map-based cloning of palmitic acid content genes. These could be used to accelerate breeding for high nutritive value cultivars via molecular marker-assisted breeding.

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Genome-wide identification and analysis of soybean acyl-ACP thioesterase gene family reveals the role of GmFAT to improve fatty acid composition in soybean seed

Cited by 22 publications

References 59 publications

Transcriptomic Analysis Reveals the Regulatory Networks and Hub Genes Controlling the Unsaturated Fatty Acid Contents of Developing Seed in Soybean

Transcriptomic Analysis Reveals the Regulatory Networks and Hub Genes Controlling the Unsaturated Fatty Acid Contents of Developing Seed in Soybean

4D genetic networks reveal the genetic basis of metabolites and seed oil-related traits in 398 soybean RILs

QTL Mapping of Palmitic Acid Content Using Specific-Locus Amplified Fragment Sequencing (SLAF-Seq) Genotyping in Soybeans (Glycine max L.)

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