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. 2022 Nov 4;11(21):2980.
doi: 10.3390/plants11212980.

Longer Duration of Active Oil Biosynthesis during Seed Development Is Crucial for High Oil Yield-Lessons from Genome-Wide In Silico Mining and RNA-Seq Validation in Sesame

Bhagwat Nawade  1 , Ajay Kumar  1 , Rasna Maurya  1 , Rajkumar Subramani  1 , Rashmi Yadav  2 , Kuldeep Singh  1 , Parimalan Rangan  1   3
Affiliations

Longer Duration of Active Oil Biosynthesis during Seed Development Is Crucial for High Oil Yield-Lessons from Genome-Wide In Silico Mining and RNA-Seq Validation in Sesame

Bhagwat Nawade et al. Plants (Basel). .

Abstract

Sesame, one of the ancient oil crops, is an important oilseed due to its nutritionally rich seeds with high protein content. Genomic scale information for sesame has become available in the public databases in recent years. The genes and their families involved in oil biosynthesis in sesame are less studied than in other oilseed crops. Therefore, we retrieved a total of 69 genes and their translated amino acid sequences, associated with gene families linked to the oil biosynthetic pathway. Genome-wide in silico mining helped identify key regulatory genes for oil biosynthesis, though the findings require functional validation. Comparing sequences of the SiSAD (stearoyl-acyl carrier protein (ACP)-desaturase) coding genes with known SADs helped identify two SiSAD family members that may be palmitoyl-ACP-specific. Based on homology with lysophosphatidic acid acyltransferase (LPAAT) sequences, an uncharacterized gene has been identified as SiLPAAT1. Identified key regulatory genes associated with high oil content were also validated using publicly available transcriptome datasets of genotypes contrasting for oil content at different developmental stages. Our study provides evidence that a longer duration of active oil biosynthesis is crucial for high oil accumulation during seed development. This underscores the importance of early onset of oil biosynthesis in developing seeds. Up-regulating, identified key regulatory genes of oil biosynthesis during early onset of seed development, should help increase oil yields.

Keywords: ACCase; DGAT; FAD; KAS; Kennedy pathway; LACS; LPAAT; SAD; early onset; longer duration; oil biosynthesis; sesame.

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Conflict of interest statement

All authors declare that there are no direct or indirect, including financial and non-financial, competing interests, with reference to this article.

Figures

Figure 1
Figure 1
Schematic diagram depicting the oil biosynthesis pathway in plants (adapted from: [5,6,7,8,9,10]). The black dotted arrow indicates multiple steps in the conversion of FFA to acyl-CoA and transport; the blue dotted arrow indicates steps involved in the conversion of acyl-CoA to LPA; the red dotted arrow indicates conversion of TAG to oil bodies or lipid droplets. ACCase: acetyl-CoA carboxylase; ACP: acyl-carrier protein; CPT: CDP-choline:DAG cholinephosphotransferase; DAG: diacylglycerol; DGAT: diacylglycerol acyltransferase; EAR: enoyl-ACP reductase; FAD2: oleate desaturase; FAD3: linoleate desaturase; FAD6: oleate desaturase; FAD7/8: linoleate desaturase; FATA: fatty acid thioesterase A; FATB: fatty acid thioesterase B; FFA: free fatty acid; G3PDH: glycerol-3-phosphate dehydrogenase; G3P: glycerol-3-phosphate; GPAT: glycerol-3-phosphate acyltransferase; HAD: 3-hydroxyacyl-ACP dehydratase; KASI: 3-ketoacyl-ACP synthase I; KASII: 3-ketoacyl-ACP synthase II; KASIII: 3-ketoacyl-ACP synthase III; KAR: 3-ketoacyl-ACP reductase; LACS: long-chain acyl-CoA synthetase; LPAAT: lysophosphaditic acid acyltransferase; LPCAT: acyl-CoA:lysophosphatidylcholine acyltransferase; LPAP: lyso-phosphatidic acid phosphatase; LPA: lyso-phosphatidic acid; LPC: lyso-phosphatidylcholine; MAG: monoacylglycerol; MAGAT: monoacylglycerol acyltransferase; MCAT: malonyl Coenzyme A-ACP transacylase; mFA: PC-modified FA; PAP: phosphatic acid phosphohydrolase; PA: phosphatidic acid; PC: phosphatidylcholine; PDH: pyruvate dehydrogenase; PCH: palmitoyl-CoA hydrolase; PDAT: phospholipid:diacylglycerol acyltransferase; PDCT: PC:DAG cholinephosphotransferase; SAD: stearoyl-ACP desaturase; TAG: triacylglycerol.
Figure 2
Figure 2
Circular dendrogram for the gene products involved in oil biosynthesis constructed using the N–J method with 10,000 bootstraps using MEGAv10 [27]. For accession number details of each gene product, please refer to Supplementary Table S1. Bootstrap values are represented by grey circles on the branches. The subfamily names of gene products are denoted on the outermost circle of the tree. Ah—Arachis hypogaea, At—Arabidopsis thaliana, Bn—Brassica napus, Br—Brassica rapa, Co—Camellia oleifera, Cs—Camelina sativa, Eg—Elaeis guineensis, Gh—Gossypium hirsutum, Gm—Glycine max, Ha—Helianthus annuus, Hi—Handroanthus impetiginosus, Ji—Jatropha curcas, Jr—Juglans regia, Muc—Macfadyena unguis-cati, Nt—Nicotiana tabacum, Oe—Olea europaea, Pf—Perilla frutescens, Rc—Ricinus communis, Sa—Striga asiatica, Sh—Salvia hispanica, Si—Sesamum indicum, Tm—Tropaeolum majus.
Figure 3
Figure 3
Distribution of cis-acting regulatory elements (CAREs) in the promoters of selected genes detected in the PlantCare tool.
Figure 4
Figure 4
The number of binding sites identified using PLACE and PlantPAN 3.0 tools for each of the CARE (cis-acting regulatory elements) associated with oil accumulation (represented in a heat map).
Figure 5
Figure 5
Expression profiles (in FPKM values, Y-axis) for key regulatory genes of oil biosynthesis in sesame using the transcriptome dataset of Wang et al. (2019). The X-axis represents the developmental stages in days post anthesis (DPA). (A): Sad; (B): Fad2; (C): Oleosin 5-like; (D): Oleosin 1-like; (E): Oleosin 1-like; (F): Oleosin 18.2 kDa-like; (G): Dgat; (H): Lpaat4; (I): Fad4L2; (J): nsLTP; (K): DIR1; (L): KCS; (M,N): Set of genes that are expressed significantly less at 10 DPA in both of the low oil yielding genotypes (indicated with a red colored down arrow at 10 DPA); (O): Set of genes that are significantly less expressed at 30 DPA in both of the low oil yielding genotypes (indicated with a red colored down arrow at 30 DPA).
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