Selection for a Zinc-Finger Protein Contributes to Seed Oil Increase during Soybean Domestication

Integrative omics analysis elucidates the genetic basis underlying seed weight and oil content in soybean

Synergistic optimization of key agronomic traits by traditional breeding has dramatically enhanced crop productivity in the past decades. However, the genetic basis underlying coordinated regulation of yield- and quality-related traits remains poorly understood. Here, we dissected the genetic architectures of seed weight and oil content by combining genome-wide association studies (GWAS) and transcriptome-wide association studies (TWAS) using 421 soybean (Glycine max) accessions. We identified 26 and 33 genetic loci significantly associated with seed weight and oil content by GWAS, respectively, and detected 5,276 expression quantitative trait loci (eQTLs) regulating expression of 3,347 genes based on population transcriptomes. Interestingly, a gene module (IC79), regulated by two eQTL hotspots, exhibited significant correlation with both seed weigh and oil content. Twenty-two candidate causal genes for seed traits were further prioritized by TWAS, including Regulator of Weight and Oil of Seed 1 (GmRWOS1), which encodes a sodium pump protein. GmRWOS1 was verified to pleiotropically regulate seed weight and oil content by gene knockout and overexpression. Notably, allelic variations of GmRWOS1 were strongly selected during domestication of soybean. This study uncovers the genetic basis and network underlying regulation of seed weight and oil content in soybean and provides a valuable resource for improving soybean yield and quality by molecular breeding.

The tree peony DREB transcription factor PrDREB2D regulates seed α-linolenic acid accumulation

α-Linolenic acid (ALA), an essential fatty acid (FA) for human health, serves as the precursor of 2 nutritional benefits, docosahexaenoic acid and eicosapentaenoic acid, and can only be obtained from plant foods. We previously found that phospholipid:diacylglycerol acyltransferase 2 (PrPDAT2) derived from ALA-rich tree peony (Paeonia rockii) can promote seed ALA accumulation. However, the regulatory mechanism underlying its promoting effect on ALA accumulation remains unknown. Here, we revealed a tree peony dehydration-responsive element binding transcription factor, PrDREB2D, as an upstream regulator of PrPDAT2, which is involved in regulating seed ALA accumulation. Our findings demonstrated that PrDREB2D serves as a nucleus-localized transcriptional activator that directly activates PrPDAT2 expression. PrDREB2D altered the FA composition in transient overexpression Nicotiana benthamiana leaves and stable transgenic Arabidopsis (Arabidopsis thaliana) seeds. Repressing PrDREB2D expression in P. rockii resulted in decreased PrPDAT2 expression and ALA accumulation. In addition, PrDREB2D strengthened its regulation of ALA accumulation by recruiting the cofactor ABA-response element binding factor PrABF2b. Collectively, the study findings provide insights into the mechanism of seed ALA accumulation and avenues for enhancing ALA yield via biotechnological manipulation.

Regulation of seed traits in soybean

Soybean (Glycine max) is an essential economic crop that provides vegetative oil and protein for humans, worldwide. Increasing soybean yield as well as improving seed quality is of great importance. Seed weight/size, oil and protein content are the three major traits determining seed quality, and seed weight also influences soybean yield. In recent years, the availability of soybean omics data and the development of related techniques have paved the way for better research on soybean functional genomics, providing a comprehensive understanding of gene functions. This review summarizes the regulatory genes that influence seed size/weight, oil content and protein content in soybean. We also provided a general overview of the pleiotropic effect for the genes in controlling seed traits and environmental stresses. Ultimately, it is expected that this review will be beneficial in breeding improved traits in soybean.

Global analysis of seed transcriptomes reveals a novel PLATZ regulator for seed size and weight control in soybean

Seed size and weight are important factors that influence soybean yield. Combining the weighted gene co-expression network analysis (WGCNA) of 45 soybean accessions and gene dynamic changes in seeds at seven developmental stages, we identified candidate genes that may control the seed size/weight. Among these, a PLATZ-type regulator overlapping with 10 seed weight QTLs was further investigated. This zinc-finger transcriptional regulator, named as GmPLATZ, is required for the promotion of seed size and weight in soybean. The GmPLATZ may exert its functions through direct binding to the promoters and activation of the expression of cyclin genes and GmGA20OX for cell proliferation. Overexpression of the GmGA20OX enhanced seed size/weight in soybean. We further found that the GmPLATZ binds to a 32-bp sequence containing a core palindromic element AATGCGCATT. Spacing of the flanking sequences beyond the core element facilitated GmPLATZ binding. An elite haplotype Hap3 was also identified to have higher promoter activity and correlated with higher gene expression and higher seed weight. Orthologues of the GmPLATZ from rice and Arabidopsis play similar roles in seeds. Our study reveals a novel module of GmPLATZ-GmGA20OX/cyclins in regulating seed size and weight and provides valuable targets for breeding of crops with desirable agronomic traits.

Genome scans capture key adaptation and historical hybridization signatures in tetraploid wheat

Tetraploid wheats (Triticum turgidum L.), including durum wheat (T. turgidum ssp. durum (Desf.) Husn.), are important crops with high nutritional and cultural values. However, their production is constrained by sensitivity to environmental conditions. In search of adaptive genetic signatures tracing historical selection and hybridization events, we performed genome scans on two datasets: (1) Durum Global Diversity Panel comprising a total of 442 tetraploid wheat and wild progenitor accessions including durum landraces (n = 286), domesticated emmer (T. turgidum ssp. dicoccum (Schrank) Thell.; n = 103) and wild emmer (T. turgidum ssp. dicoccoides (Korn. ex Asch. & Graebn.) Thell.; n = 53) wheats genotyped using the 90K single nucleotide polymorphism (SNP) array, and (2) a second dataset comprising a total 121 accessions of nine T. turgidum subspecies including wild emmer genotyped with >100 M SNPs from whole-genome resequencing. The genome scan on the first dataset detected six outlier loci on chromosomes 1A, 1B, 3A (n = 2), 6A, and 7A. These loci harbored important genes for adaptation to abiotic stresses, phenological responses, such as seed dormancy, circadian clock, flowering time, and key yield-related traits, including pleiotropic genes, such as HAT1, KUODA1, CBL1, and ZFN1. The scan on the second dataset captured a highly differentiated region on chromosome 2B that shows significant differentiation between two groups: one group consists of Georgian (T. turgidum ssp. paleocolchicum A. Love & D. Love) and Persian (T. turgidum ssp. carthlicum (Nevski) A. Love & D. Love) wheat accessions, while the other group comprises all the remaining tetraploids including wild emmer. This is consistent with a previously reported introgression in this genomic region from T. timopheevii Zhuk. which naturally cohabit in the Georgian and neighboring areas. This region harbored several adaptive genes, including the thermomorphogenesis gene PIF4, which confers temperature-resilient disease resistance and regulates other biological processes. Genome scans can be used to fast-track germplasm housed in gene banks and in situ; which helps to identify environmentally resilient accessions for breeding and/or to prioritize them for conservation.

Non-Tandem CCCH-Type Zinc-Finger Protein CpZF_CCCH1 Improves Fatty Acid Desaturation and Stress Tolerance in Chlamydomonas reinhardtii

The properties and nutritional value of microalgal bioproducts depend significantly on fatty acid desaturation, which is generally modulated by manipulating the culture conditions or associated gene expressions. Here, we investigated the role of CpZF_CCCH1, a non-tandem CCCH-type zinc-finger (non-TZF) protein, in elevating polyunsaturated fatty acid (PUFA) content (11.00-16.36%) in Chlamydomonas reinhardtii. Through lipidomic and flow cytometry analyses, we observed reduced triacylglycerol accumulation (7.01-21.15%) and elevated levels of membrane lipids containing PUFAs (7.81-46.18%) in C. reinhardtii overexpressing CpZF_CCCH1. Additionally, overexpression of nucleus-located CpZF_CCCH1 downregulated genes associated with triacylglycerol assembly and lipid turnover from 2.00- to 2.90-fold, likely by binding to GCN4 motif and promoter of 3-phosphate-glycerol acyltransferase. Furthermore, overexpression of CpZF_CCCH1 alleviated reactive oxygen species levels by 59.28-73.26% and enhanced stress tolerance under adverse conditions. These findings expanded the roles of non-TZF proteins in lipid metabolism, opening new avenues for metabolic engineering to enhance the nutritional value and stress tolerance of microalgae and agricultural crops.

Genome-wide scan for oil quality reveals a coregulation mechanism of tocopherols and fatty acids in soybean seeds

Tocopherols (vitamin E) play essential roles in human health because of their antioxidant activity, and plant-derived oils are the richest sources of tocopherols in the human diet. Although soybean (Glycine max) is one of the main sources of plant-derived oil and tocopherol in the world, the relationship between tocopherol and oil in soybean seeds remains unclear. Here, we focus on dissecting tocopherol metabolism with the long-term goal of increasing α-tocopherol content and soybean oil quality. We first collected tocopherol and fatty acid profiles in a soybean population (>800 soybean accessions) and found that tocopherol content increased during soybean domestication. A strong positive correlation between tocopherol and oil content was also detected. Five tocopherol pathway-related loci were identified using a metabolite genome-wide association study strategy. Genetic variations in three tocopherol pathway genes were responsible for total tocopherol content and composition in the soybean population through effects on enzyme activity, mainly caused by non-conserved amino acid substitution or changes in gene transcription level. Moreover, the fatty acid regulatory transcription factor GmZF351 directly activated tocopherol pathway gene expression, increasing both fatty acid and tocopherol contents in soybean seeds. Our study reveals the functional differentiation of tocopherol pathway genes in soybean populations and provides a framework for development of new soybean varieties with high α-tocopherol content and oil quality in seeds.

Deciphering the fertilizing and disease suppression potential of phytofabricated zinc oxide nanoparticles on Brassicajuncea

Every year 30-50% of crops suffer from fungal and bacterial diseases. Use of various chemically synthesized fungicides and bactericides make the soil environment more toxic and harmful to the plant health. Therefore, there is need to find non-toxic and cost effective alternative against plant pathogen. In recent years, nanotechnology has got attention because of its wide application in different areas of agriculture. Various nanoparticles have been used in agriculture for their fertilizing and antimicrobial potential. Among them zinc oxide nanoparticles (ZnO NPs) have gained the attention of agriculturists as zinc is an essential micronutrient for plants. Antifungal activity of Tb-ZnO NPs (Terminalia bellerica synthesized zinc oxide nanoparticles) against Alternaria brassicae causative agent of blight disease in Brassica juncea has been reported in our previous study. To use Tb-ZnO NPs as nanofungicides and simultaneously as nanofertilizers, the doses of Tb-ZnO NPs beneficial to the Brassica juncea crop is need to be known. Therefore, experiment has been designed to see the protective and curative potential of Tb-ZnO NPs in alluvial and calcareous soil. Biochemical constituents and stress enzymes analysis has shown significant potential of Tb-ZnO NPs at 200 ppm concentration in alleviating the stress caused by A. brassicae by modulating the photosynthetic, biochemical and enzymatic characteristics. Growth parameter analysis confirmed the role of Tb-ZnO NPs in increasing root and shoot length of B. juncea. Yield component such as seed number, seed weight and oil content of B. juncea crop also has been increased. There was one-fold increase in oil content of B. juncea as compared to control. Maximum percent disease control was found to be 70% in alluvial soil (protective method) grown plants. Therefore, present study supports the hypothesis of a relationship between nutrients and disease suppression.

GmJAZ3 interacts with GmRR18a and GmMYC2a to regulate seed traits in soybean

Seed weight is usually associated with seed size and is one of the important agronomic traits that determine yield. Understanding of seed weight control is limited, especially in soybean plants. Here we show that Glycine max JASMONATE-ZIM DOMAIN 3 (GmJAZ3), a gene identified through gene co-expression network analysis, regulates seed-related traits in soybean. Overexpression of GmJAZ3 promotes seed size/weight and other organ sizes in stable transgenic soybean plants likely by increasing cell proliferation. GmJAZ3 interacted with both G. max RESPONSE REGULATOR 18a (GmRR18a) and GmMYC2a to inhibit their transcriptional activation of cytokinin oxidase gene G. max CYTOKININ OXIDASE 3-4 (GmCKX3-4), which usually affects seed traits. Meanwhile, the GmRR18a binds to the promoter of GmMYC2a and activates GmMYC2a gene expression. In GmJAZ3-overexpressing soybean seeds, the protein contents were increased while the fatty acid contents were reduced compared to those in the control seeds, indicating that the GmJAZ3 affects seed size/weight and compositions. Natural variation in JAZ3 promoter region was further analyzed and Hap3 promoter correlates with higher promoter activity, higher gene expression and higher seed weight. The Hap3 promoter may be selected and fixed during soybean domestication. JAZ3 orthologs from other plants/crops may also control seed size and weight. Taken together, our study reveals a novel molecular module GmJAZ3-GmRR18a/GmMYC2a-GmCKXs for seed size and weight control, providing promising targets during soybean molecular breeding for better seed traits.

Interaction of iron and zinc fortification and late-season water deficit on yield and fatty acid composition of Dragon's Head (Lallemantia iberica L.)

Dragon's head (Lallemantia iberica) is a rich source of alpha-linolenic acid, linoleic acid, essential oil, protein, and mucilage. Therefore, the aim of this study was to evaluate the effects of foliar application of three different concentrations of Fe and Zn (control, 4, and 8 g lit-1) at two different developmental stages (vegetative stage (VS) and reproductive stage (RS)) on the quantity and quality of dragon's head seed yield and fatty acid composition in two crop seasons (2018 and 2019) under two environments (normal irrigation as control (NI) and post-anthesis water deficit (WD). In NI, average yields of seed, oil, and protein were 1155, 340, and 183 kg ha-1, respectively, and in the WD, they were 879, 283, and 148 kg ha-1, respectively. By applying Zn and Fe, the mean values of seed, oil, and protein yields in the NI were 1425, 478, and 264 kg ha-1, while in the WD, they were 1011, 354, and 200 kg ha-1, respectively. Furthermore, the application of WD resulted in a significant increase in zinc concentration, protein percentage, and saturated fatty acid percentage in seeds. Unlike WD, iron and zinc treatments decreased the percentage of saturated fatty acids and increased the percentage of unsaturated fatty acids. The number of capsules per plant had the most positive indirect effect on grain yield. The results showed that foliar spraying of Fe and Zn could effectively mitigate the adverse effects of WD on the quality and quantity of seed and oil yield dragon's head.

Genome-Wide Identification and Analysis of the Plant Cysteine Oxidase (PCO) Gene Family in Brassica napus and Its Role in Abiotic Stress Response

Plant Cysteine Oxidase (PCO) is a plant O₂-sensing enzyme catalyzing the oxidation of cysteine to Cys-sulfinic acid at the N-termini of target proteins. To better understand the Brassica napus PCO gene family, PCO genes in B. napus and related species were analyzed. In this study, 20, 7 and 8 PCO genes were identified in Brassica napus, Brassica rapa and Brassica oleracea, respectively. According to phylogenetic analysis, the PCOs were divided into five groups: PCO1, PCO2, PCO3, PCO4 and PCO5. Gene organization and motif distribution analysis suggested that the PCO gene family was relatively conserved during evolution. According to the public expression data, PCO genes were expressed in different tissues at different developmental stages. Moreover, qRT-PCR data showed that most of the Bna/Bra/BoPCO5 members were expressed in leaves, roots, flowers and siliques, suggesting an important role in both vegetative and reproductive development. Expression of BnaPCO was induced by various abiotic stress, especially waterlogging stress, which was consistent with the result of cis-element analysis. In this study, the PCO gene family of Brassicaceae was analyzed for the first time, which contributes to a comprehensive understanding of the origin and evolution of PCO genes in Brassicaceae and the function of BnaPCO in abiotic stress responses.

Integrative lipidomics profile uncovers the mechanisms underlying high-level α-linolenic acid accumulation in Paeonia rockii seeds

Tree peony (Paeonia rockii) is an excellent woody oilseed crop, known for its high α-linolenic acid (ALA, ~45%) content, which is of great value for human health. However, the mechanisms underlying this high-level ALA accumulation in tree peony seeds are poorly understood. In this study, we evaluated the dynamic changes in the lipidomic profile of P. rockii seeds during development. A total of 760 lipid molecules were identified in P. rockii seeds; triacylglycerol (TAG) lipid molecules showed the highest abundance and diversity, both increasing during seed development. Particularly, ALA was the predominant fatty acid at the TAG sn-3 position. We further characterized two diacylglycerol acyltransferase (DGAT) genes and three phospholipid:diacylglycerol acyltransferase (PDAT) genes involved in the transfer of fatty acids to the TAG sn-3 position. Gene expression and subcellular localization analyses suggested that PrDGATs and PrPDATs may function as endoplasmic reticulum-localized proteins in seed TAG biosynthesis. In vitro functional complementation analysis showed different substrate specificities, with PrPDAT2 having a specific preference for ALA. Multiple biological assays demonstrated that PrDGAT1, PrDGAT2, PrPDAT1-2, and PrPDAT2 promote oil synthesis. Specifically, PrPDAT2 leads to preferential ALA in the oil. Our findings provide novel functional evidence of the roles of PrDGAT1 and PrPDAT2, which are potential targets for increasing the ALA yield in tree peony and other oilseed crops.

Addressing global food insecurity: Soil-applied zinc oxide nanoparticles promote yield attributes and seed nutrient quality in Glycine max L

Consumed globally, oilseeds serve as a major source of proteins and oils in human and animal nutrition, supporting global food security. Zinc (Zn) is an essential micronutrient critical for oil and protein synthesis in plants. In this study, we synthesized three distinct sized zinc oxide nanoparticles (nZnO: 38 nm = S [small], 59 nm = M [medium], and > 500 nm = L [large], and assessed the potential effects of varied particle sizes and concentrations (0, 50, 100, 200, and 500 mg/kg-soil) on seed yield attributes, nutrient quality and oil and protein yield in soybean (Glycine max L.) grown for a full lifecycle of 120 days, and compared with soluble Zn²⁺ ions (ZnCl₂) and water-only controls. We observed particle size- and concentration-dependent influence of nZnO on photosynthetic pigments, pod formation, potassium and phosphorus accumulation in seed, and protein and oil yields. Overall, soybean showed significant stimulatory responses to nZnO-S for most of the parameters tested compared to nZnO-M, nZnO-L, and Zn²⁺ ions treatments up to 200 mg/kg, suggesting the potential for small size nZnO to improve seed quality and production in soybean. At 500 mg/kg, however, for all endpoints (except for carotenoids and seed formation) toxicity was observed with all Zn compounds. Further, TEM analysis of seed ultrastructure indicated potential alterations in seed oil bodies and protein storage vacuoles at a toxic concentration (500 mg/kg) of nZnO-S compared to control. These findings suggest 200 mg/kg as an optimal dose for the smallest size nZnO-S (38 nm) to significantly improve seed yield, nutrient quality, and oil and protein yield, paving a path for addressing global food insecurity using small sized nZnO as a novel nano-fertilizer to promote crop yield and nutrient quality, in soil-grown soybean.

Genetic regulatory networks of soybean seed size, oil and protein contents

As a leading oilseed crop that supplies plant oil and protein for daily human life, increasing yield and improving nutritional quality (high oil or protein) are the top two fundamental goals of soybean breeding. Seed size is one of the most critical factors determining soybean yield. Seed size, oil and protein contents are complex quantitative traits governed by genetic and environmental factors during seed development. The composition and quantity of seed storage reserves directly affect seed size. In general, oil and protein make up almost 60% of the total storage of soybean seed. Therefore, soybean's seed size, oil, or protein content are highly correlated agronomical traits. Increasing seed size helps increase soybean yield and probably improves seed quality. Similarly, rising oil and protein contents improves the soybean's nutritional quality and will likely increase soybean yield. Due to the importance of these three seed traits in soybean breeding, extensive studies have been conducted on their underlying quantitative trait locus (QTLs) or genes and the dissection of their molecular regulatory pathways. This review summarized the progress in functional genome controlling soybean seed size, oil and protein contents in recent decades, and presented the challenges and prospects for developing high-yield soybean cultivars with high oil or protein content. In the end, we hope this review will be helpful to the improvement of soybean yield and quality in the future breeding process.

Zinc-finger protein GmZF351 improves both salt and drought stress tolerance in soybean

Abiotic stress is one of the most important factors reducing soybean yield. It is essential to identify regulatory factors contributing to stress responses. A previous study found that the tandem CCCH zinc-finger protein GmZF351 is an oil level regulator. In this study, we discovered that the GmZF351 gene is induced by stress and that the overexpression of GmZF351 confers stress tolerance to transgenic soybean. GmZF351 directly regulates the expression of GmCIPK9 and GmSnRK, leading to stomata closing, by binding to their promoter regions, which carry two CT(G/C)(T/A)AA elements. Stress induction of GmZF351 is mediated through reduction in the H3K27me3 level at the GmZF351 locus. Two JMJ30-demethylase-like genes, GmJMJ30-1 and GmJMJ30-2, are involved in this demethylation process. Overexpression of GmJMJ30-1/2 in transgenic hairy roots enhances GmZF351 expression mediated by histone demethylation and confers stress tolerance to soybean. Yield-related agronomic traits were evaluated in stable GmZF351-transgenic plants under mild drought stress conditions. Our study reveals a new mode of GmJMJ30-GmZF351 action in stress tolerance, in addition to that of GmZF351 in oil accumulation. Manipulation of the components in this pathway is expected to improve soybean traits and adaptation under unfavorable environments.

A multi-locus linear mixed model methodology for detecting small-effect QTLs for quantitative traits in MAGIC, NAM, and ROAM populations

Although multi-parent populations (MPPs) integrate the advantages of linkage and association mapping populations in the genetic dissection of complex traits and especially combine genetic analysis with crop breeding, it is difficult to detect small-effect quantitative trait loci (QTL) for complex traits in multiparent advanced generation intercross (MAGIC), nested association mapping (NAM), and random-open-parent association mapping (ROAM) populations. To address this issue, here we proposed a multi-locus linear mixed model method, namely mppQTL, to detect QTLs, especially small-effect QTLs, in these MPPs. The new method includes two steps. The first is genome-wide scanning based on a single-locus linear mixed model; the P-values are obtained from likelihood-ratio test, the peaks of negative logarithm P-value curve are selected by group-lasso, and all the selected peaks are regarded as potential QTLs. In the second step, all the potential QTLs are placed on a multi-locus linear mixed model, all the effects are estimated using expectation-maximization empirical Bayes algorithm, and all the non-zero effect vectors are further evaluated via likelihood-ratio test for significant QTLs. In Monte Carlo simulation studies, the new method has higher power in QTL detection, lower false positive rate, lower mean absolute deviation for QTL position estimate, and lower mean squared error for the estimate of QTL size (r²) than existing methods because the new method increases the power of detecting small-effect QTLs. In real dataset analysis, the new method (19) identified five more known genes than the existing three methods (14). This study provides an effective method for detecting small-effect QTLs in any MPPs.

Identification of QTN-by-environment interactions and their candidate genes for soybean seed oil-related traits using 3VmrMLM

INTRODUCTION

Although seed oil content and its fatty acid compositions in soybean were affected by environment, QTN-by-environment (QEIs) and gene-by-environment interactions (GEIs) were rarely reported in genome-wide association studies.

METHODS

The 3VmrMLM method was used to associate the trait phenotypes, measured in five to seven environments, of 286 soybean accessions with 106,013 SNPs for detecting QTNs and QEIs.

RESULTS

Seven oil metabolism genes (GmSACPD-A, GmSACPD-B, GmbZIP123, GmSWEET39, GmFATB1A, GmDGAT2D, and GmDGAT1B) around 598 QTNs and one oil metabolism gene GmFATB2B around 54 QEIs were verified in previous studies; 76 candidate genes and 66 candidate GEIs were predicted to be associated with these traits, in which 5 genes around QEIs were verified in other species to participate in oil metabolism, and had differential expression across environments. These genes were found to be related to soybean seed oil content in haplotype analysis. In addition, most candidate GEIs were co-expressed with drought response genes in co-expression network, and three KEGG pathways which respond to drought were enriched under drought stress rather than control condition; six candidate genes were hub genes in the co-expression networks under drought stress.

DISCUSSION

The above results indicated that GEIs, together with drought response genes in co-expression network, may respond to drought, and play important roles in regulating seed oil-related traits together with oil metabolism genes. These results provide important information for genetic basis, molecular mechanisms, and soybean breeding for seed oil-related traits.

GmWRI1c Increases Palmitic Acid Content to Regulate Seed Oil Content and Nodulation in Soybean (Glycine max)

Soybean (Glycine max) is an important oil crop, but the regulatory mechanisms underlying seed oil accumulation remain unclear. We identified a member of the GmWRI1s transcription factor family, GmWRI1c, that is involved in regulating soybean oil content and nodulation. Overexpression of GmWRI1c in soybean hairy roots increased the expression of genes involved in glycolysis and de novo lipogenesis, the proportion of palmitic acid (16:0), and the number of root nodules. The effect of GmWRI1c in increasing the number of root nodules via regulating the proportion of palmitic acid was confirmed in a recombinant inbred line (RIL) population. GmWRI1c shows abundant sequence diversity and has likely undergone artificial selection during domestication. An association analysis revealed a correlation between seed oil content and five linked natural variations (Hap1/Hap2) in the GmWRI1c promoter region. Natural variations in the GmWRI1c promoter were strongly associated with the GmWRI1c transcript level, with higher GmWRI1c transcript levels in lines carrying GmWRI1c^Hap1 than in those carrying GmWRI1c^Hap2. The effects of GmWRI1c alleles on seed oil content were confirmed in natural and RIL populations. We identified a favourable GmWRI1c allele that can be used to breed new varieties with increased seed oil content and nodulation.

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

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.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13068-022-02191-1.

Responses of soybean (Glycine max [L.] Merr.) to zinc oxide nanoparticles: Understanding changes in root system architecture, zinc tissue partitioning and soil characteristics

Addressing global Zinc (Zn) deficiency in food and feed requires innovation in Zn fertilizer. Recently, Zn oxide nanoparticles (ZnONPs) have piqued interest for potential use as a novel nano-Zn fertilizer. However, little is known about potential factors influencing ZnONPs partitioning in different plant tissues, and changes in root system architecture (RSA) and soil characteristics. Herein, we tested the effects of particle size (38, 59, and > 500 nm) and concentration (0-500 mg/kg) of ZnONPs on Zn bioaccumulation in multiple tissues in soil-grown soybean (Glycine max) grown for 120 days, including changes in RSA (root biomass, length, area, volume, and density) and soil characteristics (pH and electrical conductance [EC]). Our results showed significant effects of Zn compound types, Zn concentrations and their interaction on RSA, and Zn uptake by root, stem, leaf, and seed, in soybean. Concentration-response curves for root structures with varied sized ZnONPs and Zn2+ ions were deemed nonlinear, whereas for Zn distribution between different tissues the concentration-response curves were linear. Interestingly, ZnONPs and Zn2+ ions up to 200 mg/kg showed beneficial effects on root growth and development, but toxic response was observed at higher concentrations for both compounds. Root dry weight, length, volume, and area with 200 mg/kg ZnONPs-38 nm were higher by 48%, 56%, 33% and 44%, respectively, compared to control, and were higher by 15%, 23%, 15% and 19%, respectively, compared to 200 mg/kg ZnCl2. In general, soybean responses to the smallest size ZnONPs-38 nm were higher for all parameters evaluated compared to the larger-sized ZnONPs (59 and > 500 nm) and Zn2+ ions. Zn bioaccumulation varied among tissues in the order: root > seed > leaf > stem. A minor but steady decrease in soil pH and EC occurred among different concentrations for both ZnONPs and Zn2+ ions. Improved RSA can facilitate water and nutrient uptake in soybean, promoting growth and yield, especially considering arid and semi-arid climates where water is a limiting factor. Further, improving seed and shoot Zn levels, as demonstrated herein using ZnONPs, is paramount to addressing Zn deficiency in food and feed. Future studies assessing potential impacts on soil microbes, soil health and food safety upon ZnONPs application is critical for risk assessment of the novel nanofertilizer.

Acyl-CoA:diacylglycerol acyltransferase: Properties, physiological roles, metabolic engineering and intentional control

Acyl-CoA:diacylglycerol acyltransferase (DGAT, EC 2.3.1.20) catalyzes the last reaction in the acyl-CoA-dependent biosynthesis of triacylglycerol (TAG). DGAT activity resides mainly in membrane-bound DGAT1 and DGAT2 in eukaryotes and bifunctional wax ester synthase-diacylglycerol acyltransferase (WSD) in bacteria, which are all membrane-bound proteins but exhibit no sequence homology to each other. Recent studies also identified other DGAT enzymes such as the soluble DGAT3 and diacylglycerol acetyltransferase (EaDAcT), as well as enzymes with DGAT activities including defective in cuticular ridges (DCR) and steryl and phytyl ester synthases (PESs). This review comprehensively discusses research advances on DGATs in prokaryotes and eukaryotes with a focus on their biochemical properties, physiological roles, and biotechnological and therapeutic applications. The review begins with a discussion of DGAT assay methods, followed by a systematic discussion of TAG biosynthesis and the properties and physiological role of DGATs. Thereafter, the review discusses the three-dimensional structure and insights into mechanism of action of human DGAT1, and the modeled DGAT1 from Brassica napus. The review then examines metabolic engineering strategies involving manipulation of DGAT, followed by a discussion of its therapeutic applications. DGAT in relation to improvement of livestock traits is also discussed along with DGATs in various other eukaryotic organisms.

Can omic tools help generate alternative newer sources of edible seed oil?

There are three pathways for triacylglycerol (TAG) biosynthesis: De novo TAG biosynthesis, phosphatidylcholine-derived biosynthesis, and cytosolic TAG biosynthesis. Variability in fatty acid composition is mainly associated with phosphatidylcholine-derived TAG pathway. Mobilization of TAG-formed through cytosolic pathway into lipid droplets is yet unknown. There are multiple regulatory checkpoints starting from acetyl-CoA carboxylase to the lipid droplet biogenesis in TAG biosynthesis. Although a primary metabolism, only a few species synthesize oil in seeds for storage, and less than 10 species are commercially exploited. To meet out the growing demand for oil, diversifying into newer sources is the only choice left. The present review highlights the potential strategies targeting species like Azadirachta, Callophyllum, Madhuca, Moringa, Pongamia, Ricinus, and Simarouba, which are not being used for eating but are otherwise high yielding (ranging from 1.5 to 20 tons per hectare) with seeds having a high oil content (40-60%). Additionally, understanding the toxin biosynthesis in Ricinus and Simarouba would be useful in developing toxin-free oil plants. Realization of the importance of cell cultures as "oil factories" is not too far into the future and would soon be a commercially viable option for producing oils in vitro, round the clock.

CCCH Zinc finger genes in Barley: genome-wide identification, evolution, expression and haplotype analysis

BACKGROUND

CCCH transcription factors are important zinc finger transcription factors involved in the response to biotic and abiotic stress and physiological and developmental processes. Barley (Hordeum vulgare) is an agriculturally important cereal crop with multiple uses, such as brewing production, animal feed, and human food. The identification and assessment of new functional genes are important for the molecular breeding of barley.

RESULTS

In this study, a total of 53 protein-encoding CCCH genes unevenly dispersed on seven different chromosomes were identified in barley. Phylogenetic analysis categorized the barley CCCH genes (HvC3Hs) into eleven subfamilies according to their distinct features, and this classification was supported by intron-exon structure and conserved motif analysis. Both segmental and tandem duplication contributed to the expansion of CCCH gene family in barley. Genetic variation of HvC3Hs was characterized using publicly available exome-capture sequencing datasets. Clear genetic divergence was observed between wild and landrace barley populations in HvC3H genes. For most HvC3Hs, nucleotide diversity and the number of haplotype polymorphisms decreased during barley domestication. Furthermore, the HvC3H genes displayed distinct expression profiles for different developmental processes and in response to various types of stresses. The HvC3H1, HvC3H2 and HvC3H13 of arginine-rich tandem CCCH zinc finger (RR-TZF) genes were significantly induced by multiple types of abiotic stress and/or phytohormone treatment, which might make them as excellent targets for the molecular breeding of barley.

CONCLUSIONS

Overall, our study provides a comprehensive characterization of barley CCCH transcription factors, their diversity, and their biological functions.

Large-Scale Integrative Analysis of Soybean Transcriptome Using an Unsupervised Autoencoder Model

Plant tissues are distinguished by their gene expression patterns, which can help identify tissue-specific highly expressed genes and their differential functional modules. For this purpose, large-scale soybean transcriptome samples were collected and processed starting from raw sequencing reads in a uniform analysis pipeline. To address the gene expression heterogeneity in different tissues, we utilized an adversarial deconfounding autoencoder (AD-AE) model to map gene expressions into a latent space and adapted a standard unsupervised autoencoder (AE) model to help effectively extract meaningful biological signals from the noisy data. As a result, four groups of 1,743, 914, 2,107, and 1,451 genes were found highly expressed specifically in leaf, root, seed and nodule tissues, respectively. To obtain key transcription factors (TFs), hub genes and their functional modules in each tissue, we constructed tissue-specific gene regulatory networks (GRNs), and differential correlation networks by using corrected and compressed gene expression data. We validated our results from the literature and gene enrichment analysis, which confirmed many identified tissue-specific genes. Our study represents the largest gene expression analysis in soybean tissues to date. It provides valuable targets for tissue-specific research and helps uncover broader biological patterns. Code is publicly available with open source at https://github.com/LingtaoSu/SoyMeta.

Progress in soybean functional genomics over the past decade

Soybean is one of the most important oilseed and fodder crops. Benefiting from the efforts of soybean breeders and the development of breeding technology, large number of germplasm has been generated over the last 100 years. Nevertheless, soybean breeding needs to be accelerated to meet the needs of a growing world population, to promote sustainable agriculture and to address future environmental changes. The acceleration is highly reliant on the discoveries in gene functional studies. The release of the reference soybean genome in 2010 has significantly facilitated the advance in soybean functional genomics. Here, we review the research progress in soybean omics (genomics, transcriptomics, epigenomics and proteomics), germplasm development (germplasm resources and databases), gene discovery (genes that are responsible for important soybean traits including yield, flowering and maturity, seed quality, stress resistance, nodulation and domestication) and transformation technology during the past decade. At the end, we also briefly discuss current challenges and future directions.

Integrating omics approaches to discover and prioritize candidate genes involved in oil biosynthesis in soybean

Soybean is a major source of edible protein and oil. Oil content is a quantitative trait that is significantly determined by genetic and environmental factors. Over the past 30 years, a large volume of soybean genetic, genomic, and transcriptomic data have been accumulated. Nevertheless, integrative analyses of such data remain scarce, in spite of their importance for crop improvement. We hypothesized that the co-occurrence of genomic regions for oil-related traits in different studies may reveal more stable regions encompassing important genetic determinants of oil content and quality in soybean. We integrated publicly available data, obtained with distinct techniques, to discover and prioritize candidate genes involved in oil biosynthesis and regulation in soybean. We detected key fatty acid biosynthesis genes (e.g., BCCP2 and ACCase, FADs, KAS family proteins) and several transcription factors, which are likely regulators of oil biosynthesis. In addition, we identified new candidates for seed oil accumulation and quality, such as Glyma.03G213300 and Glyma.19G160700, which encode a translocator protein homolog and a histone acetyltransferase, respectively. Further, oil and protein genomic hotspots are strongly associated with breeding and not with domestication, suggesting that soybean domestication prioritized other traits. The genes identified here are promising targets for breeding programs and for the development of soybean lines with increased oil content and quality.

Domestication and improvement genes reveal the differences of seed size- and oil-related traits in soybean domestication and improvement

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Due to reduced diversity, it is essential to map domesticated and improved genes.

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13 known and 442 candidate genes were mined for seed size- and oil-related traits.

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All the genes were used to explain trait changes in domestication and improvement.

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56 domesticated and 15 improved genes may be valuable for future soybean breeding.

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This study provides useful gene resources for future breeding and biology research.

To address domestication and improvement studies of soybean seed size- and oil-related traits, a series of domesticated and improved regions, loci, and candidate genes were identified in 286 soybean accessions using domestication and improvement analyses, genome-wide association studies, quantitative trait locus (QTL) mapping and bulked segregant analyses in this study. As a result, 534 candidate domestication regions (CDRs) and 458 candidate improvement regions (CIRs) were identified in this study and integrated with those in five and three previous studies, respectively, to obtain 952 CDRs and 538 CIRs; 1469 loci for soybean seed size- and oil-related traits were identified in this study and integrated with those in Soybase to obtain 433 QTL clusters. The two results were intersected to obtain 245 domestication and 221 improvement loci for the above traits. Around these trait-related domestication and improvement loci, 7 domestication and 7 improvement genes were found to be truly associated with these traits, and 372 candidate domestication and 87 candidate improvement genes were identified using gene expression, SNP variants in genome, miRNA binding, KEGG pathway, DNA methylation, and haplotype analysis. These genes were used to explain the trait changes in domestication and improvement. As a result, the trait changes can be explained by their frequencies of elite haplotypes, base mutations in coding region, and three factors affecting their expression levels. In addition, 56 domestication and 15 improvement genes may be valuable for future soybean breeding. This study can provide useful gene resources for future soybean breeding and molecular biology research.

Nuclear factor Y subunit GmNFYA competes with GmHDA13 for interaction with GmFVE to positively regulate salt tolerance in soybean

Soybean is an important crop worldwide, but its production is severely affected by salt stress. Understanding the regulatory mechanism of salt response is crucial for improving the salt tolerance of soybean. Here, we reveal a role for nuclear factor Y subunit GmNFYA in salt tolerance of soybean likely through the regulation of histone acetylation. GmNFYA is induced by salt stress. Overexpression of GmNFYA significantly enhances salt tolerance in stable transgenic soybean plants by inducing salt-responsive genes. Analysis in soybean plants with transgenic hairy roots also supports the conclusion. GmNFYA interacts with GmFVE, which functions with putative histone deacetylase GmHDA13 in a complex for transcriptional repression possibly by reducing H3K9 acetylation at target loci. Under salt stress, GmNFYA likely accumulates and competes with GmHDA13 for interaction with GmFVE, leading to the derepression and maintenance of histone acetylation for activation of salt-responsive genes and finally conferring salt tolerance in soybean plants. In addition, a haplotype I GmNFYA promoter is identified with the highest self-activated promoter activity and may be selected during future breeding for salt-tolerant cultivars. Our study uncovers the epigenetic regulatory mechanism of GmNFYA in salt-stress response, and all the factors/elements identified may be potential targets for genetic manipulation of salt tolerance in soybean and other crops.

The role of glutathione-mediated triacylglycerol synthesis in the response to ultra-high cadmium stress in Auxenochlorella protothecoides

Under ultra-high cadmium (Cd) stress, large amounts of glutathione are produced in Auxenochlorella protothecoides UTEX 2341, and the lipid content increases significantly. Glutathione is the best reductant that can effectively remove Cd, but the relationship between lipid accumulation and the cellular response to Cd stress has not been ascertained. Integrating analyses of the transcriptomes and lipidomes, the mechanism of lipid accumulation to Cd tolerance were studied from the perspectives of metabolism, transcriptional regulation and protein glutathionylation. Under Cd stress, basic metabolic pathways, such as purine metabolism, translation and pre-mRNA splicing process, were inhibited, while the lipid accumulation pathway was significantly activated. Further analysis revealed that the transcription factors (TFs) and genes related to lipid accumulation were also activated. Analysis of the TF interaction sites showed that ABI5, MYB_rel and NF-YB could further regulate the expression of diacylglycerol acyltransferase through glutathionylation/deglutathionylation, which led to increase of the triacylglycerol (TAG) content. Lipidomes analysis showed that TAG could help maintain lipid homeostasis by adjusting its saturation/unsaturation levels. This study for the first time indicated that glutathione could activate TAG synthesis in microalga A. protothecoides, leading to TAG accumulation and glutathione accumulation under Cd stress. Therefore, the accumulation of TAG and glutathione can confer resistance to high Cd stress. This study provided insights into a new operation mode of TAG accumulation under heavy metal stress.

The CCCH zinc finger family of soybean (Glycine max L.): genome-wide identification, expression, domestication, GWAS and haplotype analysis

BACKGROUND

The CCCH zinc finger (zf_CCCH) is a unique subfamily featured one or more zinc finger motif(s) comprising of three Cys and one His residues. The zf_CCCH family have been reported involving in various processes of plant development and adaptation.

RESULTS

In this study, the zf_CCCH genes were identified via a genome-wide search and were systematically analyzed. 116 Gmzf_CCCHs were obtained and classified into seventeen subfamilies. Gene duplication and expansion analysis showed that tandem and segmental duplications contributed to the expansion of the Gmzf_CCCH gene family, and that segmental duplication play the main role. The expression patterns of Gmzf_CCCH genes were tissue-specific. Eleven domesticated genes were detected involved in the regulation of seed oil and protein synthesis as well as growth and development of soybean through GWAS and haplotype analysis for Gmzf_CCCH genes among the 164 of 302 soybeans resequencing data. Among which, 8 genes play an important role in the synthesis of seed oil or fatty acid, and the frequency of their elite haplotypes changes significantly among wild, landrace and improved cultivars, indicating that they have been strongly selected in the process of soybean domestication.

CONCLUSIONS

This study provides a scientific foundation for the comprehensive understanding, future cloning and functional studies of Gmzf_CCCH genes in soybean, meanwhile, it was also helpful for the improvement of soybean with high oil content.

A transcriptional regulatory module controls lipid accumulation in soybean

Soybean (Glycine max) is one of the most important oilseed crops. However, the regulatory mechanism that governs the process of oil accumulation in soybean remains poorly understood. In this study, GmZF392, a tandem CCCH zinc finger (TZF) protein which was identified in our previous RNA-seq analysis of seed-preferred transcription factors, was found to function as a positive regulator of lipid production. GmZF392 promotes seed oil accumulation in both transgenic Arabidopsis and stable transgenic soybean plants by binding to a bipartite cis-element, containing TG- and TA-rich sequences, in promoter regions, activating the expression of genes in the lipid biosynthesis pathway. GmZF392 physically interacts with GmZF351, our previously identified transcriptional regulator of lipid biosynthesis, to synergistically promote downstream gene expression. Both GmZF392 and GmZF351 are further upregulated by GmNFYA, another transcription factor involved in lipid biosynthesis, directly (in the former case) and indirectly (in the latter case). Promoter sequence diversity analysis showed that the GmZF392 promoter may have been selected at the origin of the Glycine genus and further mildly selected during domestication from wild soybeans to cultivated soybeans. Our study reveals a regulatory module containing three transcription factors in the lipid biosynthesis pathway, and manipulation of the module may improve oil production in soybean and other oilseed crops.

Analysis and Functional Verification of PoWRI1 Gene Associated with Oil Accumulation Process in Paeonia ostii

The plant transcription factor WRINKLED1 (WRI1), a member of AP2/EREBP, is involved in the regulation of glycolysis and the expression of genes related to the de novo synthesis of fatty acids in plastids. In this study, the key regulator of seed oil synthesis and accumulation transcription factor gene PoWRI1 was identified and cloned, having a complete open reading frame of 1269 bp and encoding 422 amino acids. Subcellular localization analysis showed that PoWRI1 is located at the nucleus. After the expression vector of PoWRI1 was constructed and transformed into wild-type Arabidopsis thaliana, it was found that the overexpression of PoWRI1 increased the expression level of downstream target genes such as BCCP2, KAS1, and PKP-β1. As a result, the seeds of transgenic plants became larger, the oil content increased significantly, and the unsaturated fatty acid content increased, which provide a scientific theoretical basis for the subsequent use of genetic engineering methods to improve the fatty acid composition and content of plant seeds.

Transcriptomic analysis of α-linolenic acid content and biosynthesis in Paeonia ostii fruits and seeds

Background

Paeonia ostii is a potentially important oilseed crop because its seed yield is high, and the seeds are rich in α-linolenic acid (ALA). However, the molecular mechanisms underlying ALA biosynthesis during seed kernel, seed testa, and fruit pericarp development in this plant are unclear. We used transcriptome data to address this knowledge gap.

Results

Gas chromatograph-mass spectrometry indicated that ALA content was highest in the kernel, moderate in the testa, and lowest in the pericarp. Therefore, we used RNA-sequencing to compare ALA synthesis among these three tissues. We identified 227,837 unigenes, with an average length of 755 bp. Of these, 1371 unigenes were associated with lipid metabolism. The fatty acid (FA) biosynthesis and metabolism pathways were significantly enriched during the early stages of oil accumulation in the kernel. ALA biosynthesis was significantly enriched in parallel with increasing ALA content in the testa, but these metabolic pathways were not significantly enriched during pericarp development. By comparing unigene transcription profiles with patterns of ALA accumulation, specific unigenes encoding crucial enzymes and transcription factors (TFs) involved in de novo FA biosynthesis and oil accumulation were identified. Specifically, the bell-shaped expression patterns of genes encoding SAD, FAD2, FAD3, PDCT, PDAT, OLE, CLE, and SLE in the kernel were similar to the patterns of ALA accumulation in this tissue. Genes encoding BCCP, BC, KAS I– III, and FATA were also upregulated during the early stages of oil accumulation in the kernel. In the testa, the upregulation of the genes encoding SAD, FAD2, and FAD3 was followed by a sharp increase in the concentrations of ALA. In contrast, these genes were minimally expressed (and ALA content was low) throughout pericarp development.

Conclusions

We used three tissues with high, moderate, and low ALA concentrations as an exemplar system in which to investigate tissue-specific ALA accumulation mechanisms in P. ostii. The genes and TFs identified herein might be useful targets for future studies of ALA accumulation in the tree peony. This study also provides a framework for future studies of FA biosynthesis in other oilseed plants.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07594-2.

Enhanced separation and analysis of low abundant soy proteins by dual washing extraction process

Soybean seeds provide a rich source of proteins, fats, carbohydrates, and micronutrients. Extraction and analysis of low abundant soybean seed proteins are challenging because of its complex seed composition. For characterizing various proteins, it is paramount to remove the other interfering components, primarily oils, and carbohydrates. In the present study, we used a sequential dual washing process initially with hexane to remove oil and non-polar interferences, followed by 80% ethanol washing to remove about 60% of the total soluble sugars. The extracted soluble sugars were quantified using a newly developed and validated high-performance liquid chromatography-evaporative light scattering detector (HPLC-ELSD). This newly developed combined washings process significantly enhanced the separation of both low molecular weight and low abundant proteins using 1D (one dimensional)- and 2D (two dimensional) gel electrophoresis. The separated proteins were trypsinized and analyzed by using Bruker amazon speed ion trap mass spectrometer equipped with an ESI source. This combined washing process allowed the identification of 18 additional low abundant soy proteins as compared to the simple hexane washed samples. This purification process will allow researchers to identify and investigate the role of low molecular weight and low abundant proteins as it relates to plant functions, nutrition, and health.

Accelerating gene function discovery by rapid phenotyping of fatty acid composition and oil content of single transgenic T1 Arabidopsis and camelina seeds

Arabidopsis is wildly used as a model plant and camelina is increasingly used for oilseed research and applications. Although the Arabidopsis genome has been sequenced for two decades, the functions of many lipid-related genes and their regulators have not been well characterized. Improvements in the efficiency and accuracy of gene investigations are key to effective discovery of gene function and downstream bioengineering of plant oil quantity and quality. In this study, a visible marker was used to quickly identify transgenic T1 seeds and a method has been developed to phenotype fatty acid compositions and oil content of single T1 seeds. A whole seed direct transmethylation method was first optimized with multiple seeds and incubation at 85°C for 2 hours in a transmethylation solvent (5% H2SO4 in methanol with 30% toluene cosolvent) is recommended. Based on this method, a single Arabidopsis seed mini-transmethylation (SAST) method has been established in a 1.5 ml GC sample vial with 200 μl transmethylation solvent. Characteristics of the method were evaluated and it was used to phenotype transgenic T1 seeds expressing AtFAD2 or RcWRI1. Our results indicate that fatty acid composition of T1 individual seeds are consistent with those of pools of multiple seeds from higher generations. However, oil content per individual seed varied substantially and therefore pooling five seeds is recommended for phenotyping oil content of T1 seeds. Additionally, a whole camelina single-seed direct transmethylation was evaluated and results confirm its feasibility. The suitability of partial seed analysis of camelina was investigated but variation in composition of different seed tissues limits this approach.

Genetic variants and underlying mechanisms influencing variance heterogeneity in maize

Traditional genetic studies focus on identifying genetic variants associated with the mean difference in a quantitative trait. Because genetic variants also influence phenotypic variation via heterogeneity, we conducted a variance-heterogeneity genome-wide association study to examine the contribution of variance heterogeneity to oil-related quantitative traits. We identified 79 unique variance-controlling single nucleotide polymorphisms (vSNPs) from the sequences of 77 candidate variance-heterogeneity genes for 21 oil-related traits using the Levene test (P < 1.0 × 10^-5 ). About 30% of the candidate genes encode enzymes that work in lipid metabolic pathways, most of which define clear expression variance quantitative trait loci. Of the vSNPs specifically associated with the genetic variance heterogeneity of oil concentration, 89% can be explained by additional linked mean-effects genetic variants. Furthermore, we demonstrated that gene × gene interactions play important roles in the formation of variance heterogeneity for fatty acid compositional traits. The interaction pattern was validated for one gene pair (GRMZM2G035341 and GRMZM2G152328) using yeast two-hybrid and bimolecular fluorescent complementation analyses. Our findings have implications for uncovering the genetic basis of hidden additive genetic effects and epistatic interaction effects, and we indicate opportunities to stabilize efficient breeding and selection of high-oil maize (Zea mays L.).

Three-dimensional genetic networks among seed oil-related traits, metabolites and genes reveal the genetic foundations of oil synthesis in soybean

Although the biochemical and genetic basis of lipid metabolism is clear in Arabidopsis, there is limited information concerning the relevant genes in Glycine max (soybean). To address this issue, we constructed three-dimensional genetic networks using six seed oil-related traits, 52 lipid metabolism-related metabolites and 54 294 SNPs in 286 soybean accessions in total. As a result, 284 and 279 candidate genes were found to be significantly associated with seed oil-related traits and metabolites by phenotypic and metabolic genome-wide association studies and multi-omics analyses, respectively. Using minimax concave penalty (MCP) and smoothly clipped absolute deviation (SCAD) analyses, six seed oil-related traits were found to be significantly related to 31 metabolites. Among the above candidate genes, 36 genes were found to be associated with oil synthesis (27 genes), amino acid synthesis (four genes) and the tricarboxylic acid (TCA) cycle (five genes), and four genes (GmFATB1a, GmPDAT, GmPLDα1 and GmDAGAT1) are already known to be related to oil synthesis. Using this information, 133 three-dimensional genetic networks were constructed, 24 of which are known, e.g. pyruvate-GmPDAT-GmFATA2-oil content. Using these networks, GmPDAT, GmAGT and GmACP4 reveal the genetic relationships between pyruvate and the three major nutrients, and GmPDAT, GmZF351 and GmPgs1 reveal the genetic relationships between amino acids and seed oil content. In addition, GmCds1, along with average temperature in July and the rainfall from June to September, influence seed oil content across years. This study provides a new approach for the construction of three-dimensional genetic networks and reveals new information for soybean seed oil improvement and the identification of gene function.

Molecular and functional characterization of two DELLA protein-coding genes in litchi

DELLA proteins are members of the plant-specific GRAS family, acting as negative regulators of plant growth. In this study, we identified two DELLA protein-coding genes in litchi, denoted as LcGAI and LcRGL1. Motif analysis showed that LcGAI and LcRGL1 proteins both contain a conserved DELLA and TVHYNP motif at the N-terminus as well as LHR1, VHIID, LHR2, PFYRE, and SAW motifs at the C terminus. The fused proteins of LcGAI-GFP and LcRGL1-GFP were both localized in the nucleus. Overexpression of LcGAI and LcRGL1 in Arabidopsis substantially inhibits leaf growth. Expression analysis showed that HLH factors, PRE1 and PRE5, were restrained, whereas gibberellin (GA) receptors GID1a and LcGID1b were enhanced in LcGAI and LcRGL1 overexpression lines. Results of the yeast two-hybrid assay showed that LcGAI and LcRGL1 interact with LcGID1b/LcGID1c in a GA dose-dependent manner, whereas LcGAI and LcRGL1 had a greater binding capacity to LcGID1b than LcGID1c. These observations suggested that LcGAI and LcRGL1 proteins are nuclear growth repressors.

Molecular Basis of Plant Oil Biosynthesis: Insights Gained From Studying the WRINKLED1 Transcription Factor

Most plant species generate and store triacylglycerol (TAG) in their seeds, serving as a core supply of carbon and energy to support seedling development. Plant seed oils have a wide variety of applications, from being essential for human diets to serving as industrial renewable feedstock. WRINKLED1 (WRI1) transcription factor plays a central role in the transcriptional regulation of plant fatty acid biosynthesis. Since the discovery of Arabidopsis WRI1 gene (AtWRI1) in 2004, the function of WRI1 in plant oil biosynthesis has been studied intensively. In recent years, the identification of WRI1 co-regulators and deeper investigations of the structural features and molecular functions of WRI1 have advanced our understanding of the mechanism of the transcriptional regulation of plant oil biosynthesis. These advances also help pave the way for novel approaches that will better utilize WRI1 for bioengineering oil production in crops.

Research advances of WRINKLED1 (WRI1) in plants

WRINKLED 1 (WRI1), a member of the AP2/EREBP class of transcription factors, regulates carbon allocation between the glycolytic and fatty acid biosynthetic pathways and plays important roles in other biological events. Previous studies have suggested that post-translational modifications and interacting partners modulate the activity of WRI1. We systematically summarised the structure of WRI1 as well as its molecular interactions during transcription and translation in plants. This work elucidates the genetic evolution and regulatory functions of WRI1 at the molecular level and describes a new pathway involving WRI1 that can be used to produce triacylglycerols (TAGs) in plants.

Natural variation and selection in GmSWEET39 affect soybean seed oil content

Soybean (Glycine max) is a major contributor to the world oilseed production. Its seed oil content has been increased through soybean domestication and improvement. However, the genes underlying the selection are largely unknown. The present contribution analyzed the expression patterns of genes in the seed oil quantitative trait loci with strong selective sweep signals, then used association, functional study and population genetics to reveal a sucrose efflux transporter gene, GmSWEET39, controlling soybean seed oil content and under selection. GmSWEET39 is highly expressed in soybean seeds and encodes a plasma membrane-localized protein. Its expression level is positively correlated with soybean seed oil content. The variation in its promoter and coding sequence leads to different natural alleles of this gene. The GmSWEET39 allelic effects on total oil content were confirmed in the seeds of soybean recombinant inbred lines, transgenic Arabidopsis, and transgenic soybean hairy roots. The frequencies of its superior alleles increased from wild soybean to cultivated soybean, and are much higher in released soybean cultivars. The findings herein suggest that the sequence variation in GmSWEET39 affects its relative expression and oil content in soybean seeds, and GmSWEET39 has been selected to increase seed oil content during soybean domestication and improvement.

A class B heat shock factor selected for during soybean domestication contributes to salt tolerance by promoting flavonoid biosynthesis

Soybean (Glycine max) production is severely affected in unfavorable environments. Identification of the regulatory factors conferring stress tolerance would facilitate soybean breeding. In this study, through coexpression network analysis of salt-tolerant wild soybeans, together with molecular and genetic approaches, we revealed a previously unidentified function of a class B heat shock factor, HSFB2b, in soybean salt stress response. We showed that HSFB2b improves salt tolerance through the promotion of flavonoid accumulation by activating one subset of flavonoid biosynthesis-related genes and by inhibiting the repressor gene GmNAC2 to release another subset of genes in the flavonoid biosynthesis pathway. Moreover, four promoter haplotypes of HSFB2b were identified from wild and cultivated soybeans. Promoter haplotype II from salt-tolerant wild soybean Y20, with high promoter activity under salt stress, is probably selected for during domestication. Another promoter haplotype, III, from salt-tolerant wild soybean Y55, had the highest promoter activity under salt stress, had a low distribution frequency and may be subjected to the next wave of selection. Together, our results revealed the mechanism of HSFB2b in soybean salt stress tolerance. Its promoter variations were identified, and the haplotype with high activity may be adopted for breeding better soybean cultivars that are adapted to stress conditions.

WRINKLED1, a "Master Regulator" in Transcriptional Control of Plant Oil Biosynthesis

A majority of plant species generate and accumulate triacylglycerol (TAG) in their seeds, which is the main resource of carbon and energy supporting the process of seedling development. Plant seed oils have broad ranges of uses, being not only important for human diets but also renewable feedstock of industrial applications. The WRINKLED1 (WRI1) transcription factor is vital for the transcriptional control of plant oil biosynthetic pathways. Since the identification of the Arabidopsis WRI1 gene (AtWRI1) fifteen years ago, tremendous progress has been made in understanding the functions of WRI1 at multiple levels, ranging from the identification of AtWRI1 target genes to location of the AtWRI1 binding motif, and from discovery of intrinsic structural disorder in WRI1 to fine-tuning of WRI1 modulation by post-translational modifications and protein-protein interactions. The expanding knowledge on the functional understanding of the WRI1 regulatory mechanism not only provides a clearer picture of transcriptional regulation of plant oil biosynthetic pathway, but also helps generate new strategies to better utilize WRI1 for developing novel oil crops.

Artificial selection on GmOLEO1 contributes to the increase in seed oil during soybean domestication

Increasing seed oil content is one of the most important breeding goals for soybean due to a high global demand for edible vegetable oil. However, genetic improvement of seed oil content has been difficult in soybean because of the complexity of oil metabolism. Determining the major variants and molecular mechanisms conferring oil accumulation is critical for substantial oil enhancement in soybean and other oilseed crops. In this study, we evaluated the seed oil contents of 219 diverse soybean accessions across six different environments and dissected the underlying mechanism using a high-resolution genome-wide association study (GWAS). An environmentally stable quantitative trait locus (QTL), GqOil20, significantly associated with oil content was identified, accounting for 23.70% of the total phenotypic variance of seed oil across multiple environments. Haplotype and expression analyses indicate that an oleosin protein-encoding gene (GmOLEO1), colocated with a leading single nucleotide polymorphism (SNP) from the GWAS, was significantly correlated with seed oil content. GmOLEO1 is predominantly expressed during seed maturation, and GmOLEO1 is localized to accumulated oil bodies (OBs) in maturing seeds. Overexpression of GmOLEO1 significantly enriched smaller OBs and increased seed oil content by 10.6% compared with those of control seeds. A time-course transcriptomics analysis between transgenic and control soybeans indicated that GmOLEO1 positively enhanced oil accumulation by affecting triacylglycerol metabolism. Our results also showed that strong artificial selection had occurred in the promoter region of GmOLEO1, which resulted in its high expression in cultivated soybean relative to wild soybean, leading to increased seed oil accumulation. The GmOLEO1 locus may serve as a direct target for both genetic engineering and selection for soybean oil improvement.

Whole-genome mapping identified novel "QTL hotspots regions" for seed storability in soybean (Glycine max L.)

BACKGROUND

Seed aging in soybean is a serious challenge for agronomic production and germplasm preservation. However, its genetic basis remains largely unclear in soybean. Unraveling the genetic mechanism involved in seed aging, and enhancing seed storability is an imperative goal for soybean breeding. The aim of this study is to identify quantitative trait loci (QTLs) using high-density genetic linkage maps of soybean for seed storability. In this regard, two recombinant inbred line (RIL) populations derived from Zhengyanghuangdou × Meng 8206 (ZM6) and Linhefenqingdou × Meng 8206 (LM6) crosses were evaluated for three seed-germination related traits viz., germination rate (GR), normal seedling length (SL) and normal seedling fresh weight (FW) under natural and artificial aging conditions to map QTLs for seed storability.

RESULTS

A total of 34 QTLs, including 13 QTLs for GR, 11 QTLs for SL and 10 QTLs for FW, were identified on 11 chromosomes with the phenotypic variation ranged from 7.30 to 23.16% under both aging conditions. All these QTLs were novel, and 21 of these QTLs were clustered in five QTL-rich regions on four different chromosomes viz., Chr3, Chr5, Chr17 &Chr18, among them the highest concentration of seven and six QTLs were found in "QTL hotspot A" (Chr17) and "QTL hotspot B" (Chr5), respectively. Furthermore, QTLs within all the five QTL clusters are linked to at least two studied traits, which is also supported by highly significant correlation between the three germination-related traits. QTLs for seed-germination related traits in "QTL hotspot B" were found in both RIL populations and aging conditions, and also QTLs underlying "QTL hotspot A" are identified in both RIL populations under artificial aging condition. These are the stable genomic regions governing the inheritance of seed storability in soybean, and will be the main focus for soybean breeders.

CONCLUSION

This study uncovers the genetic basis of seed storability in soybean. The newly identified QTLs provides valuable information, and will be main targets for fine mapping, candidate gene identification and marker-assisted breeding. Hence, the present study is the first report for the comprehensive and detailed investigation of genetic architecture of seed storability in soybean.

Metabolic engineering for enhanced oil in biomass

The world is hungry for energy. Plant oils in the form of triacylglycerol (TAG) are one of the most reduced storage forms of carbon found in nature and hence represent an excellent source of energy. The myriad of applications for plant oils range across foods, feeds, biofuels, and chemical feedstocks as a unique substitute for petroleum derivatives. Traditionally, plant oils are sourced either from oilseeds or tissues surrounding the seed (mesocarp). Most vegetative tissues, such as leaves and stems, however, accumulate relatively low levels of TAG. Since non-seed tissues constitute the majority of the plant biomass, metabolic engineering to improve their low-intrinsic TAG-biosynthetic capacity has recently attracted significant attention as a novel, sustainable and potentially high-yielding oil production platform. While initial attempts predominantly targeted single genes, recent combinatorial metabolic engineering strategies have focused on the simultaneous optimization of oil synthesis, packaging and degradation pathways (i.e., 'push, pull, package and protect'). This holistic approach has resulted in dramatic, seed-like TAG levels in vegetative tissues. With the first proof of concept hurdle addressed, new challenges and opportunities emerge, including engineering fatty acid profile, translation into agronomic crops, extraction, and downstream processing to deliver accessible and sustainable bioenergy.

DA-6 promotes germination and seedling establishment from aged soybean seeds by mediating fatty acid metabolism and glycometabolism

Soybean seeds contain higher concentrations of oil (triacylglycerol) and fatty acids than do cereal crop seeds, and the oxidation of these biomolecules during seed storage significantly shortens seed longevity and decreases germination ability. Here, we report that diethyl aminoethyl hexanoate (DA-6), a plant growth regulator, increases germination and seedling establishment from aged soybean seeds by increasing fatty acid metabolism and glycometabolism. Phenotypic analysis showed that DA-6 treatment markedly promoted germination and seedling establishment from naturally and artificially aged soybean seeds. Further analysis revealed that DA-6 increased the concentrations of soluble sugars during imbibition of aged soybean seeds. Consistently, the concentrations of several different fatty acids in DA-6-treated aged seeds were higher than those in untreated aged seeds. Subsequently, quantitative PCR analysis indicated that DA-6 induced the transcription of several key genes involved in the hydrolysis of triacylglycerol to sugars in aged soybean seeds. Furthermore, the activity of invertase in aged seeds, which catalyzes the hydrolysis of sucrose to form fructose and glucose, increased following DA-6 treatment. Taken together, DA-6 promotes germination and seedling establishment from aged soybean seeds by enhancing the hydrolysis of triacylglycerol and the conversion of fatty acids to sugars.

An integrated omics analysis reveals molecular mechanisms that are associated with differences in seed oil content between Glycine max and Brassica napus

BACKGROUND

Rapeseed (Brassica napus L.) and soybean (Glycine max L.) seeds are rich in both protein and oil, which are major sources of biofuels and nutrition. Although the difference in seed oil content between soybean (~ 20%) and rapeseed (~ 40%) exists, little is known about its underlying molecular mechanism.

RESULTS

An integrated omics analysis was performed in soybean, rapeseed, Arabidopsis (Arabidopsis thaliana L. Heynh), and sesame (Sesamum indicum L.), based on Arabidopsis acyl-lipid metabolism- and carbon metabolism-related genes. As a result, candidate genes and their transcription factors and microRNAs, along with phylogenetic analysis and co-expression network analysis of the PEPC gene family, were found to be largely associated with the difference between the two species. First, three soybean genes (Glyma.13G148600, Glyma.13G207900 and Glyma.12G122900) co-expressed with GmPEPC1 are specifically enriched during seed storage protein accumulation stages, while the expression of BnPEPC1 is putatively inhibited by bna-miR169, and two genes BnSTKA and BnCKII are co-expressed with BnPEPC1 and are specifically associated with plant circadian rhythm, which are related to seed oil biosynthesis. Then, in de novo fatty acid synthesis there are rapeseed-specific genes encoding subunits β-CT (BnaC05g37990D) and BCCP1 (BnaA03g06000D) of heterogeneous ACCase, which could interfere with synthesis rate, and β-CT is positively regulated by four transcription factors (BnaA01g37250D, BnaA02g26190D, BnaC01g01040D and BnaC07g21470D). In triglyceride synthesis, GmLPAAT2 is putatively inhibited by three miRNAs (gma-miR171, gma-miR1516 and gma-miR5775). Finally, in rapeseed there was evidence for the expansion of gene families, CALO, OBO and STERO, related to lipid storage, and the contraction of gene families, LOX, LAH and HSI2, related to oil degradation.

CONCLUSIONS

The molecular mechanisms associated with differences in seed oil content provide the basis for future breeding efforts to improve seed oil content.

The CCCH-type transcription factor BnZFP1 is a positive regulator to control oleic acid levels through the expression of diacylglycerol O-acyltransferase 1 gene in Brassica napus

In China, the high-oleic acid rapeseed has an oil content of ∼42% and oleic acid (18:1) content of ∼80%. Compared to ordinary rapeseed, high-oleic acid rapeseed has higher levels of monounsaturated fatty acids and lower levels of saturated fatty acid and polyunsaturated fatty acids, and thus is of high nutritional and health value. In addition, high-oleic acid rapeseed oil imparts cardiovascular protective effects. Based on these properties, high-oleic acid oil crops have been extensively investigated and cultivated. We previously identified a CCCH-type transcription factor (BnZFP1, GenBank accession number XM_013796508) that is associated with high oleic acid traits from a Brassica napus subtractive hybridization library. In the present study, we overexpressed and silenced the BnZFP1 gene of B. napus. BnZFP1-overexpressing plants exhibited an 18.8% increase in oleic acid levels and a 3.8% increase in oil content. However, BNZFP1-silenced plants showed a 4.5% decrease in oleic acid levels, whereas no significant change in oil content was observed. Microarray and pull-down assays indicated that BnZFP1 has a total of thirty potential target genes. Further analysis and validation of one of the potential target genes, namely, diacylglycerol O-acyltransferases 1 (DGAT1) gene, indicated that it is positively regulated by BnZFP1. We also observed a correlation between elevated DGAT1 gene expression levels and higher oil content and oleic acid levels in rapeseed.