Integration of proteomic and genomic approaches to dissect seed germination vigor in Brassica napus seeds differing in oil content

A Golden2-like transcription factor regulates Brassica napus seed vigor after artificial aging

KEY MESSAGE

A novel GLK transcription factor, BnaA03.G2-like, regulates seed vigor after aging by affecting FAs composition in B. napus. Seeds, a most crucial materials for crop production, constitute the basis of agriculture. Seed aging usually occurs during storage, especially for seeds with high oil content. However, the genes and mechanisms underlying seed aging in Brassica napus, a widely grown oilseed crop, remain largely unexplored. In this study, nine SNPs associated with seed vigor after aging were identified through a genome-wide association study, and transgenic seeds confirmed that BnaA03.G2-like negatively regulated seed vigor after aging. Haplotype and gene-based association analyses revealed that S_A3.16900957 and S_A3.16901008 were two core variants located within BnaA03.G2-like. Transcriptome analysis and gas chromatography results suggested that BnaA03.G2-like regulated fatty acid biosynthesis, and the linoleic acid content significantly increased in the seeds of BnaA03.G2-like overexpression lines but decreased in the seeds of BnaA03.G2-like RNA interference lines. Further correlation analysis and malondialdehyde determination revealed that BnaA03.G2-like regulated seed vigor by affecting the linoleic acid content in mature seeds and the degree of membrane lipid peroxidation during seed aging. This study initially reported the function of BnaA03.G2-like and its favorable alleles, providing genetic resources for seed antiaging breeding in B. napus.

Exploration of advanced omics tools and resources for the improvement of industrial oil crops

The rapid advancement in the field of omics approaches plays a crucial role in the development of improved industrial oil crops. Industrial oil crops are important for many sectors like food processing, biofuels, cosmetics, and pharmaceuticals, making them indispensable contributors to global economies and these crops serve as vital elements in a multitude of industrial processes. Significant improvements in genomics have revolutionized the agricultural sector, particularly in the realm of oil crops. Cutting-edge advancements have facilitated the efficient sequencing of genomes for key commercial oil crops. This breakthrough not only enhances our understanding of the genetic makeup of these crops but also empowers breeders with invaluable insights for targeted genetic manipulation and breeding programs. Moreover, integrating transcriptomics with genomic data has assisted in a new era of precision agriculture. This approach provides an in-depth understanding of molecular mechanisms involved in traits of interest, such as oil content, yield potential, and resistance to biotic and abiotic stresses. Proteomics methods are instrumental in deciphering the intricacies of protein structure, interactions, and function, while metabolomics and ionomics shed light on the intricate network of metabolites and ions within biological systems. Each omics discipline offers unique insights, and their integration holds the promise of enriching our understanding and furnishing invaluable insights for enhancing oil crops. This review delves into the efficacy and constraints of various omics approaches in the context of refining industrial oil crops. Moreover, it underscores the importance of multi-omics strategies and explores their convergence with genetic engineering techniques to cultivate superior oil crop varieties.

Unravelling the Significance of Seed Proteomics: Insights into Seed Development, Function, and Agricultural Applications

Seeds are essential for plant reproduction, ensuring species survival and dispersal while adapting to diverse environments throughout a plant's life. Proteomics has emerged as a powerful tool for deciphering the complexities of seed growth, germination, and stress responses. Advanced proteomic technologies enable the analysis of protein changes during germination, dormancy, and ageing, enhancing our understanding of seed lifespan and vitality. Recent studies have revealed detailed insights into metabolic processes and storage protein profiles across various plant species. This knowledge is crucial for improving seed storage, conserving quality, and maintaining viability. Additionally, it contributes to sustainable agriculture by identifying stress-responsive proteins and signalling pathways that can mitigate stress and enhance farming practices. This review highlights significant advancements in seed proteomics over the past decade, discussing critical discoveries related to storage proteins, protein interactions, and proteome modifications due to stress. It illustrates how these insights transform seed biology, boosting productivity, food security, and environmentally friendly practices. The review also identifies existing knowledge gaps and provides direction for future research, underscoring the need for continued interdisciplinary collaboration in this dynamic field.

Dynamic responses of germination characteristics and antioxidant systems to alfalfa (Medicago sativa) seed aging based on transcriptome

Seed aging poses a significant challenge to agronomic production and germplasm conservation. Reactive oxygen species (ROS) are highly involved in the aging process. However, dynamic response of germination characteristics and antioxidant system to seed aging are not yet very clear. This study explored the potential physiological mechanisms responsible for the reduced and rapid loss of seed vigor in alfalfa, and identified key genes regulating seed vigor. The germination percentage exhibited a decreased trend with the prolongation of aging duration. From 16 to 32 days of aging, the antioxidant enzyme activities of SOD, POD, CAT, DHAR and MDHAR declined significantly, which lead to the disruption of ROS balance and a significant increase in ROS levels, exacerbating seed aging. Based on transcriptome, 29 differentially expressed genes (DEGs) including SOD1, APX-2 and GST-7 within the ROS scavenging system showed a significantly down-regulated expression trend at aging of 16 and 24 days, indicating the abnormal function of antioxidant metabolism. Furthermore, some related genes including ATPF1B, ATPeF0C-3, NDUFS1, NDUFS3 and ND2 in the mitochondrial ETC exhibited a downturn following seed aging, which would result in the losing of seed vigor. This study has uncovered a significant array of potential target genes within the seed antioxidant system and mitochondrial ETC. These discoveries offer a wider lens for delving into the molecular regulatory mechanisms of seed aging. Further research is crucial to comprehensively elucidate the precise pathways through which these pivotal genes regulate seed vigor.

Determination and Prediction of Amino Acid Digestibility in Rapeseed Cake for Growing-Finishing Pigs

OBJECTIVE

The experiment was conducted to determine the apparent or standardized ileal digestibility (AID or SID) of crude protein (CP) and amino acids (AA) in 10 rapeseed cake samples fed to pigs, and to construct predictive models for the SID of CP and AA based on the chemical composition of rapeseed cakes.

METHODS

Twenty-two cannulated pigs (initial body weight: 39.8 ± 1.2 kg) were assigned to two 11 × 3 incomplete Latin square designs, including an N-free diet and 10 diets containing rapeseed cake. Each experimental period included 5 days of adaptation and 2 days of ileal digesta collection. Titanium dioxide (TiO2) was added at 0.3% to all the diets as an indigestible marker for calculating the ileal CP and AA digestibility.

RESULTS

The coefficients of variation (CV) of the content of crude fat (EE), crude fiber (CF), neutral detergent fiber (NDF), acid detergent fiber (ADF), and total glucosinolates (TGS) in 10 samples of rapeseed cake were greater than 10%. The standardized ileal digestibility (SID) of crude protein (CP), lysine (Lys), methionine (Met), threonine (Thr), and tryptophan (Trp) in rapeseed cake was 73.34% (61.49 to 81.12%), 63.01% (41.41 to 73.10%), 69.47% (50.55 to 88.16%), 79.61% (74.41 to 87.58%), and 94.43% (91.34 to 97.20%), respectively. The best prediction equations for SIDCP, SIDLys, and SIDVal were as follows: SIDCP = 90.124 - 0.54NDF (R2 = 0.58), SIDLys = 100.107 - 1.229NDF (R2 = 0.94), and SIDVal = 151.012 - 2.990TGS (R2 = 0.57).

CONCLUSION

Overall, great variation exists among the 10 rapeseed cakes, and the NDF, TGS, and heating temperature can be used as the key predictors for the SID of CP and AA.

Full-Length Transcriptome Sequencing Reveals the Molecular Mechanism of Metasequoia glyptostroboides Seed Responding to Aging

Metasequoia glyptostroboides, Hu and W. C. Cheng, as the only surviving relict species of the Taxodiaceae Metasequoia genus, is a critically endangered and protected species in China. There is a risk of extinction due to the low vigor of M. glyptostroboides seeds, and the physiological mechanism of seed aging in M. glyptostroboides is not yet clear. In order to investigate the physiological and molecular mechanisms underlying the aging process of M. glyptostroboides seeds, we analyzed the antioxidant system and transcriptome at 0, 2, 4, 6, and 8 days after artificial accelerated aging treatment at 40 °C and 100% relative humidity. It was found that the germination percentage of fresh dried M. glyptostroboides seeds was 54 ± 5.29%, and significantly declined to 9.33 ± 1.88% after 6 days of aging, and then gradually decreased until the seed died on day 8. Superoxide dismutase (SOD) activity, ascorbic acid (AsA), glutathione (GSH) content and superoxide anion (O₂^·-) content and production rate significantly decreased, while malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) content and glutathione peroxidase (GPX) and catalase (CAT) activity gradually increased during the aging process. A total of 42,189 unigenes were identified in the whole transcriptome, and 40,446 (95.86%) unigenes were annotated in at least one protein database. A total of 15,376 differentially expressed genes (DEGs) were obtained; KEGG enrichment analysis results revealed that seed aging may be mainly involved in the protein-processing pathways in endoplasmic reticulum, oxidative phosphorylation, and ascorbate and aldarate metabolism. Weighted gene co-expression network analysis (WGCNA) revealed that the dark magenta, orange, and medium purple modules were highly correlated with physiological indicators such as SOD, CAT, and GSH and further identified 40 hub genes such as Rboh, ACO, HSF, and CML as playing important roles in the antioxidant network of M. glyptostroboides seeds. These findings provide a broader perspective for studying the regulatory mechanism of seed aging and a large number of potential target genes for the breeding of other endangered gymnosperms.

Proteome Landscape during Ripening of Solid Endosperm from Two Different Coconut Cultivars Reveals Contrasting Carbohydrate and Fatty Acid Metabolic Pathway Modulation

Cocos nucifera L. is a crop grown in the humid tropics. It is grouped into two classes of varieties: dwarf and tall; regardless of the variety, the endosperm of the coconut accumulates carbohydrates in the early stages of maturation and fatty acids in the later stages, although the biochemical factors that determine such behavior remain unknown. We used tandem mass tagging with synchronous precursor selection (TMT-SPS-MS3) to analyze the proteomes of solid endosperms from Yucatan green dwarf (YGD) and Mexican pacific tall (MPT) coconut cultivars. The analysis was conducted at immature, intermediate, and mature development stages to better understand the regulation of carbohydrate and lipid metabolisms. Proteomic analyses showed 244 proteins in YGD and 347 in MPT; from these, 155 proteins were shared between both cultivars. Furthermore, the proteomes related to glycolysis, photosynthesis, and gluconeogenesis, and those associated with the biosynthesis and elongation of fatty acids, were up-accumulated in the solid endosperm of MPT, while in YGD, they were down-accumulated. These results support that carbohydrate and fatty acid metabolisms differ among the developmental stages of the solid endosperm and between the dwarf and tall cultivars. This is the first proteomics study comparing different stages of maturity in two contrasting coconut cultivars and may help in understanding the maturity process in other palms.

Characterization of novel loci controlling seed oil content in Brassica napus by marker metabolite-based multi-omics analysis

BACKGROUND

Seed oil content is an important agronomic trait of Brassica napus (B. napus), and metabolites are considered as the bridge between genotype and phenotype for physical traits.

RESULTS

Using a widely targeted metabolomics analysis in a natural population of 388 B. napus inbred lines, we quantify 2172 metabolites in mature seeds by liquid chromatography mass spectrometry, in which 131 marker metabolites are identified to be correlated with seed oil content. These metabolites are then selected for further metabolite genome-wide association study and metabolite transcriptome-wide association study. Combined with weighted correlation network analysis, we construct a triple relationship network, which includes 21,000 edges and 4384 nodes among metabolites, metabolite quantitative trait loci, genes, and co-expression modules. We validate the function of BnaA03.TT4, BnaC02.TT4, and BnaC05.UK, three candidate genes predicted by multi-omics analysis, which show significant impacts on seed oil content through regulating flavonoid metabolism in B. napus.

CONCLUSIONS

This study demonstrates the advantage of utilizing marker metabolites integrated with multi-omics analysis to dissect the genetic basis of agronomic traits in crops.

Mitigation of the salinity stress in rapeseed (Brassica napus L.) productivity by exogenous applications of bio-selenium nanoparticles during the early seedling stage

In recent years, much attention has been directed toward using nanoparticles (NPs) as one of the most effective strategies to improve plant growth, especially under salt stress conditions. Further research has been conducted to develop NPs using various chemical ways; accordingly, knowledge about the beneficial effect of bioSeNPs in rapeseed is obscure. Selenium (Se) is a vital micronutrient with a series of physiological and antioxidative properties. Seed priming is emerging as a low-cost, efficient, and environment-friendly seed treatment in nanotechnology. The current study was carried out to examine the promising effects of nanopriming via bioSeNPs on the expression level of aquaporin genes, seed microstructure, seed germination, growth traits, physiochemical attributes, and minerals uptake of two rapeseed cultivars under salinity stress conditions. Our investigation monitored the positive effects of bioSeNPs on the expression level of aquaporin genes (BnPIP1-1 and BnPIP2-1) and water uptake during the seed imbibition (4 and 8 h of priming), which indicated higher imbibition potential and germination promotion with bioSeNPs application (most effective at 150 μmol/L). The total performance index was significantly enhanced with nano-treatments in rapeseed seedlings. Collectively, nano-application improved seed microstructure, seed germination, and photosynthetic efficiency directly correlated with higher seedlings biomass, especially with a higher concentration of bioSeNPs. The enhancement in α-amylase and free amino acid contents in nanoprimed seeds resulted in rapid seed germination. Moreover, bioSeNPs increased the osmotic adjustment and enhanced the efficiency of the plant's defense system by improving the activity of enzymatic and non-enzymatic antioxidants, thus enhancing ROS scavenging under salt stress. The obtained results may indicate the strengthening of seed vigor, improving seedling growth and physiochemical attributes via bioSeNPs. Our findings displayed that bioSeNPs modulated the Na⁺ and K⁺ uptake, which improved the rapeseed growth and showed a close relationship with the low contents of toxic Na⁺ ion; thus, it prevented oxidative damage due to salt stress. This comprehensive data can add more knowledge to understand the mechanisms behind plant-bioSeNPs interaction and provide physiological evidence for the beneficial roles of nanopriming using bioSeNPs on rapeseed germination and seedling development under salinity stress conditions. Such studies can be used to develop simple prepackaged nano primer products, which can be used before sowing to boost seed germination and crop productivity under stress conditions.

Proteomic analysis of metabolic mechanisms associated with fatty acid biosynthesis during Styrax tonkinensis kernel development

BACKGROUND

Styrax tonkinensis is a white-flowered tree with considerable potential as a feedstock source for biodiesel production from the oily seed contained within its nutlike drupes. Transcriptome changes during oil accumulation have been previously reported, but not concurrent changes in the proteome.

RESULTS

Using proteomic analysis of samples collected at 50, 70, 100 and 130 days after flowering (DAF), we identified 1472 differentially expressed proteins (DEPs). Based on their expression patterns, we grouped the DEPs into nine clusters and analyzed the pathway enrichment. Proteins related to starch and sucrose metabolism were most abundant at 50 DAF. Proteins involved in fatty acid (FA) biosynthesis were mainly grouped into a cluster that peaked at 70 DAF. Proteins related to protein processing in endoplasmic reticulum had two major patterns, trending either upwards or downwards, while proteins involved in amino acid biosynthesis showed more complex relationships. We identified 42 key enzymes involved in lipid accumulation during kernel development, including the acetyl-CoA carboxylase complex (ACC) and the pyruvate dehydrogenase complex (PDC). One oil body membrane protein, oleosin, continuously increased during kernel development.

CONCLUSION

A regulatory network of oil accumulation processes was built based on protein and available transcriptome expression data, which were in good temporal agreement. This analysis placed ACC and PDC in the center of the network, suggesting that the glycolytic provision of substrate plays a central regulatory role in FA biosynthesis and oil accumulation. © 2021 Society of Chemical Industry.

Transcriptomic profiling of the high-vigour maize (Zea mays L.) hybrid variety response to cold and drought stresses during seed germination

Abiotic stresses, including cold and drought, negatively affect maize (Zea mays L.) seed field emergence and later yield and quality. In order to reveal the molecular mechanism of maize seed resistance to abiotic stress at seed germination, the global transcriptome of high- vigour variety Zhongdi175 exposed to cold- and drought- stress was analyzed by RNA-seq. In the comparison between the control and different stressed sample, 12,299 differentially expressed genes (DEGs) were detected, of which 9605 and 7837 DEGs were identified under cold- and drought- stress, respectively. Functional annotation analysis suggested that stress response mediated by the pathways involving ribosome, phenylpropanoid biosynthesis and biosynthesis of secondary metabolites, among others. Of the obtained DEGs (12,299), 5,143 genes are common to cold- and drought- stress, at least 2248 TFs in 56 TF families were identified that are involved in cold and/or drought treatments during seed germination, including bHLH, NAC, MYB and WRKY families, which suggested that common mechanisms may be originated during maize seed germination in response to different abiotic stresses. This study will provide a better understanding of the molecular mechanism of response to abiotic stress during maize seed germination, and could be useful for cultivar improvement and breeding of high vigour maize cultivars.

Modulation of salinity impact on early seedling stage via nano-priming application of zinc oxide on rapeseed (Brassica napus L.)

Salinity stress negatively affects the plant's developmental stages through micronutrient imbalance. As an essential micronutrient, ZnO can substitute Na⁺ absorption under saline conditions. Therefore, nanoparticles as technological innovation, improve the plant growth efficiency under biotic and abiotic stresses. Nano-priming has become widely applicable in agricultural research during the last decade. The current study was conducted to highlight the impact of ZnONPs priming on seedling biological processes under 150 mM of NaCl using two rapeseed cultivars during the early seedling stage. All concentrations of ZnONPs increased the germination parameters i.e., FG%, GR, VI (I), and VI (II). Meanwhile, the high concentration (ZnO 100%) showed the highest increase in shoot length (9.60% and 25.63%), root length (41.64% and 48.17%) for Yang You 9 and Zhong Shuang 11 over hydro-priming, respectively, as well as biomass. Additionally, nano-priming improved the proline, soluble sugar, and soluble protein contents as a result of osmotic protection modulation. Moreover, nano-priming alleviated ROS and biosynthesis pigments through the reduction of accumulated (H₂O₂) and (O₂^-), and chlorophyll degradation, respectively, also enhanced antioxidant adjustment via improving the plant defense system. Nano-priming substituted the Na⁺ by Zn²⁺, K⁺, and Ca²⁺, and compensated the deficit of micronutrients, thus reduced the Na⁺ toxicity in the cell cytosol. To track the effects of priming during seed imbibition, it noticed that ZnO 100% and ZnO 100%+S increased the Linoleic and Linolenic acids among the studied fatty acids composition by 12.02%, 7.59%, 13.27%, and 10.38% (Yang You 9), 7.42%, 2.77%, 2.93%, and 1.49% (Zhong Shuang 11) over the hydro-priming, respectively. Moreover, the gene expression patterns of BnCAM and BnPER reflected the enhancement of germination levels, notably under the influence of ZnO 100% priming, which increased the level of BnCAM by 70.42% and 111.9% in Yang You 9 and Zhong Shuang 11, respectively. Consequently, ZnO nano-priming enhanced the seedling development through the biosynthesis of pigments, osmotic protection, reduction of ROS accumulation, adjustment of antioxidant enzymes, and improvement of the nutrient absorption, thus enhancing the economic yield under saline conditions.

Ovarian morphological features and proteome reveal fecundity fitness disadvantages in β-cypermethrin-resistant strains of Blattella germanica (L.) (Blattodea: Blattellidae)

To evaluate whether the development of β-cypermethrin resistance in Blattella germanica (L.) (Blattaria: Blattellidae) affects the fecundity fitness of this insect and to determine the underlying mechanism, we compared fecundity differences between β-cypermethrin-resistant (R) and sensitive (S) strains of B. germanica, observed the physiological structural changes of ovaries from an visual perspective, and analyzed differences in the ovarian proteome using proteomic methods. The results showed that, compared with the S strain of B. germanica, the R strain of B. germanica had a significantly higher ootheca shedding rate, a significantly lower number of hatched and surviving nymphs, a significantly higher female proportion in the population and defective ovarian development. Ovarian proteomic analysis showed a total of 64 differentially expressed proteins in the R strain, including 18 upregulated proteins and 46 downregulated proteins. Twenty-four significantly differentially expressed proteins were further studied, and 14 were successfully identified, which were mainly classified into the following categories: immunity-related proteins, development-related proteins, structural proteins, energy metabolism-related proteins and proteins with unknown functions. The differential expression of these proteins reflects the overall changes in cell structure and metabolism associated with β-cypermethrin resistance and explains the possible molecular mechanism of fecundity fitness disadvantages. In summary, β-cypermethrin resistance can cause fecundity fitness disadvantages in B. germanica. The metabolic deviations needed to overcome the adverse effects of insecticides may result in an energy exchange that affects energy allocation and, ultimately, the basic needs of the insect. The fitness cost due to insecticide resistance is critical to the delay of the evolution of resistance.

Modelling the vigour of maize seeds submitted to artificial accelerated ageing based on ATR-FTIR data and chemometric tools (PCA, HCA and PLS-DA)

The main goals of this research were to use ATR-FTIR spectroscopy associated with multivariate analyses to identify biochemical changes in high and low vigour seed tissues (embryo and endosperm) in response to accelerated ageing and to create a model to predict seed vigour based on spectroscopic data. High-vigour seeds undergo minimal changes in biochemical composition during stress by accelerated ageing while low-vigour seeds are more sensitive to stress and this lower tolerance is associated with reduced lipid and protein content and increased amino acids, carbohydrates and phosphorus compounds in the embryo. High-vigour seeds show an increase in peaks associated with amino acids and phosphorous compounds in the endosperm after 24 h of stress while low-vigour seeds present these high-intensity peaks only after 72 h in the embryo. The results of this research provide the theoretical basis for the genetic improvement of maize cultivars that aim at higher physiological seed quality.

Genetic mechanisms of salt stress responses in halophytes

Abiotic stress is a major threat to plant growth and development, resulting in extensive crop loss worldwide. Plants react to abiotic stresses through physiological, biochemical, molecular, and genetic adaptations that promote survival. Exploring the molecular mechanisms involved in abiotic stress responses across various plant species is essential for improving crop yields in unfavorable environments. Halophytes are characterized as plants that survive to reproduce in soils containing high salt concentrations, and thus act as an ideal model to comprehend complicated genetic and physiological mechanisms of salinity stress tolerance. Plant ecologists classify halophytes into three main groups: euhalophytes, recretohalophytes, and pseudo-halophytes. Recent genetic and molecular research has showed complicated regulatory networks by which halophytes coordinate stress adaptation and tolerance. Furthermore, investigation of natural variations in these stress responses has supplied new perspectives on the evolution of mechanisms that regulate tolerance and adaptation. This review discusses the current understanding of the genetic mechanisms that contribute to salt-stress tolerance among different classes of halophytes.

An Integrative Approach to Analyze Seed Germination in Brassica napus

Seed germination is a complex trait determined by the interaction of hormonal, metabolic, genetic, and environmental components. Variability of this trait in crops has a big impact on seedling establishment and yield in the field. Classical studies of this trait in crops have focused mainly on the analyses of one level of regulation in the cascade of events leading to seed germination. We have carried out an integrative and extensive approach to deepen our understanding of seed germination in Brassica napus by generating transcriptomic, metabolic, and hormonal data at different stages upon seed imbibition. Deep phenotyping of different seed germination-associated traits in six winter-type B. napus accessions has revealed that seed germination kinetics, in particular seed germination speed, are major contributors to the variability of this trait. Metabolic profiling of these accessions has allowed us to describe a common pattern of metabolic change and to identify the levels of malate and aspartate metabolites as putative metabolic markers to estimate germination performance. Additionally, analysis of seed content of different hormones suggests that hormonal balance between ABA, GA, and IAA at crucial time points during this process might underlie seed germination differences in these accessions. In this study, we have also defined the major transcriptome changes accompanying the germination process in B. napus. Furthermore, we have observed that earlier activation of key germination regulatory genes seems to generate the differences in germination speed observed between accessions in B. napus. Finally, we have found that protein-protein interactions between some of these key regulator are conserved in B. napus, suggesting a shared regulatory network with other plant species. Altogether, our results provide a comprehensive and detailed picture of seed germination dynamics in oilseed rape. This new framework will be extremely valuable not only to evaluate germination performance of B. napus accessions but also to identify key targets for crop improvement in this important process.