Complementary transcriptome and proteome profiling in the mature seeds of Camellia oleifera from Hainan Island

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.

High-Density Genetic Map Construction and Quantitative Trait Locus Analysis of Fruit- and Oil-Related Traits in Camellia oleifera Based on Double Digest Restriction Site-Associated DNA Sequencing

Camellia oleifera, an important tree species and source of edible oil in China, has received significant attention owing to the oil's high unsaturated fatty acid content, which has benefits for human health. However, the mechanisms underlying C. oleifera yield and oil quality are largely unknown. In this study, 180 F1 progenies were obtained from two parents with obvious differences in fruit- and oil-related traits. We constructed a high-density genetic map using a double digest restriction site-associated DNA sequencing (ddRAD-Seq) strategy in C. oleifera. This map spanned 3327 cM and anchored 2780 markers in 15 linkage groups (LGs), with an average marker interval of 1.20 cM. A total of 221 quantitative trait loci (QTLs) associated with fruit- and oil-related traits were identified across three years' worth of phenotypic data. Nine QTLs were detected simultaneously in at least two different years, located on LG02, LG04, LG05, LG06, and LG11, and explained 8.5-16.6% of the phenotypic variation in the corresponding traits, respectively. Seventeen major QTLs were obtained that explained 13.0-16.6% of the phenotypic variance. Eleven and five flanking SNPs of major QTLs for fruit- and oil-related traits were detected which could be used for marker-assisted selection in C. oleifera breeding programs. Furthermore, 202 potential candidate genes in QTL regions were identified based on the collinearity of the genetic map and the C. oleifera "CON" genome. A potential regulatory network controlling fruit development and oil biosynthesis was constructed to dissect the complex mechanism of oil accumulation. The dissection of these QTLs will facilitate the gene cloning underlying lipid synthesis and increase our understanding in order to enhance C. oleifera oil yield and quality.

Genome-Wide Analyses of MADS-Box Genes Reveal Their Involvement in Seed Development and Oil Accumulation of Tea-Oil Tree (Camellia oleifera)

The seeds of Camellia oleifera produce high amount of oil, which can be broadly used in the fields of food, industry, and medicine. However, the molecular regulation mechanisms of seed development and oil accumulation in C. oleifera are unclear. In this study, evolutionary and expression analyses of the MADS-box gene family were performed across the C. oleifera genome for the first time. A total of 86 MADS-box genes (ColMADS) were identified, including 60 M-type and 26 MIKC members. More gene duplication events occurred in M-type subfamily (6) than that in MIKC subfamily (2), and SEP-like genes were lost from the MIKCC clade. Furthermore, 8, 15, and 17 differentially expressed ColMADS genes (DEGs) were detected between three developmental stages of seed (S1/S2, S2/S3, and S1/S3), respectively. Among these DEGs, the STK-like ColMADS12 and TT16-like ColMADS17 were highly expressed during the seed formation (S1 and S2), agreeing with their predicted functions to positively regulate the seed organogenesis and oil accumulation. While ColMADS57 and ColMADS07 showed increasing expression level with the seed maturation (S2 and S3), conforming to their potential roles in promoting the seed ripening. In all, these results revealed a critical role of MADS-box genes in the C. oleifera seed development and oil accumulation, which will contribute to the future molecular breeding of C. oleifera.

The Antioxidant, Anti-Inflammatory and Moisturizing Effects of Camellia oleifera Oil and Its Potential Applications

Camellia oleifera oil (CO oil) extracted from C. oleifera seeds has a 2300-year consumption history in China. However, there is relatively little research regarding its non-edible uses. This study determined the physicochemical properties of CO oil extracted via direct pressing, identified its main components using GC-MS, and evaluated its antioxidant, moisturizing, and anti-inflammatory activities. The results revealed that CO oil's acid, peroxide, iodine, and saponification values were 1.06 ± 0.031 mg/g, 0.24 ± 0.01 g/100 g, 65.14 ± 8.22 g/100 g, and 180.41 ± 5.60 mg/g, respectively. CO oil's tocopherol, polyphenol, and squalene contents were 82.21 ± 9.07 mg/kg, 181.37 ± 3.76 mg/kg, and 53.39 ± 6.58 mg/kg, respectively; its unsaturated fatty acid (UFA) content was 87.44%, and its saturated fatty acid (SFA) content was 12.56%. CO oil also demonstrated excellent moisture retention properties, anti-inflammatory effects, and certain free radical scavenging. A highly stable CO oil emulsion with competent microbiological detection was developed using formulation optimization. Using CO oil in the emulsion significantly improved the formulation's antioxidant and moisturizing properties compared with those of the emulsion formulation that did not include CO oil. The prepared emulsion was not cytotoxic to cells and could reduce cells' NO content; therefore, it may have potential nutritional value in medicine and cosmetics.

Structural elucidation of hemicelluloses from oil-tea camellia fruit shell

Oil-tea camellia fruit shell (CFS) is a very abundant waste lignocellulosic resource. The current treatments of CFS, i.e. composting and burning, pose a severe threat on environment. Up to 50 % of the dry mass of CFS is composed of hemicelluloses. However, chemical structures of the hemicelluloses in CFS have not been extensively studied, which limits their high-value utilization. In this study, different types of hemicelluloses were isolated from CFS through alkali fractionation with the assistance of Ba(OH)2 and H3BO3. Xylan, galacto-glucomannan and xyloglucan were found to be the major hemicelluloses in CFS. Through methylation, HSQC and HMBC analyses, we have found that the xylan in CFS is composed of →4)-β-D-Xylp-(1→ and →3,4)-β-D-Xylp-(1→ linked by (1→4)-β glycosidic bond as the main chain; the side chains are α-L-Fucp-(1→, →5)-α-L-Araf-(1→, β-D-Xylp-(1→, α-L-Rhap-(1→ and 4-O-Me-α-D-GlcpA-(1→, connected to the main chain through (1→3) glycosidic bond. The main chain of galacto-glucomannan in CFS consists of →6)-β-D-Glcp-(1→, →4)-β-D-Glcp-(1→, →4,6)-β-D-Glcp-(1→ and →4)-β-D-Manp-(1→; the side chains are β-D-Glcp-(1→, →2)-β-D-Galp-(1→, β-D-Manp-(1→ and →6)-β-D-Galp-(1→ connected to the main chain through (1→6) glycosidic bonds. Moreover, galactose residues are connected by α-L-Fucp-(1→. The main chain of xyloglucan is composed of →4)-β-D-Glcp-(1→, →4,6)-β-D-Glcp-(1→ and →6)-β-D-Glcp-(1→; the side groups, i.e. β-D-Xylp-(1→ and →4)-β-D-Xylp-(1→, are connected to the main chain by (1→6) glycosidic bond; →2)-β-D-Galp-(1→ and α-L-Fucp-(1→ can also connect to →4)-β-D-Xylp-(1→ forming di- or trisaccharide side chains.

Effects of tea oil camellia (Camellia oleifera Abel.) shell-based organic fertilizers on the physicochemical property and microbial community structure of the rhizosphere soil

Soil microorganisms play important roles in promoting soil ecosystem restoration, but much of the current research has been limited to changes in microbial community structure in general, and little is known regarding the soil physicochemical property and microbial community structure. In this study, four organic fertilizers were first prepared based on tea oil camellia shell (TOCS). Our findings indicate that the application of BOFvo increased both total pore volume and BET surface area of the rhizosphere soils, as well there was a remarkable enhancement in total organic matter (TOM), total nitrogen (TN), available nitrogen (AN), total phosphorus (TP), total potassium (TK), and available potassium (AK) contents of the rhizosphere soils. Meanwhile, in comparison to the CK and CF groups, the utilization of BOFvo led to a substantial increase in both average yield and fruiting rate per plant at maturity, as well resulted in a significant increase in TN and TP contents of tea oil camellia leaves. Furthermore, our findings suggest that the application of TOCS-based organic fertilizers significantly enhances the microbial diversity in the rhizosphere soils with Proteobacteria and Ascomycota being the dominant bacterial and fungal phyla, respectively, and Rhodanobacter and Fusarium being the dominant bacterial and fungal genus, respectively. Redundancy analysis (RDA) indicates that the physicochemical characteristics of TOCS-based organic fertilizers had a significant impact on the composition and distribution of microbial communities in the rhizosphere soils. This study will facilitate the promotion and application of TOCS-based organic fertilizers, thereby establishing a foundation for the reuse of tea oil camellia waste resources.

Assessment of the Genetic Relationship and Population Structure in Oil-Tea Camellia Species Using Simple Sequence Repeat (SSR) Markers

Oil-tea camellia trees, the collective term for a class of economically valuable woody oil crops in China, have attracted extensive attention because of their rich nutritional and pharmaceutical value. This study aimed to analyze the genetic relationship and genetic diversity of oil-tea camellia species using polymorphic SSR markers. One-hundred and forty samples of five species were tested for genetic diversity using twenty-four SSR markers. In this study, a total of 385 alleles were identified using 24 SSR markers, and the average number of alleles per locus was 16.0417. The average Shannon's information index (I) was 0.1890, and the percentages of polymorphic loci (P) of oil-tea camellia trees were 7.79-79.48%, indicating that oil-tea camellia trees have low diversity. Analysis of molecular variance (AMOVA) showed that the majority of genetic variation (77%) was within populations, and a small fraction (23%) occurred among populations. Principal coordinate analysis (PCoA) results indicated that the first two principal axes explained 7.30% (PC1) and 6.68% (PC2) of the total variance, respectively. Both UPGMA and PCoA divided the 140 accessions into three groups. Camellia oleifera clustered into one class, Camellia vietnamensis and Camellia gauchowensis clustered into one class, and Camellia crapnelliana and Camellia chekiangoleosa clustered into another class. It could be speculated that the genetic relationship of C. vietnamensis and C. gauchowensis is quite close. SSR markers could reflect the genetic relationship among oil-tea camellia germplasm resources, and the results of this study could provide comprehensive information on the conservation, collection, and breeding of oil-tea camellia germplasms.

Comparison of the Main Metabolites in Different Maturation Stages of Camelliavietnamensis Huang Seeds

Camellia vietnamensis Huang is an important woody oil crop in China, which has attracted much attention because of its abundant nutritional components and pharmaceutical value. Its seeds undergo a complex series of physiological and biochemical changes during maturation, with consequent alterations in metabolites. In order to investigate the endogenous metabolism of C. vietnamensis on Hainan Island during seed development, in this study, ultra-high-performance liquid tandem chromatography coupled with quadrupole time-of-flight mass spectrometry (UHPLC/Q-TOF-MS) and multivariate statistical analysis (MSA) were used to analyze the differences in the chemical compounds of C. vietnamensis seeds among the four maturation stages. A total of 293 metabolites were identified from the methanol extract of the seeds of C. vietnamensis. Five metabolites, belonging to benzene and substituted derivatives, 5′-deoxyribonucleosides and linear 1,3-diarylpropanoids, were found in all three comparison groups, with consistently down-regulated trends. The Kyoto Encyclopedia of Genes and Genomes (KEGG) results showed that phloretin and 5′-methylthioadenosine were the differentially expressed metabolites when seeds were in the growth periods of S2 and S3, and indole and L-tryptophan were the differentially expressed metabolites when seeds were in the growth periods of S3 and S4. In addition, 34 flavonoid metabolites were detected, of which 4 were differentially expressed. It was indicated that flavonoids dynamically change during all the oil-tea camellia seed development stages. The findings provide data for the better understanding of endogenous metabolic pathways during C. vietnamensis seed development.

A High-Quality Genome Assembly of the Mitochondrial Genome of the Oil-Tea Tree Camellia gigantocarpa (Theaceae)

Camellia gigantocarpa is one of the oil-tea trees whose seeds can be used to extract high-quality vegetable oil. To date, there are no data on the mitochondrial genome of the oil-tea tree, in contrast to the tea-tree C. sinensis, which belongs to the same genus. In this paper, we present the first complete mitochondrial genomes of C. gigantocarpa obtained using PacBio Hi-Fi (high-fidelity) and Hi-C sequencing technologies to anchor the 970,410 bp genome assembly into a single sequence. A set of 44 protein-coding genes, 22 non-coding genes, 746 simple sequence repeats (SSRs), and more than 201 kb of repetitive sequences were annotated in the genome assembly. The high percentage of repetitive sequences in the mitochondrial genome of C. gigantocarpa (20.81%) and C.sinensis (22.15%, tea tree) compared to Arabidopsis thaliana (4.96%) significantly increased the mitogenome size in the genus Camellia. The comparison of the mitochondrial genomes between C. gigantocarpa and C. sinensis revealed genes exhibit high variance in gene order and low substitution rate within the genus Camellia. Information on the mitochondrial genome provides a better understanding of the structure and evolution of the genome in Camellia and may contribute to further study of the after-ripening process of oil-tea trees.

Critical metabolic pathways and SAD/FADs, WRI1s, and DGATs cooperate for high-oleic acid oil production in developing oil tea (Camellia oleifera) seeds

Oil tea trees produce high-quality edible oils with desirably high oleic acid (18:1) and low linoleic (18:2) and linolenic (18:3) fatty acid (FA) levels, but limited understanding of tea oil biosynthesis and regulation has become a significant obstacle for the breeding of high-yield and -quality oil tea varieties. By integrating metabolite and transcriptome analyses of developing oil tea seeds, we dissected the critical metabolic pathways, including glycolysis, fatty acid, and triacylglycerol (TAG) biosynthesis, as well as genes essential for tea seed oil production. Two plastidic stearoyl-acyl carrier protein desaturases (CoSAD1 and 2) and two endoplasmic reticulum-localized FA desaturases (CoFAD2 and 3) were functionally characterized as responsible for high 18:1 and low 18:2 and 18:3 proportions in tea oils. Two diacylglycerol O-acyltransferases (CoDGAT1 and 2) that may prefer to synthesize 18:1-TAG were functionally characterized and might be also important for high 18:1-TAG production. The highly expressed CoWRI1a and b were identified and characterized as activators of glycolysis and regulators of directing source carbon flux into FA biosynthesis in developing oil tea seeds. The upregulated CoSADs with downregulated CoFAD2 and CoFAD3 at the late seed developmental stages mainly accounted for high 18:1 levels. Two CoDGATs might be responsible for assembling TAGs with oleoyl acyl chains, whilst two CoWRI1s regulated carbons from parental sources, partitioning into oil production in oil tea embryo sinks. This study provides a deep understanding of the biosynthesis of tea seed oils and information on genes that may be used as molecular markers to breed oil tea varieties with higher oil yield and quality.

Shotgun proteomics of Brassica rapa seed proteins identifies vicilin as a major seed storage protein in the mature seed

Proteins make up a large percentage of the Brassica seed and are second only to the oil in economic importance with uses for both animal and human nutrition. The most abundant proteins reported in the seeds of Brassica are the seed storage proteins cruciferin and napin, belonging to the 12S globulin and 2S albumin families of proteins, respectively. To gain insight into the Brassica rapa seed proteome and to confirm the presence and relative quantity of proteins encoded by candidate seed storage genes in the mature seed, shotgun proteomics was carried out on protein extracts from seeds of B. rapa inbred line R-o-18. Following liquid chromatography tandem mass spectrometry, a total of 34016 spectra were mapped to 323 proteins, where 233 proteins were identified in 3 out of 4 biological replicates by at least 2 unique peptides. 2S albumin like napin seed storage proteins (SSPs), 11/12S globulin like cruciferin SSPs and 7S globulin like vicilin SSPs were identified in the samples, along with other notable proteins including oil body proteins, namely ten oleosins and two oil body-associated proteins. The identification of vicilin like proteins in the mature B. rapa seed represents the first account of these proteins in the Brassicaceae and analysis indicates high conservation of sequence motifs to other 7S vicilin-like allergenic proteins as well as conservation of major allergenic epitopes in the proteins. This study enriches our existing knowledge on rapeseed seed proteins and provides a robust foundation and rational basis for plant bioengineering of seed storage proteins.

Integrative iTRAQ-based proteomic and transcriptomic analysis reveals the accumulation patterns of key metabolites associated with oil quality during seed ripening of Camellia oleifera

Camellia oleifera (C. oleifera) is one of the four major woody oil-bearing crops in the world and has relatively high ecological, economic, and medicinal value. Its seeds undergo a series of complex physiological and biochemical changes during ripening, which is mainly manifested as the accumulation and transformation of certain metabolites closely related to oil quality, especially flavonoids and fatty acids. To obtain new insights into the underlying molecular mechanisms, a parallel analysis of the transcriptome and proteome profiles of C. oleifera seeds at different maturity levels was conducted using RNA sequencing (RNA-seq) and isobaric tags for relative and absolute quantification (iTRAQ) complemented with gas chromatography-mass spectrometry (GC-MS) data. A total of 16,530 transcripts and 1228 proteins were recognized with significant differential abundances in pairwise comparisons of samples at various developmental stages. Among these, 317 were coexpressed with a poor correlation, and most were involved in metabolic processes, including fatty acid metabolism, α-linolenic acid metabolism, and glutathione metabolism. In addition, the content of total flavonoids decreased gradually with seed maturity, and the levels of fatty acids generally peaked at the fat accumulation stage; these results basically agreed with the regulation patterns of genes or proteins in the corresponding pathways. The expression levels of proteins annotated as upstream candidates of phenylalanine ammonia-lyase (PAL) and chalcone synthase (CHS) as well as their cognate transcripts were positively correlated with the variation in the flavonoid content, while shikimate O-hydroxycinnamoyltransferase (HCT)-encoding genes had the opposite pattern. The increase in the abundance of proteins and mRNAs corresponding to alcohol dehydrogenase (ADH) was associated with a reduction in linoleic acid synthesis. Using weighted gene coexpression network analysis (WGCNA), we further identified six unique modules related to flavonoid, oil, and fatty acid anabolism that contained hub genes or proteins similar to transcription factors (TFs), such as MADS intervening keratin-like and C-terminal (MIKC_MADS), type-B authentic response regulator (ARR-B), and basic helix-loop-helix (bHLH). Finally, based on the known metabolic pathways and WGCNA combined with the correlation analysis, five coexpressed transcripts and proteins composed of cinnamyl-alcohol dehydrogenases (CADs), caffeic acid 3-O-methyltransferase (COMT), flavonol synthase (FLS), and 4-coumarate: CoA ligase (4CL) were screened out. With this exploratory multiomics dataset, our results presented a dynamic picture regarding the maturation process of C. oleifera seeds on Hainan Island, not only revealing the temporal specific expression of key candidate genes and proteins but also providing a scientific basis for the genetic improvement of this tree species.

Genetic relationships and low diversity among the tea-oil Camellia species in Sect. Oleifera, a bulk woody oil crop in China

Tea-oil Camellia is one of the four woody oil crops in the world and has high ecological, economic and medicinal values. However, there are great differences in the classification and merging of tea-oil Camellia Sect. Oleifera species, which brings difficulties to the innovative utilization and production of tea-oil Camellia resources. Here, ISSR, SRAP and chloroplast sequence markers were analyzed in 18 populations of tea-oil Camellia Sect. Oleifera species to explore their phylogenetic relationships and genetic diversity. The results showed that their genetic diversity were low, with mean H and π values of 0.16 and 0.00140, respectively. There was high among-population genetic differentiation, with ISSR and SRAP markers showing an Fst of 0.38 and a high Nm of 1.77 and cpDNA markers showing an Fst of 0.65 and a low Nm of 0.27. The C. gauchowensis, C. vietnamensis and Hainan Island populations formed a single group, showing the closest relationships, and supported being the same species for them with the unifying name C. drupifera and classifying the resources on Hainan Island as C. drupifera. The tea-oil Camellia resources of Hainan Island should be classified as a special ecological type or variety of C. drupifera. However, cpDNA marker-based STRUCTURE analysis showed that the genetic components of the C. osmantha population formed an independent, homozygous cluster; hence, C. osmantha should be a new species in Sect. Oleifera. The C. oleifera var. monosperma and C. oleifera populations clustered into two distinct clades, and the C. oleifera var. monosperma populations formed an independent cluster, accounting for more than 99.00% of its genetic composition; however, the C. oleifera populations contained multiple different cluster components, indicating that C. oleifera var. monosperma significantly differs from C. oleifera and should be considered the independent species C. meiocarpa. Haplotype analysis revealed no rapid expansion in the tested populations, and the haplotypes of C. oleifera, C. meiocarpa and C. osmantha evolved from those of C. drupifera. Our results support the phylogenetic classification of Camellia subgenera, which is highly significant for breeding and production in tea-oil Camellia.