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Abstract Astaxanthin biosynthesis in Haematococcus pluvialis is driven by energy. However, the effect of the flagella-mediated energy-consuming movement process on astaxanthin accumulation has not been well studied. In this study, the profiles of astaxanthin and NADPH contents in combination with the photosynthetic parameters with or without flagella enabled by pH shock were characterized. The results demonstrated that there was no significant alteration in cell morphology, with the exception of the loss of flagella observed in the pH shock treatment group. In contrast, the astaxanthin content in the flagella removal groups was 62.9%, 62.8% and 91.1% higher than that of the control at 4, 8 and 12 h, respectively. Simultaneously, the increased Y(II) and decreased Y(NO) suggest that cells lacking the flagellar movement process may allocate more energy towards astaxanthin biosynthesis. This finding was verified by NADPH analysis, which revealed higher levels in flagella removal cells. These results provide preliminary insights into the underlying mechanism of astaxanthin accumulation enabled by energy reassignment in movement-lacking cells.

Abstract Green manufacture of steroid precursors from diosgenin by microbial replacing multistep chemical synthesis has been elusive. It is currently limited by the lack of strain and degradation mechanisms. Here, we demonstrated the feasibility of this process using a novel strain Mycolicibacterium sp. HK‐90 with efficiency in diosgenin degradation. Diosgenin degradation by strain HK‐90 involves the selective removal of 5,6‐spiroketal structure, followed by the oxygenolytic cleavage of steroid nuclei. Bioinformatic analyses revealed the presence of two complete steroid catabolic gene clusters, SCG‐1 and SCG‐2, in the genome of strain HK‐90. SCG‐1 cluster was found to be involved in classic phytosterols or cholesterol catabolic pathway through the deletion of key kstD1 gene, which promoted the mutant m‐∆kstD1 converting phytosterols to intermediate 9α‐hydroxyandrostenedione (9‐OHAD). Most impressively, global transcriptomics and characterization of key genes suggested SCG‐2 as a potential gene cluster encoding diosgenin degradation. The gene inactivation of kstD2 in SCG‐2 resulted in the conversion of diosgenin to 9‐OHAD and 9,16‐dihydroxy‐pregn‐4‐ene‐3,20‐dione (9,16‐(OH)2‐PG) in mutant m‐ΔkstD2. Moreover, the engineered strain mHust‐ΔkstD1,2,3 with a triple deletion of kstDs was constructed, which can stably accumulate 9‐OHAD by metabolizing phytosterols, and accumulate 9‐OHAD and 9,16‐(OH)2‐PG from diosgenin. Diosgenin catabolism in strain mHust‐ΔkstD1,2,3 was revealed as a progression through diosgenone, 9,16‐(OH)2‐PG, and 9‐OHAD to 9α‐hydroxytestosterone (9‐OHTS). So far, this work is the first report on genetically engineered strain metabolizing diosgenin to produce 21‐carbon and 19‐carbon steroids. This study presents a promising biosynthetic platform for the green production of steroid precursors, and provide insights into the complex biochemical mechanism of diosgenin catabolism.

Xylanase is the key enzyme responsible for the degradation of hemicellulose and plays an important role in ramie degumming. In this study, an endo-β-1,4-xylanase xyl-1 of GH11 family from Aspergillus terreus HG-52 was cloned and identified for the first time. The protein was heterologously expressed in Escherichia coli BL21, then purified and analyzed for its biochemical properties. The optimal temperature and pH of xyl-1 are 45°C and pH 5, respectively, with a specific activity as high as 1505.11 U/mg. The immunofluorescence staining combined in-situ catalysis of ramie slices revealed that xyl-1 could degrade ramie xylan fraction. The scanning electron microscopy, X-ray diffraction, and Fourier-transform infrared spectroscopy analysis of ramie fibers treated by xyl-1 showed that the treated fibers were more dispersed, the crystallinity was improved, the absorption peak of hemicellulose functional group was reduced. Residual hemicellulose content reduced from 14.93% to 5.75% and whiteness was reached 45.4, indicating xyl-1 had high-efficiency degumming ability for ramie hemicellulose. This work excavated a promising endo-β-1,4-xylanase for ramie fibers degumming applications and has good potential for commercial application.

Flax is an economically important fiber crop, however, it requires degumming to yield usable fibers. The degumming process of flax roving is a key step in flax processing and production. In this study, deep eutectic solvent (DES; choline chloride–urea) pretreatment was combined with microbial treatment to develop an ecofriendly and effective degumming method for flax roving. The optimal conditions for DES pretreatment (100°C for 120 min with 90% DES) were obtained through orthogonal tests. DES combine microbial treatment could effectively remove gum from the flax fibers. The flax roving fibers were characterized by chemical analyses, scanning electron microscopy, Fourier transform infrared spectroscopy, X-ray diffractometry, and thermogravimetric analysis. Compared with fibers treated with microbes alone, flax roving fibers subjected to DES combine microbial treatment showed better breaking tenacity (16.77 cN/tex) and average pectin, hemicellulose, and lignin removal rates of approximately 86.4%, 26.7%, and 55.1%, respectively. NMR revealed that the composition of DES was not damaged during pretreatment, which means the bulk solution could be reused. This research showed that DES combine microbial treatment is feasible and effective method for flax roving degumming.

Karst wetlands are important in the global carbon and nitrogen cycles as well as in security of water resources. Huixian wetland (Guilin) is the largest natural karst wetland in China. In recent years, groundwater nitrogen pollution has increasingly affected the wetland ecosystem integrity due to anthropogenic activities. In this study, it was hypothesized that autotrophic microbial diversity is impacted with the advent of pollution, adversely affecting autotrophs in the carbon and nitrogen cycles. Autotrophic microbes have important roles in abating groundwater nitrogen pollution. Thus, it is of great significance to study the characteristics of autotrophic bacterial communities and their responses to environmental parameters in nitrogen-polluted karst groundwaters. The abundances of the Calvin–Benson cycle functional genes cbbL and cbbM as well as the autotrophic CO2-fixing bacterial communities were characterized in the karst groundwater samples with different levels of nitrogen pollution. The cbbM gene was generally more abundant than the cbbL gene in the groundwater samples. The cbbL gene abundance was significantly positively correlated with dissolved inorganic nitrogen (DIN) concentration (P < 0.01). In the autotrophic CO2-fixing bacterial communities, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria of the phylum Proteobacteria were predominant. At the genus level, Rubrivivax and Methylibium were the dominant cbbL gene containing genera, while Halothiobacillus and Endothiovibrio were the dominant genera for the cbbM gene. The abundance of autotrophic CO2-fixing bacterial communities increased but their diversity decreased with the inflow of nitrogen into the karst groundwater system. The community structure of autotrophic CO2-fixing bacteria in the groundwaters was also significantly affected by environmental factors such as the carbonic anhydrase (CA) activity, dissolved inorganic carbon (DIC) concentration, temperature, and oxidation-reduction potential (ORP). Nitrogen inflow significantly changed the characteristics of autotrophic CO2-fixing bacterial communities in the karst groundwaters. Some key genera such as Nitrosospira and Thiobacillus were clearly abundant in the karst groundwaters with high nitrogen levels. Their respective roles in nitrification and denitrification impact nitrogen removal in this ecosystem. The findings in this study provide an important reference for biological abatement of nitrogen pollution in the karst groundwater system.

Abstract Background Taxus cells are a potential sustainable and environment-friendly source of taxol, but they have low survival ratios and slow grow rates. Despite these limitations, Taxus callus cells induced through 6 months of culture contain more taxol than their parent tissues. In this work, we utilized 6-month-old Taxus media calli to investigate their regulatory mechanisms of taxol biosynthesis by applying multiomics technologies. Our results provide insights into the adaptation strategies of T. media by transcriptional reprogramming when induced into calli from parent tissues. Results Seven out of 12 known taxol, most of flavonoid and phenylpropanoid biosynthesis genes were significantly upregulated in callus cells relative to that in the parent tissue, thus indicating that secondary metabolism is significantly strengthened. The expression of genes involved in pathways metabolizing biological materials, such as amino acids and sugars, also dramatically increased because all nutrients are supplied from the medium. The expression level of 94.1% genes involved in photosynthesis significantly decreased. These results reveal that callus cells undergo transcriptional reprogramming and transition into heterotrophs. Interestingly, common defense and immune activities, such as “plant–pathogen interaction” and salicylic acid- and jasmonic acid-signaling transduction, were repressed in calli. Thus, it’s an intelligent adaption strategy to use secondary metabolites as a cost-effective defense system. MiRNA- and degradome-sequencing results showed the involvement of a precise regulatory network in the miRNA-mediated transcriptional reprogramming of calli. MiRNAs act as direct regulators to enhance the metabolism of biological substances and repress defense activities. Given that only 17 genes of secondary metabolite biosynthesis were effectively regulated, miRNAs are likely to play intermediate roles in the biosynthesis of secondary metabolites by regulating transcriptional factors (TFs), such as ERF, WRKY, and SPL. Conclusion Our results suggest that increasing the biosynthesis of taxol and other secondary metabolites is an active regulatory measure of calli to adapt to heterotrophic culture, and this alteration mainly involved direct and indirect miRNA-induced transcriptional reprogramming. These results expand our understanding of the relationships among the metabolism of biological substances, the biosynthesis of secondary metabolites, and defense systems. They also provide a series of candidate miRNAs and transcription factors for taxol biosynthesis.

Distributed self-organization and self-management is an ideal way to achieve an autonomous and efficient operation of large-scale remote sensing satellite swarm. A distributed task allocation method based on the improved contract network algorithm is designed, orienting typical mission-level tasks. And the satellite swarm task allocation and planning model of potential target searching, moving target tracking, and sensitive target feature confirmation is given. The model is composed of observation requirement generation, observing area decomposition, and task allocation between different satellites. Simulation results confirm that the improved contract network algorithm can optimally solve the problem of mission-level task allocation autonomously in distributed swarm. This paper verifies that the self-organization method has the potential for engineering applications with simple realization theory and high calculation efficiency.

Docosahexaenoic acid (DHA) is an important omega-3 polyunsaturated fatty acid (PUFA) that plays a critical physiological role in human health. Schizochytrium sp. is considered an excellent strain for DHA production, but the synthesis of DHA is limited by the availability of nicotinamide adenine dinucleotide phosphate (NADPH). In this study, the endogenous glucose-6-phosphate dehydrogenase (G6PD) gene was overexpressed in Schizochytrium sp. H016. Results demonstrated that G6PD overexpression increased the availability of NADPH, which ultimately altered the fatty acid profile, resulting in a 1.91-fold increase in DHA yield (8.81 g/L) and increased carbon flux by shifting it from carbohydrate and protein synthesis to lipid production. Thus, G6PD played a vital role in primary metabolism. In addition, G6PD significantly increased DHA content and lipid accumulation by 31.47% and 40.29%, respectively. The fed-batch fermentation experiment results showed that DHA production reached 17.01 g/L in the overexpressing G6PD strain. These results elucidated the beneficial effects of NADPH on the synthesis of PUFA in Schizochytrium sp. H016, which may be a potential target for metabolic engineering. Furthermore, this study provides a promising regulatory strategy for the large-scale production of DHA in Schizochytrium sp.

Taxol is a rare secondary metabolite that accumulates considerably in Taxus species under salicylic acid (SA) and methyl jasmonate treatment. However, the molecular mechanism of its accumulation remains unclear. We investigated TcWRKY33, a nuclear-localized group I WRKY transcription factor, as an SA-responsive regulator of taxol biosynthesis. Overexpression and RNA interference of TcWRKY33 confirmed that TcWRKY33 regulates the expression of most taxol biosynthesis genes, especially 10-deacetylbaccatin III-10-O-acetyltransferase (DBAT) and taxadiene synthase (TASY), which were considered as key enzymes in taxol biosynthesis. Transient overexpression of TcWRKY33 in Taxus chinensis leaves resulted in increased taxol and 10-deacetylbaccatin accumulation by 1.20 and 2.16 times compared with the control, respectively. Furthermore, TcWRKY33, DBAT, and TASY were confirmed to respond positively to SA signals. These results suggested that TcWRKY33 was the missing component of taxol biosynthesis that responds to SA. The sequence analysis identified two W-box motifs in the promoter of DBAT but not in the TASY. Yeast one-hybrid and dual-luciferase activity assays confirmed that TcWRKY33 can bind to the two W-boxes in the promoter of DBAT, upregulating its expression level. Hence, DBAT is a direct target of TcWRKY33. Furthermore, TcERF15, encoding a TASY activator, also contains two W-boxes in its promoter. Yeast one-hybrid and dual-luciferase activity assays further confirmed that TcWRKY33 can upregulate TASY expression through the activation of TcERF15. In summary, TcWRKY33 transmits SA signals and positively regulates taxol biosynthesis genes in two ways: directly and through the activation of other activators. Therefore, TcWRKY33 is an excellent candidate for genetically engineering regulation of taxol biosynthesis in Taxus plants.

Abstract Background Taxus spp. produces the anticancer drug, taxol, and hence is planted as an industrial crop in China. APETALA2/ethylene response element binding proteins (AP2/EREBPs) are the key regulators of plant development, growth, and stress responses. Several homologues control taxol biosynthesis. Identifying the AP2/EREBP proteins from Taxus is important to increase breeding and production and clarify their evolutionary processes. Results Among the 90 genes from multi Taxus chinensis transcriptome datasets, 81 encoded full-length AP2-containing proteins. A domain structure highly similar to that of angiosperm AP2/EREBPs was found in 2 AP2, 2 ANT, 1 RAV, 28 dehydration-responsive element-binding proteins, and 47 ethylene-responsive factors contained, indicating that they have extremely conservative evolution processes. A new subgroup protein, TcA3Bz1, contains three conserved AP2 domains and, a new domain structure of AP2/EREBPs that is different from that of known proteins. The new subtype AP2 proteins were also present in several gymnosperms (Gingko biloba) and bryophytes (Marchantia polymorpha). However, no homologue was found in Selaginella moellendorffii, indicating unknown evolutionary processes accompanying this plant’s evolution. Moreover, the structures of the new subgroup AP2/EREBPs have different conserved domains, such as B3, zf-C3Hc3H, and agent domains, indicating their divergent evolution in bryophytes and gymnosperms. Interestingly, three repeats of AP2 domains have separately evolved from mosses to gymnosperms for most of the new proteins, but the AP2 domain of Gb_11937 has been replicated. Conclusion The new subtype AP2/EREBPs have different origins and would enrich our knowledge of the molecular structure, origin, and evolutionary processes of AP2/EREBP transcription factors in plants.

We provide detailed datasets from our analysis of proteins that are identified in human liver, lung, kidney and intestine microsomes by MS-based proteomics. Also included is a set of CYP450 enzymes and microsomal glutathione-S-transferase (MGSTs) activities in human liver microsomes. The data presented in this paper support the research article “Targeted label-free approach for quantification of epoxide hydrolase and glutathione transferases in microsomes” (Song et al., 2015) [1]. We expect that the data will contribute to the study of metabolism enzymes.

Brassica napus L. is a vegetable oil crop, commonly known as rapeseed (or canola). It is widely used as a source of oil and protein for food and industrial applications, but also as a remedy, and in a field of attraction or as an ornament due to its diverse flower colors. Every part of rapeseed is useful, even the waste, which could be used to feed animals, or recycled. In this review, the use of rapeseed in these applications is presented, starting with the preparation of oil and protein from the seeds, before their release in the market, to the utilization of natural unprocessed rapeseed. Progress in rapeseed exploitation for food, remedy, energy source, and industrial applications are analyzed to show variability in diverse findings, to provide insights and progressive descriptions of rapeseed usage to other scholars. Moreover, advancements in breeding for rapeseed improvement were described. In the future, strategies could be developed or improved to avoid or decrease crop losses, but also to increase interest in propagating the valuable traits of rapeseed.

Abstract Background Deciphering the genetic architecture of a species is a good way to understand its evolutionary history, but also to tailor its profile for breeding elite cultivars with desirable traits. Aligning QTLs from diverse population in one map and utilizing it for comparison, but also as a basis for multiple analyses assure a stronger evidence to understand the genetic system related to a given phenotype. Results In this study, 439 genes involved in fatty acid (FA) and triacylglycerol (TAG) biosyntheses were identified in Brassica napus. B. napus genome showed mixed gene loss and insertion compared to B. rapa and B. oleracea, and C genome had more inserted genes. Identified QTLs for oil (OC-QTLs) and fatty acids (FA-QTLs) from nine reported populations were projected on the physical map of the reference genome “Darmor-bzh” to generate a map. Thus, 335 FA-QTLs and OC-QTLs could be highlighted and 82 QTLs were overlapping. Chromosome C3 contained 22 overlapping QTLs with all trait studied except for C18:3. In total, 218 candidate genes which were potentially involved in FA and TAG were identified in 162 QTLs confidence intervals and some of them might affect many traits. Also, 76 among these candidate genes were found inside 57 overlapping QTLs, and candidate genes for oil content were in majority (61/76 genes). Then, sixteen genes were found in overlapping QTLs involving three populations, and the remaining 60 genes were found in overlapping QTLs of two populations. Interaction network and pathway analysis of these candidate genes indicated ten genes that might have strong influence over the other genes that control fatty acids and oil formation. Conclusion The present results provided new information for genetic basis of FA and TAG formation in B. napus. A map including QTLs from numerous populations was built, which could serve as reference to study the genome profile of B. napus, and new potential genes emerged which might affect seed oil. New useful tracks were showed for the selection of population or/and selection of interesting genes for breeding improvement purpose.

Worldwide consumption of oil is increasing with the growing population in need for edible oil and the expansion of industry using biofuels. Then, demand for high yielding varieties of oil crops is always increasing. Brassica napus (rapeseed) is one of the most important oil crop in the world, therefore, increasing rapeseed yield through breeding is inevitable in order to cater for the high demand of vegetable oil and high-quality protein for live stocks. Quantitative trait loci (QTL) analysis is a powerful tool to identify important loci and which is also valuable for molecular marker assisted breeding. Seed-yield (SY) is a complex trait that is controlled by multiple loci and is affected directly by seed weight, seeds per silique and silique number. Some yield-related traits, such as plant height, biomass yield, flowering time, and so on, also affect the SY indirectly. This study reports the assembly of QTLs identified for seed-yield and yield-related traits in rapeseed, in one unique map. A total of 972 QTLs for seed-yield and yield-related were aligned into the physical map of B. napus Darmor-bzh and 92 regions where 198 QTLs overlapped, could be discovered on 16 chromosomes. Also, 147 potential candidate genes were discovered in 65 regions where 131 QTLs overlapped, and might affect nine different traits. At the end, interaction network of candidate genes was studied, and showed nine genes that could highly interact with the other genes, and might have more influence on them. The present results would be helpful to develop molecular markers for yield associated traits and could be used for breeding improvement in B. napus.

The multitherapeutic taxol, which can be obtained from Taxus spp., is the most widely used anticancer drug. Taxol biosynthesis is significantly regulated by jasmonate acid (JA), one of the most important endogenous hormones in land plants. Nevertheless, the JA-inducing mechanism remains poorly understood. MYC2 is one of the key regulators of JA signal transfer and the biosynthesis of various secondary metabolites. Here, TcMYC2a was identified to contain a basic helix–loop–helix (bHLH)-leucine zipper domain, a bHLH-MYC_N domain, and a BIF/ACT-like domain. TcMYC2a was also found to bind with TcJAZ3 in yeast, which was a homolog of Arabidopsis JASMONATE ZIM-domain JAZ proteins, indicating that TcMYC2a had a similar function to AtMYC2 of JA signal transduction. TcMYC2a was able to affect the expression of GUS reporter gene by binding with the T/G-box, G-box, and E-box, which were the key cis-elements of TASY and TcERF12/15 promoter. TcMYC2a overexpression also led to significantly increased expression of TASY, tat, dbtnbt, t13h, and t5h genes. Additionally, TcERF15, which played the positive role to regulate tasy gene, was up-regulated by TcMYC2a. All these results revealed that TcMYC2a can regulate taxol biosynthesis either directly or via ERF regulators depending on JA signaling transduction.

Diversities in structure and function of ACBP were discussed in this review. ACBP are important proteins that could transport newly synthesized fatty acid, activated into -coA, from plastid to endoplasmic reticulum, where oil in the form of triacylglycerol occurs. ACBP were detected in various animal and plants species, which indicated their importance in biological function. In fact, involvement of ACBP in important process such as lipid metabolism, regulation of enzyme and gene expression, and in response to plant stresses has been proven in several studies. In this review, findings on ACBP of 11 well-known oil crops were reviewed to comprehend diversity, comparative analyses on ACBP structure were made, and link between structure and function, tissue expression and subcellular location of ACBP were also observed. Incomplete reports in some species were mentioned, which might be encouraging to start or to perform deeper studies. Similar characteristics were found in paralogs ACBP, and orthologs ACBP had different functions, despite the high identity in amino acid sequence. At the end, it is confirmed that ortholog proteins could not necessarily display the same function, even from closely related species.

Taxus spp. is a highly valuable medicinal plant with multiple pharmacological effects on various cancers. Cytochrome P450s (CYP450s) play important roles in the biosynthesis of active compounds in Taxus spp., such as the famous diterpenoid, Taxol. However, some specific CYP450 enzymes involved in the biosynthesis of Taxol remain unknown, and the systematic identification of CYP450s in Taxus has not been reported. In this study, 118 full-length and 175 partial CYP450 genes were identified in Taxus chinensis transcriptomes. The 118 full-length genes were divided into 8 clans and 29 families. The CYP71 clan included all A-type genes (52) belonging to 11 families. The other seven clans possessed 18 families containing 66 non-A-type genes. Two new gymnosperm-specific families were discovered, and were named CYP864 and CYP947 respectively. Protein sequence alignments revealed that all of the T. chinensis CYP450s hold distinct conserved domains. The expression patterns of all 118 CYP450 genes during the long-time subculture and MeJA elicitation were analyzed. Additionally, the expression levels of 15 novel CYP725 genes in different Taxus species were explored. Considering all the evidence, 6 CYP725s were identified to be candidates for Taxol biosynthesis. The cis-regulatory elements involved in the transcriptional regulation were also identified in the promoter regions of CYP725s. This study presents a comprehensive overview of the CYP450 gene family in T. chinensis and can provide important insights into the functional gene studies of Taxol biosynthesis.

Lycoris species have been known since long ago as a multi-utility ethnomedicinal herbal in China. It has been reported to exhibit a number of properties such as anticancer, neuroprotective, and antibacterial activities. In the present study, the anticancer efficacy of dichloromethane extracts of Lycoris aurea (DELA), was evaluated both in vivo and in vitro using murine sarcoma 180 cells. To evaluate the effects of DELA on apoptotic cell death, flow cytometry and Western blotting were performed. DELA demonstrated promising inhibition effects on sarcoma 180 cells in vitro and a 53.49% inhibitory rate on cancer cells in vivo. DELA treatment increased thymus indices and spleen indices in vivo, indicating that it reduced tumours, but did not damage the main immune organs. The DELA-evoked increase in apoptotic cell death was accompanied by occurrence of cleaved caspase-3 and decreases in the ratio of Bcl-2/Bax. Further purification and LCMS analysis showed DELA contained homolycorine, 2α-hydroxyoduline, oduline, hippeastrine, 2α-hydroxy-6-O- methyloduline, and 2α-methoxy-6-O-methyloduline. These results indicate that DELA exerted its anticancer effects, at least in part, by inducing cancer cell apoptosis and thus can be considered as a potential candidate agent for treatment of cancer.

MiRNAs function in post-transcriptional regulation of gene expression and play very important roles in plant development. Lonicera japonica is one of the important medicinal plants in China. However, few studies on the discovery of conserved and novel miRNAs from L. japonica were reported. In this study, we employed deep sequencing technology to identify miRNAs in leaf and flower tissues of L. japonica. A total of 22.97 million clean reads from flower and leaf tissues were obtained, which generated 146 conserved miRNAs distributed in 20 families and 110 novel miRNAs. Accordingly, 72 differentially expressed miRNAs (P≤0.001) between leaves and flowers and their potential target genes were identified and validated. The qRT-PCR validation showed that majority of the differentially expressed miRNAs showed significant tissue-specific expression in L. japonica. Furthermore, the miRNA-mRNA and mRNA-mRNA regulatory networks were constructed using Cytoscape software. Taken together, this study identified a large number of miRNAs and target genes in L. japonica, which not only provides the first global miRNA expression profiles, but also sheds light on functional genomics research on L. japonica in the future.

The prediction of the flowering time (FT) trait in Brassica napus based on genome-wide markers and the detection of underlying genetic factors is important not only for oilseed producers around the world but also for the other crop industry in the rotation system in China. In previous studies the low density and mixture of biomarkers used obstructed genomic selection in B. napus and comprehensive mapping of FT related loci. In this study, a high-density genome-wide SNP set was genotyped from a double-haploid population of B. napus. We first performed genomic prediction of FT traits in B. napus using SNPs across the genome under ten environments of three geographic regions via eight existing genomic predictive models. The results showed that all the models achieved comparably high accuracies, verifying the feasibility of genomic prediction in B. napus. Next, we performed a large-scale mapping of FT related loci among three regions, and found 437 associated SNPs, some of which represented known FT genes, such as AP1 and PHYE. The genes tagged by the associated SNPs were enriched in biological processes involved in the formation of flowers. Epistasis analysis showed that significant interactions were found between detected loci, even among some known FT related genes. All the results showed that our large scale and high-density genotype data are of great practical and scientific values for B. napus. To our best knowledge, this is the first evaluation of genomic selection models in B. napus based on a high-density SNP dataset and large-scale mapping of FT loci.

Lonicera confusa was a medical plant which could adapt to the Ca-rich environment in the karst area of China. The photosynthesis, relative chlorophyll content,differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) of L. confusa that cultivated in calcareous and sandstone soils were investigated. The results showed that the relative chlorophyll content and net photosynthesis rate of L. confusa in calcareous soil are much higher than that planted in sandstone soil, the higher content of calcium might play a role in keeping the chloroplast from harm and showed higher photosynthesis rate. The transpiration and stomata conductance were decreased in calcareous soil, which might result from the closure of stomata. The GeneFishing and proteomic results showed that the expression of DEGs and DEPs were critical for photosynthesis and stomata closure, such as RuBisCO, photosynthetic electron transfer c and malate dehydrogenase varied in the leaves of L. confusa that cultivated in different soils. These DEGs or DEPs were further found to be directly or indirectly regulated by calcium sensor proteins. This study enriched our knowledge of the molecular mechanism of high net photosynthesis rate and lower transpiration of L. confusa that cultivated in the calcareous soil in some degree.

Increasing seed oil content is one of the most important goals in breeding of rapeseed (B. napus L.). To dissect the genetic basis of oil content in B. napus, a large and new double haploid (DH) population containing 348 lines was obtained from a cross between 'KenC-8' and 'N53-2', two varieties with >10% difference in seed oil content, and this population was named the KN DH population. A genetic linkage map consisting of 403 markers was constructed, which covered a total length of 1783.9 cM with an average marker interval of 4.4 cM. The KN DH population was phenotyped in eight natural environments and subjected to quantitative trait loci (QTL) analysis for oil content. A total of 63 identified QTLs explaining 2.64-17.88% of the phenotypic variation were identified, and these QTLs were further integrated into 24 consensus QTLs located on 11 chromosomes using meta-analysis. A high-density consensus map with 1335 marker loci was constructed by combining the KN DH map with seven other published maps based on the common markers. Of the 24 consensus QTLs in the KN DH population, 14 were new QTLs including five new QTLs in A genome and nine in C genome. The analysis revealed that a larger population with significant differences in oil content gave a higher power detecting new QTLs for oil content, and the construction of the consensus map provided a new clue for comparing the QTLs detected in different populations. These findings enriched our knowledge of QTLs for oil content and should be a potential in marker-assisted breeding of B. napus.

The Pythium splendens is a potentially useful organism for the synthesis of large amounts of eicosapentaenoic acid. Peak biomass and lipid accumulation do not occur at the same time and growth temperature has an effect on the fatty acid composition. Little is known about the pathway or the genes involved in growth, lipid synthesis or temperature resistance in P. splendens. Analysis of the transcriptome and expression profile data for P.splendensRBB-5 were used to extend genetic information for this strain and to contribute to a comprehensive understanding of the molecular mechanisms involved in specific biological processes.This study used transcriptome assembly and gene expression analysis with short-read sequencing technology combined with a tag-based digital gene expression (DGE) system. Assembled sequences were annotated with gene descriptions, such as gene ontology (GO), clusters of orthologous group (COG) terms and KEGG orthology (KO) to generate 23,796 unigenes. In addition, we obtained a larger number of genes at different stages of fermentation (48, 100 and 148 h). The genes related to growth characteristics and lipid biosynthesis were analyzed in detail. Some genes associated with lipid and fatty acid biosynthesis were selected to confirm the digital gene expression (DGE) results by quantitative real-time PCR (qRT-PCR).The transcriptome improves our genetic understanding of P.splendensRBB-5 greatly and makes a large number of gene sequences available for further study. Notably, the transcriptome and DGE profiling data of P.splendensRBB-5 provide a comprehensive insight into gene expression profiles at different stages of fermentation and lay the foundation for the study of optimizing lipid content and growth speed at the molecular level.