Mediating role of loneliness and emotional disturbance in the association between childhood trauma and occupational burnout among nurses: a cross-sectional study.

Background: The occupational burnout status of nurses in China warrants attention. Childhood trauma, loneliness, and emotional disturbance are significant predictors of this burnout, yet few studies have delved into the underlying mechanisms. This study seeks to explore the mediating pathway from childhood trauma to loneliness, emotional disturbance, and ultimately occupational burnout among nurses through a cross-sectional analysis. Method: Data for the study were collected from Yunnan province, China, from 11 July to 26 July 2022. Key variables were measured using standardized scales: the Childhood Trauma Questionnaire Short Form for childhood trauma, the three-item loneliness scale for loneliness, the Patient Health Questionnaire and the Generalized Anxiety Disorder questionnaire for emotional disturbance, and the Maslach Burnout Inventory-Human Service Survey for occupational burnout. Mediation modeling analysis was employed for data analysis to test the effect of loneliness and emotional disturbance on the association between childhood trauma and occupational burnout. Data analysis was conducted using AMOS and SPSS software. Results: Loneliness and emotional disturbance fully mediated the association between childhood trauma and emotional exhaustion [indirect effect (95% CI) = 0.228 (0.196, 0.270)]. Loneliness and emotional disturbance partially mediated the association between childhood trauma [indirect effect (95% CI) = -0.020 (-0.039, 0.002)] and personal accomplishment or depersonalization [indirect effect (95% CI) = 0.221 (0.186, 0.255)]. Conclusion: Childhood trauma could affect occupational burnout through loneliness and emotional disturbance among nurses. Preventive strategies could include protective interventions like treatment of loneliness and emotional disturbance, especially in nurses who experienced childhood trauma.

Multi-omics strategies uncover the molecular mechanisms of nitrogen, phosphorus and potassium deficiency responses in Brassica napus.

BACKGROUND: Nitrogen (N), phosphorus (P) and potassium (K) are critical macronutrients in crops, such that deficiency in any of N, P or K has substantial effects on crop growth. However, the specific commonalities of plant responses to different macronutrient deficiencies remain largely unknown. METHODS: Here, we assessed the phenotypic and physiological performances along with whole transcriptome and metabolomic profiles of rapeseed seedlings exposed to N, P and K deficiency stresses. RESULTS: Quantities of reactive oxygen species were significantly increased by all macronutrient deficiencies. N and K deficiencies resulted in more severe root development responses than P deficiency, as well as greater chlorophyll content reduction in leaves (associated with disrupted chloroplast structure). Transcriptome and metabolome analyses validated the macronutrient-specific responses, with more pronounced effects of N and P deficiencies on mRNAs, microRNAs (miRNAs), circular RNAs (circRNAs) and metabolites relative to K deficiency. Tissue-specific responses also occurred, with greater effects of macronutrient deficiencies on roots compared with shoots. We further uncovered a set of common responders with simultaneous roles in all three macronutrient deficiencies, including 112 mRNAs and 10 miRNAs involved in hormonal signaling, ion transport and oxidative stress in the root, and 33 mRNAs and 6 miRNAs with roles in abiotic stress response and photosynthesis in the shoot. 27 and seven common miRNA-mRNA pairs with role in miRNA-mediated regulation of oxidoreduction processes and ion transmembrane transport were identified in all three macronutrient deficiencies. No circRNA was responsive to three macronutrient deficiency stresses, but two common circRNAs were identified for two macronutrient deficiencies. Combined analysis of circRNAs, miRNAs and mRNAs suggested that two circRNAs act as decoys for miR156 and participate in oxidoreduction processes and transmembrane transport in both N- and P-deprived roots. Simultaneously, dramatic alterations of metabolites also occurred. Associations of RNAs with metabolites were observed, and suggested potential positive regulatory roles for tricarboxylic acids, azoles, carbohydrates, sterols and auxins, and negative regulatory roles for aromatic and aspartate amino acids, glucosamine-containing compounds, cinnamic acid, and nicotianamine in plant adaptation to macronutrient deficiency. CONCLUSIONS: Our findings revealed strategies to rescue rapeseed from macronutrient deficiency stress, including reducing the expression of non-essential genes and activating or enhancing the expression of anti-stress genes, aided by plant hormones, ion transporters and stress responders. The common responders to different macronutrient deficiencies identified could be targeted to enhance nutrient use efficiency in rapeseed.

Application of image overlapping in percutaneous nephrolithotomy.

OBJECTIVE: To investigate the application of ultrasound and CT image overlap in percutaneous nephrolithotomy (PCNL). METHODS: A total of 140 patients with complicated kidney stones requiring PCNL were prospectively enrolled, from January 2020 to December 2022. These patients were randomly divided into 2 groups, with 70 patients each in the research group and the control group. All participants underwent dual-source, non-contrast CT scan of both kidneys and pelvis before surgery. Preoperative three-dimensional CT reconstruction and simulated puncture were performed in patients from the research group. The best puncture path was determined through ultrasound and CT image overlap. Puncture guided by regular CT and ultrasound was conducted in patients from the control group. Differences in the surgical outcomes between the two groups were compared. RESULTS: Compared to the control group, the research group had higher stone clearance rate in stage I PCNL, success rate of one-time puncture, less percutaneous channels, less reduction of hemoglobin and shorter procedure time. Complications in stage I PCNL were comparable in the two groups, and there was no significant change in the final stone clearance rates between the two groups. CONCLUSION: An optimal puncture channel can be chosen using ultrasound and CT image overlap. PCNL can be achieved with precise puncturing, thus achieving coincidence between imaging and anatomy and reducing the amount of blood loss during stage I of PCNL. It also shortens the procedure time and improves stone clearance rate of PCNL.

Research progress and applications of colorful Brassica crops.

MAIN CONCLUSION: We review the application and the molecular regulation of anthocyanins in colorful Brassica crops, the creation of new germplasm resources, and the development and utilization of colorful Brassica crops. Brassica crops are widely cultivated: these include oilseed crops, such as rapeseed, mustards, and root, leaf, and stem vegetable types, such as turnips, cabbages, broccoli, and cauliflowers. Colorful variants exist of these crop species, and asides from increased aesthetic appeal, these may also offer advantages in terms of nutritional content and improved stress resistances. This review provides a comprehensive overview of pigmentation in Brassica as a reference for the selection and breeding of new colorful Brassica varieties for multiple end uses. We summarize the function and molecular regulation of anthocyanins in Brassica crops, the creation of new colorful germplasm resources via different breeding methods, and the development and multifunctional utilization of colorful Brassica crop types.

Mapping and Identifying Candidate Genes Enabling Cadmium Accumulation in Brassica napus Revealed by Combined BSA-Seq and RNA-Seq Analysis.

Rapeseed has the ability to absorb cadmium in the roots and transfer it to aboveground organs, making it a potential species for remediating soil cadmium (Cd) pollution. However, the genetic and molecular mechanisms underlying this phenomenon in rapeseed are still unclear. In this study, a 'cadmium-enriched' parent, 'P1', with high cadmium transport and accumulation in the shoot (cadmium root: shoot transfer ratio of 153.75%), and a low-cadmium-accumulation parent, 'P2', (with a cadmium transfer ratio of 48.72%) were assessed for Cd concentration using inductively coupled plasma mass spectrometry (ICP-MS). An F2 genetic population was constructed by crossing 'P1' with 'P2' to map QTL intervals and underlying genes associated with cadmium enrichment. Fifty extremely cadmium-enriched F2 individuals and fifty extremely low-accumulation F2 individuals were selected based on cadmium content and cadmium transfer ratio and used for bulk segregant analysis (BSA) in combination with whole genome resequencing. This generated a total of 3,660,999 SNPs and 787,034 InDels between these two segregated phenotypic groups. Based on the delta SNP index (the difference in SNP frequency between the two bulked pools), nine candidate Quantitative trait loci (QTLs) from five chromosomes were identified, and four intervals were validated. RNA sequencing of 'P1' and 'P2' in response to cadmium was also performed and identified 3502 differentially expressed genes (DEGs) between 'P1' and 'P2' under Cd treatment. Finally, 32 candidate DEGs were identified within 9 significant mapping intervals, including genes encoding a glutathione S-transferase (GST), a molecular chaperone (DnaJ), and a phosphoglycerate kinase (PGK), among others. These genes are strong candidates for playing an active role in helping rapeseed cope with cadmium stress. Therefore, this study not only sheds new light on the molecular mechanisms of Cd accumulation in rapeseed but could also be useful for rapeseed breeding programs targeting this trait.

Characterization of the Internal Stress Evolution of an EB-PVD Thermal Barrier Coating during a Long-Term Thermal Cycling.

Electron beam physical vapour deposition (EB-PVD) technology is a standard industrial method for the preparation of a thermal barrier coating (TBC) deposition on aeroengines. The internal stress of EB-PVD TBCs, including stress inside the top coating (TC) and thermal oxidation stress during long-term service is one of the key reasons for thermal barrier failures. However, research on the synergistic characterization of the internal stress of EB-PVD TBCs is still lacking. In this work, the stress inside the TC layer and the thermal oxidation stress of EB-PVD TBC during long-term thermal cycles were synergistically detected, combining Cr3+-PLPS and THz-TDS technologies. Based on a self-built THz-TDS system, stress-THz coefficients c1 and c2 of the EB-PVD TBC, which are the core parameters for stress characterization, were calibrated for the first time. According to experimental results, the evolution law of the internal stress of the TC layer was similar to that of the TGO stress, which were interrelated and influenced by each other. In addition, the internal stress of the TC layer was less than that of the TGO stress due to the columnar crystal microstructure of EB-PVD TBCs.

The characterization of bovine compact bone fatigue damage using terahertz spectroscopy.

Fatigue can cause cracks to propagate from the micro- to the macroscale, which results in a decrease of Young's modulus of the bone. Non-destructive measurements of bone fatigue damage are of great importance for bone quality assessment and fracture prevention. Unfortunately, there is still a lack of effective nondestructive methods sensitive to the initial deterioration during damage accumulation, particularly in the field of orthopedics and biomechanics. In this study, terahertz spectroscopy was adopted to evaluate microscale bone damage. Specifically, the refractive index and Young's modulus of bone samples subjected to different degrees of fatigue damage were tested at a fixed area. Both parameters are found to decrease in two stages under cycled fatigue loading, which is attributed to the initial onset and subsequent development of microdamage during fatigue loading. The change in refractive index reflects the accumulation of fatigue damage as well as the decrease in Young's modulus.

Stress Component Decoupling Analysis Based on Large Numerical Aperture Objective Lens, an Impractical Approach.

Micro Raman spectroscopy is an effective method to quantitatively analyse the internal stress of semiconductor materials and structures. However, the decoupling analysis of the stress components for {100} monocrystalline silicon (c-Si) remains difficult. In the work outlined, physical and simulation experiments were combined to study the influence of the objective lens numerical aperture (NA) on the Raman stress characterization. The physical experiments and simulation experiments show that the spectral results obtained by using lenses with different NAs can accurately obtain the principal stress sum but cannot decouple the components of the in-plane stress. Even if the spectral resolution of the simulated experiment is ideal (The random errors of the polarization directions of less than ±1° and the systematic random errors of less than ±0.02 cm-1). The analysis based on the theoretical model demonstrates that the proportion of the principal stress sum in the Raman shift obtained in an actual experiment exceeded 98.7%, while the proportion of the principal stress difference part was almost negligible. This result made it difficult to identify the variable effects of different stress states from the experimental results. Further simulation experiments in this work verify that when the principal stress sum was identical, the differences in the Raman shifts caused by different stress states were much smaller than the resolution of the existing Raman microscope system, which was hardly possible to identify in the experimental results. It was proven that decoupling analysis of stress components using the large-NA objective lens lacked actual practicability.

Effects of Fatigue Damage on the Microscopic Modulus of Cortical Bone Using Nanoindentation.

Alterations to the bone structure from cycle loadings can undermine its damage resistance at multiple scales. The accumulation of fatigue damage in a bone is commonly characterized by the reduction in the elastic modulus. In this study, nano-indentation was used for investigating microscopic damage evolution of bovine tibia samples subjected to fatigue loading. Indentation tests were conducted in the same 60 µm × 120 µm area with different degrees of damage, including fracture, and the evolution of reduced modulus was observed. The results showed that bone's reduced modulus decreased significantly during the initial 40% of the life fraction, whereas it proceeded slowly during the remaining period. As the size of the residual indentations was about 4 µm in length, the degradation of bone's reduced modulus reflected the accumulation of fatigue damage at smaller scales.

Identification of genetic variation for salt tolerance in Brassica napus using genome-wide association mapping.

Soil salinity negatively impacts rapeseed (Brassica napus) crop production. In particular, high soil salinity is known to hinder seedling growth and establishment. Identifying natural genetic variation for high salt tolerance in Brassica napus seedlings is an effective way to breed for improved productivity under salt stress. To identify genetic variants involved in differential response to salt stress, we evaluated a diverse association panel of 228 Brasica napus accessions for four seedling traits under salt stress to establish stress susceptibility index (SSI) and stress tolerance index (STI) values, and performed genome-wide association studies (GWAS) using 201,817 high-quality single nucleotide polymorphic (SNP) markers. Our GWAS identified 142 significant SNP markers strongly associated with salt tolerance distributed across all rapeseed chromosomes, with 78 SNPs in the C genome and 64 SNPs in the A genome, and our analyses subsequently pinpointed both favorable alleles and elite cultivars. We identified 117 possible candidate genes associated with these SNPs: 95/117 were orthologous with Arabidopsis thaliana genes encoding transcription factors, aquaporins, and binding proteins. The expression level of ten candidate genes was validated by quantitative real-time PCR (qRT-PCR), and these genes were found to be differentially expressed between salt-tolerant and salt-susceptible lines under salt stress conditions. Our results provide new genetic resources and information for improving salt tolerance in rapeseed genotypes at the seed germination and seedling stages via genomic or marker-assisted selection, and for future functional characterization of putative gene candidates.

Differentially evolved drought stress indices determine the genetic variation of Brassica napus at seedling traits by genome-wide association mapping.

Drought seriously curtails growth, physiology and productivity in rapeseed (Brassica napus). Although drought tolerance is a complex trait, efficient phenotyping and genotyping has led to the identification of novel marker-trait associations underlying drought tolerance. A diverse panel of 228 Brassica accessions was phenotyped under normal (without stress) and water-stress conditions, simulated by polyethylene glycol (PEG-6000) (15% PEG stress) at the seedling stage; stress tolerance index (STI) and stress susceptibility index (SSI) values were acquired. Genome-wide association studies (GWAS) using 201 817 high quality SNPs identified 314 marker-trait associations strongly linked with drought indices and distributed across all nineteen chromosomes in both the A and C genomes. None of these quantitative trait loci (QTL) had been previously identified by other studies. We identified 85 genes underlying these QTL (most within 100 kb of associated SNPs) which were orthologous to Arabidopsis genes known to be associated with drought tolerance. Our study provides a novel resource for breeding drought-tolerant Brassica crops.

MicroRNA-mRNA expression profiles and their potential role in cadmium stress response in Brassica napus.

BACKGROUND: Oilseed rape is an excellent candidate for phytoremediation of cadmium (Cd) contaminated soils given its advantages of high biomass, fast growth, moderate metal accumulation, ease of harvesting, and metal tolerance, but the cadmium response pathways in this species (Brassica napus) have yet to be fully elucidated. A combined analysis of miRNA and mRNA expression to infer Cd-induced regulation has not been reported in B. napus. RESULTS: We characterized concurrent changes in miRNA and mRNA profiles in the roots and shoots of B. napus seedlings after 10 days of 10 mg/L Cd2+ treatment. Cd treatment significantly affected the expression of 22 miRNAs belonging to 11 families in the root and 29 miRNAs belonging to 14 miRNA families in the shoot. Five miRNA families (MIR395, MIR397, MIR398, MIR408 and MIR858) and three novel miRNAs were differentially expressed in both tissues. A total of 399 differentially expressed genes (DEGs) in the root and 389 DEGs in the shoot were identified, with very little overlap between tissue types. Eight anti-regulation miRNA-mRNA interaction pairs in the root and eight in the shoot were identified in response to Cd and were involved in key plant stress response pathways: for example, four genes targeted by miR398 were involved in a pathway for detoxification of superoxide radicals. Cd stress significantly impacted the photosynthetic pathway. Transcription factor activation, antioxidant response pathways and secondary metabolic processes such as glutathione (GSH) and phenylpropanoid metabolism were identified as major components for Cd-induced response in both roots and shoots. CONCLUSIONS: Combined miRNA and mRNA profiling revealed miRNAs, genes and pathways involved in Cd response which are potentially critical for adaptation to Cd stress in B. napus. Close crosstalk between several Cd-induced miRNAs and mRNAs was identified, shedding light on possible mechanisms for response to Cd stress in underground and aboveground tissues in B. napus. The pathways, genes, and miRNAs identified here will be valuable targets for future improvement of cadmium tolerance in B. napus.

Non-coding RNAs and transposable elements in plant genomes: emergence, regulatory mechanisms and roles in plant development and stress responses.

MAIN CONCLUSION: This review will provide evidence for the indispensable function of these elements in regulating plant development and resistance to biotic and abiotic stresses, as well as their evolutionary role in facilitating plant adaptation. Over millions of years of evolution, plant genomes have acquired a complex constitution. Plant genomes consist not only of protein coding sequences, but also contain large proportions of non-coding sequences. These include introns of protein-coding genes, and intergenic sequences such as non-coding RNA, repeat sequences and transposable elements. These non-coding sequences help to regulate gene expression, and are increasingly being recognized as playing an important role in genome organization and function. In this review, we summarize the known molecular mechanisms by which gene expression is regulated by several species of non-coding RNAs (microRNAs, long non-coding RNAs, and circular RNAs) and by transposable elements. We further discuss how these non-coding RNAs and transposable elements evolve and emerge in the genome, and the potential influence and importance of these non-coding RNAs and transposable elements in plant development and in stress responses.

NBS-Encoding Genes in Brassica napus Evolved Rapidly After Allopolyploidization and Co-localize With Known Disease Resistance Loci.

Genes containing nucleotide-binding sites (NBS) play an important role in pathogen resistance in plants. However, the evolutionary fate of NBS-encoding genes after formation of allotetraploid Brassica napus (AnAnCnCn, 2n = 38) is still unknown. We performed a genome-wide comparison of putatively functional NBS-encoding genes in B. napus and its progenitor species Brassica rapa (ArAr, 2n = 20) and Brassica oleracea (CoCo, 2n = 18), identifying 464, 202, and 146 putatively functional NBS-encoding genes respectively, with genes unevenly distributed in several clusters. The An-subgenome of B. napus possessed similar numbers of NBS-encoding genes (191 genes) to the Ar genome of B. rapa (202 genes) and similar clustering patterns. However, the Cn genome of B. napus had many more genes (273) than the B. oleracea Co genome (146), with different clustering trends. Only 97 NBS-encoding genes (66.4%) in B. oleracea were homologous with NBS-encoding genes in B. napus, while 176 NBS-encoding genes (87.1%) were homologous between B. rapa and B. napus. These results suggest a greater diversification of NBS-encoding genes in the C genome may have occurred after formation of B. napus. Although most NBS-encoding genes in B. napus appeared to derive from the progenitors, the birth and death of several NBS-encoding genes was also putatively mediated by non-homologous recombination. The Ka/Ks values of most homologous pairs between B. napus and the progenitor species were less than 1, suggesting purifying selection during B. napus evolution. The majority of NBS-encoding genes (60% in all species) showed higher expression levels in root tissue (out of root, leaf, stem, seed and flower tissue types). Comparative analysis of NBS-encoding genes with mapped resistance QTL against three major diseases of B. napus (blackleg, clubroot and Sclerotinia stem rot) found 204 NBS-encoding genes in B. napus located within 71 resistance QTL intervals. The majority of NBS-encoding genes were co-located with resistance QTLs against a single disease, while 47 genes were co-located with QTLs against two diseases and 3 genes were co-located with QTLs against all three. Our results revealed significant variation as well as interesting evolutionary trajectories of NBS-encoding genes in the different Brassica subgenomes, while co-localization of NBS-encoding genes and resistance QTL may facilitate resistance breeding in oilseed rape.

High Nighttime Temperature Induces Antioxidant Molecule Perturbations in Heat-Sensitive and Heat-Tolerant Coisogenic Rice ( Oryza sativa) Strains.

Global warming-associated increases in temperature, particularly at nighttime, are detrimental to rice yield and quality. Metabolomic profiling was used to examine and compare the short-term extreme high nighttime temperature-induced molecular perturbations in rice ( Oryza sativa) coisogenic strains with contrasting heat-tolerances at the first stage of seed ripening. Compared to the heat-sensitive strain, antioxidant molecules were higher in abundance in the heat-tolerant strain, whereas the abundances of molecules involved in photosynthesis, nucleotide catabolism, and the S-adenosylmethionine (SAM) cycle varied only slightly. Thus, we proposed that the high abundance of antioxidant molecules in the heat-tolerant strain alleviated cellular oxidative stress, which protected photosynthesis, nucleotide catabolism, and the SAM cycle, leading to good grain filling.

Inhibition of E-cadherin expression by lnc-RNA H19 to facilitate bladder cancer metastasis.

Bladder cancer is derived from bladder mucosa and is the most common malignant tumor in urinary system. Long non-coding RNA (lnc-RNA) has high tissue specificity and can participate in cell proliferation and differentiation at various levels, and plays critical roles in occurrence of malignant tumors. This study aims to investigate the suppression of E-cadherin expression by lnc-RNA H19 to enhance bladder cancer metastasis.qRT-PCR was applied to analyze differential expression of lnc-RNA H19 in different bladder cancer tissues and tumor adjacent tissues. Patients clinical data were collected to analyze the correlation between H19 expression level and patient's clinical stage, tumor metastasis. RNA interference was employed to examine the effect of H19 on E-cadherin expression. The regulation of cancer metastasis was investigated on an animal model. H19 expression level was significantly higher in bladder cancer tissue compared to adjacent tissues (p< 0.05), and is correlated with advanced clinical stage (p< 0.05). In those metastatic patients, H19 expression level is significantly higher than those without metastasis (p< 0.05). RNA interference is applied to knockdown H19 expression in bladder cancer cell, and found potentiated E-cadherin expression (p< 0.05), accompanied with weakened metastatic potency (p< 0.05). H19 expression is up-regulated in bladder cancer, and is probably related with cancer clinical stage and metastasis. Cell transfection reveals up-regulation of E-cadherin expression in bladder cancer cells when H19 expression is suppressed, accompanied with weakened metastasis potency.

Genome-wide identification, putative functionality and interactions between lncRNAs and miRNAs in Brassica species.

Non-coding RNA (ncRNA) is abundant in plant genomes, but is poorly described with unknown functionality in most species. Using whole genome RNA sequencing, we identified 1885, 1910 and 1299 lncRNAs and 186, 157 and 161 miRNAs at the whole genome level in the three Brassica species B. napus, B. oleracea and B. rapa, respectively. The lncRNA sequences were divergent between the three Brassica species. One quarter of lncRNAs were located in tandem repeat (TR) region. The expression of both lncRNAs and miRNAs was strongly biased towards the A rather than the C subgenome in B. napus, unlike mRNA expression. miRNAs in genic regions had higher average expression than miRNAs in non-genic regions in B. napus and B. oleracea. We provide a comprehensive reference for the distribution, functionality and interactions of lncRNAs and miRNAs in Brassica.

The genetic and molecular basis of crop height based on a rice model.

MAIN CONCLUSION: This review presents genetic and molecular basis of crop height using a rice crop model. Height is controlled by multiple genes with potential to be manipulated through breeding strategies to improve productivity. Height is an important factor affecting crop architecture, apical dominance, biomass, resistance to lodging, tolerance to crowding and mechanical harvesting. The impressive increase in wheat and rice yield during the 'green revolution' benefited from a combination of breeding for high-yielding dwarf varieties together with advances in agricultural mechanization, irrigation and agrochemical/fertilizer use. To maximize yield under irrigation and high fertilizer use, semi-dwarfing is optimal, whereas extreme dwarfing leads to decreased yield. Rice plant height is controlled by genes that lie in a complex regulatory network, mainly involved in the biosynthesis or signal transduction of phytohormones such as gibberellins, brassinosteroids and strigolactones. Additional dwarfing genes have been discovered that are involved in other pathways, some of which are uncharacterized. This review discusses our current understanding of the regulation of plant height using rice as a well-characterized model and highlights some of the most promising research that could lead to the development of new, high-yielding varieties. This knowledge underpins future work towards the genetic improvement of plant height in rice and other crops.

Earliness traits in rapeseed (Brassica napus): SNP loci and candidate genes identified by genome-wide association analysis.

Life cycle timing is critical for yield and productivity of Brassica napus (rapeseed) cultivars grown in different environments. To facilitate breeding for earliness traits in rapeseed, SNP loci and underlying candidate genes associated with the timing of initial flowering, maturity and final flowering, as well as flowering period (FP) were investigated in two environments in a diversity panel comprising 300 B. napus inbred lines. Genome-wide association studies (GWAS) using 201,817 SNP markers previously developed from SLAF-seq (specific locus amplified fragment sequencing) revealed a total of 131 SNPs strongly linked (P < 4.96E-07) to the investigated traits. Of these 131 SNPs, 40 fell into confidence intervals or were physically adjacent to previously published flowering time QTL or SNPs. Phenotypic effect analysis detected 35 elite allelic variants for early maturing, and 90 for long FP. Candidate genes present in the same linkage disequilibrium blocks (r2>0.6) or in 100 kb regions around significant trait-associated SNPs were screened, revealing 57 B. napus genes (33 SNPs) orthologous to 39 Arabidopsis thaliana flowering time genes. These results support the practical and scientific value of novel large-scale SNP data generation in uncovering the genetic control of agronomic traits in B. napus, and also provide a theoretical basis for molecular marker-assisted selection of earliness breeding in rapeseed.

Genome-Wide SNP Markers Based on SLAF-Seq Uncover Breeding Traces in Rapeseed (Brassica napus L.).

Single Nucleotide Polymorphisms (SNPs) are the most abundant and richest form of genomic polymorphism, and hence make highly favorable markers for genetic map construction and genome-wide association studies. In this study, a total of 300 rapeseed accessions (278 representative of Chinese germplasm, plus 22 outgroup accessions of different origins and ecotypes) were collected and sequenced using Specific-Locus Amplified Fragment Sequencing (SLAF-seq) technology, obtaining 660.25M reads with an average sequencing depth of 6.27 × and a mean Q30 of 85.96%. Based on the 238,711 polymorphic SLAF tags a total of 1,197,282 SNPs were discovered, and a subset of 201,817 SNPs with minor allele frequency >0.05 and integrity >0.8 were selected. Of these, 30,877 were designated SNP "hotspots," and 41 SNP-rich genomic regions could be delineated, with 100 genes associated with plant resistance, vernalization response, and signal transduction detected in these regions. Subsequent analysis of genetic diversity, linkage disequilibrium (LD), and population structure in the 300 accessions was carried out based on the 201,817 SNPs. Nine subpopulations were observed based on the population structure analysis. Hierarchical clustering and principal component analysis divided the 300 varieties roughly in accordance with their ecotype origins. However, spring-type varieties were intermingled with semi-winter type varieties, indicating frequent hybridization between spring and semi-winter ecotypes in China. In addition, LD decay across the whole genome averaged 299 kb when r2 = 0.1, but the LD decay in the A genome (43 kb) was much shorter than in the C genome (1,455 kb), supporting the targeted introgression of the A genome from progenitor species B. rapa into Chinese rapeseed. This study also lays the foundation for genetic analysis of important agronomic traits using this rapeseed population.