Genome-Wide Association Analyses Reveal Candidate Genes Controlling Harvest Index and Related Agronomic Traits in <i>Brassica napus</i> L.

Harvest index (HI) is a complex and vital agronomic trait that is closely related to the economic benefits of rapeseed. In this study, we measured the HI and 13 HI-related agronomic traits of 104 core breeding lines of rapeseed during 3 years and sequenced the populations using the Bnapus50K array. The phenotypic analyses showed the complex connections among HI and other traits. A total of 212 significant SNPs related to the traits and 22 stable SNPs were identified. Four SNPs, A01_1783685 (PH and SYP), C06_26638717 (PH and NSS), C03_4731660 (MIL and MINS), and C09_36899682 (PH and BYP), were identified as potential pleiotropic loci. Compared to previous reports, 49 consensus loci were obtained that were related to PH, TSW, NSP, BAI, NSS, SL, BN, MINS, SYP, and BYP. Twelve stable SNPs were detected as promising novel loci related to BN (A05_19368584 and A05_19764389), SL (A06_23598999, A06_23608274, and C07_38735522), PH (C04_47349279, C04_47585236, and C09_36899680), MINS (C05_6251826), NSS (C06_22559430 and C06_22570315), and HI (C05_6554451). In addition, 39 putative genes were identified in the candidate intervals. This study provides novel insights into the genetic mechanisms of HI and HI-related traits, and lays a foundation for molecular marker development and casual gene cloning to improve the harvest index of rapeseed

Uncovering the pharmacological mechanisms of Xijiao Dihuang decoction combined with Yinqiao powder in treating influenza viral pneumonia by an integrative pharmacology strategy

Xijiao Dihuang decoction combined with Yinqiao powder (XDD-YQP) is a classical combination formula; however, its therapeutic effects in treating influenza viral pneumonia and the pharmacological mechanisms remain unclear. The therapeutic effect of XDD-YQP in influenza viral pneumonia was evaluated in mice. Subsequently, an everted gut sac model coupled with UPLC/Q-TOF MS were used to screen and identify the active compounds of XDD-YQP. Furthermore, network pharmacological analysis was adopted to probe the mechanisms of the active compounds. Lastly, we verified the targets predicted from network pharmacological analysis by differential bioinformatics analysis. Animal experiments showed that XDD-YQP has a therapeutic effect on influenza viral pneumonia. Moreover, 113 active compounds were identified from intestinal absorbed solutions of XDD-YQP. Using network pharmacological analysis, 90 major targets were selected as critical in the treatment of influenza viral pneumonia through 12 relevant pathways. Importantly, the MAPK signaling pathway was found to be closely associated with the other 11 pathways. Moreover, seven key targets, EGFR, FOS, MAPK1, MAP2K1, HRAS, NRAS, and RELA, which are common targets in the MAPK signaling pathway, were investigated. These seven key targets were identified as differentially expressed genes (DEGs) between influenza virus-infected and uninfected individuals. Hence, the seven key targets in the MAPK signaling pathway may play a vital role in the treatment of influenza viral pneumonia with XDD-YQP. This research may offer an integrative pharmacology strategy to clarify the pharmacological mechanisms of traditional Chinese medicines. The results provide a theoretical basis for a broader clinical application of XDD-YQP

Protective effect of vitamin C against tetrachlorobenzoquinone-induced 5-hydroxymethylation-dependent apoptosis in HepG2 cells mainly via the mitochondrial apoptosis pathway

Tetrachlorobenzoquinone (TCBQ) is an active metabolite of pentachlorophenol, and stimulates the accumulation of ROS to trigger apoptosis. The preventive effect of vitamin C (Vc) against TCBQ-induced apoptosis in HepG2 cells is unknown. And there is little known about TCBQ-triggered 5-hydromethylcytosine (5hmC)-dependent apoptosis. Here, we confirmed that Vc alleviated TCBQ-induced apoptosis. Through investigating the underlying mechanism, we found TCBQ downregulated 5hmC levels of genomic DNA in a Tet-dependent manner, with a particularly pronounced decrease in the promoter region, using UHPLC-MS-MS analysis and hydroxymethylated DNA immunoprecipitation sequencing. Notably, TCBQ exposure resulted in alterations of 5hmC abundance to ∼91% of key genes at promoters in the mitochondrial apoptosis pathway, along with changes of mRNA expression in 87% of genes. By contrast, 5hmC abundance of genes only exhibited slight changes in the death receptor/ligand pathway. Interestingly, the pretreatment with Vc, a positive stimulator of 5hmC generation, restored 5hmC in the genomic DNA to near-normal levels. More notably, Vc pretreatment further counter-regulated TCBQ-induced alteration of 5hmC abundance in the promoter with 100% of genes, accompanying the reverse modulation of mRNA expressions in 89% of genes. These data from Vc pretreatment supported the relationship between TCBQ-induced apoptosis and the altered 5hmC abundance. Additionally, Vc also suppressed TCBQ-stimulated generation of ROS, and further increased the stability of mitochondria. Our study illuminates a new mechanism of TCBQ-induced 5hmC-dependent apoptosis, and the dual mechanisms of Vc against TCBQ-stimulated apoptosis via reversely regulating 5hmC levels and scavenging ROS. The work also provided a possible strategy for the detoxification of TCBQ

Fine-mapping and validation of the genomic region underpinning pear red skin colour

Crop genetics: What makes a pear red? Researchers in New Zealand have produced a map of genetic variants linked with red skin color in pears, opening the door to identifying the genes responsible. Satish Kumar and others at the New Zealand Institute for Plant and Food Research Limited measured the skin color of 550 hybrid pear seedlings and sequenced their genomes. Combining these data produced a map of 7,500 variants throughout the genome and identified those associated with red skin color. The most significant variant accounted for about 15% of the color variation. Further analysis of that genomic region revealed several genes which might be related to red skin color. The genomic map produced by this study will improve breeding efficiency by making it possible to screen seedlings for fruit color, but further research is necessary to characterize the candidate genes

Largely Enhanced Stretching Sensitivity of Polyurethane/Carbon Nanotube Nanocomposites via Incorporation of Cellulose Nanofiber

Stretchable sensors have drawn a great deal of attention due to their importance and necessity in high-technology areas. However, it is difficult to obtain sensors with high sensitivity accompanied by high tenacity. Taking advantage of the very large aspect ratio and amphiphilicity of nanofibrillated cellulose (NFC), in this study, we fabricated polyurethane (TPU)/multiwall carbon nanotube (CNT) nanocomposites with excellent dispersion using NFC as stabilizer. Then the mechanical and electrical properties, particularly the stretching sensitivity of the prepared TPU/NFC@CNTs nanocomposites, were investigated. It was found that the prepared TPU/NFC@CNTs has much better mechanical properties and electrical conductivity compared with those of TPU/CNTs composites. More importantly, a linear change of electrical conductivity as a function of stretching is observed for at least strains up to 300% and a very high sensitivity whose gauge factor close to 50 could be achieved. The excellent stretching sensitivity could be attributed to the unique role of NFC: (1) assisting the dispersion of CNTs, (2) enhancing the interaction between NFC and TPU matrix as due to its amphiphilicity, and (3) increasing the overall aspect ratio of CNTs via connecting many tiny CNTs bundled together along the long axis

Quantitative Trait Locus Mapping of Salt Tolerance and Identification of Salt-Tolerant Genes in Brassica napus L

Salinity stress is one of typical abiotic stresses that seriously limit crop production. In this study, a genetic linkage map based on 532 molecular markers covering 1341.1 cM was constructed to identify the loci associated with salt tolerance in Brassica napus. Up to 45 quantitative trait loci (QTLs) for 10 indicators were identified in the F2:3 populations. These QTLs can account for 4.80–51.14% of the phenotypic variation. A major QTL, qSPAD5 on LG5 associated with chlorophyll can be detected in three replicates. Two intron polymorphic (IP) markers in this QTL region were developed successfully to narrow down the QTL location to a region of 390 kb. A salt tolerance related gene Bra003640 was primary identified as the candidate gene in this region. The full length of the candidate gene was 1,063 bp containing three exons and two introns in B. napus L. The open reading frame (ORF) is 867 bp and encodes 287 amino acids. Three amino acid differences (34, 54, and 83) in the conserved domain (B-box) were identified. RT-qPCR analysis showed that the gene expression had significant difference between the two parents. The study laid great foundation for salt tolerance related gene mapping and cloning in B. napus L

Identification of Alkaline Salt Tolerance Genes in Brassica napus L. by Transcriptome Analysis

Soil salt alkalization is one major abiotic factor reducing the productivity of crops, including rapeseed, an indispensable oil crop and vegetable. The mechanism studies of alkali salt tolerance can help breed highly resistant varieties. In the current study, rapeseed (B. napus) line 2205 exhibited more tolerance to alkaline salt than line 1423 did. In line 2205, the lesser plasma membrane damage index, the accumulated osmotic solute, and higher antioxidant enzyme activities contributed to alkaline tolerance. A more integrated mesophyll-cell structure was revealed under alkali salt stress by ultrastructure observation in line 2205, which also implied a lesser injury. Transcriptome analysis showed that more genes responded to alkaline salt in line 2205. The expression of specific-response genes in line 1423 was lower than in line 2205. However, most of the specific-response genes in line 2205 had higher expression, which was mainly enriched in carbohydrate metabolism, photosynthetic processes, ROS regulating, and response to salt stress. It can be seen that the tolerance to alkaline salt is attributed to the high expression of some genes in these pathways. Based on these, twelve cross-differentially expressed genes were proposed as candidates. They provide clues for further analysis of the resistance mechanism of rapeseed