Instability of chromosome number and DNA methylation variation induced by hybridization and amphidiploid formation between Raphanus sativus L. and Brassica alboglabra Bailey

<p>Abstract</p> <p>Background</p> <p>Distant hybridization can result genome duplication and allopolyploid formation which may play a significant role in the origin and evolution of many plant species. It is unclear how the two or more divergent genomes coordinate in one nucleus with a single parental cytoplasm within allopolyploids. We used cytological and molecular methods to investigate the genetic and epigenetic instabilities associated with the process of distant hybridization and allopolyploid formation, measuring changes in chromosome number and DNA methylation across multiple generations.</p> <p>Results</p> <p>F₁plants from intergeneric hybridization between <it>Raphanus sativus </it>L. (2n = 18, RR) and <it>Brassica alboglabra </it>Bailey (2n = 18, CC) were obtained by hand crosses and subsequent embryo rescue. Random amplification of polymorphic DNA (RAPD) markers were used to identify the F₁hybrid plants. The RAPD data indicated that the hybrids produced specific bands similar to those of parents and new bands that were not present in either parent. Chromosome number variation of somatic cells from allotetraploids in the F₄to F₁₀generations showed that intensive genetic changes occurred in the early generations of distant hybridization, leading to the formation of mixopolyploids with different chromosome numbers. DNA methylation variation was revealed using MSAP (methylation-sensitive amplification polymorphism), which showed that cytosine methylation patterns changed markedly in the process of hybridization and amphidiploid formation. Differences in cytosine methylation levels demonstrated an epigenetic instability of the allopolyploid of <it>Raphanobrassica </it>between the genetically stable and unstable generations.</p> <p>Conclusions</p> <p>Our results showed that chromosome instability occurred in the early generations of allopolyploidy and then the plants were reverted to largely euploidy in later generations. During this process, DNA methylation changed markedly. These results suggest that, epigenetic mechanisms play an important role in intergeneric distant hybridization, probably by maintaining a genetic balance through the modification of existing genetic materials.</p

Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa

Background The Multinational Brassica rapa Genome Sequencing Project (BrGSP) has developed valuable genomic resources, including BAC libraries, BAC-end sequences, genetic and physical maps, and seed BAC sequences for Brassica rapa. An integrated linkage map between the amphidiploid B. napus and diploid B. rapa will facilitate the rapid transfer of these valuable resources from B. rapa to B. napus (Oilseed rape, Canola). Results In this study, we identified over 23,000 simple sequence repeats (SSRs) from 536 sequenced BACs. 890 SSR markers (designated as BrGMS) were developed and used for the construction of an integrated linkage map for the A genome in B. rapa and B. napus. Two hundred and nineteen BrGMS markers were integrated to an existing B. napus linkage map (BnaNZDH). Among these mapped BrGMS markers, 168 were only distributed on the A genome linkage groups (LGs), 18 distrubuted both on the A and C genome LGs, and 33 only distributed on the C genome LGs. Most of the A genome LGs in B. napus were collinear with the homoeologous LGs in B. rapa, although minor inversions or rearrangements occurred on A2 and A9. The mapping of these BAC-specific SSR markers enabled assignment of 161 sequenced B. rapa BACs, as well as the associated BAC contigs to the A genome LGs of B. napus. Conclusion The genetic mapping of SSR markers derived from sequenced BACs in B. rapa enabled direct links to be established between the B. napus linkage map and a B. rapa physical map, and thus the assignment of B. rapa BACs and the associated BAC contigs to the B. napus linkage map. This integrated genetic linkage map will facilitate exploitation of the B. rapa annotated genomic resources for gene tagging and map-based cloning in B. napus, and for comparative analysis of the A genome within Brassica species

MiRNA identification, characterization and integrated network analysis for flavonoid biosynthesis in Brassicacoraphanus

Brassica rapa (AA, 2n = 20) and Raphanus sativus (RR, 2n = 18) are popular vegetables containing multiple secondary metabolites, such as flavonoids and anthocyanins. Nevertheless, few studies on miRNA expression profiles and potential regulatory network of flavonoid metabolism have been reported in the intergeneric hybrid of B. rapa and R. sativus (Brassicacoraphanus, AARR, 2n = 38). Here, the miRNAs of Brassicacoraphanus and its parents were first identified by small RNA sequencing. It was revealed that 315 conserved miRNAs and 193 novel miRNAs were found in Brassicacoraphanus and its parents. Moreover, the miRNA expression profiles were characterized and 204 miRNAs with differential expression were obtained. Further analysis showed that 184 miRNAs were non-additively expressed in Brassicacoraphanus. At last, the potential regulatory network of flavonoid metabolism in Brassicacoraphanus was analyzed by multi-omics data, suggesting possible roles of miR858a and miR157a in regulating flavonoid synthesis pathway in Brassicacoraphanus. Taken together, this study provides useful resources for probing global miRNA expression patterns in Brassicacoraphanus, which facilitates regulatory mechanism research on the biosynthesis pathway of secondary metabolites in Brassicacoraphanus

Sensualità senza carne. La musica nella vita e nell'opera di d'Annunzio

High-density genetic markers are the prerequisite for understanding linkage disequilibrium (LD) and genome-wide association studies (GWASs) of complex traits in crops. To evaluate the LD pattern in oilseed rape, we sequenced a previous association panel containing 189 B. napus inbred lines using double-digested restriction-site associated DNA (ddRAD) and genotyped 19,327 RAD tags. A total of 15,921 RAD tags were assigned to a published genetic linkage map and the majority (71.1%) of these tags was uniquely mapped to the draft reference genome "Darmor-bzh." The distance of LD decay was 1,214 kb across the genome at the background level (r2 = 0.26), with the distances of LD decay being 405 kb and 2,111 kb in the A and C subgenomes, respectively. A total of 361 haplotype blocks with length > 100 kb were identified in the entire genome. The association panel could be classified into two groups, P1 and P2, which are essentially consistent with the geographical origins of varieties. A large number of group-specific haplotypes were identified, reflecting that varieties in the P1 and P2 groups experienced distinct selection in breeding programs to adapt their different growth habitats. GWAS repeatedly detected two loci significantly associated with oil content of seeds based on the developed SNPs, suggesting that the high-density SNPs were useful for understanding the genetic determinants of complex traits in GWAS

Dual-Targeting Nanosystem for Enhancing Photodynamic Therapy Efficiency

Photodynamic therapy (PDT) has been recognized as a valuable treatment option for localized cancers. Herein, we demonstrate a cellular and subcellular targeted strategy to facilitate PDT efficacy. The PDT system was fabricated by incorporating a cationic porphyrin derivative (MitoTPP) onto the polyethylene glycol (PEG)-functionalized and folic acid-modified nanographene oxide (NGO). For this PDT system, NGO serves as the carrier for MitoTPP as well as the quencher for MitoTPP’s fluorescence and singlet oxygen (¹O₂) generation. Attaching a hydrophobic cation to the photosensitizer ensures its release from NGO at lower pH values as well as its mitochondria-targeting capability. Laser confocal microscope experiments demonstrate that this dual-targeted nanosystem could preferably enter the cancer cells overexpressed with folate receptor, and release its cargo MitoTPP, which subsequently accumulates in mitochondria. Upon light irradiation, the released MitoTPP molecules generate singlet oxygen and cause oxidant damage to the mitochondria. Cell viability assays suggest that the dual-targeted nanohybrids exhibit much higher cytotoxicity toward the FR-positive cells

Transcriptome analysis of leaf tissue of Raphanus sativus by RNA sequencing.

Raphanus sativus is not only a popular edible vegetable but also an important source of medicinal compounds. However, the paucity of knowledge about the transcriptome of R. sativus greatly impedes better understanding of the functional genomics and medicinal potential of R. sativus. In this study, the transcriptome sequencing of leaf tissues in R. sativus was performed for the first time. Approximately 22 million clean reads were generated and used for transcriptome assembly. The generated unigenes were subsequently annotated against gene ontology (GO) database. KEGG analysis further revealed two important pathways in the bolting stage of R.sativus including spliceosome assembly and alkaloid synthesis. In addition, a total of 6,295 simple sequence repeats (SSRs) with various motifs were identified in the unigene library of R. sativus. Finally, four unigenes of R. sativus were selected for alignment with their homologs from other plants, and phylogenetic trees for each of the genes were constructed. Taken together, this study will provide a platform to facilitate gene discovery and advance functional genomic research of R. sativus

Physiological Mechanisms behind Differences in Pod Shattering Resistance in Rapeseed (Brassica napus L.) Varieties.

Pod shattering resistance index (SRI) is a key factor affecting the mechanical harvesting of rapeseed. Research on the differences in pod shattering resistance levels of various rapeseed varieties can provide a theoretical basis for varietal breeding and application in mechanical harvesting. The indicators on pod shattering resistance including pod morphology and wall components were evaluated on eight hybrids and open pollinators, respectively, during 2012-2014. The results showed the following: (1) From the current study, SRI varied greatly with variety, and conventional varieties had stronger resistance than hybrid according to the physiological indexes. and (2) Under the experimental conditions, the SRI was linearly related to pod wall weight and the water content in pod walls, and the goodness-of-fit measurements for the regression model of the SRI based on pod wall weight and water content were 0.584** and 0.377*, respectively, reaching the significant level. This illustrated that pod wall weight and the water content in pod walls determined the SRI. (3) Compared with the relative contents of biochemical components in pod walls, the contents of particular biochemical components in pod walls had closer correlations with SRI. Among the biochemical components, the hemicellulose content was the decisive factor for the SRI

Systemic Resistance to Powdery Mildew in Brassica napus (AACC) and Raphanus alboglabra (RRCC) by Trichoderma harzianum TH12.

Trichoderma harzianum TH12 is a microbial pesticide for certain rapeseed diseases. The mechanism of systemic resistance induced by TH12 or its cell-free culture filtrate (CF) in Brassica napus (AACC) and Raphanus alboglabra (RRCC) to powdery mildew disease caused by ascomycete Erysiphe cruciferarum was investigated. In this study, we conducted the first large-scale global study on the cellular and molecular aspects of B. napus and R. alboglabra infected with E. cruciferarum. The histological study showed the resistance of R. alboglabra to powdery mildew disease. The growth of fungal colonies was not observed on R. alboglabra leaves at 1, 2, 4, 6, 8, and 10 days post-inoculation (dpi), whereas this was clearly observed on B. napus leaves after 6 dpi. In addition, the gene expression of six plant defense-related genes, namely, PR-1, PR-2 (a marker for SA signaling), PR-3, PDF 1.2 (a marker for JA/ET signaling), CHI620, and CHI570, for both genotypes were analyzed in the leaves of B. napus and R. alboglabra after treatment with TH12 or CF and compared with the non-treated ones. The qRT-PCR results showed that the PR-1 and PR-2 expression levels increased in E. cruciferarum-infected leaves, but decreased in the TH12-treated leaves compared with leaves treated with CF. The expression levels of PR-3 and PDF1.2 decreased in plants infected by E. cruciferarum. However, expression levels increased when the leaves were treated with TH12. For the first time, we disclosed the nature of gene expression in B. napus and R. alboglabra to explore the resistance pathways in the leaves of both genotypes infected and non-infected by powdery mildew and inoculated or non-inoculated with elicitor factors. Results suggested that R. alboglabra exhibited resistance to powdery mildew disease, and the application of T. harzianum and its CF are a useful tool to facilitate new protection methods for resist or susceptible plants

Disruption of a Cartenoid Cleavage Dioxygenase 4 gene converts flower colour from white to yellow in Brassica species

In Brassica napus, yellow petals had a much higher content of carotenoids than white petals present in a small number of lines, with violaxanthin identified as the major carotenoid compound in yellow petals of rapeseed lines. Using positional cloning we identified a carotenoid cleavage dioxygenase 4 gene, BnaC3.CCD4, responsible for the formation of flower colour, with preferential expression in petals of white-flowered B. napus lines. Insertion of a CACTA-like transposable element 1 (TE1) into the coding region of BnaC3.CCD4 had disrupted its expression in yellow-flowered rapeseed lines. α-Ionone was identified as the major volatile apocarotenoid released from white petals but not from yellow petals. We speculate that BnaC3.CCD4 may use δ- and/or α-carotene as substrates. Four variations, including two CACTA-like TEs (alleles M1 and M4) and two insertion/deletions (INDELs, alleles M2 and M3), were identified in yellow-flowered Brassica oleracea lines. The two CACTA-like TEs were also identified in the coding region of BcaC3.CCD4 in Brassica carinata. However, the two INDELs were not detected in B. napus and B. carinata. We demonstrate that the insertions of TEs in BolC3.CCD4 predated the formation of the two allotetraploids

Environmental Factors Driving the Transpiration of a <i>Betula platyphylla</i> Sukaczev Forest in a Semi-arid Region in North China during Different Hydrological Years

More and more droughts happened during the last decades, threatening natural forests in the semi-arid regions of North China. The increase in drought pressure may have an impact on stand transpiration (T) in semi-arid regions due to rising temperature and changes in precipitation. It is unclear how the transpiration of natural forest in semi-arid regions respond to drought, which is regulated by environmental factors. In this study, a relatively simple but mechanism-based forest stand T model that couples the effects of the reference T, solar radiation (Rn), vapor pressure deficit (VPD), and relative extractable water (REW) in the 0–80 cm soil layer was developed to quantify the independent impacts of Rn, VPD, and REW on T. The model was established based on the observed sap flow of four sample trees, and environmental factors were observed from May to September in different hydrological years (2015, 2017, 2018, and 2021) in a pure white birch (Betula platyphylla Sukaczev) forest stand in the southern section of the Greater Khingan Mountains, northeastern China. The sap flow data were used to calculate tree transpiration (Tt) and T to calibrate the T model. The results indicated that (1) The Tt sharply declined in the ‘dry’ year compared with that in the ‘wetter’ year. The daily Tt for small trees in the ‘dry’ year was only one-fifth of that in the ‘wetter’ year, and the daily Tt of large trees was 48% lower than that in the ‘normal’ year; (2) Large trees transpired more water than small trees, e.g., the daily Tt of small trees was 89% lower than that of the large trees in the ‘normal’ year; (3) Daily T increased with the increase in Rn, and the response conformed to a binomial function. Daily T responded to the rise of VPD and REW in an exponential function, first increasing rapidly, gradually reaching the threshold or peak value, and then stabilizing; (4) The driving factors for the T shift in different hydrological years were the REW in the ‘dry’ year, but the Rn and REW in the ‘wet’, ‘normal’, and ‘wetter’ years. The REW in the ‘wet’ and ‘wetter’ years exerted positive effects on T, but in the ‘normal’ and ‘dry’ year, exerted negative effects on T. Thus, the environmental factors affecting T were not the same in different hydrological years