Seedling development traits in Brassica napus examined by gene expression analysis and association mapping

BACKGROUND: An optimal seedling development of Brassica napus plants leads to a higher yield stability even under suboptimal growing conditions and has therefore a high importance for plant breeders. The objectives of our study were to (i) examine the expression levels of candidate genes in seedling leaves of B. napus and correlate these with seedling development as well as (ii) detect genome regions associated with gene expression levels and seedling development traits in B. napus by genome-wide association mapping. RESULTS: The expression levels of the 15 candidate genes examined in the 509 B. napus inbreds showed an averaged standard deviation of 5.6 across all inbreds and ranged from 3.2 to 8.8. The gene expression differences between the 509 B. napus inbreds were more than adequate for the correlation with phenotypic variation of seedling development. The average of the absolute value correlations of the correlation coefficients of 0.11 were observed with a range from 0.00 to 0.39. The candidate genes GER1, AILP1, PECT, and FBP were strongly correlated with the seedling development traits. In a genome-wide association study, we detected a total of 63 associations between single nucleotide polymorphisms (SNPs) and the seedling development traits and 31 SNP-gene associations for the candidate genes with a P-value < 0.0001. For the projected leaf area traits we identified five different association hot spots on the chromosomes A2, A7, C3, C6, and C7. CONCLUSION: A total of 99.4% of the adjacent SNPs on the A genome and 93.0% of the adjacent SNPs on the C genome had a distance smaller than the average range of linkage disequilibrium. Therefore, this genome-wide association study is expected to result on average in 14.7% of the possible power. Compared to previous studies in B. napus, the SNP marker density of our study is expected to provide a higher power to detect SNP-trait/-gene associations in the B. napus diversity set. The large number of associations detected for the examined 14 seedling development traits indicated that these are genetically complex inherited. The results of our analyses suggested that the studied genes ribulose 1,5-bisphosphate carboxylase/oxygenase small subunit (RBC) on the chromosomes A4 and C4 and fructose-1,6-bisphosphatase precursor (FBP) on the chromosomes A9 and C8 are cis-regulated. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12870-015-0496-3) contains supplementary material, which is available to authorized users

High-throughput polymorphism detection and genotyping in <it>Brassica napus</it> using next-generation RAD sequencing

<p>Abstract</p> <p>Background</p> <p>The complex genome of rapeseed (<it>Brassica napus</it>) is not well understood despite the economic importance of the species. Good knowledge of sequence variation is needed for genetics approaches and breeding purposes. We used a diversity set of <it>B. napus</it> representing eight different germplasm types to sequence genome-wide distributed restriction-site associated DNA (RAD) fragments for polymorphism detection and genotyping.</p> <p>Results</p> <p>More than 113,000 RAD clusters with more than 20,000 single nucleotide polymorphisms (SNPs) and 125 insertions/deletions were detected and characterized. About one third of the RAD clusters and polymorphisms mapped to the <it>Brassica rapa</it> reference sequence. An even distribution of RAD clusters and polymorphisms was observed across the <it>B. rapa</it> chromosomes, which suggests that there might be an equal distribution over the <it>Brassica oleracea</it> chromosomes, too. The representation of Gene Ontology (GO) terms for unigenes with RAD clusters and polymorphisms revealed no signature of selection with respect to the distribution of polymorphisms within genes belonging to a specific GO category.</p> <p>Conclusions</p> <p>Considering the decreasing costs for next-generation sequencing, the results of our study suggest that RAD sequencing is not only a simple and cost-effective method for high-density polymorphism detection but also an alternative to SNP genotyping from transcriptome sequencing or SNP arrays, even for species with complex genomes such as <it>B. napus</it>.</p

Additional file 19 of Comparison of statistical models for nested association mapping in rapeseed (Brassica napus L.) through computer simulations

Table S11. Phenotypes for the 50 BC-NAM subpopulations in a scenario where QTLs = 50, h 2=0.8, 0.05 of explained ratio by QTL × genetic background interactions to the total genetic variance with 25 replications. (TXT 2078 kb

The effects of quantitative easing on the USA, Japan, Eurozone and Great Britain

This master thesis aims to describe problematics of the effects of unconventional monetary policy, also known as quantitative easing, on economics of USA, Japan, Eurozone and Great Britain, by using empirical analysis of events related to quantitative easing and large BVAR model. In theoretical part of the thesis there are described transmission mechanisms of conventional monetary policy still effective in conditions of interest rates close to zero, as well as channels of unconventional monetary policy. Practical part of the thesis demonstrates analysis of impact of events related to quantitative easing in all the in-scope economics by applying a method of empirical observation of interest rates reactions on every event. Further, based on the received results of the empirical analysis, broader economic effects of quantitative easing are examined by using large BVAR model and afterwards the conclusion is made

3rd generation poly(ethylene imine)s for gene delivery

In this study, a series of high molar mass poly(2-oxazoline)-based copolymers was synthesized, introducing 2-ethyl-2-oxazoline, ethylene imine, and primary amine bearing monomer units representing a new generation of PEI.</p

Fluorescent amphiphilic heterografted comb polymers comprising biocompatible PLA and PEtOx side chains

A series of amphiphilic heterografted comb polymers comprising various ratios of oligomeric polylactide (PLA) and poly(2-ethyl-2-oxazoline) (PEtOx) side chains was synthesized via the grafting-through method employing the reversible addition-fragmentation chain transfer copolymerization. Two well-defined PLA macromonomers were prepared via ring opening polymerization (ROP) of L-lactide using a calcium-based pre-catalyst, pyrenebutanol as an initiator and methacryloyl chloride as an end-capping agent. The PEtOx macromonomer was obtained from the cationic ROP of EtOx and end-capping with methacrylic acid. The amphiphilic comb polymers self-assembled in aqueous solution to form spherical and wormlike micelles, vesicles and more complex morphologies as a function of the composition, as is evident from dynamic light scattering and cryo-transmission electron microscopy studies. All polymers were found to be non-toxic to L929 cells up to a concentration of 200 mu g mL(-1). Cellular uptake studies with HEK-293 cells by live cell confocal fluorescence microscopy revealed localization in the cytosol after 4 h and suggest an energy-driven cellular uptake mechanism

The Power of Shielding: Low Toxicity and High Transfection Performance of Cationic Graft Copolymers Containing Poly(2-oxazoline) Side Chains

We show the potential of oligo­(2-ethyl-2-oxazoline) (Ox_n)-shielded graft copolymers of (2-aminoethyl)-methacrylate and <i>N</i>-methyl-(2-aminoethyl)-methacrylate for pDNA delivery in HEK cells. For the effect of grafting density and side chain length concerning improved transfection properties through the concept of shielding to be investigated, copolymers were synthesized via the macromonomer method using a combination of cationic ring opening polymerization and reversible addition–fragmentation chain transfer polymerization to vary the degree of grafting (DG = 10 and 30%) as well as the side chain degree of polymerization (DP = 5 and 20). Investigations of the polyplex formation, in vitro flow cytometry, and confocal laser scanning microscopy measurements on the copolymer library revealed classical shielding properties of the Ox side chains, including highly reduced cytotoxicity and a partial decrease in transfection efficiency, as also reported for polyethylene glycol shielding. In terms of the transfection efficiency, the best performing copolymers (<b>A-</b><i><b>g</b></i><b>-Ox</b>_<b>5</b><b>(10)</b> and <b>M-</b><i><b>g</b></i><b>-Ox</b>_<b>5</b><b>(10)</b>) revealed equal or better performances compared to those of the corresponding homopolymers. In particular, the graft copolymers with low DG and side chain DP transfected well with over 10-fold higher IC₅₀ values. In contrast, a DG of 30% resulted in a loss of transfection efficiency due to missing ability for endosomal release, and a side chain DP of 20 hampered the cellular uptake