A bi-filtering method for processing single nucleotide polymorphism array data improves the quality of genetic map and accuracy of quantitative trait locus mapping in doubled haploid populations of polyploid Brassica napus

Background

Single nucleotide polymorphism (SNP) markers have a wide range of applications in crop genetics and genomics. Due to their polyploidy nature, many important crops, such as wheat, cotton and rapeseed contain a large amount of repeat and homoeologous sequences in their genomes, which imposes a huge challenge in high-throughput genotyping with sequencing and/or array technologies. Allotetraploid Brassica napus (AACC, 2n = 4x = 38) comprises of two highly homoeologous sub-genomes derived from its progenitor species B. rapa (AA, 2n = 2x = 20) and B. oleracea (CC, 2n = 2x = 18), and is an ideal species to exploit methods for reducing the interference of extensive inter-homoeologue polymorphisms (mHemi-SNPs and Pseudo-simple SNPs) between closely related sub-genomes.

Results

Based on a recent B. napus 6K SNP array, we developed a bi-filtering procedure to identify unauthentic lines in a DH population, and mHemi-SNPs and Pseudo-simple SNPs in an array data matrix. The procedure utilized both monomorphic and polymorphic SNPs in the DH population and could effectively distinguish the mHemi-SNPs and Pseudo-simple SNPs that resulted from superposition of the signals from multiple SNPs. Compared with conventional procedure for array data processing, the bi-filtering method could minimize the pseudo linkage relationship caused by the mHemi-SNPs and Pseudo-simple SNPs, thus improving the quality of SNP genetic map. Furthermore, the improved genetic map could increase the accuracies of mapping of QTLs as demonstrated by the ability to eliminate non-real QTLs in the mapping population.

Conclusions

The bi-filtering analysis of the SNP array data represents a novel approach to effectively assigning the multi-loci SNP genotypes in polyploid B. napus and may find wide applications to SNP analyses in polyploid crops.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1559-4) contains supplementary material, which is available to authorized users.     

Phosphorus fractions in montane forest soils of the Cordillera de Piuchué, Chile: biogeochemical implications

The Hedley fractionation procedure as modified by Tiessen and Moir (1993) was used to evaluate the amounts of P in several soil chemical pools in an old, unglaciated landscape at 600 m elevation in the Cordillera de Piuchué, Chile (42° 30′ S. 74° W). This is an area of primary forests which have escaped disturbance from forest harvesting, land clearing and the deposition of anthropogenic chemicals. Two study watersheds are conifer-dominated with moorland on wind-exposed ridgetops. In a third study watershed, vegetation is dominated by evergreen broadleaf trees. Soils are thin (ca. 40 cm) and have a high organic matter content. Across all communities, most of the soil P is in non-labile forms in organic combinations or in combination with secondary soil minerals. Little P was present in primary minerals. The remainder (ca. 20%) was in labile forms extractable with anion exchange resin or bicarbonate solution. From litterfall and allometric relationships, we estimated the annual P requirement of growing vegetation to be <1 kg ha^-1 in the moorland and < 3 kg ha^-1 in the conifer and mixed forests. This is substantially less than the standing pool of resin-extractable P (ca. 20 kg ha^-1), which is considered to be P fraction most readily available to plants. Resin-extractable P was strongly correlated with soil carbon content ( R² =0.72 − 0.87, p < 0.001) suggesting that soil organic matter is the likely proximate source of plant-available P. On a kg ha^-1 basis, the most labile forms of P did not differ significantly across 3 of the 4 community types despite dramatic differences in species, live biomass and annual P requirement, suggesting little control of available P pools by forest vegetation type. On a more detailed level, resin-extractable P was strongly correlated with HCO₃-extractable organic (and inorganic) P. This is consistent with other findings of P behavior in acid soils high in organic matter in which microbial transformations are key in regulating pools of plant-available P. This revised version was published online in June 2006 with corrections to the Cover Date.     

Reproductive strategies of the larval parasitoid Microplitis croceipes

Mate choice may have important consequences for offspring sex ratio and fitness of haplodiploid insects. Mate preference of females of the solitary larval parasitoid Microplitis croceipes (Cresson) (Hymenoptera: Braconidae) for virgin and mated males, and vice versa, and the reproductive consequences (i.e., the sex ratio expressed as the proportion of male offspring) were examined in choice and non‐choice experiments. In addition, the effect of repeated rapid and daily copulation of an individual male on the sex ratio of offspring of the female mates was assessed. Males preferred virgins over mated females, whereas females copulated with a male irrespective of his mating status. In both the rapid and daily copulation assay, females copulating with a male that had copulated five times or more produced a higher sex ratio than females that had copulated with a virgin male. Females that copulated with virgin males once or twice produced a significantly and considerably lower sex ratio than females that first copulated with a sperm‐depleted male followed by a virgin male. This indicates that copulating with a sperm‐depleted male has costs and limits acquisition by the female of sperm from virgin males.     

The actin cytoskeleton of kidney podocytes is a direct target of the antiproteinuric effect of cyclosporine A

The immunosuppressive action of the calcineurin inhibitor cyclosporine A (CsA) stems from the inhibition of nuclear factor of activated T cells (NFAT) signaling in T cells. CsA is also used for the treatment of proteinuric kidney diseases. As it stands, the antiproteinuric effect of CsA is attributed to its immunosuppressive action. Here we show that the beneficial effect of CsA on proteinuria is not dependent on NFAT inhibition in T cells, but rather results from the stabilization of the actin cytoskeleton in kidney podocytes. CsA blocks the calcineurin-mediated dephosphorylation of synaptopodin, a regulator of Rho GTPases in podocytes, thereby preserving the phosphorylation-dependent synaptopodin-14-3-3 beta interaction. Preservation of this interaction, in turn, protects synaptopodin from cathepsin L-mediated degradation. These results represent a new view of calcineurin signaling and shed further light on the treatment of proteinuric kidney diseases. Novel calcineurin substrates such as synaptopodin may provide promising starting points for antiproteinuric drugs that avoid the serious side effects of long-term CsA treatment.     

Indoleamine 2, 3-dioxygenase （IDO） is essential for dendritic cell activation and chemotactic responsiveness to chemokines

Indoleamine 2, 3-dioxygenase (IDO) is a rate-limiting enzyme for the tryptophan catabolism. In human and murine cells, IDO inhibits antigen-specific T cell proliferation in vitro and suppresses T cell responses to fetal alloantigens during murine pregnancy. In mice, IDO expression is an inducible feature of specific subsets of dendritic cells (DCs),and is important for T cell regulatory properties. However, the effect of IDO and tryptophan deprivation on DC functions remains unknown. We report here that when tryptophan utilization was prevented by a pharmacological inhibitor of IDO, 1-methyl tryptophan (1MT), DC activation induced by pathogenic stimulus lipopolysaccharide (LPS) or inflammatory cytokine TNF-α was inhibited both phenotypically and functionally. Such an effect was less remarkable when DC was stimulated by a physiological stimulus, CD40 ligand. Tryptophan deprivation during DC activation also regulated the expression of CCR5 and CXCR4, as well as DC responsiveness to chemokines. These results suggest that tryptophan usage in the microenvironment is essential for DC maturation, and may also play a role in the regulation of DC migratory behaviors.     

Functional Characterization of Bacteria Isolated from Ancient Arctic Soil Exposes Diverse Resistance Mechanisms to Modern Antibiotics

Using functional metagenomics to study the resistomes of bacterial communities isolated from different layers of the Canadian high Arctic permafrost, we show that microbial communities harbored diverse resistance mechanisms at least 5,000 years ago. Among bacteria sampled from the ancient layers of a permafrost core, we isolated eight genes conferring clinical levels of resistance against aminoglycoside, β-lactam and tetracycline antibiotics that are naturally produced by microorganisms. Among these resistance genes, four also conferred resistance against amikacin, a modern semi-synthetic antibiotic that does not naturally occur in microorganisms. In bacteria sampled from the overlaying active layer, we isolated ten different genes conferring resistance to all six antibiotics tested in this study, including aminoglycoside, β-lactam and tetracycline variants that are naturally produced by microorganisms as well as semi-synthetic variants produced in the laboratory. On average, we found that resistance genes found in permafrost bacteria conferred lower levels of resistance against clinically relevant antibiotics than resistance genes sampled from the active layer. Our results demonstrate that antibiotic resistance genes were functionally diverse prior to the anthropogenic use of antibiotics, contributing to the evolution of natural reservoirs of resistance genes.     

The biotransformation of methyl ent-15-oxokaur-16-en-19-oate by Rhizopus stolonifer and Mucor plumbeus

Incubation of methyl ent-15-oxokaur-16-en-19-oate with Rhizopus stolonifer and Mucor plumbeus gave methyl ent-7β,11-dihydroxy-15-oxokauran-19-oate and methyl ent-7β,16β-dihydroxy-15-oxokauran-19-oate, respectively.     

Calmodulin in rat enterocyte: an immunogold electron-microscope study

Immunogold labeling of ultrathin sections of the epithelium of rat small intestine has been used to obtain insights into the ultrastructural localization and possible function of calmodulin in the enterocyte. Calmodulin is found mainly overlying the periphery of the microvillous core, in agreement with the location of the 110-kDa calmodulin complex. Extremely small amounts of calmodulin can be detected along the interdigitating basolateral membrane. This immunogold electron-microscope study suggests that calmodulin plays an important role in regulating the mechanochemical activity of myosin I but not in processes associated with the basolateral membrane of rat enterocyte.