Utilização de bulked segregant analysis na identificação de marcadores ligados a genes que controlam a resistência à ferrugem (Puccinia psidii Winter) em Eucalyptus sp

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Rapid genome wide mapping of phosphine resistance loci by a simple regional averaging analysis in the red flour beetle, Tribolium castaneum

Background Next-generation sequencing technology is an important tool for the rapid, genome-wide identification of genetic variations. However, it is difficult to resolve the ‘signal’ of variations of interest and the ‘noise’ of stochastic sequencing and bioinformatic errors in the large datasets that are generated. We report a simple approach to identify regional linkage to a trait that requires only two pools of DNA to be sequenced from progeny of a defined genetic cross (i.e. bulk segregant analysis) at low coverage (<10×) and without parentage assignment of individual SNPs. The analysis relies on regional averaging of pooled SNP frequencies to rapidly scan polymorphisms across the genome for differential regional homozygosity, which is then displayed graphically. Results Progeny from defined genetic crosses of Tribolium castaneum (F4 and F19) segregating for the phosphine resistance trait were exposed to phosphine to select for the resistance trait while the remainders were left unexposed. Next generation sequencing was then carried out on the genomic DNA from each pool of selected and unselected insects from each generation. The reads were mapped against the annotated T. castaneum genome from NCBI (v3.0) and analysed for SNP variations. Since it is difficult to accurately call individual SNP frequencies when the depth of sequence coverage is low, variant frequencies were averaged across larger regions. Results from regional SNP frequency averaging identified two loci, tc_rph1 on chromosome 8 and tc_rph2 on chromosome 9, which together are responsible for high level resistance. Identification of the two loci was possible with only 5-7× average coverage of the genome per dataset. These loci were subsequently confirmed by direct SNP marker analysis and fine-scale mapping. Individually, homozygosity of tc_rph1 or tc_rph2 results in only weak resistance to phosphine (estimated at up to 1.5-2.5× and 3-5× respectively), whereas in combination they interact synergistically to provide a high-level resistance >200×. The tc_rph2 resistance allele resulted in a significant fitness cost relative to the wild type allele in unselected beetles over eighteen generations. Conclusion We have validated the technique of linkage mapping by low-coverage sequencing of progeny from a simple genetic cross. The approach relied on regional averaging of SNP frequencies and was used to successfully identify candidate gene loci for phosphine resistance in T. castaneum. This is a relatively simple and rapid approach to identifying genomic regions associated with traits in defined genetic crosses that does not require any specialised statistical analysis.

Bulk geochemical analysis and planktonic foraminifera of sediment core GeoB7112-5

A multivariable approach utilising bulk sediment, planktonic Foraminifera and siliceous phytoplankton has been used to reconstruct rapid variations in palaeoproductivity in the Peru-Chile Current System off northern Chile for the past 19000 cal. yr. During the early deglaciation (19000-16000 cal. yr BP), our data point to strongest upwelling intensity and highest productivity of the past 19 000 cal. yr. The late deglaciation (16000-13000 cal. yr BP) is characterised by a major change in the oceanographic setting, warmer water masses and weaker upwelling at the study site. Lowest productivity and weakest upwelling intensity are observed from the early to the middle Holocene (13000-4000 cal. yr BP), and the beginning of the late Holocene (<4000 cal. yr BP) is marked by increasing productivity, mainly driven by silicate-producing organisms. Changes in the productivity and upwelling intensity in our record may have resulted from a large-scale compression and/or displacement of the South Pacific subtropical gyre during more productive periods, in line with a northward extension of the Antarctic Circumpolar Current and increased advection of Antarctic water masses with the Peru-Chile Current. The corresponding increase in hemispheric thermal gradient and wind stress induced stronger upwelling. During the periods of lower productivity, this scenario probably reversed.

Bulk chemical analysis of sediments ODP Hole 110-671B and 110-672A

Chemical analyses for calcium carbonate, organic carbon, and major constituents (Al, Ti, Ca, Mg, K, Fe) of bulk sediments collected in Hole 671B have been carried out. Organic carbon contents in Pleistocene through middle Miocene sediments above the zone of decollement are very low (<0.1%); below the decollement considerably higher concentrations of organic carbon occur (up to 1 %). Changes in Ti/Al and Fe/Al ratios are minor, but K/Al and Mg/Al ratios show clear trends with the age of the sediments. Preliminary comparisons of these ratios with mineralogic information on clays indicate good correspondence with clay abundances. Calculations of the mass flux of magnesium from the overlying ocean into the pore fluids suggest that addition of magnesium to the sediments is difficult to detect, especially in the absence of a background reference concentration.