Trace elements in pacific Dunlin (Calidris alpina pacifica): patterns of accumulation and concentrations in kidneys and feathers

Trace element concentrations were measured in Pacific Dunlin (Calidris alpina pacifica) to identify factors that influence accumulation and to assess toxicity risks. We report concentrations of cadmium, copper, and zinc in kidneys as well as copper, lead, mercury, selenium and zinc in feathers. Relationships between element concentrations and Dunlin age, sex, bill length, habitat preference, trophic level, and sample group were investigated with regression analyses. Stable isotope ratios of carbon and nitrogen in Dunlin muscle tissue were used to determine habitat preference and trophic level, respectively. Cadmium concentrations in kidneys were significantly related to habitat preference: [Cd] in estuarine foragers >[Cd] in terrestrial foragers. Cadmium accumulation was age-dependent as concentrations increased significantly within 10 months of hatch dates but not afterward. Concentrations of cadmium and zinc in kidneys as well as lead and mercury in feathers were below those known to cause deleterious effects in birds. In contrast, selenium concentrations in feathers (range: 2.1–14.0 µg/g) were often at levels associated with toxicity risks (>5 µg/g). Toxicity thresholds are not available for copper in kidneys or copper and zinc in feathers; however, measured concentrations of these elements were within documented ranges for sandpipers. Future studies should assess potential impacts of selenium on embryonic development in Dunlin and other sandpipers. Risk assessments would yield more conclusive results for all elements if impacts under ecologically relevant stresses (e.g. development in the wild, migration, predation) were better understood

High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis

Expression microarrays hybridized with RNA can simultaneously provide both phenotypic (gene expression) and genotypic (marker) data. We developed two types of genetic markers from Affymetrix GeneChip expression data to generate detailed haplotypes for 148 recombinant inbred lines (RILs) derived from Arabidopsis thaliana accessions Bayreuth and Shahdara. Gene expression markers (GEMs) are based on differences in transcript levels that exhibit bimodal distributions in segregating progeny, while single feature polymorphism (SFP) markers rely on differences in hybridization to individual oligonucleotide probes. Unlike SFPs, GEMs can be derived from any type of DNA-based expression microarray. Our method identifies SFPs independent of a gene’s expression level. Alleles for each GEM and SFP marker were ascertained with GeneChip data from parental accessions as well as RILs; a novel algorithm for allele determination using RIL distributions capitalized on the high level of genetic replication per locus. GEMs and SFP markers provided robust markers in 187 and 968 genes, respectively, which allowed estimation of gene order consistent with that predicted from the Col-0 genomic sequence. Using microarrays on a population to simultaneously measure gene expression variation and obtain genotypic data for a linkage map will facilitate expression QTL analyses without the need for separate genotyping. We have demonstrated that gene expression measurements from microarrays can be leveraged to identify polymorphisms across the genome and can be efficiently developed into genetic markers that are verifiable in a large segregating RIL population. Both marker types also offer opportunities for massively parallel mapping in unsequenced and less studied species