Project description:Gene copy number variations (CNVs) involved in phenotypic variations have already been shown in plants, but genome-wide testing of CNVs for adaptive variation was not doable until recent technological developments. Thus, reports of the genomic architecture of adaptation involving CNVs remain scarce to date. Here, we investigated F1 progenies of an intra-provenance cross (north-north cross, 58th parallel) and an inter-provenances cross (north-south cross, 58th/49th parallels) for CNVs using comparative genomic hybridization on arrays of probes targeting gene sequences in balsam poplar (Populus balsamifera L.), a wide-spread North American forest tree. Results: A total of 1,721 genes were found in varying copy numbers over the set of 19,823 tested genes. These gene CNVs presented an estimated average size of 8.3 kb and were distributed over poplar’s 19 chromosomes including 22 hotspot regions. Gene CNVs number was higher for the inter-provenance progeny in accordance with an expected higher genetic diversity related to the composite origin of this family. Regression analyses between gene CNVs and seven adaptive trait variations resulted in 23 significant links; among these adaptive gene CNVs, 30% were located in hotspots. One-to-five gene CNVs were found related to each of the measured adaptive traits and annotated for both biotic and abiotic stress responses. These annotations can be related to the occurrence of a higher pathogenic pressure in the southern parts of balsam poplar’s distribution, and higher photosynthetic assimilation rates and water-use efficiency at high-latitudes. Overall, our findings suggest that gene CNVs typically having higher mutation rates than SNPs, may in fact represent efficient adaptive variations against fast-evolving pathogens. Overall design: A total of 34 individuals were hybridized (17 in each dye) in addition to 12 reference DNA (6 in each dye). Reference DNAs were corrected for day and batch effect and averaged within each dye. Afterwards, each sample was compared to this average representation of the reference in the opposite dye.
Project description:Purpose: The goal of the current study was to find the candidate genes responsible for the habita specific clock variation in N. discreta. Methods: We performed RNA-seq experiment using four strains ; African parent (FGSC8831), North American parent (FGSC 8578) and two representative progeny representing African clock phenotype (N309-89) and North American clock phenotype (N309-50). Results: We identified one candidate gene that meets our criteria; confirmed it's expression by qPCR and it's expression pattern is associated with parent genotype. Conclusions: Our approach using the expression profiles and SNP data of two parents and two representative progeny led us to identify a candidate gene for a complex clock adaptation phenotype. Overall design: Samples are prepared from cells at different time of the cycling environement, 12 h light: 12 h dark; 2h dark phase (2DK), and 15m, 1h and 2h light phase. We also used the identified SNPs in the transcripts to perform association study.
Project description:To study the population genetics context of the Saqqaq individual we carried out Illumina Bead-Array-based genotyping on four native North American and twelve north Asian populations. Overall design: 169 samples are analysed on two different Illumina platforms.
Project description:Background: The idea of using whole genome microarrays to detect peripheral blood biomarkers for physiological status a fairly new and unexplored method. Identifying biomarkers that can be linked to stress and immune response would be of great importance not only in animal management practices but in humans as well. The main objective of this research was to explore this concept using the North American Red Wolf (Canis rufus) which are exposed to a wide variety of environments from free ranging to confinement. Results: Transcription profiling of peripheral blood samples from 13 red wolf individuals in the Alligator River region of North Carolina revealed a strong signal of differentiation between confined and free-range animals. 482 out of 2,980 transcripts detected on the human Illumina Ref8 oligonucleotide bead arrays were found to differentiate these groups at a false discovery rate of 5 percent. Over-representation of genes in focal adhesion, insulin signaling, proteasomal, and tryptophan metabolism pathways suggests the activation of proinflammatory and stress responses in confined animals. Conclusions: Integration of immunological and physiological signals may leave a signature of lifestyle in the patterns of gene expression in the blood and suggest the possible development of biomarkers for disease and normal conditions. Keywords: Stress Response/Disease State Overall design: 14 whole blood samples were collect from captive and free ranging red wolves. Information pertaining to sex and current holding status was obtained for each individual. In total we had 6 captive wolves (2 females and 4 males), 7 free range wolves (2 females and 5 males) and 1 free range female coyote. Total RNA was extracted from whole blood samples stored in RNAlater at -20C. Total RNA was amplified and biotin labeled using Ambion's Illumina RNA Amplification Kit (#I1755). Each labeled sample was hybridized on 4 independent arrays, giving a total of 56 arrays (4/sample). Hybridization was done at 42C overnight. Arrays were washed and stained with strepavidin linked Cy3. Arrays were scanned on Illumina's BeadStation Scanner and raw intensity data was extracted using Illumina Beadstudio. Raw intensities were log base 2 transformed and then median center standardized in SAS using the proc stdize.