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768
datasets available to search
ShareScore release 0.9.0
Dataset results
768 results for “Populus”
Populus deltoides (Salicaceae) - whole tree (or vine) - general
Image of Populus deltoides (Salicaceae) - whole tree (or vine) - general
Populus deltoides (Salicaceae) - leaf - whole upper surface
Image of Populus deltoides (Salicaceae) - leaf - whole upper surface
Populus deltoides (Salicaceae) - leaf - margin of upper + lower surface
Image of Populus deltoides (Salicaceae) - leaf - margin of upper + lower surface
Populus deltoides (Salicaceae) - twig - orientation of petioles
Image of Populus deltoides (Salicaceae) - twig - orientation of petioles
Populus tremuloides (Salicaceae) - twig - orientation of petioles
Image of Populus tremuloides (Salicaceae) - twig - orientation of petioles
Populus tremuloides (Salicaceae) - leaf - showing orientation on twig
Image of Populus tremuloides (Salicaceae) - leaf - showing orientation on twig
Populus tremuloides (Salicaceae) - whole tree (or vine) - view up trunk
Image of Populus tremuloides (Salicaceae) - whole tree (or vine) - view up trunk
Populus tremuloides (Salicaceae) - bark - of a medium tree or large branch
Image of Populus tremuloides (Salicaceae) - bark - of a medium tree or large branch
Populus tremuloides (Salicaceae) - whole tree (or vine) - general
Image of Populus tremuloides (Salicaceae) - whole tree (or vine) - general
Populus tremuloides (Salicaceae) - twig - orientation of petioles
Image of Populus tremuloides (Salicaceae) - twig - orientation of petioles
Populus tremuloides (Salicaceae) - leaf - whole upper surface
Image of Populus tremuloides (Salicaceae) - leaf - whole upper surface
Populus tremuloides (Salicaceae) - leaf - margin of upper + lower surface
Image of Populus tremuloides (Salicaceae) - leaf - margin of upper + lower surface
Populus tremuloides (Salicaceae) - leaf - whole upper surface
Image of Populus tremuloides (Salicaceae) - leaf - whole upper surface
Populus deltoides (Salicaceae) - bark - of a large tree
Image of Populus deltoides (Salicaceae) - bark - of a large tree
Populus deltoides (Salicaceae) - fruit - as borne on the plant
Image of Populus deltoides (Salicaceae) - fruit - as borne on the plant
Populus deltoides (Salicaceae) - leaf - whole upper surface
Image of Populus deltoides (Salicaceae) - leaf - whole upper surface
Populus deltoides (Salicaceae) - fruit - section or open
Image of Populus deltoides (Salicaceae) - fruit - section or open
Populus deltoides (Salicaceae) - fruit - as borne on the plant
Image of Populus deltoides (Salicaceae) - fruit - as borne on the plant
Demographic history and natural selection shape patterns of deleterious mutation load and barriers to introgression across Populus genome
<p><br> Abbreviation of species names in each folder: Palb, P. alba; Pade, P. adenopoda; Pdav, P. davidiana; Ptra, P. tremula; Ptrs, P. tremuloides; Prot, P. rotundifolia; Pqio,P. qiongdaoensis.</p> <p>1. FST<br> Relative divergence (FST) for pairwise species comparisons was calculated for all sites with 100 Kbp non-overlapping windows. </p> <p>2. dxy<br> Absolute divergence (dxy) was calculated for all sites with 100 Kbp non-overlapping windows. </p> <p>3. Nucleotide diversity<br> Nucleotide diversity (π) was calculated for all sites with 100 Kbp non-overlapping windows. </p> <p>4. Derived allele frequency<br> The derived frequencies of 4 different functional categories. Each folder contains seven Populus resluts</p> <p>5. Derived_allele_statistics<br> The statistics of homozygous and heterozygous derived alleles for loss of function, deleterious, tolerated and synonymous variants for each individual. The last two individuals in each file are outgroups </p> <p>6. dsuite-dinvestigate<br> The outputs of 10 trios using program Dinvestigate from Dsuite. The sliding window is 50 SNPs, and the step is 20 SNPs.</p> <p>7. Recombination rate<br> The result of population-scaled recombination rate was calculated by LDhat v2.2.</p> <p>8. Volcanofinder<br> Genome-wide scans of introgression sweeps within each species was implemented using VolcanFinder v.1.0 with the Model over 10 Kbp non-overlapping windows.</p> <p>9. ihh12<br> phased SNPs were used to computed ihh12 by selscan v1.3.0. </p> <p>10 populus162.phased.recode.vcf.gz<br> SNPs were phased with Beagle v.4.1 for the 162 non-hybrid individuals.</p> <p>11 populus227.snp.rm_indel.para_filter.biallelic.GQ30.max_miss20.bed.recode.vcf.gz <br> The vcf of 227 Populus samples. </p>
Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa
In order to uncover the genetic basis of phenotypic trait variation, we used 448 unrelated wild accessions of black cottonwood (Populus trichocarpa) from much of its range in western North America. Extensive data from large-scale trait phenotyping (with spatial and temporal replications within a common garden) and genotyping (with a 34 K Populus single nucleotide polymorphism (SNP) array) of all accessions were used for gene discovery in a genome-wide association study (GWAS). We performed GWAS with 40 biomass, ecophysiology and phenology traits and 29 355 filtered SNPs representing 3518 genes. The association analyses were carried out using a Unified Mixed Model accounting for population structure effects among accessions. We uncovered 410 significant SNPs using a Bonferroni-corrected threshold (P < 1.7 × 10−6). Markers were found across 19 chromosomes, explained 1–13% of trait variation, and implicated 275 unique genes in trait associations. Phenology had the largest number of associated genes (240 genes), followed by biomass (53 genes) and ecophysiology traits (25 genes). The GWAS results propose numerous loci for further investigation. Many traits had significant associations with multiple genes, underscoring their genetic complexity. Genes were also identified with multiple trait associations within and/or across trait categories. In some cases, traits were genetically correlated while in others they were not.
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