Data from: Admixture mapping of quantitative traits in Populus hybrid zones: power and limitations

Lindtke D, González-Martínez SC, Macaya-Sanz D, Lexer C

Date Published: June 12, 2013

DOI: http://dx.doi.org/10.5061/dryad.12kh6

 

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Title R code for single-locus and multivariate regression analyses used for "Admixture mapping in Populus"
Downloaded 69 times
Description R code to obtain candidate QTL and parameter estimates. Runs with example input files 'linkage_Ita_f.edited', 'linkage_Ita_ss.edited', 'Marker.csv', and 'phenotypes_Ita.txt'.
Download AdmixtureMapping.R (13.25 Kb)
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Title Microsatellite genotype data for all individuals from four Populus hybrid zones
Downloaded 20 times
Description Genotypic data are in 2 rows for each individual, in a slightly modified Structure input format. Columns: individual number; source population (Italy, Austria, Hungary, Spain); individual ID; species assignment (0, hybrid; 1, P. alba; 2, P. tremula); use population flag in Structure (0, no; 1, yes); followed by microsatellite fragment sizes for 77 loci (-9, missing data; 222, band absent for dominant markers).
Download Genotypes.csv (537.2 Kb)
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Title Phenotype measurements for all 22 traits and all individuals from four Populus hybrid zones
Downloaded 11 times
Description Columns: individual number; source population (Italy, Austria, Hungary, Spain); individual ID; species assignment (H, hybrid; A, P. alba; T, P. tremula); followed by phenotypes for all 22 phenotypic traits measured/calculated. Phenotype measurements represent averages over 5 leaves measured per tree.
Download Phenotypes.csv (174.5 Kb)
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Title Result of Structure run for Italy, using linkage model (Input file for R code; text file)
Downloaded 12 times
Description Columns: individual number; individual ID; percent missing data; proportion of ancestry from cluster 1 (P. tremula); proportion of ancestry from cluster 2 (P. alba); followed by their 90% probability intervals.
Download linkage_Ita_f.edited (8.189 Kb)
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Title Result of Structure run for Italy, using linkage model, site-by-site output (Input file for R code; text file)
Downloaded 9 times
Description Columns: individual number; locus number; followed by 4 columns for LSA estimates (probability that both alleles are from P. alba; probability that first allele is from P. alba, second from P. tremula; probability that first allele is from P. tremula, second from P. alba; probability that both alleles are from P. tremula).
Download linkage_Ita_ss.edited (369.5 Kb)
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Title Information on microsatellite markers used (Input file for R code)
Downloaded 14 times
Description Columns: locus number; abbreviated locus name used in this study; locus name published; chromosome; position on chromosome in bp; position in bp/200,000 as proxy for cM; marker type (dominant or co-dominant).
Download Marker.csv (3.161 Kb)
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Title Phenotype measurements for Italy, admixed individuals only, 8 mapping traits (Input file for R code)
Downloaded 9 times
Description Rows give measurements for individuals in the same order as in Structure files; columns give 8 main phenotypic traits used for admixture mapping. Phenotype measurements represent averages over 5 leaves measured per tree.
Download phenotypes_Ita.txt (13.67 Kb)
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When using this data, please cite the original publication:

Lindtke D, González-Martínez SC, Macaya-Sanz D, Lexer C (2013) Admixture mapping of quantitative traits in Populus hybrid zones: power and limitations. Heredity 111(6): 474–485. http://dx.doi.org/10.1038/hdy.2013.69

Additionally, please cite the Dryad data package:

Lindtke D, González-Martínez SC, Macaya-Sanz D, Lexer C (2013) Data from: Admixture mapping of quantitative traits in Populus hybrid zones: power and limitations. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.12kh6
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