10.5061/DRYAD.12KH6
Lindtke, Dorothea
University of Fribourg
González-Martínez, Santiago C.
Department of Forest Ecology and Genetics, INIA, Forest Research Centre,
Madrid, Spain
Macaya-Sanz, David
Department of Forest Ecology and Genetics, INIA, Forest Research Centre,
Madrid, Spain
Lexer, Christian
Data from: Admixture mapping of quantitative traits in Populus hybrid
zones: power and limitations
Dryad
dataset
2013
leaf morphology
Populus tremula
QTL
Admixture Mapping
Populus alba
2013-06-12T18:24:08Z
2013-06-12T18:24:08Z
en
https://doi.org/10.1038/hdy.2013.69
1119592 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Uncovering the genetic architecture of species differences is of central
importance for understanding the origin and maintenance of biological
diversity. Admixture mapping can be used to identify the number and effect
sizes of genes that contribute to the divergence of ecologically important
traits, even in taxa that are not amenable to laboratory crosses due to
their long generation time or other limitations. Here, we apply admixture
mapping to naturally occurring hybrids between two ecologically divergent
Populus species. We map quantitative trait loci (QTL) for eight leaf
morphological traits using 77 mapped microsatellite markers from all 19
chromosomes of Populus. We apply multivariate linear regression analysis
allowing the modeling of additive and non-additive gene action and
identify several candidate genomic regions associated with leaf morphology
using an information-theoretic approach. We perform simulation studies to
assess the power and limitations of admixture mapping of quantitative
traits in natural hybrid populations for a variety of genetic
architectures and modes of gene action. Our results indicate that (1)
admixture mapping has considerable power to identify the genetic
architecture of species differences if sample sizes and marker densities
are sufficiently high, (2) modeling of non-additive gene action can help
to elucidate the discrepancy between genotype and phenotype sometimes seen
in interspecific hybrids, and (3) the genetic architecture of leaf
morphological traits in the studied Populus species involves complementary
and overdominant gene action, providing the basis for rapid adaptation of
these ecologically important forest trees.
R code for single-locus and multivariate regression analyses used for
"Admixture mapping in Populus"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'.AdmixtureMapping.RMicrosatellite genotype
data for all individuals from four Populus hybrid zonesGenotypic 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).Genotypes.csvPhenotype measurements for all
22 traits and all individuals from four Populus hybrid zonesColumns:
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.Phenotypes.csvResult of Structure run for Italy, using linkage model
(Input file for R code; text file)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.linkage_Ita_f.editedResult of Structure
run for Italy, using linkage model, site-by-site output (Input file for R
code; text file)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).linkage_Ita_ss.editedInformation on microsatellite markers used
(Input file for R code)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).Marker.csvPhenotype measurements for Italy, admixed
individuals only, 8 mapping traits (Input file for R code)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.phenotypes_Ita.txt
Ticino river Italy
Duero river Spain
Danube river Austria
Tisza river Hungary