10.5061/DRYAD.MP32F
Corbi, Jonathan
University of Georgia
University of Lyon System
Baack, Eric J.
Luther College
Dechaine, Jennifer M.
Central Washington University
Seiler, Gerald
United States Department of Agriculture
Burke, John M.
University of Georgia
Data from: Genome-wide analysis of allele frequency change in sunflower
crop-wild hybrid populations evolving under natural conditions
Dryad
dataset
2017
Helianthus annuus
domestication traits
crop-wild hybridization
allele frequency
National Science Foundation
https://ror.org/021nxhr62
IOS-1444522
2017-06-13T04:39:23Z
2017-06-13T04:39:23Z
en
https://doi.org/10.1111/mec.14202
1013014 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Crop-wild hybridization occurs in numerous plant species, and could alter
the genetic structure and evolutionary dynamics of wild populations.
Studying crop-derived alleles in wild populations is also relevant to
assessing/mitigating the risks associated with transgene escape. To date,
crop-wild hybridization has generally been examined via short-term
studies, typically within a single generation, focusing on few traits or
genetic markers. Little is known about patterns of selection on
crop-derived alleles over multiple generations, particularly at a
genome-wide scale. Here, we documented patterns of natural selection in an
experimental crop × wild sunflower population that was allowed to evolve
under natural conditions for two generations at two locations. Allele
frequencies at a genome-wide collection of SNPs were tracked across
generations, and a common garden experiment was conducted to compare trait
means between generations. These data allowed us to identify instances of
selection on crop-derived alleles/traits and, in concert with QTL mapping
results, test for congruence between our genotypic and phenotypic results.
We found that natural selection overwhelmingly favors wild alleles and
phenotypes. However, crop alleles in certain genomic regions can be
favored, and these changes often occurred in parallel across locations. We
did not, however, consistently observe close agreement between our
genotypic and phenotypic results. For example, when a trait evolved
towards the wild phenotype, wild QTL alleles associated with that trait
did not consistently increase in frequency. We discuss these results in
the context of crop allele introgression into wild populations and
implications for the management of GM crops.
G1 and G3 SNP genotypesSNP genotypesInputfilerg0g3lg05Sample data file for
the 'Python script for simulation of selection drift recombination
with linked loci.py'.IOWA2011RData were collected in Decorah, IA and
Fargo, ND in 2011ND2011RData were collected in Decorah, IA and Fargo, ND
in 2011lg05dInput used by the 'Python script for simulation of
selection drift recombination with linked loci.py'python script for
simulation of selection drift recombination with linked locipython script
for simulation of selection drift recombination with linked locipython
script for simulation of selection without linkagepython script for
simulation of selection without linkageR script for analysis of 2011
common garden data setsR script for data analysis of sunflower phenotypic
datarilfreqInput file used for 'python sript for simulation of
selection without linkage.py'.RIL genotypes - generation 0RIL
genotypes - generation 0SNP loci used sorted by map positionSNP loci used
sorted by map positionSNP 278Sequences of the 278 SNP used