TY - JOUR
T1 - Association mapping of morphological traits in wild and captive zebra finches
T2 - reliable within, but not between populations
AU - Knief, Ulrich
AU - Schielzeth, Holger
AU - Backström, Niclas
AU - Hemmrich-Stanisak, Georg
AU - Wittig, Michael
AU - Franke, Andre
AU - Griffith, Simon C.
AU - Ellegren, Hans
AU - Kempenaers, Bart
AU - Forstmeier, Wolfgang
PY - 2017/3/1
Y1 - 2017/3/1
N2 - Identifying causal genetic variants underlying heritable phenotypic variation is a long-standing goal in evolutionary genetics. We previously identified several quantitative trait loci (QTL) for five morphological traits in a captive population of zebra finches (Taeniopygia guttata) by whole-genome linkage mapping. We here follow up on these studies with the aim to narrow down on the quantitative trait variants (QTN) in one wild and three captive populations. First, we performed an association study using 672 single nucleotide polymorphisms (SNPs) within candidate genes located in the previously identified QTL regions in a sample of 939 wild-caught zebra finches. Then, we validated the most promising SNP–phenotype associations (n = 25 SNPs) in 5228 birds from four populations. Genotype–phenotype associations were generally weak in the wild population, where linkage disequilibrium (LD) spans only short genomic distances. In contrast, in captive populations, where LD blocks are large, apparent SNP effects on morphological traits (i.e. associations) were highly repeatable with independent data from the same population. Most of those SNPs also showed significant associations with the same trait in other captive populations, but the direction and magnitude of these effects varied among populations. This suggests that the tested SNPs are not the causal QTN but rather physically linked to them, and that LD between SNPs and causal variants differs between populations due to founder effects. While the identification of QTN remains challenging in nonmodel organisms, we illustrate that it is indeed possible to confirm the location and magnitude of QTL in a population with stable linkage between markers and causal variants.
AB - Identifying causal genetic variants underlying heritable phenotypic variation is a long-standing goal in evolutionary genetics. We previously identified several quantitative trait loci (QTL) for five morphological traits in a captive population of zebra finches (Taeniopygia guttata) by whole-genome linkage mapping. We here follow up on these studies with the aim to narrow down on the quantitative trait variants (QTN) in one wild and three captive populations. First, we performed an association study using 672 single nucleotide polymorphisms (SNPs) within candidate genes located in the previously identified QTL regions in a sample of 939 wild-caught zebra finches. Then, we validated the most promising SNP–phenotype associations (n = 25 SNPs) in 5228 birds from four populations. Genotype–phenotype associations were generally weak in the wild population, where linkage disequilibrium (LD) spans only short genomic distances. In contrast, in captive populations, where LD blocks are large, apparent SNP effects on morphological traits (i.e. associations) were highly repeatable with independent data from the same population. Most of those SNPs also showed significant associations with the same trait in other captive populations, but the direction and magnitude of these effects varied among populations. This suggests that the tested SNPs are not the causal QTN but rather physically linked to them, and that LD between SNPs and causal variants differs between populations due to founder effects. While the identification of QTN remains challenging in nonmodel organisms, we illustrate that it is indeed possible to confirm the location and magnitude of QTL in a population with stable linkage between markers and causal variants.
KW - association study
KW - genotype–phenotype maps
KW - linkage mapping
KW - morphology
KW - quantitative trait locus
KW - standing genetic variation
UR - http://www.scopus.com/inward/record.url?scp=85013020792&partnerID=8YFLogxK
U2 - 10.1111/mec.14009
DO - 10.1111/mec.14009
M3 - Article
C2 - 28100011
AN - SCOPUS:85013020792
SN - 0962-1083
VL - 26
SP - 1285
EP - 1305
JO - Molecular Ecology
JF - Molecular Ecology
IS - 5
ER -