Data from: Association mapping of morphological traits in wild and captive zebra finches: reliable within but not between populations

Identifying causal genetic variants underlying heritable phenotypic variation is a longstanding 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 5,228 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 non-model 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.

Usage Notes
data_phenotypes_BodyMassBody mass data used for the initial linkage analysis. A detailed description of the file is in the README.data_phenotypes_TarsusDigitRatioTarsus length, body size and digit ratio data used for the initial linkage analysis. A detailed description of the file is in the README.data_phenotypes_TarsusBodySizeDigitRatio.txtdata_genotypes_SequenomGenotypic data for all individuals from the wild and multiple captive populations used for the validation study. A detailed description of the file is in the README.data_snp_annotationAdditional information for all SNPs used for the validation study. A detailed description of the file is in the README.

识别遗传变异背后的因果遗传变异，一直是进化遗传学中长期追求的目标。我们先前通过全基因组连锁图谱分析，在斑马雀（Taeniopygia guttata）的圈养种群中鉴定了五个形态性状的多个数量性状位点（QTL）。在此，我们继这些研究之后，旨在缩小一个野生种群和三个圈养种群中数量性状变异（QTN）的范围。首先，我们利用候选基因中位于先前识别的QTL区域内的672个单核苷酸多态性（SNPs）对939只野生捕获的斑马雀样本进行了关联研究。随后，我们在来自四个种群共计5,228只鸟类中验证了最有希望的SNP-表型关联（n = 25 SNPs）。在野生种群中，基因型-表型关联普遍较弱，其中连锁不平衡（LD）仅跨越短基因组距离。相比之下，在圈养种群中，LD块较大，显性SNPs对形态性状的影响（即关联）与同种群独立数据高度可重复。其中大多数SNPs还显示出与同一性状在其他圈养种群中的显著关联，但这些效应的方向和强度在种群之间存在差异。这表明，所测试的SNPs并非因果QTN，而是与其物理相连，并且由于奠基效应，SNPs与因果变异之间的连锁不平衡在种群之间存在差异。虽然识别QTN在非模式生物中仍然具有挑战性，但我们展示了确实可以在具有标记与因果变异之间稳定连锁的种群中确认QTL的位置和强度。

使用说明

data_phenotypes_BodyMass用于初始连锁分析的身体质量数据。有关文件的详细描述请参阅README。
data_phenotypes_TarsusDigitRatio用于初始连锁分析的手指长度、身体大小和手指比例数据。有关文件的详细描述请参阅README。
data_genotypes_Sequenom用于验证研究中野生和多个圈养种群所有个体的基因型数据。有关文件的详细描述请参阅README。
data_snp_annotation用于验证研究中所有SNPs的附加信息。有关文件的详细描述请参阅README。