Genetic insight into a polygenic trait using a novel Genome Wide Association approach in a wild amphibian population

# Genetic insight into a polygenic trait using a novel Genome Wide Association approach in a wild amphibian population [https://doi.org/10.5061/dryad.f4qrfj739](https://doi.org/10.5061/dryad.f4qrfj739) We utilized a ddrad sequencing approach to explore the genetic basis of polygenic traits such as body size and fecundity on a single population of Greek smooth newt, by utilizing an association analysis in Tassel with linkage disequilibrium network analysis in LDna. ## Description of the data and file structure 1.phenotypic_traits.xlx: Excel file containing phenotypic measurements for the samples used in this study. 2.females.vcf: Variant Call Format file with SNP info for 102,403 sites and 38 individuals. 3.imputed.vcf: Variant Call Format file with imputed genotypic information based on the females.vcf file 4.GRM_imputed.txt: A genetic relationship matrix generated using the imputed genotypic dataset (imputed.vcf). 5.GWAS_traits.txt: Phenotypic measurements (transformed measurements) used in the association analysis and LD (linkage disequilibrium) network analysis. ***DATA-SPECIFIC INFORMATION FOR: phenotypic_traits.xlx*** A. Number of individuals: 61 B. List of variables -id: the id name of each individual -sex: the sex of each individual, female or male -morph: the morph of each individual, metamorphic or paedomorphic -svl: snout to vent length in millimetre -logsvl: log transformed snout to vent length -weight: body weight in grams -logw: log transformed weight -body condition: Body weight was regressed on body size after log transformation, and the residual distances from the linear regression line were used to calculate Body Condition Index (BCI; Jakob et al., 1996). -egg_laying: that act of egg laying, zero no eggs and one egg laying (binary variable) -eggs: the number of eggs deposited for each individual -hatched: the number of successfully hatched eggs for each individual -stage_larvae: number of larvae that developed limps -stage_juvenile: number of larvae that reach the juvenile stage -fecundity1: squared root transformed number of laid eggs -fecundity2: squared root transformed number of successfully hatched eggs -fecundity3: squared root transformed number of survived larvae till juvenile stage C. Missing cells: None D. Empty cells: Correspond to the females that did not engage in oviposition (egg laying is zero) at the present study. ###### **DATA-SPECIFIC INFORMATION FOR: GWAS\_traits.xlx** A. Number of individuals: 38 B. List of variables -ID: the id name of each individual -sex: the sex of each individual, female or male -morph: the morph of each individual, meta (metamorphic) or paedo (paedomorphic) -size: log transformed snout to vent length (mm) -condition: Body weight was regressed on body size after log transformation, and the residual distances from the linear regression line were used to calculate Body Condition Index (BCI; Jakob et al., 1996). -fecundity1: squared root transformed number of laid eggs -fecundity2: squared root transformed number of successfully hatched eggs -fecundity3: squared root transformed number of survived larvae till juvenile stage C. Missing values are denoted by NA (data not applicable).