Supplemental Material for Sideli et al., 2020

All supplementary files from manuscript included. Additional SNP hapmap file format included. <b>FigS1 </b>contains images of walnut pellicle pigmentation variation in bi-parental population in study.<b>FigS2</b> contains PCA and scree plot used to assess the number of PC's to add to model in GWAS analysis.<b>FigS3</b> contains a diagram of genetic map for chromosome 16 in 'Chandler' with significant QTLs. <b>FigS4</b> contains a diagram of genetic map and QTL for chromosome 7 in 'Chandler'. <b>FigS5</b> contains a diagram of genetic map for chromosome 4 and QTL for 'Chandler'.<b>FigS6</b> contains a diagram of genetic map for chromosome 14 and QTLs for 'Idaho'.<b>FigS7</b> contains a diagram of genetic map for chromosome 1 and QTL for 'Idaho'.<b>FigS8</b> contains both Manhattan plots for FarmCPU and MLMM models with QQ plots for DFA phenotype. <b>File S1-S3</b> contains methods and Fiji software code for computer vision analysis of walnut pellicle pigmentation.<br><b>File S4</b> ANOVA tables for L*, a*, b*, DFA scores in the GWAS population.<br><b>File S5</b> contains both 'Chandler' and 'Idaho' genetic maps and phenotypes for QTL mapping analysis.<b>File S6 </b>contains the phenotypes for GWAS analysis.<b>File S7</b> contains the first 6 principal components for GWAS analysis. <br><b>File S8</b> Raw color score phenotypic data for individuals in the GWAS and Chandler × Idaho population.<br><b>Table S1 </b>Estimated breeding values for color phenotypes. Samples collected from 2015, 2016 harvest on 528 individual trees and display the 20 individuals possessing the lightest color scores.<b>Table S2</b> Co-localization of marker trait associations with Marrano et al. 2019. LD for SNPs displayed.<b>Table S3</b> contains all gene functional annotations from BLAST analysis of 100kb regions around significant SNPs. <b>walnut_hapmap.txt</b> is the additional file added to submission to include the SNP genotypes for GWAS analysis. <br><br>