20 files

Supplemental Material for Sideli et al., 2020

posted on 02.10.2020, 18:12 by Gina M. Sideli, Peter McAtee, Annarita Marrano, Brian J. Allen, Patrick J. Brown, Timothy Butterfield, Abhaya M. Dandekar, Charles A. Leslie, David B. Neale
All supplementary files from manuscript included. Additional SNP hapmap file format included.
FigS1 contains images of walnut pellicle pigmentation variation in bi-parental population in study.
FigS2 contains PCA and scree plot used to assess the number of PC's to add to model in GWAS analysis.
FigS3 contains a diagram of genetic map for chromosome 16 in 'Chandler' with significant QTLs.
FigS4 contains a diagram of genetic map and QTL for chromosome 7 in 'Chandler'.
FigS5 contains a diagram of genetic map for chromosome 4 and QTL for 'Chandler'.
FigS6 contains a diagram of genetic map for chromosome 14 and QTLs for 'Idaho'.
FigS7 contains a diagram of genetic map for chromosome 1 and QTL for 'Idaho'.
FigS8 contains both Manhattan plots for FarmCPU and MLMM models with QQ plots for DFA phenotype.
File S1-S3 contains methods and Fiji software code for computer vision analysis of walnut pellicle pigmentation.
File S4 ANOVA tables for L*, a*, b*, DFA scores in the GWAS population.
File S5 contains both 'Chandler' and 'Idaho' genetic maps and phenotypes for QTL mapping analysis.
File S6 contains the phenotypes for GWAS analysis.
File S7 contains the first 6 principal components for GWAS analysis.
File S8 Raw color score phenotypic data for individuals in the GWAS and Chandler × Idaho population.
Table S1 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.
Table S2 Co-localization of marker trait associations with Marrano et al. 2019. LD for SNPs displayed.
Table S3 contains all gene functional annotations from BLAST analysis of 100kb regions around significant SNPs.
walnut_hapmap.txt is the additional file added to submission to include the SNP genotypes for GWAS analysis.


Article title

Genetic Analysis of Walnut (Juglans regia L.) Pellicle Pigment Variation Through a Novel, High-Throughput Phenotyping Platform

Manuscript #


Article DOI