Datasets usually provide raw data for analysis. This raw data often comes in spreadsheet form, but can be any collection of data, on which analysis can be performed.
Contains genetic data and binary images associated with the manuscript "Morphometrics reveals complex and heritable apple leaf shapes"
Contains the genetic data (ped and map files) used in this study.
Genotype table in PLINK .ped format. Genotypes were obtained using GBS (ApeKI and PstI-EcoT221I). The PED file is a white-space (space or tab) delimited file. the first six columns are:
Family ID / Individual ID / Paternal ID / Maternal ID / Sex (1=male; 2=female; other=unknown) / Phenotype
Genotypes (biallelic) are column 7 onwards.
apple_ids (unique per cultivar) are used for Family ID and Individual ID, these can be linked with the binary images using leaf_binary_image_info.txt
Each line of the .map file describes a single marker and contains 4 columns:
chromosome (1-18, X, Y or 0 if unplaced) / rs# or snp identifier / Genetic distance (morgans) / Base-pair position (bp units)
chromosome 18 indicates contigs that are unanchored to the reference genome
Contains all binary images of apple leaves used in this study. Files are named after the nursery ID, which is the value before “-“ and can be linked with the apple IDs used in this study through the leaf_binary_image_info.txt info file.
Info file (leaf_binary_image_info.txt) which links the name of the images (image_name) with the nursery_id (unique per tree in the orchard) and apple_id (unique per cultivar) for the study. The image_name/nursery_id is used in the leaf images, but the apple IDs are used in the genotype files.