apple_leaf

Contains genetic data and binary images associated with the manuscript "Morphometrics reveals complex and heritable apple leaf shapes"

####

Folder: genetic_data

Contains the genetic data (ped and map files) used in this study.

File 1:

ApeKI_PstI-EcoT22I_Malv1.0p_bwa_maf0.01_min2alleles_noIndels_dp5_miss70_imputed_plink_leaf_miss0_maf05_hetero90.ped

Description:

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

File 2:

ApeKI_PstI-EcoT22I_Malv1.0p_bwa_maf0.01_min2alleles_noIndels_dp5_miss70_imputed_plink_leaf_miss0_maf05_hetero90.map

Description:

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

###

Folder: apple_leaf_binary_images

Description:

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.

###

Folder: leaf_genetic_image_info

Description:

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.