apple_leaf

Contains genetic data and binary images associated with the manuscript "Morphometrics reveals complex and heritable apple leaf shapes" ####Folder: genetic_dataContains 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.pedDescription: 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) / PhenotypeGenotypes (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.mapDescription: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_imagesDescription: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_infoDescription: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.本数据集包含与论文《形态计量学揭示苹果叶片形状具有复杂且可遗传的特征》相关的遗传数据与二值图像。 #### 文件夹：genetic_data 包含本研究使用的遗传数据（PED格式与MAP格式文件）。 文件1：ApeKI_PstI-EcoT22I_Malv1.0p_bwa_maf0.01_min2alleles_noIndels_dp5_miss70_imputed_plink_leaf_miss0_maf05_hetero90.ped 描述：该文件为PLINK .ped格式的基因型表格。基因型通过GBS（Genotyping-by-Sequencing，基因型分型测序）（ApeKI与PstI-EcoT22I酶切方案）获得。PED文件为空白符（空格或制表符）分隔的文本文件，其前六列依次为：家系ID/个体ID/父本ID/母本ID/性别（1=雄性；2=雌性；其余为未知）/表型。第7列及之后为双等位基因型。本研究中使用苹果品种唯一标识（apple_ids）作为家系ID与个体ID，可通过leaf_binary_image_info.txt文件与二值图像建立关联。 文件2：ApeKI_PstI-EcoT22I_Malv1.0p_bwa_maf0.01_min2alleles_noIndels_dp5_miss70_imputed_plink_leaf_miss0_maf05_hetero90.map 描述：MAP文件的每一行对应一个单核苷酸多态性（SNP）标记，包含四列信息：染色体编号（1-18、X、Y，若未锚定至参考基因组则为0）/rs编号或SNP标识符/遗传距离（单位：摩根）/碱基对位置（单位：bp）。其中染色体18代表未锚定至参考基因组的重叠群（contigs）。 #### 文件夹：apple_leaf_binary_images 包含本研究使用的全部苹果叶片二值图像。文件以苗圃ID命名，即文件名中“-”之前的部分，可通过leaf_binary_image_info.txt文件与本研究中使用的苹果品种唯一标识（apple_ids）建立关联。 #### 文件夹：leaf_genetic_image_info 包含信息文件leaf_binary_image_info.txt，该文件用于将图像名称（image_name）与苗圃ID（果园内每棵果树的唯一标识）以及苹果品种唯一标识进行关联。叶片图像中使用苗圃ID作为标识，而基因型文件中则使用苹果品种唯一标识。