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《形态计量学揭示复杂且可遗传的苹果叶片形状》相关的遗传数据与二值图像。 #### 文件夹：genetic_data 本文件夹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。基因型通过基因分型测序（Genotyping-by-Sequencing, GBS）获取，所用限制性内切酶为ApeKI与PstI-EcoT221I。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列及之后的列内容为双等位基因基因型。本研究中使用苹果品种唯一标识符（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：该文件为PLINK .map格式的遗传图谱文件。文件的每一行对应一个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）标记，包含四列信息：染色体编号（1-18、X、Y，未锚定至参考基因组的染色体标注为0）/rs编号或SNP标识符/遗传距离（单位为摩根）/碱基对位置（单位为碱基对）。其中染色体编号18代表未锚定至参考基因组的重叠群（contigs）。 #### 文件夹：apple_leaf_binary_images 本文件夹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“-”之前的字符串部分，可通过leaf_binary_image_info.txt文件与本研究使用的apple_ids建立关联。 #### 文件夹：leaf_genetic_image_info 本文件夹包含信息文件leaf_binary_image_info.txt，该文件用于建立图像名称（image_name）、果园中单棵果树的唯一标识符苗圃ID（nursery_id）以及苹果品种唯一标识符apple_id三者之间的关联。叶片图像文件使用nursery_id进行命名，而基因型文件则使用apple_ids作为个体标识。