Genotypic and phenotypic data for GWAS

This constitutes a dense and exhaustive coverage of the soybean genome using a dual genotyping approach combining both GBS and WGS for a core set of 137 Canadian soybean lines with their root system architecture (RSA)-related traits data. The entire panel was characterized via 56K GBS-derived SNPs. A Canadian soybean reference panel (102 lines, of which 56 were also present in the association panel) of 4.3M WGS-derived SNPs was used to perform imputation of untyped loci in the first catalogue. This led to a final catalogue of 2.18M SNPs (MAF ≥ 0.05) for a mean density of 1 SNP every 435 bp across the soybean genome.Automatic Root Image Analysis (ARIA) software was used to extract phenotypic data (after 10 days of growth) from the images. In total, 12 different RSA-related traits were measured from each 2D image for each soybean line including : including: total length of roots (TLR), length of primary root (LPR), length of secondary roots (LSR), distribution of total root length (DTLR), total number of roots (TNR), median number of roots (Med), maximum number of roots (Max), depth of root system (DRS), width of root system (WRS), surface of root system (SRS), diameter of primary root (DR), surface area of primary root (SAR). <br>

本数据集针对137份加拿大核心大豆品系，采用基因分型测序（Genotyping-by-Sequencing, GBS）与全基因组测序（Whole Genome Sequencing, WGS）相结合的双基因分型策略，对大豆基因组开展高密度全覆盖检测，并同步获取了其根系构型（Root System Architecture, RSA）相关性状数据。全部供试群体通过56K个GBS来源的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点完成基因分型。本研究采用包含430万个WGS来源SNP位点的加拿大大豆参考群体（共102份品系，其中56份与关联分析群体重合），对初始分型目录中未获取基因型的位点进行填充。最终得到包含218万个SNP位点（最小等位基因频率（Minor Allele Frequency, MAF）≥0.05）的最终分型目录，大豆全基因组范围内的平均标记密度为每435个碱基对分布1个SNP。本研究采用自动根系图像分析（Automatic Root Image Analysis, ARIA）软件，对生长10天后的大豆根系图像提取表型数据。针对每份大豆品系的二维根系图像，共测定了12项与根系构型相关的性状，包括：总根长（total length of roots, TLR）、主根长（length of primary root, LPR）、侧根长（length of secondary roots, LSR）、总根长分布（distribution of total root length, DTLR）、总根数（total number of roots, TNR）、根数量中位数（median number of roots, Med）、根数量最大值（maximum number of roots, Max）、根系深度（depth of root system, DRS）、根系宽度（width of root system, WRS）、根系表面积（surface of root system, SRS）、主根直径（diameter of primary root, DR）、主根表面积（surface area of primary root, SAR）。