Replication Data for: Genome-wide association study of salt tolerance at the seed germination stage in lettuce

This dataset contains genotypic data (SNP) of 445 diverse lettuce accessions (Lactuca spp.), mainly consisting of cultivated types with a few wild and primitive types, selected from the germplasm collection at the USDA-ARS, Salinas, CA. SNP genotyping was conducted by Data2Bio (Ames, IA) using Genotyping by Sequencing technology with the restriction enzyme BSP1682I.The genotypic data is presented in a variant call format (VCF) file containing 56,820 SNPs and 445 accessions. The missing values of the genotypic data were imputed using Beagle version 5.4 software with 3 Burnin iteration and 12 Phasing iteration. This dataset was used to conduct a genome-wide association study to identify SNP markers associated with salt tolerance at the seed germination stage in lettuce.

本数据集包含445份多样化莴苣属（Lactuca spp.）生菜种质材料的单核苷酸多态性（Single Nucleotide Polymorphism，SNP）基因型数据，其中以栽培类型为主，辅以少量野生与原始类型，所有材料均采自位于加利福尼亚州萨利纳斯的美国农业部农业研究服务局（USDA-ARS）种质资源库。该数据集的SNP基因分型工作由艾奥瓦州埃姆斯市的Data2Bio公司完成，采用测序分型（Genotyping by Sequencing）技术并使用限制性内切酶BSP1682I；基因型数据以变异调用格式（Variant Call Format，VCF）文件存储，共包含56820个SNP位点与445份种质材料；其缺失值通过Beagle 5.4版本软件插补，参数设置为3次烧失迭代（Burnin iteration）与12次分型迭代（Phasing iteration）；本数据集被用于开展全基因组关联分析，以筛选与生菜种子萌发期耐盐性相关的SNP标记。