GBS data of seven Brassica cultivars from Pakistan

The genotyping-by-sequencing (GBS) data was generated on seven Brassica cultivars from Pakistan as a purpose of varietal registration. After strict quality-control, only 501 high-quality SNP markers were retained with 0% missing data. These marker sites can be used for varietal identification and diversity analysis., The DNA was extracted using CTAB method, and the sequencing library was prepared following standard guidelines of two restriction enzymes based strategy. The sequencing libraries were sequenced on T7 MGI-Seq platform. The raw sequencing reads were aligned to the Reference genome sequence of Brassica napus, and the SNPs were called using GATK variant calling pipeline. The vcf file generated is being uploaded which include 501 SNPs with 100% data availability. , , # GBS data of seven Brassica cultivars from Pakistan [https://doi.org/10.5061/dryad.15dv41p4g](https://doi.org/10.5061/dryad.15dv41p4g) The GBS data of seven Brassica cultivars from Pakistan including: 1\) NIA-Canola-2023 2\) Surhan 3\) Super Canola 4\) NIA Toria Gold 5\) Rainbow 6\) Super Raya 7\) Toria Selection-A. ## Description of the data and file structure The data file consists of 501 SNPs in vcf format with SNP positions from reference genome of *Brassica napus* PRJEB5043. ## Sharing/Access information The data is only accessible from DryAd. ## Code/Software BWA-MEM Samtools GATK GATK Haplotype Caller基于测序的基因分型（genotyping-by-sequencing, GBS）数据针对7份来自巴基斯坦的芸苔属（Brassica）栽培品种生成，实验初衷为品种登记注册。经过严格的质量质控后，最终保留了501个无缺失数据的高质量单核苷酸多态性（Single Nucleotide Polymorphism, SNP）标记。该套标记可用于品种鉴定与遗传多样性分析。 基因组DNA采用CTAB法提取，测序文库依照基于双限制性内切酶的标准建库流程构建。测序文库在T7 MGI-Seq测序平台完成上机测序。原始测序读段（reads）经比对至甘蓝型油菜（Brassica napus）参考基因组序列后，使用基因组分析工具包（Genome Analysis Toolkit, GATK）的变异检测流程完成SNP位点调用。生成的变异检测格式（Variant Call Format, VCF）文件已上传，该文件包含501个数据完整率达100%的SNP位点。 # 来自巴基斯坦的7份芸苔属栽培品种GBS数据集 [https://doi.org/10.5061/dryad.15dv41p4g](https://doi.org/10.5061/dryad.15dv41p4g) 本次发布的来自巴基斯坦的7份芸苔属栽培品种GBS数据集包含以下材料： 1) NIA-Canola-2023 2) Surhan 3) Super Canola 4) NIA Toria Gold 5) Rainbow 6) Super Raya 7) Toria Selection-A ## 数据与文件结构说明 该数据文件为VCF格式，包含501个SNP位点，其位点坐标源自甘蓝型油菜（Brassica napus）参考基因组PRJEB5043。 ## 数据共享与获取说明 该数据集仅可通过Dryad平台获取。 ## 代码与软件 BWA-MEM Samtools GATK GATK Haplotype Caller