Development of Quality Control (QC) marker set, and mid-density marker set in Sorghum using Genotyping-by-Sequencing (GBS) based SNPs data of a large set of about 1900 breeding lines across several breeding programs

This dataset includes the research work on the molecular marker characterization of the 1891 breeding lines across several breeding programs. DNA for these lines was isolated from leaves of each accession at 4–6 leaf stage using the modified hexadecyltrimethyl ammonium bromide (CTAB) protocol from 12-day-old seedlings. The genotyping was done following the Genotyping-By-Sequencing (GBS) approach with ApeKI restriction enzyme used for complexity reduction. SNPs were called using GATK v4.0 and BCFTOOLS v1.9 pipeline against Sorghum assembly v3.1. The final data included a total of about 383k SNPs (obtained from 1891 breeding lines out of circa 2100 lines) obtained with filtering criteria of the minimum mean depth of 1 and minimum quality of 30 were used in this study.

本数据集涵盖了多个育种项目中1891个育种系的分子标记表征相关研究工作。所有育种系的DNA均提取自4-6叶期每份种质的叶片，采用基于12日龄幼苗改良的十六烷基三甲基溴化铵（hexadecyltrimethyl ammonium bromide, CTAB）提取方案。基因分型采用基于测序的基因分型（Genotyping-By-Sequencing, GBS）方法，使用ApeKI限制性内切酶实现基因组复杂度降低。单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点的识别依托GATK v4.0与BCFTOOLS v1.9分析流程，参照高粱参考基因组组装版本v3.1完成。最终数据集共包含约38.3万个SNP位点，该类位点由约2100个育种系中的1891个获得；本研究采用的过滤标准为最小平均深度不低于1，且最小质量值不低于30。