Amaizing Dent Panel used for breeding program simulation

This dataset corresponds to the data associated with the study: “Improving the use of plant genetic resources to sustain breeding programs efficiency” by Sanchez et al. (submitted). The data include the genotyping of 338 public lines from the Dent Amaizing Panel with the 50K SNP Illumina Infinium HD array (Ganal et al., 2011) and the result of an ADMIXTURE analysis (k=3) performed by (Rio et al., 2019). The following QC filters were applied: line call rate ≥ 0.8, marker call rate ≥ 0.9, line heterozygosity rate ≤ 0.1 and marker heterozygosity rate ≤ 0.15. Beagle V4 was used to impute missing data. 1. M. W. Ganal, et al., A Large Maize (Zea mays L.) SNP Genotyping Array: Development and Germplasm Genotyping, and Genetic Mapping to Compare with the B73 Reference Genome. PLoS ONE 6, e28334 (2011). 2. S. Rio, T. Mary-Huard, L. Moreau, A. Charcosset, Genomic selection efficiency and a priori estimation of accuracy in a structured dent maize panel. Theor Appl Genet 132, 81–96 (2019).

本数据集对应Sanchez等人（已投稿）题为《提升植物遗传资源利用以维持育种项目效率》的研究相关数据。数据包含两部分内容：一是采用50K单核苷酸多态性（Single Nucleotide Polymorphism, SNP）Illumina Infinium HD基因分型芯片（Ganal等，2011），对Dent Amaizing群体的338份公共种质系开展的基因型分型结果；二是Rio等（2019）完成的ADMIXTURE群体结构分析（k=3）结果。本数据集应用了如下质量控制（Quality Control, QC）筛选标准：系样本检出率≥0.8、标记检出率≥0.9、系内杂合率≤0.1以及标记杂合率≤0.15。采用Beagle V4软件对缺失基因型数据进行填充。
1. M. W. Ganal等. 大型玉米（Zea mays L.）SNP基因分型芯片的开发、种质资源基因分型及与B73参考基因组比对的遗传图谱构建. PLoS ONE 6, e28334 (2011).
2. S. Rio、T. Mary-Huard、L. Moreau、A. Charcosset. 结构化Dent玉米群体中的基因组选择效率与准确率先验估计. 理论与应用遗传学 132, 81–96 (2019).