NIAB DIVERSE MAGIC GENOTYPES AND PHENOTYPES

<b>SNP Genotype and Phenotype datasets for the NIAB DIVERSE MAGIC wheat population and its founders.</b> <br><br>The diverse MAGIC wheat population was developed at the National Institute for Applied Botany (NIAB), from whom germplasm is available (contact James Cockram).<br><br>Summary of the Data Sets available here:<br>(i) Founder_Consensus_Genotypes.calls.adjusted.txt, All_MAGIC_Consensus_Genotypes.calls.adjusted.txt: Tab-delimited genotypes of the 16 founders of the NIAB DIVERSE MAGIC wheat population and for 550 MAGIC lines, obtained using the 35k Wheat Breeders' Array. Calls were made using the Axiom Best Practices Genotyping Analysis workflow with an inbreeding penalty of 4. The released genotypes have consensus calls where multiple samples were genotyped from the same line. In addition, the genotypes at sites with no minor homozygous calls have been adjusted.<br>(ii) FOUNDERS.tar, MAGIC_PLINK.tar: Genotypes in PLINK format of 1.1M imputed SNPs from exome capture in the 16 founders and and low -coverage sequencing in 505 MAGIC lines.<br>(iii) MAGIC_PLINK_PRUNED.tar 55k tagging SNP genotypes of 505 MAGIC lines, suitable for GWAS<br>(iv) MAGIC_PHENOTYPES.txt Phenotypes for the MAGIC lines and founders.<br>(v) BASIC_GWAS.tar contains the genotypes and phenotypes and analysis scripts packaged into one file. We provide a simple pipeline for genetic mapping with these data.Once unpacked, the 'DATA' subdirectory contains the phenotypic data and the tagging set of ~55k SNP sites called in 504 inbred lines. In this directory, we include R functions for association mapping (file mixed.model.functions.r), including a mixed model transformation to remove the inflationary effects of unequal relatedness on genetic associations. Association mapping can be run on the basis of SNPs or the inferred founder haplotype dosages. To run, follow the steps in the R script example.analysis.r (this will run without modification if the downloaded directory is used as the R working directory). We also include a function for plotting the results as a manhattan plot (plot.functions.r). <br><br>

**NIAB DIVERSE MAGIC小麦群体及其亲本的单核苷酸多态性（Single Nucleotide Polymorphism，SNP）基因型与表型数据集**

该多样化MAGIC小麦群体由国家应用植物学研究所（NIAB）培育，种质资源可对外提供（联系方式：James Cockram）。

本数据集包含以下内容：
(i) Founder_Consensus_Genotypes.calls.adjusted.txt、All_MAGIC_Consensus_Genotypes.calls.adjusted.txt：采用35k小麦育种阵列（35k Wheat Breeders' Array）对NIAB DIVERSE MAGIC小麦群体的16个亲本及550个MAGIC株系进行基因分型得到的制表符分隔型基因型数据。基因型调用基于Axiom最佳实践基因分型分析流程，近交惩罚系数设为4。针对同一株系的多个分型样本，本数据集已整合为一致性调用结果；此外，针对未检测到次要纯合基因型的位点，已对基因型数据进行了校正调整。
(ii) FOUNDERS.tar、MAGIC_PLINK.tar：以PLINK格式存储的基因型数据，包含对16个亲本进行外显子组捕获测序后推算得到的110万个单核苷酸多态性（SNP）位点，以及对505个MAGIC株系进行低覆盖度测序得到的基因型数据。
(iii) MAGIC_PLINK_PRUNED.tar：包含505个MAGIC株系的55k标签SNP基因型数据，适用于全基因组关联分析（Genome-Wide Association Study，GWAS）。
(iv) MAGIC_PHENOTYPES.txt：MAGIC株系及其亲本的表型数据。
(v) BASIC_GWAS.tar：整合了基因型数据、表型数据及分析脚本的打包文件，配套提供了基于该数据集开展遗传作图的简易分析流程。解压后，其中的`DATA`子目录包含表型数据以及在504个自交株系中检测得到的约55k个标签SNP位点集合。该目录下提供了用于关联作图的R语言函数（文件mixed.model.functions.r），其中包含混合模型转换方法，可消除群体亲缘关系不均对遗传关联分析带来的膨胀效应。关联作图可基于SNP位点或推算得到的亲本单倍型剂量进行。运行脚本请遵循example.analysis.r中的步骤（若将下载的目录作为R工作目录，该脚本可直接运行无需修改）。此外还提供了用于将分析结果绘制为曼哈顿图的函数（plot.functions.r）。