Synbreed Biodiversity Panel Genotypes

<strong>Synbreed Diversity Panel Genotypes</strong> These data have been made available coupled with the publication of Beissinger, T., Gholami, M., Erbe, M., Weigend, S., Weigend, A., de Leon, N., Gianola, D., and Simianer, H., <em>Using the Varibility of Linkage Disequilibrium Between Populations to Infer Sweeps and Epistatic Selection in a Diverse Panel of Chickens</em>, Heredity, 2015. Please cite upon use. <strong>Synbreed – Synergistic Plant and Animal Breeding</strong> (Synbreed) was funded by the German Federal Ministry of Education and Research (BMBF) from 2009 -<br>2014 (Funding ID: 0315526) ; web address http://www.synbreed.tum.de/ ***<br>Samples were genotyped with 580K SNP Affymetrix Axiom® Genome-Wide Chicken Genotyping Array. <strong>Genotype_Matrix.Robj</strong><br>This file is a matrix of genotypes from 1,417 chickens encompassing 72 breeds, genotyped as part of the Synbreed Project. The file can be loaded into R with the load() command. Individuals are in rows and marker genotypes, coded 0, 1, and 2, are in columns. Row names are a breed index, so all rows named "1" are from breed 1, all rows named "2" are from breed 2, and so on. Column names are marker names. <strong>Genotype_Map.Robj</strong><br>This file is a map describing the 564,939 markers that were genotyped. The file can be loaded into R with the load() command. Each row describes a marker. The first column, named "SNP" provides the marker name. This column corresponds to the rows of the Genotype_Matrix.Robj file. The second column, named "Chr", is the chromosome. The third column, named "Pos", is the physical position of the marker.

**Synbreed多样性面板基因型数据（Synbreed Diversity Panel Genotypes）**
本数据集随Beissinger T.、Gholami M.、Erbe M.、Weigend S.、Weigend A.、de Leon N.、Gianola D.及Simianer H.于2015年发表于《遗传》（Heredity）的论文《利用群体间连锁不平衡的变异推断多样化鸡群中的选择性清除与上位选择（Using the Varibility of Linkage Disequilibrium Between Populations to Infer Sweeps and Epistatic Selection in a Diverse Panel of Chickens）》同步发布，使用本数据请引用该文献。

**Synbreed——动植物育种协同计划（Synbreed – Synergistic Plant and Animal Breeding）** 由德国联邦教育与研究部（German Federal Ministry of Education and Research, BMBF）于2009年至2014年资助（资助编号：0315526），项目官网为 http://www.synbreed.tum.de/ ***

本次研究的样本通过580K 单核苷酸多态性（Single Nucleotide Polymorphism, SNP）Affymetrix Axiom® 全基因组鸡基因分型芯片完成基因分型。

**Genotype_Matrix.Robj**
该文件为包含1417只鸡的基因型矩阵，涵盖72个品种，属于Synbreed项目的基因分型研究材料。可通过R语言的`load()`命令加载该文件。矩阵以行代表个体，列代表标记基因型，基因型编码为0、1、2。行名为品种索引，即所有行名标注为“1”的样本均来自品种1，行名标注为“2”的样本均来自品种2，以此类推；列名为标记名称。

**Genotype_Map.Robj**
该文件为本次基因分型所用的564939个标记的图谱信息，可通过R语言的`load()`命令加载。文件每行对应一个标记：第一列名为“SNP”，为标记名称，与Genotype_Matrix.Robj文件的行一一对应；第二列名为“Chr”，代表标记所在染色体；第三列名为“Pos”，代表标记的物理位置。