SNP genotyping of indigenous goats of Uganda based on the Goat_IGGC_65K_v2 illumina chip

Uganda's indigenous goats are characterised based on ethnic communities that raise them, average mature weight, and hair coat characteristics. Uganda's indigenous goats have  been genotyped based on the Goat_IGGC_65K_v2 illumina chip to study their population structure and genetic characteristics. Information generated from this data is vital for the sustainable utilisation, development, and conservation of Uganda's goat genetic resources.

Methods
The data was collected from genomic DNA extracted from ear tissue samples of 1032 indigenous goats from different agro-ecological zones of Uganda.  The study aimed to characterise the genetic diversity, population structure and signatures of selection of indigenous goats in different agroecological zones of Uganda. Indigenous goats were identified in their known phenotypic/ ethnic classifications of Mubende, Kigezi and Small East African goats in all the 10 agroecologies. Ear tissue samples were collected from each goat using the allflex tissue sampling system that allows for no cross contamination as each sample self locks in a single use tube after it is collected. Genomic DNA was extracted from each sample using the TANBEAD automated DNA extraction system with the 6T2 total tissue DNA extraction kit. DNA samples were genotyped based on the Goat_IGGC_65K_v2 illumina chip. 

Data processing

After genotyping, 59725 SNPs from 1032 genotypes were received in PLINK format. The data was opened in Tassel Version 5.2 and saved as VCF format for further processing. The near complete goat genome (ARS1) was used as reference to align all the SNPs to the right chromosomes and chromosome positions using R  (version 4.3.3) software. The final data set was saved as a VCF file for analysis.

乌干达本土山羊的特征分类依据为饲养其的族群、平均成年体重以及被毛特征。当前研究已基于Goat_IGGC_65K_v2 illumina基因芯片对乌干达本土山羊开展基因分型，以解析其种群结构与遗传特征。本研究产生的数据信息，对于乌干达山羊遗传资源的可持续利用、开发与保护具有重要意义。

## 研究方法
本研究的数据来源于从乌干达不同农业生态区的1032只本土山羊耳组织样本中提取的基因组DNA。本研究旨在解析乌干达不同农业生态区本土山羊的遗传多样性、种群结构以及选择信号。研究对象按照已知的表型/族群分类标准，划分为姆本德山羊（Mubende）、基格齐山羊（Kigezi）与小东非山羊（Small East African），覆盖全部10个农业生态区。每只山羊的耳组织样本均采用Allflex组织采样系统采集，该系统可实现无交叉污染，因为采集后的样本会自动锁入一次性采样管内。随后采用TANBEAD自动化DNA提取系统搭配6T2全组织DNA提取试剂盒，对每份样本进行基因组DNA提取。之后基于Goat_IGGC_65K_v2 illumina基因芯片对DNA样本完成基因分型。

## 数据处理
基因分型完成后，我们获得了1032个基因型样本对应的59725个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点数据，格式为PLINK格式。随后在Tassel 5.2版本软件中打开该数据，并另存为VCF格式以开展后续处理。我们以近乎完整的山羊参考基因组ARS1作为参照，利用R软件（版本4.3.3）将所有SNP位点比对至正确的染色体及对应染色体位置。最终数据集以VCF文件格式保存，用于后续分析。