Data from: A mix of old British and modern European breeds: Genomic prediction of breed composition of smallholder pigs in Uganda

Pig herds in Africa comprise genotypes ranging from local ecotypes to commercial breeds. Many animals are composites of these two types and the best levels of crossbreeding for particular production systems are largely unknown. These pigs are managed without structured breeding programs and inbreeding is potentially limiting. The objective of this study was to quantify ancestry contributions and inbreeding levels in a population of smallholder pigs in Uganda. The study was set in the districts of Hoima and Kamuli in Uganda and involved 422 pigs. Pig hair samples were taken from adult and growing pigs in the framework of a longitudinal study investigating productivity and profitability of smallholder pig production. The samples were genotyped using the porcine GeneSeek Genomic Profiler (GGP) 50K SNP Chip. The SNP data was analyzed to infer breed ancestry and autozygosity of the Uganda pigs. The results showed that exotic breeds (modern European and old British) contributed an average of ..., A sample of 422 pigs from the five districts in Uganda: Hoima (n = 163) Kamuli (n = 218), Kumi (n = 11), Pallisa (n = 12), and Soroti (n = 18) were involved in the study. A total of 41 animals, showing the characteristics of African pigs according to Blench (2000), were sampled from 41 households having been reported to keep local Uganda pigs by extension staff in the latter three districts. Prevalence of pigs with black coat color, long snout, short legs and popped ears, facing up and backward were criteria of selection of households keeping local pigs. Hair samples taken from the 422 pigs were genotyped using the Neogen GeneSeek Genomic Profiler (GGP) Porcine 50K array (Neogen Europe). The dataset is not qaulity controlled for both animals and SNPs., The files can be accessed with any zip/unzip program and processed with PLINK and other software

非洲猪群的基因型涵盖从地方生态型（local ecotypes）到商业品种的各类类群。多数个体为这两类的复合种群，而适配特定生产系统的最优杂交水平目前仍未明确。此类猪仅在缺乏结构化育种计划的模式下开展管理，近交问题或已成为潜在限制因素。
本研究旨在量化乌干达小农猪种群的血统贡献与近交水平。研究选址于乌干达Hoima与Kamuli两区，共纳入422头猪。样本采集自成年与育肥猪，隶属于一项探究小农生猪生产的生产力与盈利性的纵向研究框架。研究采用猪用GeneSeek基因组分型（GeneSeek Genomic Profiler, GGP）50K单核苷酸多态性（Single Nucleotide Polymorphism, SNP）芯片对样本进行基因分型，通过SNP数据解析乌干达猪群的品种血统与同源纯合性。
研究结果显示，外来品种（现代欧洲品种与古老英国品种）的平均贡献占比为……
本研究实际纳入乌干达五个县区的422头猪：Hoima区（n=163）、Kamuli区（n=218）、Kumi区（n=11）、Pallisa区（n=12）及Soroti区（n=18）。其中后三个县区的畜牧推广人员曾报告当地农户饲养乌干达地方猪，我们从41户此类农户中选取了41头符合Blench（2000）所述非洲猪特征的个体，选留标准为被毛黑色、吻部修长、四肢短小、耳向上后翻。
研究团队使用Neogen旗下GeneSeek猪用基因组分型50K芯片（Neogen Europe），对422头猪的毛发样本完成基因分型。
本数据集未针对个体与SNP进行质量控制。
相关文件可通过任意解压软件获取，并可使用PLINK及其他软件进行处理