Babigumira Brian Martin, Sölkner Johann, Mészáros Gábor, Pfeiffer Christina, Lewis Craig R G, Ouma Emily, Wurzinger Maria, Marshall Karen
Department of Sustainable Agricultural Systems, Division of Livestock Sciences, University of Natural Resources and Life Sciences, Vienna, Austria.
International Livestock Research Institute, Kampala, Uganda.
Front Genet. 2021 Jun 23;12:676047. doi: 10.3389/fgene.2021.676047. eCollection 2021.
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 22.8% with a range of 2-50% while "local" blood contributed 69.2% (36.9-95.2%) to the ancestry of the pigs. Runs of homozygosity (ROH) greater than 2 megabase (Mb) quantified the average genomic inbreeding coefficient of the pigs as 0.043. The scarcity of long ROH indicated low recent inbreeding. We conclude that the genomic background of the pig population in the study is a mix of old British and modern pig ancestries. Best levels of admixture for smallholder pigs are yet to be determined, by linking genotypes and phenotypic records.
非洲的猪群包含从本地生态型到商业品种的各种基因型。许多猪是这两种类型的混合体，而针对特定生产系统的最佳杂交水平在很大程度上尚不清楚。这些猪的管理没有结构化的育种计划，近亲繁殖可能会产生限制。本研究的目的是量化乌干达小农户猪群的祖先贡献和近亲繁殖水平。该研究在乌干达的霍伊马区和卡穆利区开展，涉及422头猪。在一项调查小农户养猪生产力和盈利能力的纵向研究框架下，采集了成年猪和生长猪的毛发样本。使用猪基因探索基因组分析器（GGP）50K单核苷酸多态性（SNP）芯片对样本进行基因分型。对SNP数据进行分析，以推断乌干达猪的品种血统和纯合性。结果表明，外来品种（现代欧洲品种和古老英国品种）平均贡献了22.8%，范围在2%-50%之间，而“本地”血统对猪的血统贡献为69.2%（36.9%-95.2%）。大于2兆碱基（Mb）的纯合子片段（ROH）将猪的平均基因组近亲繁殖系数量化为0.043。长ROH的稀缺表明近期近亲繁殖程度较低。我们得出结论，该研究中猪群的基因组背景是古老英国猪和现代猪祖先的混合。通过将基因型与表型记录联系起来，小农户猪的最佳杂交水平还有待确定。
