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

Cite this dataset

Babigumira, Brian Martin et al. (2023). Data from: A mix of old British and modern European breeds: Genomic prediction of breed composition of smallholder pigs in Uganda [Dataset]. Dryad. https://doi.org/10.5061/dryad.qnk98sfm9

Abstract

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.

Methods

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.

Usage notes

The files can be accessed with any zip/unzip program and processed with PLINK and other software

Funding

Austrian Development Agency

CGIAR