10.5061/DRYAD.QNK98SFM9
Babigumira, Brian Martin
0000-0001-8626-2658
National Agricultural Research Organisation
Sölkner, Johann
University of Natural Resources and Life Sciences
Mészáros, Gábor
University of Natural Resources and Life Sciences
Pfeiffer, Christina
Pig Austria
Lewis, Craig R. G.
Pig Improvement Company
Ouma, Emily Awuor
International Livestock Research Institute
Wurzinger, Maria
University of Natural Resources and Life Sciences
Marshall, Karen
International Livestock Research Institute
Data from: A mix of old British and modern European breeds: Genomic
prediction of breed composition of smallholder pigs in Uganda
Dryad
dataset
2022
FOS: Agricultural sciences
admixture
breed
Agricultural sciences: genomics
Sus scrofa domesticus
smallholder farmers
Uganda
Austrian Development Agency
https://ror.org/0472ppj97
CGIAR
https://ror.org/04c4bm785
2022-12-19T00:00:00Z
2022-12-19T00:00:00Z
en
https://doi.org/10.3389/fgene.2021.676047
4828530 bytes
3
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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