A Mix of Old British and Modern European Breeds: Genomic Prediction of Breed Composition of Smallholder Pigs in Uganda.

Brian Martin Babigumira,Johann Sölkner,Karen Marshall,Maria Wurzinger,Gábor Mészáros,Christina Pfeiffer,Craig R G Lewis,Emily Ouma

doi:10.3389/fgene.2021.676047

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.

Highlights

The pig (Sus scrofa domesticus), an even toed ungulate and a member of the genus Sus, was domesticated from its ancestor, the wild boar (Sus scrofa scrofa) in multiple domestication centers including the Near East, Europe, China and South-east Asia, about 9,000 years ago (Rothschild and Ruvinsky, 2011; Groenen et al, 2012)
The panel of ancestral breeds narrowed down to those potentially interesting based on their ancestry contribution in the Uganda pigs
Smallholder pig production in Uganda is constrained by several factors, mostly related to pig health, nutrition and genetics (Ouma et al, 2015)

Summary

Introduction

The pig (Sus scrofa domesticus), an even toed ungulate and a member of the genus Sus, was domesticated from its ancestor, the wild boar (Sus scrofa scrofa) in multiple domestication centers including the Near East, Europe, China and South-east Asia, about 9,000 years ago (Rothschild and Ruvinsky, 2011; Groenen et al, 2012). The pig has been genetically improved into several specialized breeds through traditional and marker assisted selective breeding. The Landrace breed originated from British foundation stock imported to Denmark and selected for leanness and fast growth. Commercial breeds such as the Large White, Berkshire, and Hampshire were developed from crossbreeding old British and Asian pigs (White, 2011; Amills et al, 2013). Sub-Saharan Africa is not within the native range of wild boar and no archeological or genetic evidence points to a domestications event there (Ramirez et al, 2009). Indian Ocean trade and eventual European settlement have been associated with the introduction of Asian and European pig breeds to East Africa (Boivin et al, 2013)

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