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. 2021 Jun 23:12:676047.
doi: 10.3389/fgene.2021.676047. eCollection 2021.

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

Brian Martin Babigumira  1   2 , Johann Sölkner  1 , Gábor Mészáros  1 , Christina Pfeiffer  1   3 , Craig R G Lewis  4 , Emily Ouma  2 , Maria Wurzinger  1 , Karen Marshall  5
Affiliations

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

Brian Martin Babigumira et al. Front Genet. .

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.

Keywords: SNP; Uganda; admixture; breed; diversity; genomic; pig.

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Conflict of interest statement

CP was employed by company PIG Austria GmbH. CL was employed by company Pig Improvement Company. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Geographical location of sampling sites. (A) Map of Africa showing the location of Uganda. (B) Map of Uganda showing the location of Hoima, Kamuli, Pallisa, Kumi, and Soroti districts. (C) Map of Hoima showing the locations of Busiisi, Kitoba, and Kizaranfumbi sub-counties. (D) Map of Kamuli showing the locations of Butansi, Mbulamuti, Namasagali, Namwendwa, and Wankole sub-counties. The black dots in panels (C) and (D) show the sampling locations.
FIGURE 2
FIGURE 2
Photographs of pigs of different breed or cross-breed types in Uganda. (A) A local sow with her litter (B) an exotic breed e.g., Camborough® sow with her litter (C) a spotted pig that could be old British (Gloucestershire) or a cross of exotic breeds (Landrace and/or Large White) (D) a local pig (E) a belted pig that could be a British Saddleback cross and (F) two red coated pigs that could be Duroc or Tamworth. Photo credit: Babigumira Brian Martin/ILRI/BOKU.
FIGURE 3
FIGURE 3
Multidimensional Scaling analysis of Uganda pigs in a global context. CMB: Camborough®; Great Britain; CNJH: Jinhua; CNLH: Laihuwei, CNLT Lantang; CNMS: Meishan-China; DEAS Angler Sattelschwein-Germany; DEBB Bunte Bentheimer-Germany; DRZ: Duroc-South Africa; DUR1: Duroc-United States; EE: Entrepelado; ER-Spain: Entrepelado × Retinto cross-Spain; HOI: Hoima-Uganda; ITCT: Casertana-Italy; ITNS: Nera Siciliana-Italy; KAM: Kamuli-Uganda; KUM: Kumi-Uganda; LDR1: Landrace-Denmark; LRA: Landrace-Austria; LRZ: Landrace-South Africa; LWA: Large White-Austria; LWT1: Large White-Denmark; LWZ: Large White-South Africa; PAL: Pallisa-Uganda; PIT2: Pietrain-German; PIT3: Pietrain-Netherlands; RE: Retinto x Entrepelado cross-Spain; RR: Retinto-Spain; RUBR: Breitov-Russia; RULV: Livni-Russia; RUMR: Murom-Russia; SOR: Soroti-Uganda; UKBK: Berkshire-Great Britain; SB: Saddleback-Great Britain; UKGO: Gloucestershire-Great Britain; UKHS: Hampshire-Great Britain; LB: Large Black-Great Britain; UKLE: Leicester-Great Britain; UKMW: Middle White-Great Britain; UKTA: Tamworth-Great Britain; UKWE: Welsh-Great Britain; USBK: Berkshire-United Sates of America; USHS: Hampshire-United Sates of America.
FIGURE 4
FIGURE 4
Multidimensional scaling analysis of Camborough® (CMB); Meishan (MS); Duroc (DRC); Uganda [Hoima (HOI), Kamuli (KAM), and Local (LOC)]; Landrace (LR); Large White (LW); Iberian (IB); Saddleback (SB); and Large Black (LB). The first Eigen vector separates the MS and IB from the rest of the population. The second eigenvector closely clusters LW and Uganda pigs and separates them from the rest.
FIGURE 5
FIGURE 5
Admixture analysis. (A) Ancestry pig populations for K = 6: the modern European consists of Large white (LW; sky blue), Landrace (LR; red) and Camborough® (CMB; nearly half sky blue/red). The old British breeds (SB: Saddleback: and LB: Large Black) share ancestries with the Iberian (IB), modern European and local Ugandan pigs (LOC). (B) The Uganda pigs Hoima (HOI) and Kamuli (KAM) have a dominant blue ancestry that we refer to as “local” shared with the old British breeds. The modern European breeds contribute most of the exotic ancestry.
FIGURE 6
FIGURE 6
Proportions contributed by surrogate populations to the minor and major sources of admixture for (A) Kamuli (KAM) and (B) Hoima (HOI) pigs. The surrogate populations are: Meishan (MS); Duroc (DRC); Iberian (IB); Large Black (LB); Saddleback (SB); local Ugandan (LOC); Large White (LW); Landrace (LR); and Camborough® (CMB). The numbers in brackets are the proportions each source contributes to the admixture in the target (recipient) population and they sum up to one. The numbers on top of the bars are the contributions of each surrogate population within each source and they sum up to one.
FIGURE 7
FIGURE 7
Analysis of autozygosity states. (A) Number of ROH distributed and along cumulative total ROH length on the pig genome in ROH. (B) Boxplot ofFROH cutoffs of 2, 4, 8, and 16 Mb for smallholder pigs from Hoima and Kamuli districts in Uganda.
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