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Timing and Extent of Inbreeding in African Goats

Timing and Extent of Inbreeding in African Goats

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dc.contributor.author Wilson Nandolo
dc.contributor.author Gábor Mészáros
dc.contributor.author Liveness Jessica Banda
dc.contributor.author Timothy N. Gondwe
dc.contributor.author Doreen Lamuno
dc.contributor.author H. Mulindwa
dc.contributor.author Helen Nakimbugwe
dc.contributor.author Maria Wurzinger
dc.contributor.author Yuri T. Utsunomiya
dc.contributor.author M. Jennifer Woodward-Greene
dc.contributor.author Mei Liu
dc.contributor.author George E. Liu
dc.contributor.author Curtis P. Van Tassell
dc.contributor.author Ino Curik
dc.contributor.author Benjamin D. Rosen
dc.contributor.author Johann Sölkner
dc.date.accessioned 2021-01-10T11:55:39Z
dc.date.available 2021-01-10T11:55:39Z
dc.date.issued 2019
dc.identifier.issn 16648021
dc.identifier.uri https://combine.alvar.ug/handle/1/49064
dc.description.abstract Genetic characterization of African goats is one of the current priorities in the improvement of goats in the continent. This study contributes to the characterization effort by determining the levels and number of generations to common ancestors (“age”) associated with inbreeding in African goat breeds and identifies regions that contain copy number variation mistyped as being homozygous. Illumina 50k single nucleotide polymorphism (SNP) genotype data for 608 goats from 31 breeds were used to compute the level and age of inbreeding at both local (marker) and global levels (FG) using a model-based approach based on a hidden Markov model (HMM). Runs of homozygosity (ROH) segments detected using the Viterbi algorithm led to ROH-based inbreeding coefficients for all ROH (FROH) and for ROH longer than 2 Mb (FROH>2Mb). Some of the genomic regions identified as having ROH are likely to be hemizygous regions (copy number deletions) mistyped as homozygous regions. Although the proportion of these miscalled ROH is small and does not substantially affect estimates of levels of inbreeding for individual animals, the inbreeding metrics were adjusted by removing these regions from the ROH. All the inbreeding metrics varied widely across breeds, with overall means of 0.0408, 0.0370, and 0.0691 and medians of 0.0125, 0.0098, and 0.0366 for FROH, FROH>2Mb and FG, respectively. Several breeds (including Menabe and Sofia from Madagascar) had high proportions of recent inbreeding, while Small East African, Ethiopian, and most of the West African breeds (including West African Dwarf) had more ancient inbreeding.
dc.description.sponsorship United States Agency for International Development
dc.publisher Frontiers Media S.A.
dc.relation.ispartof Frontiers in genetics
dc.subject Africa
dc.subject age-based inbreeding
dc.subject copy number variation
dc.subject goats
dc.subject inbreeding
dc.subject local inbreeding
dc.subject runs of homozygosity
dc.title Timing and Extent of Inbreeding in African Goats
dc.type journal article
dc.identifier.doi 10.3389/fgene.2019.00537
dc.identifier.pmid 31214253
dc.identifier.mag 2949037332
dc.identifier.pmc PMC6558083
dc.identifier.lens 032-075-081-575-41X
dc.identifier.volume 10
dc.identifier.spage 537
dc.subject.lens-fields Copy-number variation
dc.subject.lens-fields Genotype
dc.subject.lens-fields SNP
dc.subject.lens-fields Single-nucleotide polymorphism
dc.subject.lens-fields Runs of Homozygosity
dc.subject.lens-fields Inbreeding
dc.subject.lens-fields West african
dc.subject.lens-fields Evolutionary biology
dc.subject.lens-fields Biology


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