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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Genet. | doi: 10.3389/fgene.2019.00537

Timing and extent of inbreeding in African goats

  • 1Department of Sustainable Agricultural Systems, Division of Livestock Sciences, BOKU-University of Natural Resources and Life Sciences Vienna, Austria
  • 2Lilongwe university of Agriculture and Natural Resources, Malawi
  • 3National Livestock Resources Research Institute, Uganda
  • 4Kyambogo University, Uganda
  • 5Department of Preventive Veterinary Medicine and Animal Health, Faculty of Veterinary Medicine and Animal Science, University of Sao Paulo, Brazil
  • 6Animal Genomics and Improvement Laboratory (USDA-ARS), United States
  • 7Department of Animal Science and Technology, Faculty of Agriculture, University of Zagreb, Croatia

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.

Keywords: Inbreeding, Runs of homozigosity, local inbreeding, Age-based inbreeding, Goats, Africa, Copy Number Variation - CNV

Received: 31 Oct 2018; Accepted: 17 May 2019.

Edited by:

Luis Varona, University of Zaragoza, Spain

Reviewed by:

Christine Flury, Bern University of Applied Sciences, Switzerland
Mirte Bosse, Wageningen University & Research, Netherlands  

Copyright: © 2019 Nandolo, Mészáros, Banda, Gondwe, Lamuno, Mulindwa, Nakimbugwe, Wurzinger, Utsunomiya, Woodward-Greene, Liu, Liu, Van Tassell, Curik, Rosen and Sölkner. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Benjamin D. Rosen, Animal Genomics and Improvement Laboratory (USDA-ARS), Beltsville, United States,