Timing and Extent of Inbreeding in African Goats

Autor: Yuri Tani Utsunomiya, Johann Sölkner, Ino Curik, Gábor Mészáros, M. Jennifer Woodward-Greene, Doreen Lamuno, Liveness Jessica Banda, Helen Nakimbugwe, George E. Liu, Henry Mulindwa, Timothy N. Gondwe, Benjamin D. Rosen, Mei Liu, Maria Wurzinger, Curtis P. Van Tassell, Wilson Nandolo
Přispěvatelé: University of Natural Resources and Life Sciences, Lilongwe University of Agriculture and Natural Resources, Agriculture Research Service, National Livestock Resources Research Institute, Kyambogo University, Universidade Estadual Paulista (Unesp), University of Zagreb
Jazyk: angličtina
Rok vydání: 2019
Předmět:
Zdroj: Frontiers in Genetics, Vol 10 (2019)
Frontiers in Genetics
Scopus
Repositório Institucional da UNESP
Universidade Estadual Paulista (UNESP)
instacron:UNESP
ISSN: 1664-8021
DOI: 10.3389/fgene.2019.00537
Popis: Made available in DSpace on 2019-10-06T15:49:50Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-01-01 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 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. 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. Division of Livestock Sciences Department of Sustainable Agricultural Systems University of Natural Resources and Life Sciences Department of Animal Science Faculty of Agriculture Lilongwe University of Agriculture and Natural Resources Animal Genomics and Improvement Laboratory United States Department of Agriculture Agriculture Research Service National Livestock Resources Research Institute Department of Agriculture Kyambogo University School of Agricultural and Veterinarian Sciences Jaboticabal São Paulo State University (UNESP) Department of Animal Science Faculty of Agriculture University of Zagreb School of Agricultural and Veterinarian Sciences Jaboticabal São Paulo State University (UNESP)
Databáze: OpenAIRE
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