Timing and Extent of Inbreeding in African Goats.

Autor:	Nandolo W; Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria.; Department of Animal Science, Faculty of Agriculture, Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi.; Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD, United States., Mészáros G; Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria., Banda LJ; Department of Animal Science, Faculty of Agriculture, Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi., Gondwe TN; Department of Animal Science, Faculty of Agriculture, Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi., Lamuno D; Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria., Mulindwa HA; National Livestock Resources Research Institute, Tororo, Uganda., Nakimbugwe HN; Department of Agriculture, Kyambogo University, Kyambogo, Uganda., Wurzinger M; Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria., Utsunomiya YT; School of Agricultural and Veterinarian Sciences, Jaboticabal, São Paulo State University (UNESP), São Paulo, Brazil., Woodward-Greene MJ; Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD, United States., Liu M; Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD, United States., Liu G; Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD, United States., Van Tassell CP; Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD, United States., Curik I; Department of Animal Science, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia., Rosen BD; Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD, United States., Sölkner J; Division of Livestock Sciences, Department of Sustainable Agricultural Systems, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria.
Jazyk:	angličtina
Zdroj:	Frontiers in genetics [Front Genet] 2019 Jun 04; Vol. 10, pp. 537. Date of Electronic Publication: 2019 Jun 04 (Print Publication: 2019).
DOI:	10.3389/fgene.2019.00537
Abstrakt:	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 (F G ) 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 (F ROH ) and for ROH longer than 2 Mb (F ROH > 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 F ROH , F ROH > 2Mb , and F G , 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.
Databáze:	MEDLINE
Externí odkaz:	Zobrazit plný text záznamu