Timing and extent of inbreeding in African goats

Authors: NANDOLO, WILSON - University Of Natural Resources & Applied Life Sciences - Austria; MESZAROS, GABOR - University Of Natural Resources & Applied Life Sciences - Austria; BANDA, LIVENESS - Lilongwe University Of Agriculture And Natural Resources; GONDWE, TIMOTHY - Lilongwe University Of Agriculture And Natural Resources; LAMUNO, DOREEN - National Livestock Research Institute; MULINDWA, HENRY - National Livestock Research Institute; NAKIMBUGWE, HELEN - Collaborator; WURZINGER, MARIA - University Of Natural Resources & Applied Life Sciences - Austria; UTSUNOMIYA, YURI - Sao Paulo State University (UNESP); Woodward-Greene, Jennifer; LIU, MEI - Northwest Agricultural & Forestry University; Liu, Ge - George; Van Tassell, Curtis - Curt; CURIK, INO - University Of Zagreb; Rosen, Benjamin - Ben; SOLKNER, JOHANN - University Of Natural Resources & Applied Life Sciences - Austria

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/17/2019
Publication Date: 6/4/2019
Citation: Nandolo, W., Meszaros, G., Banda, L.J., Gondwe, T.N., Lamuno, D., Mulindwa, H., Nakimbugwe, H.N., Wurzinger, M., Utsunomiya, Y.T., Woodward Greene, M.J., Liu, M., Liu, G., Van Tassell, C.P., Curik, I., Rosen, B.D., Solkner, J. 2019. Timing and extent of inbreeding in African goats. Frontiers in Genetics. 10:57. https://doi.org/10.3389/fgene.2019.00537.
DOI: https://doi.org/10.3389/fgene.2019.00537

Interpretive Summary: Goats are critical to small-holder farmers in Africa and genetic characterization of goat populations is a current priority on the continent. Our study clarifies the levels and age of inbreeding in goat breeds across Sub-Saharan Africa. Using Illumina 50k SNP data for 608 goats representing 31 breeds from 11 countries, runs of homozygosity (ROH) regions were adjusted for copy number deletions (hemizygous regions) providing more accurate ROH-based inbreeding coefficients. Contrary to expectation, many African goat breeds have low levels of inbreeding with some retaining large proportions of homozygous-by-descent genome segments dating back to the beginning of domestication. This comprehensive report has practical applications for the management and improvement of goat populations through the avoidance of inbreeding depression.

Technical 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 0.691 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.