Estimation of inbreeding in Ethiopia goats using runs of homozygosity

Abstract

Received: 2016-07-14 | Accepted: 2016-07-28 | Available online: 2017-03-31 http://dx.doi.org/10.15414/afz.2017.20.01.10–12 This study was carried out to estimate the inbreeding levels in Abergelle, Gumuz, Keffa and Woytoguji goats in Ethiopia from genomic information. A total of 161 animals (53 Abergelle, 39 Gumuz, 31 Keffa and 38 Woytoguji) were genotyped using the Illumina 50K SNP chip. Runs of homozygosity were computed at cut-offs of 1MB, 2MB, 4MB, 8MB and 16MB, using cgaTOH Analysis & Clustering Suite, Version 1.0.1. The estimated levels of inbreeding based on runs of homozygosity greater than 1MB were 0.0210, 0.0209, 0.0502 and 0.0199 for Abergelle, Gumuz, Keffa and Woytoguji, respectively. The results suggest that inbreeding levels are low in the four breeds, although relatively higher in the Keffa breed than in the other three breeds. Suitable strategies may need to be implemented for reducing inbreeding when designing breeding programmes for the Keffa goats. This study was carried out to estimate the inbreeding levels in Abergelle, Gumuz, Keffa and Woytoguji goats in Ethiopia from genomic information. A total of 161 animals (53 Abergelle, 39 Gumuz, 31 Keffa and 38 Woytoguji) were genotyped using the Illumina 50K SNP chip. Runs of homozygosity were computed at cut-offs of 1MB, 2MB, 4MB, 8MB and 16MB, using cgaTOH Analysis & Clustering Suite, Version 1.0.1. The estimated levels of inbreeding based on runs of homozygosity greater than 1MB were 0.0210, 0.0209, 0.0502 and 0.0199 for Abergelle, Gumuz, Keffa and Woytoguji, respectively. The results suggest that inbreeding levels are low in the four breeds, although relatively higher in the Keffa breed than in the other three breeds. Suitable strategies may need to be implemented for reducing inbreeding when designing breeding programmes for the Keffa goats. Keywords: goats, genome, inbreeding, runs of homozygosity References FALCONER, D.S. and MACKAY, T.F.C. (1996) Introduction to quantitative genetics . 4th ed. London: Longman FERENCAKOVIC, M., et al. (2011) Runs of Homozygosity Reveal Genome-wide Autozygosity in the Austrian Fleckvieh Cattle. Agriculturae Conspectus Scientificus, vol . 76, pp. 325–329. FERENCAKOVIC, et al.(2013) Estimates of autozygosity derived from runs of homozygosity: Empirical evidence from selected cattle populations. Journal of Animal Breeding and Genetics , vol. 130, pp. 286–293. doi: http://dx.doi.org/10.1111/jbg.12012 PURCELL, S., et al. (2007) PLINK: A tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics , vol. 81, pp. 559–575. doi: http://dx.doi.org/10.1086/519795 PURFIELD, D.C., et al. (2012) Runs of homozygosity and population history in cattle. BMC Genetics , vol. 13, no. 70. 1 p. doi: http://dx.doi.org/0.1186/1471-2156-13-70 TEFERA, M. (2013) Atlas biogeography and biodiversity of indigenous wild mammals of Ethiopia . Alemaya: Haramaya University. ZHANG, L., et al. (2013) cgaTOH: Extended Approach for Identifying Tracts of Homozygosity. PLoS One, vol. 8, no. 1. doi: http://dx.doi.org/0.1371/journal.pone.0057772