Runs Of Homozygosity and Effective Population Size from Different Goat Genotypes in Kenya

Analysis of ROHs and Ne in Kenyan Goat Genotypes

Abstract

Limited genetic information in most goat populations hinders the implementation of better breeding strategies for genetic conservation and improvement. Runs of Homozygosity (ROH) were used to analyse the distribution, inbreeding coefficients and effective population size (Ne) of different goat genotypes in Kenya. This was performed from 48808 Single Nucleotide Polymorphism (SNP) that were detected for analysis after quality control. The SNP data of four goat genotypes were used; Galla (n = 12), Alpine (n = 28), Saanen (n = 24) and Toggenburg (n = 30). Across the genotypes, 348 ROHs were detected with the highest number (180) observed in Toggenburg and lowest (22) in Galla. From the ROH length categories, the highest mean length was observed on the long ROHs category (>16 Mb) suggesting a recent inbreeding. The distribution of ROHs per chromosome was breed-specific without a clear pattern across the genotypes. Furthermore, 32 genomic regions with a high frequency of ROHs were detected. Sixteen genes (missense and synonymous) associated with various phenotypic functions were identified. High inbreeding coefficient values of > 0.1 were observed in all exotic genotypes suggesting continuous use of few breeding bucks. Toggenburg was found to be the most inbred genotype with the highest inbreeding coefficient of 0.68. The effective population size decreased over time across the genotypes. Galla, Saanen and Toggenburg at recent generation (13genAgo) recorded Ne of less than the recommended threshold (Ne = 100) population indicating a limited genetic diversity. The study outcome emphasize the need to use different lines of exotic goats, improved technologies, and/or sustainable implementation of controlled breeding programs.