Genome-Wide Characterization of Selection Signatures and Runs of Homozygosity in Ugandan Goat Breeds

Abstract

Both natural and artificial selection are among the main driving forces shaping genetic variation across the genome of livestock species. Selection typically leaves signatures in the genome, which are often characterized by high genetic differentiation across breeds and/or a strong reduction in genetic diversity in regions associated with traits under intense selection pressure. In this study, we evaluated selection signatures and genomic inbreeding coefficients, FROH, based on runs of homozygosity (ROH), in six Ugandan goat breeds: Boer (n = 13), and the indigenous breeds Karamojong (n = 15), Kigezi (n = 29), Mubende (n = 29), Small East African (n = 29), and Sebei (n = 29). After genotyping quality control, 45,294 autosomal single nucleotide polymorphisms (SNPs) remained for further analyses. A total of 394 and 6 breed-specific putative selection signatures were identified across all breeds, based on marker-specific fixation index (FST-values) and haplotype differentiation (hapFLK), respectively. These regions were enriched with genes involved in signaling pathways associated directly or indirectly with environmental adaptation, such as immune response (e.g., IL10RB and IL23A), growth and fatty acid composition (e.g., FGF9 and IGF1), and thermo-tolerance (e.g., MTOR and MAPK3). The study revealed little overlap between breeds in genomic regions under selection and generally did not display the typical classic selection signatures as expected due to the complex nature of the traits. In the Boer breed, candidate genes associated with production traits, such as body size and growth (e.g., GJB2 and GJA3) were also identified. Furthermore, analysis of ROH in indigenous goat breeds showed very low levels of genomic inbreeding (with the mean FROH per breed ranging from 0.8% to 2.4%), as compared to higher inbreeding in Boer (mean FROH = 13.8%). Short ROH were more frequent than long ROH, except in Karamojong, providing insight in the developmental history of these goat breeds. This study provides insights into the effects of long-term selection in Boer and indigenous Ugandan goat breeds, which are relevant for implementation of breeding programs and conservation of genetic resources, as well as their sustainable use and management.

Conservation Status and Historical Relatedness of South African Communal Indigenous Goat Populations Using Genome-Wide Snp Marker

“…In this study, differences in terms of total number and length of ROH were short (>5Mb) were more abundant (57.61%). [48] reported results that showed lower than the F ROH > 2Mb for Kenya, Uganda, and Mozambique goat breeds when Goat 50K BeadChip was used. On the other hand, the Eastern Cape population showed very low amounts of ROH.…”

“…The Illumina goat SNP50K BeadChip includes 53 347 SNPs [59] that have found utility in South African population genetic studies in Angora [27], commercial, indigenous and village goat populations [37] as well as investigate genetic adaptation to environmental pressures [36]. The use of the tool has been described in other African countries [48,65] and in specialised breeds [32]. While much work on South African commercial, indigenous and village goat populations has focused on genetic studies and investigation on genetic adaptation, less work has focused on conservation status and historical relatedness of communal indigenous goat populations.…”

“…An increase in inbreeding (F) over generations leads to a reduction in genetic diversity [48]. Higher frequency of homozygous genotypes for deleterious alleles with a reduction in individual performance (inbreeding depression) and lower population viability [49].…”

Genome-Wide Association Study and Fine Mapping Reveals Candidate Genes for Birth Weight of Yorkshire and Landrace Pigs

“…Previous knock-out results have shown that Vav3deficient mice were protected from bone loss induced by systemic bone resorption stimuli such as parathyroid hormone or RANKL (Faccio et al, 2005). Furthermore, VAV3 is associated with hypothyroidism in humans, food conversion ratio in a male Duroc pig population, high body weight and growth rate in Boer goats, as well as sperm concentration in Holstein-Friesian bulls (Hering et al, 2014;Kwak et al, 2014;Wang et al, 2015;Onzima et al, 2018).…”

Estimates of autozygosity through runs of homozygosity in farmed coho salmon

“…For both POP A and B 284 it was possible to identify short and long segments in most of the animals analyzed, whereas 285 in the POP C a small number of animals (n = 7) presented ROH8-16 Mb and none ROH>16 Mb. 286 In recent years, some studies have investigated different genomic methods to estimate 287 inbreeding coefficients in cattle [12,25,26,45,47,48], pigs [27,28,49,50], goats [51][52][53] and 288 rainbow trout [32]. However, this is the first study aimed at characterizing the ROH patterns 289 and comparing different genomic-and pedigree-based methods to estimate inbreeding 290 coefficients in farmed coho salmon populations.…”