Genome-wide diversity and demographic dynamics of Cameroon goats and their divergence from east African, north African, and Asian conspecifics

Abstract

Indigenous goats make significant contributions to Cameroon’s national and local economy, but little effort has been devoted to identifying the populations. Here, we assessed the genetic diversity and demographic dynamics of Cameroon goat populations using mitochondrial DNA (two populations) and autosomal markers (four populations) generated with the Caprine 50K SNP chip. To infer genetic relationships at continental and global level, genotype data on six goat populations from Ethiopia and one population each from Egypt, Morocco, Iran, and China were included in the analysis. The mtDNA analysis revealed 83 haplotypes, all belonging to haplogroup A, in Cameroon goats. Four haplotypes were shared between goats found in Cameroon, Mozambique, Namibia, Zimbabwe, Kenya, and Ethiopia. Analysis of autosomal SNPs in Cameroon goats revealed the lowest H O (0.335±0.13) and H E (0.352±0.15) in the North-west Highland and Central Highland populations, respectively. Overall, the highest H O (0.401±0.12) and H E (0.422±0.12) were found for Barki and Iranian goats, respectively. Barki goats had the highest average MAF, while Central Highland Cameroon goats had the lowest. Overall, Cameroon goats demonstrated high F IS . AMOVA revealed that 13.29% of the variation was explained by genetic differences between the six population groups. Low average F ST (0.01) suggests intermixing among Cameroon goats. All measures indicated that Cameroon goats are closer to Moroccan goats than to other goat populations. PCA and STRUCTURE analyses poorly differentiated the Cameroon goats, as did genetic distance, Neighbor-Net network, and neighbor-joining tree analyses. The haplotype analysis of mtDNA showed the initial dispersion of goats to Cameroon and central Africa from north-east Africa following the Nile Delta. Whereas, the approximate Bayesian computation indicated Cameroon goats were separated from Moroccan goats after 506 generations in later times (~1518 YA), as supported by the phylogenetic net-work and admixture outputs. Overall, indigenous goats in Cameroon show weak phylogenetic structure, suggesting either extensive intermixing.

Genetic diversity, population structure and kinship relationships highlight the environmental influence on Uganda’s indigenous goat populations

“…The observed and expected heterozygosity of more than 0.37 and the average genetic distance of 0.390 indicate that Uganda’s indigenous goats are genetically diverse. Similar values of heterozygosity were observed among indigenous goats in Ethiopia ( Tarekegn et al, 2021 ), Cameroon ( Tarekegn et al, 2019 ), China ( Berihulay et al, 2019 ), and Mongolia ( Mukhina et al, 2022 ). In addition, low and positive values of F IS and F ST obtained in this study indicate high heterozygosity and no deliberate inbreeding in the goat population, which limits the impact of deleterious alleles, inbreeding depression, and loss of variance ( Berihulay et al, 2019 ).…”

Haplotype analysis of the mitochondrial DNA d‐loop region reveals the maternal origin and historical dynamics among the indigenous goat populations in east and west of the Democratic Republic of Congo

“…Average haplotype diversity and nucleotide diversity of 0.987 ± 0.002 and 0.015 ± 0.003 respectively were obtained for the three populations with an average number of nucleotide differences of 14.740. This average haplotype diversity is similar to that of Kenyan goats (0.981; Kibegwa et al, 2016), lower than that of Cameroonian (0.995 ± 0.002; Tarekegn et al, 2019), Ethiopian (0.997 ± 0.001; Tarekegn et al, 2018), European (0.994), and Iberian (0.996) goats but higher than that of South and Central American (0.963; Amills et al, 2009) and Sicilian (ranged between 0.86 and 0.969; Sardina et al, 2006) goats. These results assume that the maternal genetic diversity of Congolese indigenous goats is not at risk of loss neither through extinction nor through genetic erosion.…”

“…It also permits the faster examination of the relatedness of populations and has become important in biogeographic and anthropologic studies (Lehman & Fleagle, 2006). The mtDNA polymorphism, especially the displacement loop (d-loop) region, is one of the important tools that have been used to better understand the genetic diversity, the population structure, and the population dynamics in different animal species including goats (Phyu et al, 2017;Tarekegn et al, 2018Tarekegn et al, , 2019, sheep (Agaviezor et al, 2012), and chickens (Liu et al, 2009).…”