TY - JOUR
T1 - Genome-wide diversity and demographic dynamics of Cameroon goats and their divergence from east African, north African, and Asian conspecifics
AU - Tarekegn, Getinet Mekuriaw
AU - Wouobeng, Patrick
AU - Jaures, Kouam Simo
AU - Mrode, Raphael
AU - Edea, Zewdu
AU - Liu, Bin
AU - Zhang, Wenguang
AU - Mwai, Okeyo Ally
AU - Dessie, Tadelle
AU - Tesfaye, Kassahun
AU - Strandberg, Erling
AU - Berglund, Britt
AU - Mutai, Collins
AU - Osama, Sarah
AU - Wolde, Asaminew Tassew
AU - Birungi, Josephine
AU - Djikeng, Appolinaire
AU - Meutchieye, Félix
PY - 2019/4/1
Y1 - 2019/4/1
N2 - 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 HO (0.335 ±0.13) and HE (0.352±0.15) in the North-west Highland and Central Highland populations, respectively. Overall, the highest HO (0.401±0.12) and HE (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 FIS. AMOVA revealed that 13.29% of the variation was explained by genetic differences between the six population groups. Low average FST (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-joiningtree 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.
AB - 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 HO (0.335 ±0.13) and HE (0.352±0.15) in the North-west Highland and Central Highland populations, respectively. Overall, the highest HO (0.401±0.12) and HE (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 FIS. AMOVA revealed that 13.29% of the variation was explained by genetic differences between the six population groups. Low average FST (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-joiningtree 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.
UR - http://www.scopus.com/inward/record.url?scp=85064735910&partnerID=8YFLogxK
U2 - 10.1371/journal.pone.0214843
DO - 10.1371/journal.pone.0214843
M3 - Article
C2 - 31002664
AN - SCOPUS:85064735910
SN - 1932-6203
VL - 14
JO - PLoS ONE
JF - PLoS ONE
IS - 4
M1 - e0214843
ER -