Molecular Characterization of Ethiopian Indigenous Goat Populations: Genetic Diversity and Structure, Demogrphic Dynamics And Assessment of the Kisspeptin Gene Polymorphism
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Date
2016-06
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Addis Ababa Universty
Abstract
Ethiopia lies within the earliest geographic center for the dispersal of livestock into the African
continent. It therefore comprises a unique repository of livestock genetic diversity in the
continent. However, information relating to the origin and divergence of domestic goats in the
NOIth-East African region, and Ethiopia in particular, remains unknown despite the availability
of genomic tools to assess the same. Here, the complete mitochondrial DNA D-loop region of
309 individuals representing \3 Ethiopian indigenous populations of goats was sequenced to
investigate the maternal historical demographic dynamics of Ethiopian indigenous goats,
Similarly, genotype data were generated from 14 populations by the 50K Caprine SNP CHIP
array to investigate the genetic diversity and structure of Ethiopian indigenous goats, The
Chinese Cashmere, Cashmere-Ibex hybrid and the wild Swiss Alpine Ibex populations were also
included as outgroup for comparison, In addition, analysis of polymorphism of the KISS I gene
and its association with litter size, and haplotype and patterns of linkage disequilibrium (LD)
analysis were conducted in exon regions of the kisspeptin gene of Gondar and Woyto-Guji goat
populations. A total of 173 and 242 Sanger sequences were employed for further analysis of
exonl (1210 bp) and exon2 (325 bp) regions of the kisspeptin gene, respectively, Sequencing of
the mtDNA, 174 variable sites that generated 231 haplotypes were observed in the D-loop region
of mtDNA sequences and these haplotypes defined two haplogroups lacking a phylogeographic structure but with a high genetic diversity. In a combined analysis of reference haplotypes
representing the six globally defined Caprine haplogroups revealed out two haplogroups to be A
and G, with the former being the most predominant. The lack of phylogeographic structure and a
weak population differentiation (overall PST = 0.0245) suggest extensive gene flow amongst
indigenous Ethiopian goats. In the gcnome wide survey, high genetic diversity (HE :0: 0.35) but
low level of genetic differcntiation among the populations is revealed. Thc 14 populations were
grouped into six clusters and none of them was spccific to one population or geographic region.
Interestingly, population phylogenetic analysis did not support the classification of Ethiopian
goats based on their agro-ecological location, associated production system and phenotypic
family as suggested previously, but differentiated the Kaffa goat from the rest of 13 Ethiopian
goat populations. Based on the admixture and phylogenetic network analyses, the 14 Ethiopian
goat populations can be re-grouped into seven goat types. On the other hand, polymorphism
analysis of the KISS I gene revealed five complete substitutions and 15 polymorphic sites in both
exon regions. The overall average HE was 0.18863±0.21 for exonl and 0.031 55±0.0 I for exon2.
Among detected polymorphic sites only four SNPs contributed 18%-31 % multiple birth.
Similarly, a total of29 and three haplotypes were detected in exonl and exon2, respectively. The
overall haplotype diversity was 0.8703 for exon I and 0.0703 for exon2. Lowest (0.083 for
Woyto-Guji and 0.081 for GondaI' goats) and modest (0.656 for Woyto-Guji and 0.635 for
GondaI' goats) average estimates of R2 and ID'I were obtained in LD decay analysis in exonl,
respectively, and most of the R2 and ID'I values suffer floor and ceiling effects. The neutrality
tests showed significant and negative values of Fs for Woyto-Guji (Fs = -8.098) and for GondaI'
" goats (Fs = -12.08); whereas, the Tajima's D test was positive and non-significant. Overall, there
was high goat population dynamics that causcd to have highest level of population admixture. The KISS I gene polymorphism analysis showed importance of the gene for multiple birth in
Ethiopian goats and can be suggested for marker assisted selection breeding program.
Key words: Ethiopia, Genetic diversity, Haplogroup, High density SNP Chip, Indigenous goat,
Kisspeptin gene, Population expansion, Neutrality test
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Keywords
Ethiopia, Genetic diversity, Haplogroup, High density SNP Chip, Indigenous goat, Kisspeptin gene, Population expansion, Neutrality test