Molecular Characterization Of Ethiopian Indigenous Goat Populations Genetic Diversity And Structure Demogrphic Dynamics And Assessment Of The Kisspeptin Gene Polymorphism

Ethiopia lies within the earliest geographic center for the dispersal of livestock into the Africanrncontinent. It therefore comprises a unique repository of livestock genetic diversity in therncontinent. However, information relating to the origin and divergence of domestic goats in thernNOIth-East African region, and Ethiopia in particular, remains unknown despite the availabilityrnof genomic tools to assess the same. Here, the complete mitochondrial DNA D-loop region ofrn309 individuals representing 3 Ethiopian indigenous populations of goats was sequenced torninvestigate the maternal historical demographic dynamics of Ethiopian indigenous goats,rnSimilarly, genotype data were generated from 14 populations by the 50K Caprine SNP CHIPrnarray to investigate the genetic diversity and structure of Ethiopian indigenous goats, ThernChinese Cashmere, Cashmere-Ibex hybrid and the wild Swiss Alpine Ibex populations were alsornincluded as outgroup for comparison, In addition, analysis of polymorphism of the KISS I genernand its association with litter size, and haplotype and patterns of linkage disequilibrium (LD)rnanalysis were conducted in exon regions of the kisspeptin gene of Gondar and Woyto-Guji goatrnpopulations. A total of 173 and 242 Sanger sequences were employed for further analysis ofrnexonl (1210 bp) and exon2 (325 bp) regions of the kisspeptin gene, respectively, Sequencing ofrnthe mtDNA, 174 variable sites that generated 231 haplotypes were observed in the D-loop regionrnof mtDNA sequences and these haplotypes defined two haplogroups lacking a phylogeographic structure but with a high genetic diversity. In a combined analysis of reference haplotypesrnrepresenting the six globally defined Caprine haplogroups revealed out two haplogroups to be Arnand G, with the former being the most predominant. The lack of phylogeographic structure and arnweak population differentiation (overall PST = 0.0245) suggest extensive gene flow amongstrnindigenous Ethiopian goats. In the gcnome wide survey, high genetic diversity (HE :0: 0.35) butrnlow level of genetic differcntiation among the populations is revealed. Thc 14 populations wererngrouped into six clusters and none of them was spccific to one population or geographic region.rnInterestingly, population phylogenetic analysis did not support the classification of Ethiopianrngoats based on their agro-ecological location, associated production system and phenotypicrnfamily as suggested previously, but differentiated the Kaffa goat from the rest of 13 Ethiopianrngoat populations. Based on the admixture and phylogenetic network analyses, the 14 Ethiopianrngoat populations can be re-grouped into seven goat types. On the other hand, polymorphismrnanalysis of the KISS I gene revealed five complete substitutions and 15 polymorphic sites in bothrnexon regions. The overall average HE was 0.18863±0.21 for exonl and 0.031 55±0.0 I for exon2.rnAmong detected polymorphic sites only four SNPs contributed 18%-31 % multiple birth.rnSimilarly, a total of29 and three haplotypes were detected in exonl and exon2, respectively. Thernoverall haplotype diversity was 0.8703 for exon I and 0.0703 for exon2. Lowest (0.083 forrnWoyto-Guji and 0.081 for GondaI' goats) and modest (0.656 for Woyto-Guji and 0.635 forrnGondaI' goats) average estimates of R2 and ID'I were obtained in LD decay analysis in exonl,rnrespectively, and most of the R2 and ID'I values suffer floor and ceiling effects. The neutralityrntests showed significant and negative values of Fs for Woyto-Guji (Fs = -8.098) and for GondaI'rn" goats (Fs = -12.08); whereas, the Tajima's D test was positive and non-significant. Overall, therernwas 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 inrnEthiopian goats and can be suggested for marker assisted selection breeding program.rnKey words: Ethiopia, Genetic diversity, Haplogroup, High density SNP Chip, Indigenous goat,rnKisspeptin gene, Population expansion, Neutrality test

Get Full Work

Report copyright infringement or plagiarism