High Density SNP Chips Array Uncovers Genetic Diversity and Population Structure of 16 Ethiopian and Chinese Goat Populations

Genome wide survey was conducted to assess genetic diversity and population structure of 16 goat populations from Ethiopia and China. A total of 468 samples, which were genotyped using GoatSNP50k BeadCHIP panel were included in the study. Moreover, from the wild goat, Swiss alpine Ibex was also included as the 17^th study population for comparison. However, due to the highest monomorphic (99.6%) loci accumulation, the Swiss alpine Ibex was limited only for the SNP polymorphism and diversity study. The average Ho and H_E were 0.375±0.1 and 0.383±0.00, respectively. The level of inbreeding ranged from -0.020 (Ibex-Cashmere hybrid) to 0.073 (Nubian goat). Average monomorphic and polymorphic loci were estimated to be 1749.19±627.37(3.5%) and 48000±627.52(96.5%). Molecular variance revealed 11.92% of variation among Chinese and Ethiopian goat populations studied. However, low (≤1%) population differentiation, lowest F_ST(µ=0.026) and highest Nm (µ=24.76) were observed among Ethiopian goats. The PCA1&2 differentiated Ethiopian goats, Cashmere and Ibex hybrid. Similarly, PCA1&3 differentiated Kaffa goat from other Ethiopian goats. The ADMIXTURE analysis revealed presence of only six genetic backgrounds in Ethiopian goats. Overall, high genetic diversity and weak population structure were observed in Ethiopian goat populations. The gene flow facilitated through animal exchange could be one of the possible reasons for the observed pattern.