The genetic diversity and structure of Bolivian alpaca populations, and genetic relationship between alpacas, llamas and vicunas has been assessed using microsatellite markers. Overall alpaca and llama populations present higher genetic diversity (He = 0,73) than vicunas (He = 0,59). Genetic analysis and population structure have shown a closer relationship between alpacas and llamas, suggesting admixture at productive systems where alpacas and llamas are raised together. Alpaca productive systems have shown low differentiation values (FST = 0,026), and have been clustered into five inferred groups. Populations with higher contribution to total genetic diversity were Ulla Ulla and Catacora. These data could stablish a base line for management and conservation of alpaca populations, particularly to avoid hybridization with llamas, which may affect fiber quality, and to maintain current genetic diversity levels at the Bolivian productive systems.
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