Microsatellite-Based Genetic Diversity and Population Structure of Huacaya Alpacas (Vicugna pacos) in Southern Peru

Deyanira Figueroa; Flor-Anita Corredor; Ruben H Mamani-Cato; Roberto F Gallegos-Acero; Nicoll Condori-Rojas; Richard Estrada; Lizeth Heredia; Wilian Salazar; Carlos Quilcate; Carlos I Arbizu

doi:10.3390/ani13091552

Microsatellite-Based Genetic Diversity and Population Structure of Huacaya Alpacas (Vicugna pacos) in Southern Peru

Animals (Basel). 2023 May 5;13(9):1552. doi: 10.3390/ani13091552.

Affiliations

¹ Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru.
² Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Estación Experimental Agraria Illpa, Puno 21002, Peru.
³ Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional del Altiplano, Av. Floral 1153, Puno 21001, Peru.
⁴ Facultad de Ingeniería y Ciencias Agrarias, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas (UNTRM), Cl. Higos Urco 342, Chachapoyas 01001, Peru.

Abstract

The alpaca population mostly consists of the Huacaya phenotype and is widely distributed in Southern Peru. This study aimed to estimate the genetic diversity and population structure of two Huacaya alpaca populations (Ajoyani and Quimsachata) using fourteen and twelve microsatellite markers for each population, respectively. A total of 168 alpaca biological samples were outsourced to Peruvian laboratories for DNA extraction and genotyping. For genetic diversity, observed heterozygosity (H_o), expected heterozygosity (H_e), polymorphism information content (PIC), and fixation indices values were estimated. An admixture analysis was performed for the population structure analysis. Different programs were used for these estimations. In total, 133 (Ajoyani) and 129 (Quimsachata) alleles were found, with a range of 4 to 17 by locus. The mean H_O, H_E, and PIC per marker for Ajoyani were 0.764 ± 0.112, 0.771 ± 0.1, and 0.736; for Quimsachata, they were 0.783 ± 0.087, 0.773 ± 0.095, and 0.738, respectively. The population structure showed no structure with K = 2. This study provides useful indicators for the creation of appropriate alpaca conservation programs.

Keywords: Andean region; SSR; camelids; genetics.

Grants and funding

This research was funded by the “Programa Nacional de Innovación Agraria del Instituto Nacional de Innovación Agraria” with grant numbers 133_PI and 167-INIA-PNIA-EXT, and PP0068 “Reducción de la vulnerabilidad y atención de emergencias por desastres” of the Ministry of Agrarian Development and Irrigation (MIDAGRI). C.I.A. was funded by Vicerrectorado de Investigación of UNTRM.