Microsatellite-Based Genetic Structure and Hybrid Detection in Alpacas Bred in Poland

Abstract

This study aimed to characterize the population structure and genetic diversity of alpacas maintained in Poland using 17 microsatellite markers recommended by the International Society for Animal Genetics. The classification of llamas, alpacas, and hybrids of both based on phenotype is often difficult due to long-term admixture. Our results showed that microsatellite markers can distinguish alpacas from llamas and provide information about the level of admixture of one species in another. Alpacas admixed with llamas constituted 8.8% of the tested individuals, with the first-generation hybrid displaying only 7.4% of llama admixture. The results showed that Poland hosts a high alpaca genetic diversity as a consequence of their mixed origin. More than 200 different alleles were identified and the average observed heterozygosity and expected heterozygosity values were 0.745 and 0.768, respectively, the average coefficient of inbreeding was 0.034, and the average polymorphism information content value was 0.741. The probability of exclusion for one parent was estimated at 0.99995 and for two parents at 0.99999.

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

“…Six loci in the Ajoyani population (LCA66, LCA99, LCA37, LCA56, LCA65, and YWLL46) and five loci in the Quimsachata population (LCA66, LCA77, YWLL36, YWLL29, and YWLL40) showed lower H o than H e , less than the half of the total loci, which may indicate that there is neither an excess nor a deficiency of heterozygosity in the populations under study. This result is consistent with previous studies carried out by other authors [34,37,38].…”

Genotyping-by-sequencing (GBS) as a tool for interspecies hybrid detection

“…One of the significant problems is the hybridisation of South American Camelids (SACs), which include two wild species: guanaco (Lama guanicoe) and vicuña (Vicugna vicugna), and two domesticated species: llama (L. glama) and alpaca (V. pacos). All SACs have the same number of chromosomes (2n = 74) and can cross, producing fertile hybrids (Podbielska et al, 2021;Wheeler, 1995), and this phenomenon occurs especially often among domesticated species (Wheeler et al, 1995). The first generation of alpaca × llama hybrids is to recognise, but the most problematic is backcrossing (Di Rocco et al, 2011).…”

“…The first generation of alpaca × llama hybrids is to recognise, but the most problematic is backcrossing (Di Rocco et al, 2011). It is an unfavourable phenomenon that threatens genetic diversity and causes a significant deterioration in the quality of alpaca fibre, which is considered a luxury material (Podbielska et al, 2021;Wheeler et al, 1995). It has been proven that, despite various breeding practices, alpacas and llamas have not yet divided genetically, proving the phenomenon of hybridisation identified based on STR markers (Echalar et al, 2020;Echalar and Barreta, 2022;Podbielska et al, 2021;Varas et al, 2020), mtDNA (Barreta et al, 2013;Kadwell et al, 2001;Maté et al, 2007Maté et al, , 2004Melo et al, 2012;Podbielska and Piórkowska, 2022;Stanley et al, 1994) or even the Y chromosome (Marín et al, 2017).…”

“…Because alpacas were classified as livestock in Poland in 2021, a good breeding approach would be to systematise breeding and trying to search for hybrid individuals, especially those difficult-to-identify backcrosses. Their elimination from reproduction could effectively affect the fibre quality of future populations (Podbielska et al, 2021).…”

“…It was not possible when examining the mtDNA and Y chromosome (Podbielska and Piórkowska, 2022). When using STR markers, the F 1 hybrid had only 7.4% llama admixture, suggesting that alpaca and llama populations are genetically mixed (Podbielska et al, 2021); however, it is hypothesised that the SNP markers may be much more precise. conclusions GBS was developed and applied in the sequencing of multiplexed samples, and it combines molecular marker discovery and genotyping using NGS.…”