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Figueroa D, Corredor FA, Mamani-Cato RH, Gallegos-Acero RF, Condori-Rojas N, Estrada R, Heredia L, Salazar W, Quilcate C, Arbizu CI. Microsatellite-Based Genetic Diversity and Population Structure of Huacaya Alpacas ( Vicugna pacos) in Southern Peru. Animals (Basel) 2023; 13:ani13091552. [PMID: 37174589 PMCID: PMC10177232 DOI: 10.3390/ani13091552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/28/2023] [Accepted: 03/09/2023] [Indexed: 05/15/2023] Open
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 (Ho), expected heterozygosity (He), 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 HO, HE, 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.
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Affiliation(s)
- Deyanira Figueroa
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Flor-Anita Corredor
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Ruben H Mamani-Cato
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Estación Experimental Agraria Illpa, Puno 21002, Peru
| | - Roberto F Gallegos-Acero
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional del Altiplano, Av. Floral 1153, Puno 21001, Peru
| | - Nicoll Condori-Rojas
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Estación Experimental Agraria Illpa, Puno 21002, Peru
| | - Richard Estrada
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Lizeth Heredia
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Wilian Salazar
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Carlos Quilcate
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Carlos I Arbizu
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
- Facultad de Ingeniería y Ciencias Agrarias, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas (UNTRM), Cl. Higos Urco 342, Chachapoyas 01001, Peru
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Behavioural biology of South American domestic camelids: An overview from a welfare perspective. Small Rumin Res 2023. [DOI: 10.1016/j.smallrumres.2023.106918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Echalar J, Barreta J. Introgression in domestic camelid productive systems in Bolivia. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Podbielska A, Piórkowska K, Szmatoła T. Microsatellite-Based Genetic Structure and Hybrid Detection in Alpacas Bred in Poland. Animals (Basel) 2021; 11:ani11082193. [PMID: 34438651 PMCID: PMC8388510 DOI: 10.3390/ani11082193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/17/2021] [Accepted: 07/18/2021] [Indexed: 11/16/2022] Open
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.
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Affiliation(s)
- Angelika Podbielska
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland; (K.P.); (T.S.)
- Correspondence:
| | - Katarzyna Piórkowska
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland; (K.P.); (T.S.)
| | - Tomasz Szmatoła
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland; (K.P.); (T.S.)
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1c, 30-248 Kraków, Poland
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Price E, Larrabure D, Gonzales B, McClure P, Espinoza E. Forensic identification of the keratin fibers of South American camelids by ambient ionization mass spectrometry: Vicuña, alpaca and guanaco. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8916. [PMID: 32770752 DOI: 10.1002/rcm.8916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/14/2020] [Accepted: 08/02/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE The keratin fleece of the endangered vicuña (Vicugna vicugna) commands a high value in international markets, and this trade has caused illegal poaching and a substantial decrease in vicuña populations. Morphological analysis of hairs does not have the resolution to determine the species of origin of camelid natural fibers. In addition, commerce in camelid fleece also includes the legal trade of alpaca (Vicugna pacos) and guanaco (Lama guanicoe) wool. METHODS The keratin fiber spectra of vicuña (n = 19), guanaco (n = 20) and alpaca (n = 20) were collected using X-ray fluorescence (XRF) spectrometry, Horizontal attenuated total reflectance Fourier transform infrared (HATR-FTIR) spectroscopy and direct analysis in real time time-of-flight mass spectrometry (DART-TOFMS). Analysis with each technique evaluated the data to determine if the three taxa could be separated using either descriptive or multivariate statistics. RESULTS XRF analysis showed that the elements detected and their relative concentrations were similar in all three species, whereas HATR-FTIR analysis could identify alpaca fleece but could not differentiate vicuña from guanaco. Ions detected by ambient ionization using DART-TOFMS, in either positive- or negative-ion mode, gave the best results and showed that each taxonomic group is distinctive. Multivariate analysis of the mass spectra created robust models which resolved each species (LOOCV = 99.9%). The analyses of eight validation samples were correctly assigned to the appropriate species and demonstrated the reliability of DART-TOFMS to infer taxonomic source. CONCLUSIONS The DART-TOFMS spectra of unmodified keratin fibers infer that the chemotype of each species is heavily influenced by fatty acids, cholesterol and its analogs, and that these ions are useful in separating the fleece of vicuña, alpaca and guanaco. We posit that the etiological source of these chemotype differences is consistent with genetic modulations and is less influenced by diet. Accurate taxonomic identification of fleece is important to identify violations and assists in the protection of rare species.
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Affiliation(s)
- Erin Price
- National Fish and Wildlife Forensic Laboratory, 1490 E. Main St., Ashland, OR 97520, USA
| | | | - Benito Gonzales
- Faculty of Forest Sciences and Nature Conservation, Universidad de Chile, Chile
| | - Pamela McClure
- National Fish and Wildlife Forensic Laboratory, 1490 E. Main St., Ashland, OR 97520, USA
| | - Edgard Espinoza
- National Fish and Wildlife Forensic Laboratory, 1490 E. Main St., Ashland, OR 97520, USA
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Intraspecific genetic analysis of Bolivian alpacas and interspecific relationship with llamas and vicunas. Small Rumin Res 2020. [DOI: 10.1016/j.smallrumres.2020.106137] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Mastrangelo S, Tolone M, Montalbano M, Tortorici L, Di Gerlando R, Sardina MT, Portolano B. Population genetic structure and milk production traits in Girgentana goat breed. ANIMAL PRODUCTION SCIENCE 2017. [DOI: 10.1071/an15431] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The aim of this work was to evaluate the genetic status of the Girgentana goat, an endangered breed from Sicily (Italy), using microsatellite markers. Furthermore, as the main purpose of the Girgentana breed is milk production, quantitative milk traits were investigated, including fatty acid profile. Molecular data from CSN1S1, CSN2, CSN1S2, and CSN3 casein genes were also used to infer haplotypes. A total of 264 individuals were collected. Samples of Maltese (n = 41) and Derivata di Siria (n = 33) goat breeds were also used to understand the genetic relationship among breeds. Test-day records for milk production were collected to determine daily milk yield, fat, protein, casein, lactose, and somatic cell count. Individual milk samples were also collected for fatty acid extraction. Wright’s statistics, gene flow, Nei genetic distance, factorial correspondence analysis, and Bayesian assignment test showed the existence of genetic variability and differentiation among breeds. The AMOVA results indicated that 89.96% of the total variance was partitioned within populations. The Girgentana breed appears to have a subdivided population, and has not experienced a recent bottleneck. A high variability in milk yield was observed. Mean morning milk yield was 1448 ± 404 g, with 4.30 ± 0.87% and 3.72 ± 0.44% of fat and protein percentages, respectively. The average somatic cell count found in Girgentana goat milk was higher than the threshold of 1 500 000 cells/mL advised in Europe for fresh milk. Gross milk and fatty acid composition were similar to that reported in the literature for other local goat breeds.
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Genetic diversity and differentiation of 12 eastern Adriatic and western Dinaric native sheep breeds using microsatellites. Animal 2014; 8:200-7. [PMID: 24433957 DOI: 10.1017/s1751731113002243] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nuclear genetic diversity and differentiation of 341 sheep belonging to 12 sheep breeds from Croatia and Bosnia and Herzegovina were examined. The aim of the study was to provide the understanding of the genetic structure and variability of the analysed pramenka sheep populations, and to give indications for conservation strategies based on the population diversity and structure information. The genetic variation of the sheep populations, examined at the nuclear level using 27 microsatellite loci, revealed considerable levels of genetic diversity, similar to the diversity found in other European indigenous low-production sheep breeds. Population-specific alleles were detected at most loci and in breeds analysed. The observed heterozygosity ranged from 0.643 (in Lika pramenka) to 0.743 (in Vlasic pramenka), and the expected heterozygosity ranged from 0.646 (in Lika pramenka) to 0.756 (in Dalmatian pramenka). Significant inbreeding coefficients were found for half of the populations studied and ranged from 0.040 (Pag island sheep) to 0.091 (Kupres pramenka). Moderate genetic differentiation was found between the studied sheep populations. The total genetic variability observed between different populations was 5.29%, whereas 94.71% of the variation was found within populations. Cres island sheep, Lika pramenka and Istrian sheep were identified as the most distinct populations, which was confirmed by the factorial analysis of correspondence and supported through a bootstrapping adjustment to correct for the difference in the sample sizes. The population structure analysis distinguished 12 clusters for the 12 sheep breeds analysed. However, the cluster differentiation was low for Dalmatian, Vlasic, Stolac and Krk pramenka. This systematic study identified Lika pramenka and Rab island sheep as those with the lowest diversity, whereas Istrian sheep and Pag island sheep had the highest. Conservation actions are proposed for Istrian, Rab and Cres island sheep, Lika and Kupres pramenka because of high estimated coefficients of inbreeding.
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Genetic diversity of GH1 and LEP genes in Argentine llama (Lama glama) populations. Small Rumin Res 2014. [DOI: 10.1016/j.smallrumres.2014.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Association of microsatellite markers with fiber diameter trait in Peruvian alpacas (Vicugna pacos). Livest Sci 2014. [DOI: 10.1016/j.livsci.2013.12.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Paredes M, Membrillo A, Azor P, Machaca J, Torres D, Serrano AM. Genetic and phenotypic variation in five populations of Huacaya Alpacas (Vicugna pacos) from Peru. Small Rumin Res 2013. [DOI: 10.1016/j.smallrumres.2012.09.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Barreta J, Gutiérrez-Gil B, Iñiguez V, Romero F, Saavedra V, Chiri R, Rodríguez T, Arranz JJ. Analysis of genetic diversity in Bolivian llama populations using microsatellites. J Anim Breed Genet 2012; 130:321-30. [PMID: 23855634 DOI: 10.1111/jbg.12009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 08/27/2012] [Indexed: 11/30/2022]
Abstract
South American camelids (SACs) have a major role in the maintenance and potential future of rural Andean human populations. More than 60% of the 3.7 million llamas living worldwide are found in Bolivia. Due to the lack of studies focusing on genetic diversity in Bolivian llamas, this analysis investigates both the genetic diversity and structure of 12 regional groups of llamas that span the greater part of the range of distribution for this species in Bolivia. The analysis of 42 microsatellite markers in the considered regional groups showed that, in general, there were high levels of polymorphism (a total of 506 detected alleles; average PIC across per marker: 0.66), which are comparable with those reported for other populations of domestic SACs. The estimated diversity parameters indicated that there was high intrapopulational genetic variation (average number of alleles and average expected heterozygosity per marker: 12.04 and 0.68, respectively) and weak genetic differentiation among populations (FST range: 0.003-0.052). In agreement with these estimates, Bolivian llamas showed a weak genetic structure and an intense gene flow between all the studied regional groups, which is due to the exchange of reproductive males between the different flocks. Interestingly, the groups for which the largest pairwise FST estimates were observed, Sud Lípez and Nor Lípez, showed a certain level of genetic differentiation that is probably due to the pattern of geographic isolation and limited communication infrastructures of these southern localities. Overall, the population parameters reported here may serve as a reference when establishing conservation policies that address Bolivian llama populations.
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Affiliation(s)
- J Barreta
- Dpto. Produccion Animal, Universidad de Leon, Leon, Spain; Instituto de Biologia Molecular y Biotecnologia, UMSA, La Paz, Bolivia
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