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Neubert S, Wagener MG, Nicolaisen TJ, von Altrock A, Buchallik-Schregel J, Mikic M, Christofides D, Wohlsein P, Ganter M. [Choanal atresia in an alpaca cria (Vicugna pacos)]. Tierarztl Prax Ausg G Grosstiere Nutztiere 2024; 52:158-163. [PMID: 38925129 DOI: 10.1055/a-2324-1208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
After birth, an alpaca cria was noticed to exhibit weakness and respiratory distress, particularly when attempting to suckle milk from the dam's udder. Clinical findings indicated the presence of bilateral choanal atresia and the animal was subsequently euthanised. A computed tomography scan and a pathological examination were performed to describe the malformation in detail. Choanal atresia is a common malformation in neonatal South American camelids, surgical treatment is not recommended. This case report provides an overview of the clinical findings as well as the results of imaging and pathologic examinations and may help to raise awareness of this malformation for early recognition.
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Affiliation(s)
- Saskia Neubert
- Klinik für kleine Klauentiere und forensische Medizin und Ambulatorische Klinik, Stiftung Tierärztliche Hochschule Hannover
| | - Matthias Gerhard Wagener
- Klinik für kleine Klauentiere und forensische Medizin und Ambulatorische Klinik, Stiftung Tierärztliche Hochschule Hannover
| | - Thies Jesper Nicolaisen
- Klinik für kleine Klauentiere und forensische Medizin und Ambulatorische Klinik, Stiftung Tierärztliche Hochschule Hannover
| | - Alexandra von Altrock
- Klinik für kleine Klauentiere und forensische Medizin und Ambulatorische Klinik, Stiftung Tierärztliche Hochschule Hannover
| | - Johannes Buchallik-Schregel
- Klinik für kleine Klauentiere und forensische Medizin und Ambulatorische Klinik, Stiftung Tierärztliche Hochschule Hannover
| | - Manon Mikic
- Klinik für Kleintiere, Stiftung Tierärztliche Hochschule Hannover
| | | | - Peter Wohlsein
- Institut für Pathologie, Stiftung Tierärztliche Hochschule Hannover
| | - Martin Ganter
- Klinik für kleine Klauentiere und forensische Medizin und Ambulatorische Klinik, Stiftung Tierärztliche Hochschule Hannover
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Somenzi E, Partel E, Barbato M, Chero Osorio AM, Colli L, Franceschi N, Mantovani R, Pilla F, Komjanc M, Achilli A, Hauffe HC, Ajmone Marsan P. Genetic legacy and adaptive signatures: investigating the history, diversity, and selection signatures in Rendena cattle resilient to eighteenth century rinderpest epidemics. Genet Sel Evol 2024; 56:32. [PMID: 38698323 PMCID: PMC11064358 DOI: 10.1186/s12711-024-00900-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 04/05/2024] [Indexed: 05/05/2024] Open
Abstract
BACKGROUND Rendena is a dual-purpose cattle breed, which is primarily found in the Italian Alps and the eastern areas of the Po valley, and recognized for its longevity, fertility, disease resistance and adaptability to steep Alpine pastures. It is categorized as 'vulnerable to extinction' with only 6057 registered animals in 2022, yet no comprehensive analyses of its molecular diversity have been performed to date. The aim of this study was to analyse the origin, genetic diversity, and genomic signatures of selection in Rendena cattle using data from samples collected in 2000 and 2018, and shed light on the breed's evolution and conservation needs. RESULTS Genetic analysis revealed that the Rendena breed shares genetic components with various Alpine and Po valley breeds, with a marked genetic proximity to the Original Braunvieh breed, reflecting historical restocking efforts across the region. The breed shows signatures of selection related to both milk and meat production, environmental adaptation and immune response, the latter being possibly the result of multiple rinderpest epidemics that swept across the Alps in the eighteenth century. An analysis of the Rendena cattle population spanning 18 years showed an increase in the mean level of inbreeding over time, which is confirmed by the mean number of runs of homozygosity per individual, which was larger in the 2018 sample. CONCLUSIONS The Rendena breed, while sharing a common origin with Brown Swiss, has developed distinct traits that enable it to thrive in the Alpine environment and make it highly valued by local farmers. Preserving these adaptive features is essential, not only for maintaining genetic diversity and enhancing the ability of this traditional animal husbandry to adapt to changing environments, but also for guaranteeing the resilience and sustainability of both this livestock system and the livelihoods within the Rendena valley.
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Affiliation(s)
- Elisa Somenzi
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy.
| | - Erika Partel
- Unità risorse foraggere e produzioni zootecniche, Centro Trasferimento Tecnologico, Fondazione Edmund Mach, S. Michele all'Adige, Trento, Italy
| | - Mario Barbato
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Department of Veterinary Science, Università degli Studi di Messina, Messina, Italy
| | - Ana María Chero Osorio
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Licia Colli
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Centro di Ricerca Sulla Biodiversità e sul DNA Antico, BioDNA, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Niccolò Franceschi
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Roberto Mantovani
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padua, Padua, Italy
| | - Fabio Pilla
- Department of Agriculture Environment and Food Science, University of Molise, Campobasso, Italy
| | - Matteo Komjanc
- Unità risorse foraggere e produzioni zootecniche, Centro Trasferimento Tecnologico, Fondazione Edmund Mach, S. Michele all'Adige, Trento, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", University of Pavia, Pavia, Italy
| | - Heidi Christine Hauffe
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, Trento, Italy
| | - Paolo Ajmone Marsan
- DIANA Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy
- Centro di Ricerca Nutrigenomica e Proteomica-PRONUTRIGEN, Università Cattolica del Sacro Cuore, Piacenza, Italy
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León F, Pizarro EJ, Noll D, Pertierra LR, Gonzalez BA, Johnson WE, Marín JC, Vianna JA. History of Diversification and Adaptation from North to South Revealed by Genomic Data: Guanacos from the Desert to Sub-Antarctica. Genome Biol Evol 2024; 16:evae085. [PMID: 38761112 PMCID: PMC11102080 DOI: 10.1093/gbe/evae085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2024] [Indexed: 05/20/2024] Open
Abstract
The increased availability of quality genomic data has greatly improved the scope and resolution of our understanding of the recent evolutionary history of wild species adapted to extreme environments and their susceptibility to anthropogenic impacts. The guanaco (Lama guanicoe), the largest wild ungulate in South America, is a good example. The guanaco is well adapted to a wide range of habitats, including the Sechura Desert, the high Andes Mountains to the north, and the extreme temperatures and conditions of Navarino Island to the south. Guanacos also have a long history of overexploitation by humans. To assess the evolutionary impact of these challenging habitats on the genomic diversity, we analyzed 38 genomes (∼10 to 16×) throughout their extensive latitudinal distribution from the Sechura and Atacama Desert to southward into Tierra del Fuego Island. These included analyses of patterns of unique differentiation in the north and geographic region further south with admixture among L. g. cacsilensis and L. g. guanicoe. Our findings provide new insights on the divergence of the subspecies ∼800,000 yr BP and document two divergent demographic trajectories and to the initial expansion of guanaco into the more southern portions of the Atacama Desert. Patagonian guanacos have experienced contemporary reductions in effective population sizes, likely the consequence of anthropogenic impacts. The lowest levels of genetic diversity corresponded to their northern and western limits of distribution and some varying degrees of genetic differentiation. Adaptive genomic diversity was strongly linked with environmental variables and was linked with colonization toward the south followed by adaptation.
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Affiliation(s)
- Fabiola León
- Pontificia Universidad Católica de Chile, Facultad de Ciencias Biológicas, Instituto para el Desarrollo Sustentable, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Millennium Nucleus of Patagonian Limit of Life (LiLi), Santiago, Chile
| | - Eduardo J Pizarro
- Pontificia Universidad Católica de Chile, Facultad de Ciencias Biológicas, Instituto para el Desarrollo Sustentable, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Millennium Nucleus of Patagonian Limit of Life (LiLi), Santiago, Chile
| | - Daly Noll
- Pontificia Universidad Católica de Chile, Facultad de Ciencias Biológicas, Instituto para el Desarrollo Sustentable, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Millennium Nucleus of Patagonian Limit of Life (LiLi), Santiago, Chile
| | - Luis R Pertierra
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
| | - Benito A Gonzalez
- Laboratorio de Ecología de Vida Silvestre, Facultad de Ciencias Forestales y de la Conservación de la Naturaleza, Universidad de Chile, Santigo, Chile
| | | | - Juan Carlos Marín
- Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Universidad del Bio-Bío, Chillán, Chile
| | - Juliana A Vianna
- Pontificia Universidad Católica de Chile, Facultad de Ciencias Biológicas, Instituto para el Desarrollo Sustentable, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Millennium Nucleus of Patagonian Limit of Life (LiLi), Santiago, Chile
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Castillo-Doloriert H, Velasquez D, Matsuno Y, Hoces D, Wheeler JC. Conflict between Farmers and Guanacos ( Lama guanicoe cacsilensis): Field Surveys, Remote Sensing, and Interviews Provide Information for Conservation of a Critically Endangered Species in Southern Peru. Animals (Basel) 2024; 14:658. [PMID: 38473043 DOI: 10.3390/ani14050658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/24/2024] [Accepted: 02/02/2024] [Indexed: 03/14/2024] Open
Abstract
The Peruvian guanaco (Lama guanicoe cacsilensis) is classified as being "in critical danger of extinction" by the government. In this study, we evaluate how the conflict between farmers and guanacos in the Susapaya and Estique Districts, Tacna Department (Southern Peru) may represent a threat to their survival. To evaluate the situation, we 1. Conducted field surveys to monitor guanaco presence, 2. Used available remote sensing data to map guanaco movement, and 3. interviewed the impacted farmers concerning their losses. Remote sensing data showed that sedentary guanaco family groups located in prime steppe vegetation habitats never entered agricultural areas, while field surveys showed that bachelor bands and solitary individuals did, perhaps seeking forage due to growing population pressure. Interview data found that 90% of community farmers felt that guanacos were a problem best resolved by better fencing (45%), hunting (19%), or increased security (16%), and 92% saw no value in the conservation of the species. Hunting is illegal, given the critically endangered status of guanacos in Peru, so additional efforts are needed to both educate those who feel guanacos are a menace and involve them in efforts to preserve the species.
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Affiliation(s)
- Hugo Castillo-Doloriert
- CONOPA-Instituto de Investigación y Desarrollo de Camélidos Sudamericanos, Lima 15823, Peru
- Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima 15039, Peru
- IUCN SSC South American Camelid Specialist Group, 1196 Gland, Switzerland
| | - Daniela Velasquez
- CONOPA-Instituto de Investigación y Desarrollo de Camélidos Sudamericanos, Lima 15823, Peru
| | - Yumi Matsuno
- CONOPA-Instituto de Investigación y Desarrollo de Camélidos Sudamericanos, Lima 15823, Peru
| | - Domingo Hoces
- CONOPA-Instituto de Investigación y Desarrollo de Camélidos Sudamericanos, Lima 15823, Peru
- IUCN SSC South American Camelid Specialist Group, 1196 Gland, Switzerland
| | - Jane C Wheeler
- CONOPA-Instituto de Investigación y Desarrollo de Camélidos Sudamericanos, Lima 15823, Peru
- IUCN SSC South American Camelid Specialist Group, 1196 Gland, Switzerland
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Pallotti S, Picciolini M, Deiana G, Pediconi D, Antonini M, Napolioni V, Renieri C. Whole genome sequencing analysis of alpaca suggests TRPV3 as a candidate gene for the suri phenotype. BMC Genomics 2024; 25:185. [PMID: 38365607 PMCID: PMC10873959 DOI: 10.1186/s12864-024-10086-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 02/02/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Alpaca is a domestic South American camelid probably arising from the domestication of two wild camelids, the vicugna and the guanaco. Two phenotypes are described for alpaca, known as huacaya and suri. Huacaya fleece is characterized by compact, soft, and highly crimped fibers, while suri fleece is longer, straight, less crimped, and lustrous. The gene variants determining these phenotypes are still unknown, although previous studies suggested a dominant inheritance of the suri. Based on that, the aim of this study was the identification of the gene variants determining alpaca coat phenotypes through whole genome sequencing (WGS) analysis. RESULTS The sample used includes two test-cross alpaca families, suri × huacaya, which produced two offspring, one with the suri phenotype and one with the huacaya phenotype. The analyzed sample was expanded through the addition of WGS data from six vicugnas and six guanacos; this because we assumed the absence of the gene variants linked to the suri phenotype in these wild species. The analysis of gene variant segregation with the suri phenotype, coupled with the filtering of gene variants present in the wild species, disclosed the presence in all the suri samples of a premature termination codon (PTC) in TRPV3 (transient receptor potential cation channel subfamily V member 3), a gene known to be involved in hair growth and cycling, thermal sensation, cold tolerance and adaptation in several species. Mutations in TRPV3 were previously associated with the alteration of hair structure leading to an impaired formation of the hair canal and the hair shaft in mouse. This PTC in TRPV3, due to a G > T substitution (p.Glu475*), results in a loss of 290 amino acids from the canonical translated protein, plausibly leading to a physiological dysfunction. CONCLUSION The present results suggest that the suri phenotype may arise from a TRPV3 gene variant which may explain some of the suri features such as its longer hair fibre with lower number of cuticular scales compared to huacaya.
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Affiliation(s)
- Stefano Pallotti
- Genomic And Molecular Epidemiology (GAME) Lab, School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III Da Varano s/n, 62032, Camerino, Italy.
| | | | - Giovanni Deiana
- School of Pharmacy and Health Products, University of Camerino, Camerino, Italy
| | - Dario Pediconi
- School of Pharmacy and Health Products, University of Camerino, Camerino, Italy
| | - Marco Antonini
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA), Roma, Italy
| | - Valerio Napolioni
- Genomic And Molecular Epidemiology (GAME) Lab, School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III Da Varano s/n, 62032, Camerino, Italy
| | - Carlo Renieri
- School of Pharmacy and Health Products, University of Camerino, Camerino, Italy
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Pauciullo A, Versace C, Miretti S, Giambra IJ, Gaspa G, Letaief N, Cosenza G. Genetic variability among and within domestic Old and New World camels at the α-lactalbumin gene (LALBA) reveals new alleles and polymorphisms responsible for differential expression. J Dairy Sci 2024; 107:1068-1084. [PMID: 38122895 DOI: 10.3168/jds.2023-23813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 10/13/2023] [Indexed: 12/23/2023]
Abstract
α-Lactalbumin (α-LA), which is encoded by the LALBA gene, is a major whey protein that binds to Ca2+ and facilitates lactose synthesis as a regulatory subunit of the synthase enzyme complex. In addition, it has been shown to play central roles in immune modulation, cell-growth regulation, and antimicrobial activity. In this study, a multitechnical approach was used to fully characterize the LALBA gene and its variants in both coding and regulatory regions for domestic camelids (dromedary, Bactrian camel, alpaca, and llama). The gene analysis revealed a conserved structure among the camelids, but a slight difference in size (2,012 bp on average) due to intronic variations. Promoters were characterized for the transcription factor binding sites (11 found in total). Intraspecies sequence comparison showed 36 SNPs in total (2 in the dromedary, none in the Bactrian camel, 22 in the alpaca, and 12 in the llama), whereas interspecies comparison showed 86 additional polymorphic sites. Eight SNPs were identified as trans-specific polymorphisms, and 2 of them (g.112A>G and g.1229A>G) were particularly interesting in the New World camels. The first creates a new binding site for transcription factor SP1. An enhancing effect of the g.112G variant on the expression was demonstrated by 3 independent pGL3 gene reporter assays. The latter is responsible for the p.78Ile>Val AA replacement and represents novel allelic variants (named LALBA A and B). A link to protein variants has been established by isoelectric focusing (IEF), and bioinformatics analysis revealed that carriers of valine (g.1229G) have a higher glycosylation rate. Genotyping methods based on restriction fragment length polymorphism (PCR-RFLP) were set up for both SNPs. Overall, adenine was more frequent (0.54 and 0.76) at both loci. Four haplotypes were found, and the AA and GA were the most common with a frequency of 0.403 and 0.365, respectively. Conversely, a putative biological gain characterizes the haplotype GG. Therefore, opportunities for rapid directional selection can be realized if this haplotype is associated with favorable milk protein properties. This study adds knowledge at the gene and protein level for α-LA (LALBA) in camelids and importantly contributes to a relatively unexplored research area in these species.
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Affiliation(s)
- A Pauciullo
- Department of Agricultural, Forest and Food Sciences, University of Torino, 10095 Grugliasco (TO), Italy.
| | - C Versace
- Department of Agricultural, Forest and Food Sciences, University of Torino, 10095 Grugliasco (TO), Italy
| | - S Miretti
- Department of Veterinary Sciences, University of Torino, 10095 Grugliasco (TO), Italy
| | - I J Giambra
- Institute for Animal Breeding and Genetics, Justus Liebig University, 35390 Gießen, Germany
| | - G Gaspa
- Department of Agricultural, Forest and Food Sciences, University of Torino, 10095 Grugliasco (TO), Italy
| | - N Letaief
- Department of Agricultural, Forest and Food Sciences, University of Torino, 10095 Grugliasco (TO), Italy; Laboratory of Animal and Forage Production, National Agricultural Research Institute of Tunisia, University of Carthage, Ariana 1004, Tunisia
| | - G Cosenza
- Department of Agriculture, University of Napoli Federico II, 80055 Portici (NA), Italy
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Pallotti S, Picciolini M, Antonini M, Renieri C, Napolioni V. Genome-wide scan for runs of homozygosity in South American Camelids. BMC Genomics 2023; 24:470. [PMID: 37605116 PMCID: PMC10440933 DOI: 10.1186/s12864-023-09547-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/31/2023] [Indexed: 08/23/2023] Open
Abstract
BACKGROUND Alpaca (Vicugna pacos), llama (Lama glama), vicugna (Vicugna vicugna) and guanaco (Lama guanicoe), are the camelid species distributed over the Andean high-altitude grasslands, the Altiplano, and the Patagonian arid steppes. Despite the wide interest on these animals, most of the loci under selection are still unknown. Using whole-genome sequencing (WGS) data we investigated the occurrence and the distribution of Runs Of Homozygosity (ROHs) across the South American Camelids (SACs) genome to identify the genetic relationship between the four species and the potential signatures of selection. RESULTS A total of 37 WGS samples covering the four species was included in the final analysis. The multi-dimensional scaling approach showed a clear separation between the four species; however, admixture analysis suggested a strong genetic introgression from vicugna and llama to alpaca. Conversely, very low genetic admixture of the guanaco with the other SACs was found. The four species did not show significant differences in the number, length of ROHs (100-500 kb) and genomic inbreeding values. Longer ROHs (> 500 kb) were found almost exclusively in alpaca. Seven overlapping ROHs were shared by alpacas, encompassing nine loci (FGF5, LOC107034918, PRDM8, ANTXR2, LOC102534792, BSN, LOC116284892, DAG1 and RIC8B) while nine overlapping ROHs were found in llama with twenty-five loci annotated (ERC2, FZD9, BAZ1B, BCL7B, LOC116284208, TBL2, MLXIPL, PHF20, TRNAD-AUC, LOC116284365, RBM39, ARFGEF2, DCAF5, EXD2, HSPB11, LRRC42, LDLRAD1, TMEM59, LOC107033213, TCEANC2, LOC102545169, LOC116278408, SMIM15, NDUFAF2 and RCOR1). Four overlapping ROHs, with three annotated loci (DLG1, KAT6B and PDE4D) and three overlapping ROHs, with seven annotated genes (ATP6V1E1, BCL2L13, LOC116276952, BID, KAT6B, LOC116282667 and LOC107034552), were detected for vicugna and guanaco, respectively. CONCLUSIONS The signatures of selection revealed genomic areas potentially selected for production traits as well as for natural adaptation to harsh environment. Alpaca and llama hint a selection driven by environment as well as by farming purpose while vicugna and guanaco showed selection signals for adaptation to harsh environment. Interesting, signatures of selection on KAT6B gene were identified for both vicugna and guanaco, suggesting a positive effect on wild populations fitness. Such information may be of interest to further ecological and animal production studies.
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Affiliation(s)
- Stefano Pallotti
- Genomic And Molecular Epidemiology (GAME) Lab, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy.
| | | | - Marco Antonini
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA), Roma, Italy
| | - Carlo Renieri
- School of Pharmacy and Health Products, University of Camerino, Camerino, Italy
| | - Valerio Napolioni
- Genomic And Molecular Epidemiology (GAME) Lab, School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
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Elkin J, Martin A, Courtier-Orgogozo V, Santos ME. Analysis of the genetic loci of pigment pattern evolution in vertebrates. Biol Rev Camb Philos Soc 2023; 98:1250-1277. [PMID: 37017088 DOI: 10.1111/brv.12952] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 04/06/2023]
Abstract
Vertebrate pigmentation patterns are amongst the best characterised model systems for studying the genetic basis of adaptive evolution. The wealth of available data on the genetic basis for pigmentation evolution allows for analysis of trends and quantitative testing of evolutionary hypotheses. We employed Gephebase, a database of genetic variants associated with natural and domesticated trait variation, to examine trends in how cis-regulatory and coding mutations contribute to vertebrate pigmentation phenotypes, as well as factors that favour one mutation type over the other. We found that studies with lower ascertainment bias identified higher proportions of cis-regulatory mutations, and that cis-regulatory mutations were more common amongst animals harbouring a higher number of pigment cell classes. We classified pigmentation traits firstly according to their physiological basis and secondly according to whether they affect colour or pattern, and identified that carotenoid-based pigmentation and variation in pattern boundaries are preferentially associated with cis-regulatory change. We also classified genes according to their developmental, cellular, and molecular functions. We found a greater proportion of cis-regulatory mutations in genes implicated in upstream developmental processes compared to those involved in downstream cellular functions, and that ligands were associated with a higher proportion of cis-regulatory mutations than their respective receptors. Based on these trends, we discuss future directions for research in vertebrate pigmentation evolution.
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Affiliation(s)
- Joel Elkin
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, 800 22nd St. NW, Suite 6000, Washington, DC, 20052, USA
| | | | - M Emília Santos
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
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9
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Weihmüller MP. A look into the wild. Pathological analysis of a modern collection of guanacos from the Dry Chaco and its implications for South American camelid paleopathological studies. INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2023; 41:69-77. [PMID: 37018942 DOI: 10.1016/j.ijpp.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 06/12/2023]
Abstract
OBJECTIVE This article evaluates the prevalence of lesions in a modern osteological collection of guanacos (Lama guanicoe) and discusses the potential of paleopathological data to assess human intervention and environmental stress. MATERIALS A modern osteological collection of guanacos (NISP = 862) from north-western Córdoba, Central Argentina. METHODS The prevalence of pathological specimens per skeletal element and the pathological index (Bartosiewicz et al., 1997) was used. The prevalence of arthropathies, trauma and infections was quantified. Additionally, thorn lesions in the autopodium were recorded. RESULTS 11.03 % of the specimens presented pathological changes and the mean pathological index was 0.01. Degenerative lesions were the most prevalent type (10.34 %), followed by traumatic (0.81 %) and infectious pathologies (0.12 %). Thorn lesions (2.55 %) were recorded especially in metapodials. CONCLUSIONS Guanacos are exposed to the development of degenerative lesions, mainly in the autopodium and vertebrae. These lesions are probably common in camelids and should not be used to argue human management. Traumatic and infectious lesions are less frequent. SIGNIFICANCE This work provides baseline information for the paleopathological study of South American camelids and contributes to the characterization of a regionally endangered species. LIMITATIONS The nature of the faunal assemblage did not allow for direct correlations between pathologies and individual variables such as sex or age. SUGGESTIONS FOR FURTHER RESEARCH The comparison of our results with other wild and domesticated modern populations would be valuable to expand the baseline information for paleopathological studies. The use of quantitative methods is encouraged for future comparative and diachronic studies.
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Affiliation(s)
- María Paula Weihmüller
- Instituto de Antropología de Córdoba (IDACOR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Museo de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, 174 Hipólito Yrigoyen Av., Córdoba 5000, Argentina.
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10
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Bahbahani H, Al-Zoubi S, Ali F, Afana A, Dashti M, Al-Ateeqi A, Wragg D, Al-Bustan S, Almathen F. Signatures of purifying selection and site-specific positive selection on the mitochondrial DNA of dromedary camels (Camelus dromedarius). Mitochondrion 2023; 69:36-42. [PMID: 36690316 DOI: 10.1016/j.mito.2023.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023]
Abstract
The two species of the Old World Camelini tribe, dromedary and Bactrian camels, show superior adaptability to the different environmental conditions they populate, e.g. desert, mountains and coastal areas, which might be associated with adaptive variations on their mitochondrial DNA. Here, we investigate signatures of natural selection in the 13-mitochondrial protein-coding genes of different dromedary camel populations from the Arabian Peninsula, Africa and southwest Asia. The full mitogenome sequences of 42 dromedaries, 38 domestic Bactrian, 29 wild Bactrian camels and 31 samples representing the New World Lamini tribe reveal species-wise genetic distinction among Camelidae family species, with no evidence of geographic distinction among dromedary camels. We observe gene-wide signals of adaptive divergence between the Old World and New World camels, with evidence of purifying selection among Old World camel species. Upon comparing the different Camelidae tribes, 27 amino acid substitutions across ten mtDNA protein-coding genes were found to be under positive selection, in which, 24 codons were defined to be under positive adaptive divergence between Old World and New World camels. Seven codons belonging to three genes demonstrated positive selection in dromedary lineage. A total of 89 codons were found to be under positive selection in Camelidae family based on investigating the impact of amino acid replacement on the physiochemical properties of proteins, including equilibrium constant and surrounding hydrophobicity. These mtDNA variants under positive selection in the Camelidae family might be associated with their adaptation to their contrasting environments.
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Affiliation(s)
- Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait University, Sh. Sabah Al-Salem campus, Kuwait.
| | - Sanaa Al-Zoubi
- Department of Biological Sciences, Faculty of Science, Kuwait University, Sh. Sabah Al-Salem campus, Kuwait
| | - Fatima Ali
- Department of Biological Sciences, Faculty of Science, Kuwait University, Sh. Sabah Al-Salem campus, Kuwait
| | - Arwa Afana
- Department of Biological Sciences, Faculty of Science, Kuwait University, Sh. Sabah Al-Salem campus, Kuwait
| | - Mohammed Dashti
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Abdulaziz Al-Ateeqi
- Environment and Life Sciences research center, Kuwait Institute for Scientific Research, Kuwait City, Kuwait
| | - David Wragg
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Suzanne Al-Bustan
- Department of Biological Sciences, Faculty of Science, Kuwait University, Sh. Sabah Al-Salem campus, Kuwait
| | - Faisal Almathen
- Department of Veterinary Public Health and Animal Husbandry, College of Veterinary Medicine, King Faisal University, 400 Al-Ahsa, Saudi Arabia; Camel Research Center, King Faisal University, 400 Al-Ahsa, Saudi Arabia
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11
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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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12
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Hu L, Long J, Lin Y, Gu Z, Su H, Dong X, Lin Z, Xiao Q, Batbayar N, Bold B, Deutschová L, Ganusevich S, Sokolov V, Sokolov A, Patel HR, Waters PD, Graves JAM, Dixon A, Pan S, Zhan X. Arctic introgression and chromatin regulation facilitated rapid Qinghai-Tibet Plateau colonization by an avian predator. Nat Commun 2022; 13:6413. [PMID: 36302769 PMCID: PMC9613686 DOI: 10.1038/s41467-022-34138-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 10/14/2022] [Indexed: 12/25/2022] Open
Abstract
The Qinghai-Tibet Plateau (QTP), possesses a climate as cold as that of the Arctic, and also presents uniquely low oxygen concentrations and intense ultraviolet (UV) radiation. QTP animals have adapted to these extreme conditions, but whether they obtained genetic variations from the Arctic during cold adaptation, and how genomic mutations in non-coding regions regulate gene expression under hypoxia and intense UV environment, remain largely unknown. Here, we assemble a high-quality saker falcon genome and resequence populations across Eurasia. We identify female-biased hybridization with Arctic gyrfalcons in the last glacial maximum, that endowed eastern sakers with alleles conveying larger body size and changes in fat metabolism, predisposing their QTP cold adaptation. We discover that QTP hypoxia and UV adaptations mainly involve independent changes in non-coding genomic variants. Our study highlights key roles of gene flow from Arctic relatives during QTP hypothermia adaptation, and cis-regulatory elements during hypoxic response and UV protection.
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Affiliation(s)
- Li Hu
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Juan Long
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Yi Lin
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Zhongru Gu
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China
| | - Han Su
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Xuemin Dong
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Zhenzhen Lin
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China
| | - Qian Xiao
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China ,grid.20513.350000 0004 1789 9964Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, 100875 Beijing, China
| | - Nyambayar Batbayar
- Wildlife Science and Conservation Center, Union Building B-802, Ulaanbaatar, 14210 Mongolia
| | - Batbayar Bold
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China ,Wildlife Science and Conservation Center, Union Building B-802, Ulaanbaatar, 14210 Mongolia
| | - Lucia Deutschová
- grid.455051.0Raptor Protection of Slovakia, Trhová 54, SK-841 01, Bratislava, Slovakia
| | - Sergey Ganusevich
- Wild Animal Rescue Centre, Krasnostudencheskiy pr., 21-45, Moscow, 125422 Russia
| | - Vasiliy Sokolov
- grid.426536.00000 0004 1760 306XInstitute of Plant and Animal Ecology, Ural Division Russian Academy of Sciences, 202-8 Marta Street, Ekaterinburg, 620144 Russia
| | - Aleksandr Sokolov
- Arctic Research Station of the Institute of Plant and Animal Ecology, Ural Division Russian Academy of Sciences, 21 Zelenaya Gorka, Labytnangi, Yamalo-Nenetski District 629400 Russia
| | - Hardip R. Patel
- grid.1001.00000 0001 2180 7477The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601 Australia
| | - Paul D. Waters
- grid.1005.40000 0004 4902 0432School of Biotechnology and Biomolecular Science, Faculty of Science, UNSW Sydney, Sydney, NSW 2052 Australia
| | | | - Andrew Dixon
- Emirates Falconers’ Club, Al Mamoura Building (A), P.O. Box 47716, Muroor Road, Abu Dhabi, UAE ,grid.511767.30000 0004 5895 0922International Wildlife Consultants, P.O. Box 19, Carmarthen, SA33 5YL UK
| | - Shengkai Pan
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China
| | - Xiangjiang Zhan
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China ,grid.9227.e0000000119573309Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223 China
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13
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Genotyping-by-sequencing (GBS) as a tool for interspecies hybrid detection. ANNALS OF ANIMAL SCIENCE 2022. [DOI: 10.2478/aoas-2022-0063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
Genotyping-by-sequencing (GBS) is an extremely useful, modern and relatively inexpensive approach to discovering high-quality single-nucleotide polymorphisms (SNPs), which seem to be the most promising markers for identifying hybrid individuals between different species, especially those that can create backcrosses. In addition, GBS could become an invaluable tool in finding backcrosses, even several generations back. Its potential for the use of restriction enzymes and species is almost unlimited. It can also be successfully applied to species for which a reference genome is not established. In this paper, we describe the GBS technique, its main advantages and disadvantages, and the research carried out using this method concerning interspecies hybridisation and the identification of fertile hybrids. We also present future approaches that could be of interest in the context of the GBS method.
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14
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Anello M, Daverio MS, Di Rocco F. Genetics of coat color and fiber production traits in llamas and alpacas. Anim Front 2022; 12:78-86. [PMID: 35974792 PMCID: PMC9374512 DOI: 10.1093/af/vfac050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Melina Anello
- Laboratorio de Genética Molecular, Instituto Multidisciplinario de Biología Celular (IMBICE), CONICET-UNLP-CIC, La Plata, Argentina
| | - María Silvana Daverio
- Laboratorio de Genética Molecular, Instituto Multidisciplinario de Biología Celular (IMBICE), CONICET-UNLP-CIC, La Plata, Argentina
| | - Florencia Di Rocco
- Laboratorio de Genética Molecular, Instituto Multidisciplinario de Biología Celular (IMBICE), CONICET-UNLP-CIC, La Plata, Argentina
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15
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Changes in Neuropeptide Prohormone Genes among Cetartiodactyla Livestock and Wild Species Associated with Evolution and Domestication. Vet Sci 2022; 9:vetsci9050247. [PMID: 35622775 PMCID: PMC9144646 DOI: 10.3390/vetsci9050247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 12/10/2022] Open
Abstract
The impact of evolution and domestication processes on the sequences of neuropeptide prohormone genes that participate in cell–cell signaling influences multiple biological process that involve neuropeptide signaling. This information is important to understand the physiological differences between Cetartiodactyla domesticated species such as cow, pig, and llama and wild species such as hippopotamus, giraffes, and whales. Systematic analysis of changes associated with evolutionary and domestication forces in neuropeptide prohormone protein sequences that are processed into neuropeptides was undertaken. The genomes from 118 Cetartiodactyla genomes representing 22 families were mined for 98 neuropeptide prohormone genes. Compared to other Cetartiodactyla suborders, Ruminantia preserved PYY2 and lost RLN1. Changes in GNRH2, IAPP, INSL6, POMC, PRLH, and TAC4 protein sequences could result in the loss of some bioactive neuropeptides in some families. An evolutionary model suggested that most neuropeptide prohormone genes disfavor sequence changes that incorporate large and hydrophobic amino acids. A compelling finding was that differences between domestic and wild species are associated with the molecular system underlying ‘fight or flight’ responses. Overall, the results demonstrate the importance of simultaneously comparing the neuropeptide prohormone gene complement from close and distant-related species. These findings broaden the foundation for empirical studies about the function of the neuropeptidome associated with health, behavior, and food production.
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16
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Sosa FE, Bertoni EA, Micheloud JF, Vallejo DMNM, Olmos LH, Florin-Christensen M, Romero SR. Occurrence of sarcoptic mange in free-ranging vicuñas (Vicugna vicugna) of the Andean high plateau region of Argentina. Parasitol Res 2022; 121:1587-1595. [PMID: 35396964 DOI: 10.1007/s00436-022-07506-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/24/2022] [Indexed: 11/28/2022]
Abstract
Free-ranging vicuñas (Vicugna vicugna) are handled in some areas of the Andean high plateau region following an ancestral practice known as chaku, which consists in their transient capture and shearing of their fiber for commercialization. In this study, 807 vicuñas captured during 12 chaku events that took place in 2019 in the province of Jujuy, Argentina, were examined for typical mange skin lesions. Twenty-eight of the examined vicuñas presented alopecia with erythema, exudation, hyperkeratosis, and/or bleeding scarred lesions, mostly in the chest, rear and front legs, and inguinal zone. Most of the cases (82%) appeared in Laguna Cucho at 4900 masl, where 23% of the animals presented these skin reactions. Microscopic evaluation of skin scrapings revealed the presence of a great number of 0.1- to 0.4-mm-long mites of different life cycle stages, morphologically compatible with the species Sarcoptes scabiei. This etiological agent was confirmed by PCR amplification and sequencing of a cox-1 species-specific segment. Histopathological examination of skin biopsies showed extensive infiltration of the dermis with lymphocytes, neutrophils and eosinophils, hyperplasia at different stages, epidermis degeneration, and hyperkeratosis. This is the first characterization of sarcoptic mange in free-ranging vicuñas by clinical examination, mite morphology, histopathological studies, and molecular confirmation in the region. Mange hampers the welfare of vicuñas and the economy of the local communities that organize chaku events since infested vicuñas cannot be sheared. Its long-term effects are unknown but it might affect the fitness and survival of this iconic South American camelid.
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Affiliation(s)
- Fabiana E Sosa
- Instituto para la Pequeña Agricultura Familiar NOA, Posta de Hornillos, 4618, Jujuy, Argentina.,Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), C1425FQB, Buenos Aires, Argentina
| | - Emiliano A Bertoni
- Área de Sanidad Animal-IIACS Salta, CIAP, Instituto Nacional de Tecnología Agropecuaria (INTA), RN 68 km 172, Cerrillos, Salta, Argentina
| | - Juan F Micheloud
- Área de Sanidad Animal-IIACS Salta, CIAP, Instituto Nacional de Tecnología Agropecuaria (INTA), RN 68 km 172, Cerrillos, Salta, Argentina
| | - Diego M N Medina Vallejo
- Área de Sanidad Animal-IIACS Salta, CIAP, Instituto Nacional de Tecnología Agropecuaria (INTA), RN 68 km 172, Cerrillos, Salta, Argentina
| | - Leandro H Olmos
- Área de Sanidad Animal-IIACS Salta, CIAP, Instituto Nacional de Tecnología Agropecuaria (INTA), RN 68 km 172, Cerrillos, Salta, Argentina
| | - Mónica Florin-Christensen
- Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), C1425FQB, Buenos Aires, Argentina. .,Instituto de Patobiologia Veterinaria, INTA-CONICET, Centro de Investigaciones en Ciencias Veeterinarias y Agronomicas, INTA, Los Reseros y Nicolas Repetto S/N, 1686, Hurlingham, Argentina.
| | - Sandra R Romero
- Instituto para la Pequeña Agricultura Familiar NOA, Posta de Hornillos, 4618, Jujuy, Argentina
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17
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Examination of d-loop region and DBY gene as tools for identifying hybridisation in alpacas (Vicugna pacos) based on Polish populations. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Chen ZH, Xu YX, Xie XL, Wang DF, Aguilar-Gómez D, Liu GJ, Li X, Esmailizadeh A, Rezaei V, Kantanen J, Ammosov I, Nosrati M, Periasamy K, Coltman DW, Lenstra JA, Nielsen R, Li MH. Whole-genome sequence analysis unveils different origins of European and Asiatic mouflon and domestication-related genes in sheep. Commun Biol 2021; 4:1307. [PMID: 34795381 PMCID: PMC8602413 DOI: 10.1038/s42003-021-02817-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/27/2021] [Indexed: 02/06/2023] Open
Abstract
The domestication and subsequent development of sheep are crucial events in the history of human civilization and the agricultural revolution. However, the impact of interspecific introgression on the genomic regions under domestication and subsequent selection remains unclear. Here, we analyze the whole genomes of domestic sheep and their wild relative species. We found introgression from wild sheep such as the snow sheep and its American relatives (bighorn and thinhorn sheep) into urial, Asiatic and European mouflons. We observed independent events of adaptive introgression from wild sheep into the Asiatic and European mouflons, as well as shared introgressed regions from both snow sheep and argali into Asiatic mouflon before or during the domestication process. We revealed European mouflons might arise through hybridization events between a now extinct sheep in Europe and feral domesticated sheep around 6000-5000 years BP. We also unveiled later introgressions from wild sheep to their sympatric domestic sheep after domestication. Several of the introgression events contain loci with candidate domestication genes (e.g., PAPPA2, NR6A1, SH3GL3, RFX3 and CAMK4), associated with morphological, immune, reproduction or production traits (wool/meat/milk). We also detected introgression events that introduced genes related to nervous response (NEURL1), neurogenesis (PRUNE2), hearing ability (USH2A), and placental viability (PAG11 and PAG3) into domestic sheep and their ancestral wild species from other wild species.
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Affiliation(s)
- Ze-Hui Chen
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China ,grid.22935.3f0000 0004 0530 8290College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ya-Xi Xu
- grid.22935.3f0000 0004 0530 8290College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xing-Long Xie
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Dong-Feng Wang
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Diana Aguilar-Gómez
- grid.47840.3f0000 0001 2181 7878Center for Computational Biology, University of California at Berkeley, Berkeley, CA 94720 USA
| | | | - Xin Li
- grid.9227.e0000000119573309CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Ali Esmailizadeh
- grid.412503.10000 0000 9826 9569Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Vahideh Rezaei
- grid.412503.10000 0000 9826 9569Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Juha Kantanen
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Innokentyi Ammosov
- grid.495192.2Laboratory of Reindeer Husbandry and Traditional Industries, Yakut Scientific Research Institute of Agriculture, The Sakha Republic (Yakutia), Yakutsk, Russia
| | - Maryam Nosrati
- grid.412462.70000 0000 8810 3346Department of Agriculture, Payame Noor University, Tehran, Iran
| | - Kathiravan Periasamy
- grid.420221.70000 0004 0403 8399Animal Production and Health Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency, Vienna, Austria
| | - David W. Coltman
- grid.17089.37Department of Biological Sciences, University of Alberta, Edmonton, AB T6G2E9 Canada
| | - Johannes A. Lenstra
- grid.5477.10000000120346234Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California at Berkeley, Berkeley, CA, 94720, USA. .,Department of Statistics, UC Berkeley, Berkeley, CA, 94707, USA. .,Globe Institute, University of Copenhagen, 1350, København K, Denmark.
| | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing, China.
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19
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Passamonti MM, Somenzi E, Barbato M, Chillemi G, Colli L, Joost S, Milanesi M, Negrini R, Santini M, Vajana E, Williams JL, Ajmone-Marsan P. The Quest for Genes Involved in Adaptation to Climate Change in Ruminant Livestock. Animals (Basel) 2021; 11:2833. [PMID: 34679854 PMCID: PMC8532622 DOI: 10.3390/ani11102833] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 12/14/2022] Open
Abstract
Livestock radiated out from domestication centres to most regions of the world, gradually adapting to diverse environments, from very hot to sub-zero temperatures and from wet and humid conditions to deserts. The climate is changing; generally global temperature is increasing, although there are also more extreme cold periods, storms, and higher solar radiation. These changes impact livestock welfare and productivity. This review describes advances in the methodology for studying livestock genomes and the impact of the environment on animal production, giving examples of discoveries made. Sequencing livestock genomes has facilitated genome-wide association studies to localize genes controlling many traits, and population genetics has identified genomic regions under selection or introgressed from one breed into another to improve production or facilitate adaptation. Landscape genomics, which combines global positioning and genomics, has identified genomic features that enable animals to adapt to local environments. Combining the advances in genomics and methods for predicting changes in climate is generating an explosion of data which calls for innovations in the way big data sets are treated. Artificial intelligence and machine learning are now being used to study the interactions between the genome and the environment to identify historic effects on the genome and to model future scenarios.
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Affiliation(s)
- Matilde Maria Passamonti
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Elisa Somenzi
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Mario Barbato
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Giovanni Chillemi
- Department for Innovation in Biological, Agro-Food and Forest Systems–DIBAF, Università Della Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (G.C.); (M.M.)
| | - Licia Colli
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
- Research Center on Biodiversity and Ancient DNA—BioDNA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; (S.J.); (E.V.)
| | - Marco Milanesi
- Department for Innovation in Biological, Agro-Food and Forest Systems–DIBAF, Università Della Tuscia, Via S. Camillo de Lellis snc, 01100 Viterbo, Italy; (G.C.); (M.M.)
| | - Riccardo Negrini
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Monia Santini
- Impacts on Agriculture, Forests and Ecosystem Services (IAFES) Division, Fondazione Centro Euro-Mediterraneo Sui Cambiamenti Climatici (CMCC), Viale Trieste 127, 01100 Viterbo, Italy;
| | - Elia Vajana
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; (S.J.); (E.V.)
| | - John Lewis Williams
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
| | - Paolo Ajmone-Marsan
- Department of Animal Science, Food and Nutrition—DIANA, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy; (M.M.P.); (E.S.); (M.B.); (L.C.); (R.N.); (J.L.W.)
- Nutrigenomics and Proteomics Research Center—PRONUTRIGEN, Università Cattolica del Sacro Cuore, Via Emilia Parmense, 84, 29122 Piacenza, Italy
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20
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Chebii VJ, Mpolya EA, Muchadeyi FC, Domelevo Entfellner JB. Genomics of Adaptations in Ungulates. Animals (Basel) 2021; 11:1617. [PMID: 34072591 PMCID: PMC8230064 DOI: 10.3390/ani11061617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/22/2021] [Accepted: 05/23/2021] [Indexed: 11/16/2022] Open
Abstract
Ungulates are a group of hoofed animals that have long interacted with humans as essential sources of food, labor, clothing, and transportation. These consist of domesticated, feral, and wild species raised in a wide range of habitats and biomes. Given the diverse and extreme environments inhabited by ungulates, unique adaptive traits are fundamental for fitness. The documentation of genes that underlie their genomic signatures of selection is crucial in this regard. The increasing availability of advanced sequencing technologies has seen the rapid growth of ungulate genomic resources, which offers an exceptional opportunity to understand their adaptive evolution. Here, we summarize the current knowledge on evolutionary genetic signatures underlying the adaptations of ungulates to different habitats.
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Affiliation(s)
- Vivien J. Chebii
- School of Life Science and Bioengineering, Nelson Mandela Africa Institution of Science and Technology, P.O. Box 447, Arusha, Tanzania;
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya;
| | - Emmanuel A. Mpolya
- School of Life Science and Bioengineering, Nelson Mandela Africa Institution of Science and Technology, P.O. Box 447, Arusha, Tanzania;
| | - Farai C. Muchadeyi
- Agricultural Research Council Biotechnology Platform (ARC-BTP), Private Bag X5, Onderstepoort 0110, South Africa;
| | - Jean-Baka Domelevo Entfellner
- Biosciences Eastern and Central Africa, International Livestock Research Institute (BecA-ILRI) Hub, P.O. Box 30709, Nairobi 00100, Kenya;
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21
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Diaz-Maroto P, Rey-Iglesia A, Cartajena I, Núñez L, Westbury MV, Varas V, Moraga M, Campos PF, Orozco-terWengel P, Marin JC, Hansen AJ. Ancient DNA reveals the lost domestication history of South American camelids in Northern Chile and across the Andes. eLife 2021; 10:63390. [PMID: 33724183 PMCID: PMC8032396 DOI: 10.7554/elife.63390] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 03/15/2021] [Indexed: 01/14/2023] Open
Abstract
The study of South American camelids and their domestication is a highly debated topic in zooarchaeology. Identifying the domestic species (alpaca and llama) in archaeological sites based solely on morphological data is challenging due to their similarity with respect to their wild ancestors. Using genetic methods also presents challenges due to the hybridization history of the domestic species, which are thought to have extensively hybridized following the Spanish conquest of South America that resulted in camelids slaughtered en masse. In this study, we generated mitochondrial genomes for 61 ancient South American camelids dated between 3,500 and 2,400 years before the present (Early Formative period) from two archaeological sites in Northern Chile (Tulán-54 and Tulán-85), as well as 66 modern camelid mitogenomes and 815 modern mitochondrial control region sequences from across South America. In addition, we performed osteometric analyses to differentiate big and small body size camelids. A comparative analysis of these data suggests that a substantial proportion of the ancient vicuña genetic variation has been lost since the Early Formative period, as it is not present in modern specimens. Moreover, we propose a domestication hypothesis that includes an ancient guanaco population that no longer exists. Finally, we find evidence that interbreeding practices were widespread during the domestication process by the early camelid herders in the Atacama during the Early Formative period and predating the Spanish conquest.
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Affiliation(s)
| | - Alba Rey-Iglesia
- Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Isabel Cartajena
- Faculty of Social Sciences, University of Chile, Santiago de Chile, Chile
| | - Lautaro Núñez
- Institute of Archaeological Research and Museum, Católica del Norte University, San Pedro de Atacama, Chile
| | - Michael V Westbury
- Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Valeria Varas
- School of Science Ecology and Evolution, Faculty of Sciences, Austral of Chile University, Valdivia, Chile
| | - Mauricio Moraga
- Human Genetics Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Paula F Campos
- CIIMAR Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Pablo Orozco-terWengel
- School of Biosciences, Cardiff University, Cardiff, United Kingdom.,ICCMISAC - International Consortium for the Conservation Management and Improvement of South American Camelids, Cardiff, United Kingdom
| | - Juan Carlos Marin
- ICCMISAC - International Consortium for the Conservation Management and Improvement of South American Camelids, Cardiff, United Kingdom.,Genomic and Biodiversity Laboratory, Basic Sciences Department, Faculty of Sciences, Bio-Bio University, Chillán, Chile
| | - Anders J Hansen
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Calderon M, More MJ, Gutierrez GA, Ponce de León FA. Development of a 76k Alpaca ( Vicugna pacos) Single Nucleotide Polymorphisms (SNPs) Microarray. Genes (Basel) 2021; 12:genes12020291. [PMID: 33669871 PMCID: PMC7923280 DOI: 10.3390/genes12020291] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 11/16/2022] Open
Abstract
Small farm producers’ sustenance depends on their alpaca herds and the production of fiber. Genetic improvement of fiber characteristics would increase their economic benefits and quality of life. The incorporation of molecular marker technology could overcome current limitations for the implementation of genetic improvement programs. Hence, the aim of this project was the generation of an alpaca single nucleotide polymorphism (SNP) microarray. A sample of 150 Huacaya alpacas from four farms, two each in Puno and Cerro de Pasco were used for SNP discovery by genotyping by sequencing (GBS). Reduced representation libraries, two per animal, were produced after DNA digestion with ApeK1 and double digestion with Pst1-Msp1. Ten alpaca genomes, sequenced at depths between 12× to 30×, and the VicPac3.1 reference genome were used for read alignments. Bioinformatics analysis discovered 76,508 SNPs included in the microarray. Candidate genes SNPs (302) for fiber quality and color are also included. The microarray SNPs cover 90.5% of the genome length with a density of about 39 ± 2.51 SNPs/Mb of DNA at an average interval of 26.45 ± 18.57 kbp. The performance was evaluated by genotyping 30 family trios and comparing them to their pedigrees, as well as comparing microarray to GBS genotypes. Concordance values of 0.93 and 0.94 for ApeK1 and Pst1-Msp1 generated SNPs were observed. Similarly, 290 fiber quality and color candidate gene SNPs were validated. Availability of this microarray will facilitate genome-wide association studies, marker-assisted selection and, in time, genomic selection.
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Affiliation(s)
- Marcos Calderon
- Facultad de Zootecnia, Universidad Nacional Agraria La Molina, Lima 15024, Peru; (M.C.); (M.J.M.); (G.A.G.)
- Escuela de Formación Profesional de Zootecnia, Facultad de Ciencias Agropecuarias, Universidad Nacional Daniel Alcídes Carrión, Cerro de Pasco 19001, Peru
| | - Manuel J. More
- Facultad de Zootecnia, Universidad Nacional Agraria La Molina, Lima 15024, Peru; (M.C.); (M.J.M.); (G.A.G.)
| | - Gustavo A. Gutierrez
- Facultad de Zootecnia, Universidad Nacional Agraria La Molina, Lima 15024, Peru; (M.C.); (M.J.M.); (G.A.G.)
| | - Federico Abel Ponce de León
- Department of Animal Science, University of Minnesota, Minneapolis, MN 55108, USA
- Correspondence: ; Tel.: +1-612-419-7870
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