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Siziba VI, Scroeder MM, Wilson B, Sliwa A, Willows‐Munro S. A method for noninvasive individual genotyping of black-footed cat ( Felis nigripes). Ecol Evol 2024; 14:e11315. [PMID: 38660470 PMCID: PMC11040180 DOI: 10.1002/ece3.11315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 03/07/2024] [Accepted: 04/05/2024] [Indexed: 04/26/2024] Open
Abstract
The black-footed cat (Felis nigripes) is endemic to the arid regions of southern Africa. One of the world's smallest wild felids, the species occurs at low densities and is secretive and elusive, which makes ecological studies difficult. Genetic data could provide key information such as estimates on population size, sex ratios, and genetic diversity. In this study, we test if microsatellite loci can be successfully amplified from scat samples that could be noninvasively collected from the field. Using 21 blood and scat samples collected from the same individuals, we statistically tested whether nine microsatellites previously designed for use in domestic cats can be used to identify individual black-footed cats. Genotypes recovered from blood and scat samples were compared to assess loss of heterozygosity, allele dropout, and false alleles resulting from DNA degradation or PCR inhibitors present in scat samples. The microsatellite markers were also used to identify individuals from scats collected in the field that were not linked to any blood samples. All nine microsatellites used in this study were amplified successfully and were polymorphic. Microsatellite loci were found to have sufficient discriminatory power to distinguish individuals and identify clones. In conclusion, these molecular markers can be used to monitor populations of wild black-footed cats noninvasively. The genetic data will be able to contribute important information that may be used to guide future conservation initiatives.
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Affiliation(s)
- Vimbai I. Siziba
- School of Life SciencesUniversity of KwaZulu‐NatalScottsvilleSouth Africa
| | | | - Beryl Wilson
- McGregor MuseumKimberleyNorthern CapeSouth Africa
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Resende CF, Santos AM, Cook RF, Victor RM, Câmara RJF, Gonçalves GP, Lima JG, Maciel e Silva AG, Leite RC, dos Reis JKP. Low transmission rates of Equine infectious anemia virus (EIAV) in foals born to seropositive feral mares inhabiting the Amazon delta region despite climatic conditions supporting high insect vector populations. BMC Vet Res 2022; 18:286. [PMID: 35869474 PMCID: PMC9306203 DOI: 10.1186/s12917-022-03384-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 07/08/2022] [Indexed: 11/10/2022] Open
Abstract
Background Marajó Island, within in the Amazon River Delta, supports numerous bands of feral equids including the genetically distinct Marajoara horses. Approximately 40% of the equids on the island are infected with Equine infectious anemia virus (EIAV). This high seropositivity rate coupled with the need to preserve rare breeds such as the Marajoara horse precludes euthanasia as the primary means for controlling EIAV in this region. In the absence of iatrogenic transmission, spread of this lentivirus is mediated primarily by hematophagous insects, whose year-round prevalence on the island is supported by favorable climatic conditions. In addition, cases of vertical EIAV transmission have been observed suggesting inclusion of seropositive mares in restorative breeding programs could result in their progeny becoming infected with this virus either pre-parturition or post-partum via hematophagous insects. Therefore, the aim of this study was to evaluate EIAV vertical and post-partum insect-mediated transmission rates among foals born to seropositive feral mares until natural weaning. Serum samples from foals born to seropositive feral mares within the Soure municipality, of Marajó Island, were collected to investigate their serological status, using an indirect ELISApgp45, with positive samples confirmed using the classical agar gel immunodiffusion (AGID) assay. Results The serological status of 28 foals were monitored over a 2-year period with some subjects, depending on their date of birth, being sampled up to six times. All foals remained with their respective mares until fully weaned at approximately 10 months of age. Only 2 foals (7.14%) in the study group became seropositive against EIAV. Conclusion The results demonstrate that in most cases it is possible to obtain seronegative foals born to and eventually weaned by EIA positive mares, even in equatorial regions where substantial rainfall and high temperatures favor the proliferation of insect vectors.
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de Faria DA, do Prado Paim T, Dos Santos CA, Paiva SR, Nogueira MB, McManus C. Selection signatures for heat tolerance in Brazilian horse breeds. Mol Genet Genomics 2022; 297:449-462. [PMID: 35150300 DOI: 10.1007/s00438-022-01862-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 01/24/2022] [Indexed: 12/14/2022]
Abstract
Since domestication, horse breeds have adapted to their environments and differentiated from one another. This paper uses two methods to detect selection signatures in 23 horse breeds, eight of which are Brazilian (610 animals), both cold-blooded and warm-blooded, from temperate and tropical regions. These animals were genotyped using the GGP Equine BeadChip and we analysed the data by Principal Component Analysis (PCA). The samples were separated into groups based on their geographical area of origin and PCA results studied. The genomic regions under selection were detected by hapFLK and PCAdapt methodologies, identifying six regions under selection with at least one Brazilian horse breed. These regions contain genes associated with heat tolerance, skin colour, body size, energy production/metabolism, genes involved in protein degradation/turnover/DNA repair, genes reducing the impact of oxidative stress/cellular repair, and transcriptional regulation. This work confirmed LCORL and NCAPG gene regions in previous studies associated with body size on Equine Chromosome Autosome 3 (ECA3). On the same ECA3, a region implicating genes linked to coat colour was identified, also previously related to heat stress. Regions with genes coding heat shock proteins were found on ECA1 and 2, and many candidate genes for oxidation-reduction which are a natural response to heat stress. However, a larger sample size and whole-genome SNPs are needed to understand better and identify new candidate regions as well as their functional relation with heat tolerance.
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Affiliation(s)
- Danielle Assis de Faria
- Faculdade de Agronomia e Veterinária, Instituto Central de Ciências, Campus Darcy Ribeiro, Universidade de Brasília, Asa Norte, Brasília, DF, 70910-900, Brazil
| | - Tiago do Prado Paim
- Instituto Federal de Educação, Ciência e Tecnologia Goiano, Rodovia Sul Goiana, Km 01, Zona Rural, Rio Verde, GO, 75901-970, Brazil
| | - Camila Alves Dos Santos
- Instituto Federal de Educação, Ciência e Tecnologia Goiano, Rodovia Sul Goiana, Km 01, Zona Rural, Rio Verde, GO, 75901-970, Brazil
| | - Samuel Rezende Paiva
- Embrapa Recursos Genéticos e Biotecnologia, Final W5 Norte, Brasília, DF, 70770-917, Brasil
| | - Marcelo Bchara Nogueira
- Faculdade de Agronomia e Veterinária, Instituto Central de Ciências, Campus Darcy Ribeiro, Universidade de Brasília, Asa Norte, Brasília, DF, 70910-900, Brazil
| | - Concepta McManus
- Departamento de Ciências Fisiológicas, Instituto de Biologia, Campus Darcy Ribeiro, Universidade de Brasília, Asa Norte, Brasília, DF, 70910-900, Brazil.
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Ianella P, Albuquerque MDSM, Paiva SR, Egito AAD, Almeida LD, Sereno FTPS, Carvalho LFR, Mariante ADS, McManus CM. D-loop haplotype diversity in Brazilian horse breeds. Genet Mol Biol 2017; 40:604-609. [PMID: 28863209 PMCID: PMC5596364 DOI: 10.1590/1678-4685-gmb-2016-0166] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 03/25/2017] [Indexed: 12/03/2022] Open
Abstract
The first horses were brought to Brazil by the colonizers after 1534. Over the centuries, these animals evolved and adapted to local environmental conditions usually unsuitable for exotic breeds, thereby originating locally adapted Brazilian breeds. The present work represents the first description of maternal genetic diversity in these horse breeds based on D-loop sequences. A D-Loop HSV-I fragment of 252 bp, from 141 horses belonging to ten Brazilian breeds / genetic groups (locally adapted and specialized breeds) were analysed. Thirty-five different haplotypes belonging to 18 haplogroups were identified with 33 polymorphic sites. Haplotype diversity (varying from 0.20 to 0.96) and nucleotide diversity (varying from 0.0039 to 0.0239) was lower for locally adapted than for specialized breeds, with the same pattern observed for FST values. Haplogroups identified in Brazilian breeds are in agreement with previous findings in South American samples. The low variability observed mainly in locally adapted breeds, indicates that, to ensure conservation of these breeds, careful reproductive management is needed. Additional genetic characterization studies are required to support accurate decision-making.
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Affiliation(s)
- Patrícia Ianella
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Brasília, DF, Brazil
| | | | - Samuel Rezende Paiva
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Brasília, DF, Brazil
| | | | | | - Fabiana T P S Sereno
- Faculdade de Agronomia e Medicina Veterinária, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, Brazil
| | | | | | - Concepta Margaret McManus
- Faculdade de Agronomia e Medicina Veterinária, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, Brazil
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Cortés O, Dunner S, Gama LT, Martínez AM, Delgado JV, Ginja C, Jiménez LM, Jordana J, Luis C, Oom MM, Sponenberg DP, Zaragoza P, Vega-Pla JL. The legacy of Columbus in American horse populations assessed by microsatellite markers. J Anim Breed Genet 2017; 134:340-350. [PMID: 28194814 DOI: 10.1111/jbg.12255] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 12/21/2016] [Indexed: 11/27/2022]
Abstract
Criollo horse populations descend from horses brought from the Iberian Peninsula over the period of colonization (15th to 17th century). They are spread throughout the Americas and have potentially undergone genetic hybridization with other breeds in the recent past. In this study, 25 autosomal microsatellites were genotyped in 50 horse breeds representing Criollo populations from 12 American countries (27 breeds), breeds from the Iberian Peninsula (19), one breed each from France and Morocco and two cosmopolitan horse breeds (Thoroughbred and Arabian). The genetic relationships among breeds identified five clusters: Celtic; Iberian; North American with Thoroughbred influence; most Colombian breeds; and nearly all other Criollo breeds. The group of "all other Criollo breeds" had the closest genetic relationship with breeds originating from the Iberian Peninsula, specifically with the Celtic group. For the whole set of Criollo breeds analysed, the estimated genetic contribution from other breeds was approximately 50%, 30% and 20% for the Celtic, Iberian and Arab-Thoroughbred groups, respectively. The spatial distribution of genetic diversity indicates that hotspots of genetic diversity are observed in populations from Colombia, Ecuador, Brazil, Paraguay and western United States, possibly indicating points of arrival and dispersion of Criollo horses in the American continent. These results indicate that Criollo breeds share a common ancestry, but that each breed has its own identity.
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Affiliation(s)
- O Cortés
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - S Dunner
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain
| | - L T Gama
- CIISA, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisboa, Portugal
| | - A M Martínez
- Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
| | - J V Delgado
- Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
| | - C Ginja
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-InBIO), Universidade do Porto, Vairão, Portugal
| | - L M Jiménez
- Departamento de Producción Animal, Facultad de Medicina Veterinaria y de Zootecnia, Universidad Nacional de Colombia Sede Bogotá, Bogota, Columbia
| | - J Jordana
- Departamento de Ciencia Animal y de los Alimentos, Facultad de Veterinaria, Bellaterra, Spain
| | - C Luis
- Centro Interuniversitário de História das Ciências e da Tecnologia (CIUHCT), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal.,Museu Nacional de História Natural e da Ciência (MUHNAC), Universidade de Lisboa, Lisboa, Portugal.,CIES-UL, Instituto Universitário de Lisboa (ISCTE-IUL), Lisboa, Portugal
| | - M M Oom
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - D P Sponenberg
- Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
| | - P Zaragoza
- Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Universidad de Zaragoza, Zaragoza, Spain
| | | | - J L Vega-Pla
- Laboratorio de Investigación Aplicada, Crıa Caballar de las Fuerzas Armadas, Cordoba, Spain
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Establishment of a microsatellite set for noninvasive paternity testing in free-ranging Macaca mulatta tcheliensis in Mount Taihangshan area, Jiyuan, China. Zool Stud 2015; 54:e8. [PMID: 31966095 DOI: 10.1186/s40555-014-0100-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 12/25/2014] [Indexed: 11/10/2022]
Abstract
BACKGROUND Within multi-male and multi-female mammalian societies, paternity assignment is crucial for evaluating male reproductive success, dominance hierarchy, and inbreeding avoidance. It is, however, difficult to determine paternity because of female promiscuity during reproduction. Noninvasive molecular techniques (e.g., fecal DNA) make it possible to match the genetic father to his offspring. In the current study, a troop of free-ranging Taihangshan macaques (Macaca mulatta tcheliensis) in Mt. Taihangshan area, Jiyuan, China, was selected for studying the paternity. We successfully screened a set of microsatellite loci from fecal DNA and evaluated the efficiency of these loci for paternity testing using clearly recorded data of maternity. RESULTS The results showed that: 1) ten loci out of 18 candidate microsatellite loci were amplified successfully in the fecal samples of Taihangshan macaques. The error probability in maternity assignments and paternity testing was very low as indicated by their power of discrimination (0.70 to 0.95), power of exclusion (0.43 to 0.84), and the values of polymorphic information content ranging from 0.52 to 0.82; 2) the combined probability of exclusion in paternity testing for ten qualified loci was as high as 99.999%, and the combined probability of exclusion reached 99.99% when the seven most polymorphic loci were adopted; 3) the offspring were assigned to their biological mother correctly and also matched with their genetic father. CONCLUSIONS We concluded that the ten polymorphic microsatellite loci, especially a core set of seven most polymorphic loci, provided an effective and reliable tool for noninvasive paternity testing in free-ranging rhesus macaques.
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da Silva EC, McManus CM, de Paiva Guimarães MPSLM, Gouveia AMG, Facó O, Pimentel DM, Caetano AR, Paiva SR. Validation of a microsatellite panel for parentage testing of locally adapted and commercial goats in Brazil. Genet Mol Biol 2014; 37:54-60. [PMID: 24688291 PMCID: PMC3958326 DOI: 10.1590/s1415-47572014000100010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 12/03/2013] [Indexed: 11/22/2022] Open
Abstract
Brazilian goats are generally kept in small herds and extensive rearing systems, mainly in the northeastern region of the country. Despite production improvement in recent years, the lack of pedigree control has affected genetic progress. This study aimed to validate a panel of 16 microsatellites for parentage testing in locally adapted and commercial goats breeds raised in Brazil, as well as to compare its efficiency with the panel recommended by the Brazilian Ministry of Agriculture, Livestock and Supplies (MAPA) in 2004. The number of alleles and expected heterozygosity (He) per marker ranged from four to 18, and from 0.051 to 0.831, respectively. Using all markers, 100% of parentage cases of the validation dataset were resolved with a strict confidence level of 95%. The 16 microsatellites panel showed adequate exclusion power (99.99%) and identity accuracy (99.99%). Suggestions for improvement of the marker panel endorsed by MAPA are provided.
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Affiliation(s)
- Elizabete Cristina da Silva
- Pós-graduação em Ciências Animais, Universidade de Brasília, Brasília, DF, Brazil . ; Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
| | - Concepta Margaret McManus
- Pós-graduação em Ciências Animais, Universidade de Brasília, Brasília, DF, Brazil . ; Departamento de Zootecnia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | | | - Aurora M G Gouveia
- Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Daniel M Pimentel
- Faculdade de Agronomia e Medicina Veterinária, Universidade de Brasília, Brasília, DF, Brazil
| | - Alexandre Rodrigues Caetano
- Pós-graduação em Ciências Animais, Universidade de Brasília, Brasília, DF, Brazil . ; Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil
| | - Samuel Rezende Paiva
- Pós-graduação em Ciências Animais, Universidade de Brasília, Brasília, DF, Brazil . ; Embrapa Recursos Genéticos e Biotecnologia, Brasília, DF, Brazil . ; Embrapa Sede, Secretaria de Relações Internacionais, Brasília, DF, Brazil
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Wang H, Jia Y, Huang W, Zheng Y, Li H. Individual identification of Chinese Holstein Bull by 10 STR loci. Mol Biol Rep 2014; 41:1201-6. [DOI: 10.1007/s11033-013-2930-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 12/20/2013] [Indexed: 11/24/2022]
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Piro M, Benjouad A, Karom A, Nabich A, Benbihi N, El Allali K, Machmoum M, Ouragh L. Genetic Structure of Severe Combined Immunodeficiency Carrier Horses in Morocco Inferred by Microsatellite Data. J Equine Vet Sci 2011. [DOI: 10.1016/j.jevs.2011.03.013] [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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Li D, Cui H, Wang C, Ling S, Huang Z, Zhang H. A fast and effective method to perform paternity testing for Wolong giant pandas. ACTA ACUST UNITED AC 2011. [DOI: 10.1007/s11434-011-4571-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Genetic diversity and population structure of three Indian horse breeds. Mol Biol Rep 2010; 38:3505-11. [PMID: 21104137 DOI: 10.1007/s11033-010-0461-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Accepted: 11/09/2010] [Indexed: 10/18/2022]
Abstract
The genetic relationships of three Indian horse breeds-Marwari, Spiti, and Kathiawari were studied by genotyping 96 individuals with 20 polymorphic microsatellite markers. A total of 157 alleles were detected across 20 polymorphic loci. The Marwari population showed the highest allelic diversity (A = 5.7 and Ar = 5.14), followed by Spiti (A = 4.9 and Ar = 4.74) and Kathiawari (A = 4.1 and Ar = 3.82). The gene diversity was highest in the Spiti population (He = 0.67), followed by Marwari (He = 0.66) and Kathiawari (He = 0.59). Within population inbreeding estimates (f) in Marwari, Spiti and Kathiawari breeds were 0.18, 0.08, and 0.07, respectively, suggesting high level of inbreeding in these breeds. Analysis of bottleneck revealed evidence of recent bottleneck in Spiti and Kathiawari populations. Pair-wise Fst analysis, AMOVA and assignment tests demonstrated high genetic differentiation and low gene flow between populations. The information about genetic diversity and population structure will be useful for the future development of effective breeding management in order to preserve these Indian horse breeds.
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Ozkan E, Soysal MI, Ozder M, Koban E, Sahin O, Togan İ. Evaluation of parentage testing in the Turkish Holstein population based on 12 microsatellite loci. Livest Sci 2009. [DOI: 10.1016/j.livsci.2009.01.004] [Citation(s) in RCA: 7] [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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