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Aliakbari Z, Kayvanfar N, Rajabi‐Maham H, Ghasempouri SM. Evidence for introgressive hybridization of wild black‐necked pheasant with the exotic ring‐necked pheasant during the past 50 years in the Hyrcanian zone, an integrative molecular and morphological approach. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zohreh Aliakbari
- Environmental Science Department Tarbiat Modares University Noor Iran
| | - Nasrin Kayvanfar
- Research Department of Zoological Innovation Faculty of Sciences Institute of Applied Zoology Ferdowsi University of Mashhad Mashhad Iran
| | - Hassan Rajabi‐Maham
- Animal Sciences and Biotechnology Department Faculty of Life Sciences and Biotechnology Shahid Beheshti University Tehran Iran
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Vázquez‐Miranda H, Olson MJ, Zink RM. Evolutionary Origin and Genetic Diversity of Ring‐necked Pheasants in the Upper Midwest United States. WILDLIFE SOC B 2020. [DOI: 10.1002/wsb.1095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Hernán Vázquez‐Miranda
- School of Natural Resources, and Nebraska State Museum, University of Nebraska Lincoln NE 68583 USA
| | - Magdalena J. Olson
- School of Natural Resources, and Nebraska State Museum, University of Nebraska Lincoln NE 68583 USA
| | - Robert M. Zink
- School of Natural Resources, School of Biological Sciences, Nebraska State Museum, University of Nebraska Lincoln NE 68583 USA
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Douglas MR, Anthonysamy WJB, Mussmann SM, Davis MA, Louis W, Douglas ME. Multi-targeted management of upland game birds at the agroecosystem interface in midwestern North America. PLoS One 2020; 15:e0230735. [PMID: 32339176 PMCID: PMC7185590 DOI: 10.1371/journal.pone.0230735] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/06/2020] [Indexed: 11/18/2022] Open
Abstract
Despite its imperative, biodiversity conservation is chronically underfunded, a deficiency that often forces management agencies to prioritize. Single-species recovery thus becomes a focus (often with socio-political implications), whereas a more economical approach would be the transition to multi-targeted management (= MTM). This challenge is best represented in Midwestern North America where biodiversity has been impacted by 300+ years of chronic anthropogenic disturbance such that native tall-grass prairie is now supplanted by an agroecosystem. Here, we develop an MTM with a population genetic metric to collaboratively manage three Illinois upland gamebirds: common pheasant (Phasianus colchicus; pheasant), northern bobwhite quail (Colinus virginianus; quail), and threatened-endangered (T&E) greater prairie chicken (Tympanuchus cupido pinnatus; prairie chicken). We first genotyped our study pheasant at 19 microsatellite DNA loci and identified three captive breeding stocks (N = 143; IL Department of Natural Resources) as being significantly bottlenecked, with relatedness >1st-cousin (μR = 0.158). 'Wild' (non-stocked) pheasant [N = 543; 14 Pheasant-Habitat-Areas (PHAs)] were also bottlenecked, significantly interrelated (μR = 0.150) and differentiated (μFST = 0.047), yet distinct from propagation stock. PHAs that encompassed significantly with larger areas also reflected greater effective population sizes (μNE = 43; P<0.007). We juxtaposed these data against previously published results for prairie chicken and quail, and found population genetic structure driven by drift, habitat/climate impacts, and gender-biased selection via hunter-harvest. Each species (hunter-harvested or T&E) is independently managed, yet their composite population genetic baseline provides the quantitative criteria needed for an upland game bird MTM. Its implementation would require agricultural plots to be rehabilitated/reclaimed using a land-sharing/sparing portfolio that differs markedly from the Conservation Reserve Program (CRP), where sequestered land decreases as agricultural prices escalate. Cost-savings for an MTM would accrue by synchronizing single-species management with a dwindling hunter-harvest program, and by eliminating propagation/stocking programs. This would sustain not only native grasslands and their resident species, but also accelerate conservation at the wildlife-agroecosystem interface.
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Affiliation(s)
- Marlis R. Douglas
- Biological Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
| | | | - Steven M. Mussmann
- Biological Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Mark A. Davis
- Illinois Natural History Survey, University of Illinois, Champaign, Illinois, United States of America
| | - Wade Louis
- Illinois Department of Natural Resources, Gibson City, Illinois, United States of America
| | - Michael E. Douglas
- Biological Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
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Romanov M, Sazanov A, Smirnov A. First century of chicken gene study and mapping – a look back and forward. WORLD POULTRY SCI J 2019. [DOI: 10.1079/wps20032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- M.N. Romanov
- Department of Microbiology and Molecular Genetics, 2209 Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824–4320, USA
| | - A.A. Sazanov
- All-Russian Institute of Animal Genetics and Breeding, Russian Academy of Agricultural Science, Moskovskoye shosse 55A, St Petersburg – Pushkin 189620, Russia
- Biological Research Institute, St Petersburg State University, Oranienbaumskoye shosse 2, St Petersburg – Stary Petergof 198504, Russia
| | - A.F. Smirnov
- All-Russian Institute of Animal Genetics and Breeding, Russian Academy of Agricultural Science, Moskovskoye shosse 55A, St Petersburg – Pushkin 189620, Russia
- Biological Research Institute, St Petersburg State University, Oranienbaumskoye shosse 2, St Petersburg – Stary Petergof 198504, Russia
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Dawson DA, Ball AD, Spurgin LG, Martín-Gálvez D, Stewart IRK, Horsburgh GJ, Potter J, Molina-Morales M, Bicknell AWJ, Preston SAJ, Ekblom R, Slate J, Burke T. High-utility conserved avian microsatellite markers enable parentage and population studies across a wide range of species. BMC Genomics 2013; 14:176. [PMID: 23497230 PMCID: PMC3738869 DOI: 10.1186/1471-2164-14-176] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 02/19/2013] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Microsatellites are widely used for many genetic studies. In contrast to single nucleotide polymorphism (SNP) and genotyping-by-sequencing methods, they are readily typed in samples of low DNA quality/concentration (e.g. museum/non-invasive samples), and enable the quick, cheap identification of species, hybrids, clones and ploidy. Microsatellites also have the highest cross-species utility of all types of markers used for genotyping, but, despite this, when isolated from a single species, only a relatively small proportion will be of utility. Marker development of any type requires skill and time. The availability of sufficient "off-the-shelf" markers that are suitable for genotyping a wide range of species would not only save resources but also uniquely enable new comparisons of diversity among taxa at the same set of loci. No other marker types are capable of enabling this. We therefore developed a set of avian microsatellite markers with enhanced cross-species utility. RESULTS We selected highly-conserved sequences with a high number of repeat units in both of two genetically distant species. Twenty-four primer sets were designed from homologous sequences that possessed at least eight repeat units in both the zebra finch (Taeniopygia guttata) and chicken (Gallus gallus). Each primer sequence was a complete match to zebra finch and, after accounting for degenerate bases, at least 86% similar to chicken. We assessed primer-set utility by genotyping individuals belonging to eight passerine and four non-passerine species. The majority of the new Conserved Avian Microsatellite (CAM) markers amplified in all 12 species tested (on average, 94% in passerines and 95% in non-passerines). This new marker set is of especially high utility in passerines, with a mean 68% of loci polymorphic per species, compared with 42% in non-passerine species. CONCLUSIONS When combined with previously described conserved loci, this new set of conserved markers will not only reduce the necessity and expense of microsatellite isolation for a wide range of genetic studies, including avian parentage and population analyses, but will also now enable comparisons of genetic diversity among different species (and populations) at the same set of loci, with no or reduced bias. Finally, the approach used here can be applied to other taxa in which appropriate genome sequences are available.
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Affiliation(s)
- Deborah A Dawson
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Alexander D Ball
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
- Current address: Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Lewis G Spurgin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - David Martín-Gálvez
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
- Current address: Estación Experimental de Zonas Áridas (CSIC), Almería, E-04120, Spain
| | - Ian R K Stewart
- Department of Biology, University of Delaware, Newark, DE, 19716, USA
| | - Gavin J Horsburgh
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Jonathan Potter
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Mercedes Molina-Morales
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
- Current address: Departamento de Zoología, Universidad de Granada, Granada, E-18071, Spain
| | - Anthony W J Bicknell
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
- Current address: Plymouth University, Marine Biology and Ecology Research Centre, Davy Building, Drake Circus, Plymouth, PL4 8AA, UK
| | - Stephanie A J Preston
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Robert Ekblom
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
- Current address: Department of Ecology and Genetics, Uppsala University, Norbyv. 18D, Uppsala, SE-75236, Sweden
| | - Jon Slate
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Terry Burke
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
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Mukesh T, Rai ID, Mandhan RP, Sathyakumar S. A panel of polymorphic microsatellite markers in Himalayan monal Lophophorus impejanus developed by cross-species amplification and their applicability in other Galliformes. EUR J WILDLIFE RES 2011. [DOI: 10.1007/s10344-011-0494-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Scandura M, Iacolina L, Apollonio M, Dessì-Fulgheri F, Baratti M. Current status of the Sardinian partridge (Alectoris barbara) assessed by molecular markers. EUR J WILDLIFE RES 2009. [DOI: 10.1007/s10344-009-0286-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Küpper C, Burke T, Székely T, Dawson DA. Enhanced cross-species utility of conserved microsatellite markers in shorebirds. BMC Genomics 2008; 9:502. [PMID: 18950482 PMCID: PMC2588463 DOI: 10.1186/1471-2164-9-502] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Accepted: 10/24/2008] [Indexed: 11/24/2022] Open
Abstract
Background Microsatellite markers are popular genetic markers frequently used in forensic biology. Despite their popularity, the characterisation of polymorphic microsatellite loci and development of suitable markers takes considerable effort. Newly-available genomic databases make it feasible to identify conserved genetic markers. We examined the utility and characteristics of conserved microsatellite markers in Charadriiformes (plovers, sandpipers, gulls and auks). This order harbours many species with diverse breeding systems, life histories and extraordinary migration biology whose genetics warrant investigation. However, research has been largely restrained by the limited availability of genetic markers. To examine the utility of conserved microsatellite loci as genetic markers we collated a database of Charadriiformes microsatellites, searched for homologues in the chicken genome and tested conserved markers for amplification and polymorphism in a range of charadriiform species. Results Sixty-eight (42%) of 161 charadriiform microsatellite loci were assigned to a single location in the chicken genome based on their E-value. Fifty-five primers designed from conserved microsatellite loci with an E-value of E-10 or lower amplified across a wider range of charadriiform species than a control group of primers from ten anonymous microsatellite loci. Twenty-three of 24 examined conserved markers were polymorphic, each in on average 3 of 12 species tested. Conclusion Genomic sequence databases are useful tools to identify conserved genetic markers including those located in non-coding regions. By maximising primer sequence similarity between source species and database species, markers can be further improved and provide additional markers to study the molecular ecology of populations of non-model organisms.
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Affiliation(s)
- Clemens Küpper
- NERC Molecular Genetics Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.
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Polymorphic microsatellites in Buff-throated partridge developed by cross-species amplification. EUR J WILDLIFE RES 2008. [DOI: 10.1007/s10344-008-0217-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Saino N, Rubolini D, Romano M, Boncoraglio G. Increased egg estradiol concentration feminizes digit ratios of male pheasants (Phasianus colchicus). Naturwissenschaften 2006; 94:207-12. [PMID: 17136513 DOI: 10.1007/s00114-006-0188-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2006] [Revised: 10/20/2006] [Accepted: 10/20/2006] [Indexed: 10/23/2022]
Abstract
The length ratio between individual digits differs between males and females in humans, other mammals, lizards, and one bird species. Sexual dimorphism in digit ratios and variation among individuals of the same sex may depend on differential exposure to androgens and estrogens during embryonic life. Organizational effects of sex hormones could cause the observed correlations between digit ratios and diverse phenotypic traits in humans. However, no study has investigated experimentally the effect of prenatal estrogens on digit ratios. We analyzed the effect of estradiol injection in ring-necked pheasant (Phasianus colchicus) eggs on digit ratios. Males from control eggs had higher ratios between the second or third and the fourth digit of the right foot compared to females. Estradiol-treated eggs produced males with lower (feminized) right foot second to fourth digit ratio. Thus, we provided the first experimental evidence that prenatal exposure to physiologically high estrogen levels affects bird digit ratios.
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Affiliation(s)
- N Saino
- Dipartimento di Biologia, Università degli Studi di Milano, via Celoria 26, 20133 Milan, Italy.
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Chaves LD, Knutson TP, Krueth SB, Reed KM. Using the chicken genome sequence in the development and mapping of genetic markers in the turkey (Meleagris gallopavo). Anim Genet 2006; 37:130-8. [PMID: 16573527 DOI: 10.1111/j.1365-2052.2005.01396.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The efficacy of employing the chicken genome sequence in developing genetic markers and in mapping the turkey genome was studied. Eighty previously uncharacterized microsatellite markers were identified for the turkey using BLAST alignment to the chicken genome. The chicken sequence was then used to develop primers for polymerase chain reaction where the turkey sequence was either unavailable or insufficient. A total of 78 primer sets were tested for amplification and polymorphism in the turkey, and informative markers were genetically mapped. Sixty-five (83%) amplified turkey genomic DNA, and 33 (42%) were polymorphic in the University of Minnesota/Nicholas Turkey Breeding Farms mapping families. All but one marker genetically mapped to the position predicted from the chicken genome sequence. These results demonstrate the usefulness of the chicken sequence for the development of genomic resources in other avian species.
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Affiliation(s)
- L D Chaves
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St Paul, MN 55108, USA
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Huang Y, Zhao Y, Haley CS, Hu S, Hao J, Wu C, Li N. A genetic and cytogenetic map for the duck (Anas platyrhynchos). Genetics 2006; 173:287-96. [PMID: 16510785 PMCID: PMC1461431 DOI: 10.1534/genetics.105.053256] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A genetic linkage map for the duck (Anas platyrhynchos) was developed within a cross between two extreme Peking duck lines by linkage analysis of 155 polymorphic microsatellite markers, including 84 novel markers reported in this study. A total of 115 microsatellite markers were placed into 19 linkage groups. The sex-averaged map spans 1353.3 cM, with an average interval distance of 15.04 cM. The male map covers 1415 cM, whereas the female map covers only 1387.6 cM. All of the flanking sequences of the 155 polymorphic loci--44 monomorphic loci and a further 41 reported microsatellite loci for duck--were blasted against the chicken genomic sequence, and corresponding orthologs were found for 49. To integrate the genetic and cytogenetic map of the duck genome, 28 BAC clones were screened from a chicken BAC library using the specific PCR primers and localized to duck chromosomes by FISH, respectively. Of 28 BAC clones, 24 were detected definitely on duck chromosomes. Thus, 11 of 19 linkage groups were localized to 10 duck chromosomes. This genetic and cytogenetic map will be helpful for the mapping QTL in duck for breeding applications and for conducting genomic comparisons between chicken and duck.
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Affiliation(s)
- Yinhua Huang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, People's Republic of China
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Rubolini D, Romano M, Martinelli R, Leoni B, Saino N. Effects of prenatal yolk androgens on armaments and ornaments of the ring-necked pheasant. Behav Ecol Sociobiol 2005. [DOI: 10.1007/s00265-005-0080-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Baratti M, Ammannati M, Magnelli C, Dessì-Fulgheri F. Introgression of chukar genes into a reintroduced red-legged partridge (Alectoris rufa) population in central Italy. Anim Genet 2005; 36:29-35. [PMID: 15670128 DOI: 10.1111/j.1365-2052.2004.01219.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Insight regarding the genetic origin and composition of the studied population of the red-legged partridge (Alectoris rufa) is likely to provide general and critical information for the appropriate management and possible conservation of the species. The reintroduced population of red-legged partridges living in Pianosa Island (National Park Tuscany Archipelago) has proven to be sustainable: captive-bred individuals, morphologically assigned to the taxon A. rufa, were released to the island approximately 20 years ago, establishing an apparently well-adapted population. We have investigated this population by means of 10 microsatellite loci in order to shed light on its genetic structure. Considering that A. rufa is known to crossbreed with A. chukar, the Pianosa Island population was compared at the molecular level with a red-legged partridge breeding stock (Aulla, MS) as well as with a population of pure A. chukar. Our results indicate that the red-legged partridge population from Pianosa, morphologically identified as A. rufa, is actually partly introgressed with A. chukar, questioning its genetic purity and the possible use of this population as a starting stock for future reintroductions elsewhere.
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Affiliation(s)
- M Baratti
- Department of Animal Biology and Genetics, University of Florence, Via Romana 17, 50125 Florence, Italy.
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Baliraine FN, Bonizzoni M, Osir EO, Lux SA, Mulaa FJ, Zheng L, Gomulski LM, Gasperi G, Malacrida AR. Comparative analysis of microsatellite loci in four fruit fly species of the genus Ceratitis (Diptera: Tephritidae). BULLETIN OF ENTOMOLOGICAL RESEARCH 2003; 93:1-10. [PMID: 12593677 DOI: 10.1079/ber2002212] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The possibility to cross-species amplify microsatellites in fruit flies of the genus Ceratitis was tested with the polymerase chain reaction (PCR) by analysing 23 Ceratitis capitata (Wiedemann) microsatellite markers on the genomic DNA of three other economically important, congeneric species: C. rosa (Karsch), C. fasciventris (Bezzi) and C. cosyra (Walker). Twenty-two primer pairs produced amplification products in at least one of the three species tested. The majority of the products were similar, if not identical in size to those expected in C. capitata. The structures of the repeat motifs and their flanking sequences were examined for a total of 79 alleles from the three species. Sequence analysis revealed the same repeat type as the homologous C. capitata microsatellites in the majority of the loci, suggesting their utility for population analysis across the species range. A total of seven loci were differentially present/absent in C. capitata, C. rosa, C. fasciventris and C. cosyra, suggesting that it may be possible to differentiate these four species using a simple sequence repeat-based PCR assay. It is proposed that medfly-based microsatellite markers could be utilized in the identification and tracing of the geographical origins of colonist pest populations of the four tested species and in the assessment of their risk and invasive potentials; thereby assisting regulatory authorities in implementing quarantine restrictions and other pest control measures.
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Affiliation(s)
- F N Baliraine
- International Centre of Insect Physiology and Ecology, PO Box 30772, Nairobi, Kenya
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