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Prinz K, Hensen I, Schie S, Debener T, Weising K. Microsatellite markers for the tetraploid halophyte Suaeda maritima (L.) Dumort. (Chenopodiaceae) and cross-species amplification in related taxa. Mol Ecol Resour 2009; 9:1247-9. [PMID: 21564891 DOI: 10.1111/j.1755-0998.2009.02620.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We developed 12 polymorphic microsatellite markers for the tetraploid halophyte Suaeda maritima (Chenopodiaceae). Population genetic parameters were estimated for three populations from different habitats (coastal and inland), using the program Tetrasat. Between two and 15 alleles per locus were observed. Mean expected heterozygosities (H(E) ) and Shannon-Wiener Diversity Indices (H') per locus and population ranged from zero to 0.852, and from zero to 2.990, respectively. The two inland populations were less diverse than the coastal one at most of the loci. All markers cross-amplified in the closely related Suaeda salsa, and all but one were transferable to Suaeda spicata and Suaeda salinaria.
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Affiliation(s)
- Kathleen Prinz
- Plant Molecular Systematics, University of Kassel, D-34109 Kassel, Germany
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52
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Wang SL, Niu DH, Li JL. Isolation and characterization of 10 polymorphic microsatellites in Meretrix meretrix. CONSERV GENET RESOUR 2009. [DOI: 10.1007/s12686-009-9027-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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53
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Baier C, Guicking D, Prinz K, Fey-Wagner C, Wöhrmann T, Weising K, Debener T, Schie S, Blattner FR. Isolation and characterization of 11 new microsatellite markers for Macaranga (Euphorbiaceae). Mol Ecol Resour 2009; 9:1049-52. [PMID: 21564836 DOI: 10.1111/j.1755-0998.2009.02567.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We provide primer sequences for 11 new polymorphic microsatellite markers developed in the tropical ant-plant genus Macaranga (Euphorbiaceae), after enrichment cloning of Macaranga tanarius and Macaranga hypoleuca. Allele numbers per locus ranged from two to 16 among 20 accessions of M. tanarius, and from three to 10 among 22 accessions of M. hypoleuca. Observed and expected heterozygosities ranged from 0.150 to 0.900 and from 0.375 to 0.894 in M. tanarius, and from 0.545 to 1.000 and from 0.434 to 0.870 in M. hypoleuca, respectively. Six of the 11 primer pairs successfully cross-amplified polymorphic polymerase chain reaction products in Macaranga winkleri.
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Affiliation(s)
- Christina Baier
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany, Plant Molecular Systematics, University of Kassel, 34109 Kassel, Germany, Institute for Plant Genetics, University of Hannover, 30419 Hannover, Germany
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Tatsuta H, Yao I, Tanaka Y. Isolation of eight microsatellite markers from Moina macrocopa for assessing cryptic genetic structure in the wild. Mol Ecol Resour 2009; 9:904-6. [PMID: 21564785 DOI: 10.1111/j.1755-0998.2008.02410.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We isolated eight polymorphic microsatellite loci from the zooplankton Moina macrocopa (Straus), which is sensitive to pollutants such as insecticides and heavy metals. The isolated loci were polymorphic, with three to seven alleles among 23 individuals. Expected heterozygosities ranged from 0.167 to 0.787. These loci can be used to examine cryptic genetic structure and to infer the connectivity among metapopulations.
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Affiliation(s)
- Haruki Tatsuta
- Research Center for Environmental Risk, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki 305-8506, Japan 21st COE Program (Neoscience of Natural History), Graduate School of Science, Hokkaido University, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
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Johanet A, Picard D, Garner TWJ, Dawson DA, Morales-Hojas R, Jehle R, Peltier D, Lemaire C. Characterization of microsatellite loci in two closely related Lissotriton newt species. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9850-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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57
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CARVALHO DC, OLIVEIRA DAA, SAMPAIO I, BEHEREGARAY LB. Microsatellite markers for the Amazon peacock bass (Cichla piquiti). Mol Ecol Resour 2009; 9:239-41. [DOI: 10.1111/j.1755-0998.2008.02425.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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58
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Benichou S, Dongo A, Henni DE, Peltier D, Simoneau P. Isolation and characterization of microsatellite markers from the phytopathogenic fungus Alternaria dauci. Mol Ecol Resour 2008; 9:390-2. [PMID: 21564659 DOI: 10.1111/j.1755-0998.2008.02237.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Eleven polymorphic microsatellite markers were isolated from the necrotrophic phytopathogenic fungus Alternaria dauci based on enriched genomic libraries. In order to assess allelic variability, the microsatellite loci were analysed in a collection of 43 isolates. The number of detected alleles in 11 loci ranged from two to 24 (mean 10.4). Test of cross-species amplification and sequencing of the resulting amplicons showed that some of these microsatellites could be used in different species such as Alternaria solani, Alternaria bataticola and Alternaria zinniae.
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Affiliation(s)
- Soumaya Benichou
- IFR149 QUASAV-UMR PaVé Université d'Angers-INRA-INH, 2 Bd Lavoisier, 49045 Angers cedex, France, Laboratoire Microbiologie Appliquée, Université d'Oran Es-Senia, BP1524 El M'naouer 31000 Oran, Algeria, UMR GenHort, BP 60057, 49071 Beaucouzé cedex, France
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59
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White TA, Stamford J, Rus Hoelzel A. Nine new microsatellite loci for the roundnose grenadier (Coryphaenoides rupestris) with four showing cross-amplification in the shortbeard grenadier (C. brevibarbis). CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9751-6] [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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60
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Isolation and characterization of microsatellite loci in the Amami rabbit (Pentalagus furnessi). CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9723-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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61
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Schemerhorn BJ, Crane YM, Morton PK. Development of polymorphic microsatellite markers in Hessian fly, Mayetiola destructor (Say). Mol Ecol Resour 2008; 8:1360-2. [PMID: 21586046 DOI: 10.1111/j.1755-0998.2008.02300.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A microsatellite library was prepared from size-selected genomic DNA of Hessian fly (Mayetiola destructor). Approximately 81% of recovered clones hybridized with microsatellite motif-specific probes. Subsequently, 2350 clones were sequenced. Sixty-two individual flies from laboratory strains were used to test for reliability and polymorphism in 50 of the microsatellites by gel electrophoresis; 18 were further tested with capillary electrophoresis. Of these, 17 behaved as a polymorphic single locus appropriate for population analysis.
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Affiliation(s)
- Brandon J Schemerhorn
- USDA-ARS, Purdue University, 901 W. State Street, West Lafayette, IN 47907-2089, USA, Department of Entomology, Smith Hall, Purdue University, 901 W. State Street, West Lafayette, IN 47907-2089, USA
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Kodama K, Yamada T, Maki M. Development and characterization of 10 microsatellite markers for the semi-evergreen tree species, Ligustrum ovalifolium (Oleaceae). Mol Ecol Resour 2008; 8:1008-10. [PMID: 21585956 DOI: 10.1111/j.1755-0998.2008.02136.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Ligustrum ovalifolium is a semi-evergreen tree distributed in the western part of Japan and southern Korea. This species contains an insular endemic variety, L. ovalifolium var. pacificum; this variety occurs only on the Izu Islands located south of the Japanese mainland Honshu. We isolated 10 polymorphic microsatellite loci from the species, and characterized them for 21 individuals from a population of L. ovalifolium. The primers developed in this study yielded an average 12.2 alleles per locus and an average expected heterozygosity of 0.78. These markers will be powerful tools for studying the genetic differentiation within the species.
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Affiliation(s)
- Kosei Kodama
- Biological Institute, Faculty of Science, Division of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Aoba, Sendai, Japan 980-8578
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63
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Tada F, Yamashiro T, Maki M. Development of microsatellite markers for the endangered grassland perennial herb Vincetoxicum atratum (Apocynaceae–Asclepiadoideae). CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9687-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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64
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Knutsen H, LE Goff-Vitry M, Fiani D, Hoelzel AR. Isolation and characterization of microsatellite loci in the deep-sea marine fish, the roundnose grenadier (Coryphaenoides rupestris). Mol Ecol Resour 2008; 8:993-5. [PMID: 21585951 DOI: 10.1111/j.1755-0998.2008.02132.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We developed polymerase chain reaction primers for eight dinucleotide microsatellite loci in the marine deep sea fish, roundnose grenadier (Coryphaenoides rupestris). All markers were obtained from a partial genomic DNA library, and characterized in 90 unrelated individuals from one putative population sampled on the Mid-Atlantic Ridge. The number of alleles ranged from two to 61 with an average of 21 per locus. The observed heterozygosity levels ranged from 0.301 to 0.987 with an average of 0.672. Several of the markers amplified multiple alleles from either the Atlantic cod (Gadus morhua) or the deep-sea fish roughhead grenadier (Macrourus berglax).
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Affiliation(s)
- Halvor Knutsen
- Flødevigen Marine Research Station, Department of Coastal Zone, Institute of Marine Research, N-4817 His, Norway, School of Biological and Biomedical Sciences, Durham University, South Road, Durham, DH1 3LE UK, School of Ocean & Earth Science, University of Southampton, Southampton Oceanography Centre, European Way, Southampton SO14 3ZH, UK
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65
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McPherson H, Porter C, Rymer PD, Crayn DM, Rossetto M. Isolation and characterization of polymorphic microsatellite loci from Tetratheca ericifolia (Elaeocarpaceae). Mol Ecol Resour 2008; 8:867-9. [PMID: 21585915 DOI: 10.1111/j.1755-0998.2008.02093.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We identified 11 informative microsatellite loci in Tetratheca ericifolia from an (AG)(n) -enriched library. Using these loci on 32 individuals from two populations (16 individuals from each), we detected an average of 11.3 alleles per locus (range of five to 21, average expected heterozygosity of 0.728), of which 56% were unique to one population or the other. All loci were amplifiable in seven to 12 of a further 12 species of Tetratheca under the same reaction conditions. The markers will be useful tools for evolutionary studies of this Australian endemic group.
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Affiliation(s)
- Hannah McPherson
- National Herbarium of New South Wales, Botanic Gardens Trust, Mrs Macquaries Road, Sydney, NSW 2000, Australia, Ecosystem Management, University of New England, Armidale, NSW 2351, Australia
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66
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Feng JB, Li JL. Twelve polymorphic microsatellites in Oriental river prawn, Macrobrachium nipponense. Mol Ecol Resour 2008; 8:986-8. [PMID: 21585949 DOI: 10.1111/j.1755-0998.2008.02129.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oriental river prawn, Macrobrachium nipponense, is a commercially important freshwater prawn species in China, Japan, Korea and Vietnam. Due to overfishing for food, the wild stocks M. nipponense are endangered. Twenty microsatellite loci were isolated from the M. nipponense. Twelve of these loci were polymorphic (seven to 16 alleles per locus), with expected heterozygosity ranging from 0.68 to 0.86 (n = 48). These polymorphic loci provide a valuable tool for assessing genetic diversity of wild and cultured populations.
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Affiliation(s)
- J B Feng
- Aquaculture Division, E-Institute of Shanghai Universities, Shanghai Fisheries University, 334 Jungong Road, Shanghai 200090, China
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67
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Boontong C, Pandey M, Changtragoon S. Isolation and characterization of microsatellite markers in Indian neem (Azadirachta indica var. indica A. Juss) and cross-amplification in Thai neem (A. indica var. siamensis Valenton). CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9610-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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68
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Cuc LM, Mace ES, Crouch JH, Quang VD, Long TD, Varshney RK. Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea). BMC PLANT BIOLOGY 2008; 8:55. [PMID: 18482440 PMCID: PMC2416452 DOI: 10.1186/1471-2229-8-55] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2008] [Accepted: 05/15/2008] [Indexed: 05/18/2023]
Abstract
BACKGROUND Cultivated peanut or groundnut (Arachis hypogaea L.) is the fourth most important oilseed crop in the world, grown mainly in tropical, subtropical and warm temperate climates. Due to its origin through a single and recent polyploidization event, followed by successive selection during breeding efforts, cultivated groundnut has a limited genetic background. In such species, microsatellite or simple sequence repeat (SSR) markers are very informative and useful for breeding applications. The low level of polymorphism in cultivated germplasm, however, warrants a need of larger number of polymorphic microsatellite markers for cultivated groundnut. RESULTS A microsatellite-enriched library was constructed from the genotype TMV2. Sequencing of 720 putative SSR-positive clones from a total of 3,072 provided 490 SSRs. 71.2% of these SSRs were perfect type, 13.1% were imperfect and 15.7% were compound. Among these SSRs, the GT/CA repeat motifs were the most common (37.6%) followed by GA/CT repeat motifs (25.9%). The primer pairs could be designed for a total of 170 SSRs and were optimized initially on two genotypes. 104 (61.2%) primer pairs yielded scorable amplicon and 46 (44.2%) primers showed polymorphism among 32 cultivated groundnut genotypes. The polymorphic SSR markers detected 2 to 5 alleles with an average of 2.44 per locus. The polymorphic information content (PIC) value for these markers varied from 0.12 to 0.75 with an average of 0.46. Based on 112 alleles obtained by 46 markers, a phenogram was constructed to understand the relationships among the 32 genotypes. Majority of the genotypes representing subspecies hypogaea were grouped together in one cluster, while the genotypes belonging to subspecies fastigiata were grouped mainly under two clusters. CONCLUSION Newly developed set of 104 markers extends the repertoire of SSR markers for cultivated groundnut. These markers showed a good level of PIC value in cultivated germplasm and therefore would be very useful for germplasm analysis, linkage mapping, diversity studies and phylogenetic relationships in cultivated groundnut as well as related Arachis species.
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Affiliation(s)
- Luu M Cuc
- International Crop Research Institute for the Semi Arid Tropics (ICRISAT), Patancheru- 502 324, Greater Hyderabad, Andhra Pradesh, India
- Agriculture Genetics Institute, Vietnamese Academy Agriculture Science, Van Dien, Thanh Tri, Hanoi, Vietnam
| | - Emma S Mace
- International Crop Research Institute for the Semi Arid Tropics (ICRISAT), Patancheru- 502 324, Greater Hyderabad, Andhra Pradesh, India
- Department of Primary Industries & Fisheries, Hermitage Research Station, 604 Yangan Road, Warwick, QLD 4370, Australia
| | - Jonathan H Crouch
- International Crop Research Institute for the Semi Arid Tropics (ICRISAT), Patancheru- 502 324, Greater Hyderabad, Andhra Pradesh, India
- International Wheat and Maize Improvement Centre (CIMMYT), Apdo. Postal 6-641, 06600 Mexico, D.F., Mexico
| | - Vu D Quang
- Agriculture Genetics Institute, Vietnamese Academy Agriculture Science, Van Dien, Thanh Tri, Hanoi, Vietnam
| | - Tran D Long
- Vietnamese Academy Agriculture Science, Van Dien, Thanh Tri, Ha Noi, Vietnam
| | - Rajeev K Varshney
- International Crop Research Institute for the Semi Arid Tropics (ICRISAT), Patancheru- 502 324, Greater Hyderabad, Andhra Pradesh, India
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Zhang HM, Guo Y, Li DS, Wang PY, Fang SG. Sixteen novel microsatellite loci developed for the giant panda (Ailuropoda melanoleuca). CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9576-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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71
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Miyazaki Y, Ohnishi N, Hirayama K, Nagata J. Development and characterization of polymorphic microsatellite DNA markers for Sasa senanensis (Poaceae: Bambuseae). CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9575-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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72
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Twenty-one novel tri- and tetranucleotide microsatellite loci for the Amur tiger (Panthera tigris altaica). CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9571-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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73
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Wang CM, Lo LC, Feng F, Gong P, Li J, Zhu ZY, Lin G, Yue GH. Construction of a BAC library and mapping BAC clones to the linkage map of Barramundi, Lates calcarifer. BMC Genomics 2008; 9:139. [PMID: 18366732 PMCID: PMC2329641 DOI: 10.1186/1471-2164-9-139] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2007] [Accepted: 03/25/2008] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Barramundi (Lates calcarifer) is an important farmed marine food fish species. Its first generation linkage map has been applied to map QTL for growth traits. To identify genes located in QTL responsible for specific traits, genomic large insert libraries are of crucial importance. We reported herein a bacterial artificial chromosome (BAC) library and the mapping of BAC clones to the linkage map. RESULTS This BAC library consisted of 49,152 clones with an average insert size of 98 kb, representing 6.9-fold haploid genome coverage. Screening the library with 24 microsatellites and 15 ESTs/genes demonstrated that the library had good genome coverage. In addition, 62 novel microsatellites each isolated from 62 BAC clones were mapped onto the first generation linkage map. A total of 86 BAC clones were anchored on the linkage map with at least one BAC clone on each linkage group. CONCLUSION We have constructed the first BAC library for L. calcarifer and mapped 86 BAC clones to the first generation linkage map. This BAC library and the improved linkage map with 302 DNA markers not only supply an indispensable tool to the integration of physical and linkage maps, the fine mapping of QTL and map based cloning genes located in QTL of commercial importance, but also contribute to comparative genomic studies and eventually whole genome sequencing.
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Affiliation(s)
- Chun Ming Wang
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Singapore.
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74
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Development and characterization of 14 novel microsatellite markers from the golden pheasant (Chrysolophus pictus). CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9552-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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75
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MCPHERSON HANNAH, PORTER CAROLYN, RYMER PAULD, CRAYN DARRENM, ROSSETTO MAURIZIO. Isolation and characterization of polymorphic microsatellite loci from Tetratheca ericifolia (Elaeocarpaceae). Mol Ecol Resour 2008. [DOI: 10.1111/j.1471-8286.2008.02093.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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76
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ZHU ZEYUAN, YUE GENHUA. Eleven polymorphic microsatellites isolated from red swamp crayfish, Procambarus clarkii. Mol Ecol Resour 2008. [DOI: 10.1111/j.1471-8286.2007.02067.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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77
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YAMAMOTO HIDETOSHI, YAMADA TAKAYUKI, MAKI MASAYUKI. Isolation and characterization of microsatellite markers from the hosta species Hosta albomarginata (Liliaceae). Mol Ecol Resour 2008; 8:185-7. [DOI: 10.1111/j.1471-8286.2007.01918.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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78
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Yamada T, Maki M. Isolation and characterization of microsatellite loci from Weigela coraeensis (Caprifoliaceae). Mol Ecol Resour 2008; 8:155-7. [PMID: 21585743 DOI: 10.1111/j.1471-8286.2007.01908.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Weigela coraeensis var. coraeensis is a deciduous shrub species distributed in Japan on the mainland, Honshu, whereas its variety W. coraeensis var. fragrans is endemic to the Izu Islands located south of Honshu. We isolated eight polymorphic microsatellite loci from the species and characterized these loci for 20 individuals from a population in Honshu. The number of alleles per locus ranged from 7 to 15 and the observed and expected heterozygosities ranged from 0.60 to 0.90 and from 0.65 to 0.90, respectively. These eight polymorphic microsatellites will be useful for examining intraspecific genetic differentiation in W. coraeensis.
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Affiliation(s)
- Takayuki Yamada
- Division of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Aoba, Sendai 980-8578, Japan
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DUFOUR BRADLEYA, HOGAN TERRYM, HEATH DANIELD. Ten polymorphic microsatellite markers in the invasive round goby (Neogobius melanostomus) and cross-species amplification. ACTA ACUST UNITED AC 2007. [DOI: 10.1111/j.1471-8286.2007.01833.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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81
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HAMAGUCHI K, MATSUMOTO T, MARUYAMA M, HASHIMOTO Y, YAMANE S, ITIOKA T. Isolation and characterization of eight microsatellite loci in two morphotypes of the Southeast Asian army ant, Aenictus laeviceps. ACTA ACUST UNITED AC 2007. [DOI: 10.1111/j.1471-8286.2007.01746.x] [Citation(s) in RCA: 8] [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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82
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LI JIALE, ZHU ZEYUAN, WANG GUILING, BAI ZHIYI, YUE GENHUA. Isolation and characterization of 17 polymorphic microsatellites in grass carp. ACTA ACUST UNITED AC 2007. [DOI: 10.1111/j.1471-8286.2007.01797.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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83
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BRODERICK DAMIEN, OVENDEN JENNY, SLADE ROB, LANYON JANETM. Characterization of 26 new microsatellite loci in the dugong (Dugong dugon). ACTA ACUST UNITED AC 2007. [DOI: 10.1111/j.1471-8286.2007.01853.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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84
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LI JIALE, WANG GUILING, BAI ZHIYI, YUE GENERALHUA. Ten polymorphic microsatellites from freshwater pearl mussel, Hyriopsis cumingii. ACTA ACUST UNITED AC 2007. [DOI: 10.1111/j.1471-8286.2007.01880.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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85
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Smith S, Hughes J. Microsatellite and mitochondrial DNA variation defines island genetic reservoirs for reintroductions of an endangered Australian marsupial, Perameles bougainville. CONSERV GENET 2007. [DOI: 10.1007/s10592-007-9368-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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86
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Zhao SS, Chen X, Fang SG, Wan QH. Development and characterization of 15 novel microsatellite markers from forest musk deer (Moschus berezovskii). CONSERV GENET 2007. [DOI: 10.1007/s10592-007-9362-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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87
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Zhu ZY, Wang CM, Lo LC, Feng F, Lin G, Yue GH. Isolation, characterization, and linkage analyses of 74 novel microsatellites in Barramundi (Lates calcarifer). Genome 2007; 49:969-76. [PMID: 17036072 DOI: 10.1139/g06-080] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Barramundi (Lates calcarifer) is an important marine food fish species in Southeast Asia and Australia. Seventy-four novel microsatellites were isolated from a genomic DNA library enriched for CA repeats and were characterized in 24 unrelated individuals. Among the 74 microsatellites, 71 were polymorphic, with an average allele number of 7.0 +/- 3.6/locus. The average expected heterozygosity of these polymorphic markers was 0.66. Sixty-three of the 71 polymorphic microsatellites conformed to Hardy-Weinberg equilibrium. Linkage analyses were conducted in a reference family, leading to the assignment of 34 novel microsatellites and 16 published markers in 16 linkage groups. The novel microsatellites developed in this study will contribute significantly to the construction of a first-generation linkage map for mapping of quantitative trait loci in Barramundi, and supply a large choice of markers for studies on population genetics, stock management, and pedigree reconstruction.
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Affiliation(s)
- Z Y Zhu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore
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88
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BENETEAU COURTNEYL, MANDRAK NICHOLASE, HEATH DANIELD. Characterization of eight polymorphic microsatellite DNA markers for the greenside darter,Etheostoma blennioides(Percidae). ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1471-8286.2006.01661.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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89
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Wang CM, Zhu ZY, Lo LC, Feng F, Lin G, Yang WT, Li J, Yue GH. A microsatellite linkage map of Barramundi, Lates calcarifer. Genetics 2006; 175:907-15. [PMID: 17179079 PMCID: PMC1800599 DOI: 10.1534/genetics.106.059972] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Barramundi (Lates calcarifer) is an important farmed marine food fish species. Its compact genome (approximately 700 Mb) is among the smallest genomes of food fish species. We established a first-generation genetic linkage map of Barramundi with a mapping panel containing three parents (two males and one female) and 93 progeny. A total of 240 microsatellite markers were mapped into 24 linkage groups. Among these markers, 10 were located in ESTs and known genes. The total lengths of the female and male maps were 873.8 and 414.5 cM with an average marker spacing of 6.20 and 4.70 cM, respectively. Comparing the flanking sequences of the 240 Barramundi microsatellites with the assembled whole-genome sequences of Tetraodon nigrovidiris revealed 55 homologous sequences located in 19 of the 21 chromosomes of T. nigrovidiris. The map will not only enable the mapping of quantitative trait loci, but also provide new resources for understanding the evolution of fish genomes.
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Affiliation(s)
- Chun Ming Wang
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, National University of Singapore, 117604 Singapore, Republic of Singapore
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90
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WANG XW, TRIGIANO RN, WINDHAM MT, DEVRIES RE, SCHEFFLER BE, RINEHART TA, SPIERS JM. A simple PCR procedure for discovering microsatellites from small insert libraries. ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1471-8286.2006.01655.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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91
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SCHWARTZ TONIAS, WARNER DANIELA, BEHEREGARAY LUCIANOB, OLSSON MATS. PRIMER NOTE: Microsatellite loci for Australian agamid lizards. ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1471-8286.2006.01644.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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92
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HADRYS HEIKE, TIMM JANNE, STREIT BRUNO, GIERE SANDRA. A panel of microsatellite markers to study sperm precedence patterns in the emperor dragonflyAnax imperator(Odonata: Anisoptera). ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1471-8286.2006.01585.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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93
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BANKS SAMC, PIGGOTT MAXINEP, WILLIAMSON JANEE, BEHEREGARAY LUCIANOB. Microsatellite DNA markers for analysis of population structure in the sea urchinCentrostephanus rodgersii. ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1471-8286.2006.01594.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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94
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Characterization of one trinucleotide and six dinucleotide microsatellite markers in bicolor damselfish, Stegastes partitus, a common coral reef fish. CONSERV GENET 2006. [DOI: 10.1007/s10592-006-9207-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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95
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BEHEREGARAY LB, PIGGOTT M, CHAO NL, CACCONE A. Development and characterization of microsatellite markers for the Amazonian blackwing hatchetfish, Carnegiella marthae (Teleostei, Gasteropelecidae). ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1471-8286.2006.01344.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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96
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YUE GH, LAM-CHAN LT, HONG Y. Development of simple sequence repeat (SSR) markers and their use in identification of Dendrobium varieties. ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1471-8286.2006.01361.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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97
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ZHU ZY, SHI YH, LE GW. Isolation and characterization of polymorphic microsatellites from Chinese mitten crab, Eriocheir sinensis. ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1471-8286.2006.01363.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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98
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TERAKAWA M, KIKUCHI S, KANETANI S, MATSUI K, YUMOTO T, YOSHIMARU H. Characterization of 13 polymorphic microsatellite loci for an evergreen tree, Myrica rubra. ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1471-8286.2006.01318.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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99
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PIGGOTT MAXINEP, BANKS SAMC, BEHEREGARAY LUCIANOB. Use of SSCP to improve the efficiency of microsatellite identification from microsatellite-enriched libraries. ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1471-8286.2006.01333.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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100
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FELDHAAR HEIKE, DRESCHER JOCHEN, BLUTHGEN NICO. Characterization of microsatellite markers for the invasive ant species Anoplolepis gracilipes. ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1471-8286.2006.01397.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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