Development and multiplexing of microsatellite markers using pyrosequencing in the clonal plant Comarum palustre (Rosaceae)

Molecular Ecology Resources

Volumn 12, Issue 1, 2012, Pages 91-97

  Somme, L ^a   Raabova J ^b,c   Jacquemart, A L ^a   Raspe O ^b  

^a UNIVERSITÉ CATHOLIQUE DE LOUVAIN   (Belgium)

^b BOTANIC GARDEN MEISE   (Belgium)

^c DEPARTMENT OF ENTOMOLOGY   (Czech Republic)

Author keywords

Clonal growth; Genetic structure; Multiplex PCR; Pyrosequencing; SSR

Indexed keywords

MICROSATELLITE DNA;

ARTICLE; CLASSIFICATION; DNA SEQUENCE; EVALUATION; GENETIC MARKER; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENETICS; METHODOLOGY; MOLECULAR GENETICS; MULTIPLEX POLYMERASE CHAIN REACTION; PHYLOGENY; ROSACEAE;

GENETIC MARKERS; GENETIC VARIATION; MICROSATELLITE REPEATS; MOLECULAR SEQUENCE DATA; MULTIPLEX POLYMERASE CHAIN REACTION; PHYLOGENY; POLYMORPHISM, GENETIC; ROSACEAE; SEQUENCE ANALYSIS, DNA;

COMARUM PALUSTRE; ROSACEAE;

EID: 83955161718     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/j.1755-0998.2011.03072.x     Document Type: Article

References (27)

1. Abdelkrim J, Robertson B, Stanton JA, Gemmell N (2009) Fast, cost-effective development of species-specific microsatellite markers by genomic sequencing. BioTechniques, 46, 185-192.
2. Arif IA, Bakir MA, Khan HA et al. (2010) A brief review of molecular techniques to assess plant diversity. International Journal of Molecular Science, 11, 2079-2096.
3. Arnaud-Haond S, Duarte CM, Alberto F, Serrão EA (2007) Standardizing methods to address clonality in population studies. Molecular Ecology, 16, 5115-5139.
4. Bournérias M, Arnal G, Bock C (2001) Guide des groupements végétaux de la région parisienne. Belin, Paris.
5. Brookfield JFY (1996) A simple new method for estimating null allele frequency from heterozygote deficiency. Molecular Ecology, 5, 453-455.
6. Buehler D, Graf R, Holderegger R, Gugerli F (2011) Using the 454 pyrosequencing-based technique in the development of nuclear microsatellite loci in the alpine plant Arabis alpina (Brassicaceae). American Journal of Botany, 98, E103-E105.
7. Csencsics D, Brodbeck S, Holderegger R (2010) Cost-effective, species-specific microsatellite development for the endangered Dwarf Bulrush (Typha minima) using next-generation sequencing technology. Journal of Heredity, 101, 789-93.
8. Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus (San Francisco, California), 12, 13-15.
9. Dubut V, Grenier R, Meglécz E et al. (2010) Development of 55 novel polymorphic microsatellite loci for the critically endangered Zingel asper L. (Actinopterygii: Perciformes: Percidae) and cross-species amplification in five other percids. European Journal of Wildlife Research, 56, 931-938.
10. Duran C, Appleby N, Edwards D, Batley J (2009) Molecular genetic markers: discovery, applications, data storage and visualisation. Current Bioinformatics, 4, 16-27.
11. Faircloth BC (2008) MSATCOMMANDER: detection of microsatellite repeat arrays and automated, locus-specific primer design. Molecular Ecology Resources, 8, 92-94.
12. Frankard P, Ghiette P, Hindryckx MN, Schumacker R, Wastiaux C (1998) Peatlands of Wallony (S-Belgium). Suo, 49, 33-47.
13. Guillén A, Rico E, Castroviejo S (2005) Reproductive biology of the Iberian species of Potentilla L. (Rosaceae). Anales del Jardín Botánico de Madrid, 62, 9-21.
14. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41, 95-98.
15. Lagercrantz U, Ellegren H, Andersson L (1993) The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates. Nucleic Acids Research, 21, 1111-1115.
16. Lambinon J, Delvosalle L, Duvigneaud J (2004) Nouvelle Flore de la Belgique, du Grand-Duché de Luxembourg, du Nord de la France et des régions voisines, 5th edn. Jardin botanique national de Belgique. Meise.
17. Lawalrée A (1961) Rosaceae-Comarum, Fragaria, Filipendula, Agrimonia, Sanguisorba, Alchemilla, Aphanes, RosaVol II. Jardin botanique national de Belgique. Bruxelles.
18. Ma ZQ, Röder M, Sorells ME (1996) Frequencies and sequence characteristics of di-, tri-, and tetra nucleotide in wheat. Genome, 39, 123-130.
19. Macek P, Leps J (2007) Environmental correlates of growth traits of the stoloniferous plant Potentilla palustris. Evolutionary Ecology, 22, 419-435.
20. Martin J-F, Pech N, Meglécz E et al. (2010) Representativeness of microsatellite distributions in genomes, as revealed by 454 GS-FLX Titanium pyrosequencing. BMC Genomics, 11, e560.
21. Olesen I, Warncke E (1992) Breeding system and seasonal variation in seed set in a population of Potentilla palustris. Nordic Journal of Botany, 12, 373-380.
22. Oliveira EJ, Pádua JG, Zucchi MI, Vencovsky R, Carneiro Vieira ML (2006) Origin, evolution and genome distribution of microsatellites. Genetics and Molecular Biology, 29, 294-307.
23. van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) Micro-checker: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes, 4, 535-538.
24. Rozen S, Skaletsky HJ (2000) PRIMER3 on the WWW for general users and for biologist programmers. In: Bioinformatics Methods and Protocols: Methods in Molecular Biology (eds Krawetz S & Misener S), pp. 365-386. Humana Press, Totowa, New Jersey.
25. Schwarz D, Robertson HM, Feder JL et al. (2009) Sympatric ecological speciation meets pyrosequencing: sampling the transcriptome of the apple maggot Rhagoletis pomonella. BMC Genomics, 10, e633.
26. Verté P (2007) Les marais de la Haute-Semois, 40 années de conservation d'un site de très grand intérêt biologique. Echo des Réserves, 3, 4-9.
27. Zane L, Bargelloni L, Patarnello T (2002) Strategies fro microsatellite isolation: a review. Molecular Ecology, 11, 1-16.