Empirical evaluation of DArT, SNP, and SSR marker-systems for genotyping, clustering, and assigning sugar beet hybrid varieties into populations

Plant Science

Volumn 184, Issue , 2012, Pages 54-62

  Simko, Ivan ^a   Eujayl, Imad ^a   van Hintum, Theo J L ^b  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

Assignment into a population; Data resolution; Genotypic diversity; Molecular markers; Population structure; Sugar beet

Indexed keywords

MICROSATELLITE DNA;

AREA UNDER THE CURVE; ARTICLE; BEET; CLASSIFICATION; CLUSTER ANALYSIS; GENE LOCUS; GENETIC MARKER; GENETICS; GENOTYPING TECHNIQUE; HYBRIDIZATION; METHODOLOGY; POPULATION DYNAMICS; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICS;

AREA UNDER CURVE; BETA VULGARIS; CLUSTER ANALYSIS; GENETIC LOCI; GENETIC MARKERS; GENETICS, POPULATION; GENOTYPING TECHNIQUES; HYBRIDIZATION, GENETIC; MICROSATELLITE REPEATS; POLYMORPHISM, SINGLE NUCLEOTIDE; POPULATION DYNAMICS; STATISTICS AS TOPIC;

BETA VULGARIS; BETA VULGARIS SUBSP. VULGARIS;

EID: 84855803194     PISSN: 01689452     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.plantsci.2011.12.009     Document Type: Article

References (27)

1. Simko I., Haynes K.G., Jones R.W. Assessment of linkage disequilibrium in potato genome with single nucleotide polymorphism markers. Genetics 2006, 173:2237-2245.
2. Mariette S., Le Corre V., Austerlitz F., Kremer A. Sampling within the genome for measuring within-population diversity: trade-offs between markers. Molecular Ecology 2002, 11:1145-1156.
3. Guillot G., Carpentier-Skandalis A. On the informativeness of dominant and co-dominant genetic markers for Bayesian supervised clustering. The Open Statistics & Probability Journal 2011, 3:7-12.
4. Tautz D., Renz M. Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Research 1984, 12:4127-4138.
5. Simko I. Development of EST-SSR markers for the study of population structure in lettuce (Lactuca sativa L.). Journal of Heredity 2009, 100:256-262.
6. Wenzl P., Carling J., Kudrna D., Jaccoud D., Huttner E., Kleinhofs A., Kilian A. Diversity Arrays Technology (DArT) for whole-genome profiling of barley. Proceedings of the National Academy of Sciences of the United States of America 2004, 101:9915-9920.
7. Hurtado P., Olsen K.M., Buitrago C., Ospina C., Marin J., Duque M., De Vicente C., Wongtiem P., Wenzel P., Killian A., Adeleke M., Fregene M. Comparison of simple sequence repeat (SSR) and diversity array technology (DArT) markers for assessing genetic diversity in cassava (Manihot esculenta Crantz). Plant Genetic Resources: Characterisation and Utilisation 2008, 6:208-214.
8. Laurent V., Devaux P., Thiel T., Viard F., Mielordt S., Touzet P., Quillet M.C. Comparative effectiveness of sugar beet microsatellite markers isolated from genomic libraries and GenBank ESTs to map the sugar beet genome. Theoretical and Applied Genetics 2007, 115:793-805.
9. Schneider K., Kulosa D., Soerensen T.R., Möhring S., Heine M., Durstewitz G., Polley A., Weber E., Jamsari, Lein J., Hohmann U., Tahiro E., Weisshaar B., Schulz B., Koch G., Jung C., Ganal M. Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes. Theoretical and Applied Genetics 2007, 115:601-615.
10. Jaccoud D., Peng K., Feinstein D., Kilian A. Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Research 2001, 29:e25.
11. Botstein D., White R.L., Skolnick M., Davis R.W. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics 1980, 32:314-331.
12. van Hintum T.J.L. Data resolution: a jackknife procedure for determining the consistency of molecular marker datasets. Theoretical and Applied Genetics 2007, 115:343-349.
13. Falush D., Stephens M., Pritchard J.K. Inference of population structure using multilocus genotype data: dominant markers and null alleles. Molecular Ecology Notes 2007, 7:574-578.
14. Pritchard J.K., Stephens M., Donnelly P. Inference of population structure using multilocus genotype data. Genetics 2000, 155:945-959.
15. Meirmans P.G., Van Tienderen P.H. GENOTYPE and GENODIVE: two programs for the analysis of genetic diversity of asexual organisms. Molecular Ecology Notes 2004, 4:792-794.
16. Evanno G., Regnaut S., Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 2005, 14:2611-2620.
17. Calinski R.B., Harabasz J. A dendrite method for cluster analysis. Communications in Statistics - Theory and Methods 1974, 3:1-27.
18. Guinand B., Topchy A., Page K.S., Burnham-Curtis M.K., Punch W.F., Scribner K.T. Comparisons of likelihood and machine learning methods of individual classification. Journal of Heredity 2002, 93:260-269.
19. Guillot G., Santos F. Using AFLP markers and the Geneland program for the inference of population genetic structure. Molecular Ecology Resources 2010, 10:1082-1084.
20. Hubisz M.J., Falush D., Stephens M., Pritchard J.K. Inferring weak population structure with the assistance of sample group information. Molecular Ecology Resources 2009, 9:1322-1332.
21. Paetkau D., Calvert W., Stirling I., Strobeck C. Microsatellite analysis of population structure in Canadian polar bears. Molecular Ecology 1995, 4:347-354.
22. Agapow P.M., Burt A. Indices of multilocus linkage disequilibrium. Molecular Ecology Notes 2001, 1:101-102.
23. Smulders M.J.M., Esselink G.D., Everaert I., De Riek J., Vosman B. Characterisation of sugar beet (Beta vulgaris L. ssp. vulgaris) varieties using microsatellite markers. BMC Genetics 2010, 11:41.
24. Rosenberg N.A., Burke T., Elo K., Feldman M.W., Freidlin P.J., Groenen M.A.M., Hillel J., Mäki-Tanila A., Tixier-Boichard M., Vignal A., Wimmers K., Weigend S. Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds. Genetics 2001, 159:699-713.
25. De Riek J., Everaert I., Esselink D., Calsyn E., Smulders M.J.M., Vosman B. Assignment tests for variety identification compared to genetic similarity-based methods using experimental datasets from different marker systems in sugar beet. Crop Science 2007, 47:1964-1974.
26. Van Inghelandt D., Melchinger A.E., Lebreton C., Stich B. Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers. Theoretical and Applied Genetics 2010, 120:1289-1299.
27. Jones E.S., Sullivan H., Bhattramakki D., Smith J.S.C. A comparison of simple sequence repeat and single nucleotide polymorphism marker technologies for the genotypic analysis of maize (Zea mays L.). Theoretical and Applied Genetics 2007, 115:361-371.