Gene-based microsatellite development for mapping and phylogeny studies in eggplant

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Stàgel, Anikò ^a   Portis, Ezio ^a   Toppino, Laura ^b   Rotino, Giuseppe Leonardo ^b   Lanteri, Sergio ^a  

^a UNIVERSITY OF TURIN   (Italy)

^b CRA ORL Research Unit for Vegetable Crops   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUBERGINE; COMPUTER MODEL; CONTROLLED STUDY; DNA POLYMORPHISM; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENE MAPPING; GENETIC VARIABILITY; MICROSATELLITE MARKER; NONHUMAN; NUCLEOTIDE SEQUENCE; PEPPER; PHENOTYPE; PHYLOGENY; PLANT GENETICS; POTATO; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; TAXONOMY; TOMATO; ALGORITHM; BIOLOGY; CHROMOSOME MAP; GENE; GENETIC DATABASE; GENETICS; GENOTYPE; METHODOLOGY; REPRODUCIBILITY;

LYCOPERSICON ESCULENTUM; SOLANACEAE; SOLANUM; SOLANUM MELONGENA; SOLANUM TUBEROSUM;

MICROSATELLITE DNA;

ALGORITHMS; BASE SEQUENCE; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENES, PLANT; GENOTYPE; MICROSATELLITE REPEATS; PHYLOGENY; REPRODUCIBILITY OF RESULTS; SOLANUM MELONGENA; VARIATION (GENETICS);

EID: 50549097320     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-357     Document Type: Article

References (60)

1. Daunay MC Lester RN Ano G Cultivated eggplants tropical plant breeding Oxford university press, Oxford Charpier A, Jacquot M, Hamon S, Nicolas D 2001, 200-225.
2. Hinata H Eggplant (Solanum melongena L.) Biotechnology in agriculture and Forestry, Crop I Springer, Berlin Bajaj YPS 1986, 2:363-370.
3. Barchi L Bonnet J Boudet C Signoret P Nagy I Lanteri S Palloix A Lefebvre V A high-resolution intraspecific linkage map of pepper (Capsicum annuum L.) and selection of reduced RIL subsets for fast mapping Genome 2007, 50:51-60. 10.1139/G06-140 17546071
4. Jacobs JME Van Eck HJ Arens P Verkerk-Bakker B Lintel B Hekkert HJM Bastiaanssen A El-Kharbotly A Pereira E Jacobsen E Stiekema WJ A genetic map of potato (Solanum tuberosum) integrating molecular markers, including transposons, and classical markers TAG 2004, 91:289-300.
5. Tanksley SD Ganal MW Prince JP Vicente MC Bonierbale MW Broun P Fulton TM Giovannoni JJ Grandillo S Martin GB Messeguer R Miller JC Miller L Paterson AH Pineda O Roder MS Wing RA Wu W Young ND High density molecular linkage maps of the tomato and potato genomes Genetics 1992, 132:1141-1160. 1205235 1360934
6. Livingstone KD Lackney VK Blauth JR Wijk RV Jahn MK Genome mapping in Capsicum and the evolution of genome structure in the Solanaceae Genetics 1999, 152:1183-1202. 1460652 10388833
7. Karihaloo JL Brauner S Gottlieb LD Random amplified polymorphic DNA variation in the eggplant, Solanum melongena L. (Solanaceae) Theor Appl Genet 1995, 90:767-770.
8. Mace ES Lester RN Gebhardt CG AFLP analysis of genetic relationship among the cultivated eggplant Solanum melongena L. and wild relatives (Solanaceae) Theor Appl Genet 1999, 99:626-633. 10.1007/s001220051277
9. Furini A Wunder J Analysis of eggplant (Solanum melongena) - related germplasm: Morphological and AFLP data contribute to phylogenetic interpretations and germplasm utilizations Theor Appl Genet 2004, 108:197-208. 10.1007/s00122-003-1439-1 14564389
10. Nunome T Suwabe K Ohyama A Fukuoka H Characterization of trinucleotide microsatellites in Eggplant Breeding Science 2003, 53:77-83. 10.1270/ jsbbs.53.77
11. Nunome T Suwabe K Iketani H Hirai M Identification and characterization of microsatellites in eggplant Plant Breeding 2003, 122:256-262. 10.1046/ j.1439-0523.2003.00816.x
12. Nunome T Ishiguro K Yoshida T Hirai M Mapping of fruit shape and color development traits in eggplant (Solanum melongena L.) based on RAPD and AFLP markers Breeding Science 2001, 51:19-26. 10.1270/jsbbs.51.19
13. Doganlar S Frary A Daunay MC Lester RN Tanksley SD A comparative genetic linkage map of Eggplant (Solanum melongena) and its implications for genome evolution in the Solanaceae Genetics 2002, 161:1697-1711. 1462225 12196412
14. Powell W Machray G Provan J Polymorphism revealed by simple sequence repeats Trends Plant Sci 1996, 1:215-222. 10.1016/1360-1385(96)86898-1
15. Morgante M Hanafey M Powell W Microsatellites are preferentially associated with nonrepetitive DNA in plant genome Nat Genet 2002, 30:194-200. 10.1038/ng822 11799393
16. Toth G Gaspari Z Jurka J Microsatellites in different eukaryotic genomes: Survey and analysis Genom Res 2000, 10:967-981. 10.1101/ gr.10.7.967
17. Varshney RK Sigmund R Boerner A Korzun V Stein N Sorrells M Langridge P Graner A Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice Plant Sci 2005, 168:195-202. 10.1016/j.plantsci.2004.08.001
18. Cho YG Ishii T Temnykh S Chen X Lipovich L McCouch SR Park WD Ayer N Cartinhour S Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa) Theor Appl Genet 2000, 100:713-722. 10.1007/s001220051343
19. Chabane K Ablett A Cordeiro GM Valkoun J Henry RJ EST versus genomic derived microsatellite markers for genotyping wild and cultivated barley Genet Resour Crop Evol 2005, 52:903-909. 10.1007/s10722-003-6112-7
20. Andersen JR Lubberstedt T Functional markers in plants Trends Plant Sci 2003, 8:554-560. 10.1016/j.tplants.2003.09.010 14607101
21. Varshney RK Thiel T Stein N Langridge P Graner A In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species Cell Mol Biol Lett 2002, 7:537-546. 12378259
22. Kumpatla PS Mukhopadhyay S Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species Genome 2005, 48:985-998. 10.1139/g05-060 16391668
23. Chen C Zhou P Choi YA Huang S Gmitter FG Jr Mining and characterizing microsatellites from citrus ESTs Theor Appl Genet 2006, 112:1248-1257. 10.1007/s00122-006-0226-1 16474971
24. Thiel T Michalek W Varshney RK Graner A Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.) Theor Appl Genet 2003, 106:411-422. 12589540
25. Metzgar D Bytof J Willis C Selection against frameshift mutations limits microsatellite expansion in coding DNA Genome Res 2000, 10:72-80. 310501 10645952
26. Nagy I Stágel A Sasvári Z Röder M Ganal M Development, characterization, and transferability to other Solanaceae of microsatellite markers in pepper (Capsicum annuum L.) Genome 2007, 50:668-688. 10.1139/G07-047 17893745
27. Portis E Nagy I Sasvári Z Stágel A Barchi L Lanteri S The design of Capsicum spp. SSR assays via analysis of in silico DNA sequence, and their potential utility for genetic mapping Plant Science 2007, 172:640-648. 10.1016/j.plantsci.2006.11.016
28. Katti MV Prabhakar KR Gupta VS Differential distribution of simple sequence repeats in eukaryotic genome sequences Mol Biol Evol 2001, 18:1161-1167. 11420357
29. Chin ECL Maize simple repetitive DNA sequences: Abundance and allele variation Genome 1996, 39:866-873. 10.1139/g96-109 8890517
30. Kanety RV Rota ML Matthews DE Sorrells ME Data mining for simple sequence repeats in expressed sequence tags from barely, maize, rice, sorghum and wheat Plant Mol Biol 2002, 48:501-510. 10.1023/ A:1014875206165 11999831
31. Lewin BV Genes, Oxford University Press, New York 1994.
32. Lagercrantz U Ellegren H Andersson L The abundance of various polymorphic microsatellite motifs differs between plants and vertebrates Nucleic Acids Res 1993, 21:1111-1115. 309270 8464696 10.1093/nar/ 21.5.1111
33. Morgante M Olivieri AM PCR-amplified microsatellites as markers in plant genetics Plant J 1993, 3:175-182. 10.1111/j.1365-313X.1993.tb00020.x 8401603
34. Nicot N Chiquet V Gandon B Amilhat L Legeai F Leroy P Bernard M Sourdille P Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs) Theor Appl Genet 2004, 109:800-805. 10.1007/s00122-004-1685-x 15146317
35. Weber JL Informativeness of human (dC-dA)n.(dG-dT)n polymorphism Genomics 1990, 7:524-530. 10.1016/0888-7543(90)90195-Z 1974878
36. Liewlaksaneeyanawin C Ritland CE El-Kassaby YA Ritland K Single-copy, species-transferable microsatellite markers developed from loblolly pine ESTs Theor Appl Genet 2004, 109:361-369. 10.1007/s00122-004-1635-7 15045175
37. Eujayl I Sorrells ME Baum M Wolters P Powell W Isolation of EST-derived microsatellite markers for genotyping the A and B genomes of wheat Theor Appl Genet 2002, 104:399-407. 10.1007/s001220100738 12582712
38. Park YH Alabady MS Ulloa M Sickler B Wilkins TA Yu J Stelly DM Kohel RJ El-Shihy OM Cantrell RG Genetic mapping of new cotton fiber loci using EST-derived microsatellites in an interspecific recombinant inbred line cotton population Mol Genet Genom 2005, 274:428-441. 10.1007/ s00438-005-0037-0
39. Han Z Guo W Song X Zhang T Genetic mapping of EST-derived microsatellites from the diploid Gossypium arboreum in allotetraploid cotton Mol Genet Genom 2004, 272:308-327. 10.1007/s00438-004-1059-8
40. Reddy OU Pepper AE Abdurakhmonov I Saha S Jenkins JN Brooks T Bolek Y El-Zik KM New dinucleotide and trinucleotide microsatellite marker resources for cotton genome research J Cotton Sci 2001, 5:103-113. http://www.cotton.org/journal/2001-05/2/103.cfm
41. Nguyen TB Giband M Brottier P Risterucci AM Lacape JM Wide coverage of the tetraploid cotton genome using newly developed microsatellite markers Theor Appl Genet 2004, 109:167-175. 10.1007/s00122-004-1612-1 14997301
42. Isshiki S Uchiyama T Tashiro Y Miyazaki S RFLP analysis of a PCR amplified region of chloroplast DNA in eggplant and related Solanum species Euphytica 1998, 102:295-299. 10.1023/A:1018304308608
43. Isshiki S Suzuki S Yamashita K RFLP analysis of mithocondrial DNA in eggplant and related Solanum species Genetic research and crop evolution 2003, 50:133-137. 10.1023/A:1022954229295
44. Olmstead RG Palmer JD Implications for the phylogeny, classification, and biogeography of Solanum from cpDNA restriction site variation Syst Bot 1997, 22:19-29. 10.2307/2419675
45. Provan J Powel W Waugh R Microsatellite analysis of relationships within cultivated potato (Solanum tuberosum) Theor Appl Genet 1996, 92:1078-1084. 10.1007/BF00224052
46. Smulders MJM Bredemeijer G Rus-Kortekaas W Arens P Vosman B Use of short microsatellites from database sequences to generate polymorphisms among Lycopersicon esculentum cultivars and accessions of other Lycopersicon species Theor Appl Genet 1997, 94:264-272. 10.1007/s001220050409
47. Varshney RK Graner A Sorrells ME Genic microsatellite markers: Their characteristics, development and application to plant breeding and genetics Trends Biotech 2005, 23:48-55. 10.1016/j.tibtech.2004.11.005
48. Scott KD Eggler P Seaton P Rossetto M Ablett EM Lee LS Henry RJ Analysis of SSRs derived from grape ESTs Theor Appl Genet 2000, 100:723-726. 10.1007/s001220051344
49. Portis E Nervo G Cavallanti F Barchi L Lanteri S Multivariate analysis of genetic relationships between Italian pepper landraces Crop Sci 2006, 6:2517-2525. 10.2135/cropsci2006.04.0216
50. Mazzucato A Papa R Bitocchi E Mosconi P Nanni L Negri V Picarella ME Siligato F Soressi GP Tiranti B Veronesi F Genetic diversity, structure and marker-trait associations in a collection of Italian tomato (Solanum lycopersicum L.) landraces Theor Appl Genet 2008, 5:657-669. 10.1007/ s00122-007-0699-6
51. Altschul SF Madden TL Schaffer AA Zhang J Zhang Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Res 1997, 25:3389-3402. 146917 9254694 10.1093/ nar/25.17.3389
52. Thompson JD Higgins DG Gibson TJ Clustal W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weighting matrix choice Nucleic Acids Res 1994, 22:4673-4680. 308517 7984417 10.1093/nar/22.22.4673
53. Rozen S Skaletsky HJ Primer3 on the WWW for general users and for biologist programmers Bioinformatics Methods and Protocols: Methods in Molecular Biology Humana Press, Totowa NJ Krawetz S, Misener S 2000, 365-386. http://primer3.sourceforge.net/
54. Doyle JJ Doyle JL Isolation of plant DNA from fresh tissue Focus 1990, 12:13-14.
55. Jackson JA Matthews D Modified inter-simple sequence repeat PCR protocol for use in conjunction with the Li-Cor gene ImagIR(2) DNA analyzer BioTechniques 2000, 28:914-917. 10818697
56. Botstein D White RL Skolnick M Davis RW Construction of a genetic linkage map in man using restriction fragment length polymorphism Am J Hum Genet 1980, 32:314-331. 1686077 6247908
57. Anderson JA Churcill GA Autrique JE Tanksley SD Sorrels ME Optimizing parental selection for genetic linkage maps Genome 1992, 36:181-186. 10.1139/g93-024
58. Nei M Li WH Mathematical model for studying genetic variation in terms of restriction endonucleases Proc Natl Acad Sci USA 1979, 76:5269-5273. 413122 291943 10.1073/pnas.76.10.5269
59. Sneath PHA Sokal RR Numerical taxonomy Freeman WH, San Francisco 1973.
60. Rohlf FJ NTSYS-pc Numerical Taxonomy and Multivariate Analysis System version 2.02 User Guide 1998.