The Mining of Citrus EST-SNP and Its Application in Cultivar Discrimination

Agricultural Sciences in China

Volumn 9, Issue 2, 2010, Pages 179-190

  JIANG, Dong ^a   YE, Qing liang ^a   WANG, Fu sheng ^a   CAO, Li ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

citrus; cleaved amplified polymorphic sequences (CAPS); EST SNP; single nucleotide polymorphisms (SNPs)

Indexed keywords

CITRUS; CITRUS SINENSIS;

EID: 76549084374     PISSN: 16712927     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1671-2927(09)60082-1     Document Type: Article

References (35)

1. Bang H., Kim S., Leskovar D., and King S. Development of a codominant CAPS marker for allelic selection between canary yellow and red watermelon based on SNP in lycopene β-cyclase (LCYB) gene. Molecular Breeding 20 (2007) 63-72
2. Barkley N.A., Roose M.L., Krueger R.R., and Federici C.T. Assessing genetic diversity and population structure in a citrus germplasm collection utilizing simple sequence repeat markers (SSRs). Theoretical and Applied Genetics 112 (2006) 1519-1531
3. Batley J., Barker G., Sullivan H.O., Edwards K.J., and Edwards D. Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiology 132 (2003) 84-91
4. Bhattramakki D., Dolan M., Hanafey M., Wineland R., Vaske D., Register III J.C., Tingey S.V., and Rafalski A. Insertion-deletion polymorphisms in 3′ regions of maize genes occur frequently and can be used as highly informative genetic markers. Plant Molecular Biology 48 (2002) 539-547
5. Cheng Y.J., Guo W.W., Yi H.L., Pang X.M., and Deng X.X. An efficient protocol for genomic DNA extraction from Citrus species. Plant Molecular Biology Reporter 21 (2003) 177a 177g
6. Ching A., Caldwell K.S., Jung M., Dolan M., Smith O.S., Tingey S., Morgante M., and Rafalski A.J. SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genetics 3 (2002) 19
7. Duran C., Appleby N., Vardy M., Imelfort M., Edwards D., and Batley J. Single nucleotide polymorphism discovery in barley using autoSNPdb. Plant Biotechnology Journal 7 (2009) 326-333
8. Fang D.Q., and Roose M.L. Identification of closely related citrus cultivars with inter-simple sequence repeat markers. Theoretical and Applied Genetics 95 (1997) 408-417
9. Haga H., Yamada R., Ohnishi Y., Nakamura Y., and Tanaka T. Gene-based SNP discovery as part of the Japanese millennium genome project: identification of 190 562 genetic variations in the human genome. Journal of Human Genetics 47 (2002) 605-610
10. Huang X.Q., and Madan A. Cap3: A DNA sequence assembly program. Genome Research 9 (1999) 868-877
11. Jorde L.B. Linkage disequilibrium and the search for complex disease genes. Genome Research 10 (2000) 1435-1444
12. Lijavetzky D., Cabezas J.A., Ibáñez A., Rodríguez V., and Martínez-Zapater J.M. High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a re-sequencing approach and SNPlex technology. BMC Genomics 8 (2007) 424
13. Monna L., Ohta R., Masuda H., Koike A., and Minobe Y. Genome-wide searching of single-nucleotide polymorphisms among eight distantly and closely related rice cultivars (Oryza sativa L.) and a wild accession (Oryza rufipogon Griff.). DNA Research 13 (2006) 43-51
14. Nakano M., Shimizu T., Fujii H., Shimada T., Endo T., Nesumi H., Kuniga T., and Omura M. Marker enrichment and construction of haplotype-specific BAC contigs for the polyembryony genomic region in Citrus. Breeding Science 58 (2008) 375-383
15. Nasu S., Suzuki J., Ohta R., Hasegawa K., Yui R., Kitazawa N., Monna L., and Minobe Y. Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza sativa, Oryza rufipogon) and establishment of SNP markers. DNA Research 9 (2002) 163-171
16. Nicolosi E., Deng Z.N., Gentile A., Malfa S.L., Continella G., and Tribulato E. Citrus phylogeny and genetic origin of important species as investigated by molecular markers. Theoretical and Applied Genetics 100 (2000) 1155-1166
17. Novelli V.M., Cristofani M., Souza A.A., and Machado M.A. Development and characterization of polymorphic microsatellite markers for the sweet orange (Citrus sinensis L. Osbeck). Genetics and Molecular Biology 29 (2006) 90-96
18. Novelli V.M., Takita M.A., and Machado M.A. Identification and analysis of single nucleotide polymorphisms (SNPs) in citrus. Euphytica 138 (2004) 227-237
19. Orford S.J., Scott N.S., and Temmis J.N. A hypervariable middle repetitive DNA sequence from citrus. Theoretical and Applied Genetics 91 (1995) 1248-1252
20. Pedrosa A., Schweizer D., and Guerra M. Cytological heterozygosity and the hybrid origin of sweet orange (Citrus sinensis L. Osbeck). Theoretical and Applied Genetics 100 (2000) 361-367
21. Picoult-Newberg L., Ideker T.E., Pohl M.G., Taylor S.L., Donaldson M.A., Nickerson D.A., and Boyce-Jacino M. Mining SNPs from EST databases. Genome Research 9 (1999) 167-174
22. Pindo M., Vezzulli S., Coppola G., Cartwright D.A., Zharkikh A., Velasco R., and Troggio M. SNP high-throughput screening in grapevine using the SNPlex™ genotyping system. BMC Plant Biology 8 (2008) 12
23. Ravel C., Praud S., Murigneux A., Canaguier A., Sapet F., Samson D., Francois B., Dufour P., Chalhoub B., Brunel D., Beckert M., and Charmet G. Single-nucleotide polymorphism frequency in a set of selected lines of bread wheat (Triticum aestivum L.). Genome 49 (2006) 1131-1139
24. Ramírez M., Graham M.A., Blanco-López L., Silvente S., Medrano-Soto A., Blair M.W., Hernández G., Vance C.P., and Lara M. Sequencing and analysis of common bean ESTs. Building a foundation for functional genomics. Plant Physiology 137 (2005) 1211-1227
25. Shen R., Fan J.B., Campbell D., Chang W.H., Chen J., Doucet D., Yeakley J., Bibikova M., Garcia E.W., McBride C., Steemers F., Garcia F., Kermani B.G., Gunderson K., and Oliphant A. High-throughput SNP genotyping on universal bead arrays. Mutation Research 573 (2005) 70-82
26. Shirasawa K., Maeda H., Monna L., Kishitani S., and Nishio T. The number of genes having different alleles between rice cultivars estimated by SNP analysis. Theoretical and Applied Genetics 115 (2007) 1067-1074
27. Syvänen A.C. Accessing genetic variation: genotyping single nucleotide polymorphisms. Nature Reviews Genetics 2 (2001) 930-942
28. Tang J.F., Leunissen J.A., Voorrips R.E., van der Linden C.G., and Vosman B. HaploSNPer: A web-based allele and SNP detection tool. BMC Genetics 9 (2008) 23
29. Tang J.F., Vosman B., Voorrips R.E., Linden C.G., and Leunissen J. QualitySNP: A pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species. BMC Bioinformatics 7 (2006) 438
30. Targon N.M.L.P., Machado M.A., Filho H.D.C., and Cristofani M. Genetic polymorphism of sweet orange (Citrus sinensis L. Osbeck) varieties evaluated by random amplified polymorphic DNA. ISHS Acta Horticulturae 535 (2000) 51-53
31. Tenaillon M.I., Sawkins M.C., Long A.D., Gaut R.L., Doebley J.F., and Gaut B.S. Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proceedings of the National Academy of Sciences of the USA 98 (2001) 9161-9166
32. Terol J., Naranjo M.A., Ollitrault P., and Talon M. Development of genomic resources for Citrus clementina: characterization of three deep-coverage BAC libraries and analysis of 46 000 BAC end sequences. BMC Genomics 9 (2008) 423
33. Thornsberry J.M., Goodman M.M., Doebley J., Kresovich S., Nielsen D., and Buckler E. Dwarf8 polymorphisms associate with variation in flowering time. Nature Genetics 28 (2001) 286-289
34. Troggio M., Malacarne G., Coppola G., Segala C., Cartwright D.A., Pindo M., Stefanini M., Mank R., Moroldo M., Morgante M., Grando M.S., and Velasco R. A dense single-nucleotide polymorphism-based genetic linkage map of grapevine (Vitis vinifera L.) anchoring Pinot Noir bacterial artificial chromosome contigs. Genetics 176 (2007) 2637-2650
35. Vignal A., Milan D., Cristobal M.S., and Eggen A. A review on SNP and other types of molecular markers and their use in animal genetics. Genetics Selection Evoution 34 (2002) 275-305