Genome-wide scan of the soybean genome using degenerate oligonucleotide primed pcr: An example for studying large complex genome structure

Genes and Genomics

Volumn 34, Issue 5, 2012, Pages 467-474

  Van, Kyujung ^a   Kang, Yang Jae ^a   Shim, Sang Rea ^a   Lee, Suk Ha ^a,b  

^a Seoul National University   (South Korea)

^b Seoul National University   (South Korea)

Author keywords

DOP PCR; Genome duplication; GS FLX; Less studied orphan crops; Retrotransposons; Soybean

Indexed keywords

CONTIG; RIBONUCLEASE H; TAQ POLYMERASE;

ARTICLE; GENOTYPE; LONG TERMINAL REPEAT; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT CHROMOSOME; PLANT GENOME; POLYMERASE CHAIN REACTION; RETROPOSON; SINGLE NUCLEOTIDE POLYMORPHISM; SOYBEAN;

EID: 84865557251     PISSN: 19769571     EISSN: 20929293     Source Type: Journal    
DOI: 10.1007/s13258-011-0238-3     Document Type: Article

References (39)

1. Barabaschi D, Guerra D, Lacrima K, Laino P, Michelotti V, Urso S, Vale G, and Cattivelli L (2011) Emerging knowledge from genome sequencing of crop species. Mol. Biotechnol. DOI 10.1007/s12033-011-9443-1.
2. Bennetzen JL, Ma J, and Devos KM (2005) Mechanisms of recent genome size variation in flowering plants. Ann. Bot. 95: 127-132.
3. Brookes AJ (1999) The essence of SNPs. Gene 234: 177-186.
4. Cho RJ, Mindrinos M, Richards DR, Sapolsky RJ, Anderson M, Drenkard E, Dewdney J, Reuber TL, Stammers M, Federspiel N, et al. (1999) Genome-wide mapping with biallelic markers in Arabidopsis thaliana. Nat. Genet. 23: 203-207.
5. Choulet F, Wicker T, Rustenholz C, Paux E, Salse J, Leroy P, Schlub S, Le Paslier M-C, Magdelenat G, Gonthier C, et al. (2010) Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces. Plant Cell 22: 1686-1701.
6. Collins FS, Brookes LD, and Charkravati A (1998) A DNA polymorphism discovery resource for research on human genetic variation. Genome Res. 8: 1229-1231.
7. Du J, Tian Z, Hans CS, Laten HM, Cannon SB, Jackson SA,
8. Shoemaker RC, and Ma J (2010) Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison. Plant J. 63: 584-598.
9. Feuillet C, Leach JE, Rogers J, Schnable PS, and Eversole K (2011) Crop genome sequencing: lessons and rationales. Trends Plant Sci. 16: 77-88.
10. Godfray HCJ, Beddington JR, Crute IR, Haddad L, Lawrence D, Muir JF, Pretty J, Robinson S, Thomas SM, and Toulmin C (2010) Food security, the challenge of feeding 9 billion people. Science 327: 812-818.
11. Iqbal SM and Bashir R (2011) Nanopores: sensing and fundamental biological interactions. Springer, New York
12. Janiak A, Kim MY, Van K, and Lee S-H (2008) Application of degenerate oligonucleotide primed PCR (DOP-PCR) for SNP discovery in soybean. Euphytica 162: 249-256
13. Jordan B, Charest A, Dowd JF, Blumenstiel JP, Yeh R-F, Osman A, Housman DE, and Landers JE (2002) Genome complexity reduction for SNP genotyping analysis. Proc. Natl. Acad. Sci. USA 99: 2942-2947.
14. Kalendar R, Flavell AJ, Ellis THN, Sjakste T, Moisy C, and Schuman AH (2011) Analysis of plant diversity with retrotransposon-based molecular markers. Heredity 106: 520-530.
15. Kashkush K and Khasdan V (2007) Large-scale survey of cytosine methylation of retrotransposons and the impact of readout transcription from long terminal repeats on expression of adjacent rice genes. Genetics 177: 1975-1985.
16. Kashkush K, Feldman M, and Levy AA (2003) Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat. Nat. Genet. 33: 102-106.
17. Kim KD, Shin JH, Van K, Kim DH, and Lee S-H (2009) Dynamic rearrangements determine genome organization and useful traits in soybean. Plant Physiol. 151: 1066-1076.
18. Kim MY, Ha BK, Jun TH, Hwang EY, Van K, Kuk YI, and Lee S-H (2004) Single nucleotide polymorphism discovery and linkage mapping of lipoxygeanse-2 gene (Lx2) in soybean. Euphytica 135: 169-177.
19. Kim SD, Hong EH, Song YG, Kim YH, Lee YH, Hwang YH, Kim HS, Lee SH, Kim WH, Ryu YH, Park RK (1994) New soybean variety resistant to disease and lodging, with adapted high yielding “Sinpaldalkong 2”. RDA J. Agric. Sci. 36: 153-157.
20. Krzywinski MI, Schein JE, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, and Marra MA (2009) Circos: An information aesthetic for comparative genomics. Genome Res. 19: 1639-1645.
21. Kuppuswamy MN, Hoffman JW, Kasper CK, Spitzer SG, Groce SL, and Bajaj SP (1991) Single nucleotide primer extension to detect genetic disease: Experimental application to hemophilia B (factor IX) and cystic fibrosis genes. Proc. Natl. Acad. Sci. USA 88: 1143-1147.
22. Kwok P-Y and Gu Z (1999) Single nucleotide polymorphism libraries: why and how are we building them? Mol. Med. Today 5: 538-543.
23. Lam HM, Xu X, Liu X, Chen W, Yang G, Wong F-L, Li M-W, He W, Qin N, Wang B, et al. (2010) Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Journal naNature Genet. 42: 1053-1059.
24. Li H and Durbin R (2010) Fast and accurate long-read alignment with Burrows-Wheeler Transform. Bioinformatics 26: 589-595.
25. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, and Durbin R, 1000 Genome Project Data Processing Subgroup. (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25: 2078-2079.
26. Martinez-Zapater JM, Carmona MJ, Diaz-Riquelme J, Fernandez L, and Lijavetzky D (2010) Grapevine genetics after the genome sequence: Challenges and limitations. Aust. J. Grape Wine Res. 16: 33-46.
27. Matthias M, Stenzel U, Myles S, Prüfer K, and Hofreiter M (2007) Targeted high-throughput sequencing of tagged nucleic acid samples. Nucleic Acids Res. 35: e97.
28. McMullen MD, Kresovich S, Villeda HS, Bradbury P, Li H, Sun Q, Flint-Garcia S, Thornsberry J, Acharya C, Bottoms C, et al. (2009) Genetic properties of the maize nested association mapping population. Science 325: 737-740.
29. Nielsen KL, Høgh AL, and Emmersen J (2006) DeepSAGE-digital transcriptomics with high sensitivity, simple experimental protocol and multiplexing of samples. Nucl. Acids Res. 34: e133.
30. Rafalski A (2002) Application of single nucleotide polymorphisms in crop genetics. Curr. Opin. Plant Biol. 5: 94-100.
31. Rusk N (2009) Cheap third-generation sequencing. Nature Methods 6: 244-245.
32. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, et al. (2010) Genome sequence of the palaeopolyploid soybean. Nature 463: 178-183.
33. Tester M and Langridge P (2010) Breeding technologies to increase crop production in a changing world. Science 327: 818-822.
34. Van K, Kim D, Cai C.M, Kim MY, Shin JH, Graham MA, Shoemaker RC, Choi B-S, Yang T-J, Lee S-H (2008) Sequence level analysis of recently duplicated regions in soybean [Glycine max (L.) Merr.] genome. DNA Res. 15: 93-102.
35. Van K, Kim DH, Shin JH, and Lee S-H (2011) Genomics of plant genetic resources: past, present and future. Plant Genet. Resour. 9: 155-158.
36. Varshney RK, Close TJ, Singh NK, Hoisington DA, and Cook DR (2009) Orphan legume crops enter the genomics era! Curr. Opin. Plant Biol. 12: 202-210.
37. Varshney RK, Glaszmann J-C, Leung H, and Ribaut J-M (2010) More genomic resources for less-studied crops. Trends Biotechnol. 28: 452-460.
38. Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, Flavell A, Leroy P, Morgante M, Panaud O, et al. (2007) A unified classification system for eukaryotic transposable elements. Nat. Rev. Genet. 8: 973-982.
39. Zhu, YL, Song QJ, Hyten DL, Van Tassell CP, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young N, and Cregan PB (2003) Single-nucleotide polymorphisms in soybean. Genetics 163: 1123-1134.