Screening of a Brassica napus bacterial artificial chromosome library using highly parallel single nucleotide polymorphism assays

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Cao, Hieu X ^a   Schmidt, Renate ^a  

^a LEIBNIZ INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH IPK   (Germany)

Author keywords

BAC library; Brassica napus; Genotyping; Multidimensional pools; PCR screening; Polyploidy; SNP

Indexed keywords

ARABIDOPSIS THALIANA; ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; BRASSICA OLERACEA; BRASSICA RAPA; CONTROLLED STUDY; GENE FREQUENCY; GENE IDENTIFICATION; GENE LOCUS; GENE MAPPING; GENE SEQUENCE; GENETIC SCREENING; GENOME ANALYSIS; GENOTYPING TECHNIQUE; NONHUMAN; PLANT GENOME; POLYMERASE CHAIN REACTION; RAPESEED; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES DIFFERENCE;

BACTERIA (MICROORGANISMS); BRASSICA NAPUS;

ALGORITHMS; BRASSICA NAPUS; CHROMOSOMES, ARTIFICIAL, BACTERIAL; DNA, PLANT; GENE LIBRARY; GENOME, PLANT; GENOTYPING TECHNIQUES; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 84883867953     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-603     Document Type: Article

References (40)

1. Lagercrantz U, Lydiate DJ. Comparative genome mapping in Brassica. Genetics 1996, 144:1903-1910. 1207737, 8978073.
2. Lagercrantz U. Comparative mapping between Arabidopsis thaliana and Brassica nigra indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusions and frequent rearrangements. Genetics 1998, 150:1217-1228. 1460378, 9799273.
3. Parkin IA, Gulden SM, Sharpe AG, Lukens L, Trick M, Osborn TC, Lydiate DJ. Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana. Genetics 2005, 171:765-781. 10.1534/genetics.105.042093, 1456786, 16020789.
4. O'Neill CM, Bancroft I. Comparative physical mapping of segments of the genome of Brassica oleracea var. alboglabra that are homoeologous to sequenced regions of chromosomes 4 and 5 of Arabidopsis thaliana. Plant J 2000, 23:233-243. 10.1046/j.1365-313x.2000.00781.x, 10929117.
5. Rana D, van den-Boogaart T, O'Neill CM, Hynes L, Bent E, Macpherson L, Park JY, Lim YP, Bancroft I. Conservation of the microstructure of genome segments in Brassica napus and its diploid relatives. Plant J 2004, 40:725-733. 10.1111/j.1365-313X.2004.02244.x, 15546355.
6. Park JY, Koo DH, Hong CP, Lee SJ, Jeon JW, Lee SH, Yun PY, Park BS, Kim HR, Bang JW, Plaha P, Bancroft I, Lim YP. Physical mapping and microsynteny of Brassica rapa ssp. pekinensis genome corresponding to a 222 kbp gene-rich region of Arabidopsis chromosome 4 and partially duplicated on chromosome 5. Mol Genet Genomics 2005, 274:579-588. 10.1007/s00438-005-0041-4, 16283385.
7. Navabi ZK, Huebert T, Sharpe AG, Bancroft I, Parkin IA, Neill CM O. Conserved microstructure of the Brassica B Genome of Brassica nigra in relation to homologous regions of Arabidopsis thaliana, B. rapa and B. oleracea. BMC Genomics 2013, 14:250. 10.1186/1471-2164-14-250, 3765694, 23586706.
8. Lysak MA, Koch MA, Pecinka A, Schubert I. Chromosome triplication found across the tribe Brassiceae. Genome Res 2005, 15:516-525. 10.1101/gr.3531105, 1074366, 15781573.
9. Lysak MA, Cheung K, Kitschke M, Bures P. Ancestral chromosomal blocks are triplicated in Brassiceae species with varying chromosome number and genome size. Plant Physiol 2007, 145:402-410. 10.1104/pp.107.104380, 2048728, 17720758.
10. U N Genomic analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilisation. Jpn J Bot 1935, 7:389-452. U N.
11. Inaba R, Nishio T. Phylogenetic analysis of Brassiceae based on the nucleotide sequences of the S-locus related gene, SLR1. Theor Appl Genet 2002, 105:1159-1165. 10.1007/s00122-002-0968-3, 12582894.
12. Town C, Schmidt R, Bancroft I. Comparative genome analysis at the sequence level in the Brassicaceae. Genetics and Genomics of the Brassicaceae 2011, 171-194. New York Dordrecht Heidelberg London: Springer, Schmidt R, Bancroft I.
13. Cheung F, Trick M, Drou N, Lim YP, Park JY, Kwon SJ, Kim JA, Scott R, Pires JC, Paterson AH, Town C, Bancroft I. Comparative analysis between homoeologous genome segments of Brassica napus and its progenitor species reveals extensive sequence-level divergence. Plant Cell 2009, 21:1912-1928. 10.1105/tpc.108.060376, 2729604, 19602626.
14. Cho K, O'Neill CM, Kwon SJ, Yang TJ, Smooker AM, Fraser F, Bancroft I. Sequence level comparative analysis of the Brassica napus genome around two stearoyl-ACP desaturase loci. Plant J 2010, 61:591-599. 10.1111/j.1365-313X.2009.04084.x, 19929877.
15. The Brassica rapa Genome Sequencing Project Consortium The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 2011, 43:1035-1039. 10.1038/ng.919, 21873998, The Brassica rapa Genome Sequencing Project Consortium.
16. Ayele M, Haas BJ, Kumar N, Wu H, Xiao Y, Van Aken S, Utterback TR, Wortman JR, White OR, Town CD. Whole genome shotgun sequencing of Brassica oleracea and its application to gene discovery and annotation in Arabidopsis. Genome Res 2005, 15:487-495. 10.1101/gr.3176505, 1074363, 15805490.
17. Katari MS, Balija V, Wilson RK, Martienssen RA, McCombie WR. Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana. Genome Res 2005, 15:496-504. 10.1101/gr.3239105, 1074364, 15805491.
18. Schmidt R, Bancroft I. Perspectives on Genetics and Genomics of the Brassicaceae. Genetics and Genomics of the Brassicaceae 2011, 617-632. New York Dordrecht Heidelberg London: Springer, Schmidt R, Bancroft I.
19. Kaur S, Francki MG, Forster JW. Identification, characterisation and interpretation of single-nucleotide sequence variation in allopolyploid crop species. Plant Biotech J 2012, 10:125-138.
20. Durstewitz G, Polley A, Plieske J, Luerssen H, Graner EM, Wieseke R, Ganal MW. SNP discovery by amplicon sequencing and multiplex SNP genotyping in the allopolyploid species Brassica napus. Genome 2010, 53:948-995. 10.1139/G10-079, 21076510.
21. Trick M, Long Y, Meng J, Bancroft I. Single nucleotide polymorphism (SNP) discovery in the polyploidy Brassica napus using Solexa transcriptome sequencing. Plant Biotech J 2009, 7:334-346.
22. Qiu D, Morgan C, Shi J, Long Y, Liu J, Li R, Zhuang X, Wang Y, Tan X, Dietrich E, Weihmann T, Everett C, Vanstraelen S, Beckett P, Fraser F, Trick M, Barnes S, Wilmer J, Schmidt R, Li J, Li D, Meng J, Bancroft I. A comparative linkage map of oilseed rape and its use for QTL analysis of seed oil and erucic acid content. Theor Appl Genet 2006, 114:67-80. 10.1007/s00122-006-0411-2, 17033785.
23. Westermeier P, Wenzel G, Mohler V. Development and evaluation of single-nucleotide polymorphism markers in allotetraploid rapeseed (Brassica napus L.). Theor Appl Genet 2009, 119:1301-1311. 10.1007/s00122-009-1135-x, 19756476.
24. Delourme R, Falentin C, Fopa Fomeju B, Boillot M, Lassalle G, André I, Duarte J, Gauthier V, Lucante N, Marty A, Pauchon M, Pichon J-P, Ribière N, Trotoux G, Blanchard P, Rivière N, Martinant J-P, Pauquet J. High-density SNP based genetic map development and linkage disequilibrium assessment in Brassica napus L. BMC Genomics 2013, 14:120. 10.1186/1471-2164-14-120, 3600037, 23432809.
25. Hu Z, Huang S, Sun M, Wang H, Hua W. Development and application of single nucleotide polymorphism markers in the polyploid Brassica napus by 454 sequencing of expressed sequence tags. Plant Breeding 2012, 131:293-299.
26. Bancroft I, Morgan C, Fraser F, Higgins J, Wells R, Clissold L, Baker D, Long Y, Meng J, Wang X, Liu S, Trick M. Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing. Nat Biotechnol 2011, 29:762-766. 10.1038/nbt.1926, 21804563.
27. Fan JB, Oliphant A, Shen R, Kermani BG, Garcia F, Gunderson KL, Hansen M, Steemers F, Butler SL, Deloukas P, Galver L, Hunt S, McBride C, Bibikova M, Rubano T, Chen J, Wickham E, Doucet D, Chang W, Campbell D, Zhang B, Kruglyak S, Bentley D, Haas J, Rigault P, Zhou L, Stuelpnagel J, Chee MS. Highly parallel SNP genotyping. Cold Spring Harb Symp Quant Biol 2003, 68:69-78. 10.1101/sqb.2003.68.69, 15338605.
28. Fan JB, Chee MS, Gunderson KL. Highly parallel genomic assays. Nat Rev Genet 2006, 7:632-644. 10.1038/nrg1901, 16847463.
29. Fan JB, Gunderson KL, Bibikova M, Yeakley JM, Chen J, Wickham Garcia E, Lebruska LL, Laurent M, Shen R, Barker D. Illumina universal bead arrays. Methods Enzymol 2006b, 410:57-73.
30. Akhunov E, Nicolet C, Dvorak J. Single nucleotide polymorphism genotyping in polyploid wheat with the Illumina GoldenGate assay. Theor Appl Genet 2009, 119:507-517. 10.1007/s00122-009-1059-5, 2715469, 19449174.
31. Luo MC, Xu K, Ma Y, Deal KR, Nicolet CM, Dvorak J. A high-throughput strategy for screening of bacterial artificial chromosome libraries and anchoring of clones on a genetic map constructed with single nucleotide polymorphisms. BMC Genomics 2009, 10:28. 10.1186/1471-2164-10-28, 2647554, 19149906.
32. Bach K. Duplizierte Gene in Brassica napus - genetische Vielfalt in Kandidatengenen für Ölgehalt. PhD thesis 2007, University of Potsdam: Faculty of Mathematics and Natural Sciences.
33. Klein PE, Klein RR, Cartinhour SW, Ulanch PE, Dong J, Obert JA, Morishige DT, Schlueter SD, Childs KL, Ale M, Mullet JE. A high-throughput AFLP-based method for constructing integrated genetic and physical maps: progress toward a sorghum genome map. Genome Res 2000, 10:789-807. 10.1101/gr.10.6.789, 310885, 10854411.
34. Cheng F, Liu S, Wu J, Fang L, Sun S, Liu B, Li P, Hua W, Wang X. BRAD, the genetics and genomics database for Brassica plants. BMC Plant Biol 2011, 11:136. http://brassicadb.org/brad/, 10.1186/1471-2229-11-136, 3213011, 21995777.
35. Sambrook J, Fitsch EF, Maniatis T. Molecular Cloning: A Laboratory Manual 1989, Cold Spring Harbor: Cold Spring Harbor Press.
36. Arumuganathan K, Earle ED. Nuclear DNA content of some important plant species. Plant Mol Biol Rep 1991, 9:208-218.
37. Ostergaard L, King GJ. Standardized gene nomenclature for the Brassica genus. Plant Methods 2008, 4:10. 10.1186/1746-4811-4-10, 2408569, 18492252.
38. Brudno M, Steinkamp R, Morgenstern B. The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences. Nucleic Acids Res 2004, 32:W41-44. http://dialign.gobics.de/chaos-dialign-submission, 10.1093/nar/gkh361, 441499, 15215346.
39. Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 2000, 132:365-386.
40. Hall T. BioEdit http://www.mbio.ncsu.edu/BioEdit/bioedit.html.