Genome-wide discovery of DNA polymorphism in Brassica rapa

Molecular Genetics and Genomics

Volumn 283, Issue 2, 2010, Pages 135-145

  Park, Soomin ^a   Yu, Hee Ju ^a   Mun, Jeong Hwan ^b   Lee, Seung Chan ^a  

^a Rural Development Administration   (South Korea)

^b National Institute of Animal Science   (South Korea)

Author keywords

Brassica rapa genome; Gene based genetic map; Insertion deletions; Single nucleotide polymorphisms

Indexed keywords

ARTICLE; CONTROLLED STUDY; DNA POLYMORPHISM; GENE AMPLIFICATION; GENE IDENTIFICATION; GENE LOCUS; GENE SEQUENCE; GENETICS; GENOME; GENOTYPE; MOLECULAR CLONING; NONHUMAN; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; TURNIP; BACTERIAL ARTIFICIAL CHROMOSOME; BREEDING; DNA SEQUENCE; GENETIC ASSOCIATION; INDEL MUTATION; PLANT GENOME;

BACTERIA (MICROORGANISMS); BRASSICA RAPA;

PLANT DNA;

BRASSICA RAPA; BREEDING; CHROMOSOMES, ARTIFICIAL, BACTERIAL; DNA, PLANT; GENOME, PLANT; GENOME-WIDE ASSOCIATION STUDY; INDEL MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 75649111250     PISSN: 16174615     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00438-009-0504-0     Document Type: Article

References (63)

1. F Absalan M Ronaghi 2008 Molecular inversion probe assay Comp Genomics 396 315 330 10.1007/978-1-59745-515-2-20
2. E Baudry C Kerdelhue H Innan W Stephan 2001 Species and recombination effects on DNA variability in the tomato Genus Genetics 158 1725 1735 11514458 1:CAS:528:DC%2BD3MXmvFKgsbs%3D
3. MA Beilstein IA Al-Shehbaz EA Kellogg 2006 Brassicaceae phylogeny and trichome evolution Am J Bot 93 607 619 10.3732/ajb.93.4.607 1:CAS:528: DC%2BD28XjvFWjs78%3D
4. RT Brumfield P Beerli DA Nickerson SV Edwards 2003 The utility of single nucleotide polymorphisms in inferences of population history Trends Ecol Evol 18 249 256 10.1016/S0169-5347(03)00018-1 (Pubitemid 36551230)
5. CR Cantor MR Nelson 2005 Haplotyping in biomedicine-practical challenges Nat Biotechnol 23 21 22 10.1038/nbt0105-21 15637611 1:CAS:528: DC%2BD2MXhsFGhuw%3D%3D (Pubitemid 41724619)
6. M Cargill D Altshuler J Ireland P Sklar K Ardlie N Patil N Shaw CR Lane EP Lim N Kalyanaraman J Nemesh L Ziaugra L Friedland A Rolfe J Warrington R Lipshutz GQ Daley ES Lander 1999 Characterization of single-nucleotide polymorphisms in coding regions of human genes Nat Genet 22 231 238 10.1038/10290 10391209 1:CAS:528:DyaK1MXkt1eqsb4%3D (Pubitemid 29297248)
7. D Chen A Ahlford F Schnorrer I Kalchhauser M Fellner E Viragh I Kiss A-C Syvanen BJ Dickson 2008 High-resolution, high-throughput SNP mapping in Drosophila melanogaster Nat Methods 5 323 329 10.1038/nmeth1148 18327265 1:CAS:528:DC%2BD1cXht1SksQ%3D%3D
8. A Ching KS Caldwell M Jung M Dolan OS Smith S Tingey M Morgante AJ Rafalski 2002 SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines BMC Genet 3 19 10.1186/1471-2156-3-19 12366868 (Pubitemid 38751030)
9. Choi W (2003) Genetic analysis on disease resistance to Turnip mosaic virus, Clubroot and Soft rot, and rapid development of multiple resistant inbreds in Chinese cabbage (Brassica rapa ssp. pekinensis). PhD thesis, Horticultural science, Chung-Ang University, Anseong, pp 1-96
10. IY Choi DL Hyten LK Matukumalli Q Song JM Chaky CV Quigley K Chase KG Lark RS Reiter MS Yoon EY Hwang SI Yi ND Young RC Shoemaker CP van Tassell JE Specht PB Cregan 2007 A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis Genetics 176 685 696 10.1534/genetics.107.070821 17339218 1:CAS:528:DC%2BD2sXntlOgtrw%3D (Pubitemid 350021056)
11. S Choi G Teakle P Plaha J Kim C Allender E Beynon Z Piao P Soengas T Han G King G Barker P Hand D Lydiate J Batley D Edwards D Koo J Bang B-S Park Y Lim 2007 The reference genetic linkage map for the multinational Brassica rapa genome sequencing project Theor Appl Genet 115 777 792 10.1007/s00122-007-0608-z 17646962 1:CAS:528:DC%2BD2sXhtVKru7%2FK (Pubitemid 47460474)
12. DN Cooper BA Smith HJ Cooke S Niemann J Schmidtke 1985 An estimate of unique DNA sequence heterozygosity in the human genome Hum Genet 69 201 205 10.1007/BF00293024 2984104 1:CAS:528:DyaL2MXksVyqtLk%3D (Pubitemid 15142094)
13. HBSM Côrte-Real DR Dixon PWH Holland 1994 Intron-targeted PCR: a new approach to survey neutral DNA polymorphism in bivalve populations Marine Biol 120 407 413 10.1007/BF00680214
14. LL Dantec D Chagné D Pot O Cantin P Garnier-Géré F Bedon J-M Frigerio P Chaumeil P Léger V Garcia F Laigret A de Daruvar C Plomion 2004 Automated SNP detection in expressed sequence tags: statistical considerations and application to maritime pine sequences Plant Mol Biol 54 461 470 10.1023/B:PLAN.0000036376.11710.6f 15284499 (Pubitemid 39059569)
15. B Ewing P Green 1998 Base-calling of automated sequencer traces using phred. II. Error probabilities Genome Res 8 186 194 9521922 1:CAS:528: DyaK1cXitlWlu7g%3D (Pubitemid 28177230)
16. N Goldman Z Yang 1994 A codon-based model of nucleotide substitution for protein-coding DNA sequences Mol Biol Evol 11 725 736 7968486 1:CAS:528:DyaK2cXmt1eit70%3D
17. D Gordon C Abajian P Green 1998 Consed: a graphical tool for sequence finishing Genome Res 8 195 202 9521923 1:CAS:528:DyaK1cXitlWksr0%3D
18. MAM Groenen P Wahlberg M Foglio HH Cheng H-J Megens RPMA Crooijmans F Besnier M Lathrop WM Muir GK-S Wong I Gut L Andersson 2009 A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate Genome Res 19 510 519 10.1101/gr.086538.108 19088305 1:CAS:528:DC%2BD1MXjt12ku74%3D
19. PK Gupta S Rustgi RR Mir 2008 Array-based high-throughput DNA markers for crop improvement Heredity 101 5 18 10.1038/hdy.2008.35 18461083 1:CAS:528:DC%2BD1cXnt1eis7Y%3D (Pubitemid 351861524)
20. Hong CP, Kwon SJ, Kim JS, Yang TJ, Park BS, Lim YP (2008) Progress in understanding and sequencing the genome of Brassica rapa. Int J Plant Genomics 9 (Article ID 582837)
21. G Jander SR Norris SD Rounsley DF Bush IM Levin RL Last 2002 Arabidopsis map-based cloning in the post-genome era Plant Physiol 129 440 450 10.1104/pp.003533 12068090 1:CAS:528:DC%2BD38XkvV2jsLk%3D (Pubitemid 34689134)
22. JS Johston AE Pepper AE Hall ZJ Chen G Hodnett J Drabek R Lopez HJ Price 2005 Evolution of genome size in Brassicaceae Ann Bot 95 229 235 10.1093/aob/mci016 1:CAS:528:DC%2BD2MXht1Kiu74%3D (Pubitemid 41214463)
23. E Jorgenson JS Witte 2006 A gene-centric approach to genome-wide association studies Nat Rev Genet 7 885 891 10.1038/nrg1962 17047687 1:CAS:528:DC%2BD28XhtVyktLnO (Pubitemid 44607104)
24. V Kanazin H Talbert D See P DeCamp E Nevo T Blake 2002 Discovery and assay of single-nucleotide polymorphisms in barley (Hordeum vulgare) Plant Mol Biol 48 529 537 10.1023/A:1014859031781 11999833 1:CAS:528:DC%2BD38XjsFWrtr8%3D (Pubitemid 34431992)
25. JS Kim TY Chung GJ King M Jin TJ Yang YM Jin HI Kim BS Park 2006 A sequence-tagged linkage map of Brassica rapa Genetics 174 29 39 10.1534/genetics.106.060152 16988107 1:CAS:528:DC%2BD28XhtFGgsrjM (Pubitemid 44427651)
26. EP Lessa 1992 Rapid surveying of DNA sequence variation in natural populations Mol Biol Evol 9 323 330 1560767 1:CAS:528:DyaK38XhvVyktLY%3D
27. D Lijavetzky JA Cabezas A Ibanez V Rodriguez JM Martinez-Zapater 2007 High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a re-sequencing approach and SNPlex technology BMC Genomics 8 424 10.1186/1471-2164-8-424 18021442 (Pubitemid 351150064)
28. F Liu D Charlesworth M Kreitman 1999 The effect of mating system differences on nucleotide diversity at the phosphoglucose isomerase Locus in the plant genus Leavenworthia Genetics 151 343 357 9872972 1:CAS:528: DyaK1MXovVCnsw%3D%3D
29. L Lukens F Zou D Lydiate I Parkin T Osborn 2003 Comparison of a Brassica oleracea genetic map with the genome of Arabidopsis thaliana Genetics 164 359 372 12750346 1:CAS:528:DC%2BD3sXkvFOiurk%3D
30. MA Lysak MA Koch A Pecinka I Schubert 2005 Chromosome triplication found across the tribe Brassiceae Genome Res 15 516 525 10.1101/gr.3531105 15781573 1:CAS:528:DC%2BD2MXjsVahtbo%3D (Pubitemid 41065010)
31. G Marth I Korf M Yandell R Yeh Z Gu H Zakeri N Stitziel L Hillier P Kwok W Gish 1999 A general approach to single-nucleotide polymorphism discovery Nat Genet 23 452 456 10.1038/70570 10581034 1:CAS:528:DyaK1MXnvFOkur4%3D
32. L Matukumalli J Grefenstette D Hyten I-Y Choi P Cregan C Van Tassell 2006 SNP-PHAGE-high throughput SNP discovery pipeline BMC Bioinform 7 468 10.1186/1471-2105-7-468 1:CAS:528:DC%2BD28Xht1Wgs73F (Pubitemid 44688208)
33. E Moriyama J Powell 1996 Intraspecific nuclear DNA variation in Drosophila Mol Biol Evol 13 261 277 8583899 1:CAS:528:DyaK28XhtVylu7k%3D
34. J-H Mun S-J Kwon T-J Yang Y-J Seol M Jin J-A Kim M-H Lim JS Kim S Baek B Choi H-J Yu D-S Kim N Kim K Lim S-I Lee Y Lim I Bancroft J-H Hahn B Park 2009 Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication Genome Biol 10 R111 10.1186/gb-2009-10-10-r111 19821981 1:CAS:528:DC%2BD1MXhsVSju7vI
35. CM O'neill I Bancroft 2000 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 23 233 243 10.1046/j.1365-313x.2000.00781.x 10929117 (Pubitemid 30597283)
36. Panjabi P, Jagannath A, Bisht N, Padmaja KL, Sharma S, Gupta V, Pradhan A, Pental D (2008) Comparative mapping of Brassica juncea and Arabidopsis thaliana using Intron Polymorphism (IP) markers: homoeologous relationships, diversification and evolution of the A, B and C Brassica genomes. BMC Genomics 9:113
37. N Pavy L Parsons C Paule J MacKay J Bousquet 2006 Automated SNP detection from a large collection of white spruce expressed sequences: contributing factors and approaches for the categorization of SNPs BMC Genomics 7 174 10.1186/1471-2164-7-174 16824208 1:CAS:528:DC%2BD28XnvFagsrk%3D (Pubitemid 44314300)
38. J Piquemal E Cinquin F Couton C Rondeau E Seignoret I Doucet D Perret MJ Villeger P Vincourt P Blanchard 2005 Construction of an oilseed rape (Brassica napus L.) genetic map with SSR markers Theor Appl Genet 111 1514 1523 10.1007/s00122-005-0080-6 16187118 1:CAS:528:DC%2BD2MXht1SqtLvL (Pubitemid 41618652)
39. E Pollak 1987 On the theory of partially inbreeding finite populations. I. Partial selfing Genetics 117 353 360 3666446 1:STN:280:DyaL1c%2FjtVKmug%3D%3D
40. A Rafalski 2002 Applications of single nucleotide polymorphisms in crop genetics Curr Opin Plant Biol 5 94 100 10.1016/S1369-5266(02)00240-6 11856602 1:CAS:528:DC%2BD38XhtlGnsLg%3D (Pubitemid 34190373)
41. Rozen S, Skaletsky H (1999) Primer3 on the WWW for general users and for biologist programmers. In: Bioinformatics methods and protocols, pp 365-386
42. KJ Schmid TR Sorensen R Stracke O Torjek T Altmann T Mitchell-Olds B Weisshaar 2003 Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana Genome Res 13 1250 1257 10.1101/gr.728603 12799357 (Pubitemid 36764205)
43. KJ Schmid S Ramos-Onsins H Ringys-Beckstein B Weisshaar T Mitchell-Olds 2005 A multilocus sequence survey in Arabidopsis thaliana reveals a genome-wide departure from a neutral model of DNA sequence polymorphism Genetics 169 1601 1615 10.1534/genetics.104.033795 15654111 1:CAS:528:DC%2BD2MXktFGjtrk%3D (Pubitemid 40547468)
44. K Schneider B Weisshaar DC Borchardt F Salamini 2001 SNP frequency and allelic haplotype structure of Beta vulgaris expressed genes Mol Breed 8 63 74 10.1023/A:1011902916194 1:CAS:528:DC%2BD3MXotl2ks7c%3D (Pubitemid 32996996)
45. P Soengas P Hand J Vicente J Pole D Pink 2007 Identification of quantitative trait loci for resistance to Xanthomonas campestris pv. campestris in Brassica rapa Theor Appl Genet 114 637 645 10.1007/s00122-006-0464-2 17160671 1:STN:280:DC%2BD2s%2FnsFSisA%3D%3D (Pubitemid 46214061)
46. BE Stranger AC Nica MS Forrest A Dimas CP Bird C Beazley CE Ingle M Dunning P Flicek D Koller S Montgomery S Tavare P Deloukas ET Dermitzakis 2007 Population genomics of human gene expression Nat Genet 39 1217 1224 10.1038/ng2142 17873874 1:CAS:528:DC%2BD2sXhtV2isL7N (Pubitemid 47482691)
47. K Suwabe H Tsukazaki H Iketani K Hatakeyama M Kondo M Fujimura T Nunome H Fukuoka M Hirai S Matsumoto 2006 Simple sequence repeat-based comparative genomics between Brassica rapa and Arabidopsis thaliana: the genetic origin of clubroot resistance Genetics 173 309 319 10.1534/genetics.104.038968 16723420 1:CAS:528:DC%2BD28XlvF2itr4%3D (Pubitemid 43804584)
48. AC Syvanen 2001 Accessing genetic variation: genotyping single nucleotide polymorphisms Nat Rev Genet 2 930 942 10.1038/35103535 11733746 1:CAS:528:DC%2BD38Xmt1Whu7Y%3D (Pubitemid 33691090)
49. AC Syvanen 2005 Toward genome-wide SNP genotyping Nat rev genet 37 S5 S10 10.1038/ng1558 1:CAS:528:DC%2BD2MXksFeisLs%3D (Pubitemid 40770397)
50. F Tajima 1983 Evolutionary relationship of DNA sequences in finite populations Genetics 105 437 460 6628982 1:CAS:528:DyaL3sXlsFCjs74%3D
51. CD Town F Cheung R Maiti J Crabtree BJ Haas JR Wortman EE Hine R Althoff TS Arbogast LJ Tallon M Vigouroux M Trick I Bancroft 2006 Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy Plant Cell 18 1348 1359 10.1105/tpc.106.041665 16632643 1:CAS:528:DC%2BD28XlvVCnsrc%3D (Pubitemid 43956101)
52. UN 1935 Genome analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization Jpn J Bot 7 389 452
53. JC Venter MD Adams EW Myers PW Li RJ Mural, et al. 2001 The sequence of the human genome Science 291 1304 1351 10.1126/science.1058040 11181995 1:CAS:528:DC%2BD3MXhtlSgsbo%3D (Pubitemid 32173090)
54. DG Wang J-B Fan C-J Siao A Berno P Young R Sapolsky G Ghandour N Perkins E Winchester J Spencer L Kruglyak L Stein L Hsie T Topaloglou E Hubbell E Robinson M Mittmann MS Morris N Shen D Kilburn J Rioux C Nusbaum S Rozen TJ Hudson R Lipshutz M Chee ES Lander 1998 Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome Science 280 1077 1082 10.1126/science.280.5366.1077 9582121 1:CAS:528:DyaK1cXjt1egsb0%3D (Pubitemid 28234949)
55. X Wang X Zhao J Zhu W Wu 2005 Genome-wide investigation of intron length polymorphisms and their potential as molecular markers in rice (Oryza sativa L.) DNA Res 12 417 427 10.1093/dnares/dsi019 16769698 1:CAS:528: DC%2BD28XjsFCns78%3D (Pubitemid 43843811)
56. GA Watterson 1975 On the number of segregating sites in genetical models without recombination Theor Popul Biol 7 256 276 10.1016/0040-5809(75)90020-9 1145509 1:STN:280:DyaE2M7pvFSquw%3D%3D
57. SI Wright B Lauga D Charlesworth 2002 Rates and patterns of molecular evolution in inbred and outbred Arabidopsis Mol Biol Evol 19 1407 1420 12200469 1:CAS:528:DC%2BD38XntVyht74%3D
58. SI Wright IV Bi SG Schroeder M Yamasaki JF Doebley MD McMullen BS Gaut 2005 The effects of artificial selection on the maize genome Science 308 1310 1314 10.1126/science.1107891 15919994 1:CAS:528:DC%2BD2MXks1Ciur0%3D (Pubitemid 40746127)
59. KS Wydner HC Passmore JL Sechler CD Boyd 1994 Use of an intron length polymorphism to localize the tropoelastin gene to mouse Chromosome 5 in a region of linkage conservation with human Chromosome 7 Genomics 23 125 131 10.1006/geno.1994.1467 7829060 1:CAS:528:DyaK2MXptVGmtg%3D%3D (Pubitemid 24296943)
60. Z Yang 2007 PAML 4: phylogenetic analysis by maximum likelihood Mol Biol Evol 24 1586 1591 10.1093/molbev/msm088 17483113 1:CAS:528:DC%2BD2sXpsVGrs7c%3D (Pubitemid 47236688)
61. T-J Yang JS Kim S-J Kwon K-B Lim B-S Choi J-A Kim M Jin JY Park M-H Lim H-I Kim YP Lim JJ Kang J-H Hong C-B Kim J Bhak I Bancroft B-S Park 2006 Sequence-level analysis of the diploidization process in the triplicated FLOWERING LOCUS C region of Brassica rapa Plant Cell 18 1339 1347 10.1105/tpc.105.040535 16632644 1:CAS:528:DC%2BD28XlvVCnsrY%3D (Pubitemid 43959288)
62. L Zhang TJ Vision BS Gaut 2002 Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana Mol Biol Evol 19 1464 1473 12200474 1:CAS:528:DC%2BD38XntVyht7g%3D
63. Y Zhu Q Song D Hyten C Van Tassell L Matukumalli D Grimm S Hyatt E Fickus N Young P Cregan 2003 Single-nucleotide polymorphisms in soybean Genetics 163 1123 1134 12663549 1:CAS:528:DC%2BD3sXjtlOgsL0%3D