Genetic marker anchoring by six-dimensional pools for development of a soybean physical map

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Wu, Xiaolei ^a   Zhong, Guohua ^a   Findley, Seth D ^a   Cregan, Perry ^b   Stacey, Gary ^a,c   Nguyen, Henry T ^a  

^a UNIVERSITY OF MISSOURI   (United States)

^b AGRICULTURAL RESEARCH SERVICE   (United States)

^c University of Missouri   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PLANT DNA;

ARTICLE; COMPUTER MODEL; DNA FINGERPRINTING; GENBANK; GENE DUPLICATION; GENE LIBRARY; GENE LOCUS; GENE MAPPING; GENE POOL; GENE SEQUENCE; GENETIC MARKER; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENETICS; POLYMERASE CHAIN REACTION; PROMOTER REGION; SEQUENCE ANALYSIS; SOYBEAN; BACTERIAL ARTIFICIAL CHROMOSOME; BIOLOGICAL MODEL; CHROMOSOME MAP; EVALUATION; EXPRESSED SEQUENCE TAG; GENETICS; GENOME; METHODOLOGY; PHYSIOLOGY; SEQUENCE HOMOLOGY;

GLYCINE MAX;

BASE SEQUENCE; CHROMOSOMES, ARTIFICIAL, BACTERIAL; EXPRESSED SEQUENCE TAGS; GENETIC MARKERS; GENOME, PLANT; GENOMIC LIBRARY; MODELS, BIOLOGICAL; PHYSICAL CHROMOSOME MAPPING; POLYMERASE CHAIN REACTION; SEQUENCE HOMOLOGY, NUCLEIC ACID; SOYBEANS;

EID: 40149092542     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-28     Document Type: Article

References (34)

1. Gepts P Beavis WD Brummer EC Shoemaker RC Stalker HT Weeden NF Young ND Legumes as a model plant family. Genomics for food and feed report of the Cross-Legume Advances Through Genomics Conference Plant Physiol 2005, 137:1228-1235. 1088316 15824285 10.1104/pp.105.060871
2. Stacey G Vodkin L Parrott WA Shoemaker RC National Science Foundation - sponsored workshop report. Draft plan for soybean genomics Plant Physiol 2004, 135:59-70. 429333 15141067 10.1104/pp.103.037903
3. Jackson SA Rokhsar D Stacey G Shoemaker RC Schmutz J Grimwood J Toward a reference sequencing of the soybean genome: A multiagency effort Crop Sci 2006, 46:S55-S61.
4. Arumuganathan K Earle ED Nuclear DNA content of some important plant species Plant Mol Biol Rep 1991, 9:208-219.
5. Shoemaker RC Polzin K Labate J Specht J Brummer EC Olson T Young N Concibido V Wilcox J Tamulonis JP Kochert G Boerma HR Genome duplication in soybean (Glycine subgenus soja) Genetics 1996, 144:329-338. 1207505 8878696
6. Blanc G Wolfe KH Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes Plant Cell 2004, 16:1667-1678. 514152 15208399 10.1105/tpc.021345
7. Schlueter JA Dixon P Granger C Grant D Clark L Doyle JJ Shoemaker RC Mining EST databases to resolve evolutionary events in major crop species Genome 2004, 47:868-876. 10.1139/g04-047 15499401
8. Mudge J Huihuang Y Denny RL Howe DK Danesh D Marek LF Retzel E Shoemaker RC Young ND Soybean bacterial artificial chromosome contigs anchored with RFLPs: Insights into genome duplication and gene clustering Genome 2004, 47:361-372. 15060589
9. Foster-Hartnett D Mudge J Danesh D Yan H Larsen D Comparative genomic analysis of sequences sampled from a small region on soybean molecular linkage group 'G' Genome 2002, 45:634-645. 10.1139/g02-027 12175066
10. Song QJ Marek LF Shoemaker RC Lark KG Concibido VC Delannay X Specht JE Cregan PB A new integrated genetic linkage map of the soybean Theor Appl Genet 2004, 109:122-128. 10.1007/s00122-004-1602-3 14991109
11. Choi IY Hyten DL Matukumalli LK Song Q Chaky JM Quigley CV Chase K Lark KG Reiter RS Yoon MS Hwang EY Yi SI Young ND Shoemaker RC van Tassell CP Specht JE Cregan PB A Soybean Transcript Map: Gene Distribution, Haplotype and SNP Analysis Genetics 2007, 176:685-696. 1893076 17339218 10.1534/genetics.107.070821
12. Wu C Sun S Nimmakayala P Santos FA Meksem K Springman R Ding K Lightfoot DA Zhang HB A BAC- and BIBAC-based physical map of the soybean genome Genome Res 2004, 14:319-326. 327108 14718376 10.1101/gr.1405004
13. Soybean Cultivar "Williams" Physical Map - integrating the soybean genetic and physical maps http://soybeanphysicalmap.org/
14. Shoemaker R Grant D Olson T Warren WC Wing R Yu Y Kim H Cregan P Joseph B Futrell-Griggs M Nelson W Davito J Walker J Wallis J Kremitski C Scheer D Clifton S Graves T Nguyen HT Wu XL Luo MC Dvorak J Nelson R Cannon S Thomkins J Schmutz J Stacey G Jackson S Microsatellite discovery from BAC end sequences and genetic mapping to anchor the soybean physical and genetic maps Genome.
15. Gardiner J Schroeder S Polacco ML Sanchez-Villeda H Fang Z Morgante M Landewe T Fengler K Useche F Hanafey M Tingey S Chou H Wing R Soderlund C Coe EH Jr Anchoring 9,371 maize expressed sequence tagged unigenes to the bacterial artificial chromosome contig map by two-dimensional overgo hybridization Plant Physiol 2004, 134:1317-1326. 419808 15020742 10.1104/ pp.103.034538
16. Romanov MN Price JA Dodgson JB Integration of animal linkage and BAC contig maps using overgo hybridization Cytogenet Genome Res 2003, 102:277-281. 10.1159/000075763 14970717
17. Barillot E Lacroix B Cohen D Theoretical analysis of library screening using a N-dimensional pooling strategy Nucleic Acids Res 1991, 19:6241-6247. 329134 1956784 10.1093/nar/19.22.6241
18. Bruno WJ Knill E Balding DJ Bruce DC Doggett NA Sawhill WW Stallings RL Whittaker CC Torney DC Efficient pooling designs for library screening Genomics 1995, 26:21-30. 10.1016/0888-7543(95)80078-Z 7782082
19. 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. 310885 10854411 10.1101/gr.10.6.789
20. Yim YS Moak P Sanchez-Villeda H Musket TA Close P Klein PE Mullet JE McMullen MD Fang Z Schaeffer ML Gardiner JM Coe EH Jr Davis GL A BAC pooling strategy combined with PCR-based screenings in a large, highly repetitive genome enables integration of the maize genetic and physical maps BMC Genomics 2007, 8:47. 1821331 17291341 10.1186/1471-2164-8-47
21. Asakawa S Abe I Kudoh Y Kishi N Wang Y Kubota R Kudoh J Kawasaki K Minoshima S Shimizu N Human BAC library: Construction and rapid screening Gene 1997, 191:69-79. 10.1016/S0378-1119(97)00044-9 9210591
22. Eggen A Gautier M Billaut A Petit E Hayes H Laurent P Urban C Pfister-Genskow M Eilertsen K Bishop MD Construction and characterization of a bovine BAC library with four genome-equivalent coverage Genet Sel Evol 2001, 33:543-548. 10.1051/gse:2001132 11712974
23. Lamoureux D Bernole A Le Clainche I Tual S Thareau V Paillard S Legeai F Dossat C Wincker P Oswald M Merdinoglu D Vignault C Delrot S Caboche M Chalhoub B Adam-Blondon AF Anchoring of a large set of markers onto a BAC library for the development of a draft physical map of the grapevine genome Theor Appl Genet 2006, 113:344-356. 10.1007/s00122-006-0301-7 16791700
24. Bouzidi MF Franchel J Tao Q Stormo K Mraz A Nicolas P Mouzeyar S A sunflower BAC library suitable for PCR screening and physical mapping of targeted genomic regions Theor Appl Genet 2006, 113:81-89. 10.1007/ s00122-006-0274-6 16783592
25. Yuan Q Liang F Hsiao J Zismann V Benito MI Quackenbush J Wing R Buell R Anchoring of rice BAC clones to the rice genetic map in silico Nucleic Acids Res 2000, 28:3636-3641. 110739 10982886 10.1093/nar/28.18.3636
26. Leeb T Vogl C Zhu B de Jong PJ Binns MM Chowdhary BP Scharfe M Jarek M Nordsiek G Schrader F Blocker H A human-horse comparative map based on equine BAC end sequences Genomics 2006, 87:772-776. 10.1016/ j.ygeno.2006.03.002 16603334
27. Schuler GD Sequence mapping by electronic PCR Genome Res 1997, 7:541-550. 310656 9149949
28. Murphy K Raj T Winters RS White PS me-PCR: A refined ultrafast algorithm for identifying sequence-defined genomic elements Bioinformatics 2004, 20:588-590. 10.1093/bioinformatics/btg466 14990458
29. National Center for Biotechnology Information(NCBI) http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=unigene
30. SoyMap http://www.soymap.org/
31. Krzywinski M Wallis J Gosele C Bosdet I Chiu R Graves T Hummel O Layman D Mathewson C Wye N Zhu B Albracht D Asano J Barber S Brown-John M Chan S Chand S Cloutier A Davito J Fjell C Gaige T Ganten D Girn N Guggenheimer K Himmelbauer H Kreitler T Leach S Lee D Lehrach H Mayo M Mead K Olson T Pandoh P Prabhu AL Shin H Tanzer S Thompson J Tsai M Walker J Yang G Sekhon M Hillier L Zimdahl H Marziali A Osoegawa K Zhao S Siddiqui A de Jong PJ Warren W Mardis E McPherson JD Wilson R Hubner N Jones S Marra M Schein J Integrated and sequence-ordered BAC- and YAC-based physical maps for the rat genome Genome Res 2004, 14:766-779. 383324 15060021 10.1101/gr.2336604
32. Chappell AS Scaboo AM Wu X Nguyen H Pantalone VR Bilyeu KD Characterization of the MIPS gene family in Glycine max Plant Breeding 2006, 125:493-500. 10.1111/j.1439-0523.2006.01264.x
33. Zhang XC Wu X Findley S Wan J Libault M Nguyen HT Cannon SB Stacey G Molecular evolution of lysine motif-type receptor-like kinases in Plants Plant Physiol 2007, 144:623-636. 1914208 17449649 10.1104/pp.107.097097
34. The Soybean Breeders Toolbox http://soybeanbreederstoolbox.org/