Construction of BAC and BIBAC libraries and their applications for generation of SSR markers for genome analysis of chickpea, Cicer arietinum L.

Theoretical and Applied Genetics

Volumn 110, Issue 3, 2005, Pages 492-510

  Lichtenzveig, J ^a,c,d   Scheuring, C ^b   Dodge, J ^b   Abbo, S ^a   Zhang, H B ^b  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

^b TEXAS A AND M UNIVERSITY   (United States)

^c MURDOCH UNIVERSITY   (Australia)

^d CSIRO   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; BIOMARKERS; CHROMOSOMES; CLONING; DNA; RESEARCH;

BACTERIAL ARTIFICIAL CHROMOSOMES (BAC); BINARY BACTERIAL ARTIFICIAL CHROMOSOMES (BIBAC); INSERT SIZE; SIMPLE SEQUENCE REPEAT (SSR) MARKERS;

PLANTS (BOTANY);

BACTERIA (MICROORGANISMS); CICER ARIETINUM;

OLIGONUCLEOTIDE; PRIMER DNA;

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CHICKPEA; COMPARATIVE STUDY; DNA SEQUENCE; GENE LIBRARY; GENETIC MARKER; GENETICS; GENOME; MOLECULAR CLONING; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; VARIABLE NUMBER OF TANDEM REPEAT;

BASE SEQUENCE; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CICER; CLONING, MOLECULAR; DNA PRIMERS; GENE LIBRARY; GENETIC MARKERS; GENOME, PLANT; MINISATELLITE REPEATS; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDES; SEQUENCE ANALYSIS, DNA;

EID: 16244367453     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-004-1857-8     Document Type: Article

References (49)

1. Ahmad F, Gaur PM, Slinkard AE (1992) Isozyme polymorphism and phylogenetic interpretation in the genus Cicer L. Theor Appl Genet 83:620-627
2. Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Rep 9:208-218
3. Bhattramakki D, Dong J, Chhabra AK, Hart GE (2000) An integrated SSR and RFLP linkage map of Sorghum bicolor (L.) Moench. Genome 43:988-1002
4. Chang YL, Tao Q, Scheuring C, Meksem K, Zhang H-B (2001) An integrated map of Arabidopsis thaliana for functional analysis of its genome sequence. Genetics 159:1231-1242
5. Chen M, Presting G, Barbazuk WB, Goicoechea JL, Blackmon B, Fang G, Kim H, Frisch D, Yu Y, Sun S, Higingbottom S, Phimphilai J, Phimphilai D, Thurmond S, Gaudette B, Li P, Liu J, Hatfield J, Main D, Farrar K, Henderson C, Barnett L, Costa R, Williams B, Walser S, Atkins M, Hall C, Budiman MA, Tomkins JP, Luo M, Bancroft I, Salse J, Regad F, Mohapatra T, Singh NK, Tyagi AK, Soderlund C, Dean RA, Wing RA (2002) An integrated physical and genetic map of the rice genome. Plant Cell 14:537-545
6. Cho S, Kumar J, Shultz JL, Anupama K, Tefera F, Muehlbauer FJ (2002) Mapping genes for double podding and other morphological traits in chickpea. Euphytica 128:285-292
7. Choumane W, Winter P, Weigand F, Kahl G (2000) Conservation and variability of sequence-tagged microsatellite sites (STMSs) from chickpea (Cicer aerietinum L.) within the genus Cicer. Theor Appl Genet 101:269-278
8. Cregan PB, Jarvik T, Bush AL, Shoemaker RC, Lark KG, Kahler, AL, Kaya N, Van Toai TT, Lohnes DJ, Chung J (1999a) The integrated map of the soybean genome. Crop Sci 39:1464-1490
9. Cregan PB, Mudge J, Fickus EW, Marek LF, Danesh D, Denny R, Shoemaker RC, Matthews BF, Jarvik T, Young ND (1999b) Targeted isolation of simple sequence repeat markers through the use of bacterial artificial chromosomes. Theor Appl Genet 98:919-928
10. Edwards KJ, Barker JHA, Daly A, Jones C, Karp A (1996) Microsatellite libraries enriched for several microsatellite sequences in plants. Biotechniques 20:758-760
11. Flandez-Galvez H, Ford R, Pang ECK, Taylor PWJ (2003) An intraspecific linkage map of the chickpea (Cicer arietinum L.) genome based on sequence tagged microsatellite and resistance gene analog markers. Theor Appl Genet 106:1447-1456
12. Hamilton CM, Frary A, Lewis C, Tanksley SD (1996) Stable transfer of intact high molecular weight DNA into plant chromosomes. Proc Natl Acad Sci USA 93:9975-9979
13. Hamilton CM, Frary A, Xu Y, Tanksley SD, Zhang H-B (1999) Construction of tomato genomic DNA libraries in a binary-BAC (BIBAC) vector. Plant J 18:223-229
14. He RF, Wang Y, Shi Z, Ren X, Zhu L, Weng Q, He GC (2003) Construction of a genomic library of wild rice and Agrobacterium-mediated transformation of large insert DNA linked to BPH resistance loci. Gene 321:113-121
15. Hüttel B, Winter P, Weising K, Choumane W, Weigand F, Kahl G (1999) Sequence-tagged microsatellite site markers for chickpea (Cicer arietinum L.). Genome 42:210-217
16. Kar S, Johnson TM, Nayak P, Sen SK (1996) Efficient transgenic plant regeneration through Agrobacterium-mediated transformation of chickpea (Cicer arietinum L.). Plant Cell Rep 16:32-37
17. Kazan K, Muehlbauer FJ, Weeden NF, Lazinsky G (1993) Inheritance and linkage relationships of morphological and isozyme loci in chickpea (Cicer arietinum L.). Theor Appl Genet 86:417-426
18. Krishnamurthy KV, Suhasini K, Sagare AP, Meixner M, de Kathen A, Pickardt T, Schieder O (2000) Agrobacterium mediated transformation of chickpea (Cicer arietinum L.) embryo axes. Plant Cell Rep 19:235-240
19. Labdi M, Robertson LD, Singh KB, Charrier A (1996) Genetic diversity and phylogenetic relationships among the annual Cicer species as revealed by isozyme polymorphisms. Euphytica 88:181-188
20. Ladizinsky G (1995) Chickpea. In: Smartt J, Simmonds NW (eds) Evolution of crop plants. Longman, New York, pp 258-261
21. Liu Y, Shirano Y, Fukaki H, Yanai Y, Tasaka M, Tabata S, Shibata D (1999) Complementation of plant mutants with large genomic DNA fragments by a transformation-competent artificial chromosome vector accelerates positional cloning. Proc Natl Acad Sci USA 96:6535-6540
22. Liu YG, Liu H, Chen L, Qiu W, Zhang Q, Wu H, Yang C, Su J, Wang Z, Tian D, Mei M (2002) Development of new transformation-competent artificial chromosome vectors and rice genomic libraries for efficient gene cloning. Gene 282:247-255
23. Rajesh PN, Tullu A, Gil J, Gupta VS, Ranjekar PK, Muehlbauer FJ (2002) Identification of an STMS marker for the double-podding gene in chickpea. Theor Appl Genet 105:604-607
24. Rajesh PN, Coyne C, Meksem K, DerSharma K, Gupta V, Muehlbauer FJ (2004) Construction of a HindIII bacterial artificial chromosome library and its use in identification of clones associated with disease resistance in chickpea. Theor Appl Genet 108:663-669
25. Ren C, Lee M-K, Yan B, Ding K, Cox B, Romanov MN, Price JA, Dodgson JB, Zhang H-B (2003) A BAC-based physical map of the chicken genome. Genome Res 13:2754-2758
26. Ren C, Xu ZY, Sun S, Lee M-K, Wu C, Zhang H-B (2004) Genomic libraries for physical mapping. In: Meksem K, Kahl G (eds) Handbook of plant genome mapping: Genetic and physical mapping. Wiley-VCH, Weinheim, in press
27. Röder MS, Korzun V, Wendehake K, Plaschke J, Tixier M-H, Leroy P, Ganal MW (1998) A microsatellite map of wheat. Genetics 149:2007-2023
28. Sharma PC, Winter P, Bunger T, Huttel B, Weigand F, Weising K, Kahl G (1995) Abundance and polymorphism of di-, tri-, and tetra-nucleotide tandem repeats in chickpea (Cicer arietinum L.). Theor Appl Genet 90:90-96
29. Simon CJ, Muehlbauer FJ (1997) Construction of a chickpea linkage map and its comparison with maps of pea and lentil. J Hered 88:115-119
30. Su XZ, Wu Y, Sifri CD, Wellems TE (1996) Reduced extension temperatures required for PCR amplification of extremely A + T-rich DNA. Nucleic Acids Res 24:1574-1575
31. Tao Q, Zhang H-B (1998) Cloning and stable maintenance of DNA fragments over 300 kb in Escherichia coli with conventional plasmid-based vectors. Nucleic Acids Res 26:4901-4909
32. Tao Q, Chang YL, Wang J, Chen H, Islam-Faridi MN, Scheuring C, Wang B, Stelly DM, Zhang H-B (2001) BAC-based physical map of the rice genome constructed by restriction fingerprint analysis. Genetics 158:1711-1724
33. Tautz D, Renz M (1984) Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res 12:4127-4138
34. Tekeoglu M, Rajesh PN, Muelhlbauer FJ (2002) Integration of sequence tagged microsatellite sites to the chickpea genetic map. Theor Appl Genet 105:847-854
35. Udupa SM, Baum M (2003) Genetic dissection of pathotype-specific resistance to ascochyta blight disease in chickpea (Cicer arietinum L.) using microsatellite markers. Theor Appl Genet 106:1196-1202
36. Udupa SM, Sharma A, Sharma AP, Pai RA (1993) Narrow genetic variability in Cicer arietinum L. as revealed by RFLP analysis. J Plant Biochem Biotechnol 2:83-86
37. n microsatellite loci in a world collection of chickpea (Cicer arietinum L.) germplasm. Mol Gen Genet 261:354-363
38. Weising K, Kaemmer D, Weigand F, Epplen JT, Kahl G (1992) Oligonucleotide fingerprinting reveals various probe-dependent levels of informativeness in chickpea (Cicer arietinum). Genome 35:436-442
39. Williams PC, Singh U (1987) The chickpea nutritional quality and evaluation of quality in breeding programs. In: Saxena MC, Singh KB (eds) The chickpea. CAB International, Wallingford, pp 329-356
40. Winter P, Pfaff T, Udupa SM, Hüttel B, Sharma PC, Sahi S, Arreguin-Espinoza R, Weigand F, Muehlbauer FJ, Kahl G (1999) Characterization and mapping of sequence-tagged microsatellite sites in the chickpea (Cicer arietinum L.) genome. Mol Gen Genet 262:90-101
41. Winter P, Benko-Iseppon A-M, Hüttel B, Ratnaparkhe M, Tullu A, Sonnante G, Pfaff T, Tekeoglu M, Santra D, Sant VJ, Rajesh PN, Kahl G, Meuhlbauer FJ (2000) A linkage map of the chickpea (Cicer arietinum L.) genome based on recombinant inbred lines from a C. arietinum x C. reticulatum cross: localization of resistance genes for Fusarium wilt races 4 and 5. Theor Appl Genet 101:1155-1163
42. Wu C, Sun S, Nimmakayala P, Santos F, Meksem K, Springman R, Ding K, Lightfoot DA, Zhang H-B (2004a) A BAC- and BIBAC-based physical map of the soybean genome. Genome Res 14:319-326
43. Wu C, Xu Z, Zhang H-B (2004b) DNA libraries. In: Meyers RA (ed) Encyclopedia of molecular cell biology and molecular medicine, vol 3, 2nd edn. Wiley-VCH, Weinheim, pp 385-425
44. Wu C, Nimmakayala P, Santos FA, Springman R, Tao Q, Meksem K, Lightfoot DA, Zhang H-B (2004c) Construction and characterization of a soybean bacterial artificial chromosome library and use of multiple complementary libraries for genome physical mapping. Theor Appl Genet 109:1041-1050
45. Wu C, Sun S, Lee M-K, Xu ZY, Ren C, Zhang H-B (2004d) Whole genome physical mapping: an overview on methods for DNA fingerprinting. In: Meksem K, Kahl G (eds) Handbook of plant genome mapping: Genetic and physical mapping. Wiley-VCH, Weinheim, in press
46. Xu ZY, Sun S, Covaleda L, Ding K, Zhang A, Scheuring C, Zhang H-B (2004) Genome physical mapping with large-insert bacterial clones by fingerprint analysis: methodologies, source clone genome coverage and contig map quality. Genomics 84:941-951
47. Zhang H-B (2000) Construction and manipulation of large-insert bacterial clone libraries manual. Texas A&M University, College Station. Available via http://hbz.tamu.edu
48. Zhang H-B, Zhao X-P, Ding X-L, Paterson AH, Wing RA (1995) Preparation of megabase-size DNA from plant nuclei. Plant J 7:175-184
49. Zhang H-B, Woo S-S, Wing RA (1996) BAC, YAC and cosmid library construction. In: Foster G, Twell D (eds) Plant gene isolation: principles and practice. Wiley, Chichester, pp 75-99