Genomic analysis and marker development for the Tsn1 locus in wheat using bin-mapped ESTs and flanking BAC contigs

Theoretical and Applied Genetics

Volumn 112, Issue 6, 2006, Pages 1132-1142

  Lu, H J ^a   Fellers, J P ^b   Friesen, T L ^c   Meinhardt, S W ^a   Faris, J D ^c  

^a NORTH DAKOTA STATE UNIVERSITY   (United States)

^b KANSAS STATE UNIVERSITY   (United States)

^c AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMARKERS; CHROMOSOMES; CLONING; FUNGI; GENES; MAPPING; TOXIC MATERIALS;

BAC CONTIGS; BIN-MAPPED ESTS; EST-BASED GENETIC MAP; MICROSATELLITE; POLYMORPHISM; TAN SPOT FUNGUS (PYRENOPHORA TRITICI-REPENTIS); TOXIN; WHEAT;

GENETIC ENGINEERING;

MICROSATELLITE DNA;

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CHROMOSOME WALKING; COMPARATIVE STUDY; CONTIG MAPPING; EXPRESSED SEQUENCE TAG; GENE; GENE LIBRARY; GENETIC MARKER; GENETICS; GENOME; PLANT CHROMOSOME; RICE; WHEAT;

CHROMOSOME WALKING; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CHROMOSOMES, PLANT; CONTIG MAPPING; EXPRESSED SEQUENCE TAGS; GENE LIBRARY; GENES, PLANT; GENETIC MARKERS; GENOME, PLANT; MICROSATELLITE REPEATS; ORYZA SATIVA; TRITICUM;

FUNGI; LANGDON DURUM; PYRENOPHORA TRITICI-REPENTIS; TRITICUM AESTIVUM;

EID: 33645411213     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-006-0215-4     Document Type: Article

References (39)

1. Akhunov ED, Goodyear AW, Geng S, Qi LL, Echalier B, Gill BS, Miftahudin, Gustafson JP, Lazo G, Chao S, Anderson OD, Linkiewicz AM, Dubcovsky J, La Rota M, Sorrells ME, Zhang D, Nguyen HT, Kalavacharla V, Hossain K, Kianian SF, Peng J, Lapitan NL, Gonzalez-Hernandez JL, Anderson JA, Choi DW, Close TJ, Dilbirligi M, Gill KS, Walker-Simmons MK, Steber C, McGuire PE, Qualset CO Dvorak J (2003) The organization and rate of evolution of wheat genomes are correlated with recombination rates along chromosome arms. Genome Res 13:753-763
2. Anderson JA, Effertz RJ, Faris JD, Francl LJ, Meinhardt SW, Gill BS (1999) Genetic analysis of sensitivity to Pyrenophora triticirepentis necrosis-inducing toxin in durum and common wheat. Phytopathology 89:293-287
3. Ballance GM, Lamari L, Bernier CC (1989) Purification and characterization of a host selective toxin from Pyrenophora tritici-repentis. Physiol Mol Plant Pathol 35:203-213
4. Bennett MD, Leitch IJ (1995) Nuclear DNA amounts in angiosperms. Ann Bot 76:113-176
5. Cenci A, Chantret N, Kong X, Gu Y, Anderson OD, Fahima T, Distelfeld A, Dubcovsky J (2003) Construction and characterization of a half million clone BAC library of durum wheat (Triticum turgidum ssp. durum). Theor Appl Genet 107:931-939
6. DeWolfe ED, Effertz RJ, Ali S, Francl LJ (1998) Vistas of tan spot research. Can J Plant Pathol 20:349-444
7. Endo TR, Gill BS (1996) The deletion stocks of common wheat. J Hered 87:295-307
8. Erayman M, Sandhu D, Sidhu D, Dilbirligi M, Baenziger PS, Gill KS (2004) Demarcating the gene-rich regions of the wheat genome. Nucleic Acids Res 32:3546-3565
9. Faris JD, Gill BS (2002) Genomic targeting and high-resolution mapping of the domestication gene Q in wheat. Genome 45:706-718
10. Faris JD, Anderson JA, Francl LJ, Jordahl JG (1996) Chromosomal location of a gene conditioning insensitivity in wheat to a necrosis-inducing culture filtrate from Pyrenophora triticirepentis. Phytopathology 86:459-463
11. Faris JD, Haen KM, Gill BS (2000) Saturation mapping of a gene-rich recombination hot spot region in wheat. Genetics 154:823-835
12. Faris JD, Fellers JP, Brooks SA, Gill BS (2003) A bacterial artificial chromosome contig spanning the major domestication locus Q in wheat and identification of a candidate gene. Genetics 164:311-321
13. Gill BS, Friebe B, Endo TR (1991) Standard karyotype and nomenclature system for description of chromosome bands and structural aberrations in wheat (Triticum aestivum). Genome 34:830-839
14. Gill KS, Gill BS, Endo TR, Boyko EV (1996) Identification and high-density mapping of gene-rich regions in chromosome group 5 of wheat. Genetics 143:1001-1012
15. Haen KM, Lu H-J, Friesen TL, Faris JD (2004) Genomic targeting and high-resolution mapping of the Tsn1 gene in wheat. Crop Sci 44:951-962
16. Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172-175
17. Lamari L, Bernier CC (1989) Toxin of Pyrenophora tritici-repentis: host-specificity significance in disease, and inheritance of host reaction. Phytopathology 79:740-744
18. Lamari L, Bernier CC (1991) Genetics of tan necrosis and extensive chlorosis in tan spot of wheat caused by Pyrenophora triticirepentis. Phytopathology 81:1092-1095
19. Lander ES, Green P, Abranhamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) Mapmaker: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174-181
20. La Rota M, Sorrells ME (2004) Comparative DNA sequence analysis of mapped wheat ESTs reveals the complexity of genome relationships between rice and wheat. Funct Integr Genomics 4:34-36
21. Ling H-Q, Zhu Y, Keller B (2003) High-resolution mapping of the leaf rust resistance gene Lr1 in wheat and characterization of BAC clones from the Lr1 locus. Theor Appl Genet 106:875-882
22. Linkiewicz AM, Qi LL, Gill BS, Ratnasiri A, Echalier B, Chao S, Lazo GR, Hummel DD, Anderson OD, Akhunov ED, Dvorak J, Pathan MS, Nguyen HT, Peng JH, Lapitan NL, Miftahudin, Gustafson JP, La Rota CM, Sorrells ME, Hossain KG, Kalavacharla V, Kianian SF, Sandhu D, Bondareva SN, Gill KS, Conley EJ, Anderson JA, Fenton RD, Close TJ, McGuire PE, Qualset CO, Dubcovsky J (2004) A 2500-locus bin map of wheat homoeologous group 5 provides insights on gene distribution and colinearity with rice. Genetics 168:665-676
23. Liu ZH, Anderson JA, Hu J, Friesen TL, Rasmussen JB, Faris JD (2005) A wheat intervarietal genetic linkage map based on microsatellite and target region amplified polymorphism markers and its utility for detecting quantitative trait loci. Theor Appl Genet 111(4):782-794
24. Orita M, Iwahana H, Kanazawa H, Hayash K, Sekiya T (1989) Detection of polymorphism of human DNA by gel electrophoresis as single-stranded conformation polymorphism. Proc Natl Acad Sci USA 86:2766-2770
25. Plaschke J, Ganal M, Röder M (1995) Detection of genetic diversity in closely related bread wheat using microsatellite markers. Theor Appl Genet 91:1001-1007
26. Qi LL, Echlier B, Friebe B, Gill BS (2003) Molecular characterization of a set of wheat deletion stocks for use in chromosome bin mapping of ESTs. Funct Integr Genomics 3:39-55
27. Qi LL, Echalier B, Chao S, Lazo GR, Butler GE, Anderson OD, Akhunov ED, Dvorak J, Linkiewicz AM, Ratnasiri A, Dubcovsky J, Bermudez-Kandianis CE, Greene RA, Kantety R, La Rota CM, Munkvold JD, Sorrells SF, Sorrells ME, Dilbirligi M, Sidhu D, Erayman M, Randhawa HS, Sandhu D, Bondareva SN, Gill KS, Mahmoud AA, Ma XF, Miftahudin, Gustafson JP, Conley EJ, Nduati V, Gonzalez-Hernandez JL, Anderson JA, Peng JH, Lapitan NL, Hossain KG, Kalavacharla V, Kianian SF, Pathan MS, Zhang DS, Nguyen HT, Choi DW, Fenton RD, Close TJ, McGuire PE, Qualset CO, Gill BS (2004) A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat. Genetics 168:701-712
28. Röder MS, Plaschke J, König SU, Börner A, Sorrells ME, Ganal MW (1995) Abundance, variability and chromosomal location of microsatellites in wheat. Mol Gen Genet 246:327-333
29. Röder MS, Korzun V, Wendehake K, Plaschke J, Tixier MH, Leroy P, Ganal MW (1998) A microsatellite map of wheat. Genetics 149:2007-2023
30. Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana, Totawa, NJ, pp 365-386
31. m. Funct Integr Genomics 2:70-80
32. Sorrells ME, La Rota M, Bermudez-Kandianis CE, Greene RA, Kantety R, Munkvold JD, Miftahudin, Mahmoud A, Ma X, Gustafson PJ, Qi LL, Echalier B, Gill BS, Matthews DE, Lazo GR, Chao S, Anderson OD, Edwards H, Linkiewicz AM, Dubcovsky J, Akhunov ED, Dvorak J, Zhang D, Nguyen HT, Peng J, Lapitan NL, Gonzalez-Hernandez JL, Anderson JA, Hossain K, Kalavacharla V, Kianian SF, Choi DW, Close TJ, Dilbirligi M, Gill KS, Steber C, Walker-Simmons MK, McGuire PE, Qualset CO (2003) Comparative DNA sequence analysis of wheat and rice genomes. Genome Res 13:1818-1827
33. Spielmeyer W, Moullet O, Laroche A, Lagudah E (2000) Highly recombinogenic regions at seed storage protein loci on chromosome 1DS of Aegilops tauschii, the D-genome donor of wheat. Genetics 155:361-367
34. Stein N, Feuillet C, Wicker T, Schlagenhauf E, Keller B (2000) Subgenome chromosome walking in wheat: A 450-kb physical contig in Triticum monococcum L. spans the Lr10 resistance locus in hexaploid wheat (Triticum aestivum L.). Proc Natl Acad Sci USA 97:13436-13441
35. Tomás A, Bockus WW (1987) Cultivar specific toxicity of culture filtrate of Pyrenophora tritici-repentis. Phytopathology 77:1337-1366
36. Touri RP, Wolpert TJ, Ciuffetti LM (1995) Purification and immunological characterization of toxic components from cultures of Pyrenophora tritici-repentis. Mol Plant Microbe Interact 8:41-48
37. Wicker T, Stein N, Albar L, Feuillet C, Schlagenhauf E, Keller B (2001) Analysis of a contiguous 211 kb sequence in diploid wheat (Triticum monococcum L.) reveals multiple mechanisms of genome evolution. Plant J 26:307-316
38. Yan L, Loukoianov A, Tranquilli G, Helguera M, Fahima T, Dubcovsky J (2003) Positional cloning of the wheat vernalization gene VRN1. Proc Natl Acad Sci USA 100:6263-6268
39. Zhang H, Francl LJ, Jordahl JG, Meinhardt SW (1997) Structural and physical properties of a necrosis-inducing toxin from Pyrenophora tritici-repentis. Phytopathology 87:154-160