Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat

Genome

Volumn 52, Issue 6, 2009, Pages 576-587

  Wanjugi, Humphrey ^a   Coleman Derr, Devin ^a   Huo, Naxin ^a   Kianian, Shahryar F ^b   Luo, Ming Cheng ^c   Wu, Jiajie ^c   Anderson, Olin ^a   Gu, Yong Qiang ^a  

^a WESTERN REGIONAL RESEARCH CENTER   (United States)

^b NORTH DAKOTA STATE UNIVERSITY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Genetic and physical mapping; Genome specific marker; Repeat DNA junction; Retrotransposon; Wheat genome

Indexed keywords

PLANT DNA;

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CHROMOSOME MAP; GENETIC MARKER; GENETICS; METHODOLOGY; NUCLEOTIDE REPEAT; PLANT CHROMOSOME; PLANT GENOME; PLOIDY; POLYMERASE CHAIN REACTION; TRANSPOSON; WHEAT;

CHROMOSOME MAPPING; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CHROMOSOMES, PLANT; DNA TRANSPOSABLE ELEMENTS; DNA, PLANT; GENETIC MARKERS; GENOME, PLANT; PLOIDIES; POLYMERASE CHAIN REACTION; REPETITIVE SEQUENCES, NUCLEIC ACID; TRITICUM;

AEGILOPS TAUSCHII; TRITICUM AESTIVUM;

EID: 67650338287     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/G09-033     Document Type: Article

References (46)

1. Bennetzen, J.L. 2000. Transposable element contributions to plant gene and genome evolution. Plant Mol. Biol. 42: 251-269. doi:10.1023/A: 1006344508454. PMID:10688140.
2. Blake, N.K., Lehfeldt, B.R., Lavin, M., and Talbert, L.E. 1999. Phylogenetic reconstruction based on low copy DNA sequence data in an allopolyploid: the B genome of wheat. Genome, 42: 351-360. doi:10.1139/gen-42-2-351. PMID:10231966.
3. Boyko, E.V., Gill, K.S., Mickelson-Young, L., Nasuda, S., Raupp, W.J., Ziegle, J.N., et al. 1999. A high-density genetic linkage map of Ae. tauschii, the D-genome progenitor of bread wheat. Theor. Appl. Genet. 99: 16-26. doi:10.1007/s001220051204.
4. Bureau, T.E., and Wessler, S.R. 1994. Stowaway: a new family of inverted repeat elements associated with the genes of both monocotyledonous and dicotyledonous plants. Plant Cell, 6: 907-916. doi:10.1105/tpc.6.6.907. PMID:8061524.
5. Casa, A.M., Brouwer, C., Nagel, A., Wang, L., Zhang, Q., Kresovich, S., and Wessler, S.R. 2000. The MITE family Heart-breaker (Hbr): molecular markers in maize. Proc. Natl. Acad. Sci. U.S.A. 97: 10083-10089. doi:10.1073/pnas.97.18.10083. PMID:10963671.
6. Chantret, N., Salse, J., Sabot, F., Rahman, S., Bellec, A., Laubin, B., et al. 2005. Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (Triticum and Aegilops). Plant Cell, 17: 1033-1045. doi:10.1105/tpc.104.029181. PMID:15749759.
7. Devos, K.M., Brown, J.K.M., and Bennetzen, J.L. 2002. Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res. 12: 1075-1079. doi:10.1101/gr.132102. PMID:12097344.
8. Devos, K.M., Ma, J., Pontaroli, A.C., Pratt, L.H., and Bennetzen, J.L. 2005. Analysis and mapping of randomly chosen bacterial artificial chromosome clones from hexaploid bread wheat. Proc. Natl. Acad. Sci. U.S.A. 102: 19243-19248. doi:10.1073/pnas. 0509473102. PMID:16357197.
9. Ellis, T.H., Poyser, S.J., Knox, M.R., Vershinin, A.V., and Ambrose, M.J. 1998. Polymorphism of insertion sites of Ty1-copia class retrotransposons and its use for linkage and diversity analysis in pea. Mol. Gen. Genet. 260: 9-19. PMID:9829823.
10. Endo, T.R., and Gill, B.S. 1996. The deletion stocks of common wheat. J. Hered. 87: 295-307.
11. Erayman, M., Sandhu, D., Sidhu, D., Dilbirligi, M., Baenziger, P.S., and Gill, K.S. 2004. Demarcating the gene-rich regions of the wheat genome. Nucleic Acids Res. 32: 3546-3565. doi:10. 1093/nar/gkh639. PMID:15240829.
12. Feldman, M., Lupton, F.G.H., and Miller, T.E. 1995. Wheats. In Evolution of crops. 2nd ed. Edited by J. Smartt and N.W. Sim-monds. Longman Scientific, London. pp. 184-192.
13. Flavell, A.J., Knox, M.R., Pearce, S.R., and Ellis, T.H.N. 1998. Retrotransposon-based insertion polymorphisms (RBIP) for high throughput marker analysis. Plant J. 16: 643-650. doi:10.1046/j. 1365-313x.1998.00334.x. PMID:10036780.
14. Gill, B.S., and Raupp, W.J. 1987. Direct genetic transfers from Ae. squarrosa L. to hexaploid wheat. Crop Sci. 27: 445-450.
15. Gill, K.S., Gill, B.S., Endo, T.R., Boyko, E.V. 1996. Identification and high-density mapping of gene-rich regions in chromosome group 5 of wheat. Genetics, 143: 1001-1012. PMID:8725245.
16. Gu, Y.Q., Coleman-Derr, D., Kong, X., and Anderson, O.D. 2004. Rapid genome evolution revealed by comparative sequence analysis of orthologous regions from four Triticeae genomes. Plant Physiol. 135: 459-470. doi:10.1104/pp.103.038083. PMID:15122014.
17. Gu, Y.Q., Salse, J., Coleman-Derr, D., Dupin, A., Crossman, C., Lazo, G.R., et al. 2006. Types and rates of sequence evolution at the high-molecular-weight glutenin locus in hexaploid wheat and its ancestral genomes. Genetics, 174: 1493-1504. doi:10. 1534/genetics.106.060756. PMID:17028342.
18. Gupta, P.K., Mir, R.R., Mohan, A., and Kumar, J. 2008. Wheat genomics: present status and future prospects. Int. J. Plant Genomics, 2008: 896451. doi:10.1155/2008/896451.
19. Huo, N., Gu, Y.Q., Lazo, G.R., Vogel, J.P., Coleman-Derr, D., Luo, M., et al. 2006. Construction and characterization of two BAC libraries from Brachypodium distachyon, a new model for grass genomics. Genome, 49: 1099-1108. doi:10.1139/G06-087. PMID:17110990.
20. Kalavacharla, V., Hossain, K., Gu, Y., Riera-Lizarazu, O., Vales, M.I., Bhamidimarri, S., et al. 2006. High-resolution radiation hybrid map of wheat chromosome 1D. Genetics, 173: 1089-1099. doi:10.1534/genetics.106.056481. PMID:16624903.
21. Kalendar, R., Grob, T., Regina, M., Suoniemi, A., and Schulman, A. 1999. IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Proc. Natl. Acad. Sci. U.S.A. 98: 704-711. doi:10.1007/s001220051124.
22. Kimber, G., and Feldman, M. 1987. Wild wheat: an introduction. University of Missouri Press, Columbia, Mo.
23. Kumar, A., and Bennetzen, J.L. 1999. Plant retrotransposons. Annu. Rev. Genet. 33: 479-532. doi:10.1146/annurev.genet.33. 1.479. PMID:10690416.
24. Landjeva, S., Korzun, V., and Börner, A. 2007. Molecular markers: actual and potential contributions to wheat genome characterization and breeding. Euphytica, 156: 271-296. doi:10.1007/ s10681-007-9371-0.
25. Li, W., Zhang, P., Fellers, J.P., Friebe, B., and Gill, B.S. 2004. Sequence composition, organization, and evolution of the core Triticeae genome. Plant J. 40: 500-511. doi:10.1111/j.1365-313X. 2004.02228.x. PMID:15500466.
26. McNeil, M.D., Kota, R., Paux, E., Dunn, D., McLean, R., Feuillet, C., et al. 2008. BAC-derived markers for assaying the stem rust resistance gene, Sr2, in wheat breeding programs. Mol. Breed. 22: 15-24. doi:10.1007/s11032-007-9152-4.
27. Paux, E., Roger, D., Badaeva, E., Gay, G., Bernard, M., Sourdille, P., and Feuillet, C. 2006. Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B. Plant J. 48: 463-474. doi:10.1111/j.1365-313X.2006.02891.x. PMID: 17010109.
28. Paux, E., Sourdille, P., Salse, J., Saintenac, C., Choulet, F., Leroy, P., et al. 2008. A physical map of the 1-gigabase bread wheat chromosome 3B. Science, 322: 101-104. doi:10.1126/science. 1161847. PMID:18832645.
29. Pereira, A., Cuypers, H., Gierl, A., Schwarz-Sommer, Z., and Saedler, H. 1986. Molecular analysis of the En/Spm transposable element system of Zea mays. EMBO J. 5: 835-841. PMID: 15957213.
30. Pestsova, E., Ganal, M.W., and Röder, M.S. 2000. Isolation and mapping of microsatellite markers specific for the D genome of bread wheat. Genome, 43: 689-697. doi:10.1139/gen-43-4-689. PMID:10984182.
31. Porceddu, A., Albertini, E., Barcaccia, G., Marconi, G., Bertoli, F., and Veronesi, F. 2002. Development of S-SAP markers based on an LTR-like sequence from Medicago sativa L. Mol. Genet. Genomics, 267: 107-114. doi:10.1007/s00438-002-0643-z. PMID:11919721.
32. Qi, L., Echalier, B., Friebe, B., and Gill, B.S. 2003. Molecular characterization of a set of wheat deletion stocks for use in chromosome bin mapping of ESTs. Funct. Integr. Genomics, 3: 39-55. doi:10.1007/s10142- 002-0063-5. PMID:12590342.
33. Qi, L.L., Echalier, B., Chao, S., Lazo, G.R., Butler, G.E., Anderson, O.D., et al. 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. doi:10.1534/genetics.104.034868. PMID:15514046.
34. Riede, C.R., and Anderson, J.A. 1996. Linkage of RFLP markers to an aluminum tolerance gene in wheat. Crop Sci. 36: 905-909.
35. Röder, M.S., Korzun, V., Wendehake, K., Plaschke, J., Tixier, M.H., Leroy, P., and Ganal, M.W. 1998. A microsatellite map of wheat. Genetics, 149: 2007-2023. PMID:9691054.
36. SanMiguel, P., and Bennetzen, J.L. 1998. Evidence that a recent increase in maize genome size was caused by the massive amplification of intergene retrotransposons. Ann. Bot. (Lond.), 82: 37-44. doi:10.1006/anbo.1998. 0746.
37. m. Funct. Integr. Genomics, 2: 70-80. doi:10.1007/s10142-002-0056-4. PMID:12021852.
38. Sears, E.R. 1954. The aneuploids of common wheat. Bull. 572. University of Missouri Agricultural Experiment Station, Columbia, Mo.
39. Shirasu, K., Schulman, A.H., Lahaye, T., and Schulze-Lefert, P. 2000. A contiguous 66-kb barley DNA sequence provides evidence for reversible genome expansion. Genome Res. 10: 908-915. doi:10.1101/gr.10.7.908. PMID:10899140.
40. Sumner, A.T., Torre, J.D.L., and Stuppia, L. 1993. The distribution of genes on chromosomes: a cytological approach. J. Mol. Evol. 37: 117-122. doi:10.1007/BF02407346. PMID:8411200.
41. Waugh, R., McLean, K., Flavell, A.J., Pearce, S.R., Kumar, A., Thomas, B.B., and Powell, W. 1997. Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP). Mol. Genet. Genomics, 253: 687-694. PMID:9079879.
42. Wessler, S.R., Bureau, T.E., and White, S.E. 1995. LTR-retrotransposons and MITEs: important players in the evolution of plant genomes. Curr. Opin. Genet. Dev. 5: 814-821. doi:10.1016/ 0959-437X(95)80016-X. PMID:8745082.
43. Wicker, T., Stein, N., Albar, L., Feuillet, C., Schlagenhauf, E., and Keller, B. 2001. Analysis of a contiguous 211 kb sequence in diploid wheat (T. monococcum L.) reveals multiple mechanisms of genome evolution. Plant J. 26: 307-316. doi:10.1046/j.1365-313X.2001.01028.x. PMID:11439119.
44. Wicker, T., Guyot, R., Yahiaoui, N., and Keller, B. 2003a. CACTA transposons in Triticeae. A diverse family of high-copy repetitive elements. Plant Physiol. 132: 52-63. doi:10.1104/pp.102. 015743. PMID:12746511.
45. m genomes of wheat. Plant Cell, 15: 1186-1197. doi:10.1105/ tpc.011023.
46. Yu, G.X., and Wise, R.P. 2000. An anchored AFLP- and retrotran-sposon- based map of diploid Avena. Genome, 43: 736-749. doi:10.1139/gen-43-5-736. PMID:11081962.