Molecular, morphological, and cytological analysis of diverse Brachypodium distachyon inbred lines

Genome

Volumn 52, Issue 10, 2009, Pages 876-890

  Filiz, E ^a   Ozdemir, B S ^a   Budak, F ^b   Vogel, J P ^c   Tuna, M ^d   Budak, H ^a  

^a SABANCI UNIVERSITY   (Turkey)

^b IGDIR UNIVERSITY   (Turkey)

^c WESTERN REGIONAL RESEARCH CENTER   (United States)

^d NAMIK KEMAL UNIVERSITY   (Turkey)

Author keywords

AFLP analysis; CpDNA; Karyotyping; MtDNA

Indexed keywords

PLANT DNA;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ARTICLE; COMPARATIVE STUDY; CYTOLOGY; GENETIC VARIABILITY; GENETICS; GENOTYPE; HISTOLOGY; INBREEDING; PHENOTYPE; PLANT CHROMOSOME; PLANT GENOME; POACEAE; TURKEY (REPUBLIC);

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS; CHROMOSOMES, PLANT; DNA, PLANT; GENETIC VARIATION; GENOME, PLANT; GENOTYPE; INBREEDING; PHENOTYPE; POACEAE; TURKEY;

BRACHYPODIUM; BRACHYPODIUM DISTACHYON; HORDEUM; MISCANTHUS; PANICUM VIRGATUM; POACEAE; TRITICUM AESTIVUM;

EID: 70349829834     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/G09-062     Document Type: Article

References (35)

1. Arumuganathan, K., and Earle, E.D. 1991. Estimation of nuclear DNA contents of plants by flow cytometry. Plant Mol. Biol. Rep. 9(3): 229-241. doi:10.1007/BF02672073.
2. Bennett, M.D., and Leitch, I.J. 2007. Plant DNA C-values Database (release 3.0, December 2004) [online]. Available from http:// urlwww.rbgkew.org.uk/cval/homepage.html [accessed 20 May 2007].
3. Bennett, M.D., and Leitch, I.J. 2005. Nuclear DNA amounts in an- giosperms: progress, problems and prospects. Ann. Bot. (Lond.), 95(1): 45-90. doi:10.1093/aob/mci003. PMID:15596457.
4. Budak, H., Shearman, R.C., Parmaksiz, I., and Dweikat, I. 2004a. Comparative analysis of seeded and vegetative biotype buffalo- grasses based on phylogenetic relationship using ISSRs, SSRs, RAPDs, and SRAPs. Theor. Appl. Genet. 109(2): 280-288. doi:10.1007/s00122-004-1630-z. PMID:15024466.
5. Budak, H., Shearman, R.C., Parmaksiz, I., Gaussoin, R.E., Riordan, T.P., and Dweikat, I. 2004b. Molecular characterization of buf- falograss germplasm using sequence-related amplified poly- morphism markers. Theor. Appl. Genet. 108(2): 328-334. doi:10.1007/s00122-003-1428-4. PMID:13679978.
6. Budak, H., Shearman, R.C., Gulsen, O., and Dweikat, I. 2005a. Understanding ploidy complex and geographic origin of the Bu- chloe dactyloides genome using cytoplasmic and nuclear marker systems. Theor. Appl. Genet. 111(8): 1545-1552. doi:10.1007/ s00122-005-0083-3. PMID:16208501.
7. Budak, H., Shearman, R.C., and Dweikat, I. 2005b. Evolution of Buchloe dactyloides based on cloning and sequencing of matK, rbcL, and cob genes from plastid and mitochondrial genomes. Genome, 48(3): 411-416. doi:10.1139/g05-002. PMID: 16121238.
8. Draper, J., Mur, L.A.J., Jenkins, G., Ghosh-Biswas, G.C., Bablak, P., Hasterok, R., and Routledge, A.P.M. 2001. Brachypodium distachyon. A new model system for functional genomics in grasses. Plant Physiol. 127(4): 1539-1555. doi:10.1104/pp.010196. PMID:11743099.
9. Excoffier, L., Smouse, P.E., and Quattro, J.M. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131(2): 479-491. PMID:1644282.
10. Felsenstein, J. 2008. PHYLIP (Phylogeny Inference Package). Ver- sion 3.68 [computer program]. Distributed by the author. De- partment of Genome Sciences, University of Washington, Seattle. Available from http://evolution.gs.washington.edu/ phylip.html.
11. Filiz, E., Ozdemir, B.S., Tuna, M., and Budak, H. 2009. Diploid Brachypodium distachyon of Turkey: molecular and morpholo- gic analysis. In The Proceedings of the 5th International Sympo- sium on the Molecular Breeding of Forage and Turf. Edited by T. Yamada and G. Spangenberg. Springer. pp. 83-89.
12. Garvin, D.F., Gu, Y.Q., Hasterok, R., Hazen, S.P., Jenkins, G., Mockler, T.C., et al. 2008. Development of genetic and genomic research resources for Brachypodium distachyon, a new model system for grass crop research. Crop Sci. 48(Suppl. 1): S69- S84. doi:10.2135/cropsci2007.06.0332tpg.
13. Godelle, B., Cartier, D., Marie, D., Brown, S.C., and Siljak- Yakovlev, S. 1993. Heterochromatin study demonstrating the non-linearity of fluorometry useful for calculating genomic base composition. Cytometry, 14(6): 618-626. doi:10.1002/cyto.990140606. PMID:8404368.
14. Hasterok, R., Draper, J., and Jenkins, G. 2004. Laying the cyto- taxonomic foundations of a new model grass, Brachypodium distachyon (L.) Beauv. Chromosome Res. 12(4): 397-403. doi:10.1023/B:CHRO.0000034130.35983.99. PMID:15241018.
15. Hasterok, R., Marasek, A., Donnison, I.S., Armstead, I., Thomas, A., King, I.P., et al. 2006. Alignment of the genomes of Brachy- podium distachyon and temperate cereals and grasses using bac- terial artificial chromosome landing with fluorescence in situ hybridization. Genetics, 173: 349-362. doi:10.1534/genetics.105.049726. PMID:16489232.
16. Huff, D.R., Quinn, J.A., Higgins, B., and Palazzo, A.J. 1998. Ran- dom amplified polymorphic DNA (RAPD) variation among na- tive little bluestem [Schizachyrium scoparium (Michx.) Nash] populations from sites of high and low fertility in forest and grassland biomes. Mol. Ecol. 7(11): 1591-1597. doi:10.1046/j. 1365-294x.1998.00473.x.
17. Huo, N., Gu, Y.Q., Lazo, G.R., Vogel, J.P., Coleman-Derr, D., Luo, M.C., et al. 2006. Construction and characterization of two BAC libraries from Brachypodium distachyon, a new model for grass genomics. Genome, 49(9): 1099-1108. doi:10.1139/G06- 087. PMID:17110990.
18. Huo, N., Lazo, G.R., Vogel, J.P., You, F.M., Ma, Y., Hayden, D.M., et al. 2008. The nuclear genome of Brachypodium dis- tachyon: analysis of BAC end sequences. Funct. Integr. Genomics, 8(2): 135-147. doi:10.1007/s10142-007-0062-7. PMID:17985162.
19. Isik, Z., Parmaksiz, I., Coruh, C., Geylan-Su, Y.S., Cebeci, O., Beecher, B., and Budak, H. 2007. Organellar genome analysis of rye (Secale cereale) representing diverse geographic regions. Genome, 50(8): 724-734. doi:10.1139/G07-052. PMID:17893732.
20. Jenkins, G., Hasterok, R., and Draper, J. 2003. Building the mole- cular cytogenetic infrastructure of a new model grass. In Appli- cation of novel cytogenetic and molecular techniques in genetics and breeding of the grasses. Edited by Z. Zwierzykowski, M. Surma, and P. Kachlicki. Polish Academy of Sciences, Poznan, Poland. pp. 77-84.
21. Jenkins, G., Mur, L.A.J., Bablak, P., Hasterok, R., and Draper, J. 2005. Prospects for functional genomics in a new model grass. In Plant functional genomics. Edited by D. Leister. Haworth Press, Binghamton. pp. 305-325.
22. Nei, M. 1972. Genetic distance between populations. Am. Nat. vol 106(949):283-292. doi:10.1086/282771.
23. Nei, M., and Li, W.H. 1979. Mathematical model for studying ge- netic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. U.S.A. 76(10): 5269-5273. doi:10.1073/pnas.76.10. 5269. PMID:291943.
24. Ozdemir, B.S., Hernandez, P., Filiz, E., and Budak, H. 2008. Bra- chypodium genomics. Int. J. Plant Genomics, 2008. Article ID 536104. doi:10.1155/2008/536104.
25. Pǎcurar, D.I., Thordal-Christensen, H., Nielsen, K.K., and Lenk, I. 2008. A high-throughput Agrobacterium-mediated transformation system for the grass model species Brachypodium distach- yon L. Transgenic Res. 17(5): 965-975. doi:10.1007/s11248-007-9159-y. PMID:18064538.
26. Rohlf, J.F. 2000. NTSYSpc: numerical taxonomy and multivariate analysis system. Exeter Software, Setauket, N.Y.
27. Sharma, H.C., and Gill, B.S. 1983. Current status of wide hybridi- zation in wheat. Euphytica, 32(1): 17-31. doi:10.1007/BF00036860.
28. Sneath, P.H.A., and Sokal, R.R. 1973. Numerical taxonomy. Free- man, San Francisco.
29. Unver, T., and Budak, H. 2009. Conserved miRNA and their tar- gets in model grass species, Brachypodium distachyon. Planta, 230: 659-669. doi:10.1007/s00425-009-0974-7. PMID:19585143.
30. Vain, P., Worland, B., Thole, V., McKenzie, N., Alves, S.C., Opa- nowicz, M., et al. 2008. Agrobacterium-mediated transformation of the temperate grass Brachypodium distachyon (genotype Bd21) for T-DNA insertional mutagenesis. Plant Biotechnol. J. 6(3): 236-245. doi:10.1111/j.1467-7652.2007.00308.x. PMID:18004984.
31. Vogel, J., and Hill, T. 2008. High-efficiency Agrobacterium-mediated transformation of Brachypodium distachyon inbred line Bd21-3. Plant Cell Rep. 27(3): 471-478. doi:10.1007/s00299-007-0472-y. PMID:17999063.
32. Vogel, J.P., Gu, Y.Q., Twigg, P., Lazo, G.R., Laudencia- hingcuanco, D., Hayden, D.M., et al. 2006a. EST sequen-cing and phylogenetic analysis of the model grass Brachy-podium distachyon. Theor. Appl. Genet. 113(2): 186-195.doi:10.1007/s00122-006-0285-3. PMID:16791686.
33. Vogel, J.P., Garvin, D.F., Leong, O.M., and Hayden, D.M. 2006b. Agrobacterium-mediated transformation and inbred line devel- opment in the model grass Brachypodium distachyon. Plant Cell Tissue Organ Cult. 85: 199-211.
34. Vogel, J.P., Tuna, M., Budak, H., Huo, N., Gu, Y.Q., and Stein- wand, M.A. 2009. Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon. BMC Plant Biol. 9: 88. doi:10.1186/1471-2229-9-88. PMID: 19594938.
35. Weir, B.S. 1996. Genetic data analysis II: Methods for discrete po- pulation genetic data. 2nd ed. Sinauer Associates, Sunderland, Mass.