PCR-based Chromosome Walking: The SFR 3 Case
Abstract:
In this study, mapping experiments were initiated in a region of 34.23 cM or 2.7 Mb to map the SFR3 gene into the smallest possible region on chromosome I. Eleven new PCR markers had been designed to fine map the gene. Roughly 557 F2 plants tested in these experiments and 38 lines were then used in the fine mapping experiments. The fine mapping experiments left the SFR3 region amongst 26 genes. Finally, 13 pseudogenes and transposable elements were eliminated and this left the SFR3 gene region amongst 13 genes in a 0.19 Mb region, which is represented by 4 BAC clones. The PCR-based chromosome mapping experiments to fine map the SFR3 gene have successfully decreased the SFR3 region from 2.7 to 0.19 Mb. We concluded that PCR-based chromosome walking is a convenient method to clone SFR3 gene.
How to cite this article
Azura Amid, Garry J. Warren and Peter M. Bramley, 2006. PCR-based Chromosome Walking: The SFR 3 Case. Pakistan Journal of Biological Sciences, 9: 164-169.
REFERENCES
Ishitani, M., L. Xiong, B. Stevenson and J.K. Zhu, 1997. Genetic analysis of osmotic and cold stress signal transduction in Arabidopsis: Interactions and convergence of abscisic acid-dependent and abscisic acid-independent pathways. The Plant Cell, 9: 1935-1949.
Direct Link
Warren, G., R. McKown, A. Marin and R. Teutonico, 1996. Isolation of mutations affecting the development of freezing tolerance in Arabidopsis thaliana (L.)Heynh. Plant Physiol., 111: 1011-1019.
PubMed Direct Link
Xin, Z. and J. Browse, 1998. eskimo1 mutants of Arabidopsis are constitutively freezing-tolerance. Proc. Nat. Acad. Sci. USA., 95: 7799-7804.
Direct Link
McKown, R., G. Kuroki and G. Warren, 1996. Cold responses of Arabidopsis mutants impaired in freezing tolerance. J. Exp. Bot., 47: 1919-1925.
Direct Link
Knight, H., E.L Veale, G.J. Warren and M.R. Knight, 1999. The SFR6 mutation in Arabidopsis suppresses low-temperature induction of genes dependent on the CRT/DRE motif. Plant Cell, 11: 875-886.
PubMed Direct Link
Warren, G., G.J. Thorlby and I. Bramke, 2002. Mutants Deficient in Cold Hardiness: What Can They Reveal about Freezing Tolerance? In: Plant Cold Hardiness, Gene Regulation and Genetics Engineering, Li, P.H. and E.T. Palva (Eds.). Kluwer Academic/Plenum Publishers, USA., pp: 17-32
Thorlby, G., E. Veale, K. Butcher and G. Warren, 1999. Map position of SFR genes in relation to other freezing related genes of Arabidopsis thaliana. Plant J., 17: 445-452.
CrossRef
Lukowitz, W., C.S. Gillmor and W. Scheible, 2000. Positional cloning in Arabidopsis. Why it feels good to have a genome initiative working for you. Plant Physiol., 123: 795-805.
Direct Link
Tautz, D., 1989. Hypervariability of simple sequences as a general source of polymorphic DNA markers. Nucleic Acids Res., 17: 6463-6471.
PubMed
Konieczny, A. and F.M. Ausubel, 1993. A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J., 4: 403-410.
CrossRef PubMed Direct Link
Edwards, K., C. Johnstone and C. Thompson, 1991. A simple and rapid method for the preparation of plant genomic DNA for PCR analysis. Nucleic Acids Res., 19: 1349-1349.
Direct Link
Kosambi, D.D., 1944. The estimation of map distance from recombination values. Ann. Eugenics, 12: 172-175.
© Science Alert. All Rights Reserved