Comparing two microarray platforms for identifying mutated genes in barley (Hordeum vulgare L.)

Plant Physiology and Biochemistry

Volumn 45, Issue 8, 2007, Pages 617-622

  Zakhrabekova, Shakhira ^a   Gough, Simon P ^a   Lundqvist, Udda ^a   Hansson, Mats ^a  

^a LUND UNIVERSITY   (Sweden)

Author keywords

Barley; Cloning; Hordeum vulgare; Magnesium chelatase; Microarray; Mutant; Xantha

Indexed keywords

CHLOROPHYLL; LYASE; MAGNESIUM CHELATASE; RNA; UNCLASSIFIED DRUG; VEGETABLE PROTEIN;

ALLELE; ARTICLE; BARLEY; BIOLOGICAL MODEL; CHEMISTRY; COMPARATIVE STUDY; DNA MICROARRAY; GENE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; INSTRUMENTATION; METABOLISM; MOLECULAR CLONING; MUTATION; NUCLEIC ACID HYBRIDIZATION; NUCLEOTIDE SEQUENCE;

ALLELES; CHLOROPHYLL; CLONING, MOLECULAR; DNA MUTATIONAL ANALYSIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; HORDEUM; LYASES; MODELS, GENETIC; MUTATION; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANT PROTEINS; RNA;

HORDEUM; HORDEUM VULGARE; HORDEUM VULGARE SUBSP. VULGARE;

EID: 34547129336     PISSN: 09819428     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.plaphy.2007.05.004     Document Type: Article

References (19)

1. Lundqvist U., Franckowiak J., and Konishi T. New and revised descriptions of barley genes. Barley Genetics Newsletter 26 (1996) 22-516
2. Søgaard B., and von Wettstein-Knowles P. Barley: genes and chromosomes. Carlsberg Res. Commun 52 (1987) 123-196
3. Gadjieva R., Axelsson E., Olsson U., Vallon-Christersson J., and Hansson M. Nonsense-mediated mRNA decay in barley mutants provides a possibility to clone the mutated gene by a microarray approach. Plant Physiol. Biochem 42 (2004) 681-685
4. Zakhrabekova S., Kannangara C.G., von Wettstein D., and Hansson M. A microarray approach for identification of mutated genes. Plant Physiol. Biochem 40 (2002) 189-197
5. Park P.J., Cao Y.A., Lee S.Y., Kim J.W., Chang M.S., Hart R., and Choi S. Current issues for DNA microarrays: platform comparison, double linear amplification, and universal RNA reference. J. Biotechnol 112 (2004) 225-245
6. Petersen D., Chandramouli G.V., Geoghegan J., Hilburn J., Paarlberg J., Kim C.H., Munroe D., Gangi L., Han J., Puri R., Staudt L., Weinstein J., Barrett J.C., Green J., and Kawasaki E.S. Three microarray platforms: an analysis of their concordance in profiling gene expression. BMC Genomics 6 (2005) 63
7. Schena M., Shalon D., Davis R.W., and Brown P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270 (1995) 467-470
8. Yan W., Lewin A., and Hauswirth W. Selective degradation of nonsense beta-phosphodiesterase mRNA in the heterozygous rd mouse. Invest. Ophthalmol. Vis. Sci. 39 (1998) 2529-2536
9. Isshiki M., Yamamoto Y., Satoh H., and Shimamoto K. Nonsense-mediated decay of mutant waxy mRNA in rice. Plant Physiol. 125 (2001) 1388-1395
10. Henningsen K.W., Boynton J.E., and von Wettstein D. Mutants at xantha and albina loci in relation to chloroplast biogenesis in barley (Hordeum vulgare L.). Biologiske Skrifter (1993), The Royal Danish Academy of Sciences and Letters, Copenhagen
11. Olsson U., Sirijovski N., and Hansson M. Characterization of eight barley xantha-f mutants deficient in magnesium chelatase. Plant Physiol. Biochem. 42 (2004) 557-564
12. Yang Y.H., Dudoit S., Luu P., Lin D.M., Peng V., Ngai J., and Speed T.P. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30 (2002) e15
13. Gao Q., Das B., Sherman F., and Maquat L.E. Cap-binding protein 1-mediated and eukaryotic translation initiation factor 4E-mediated pioneer rounds of translation in yeast. Proc. Natl. Acad. Sci. USA 102 (2005) 4258-4263
14. Vrinten P., Hu Z., Munchinsky M.A., Rowland G., and Qiu X. Two FAD3 desaturase genes control the level of linolenic acid in flax seed. Plant Physiol. 139 (2005) 79-87
15. Harries L.W., Hattersley A.T., and Ellard S. Messenger RNA transcripts of the hepatocyte nuclear factor-1α gene containing premature termination codons are subject to nonsense-mediated decay. Diabetes 53 (2004) 500-504
16. Axelsson E., Lundqvist J., Sawicki A., Nilsson S., Schröder I., Al-Karadaghi S., Willows R.D., and Hansson M. Recessivity and dominance in barley mutants deficient in Mg-chelatase subunit D, an AAA-protein involved in chlorophyll biosynthesis. Plant Cell 18 (2006) 3606-3616
17. Hansson A., Kannangara C.G., von Wettstein D., and Hansson M. Molecular basis for semidominance of missense mutations in the XANTHA-H (42-kDa) subunit of magnesium chelatase. Proc. Natl. Acad. Sci. USA 96 (1999) 1744-1749
18. Hansson A., Willows R.D., Roberts T.H., and Hansson M. Three semidominant barley mutants with single amino acid substitutions in the smallest magnesium chelatase subunit form defective AAA+ hexamers. Proc. Natl. Acad. Sci. USA 99 (2002) 13944-13949
19. Rzeznicka K., Walker C.J., Westergren T., Kannangara G.C., von Wettstein D., Merchant S., Gough S.P., and Hansson M. Xantha-l encodes a membrane protein subunit of the aerobic Mg-protoporphyrin IX monomethyl ester cyclase in the chlorophyll biosynthetic pathway. Proc. Natl. Acad. Sci. USA 102 (2005) 5886-5891