Split‐plot microarray design allows sensitive detection of expression differences after ultraviolet radiation in the inbred parental lines of a key maize mapping population

Gene expression levels were quantified after ultraviolet radiation treatment in the parental inbred lines of the maize mapping (IBM) population. This allows us to take advantage of natural variation between maize lines to analyse variation in gene expression. Using a statistically sound split-plot experiment cDNAs were identified with differently regulated expression in B73 and Mo17 after UV treatment. Fewer genes were down-regulated in B73; this global strain difference in the number of genes up- and down-regulated does not appear to reflect general hybridization differences. Contrary to our expectation, there was a higher proportion of highly expressed genes (based on EST recovery) that were differently expressed by UV between lines. Genes affected by UV (but not significantly different between B73 and Mo17) include gene types proposed to function in UV acclimation and adaptation based on experiments in other species or other experiments in maize. Several new functional classes were identified as UV-regulated, including genes encoding proteins that modulate chromatin structure.

[1]  M. Schuler,et al.  Gene regulation by low level UV-B radiation: identification by DNA array analysis , 2002, Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology.

[2]  M. Brosché,et al.  Molecular events following perception of ultraviolet‐B radiation by plants , 2003 .

[3]  Rachel B. Brem,et al.  Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors , 2003, Nature Genetics.

[4]  M. Caldwell.  Plants and UV-B: Alterations in competitive balance , 1997 .

[5]  C. Ballaré,et al.  Functional significance and induction by solar radiation of ultraviolet-absorbing sunscreens in field-grown soybean crops. , 2000, Plant physiology.

[6]  Aurelian Radu,et al.  Oligonucleotide microarray data mining: search for age-dependent gene expression. , 2002, Biochemical and biophysical research communications.

[7]  D. Hartl,et al.  Population genetic variation in genome-wide gene expression. , 2003, Molecular biology and evolution.

[8]  G. Churchill,et al.  Variation in gene expression within and among natural populations , 2002, Nature Genetics.

[9]  Charles C. Kim,et al.  Significance analysis of lexical bias in microarray data , 2003, BMC Bioinformatics.

[10]  B. Jordan.  Review: Molecular response of plant cells to UV-B stress. , 2002, Functional plant biology : FPB.

[11]  Ritsert C. Jansen,et al.  Studying complex biological systems using multifactorial perturbation , 2003, Nature Reviews Genetics.

[12]  E. Schäfer,et al.  Signal transduction in the photocontrol of chalcone synthase gene expression , 1997 .

[13]  M. Caldwell,et al.  LAMP/FILTER SYSTEMS FOR SIMULATION OF SOLAR UV IRRADIANCE UNDER REDUCED ATMOSPHERIC OZONE * , 1975 .

[14]  G. Churchill,et al.  Statistical design and the analysis of gene expression microarray data. , 2001, Genetical research.

[15]  L. Greene,et al.  Nerve growth factor selectively regulates expression of transcripts encoding ribosomal proteins , 2002, BMC Neuroscience.

[16]  Jason E. Stewart,et al.  Minimum information about a microarray experiment (MIAME)—toward standards for microarray data , 2001, Nature Genetics.

[17]  R. Stoughton,et al.  Genetics of gene expression surveyed in maize, mouse and man , 2003, Nature.

[18]  E. Schäfer,et al.  CPRF4a, a novel plant bZIP protein of the CPRF family: comparative analyses of light-dependent expression, post-transcriptional regulation, nuclear import and heterodimerisation , 1998, Molecular and General Genetics MGG.

[19]  E. Schäfer,et al.  Light perception and signalling in higher plants. , 2003, Current opinion in plant biology.

[20]  M Koornneef,et al.  Naturally occurring variation in Arabidopsis: an underexploited resource for plant genetics. , 2000, Trends in plant science.

[21]  V. Walbot,et al.  Gene Expression Profiling in Response to Ultraviolet Radiation in Maize Genotypes with Varying Flavonoid Content1[w] , 2003, Plant Physiology.

[22]  Joshua M. Stuart,et al.  A Gene-Coexpression Network for Global Discovery of Conserved Genetic Modules , 2003, Science.

[23]  Terence P. Speed,et al.  Comparison of Methods for Image Analysis on cDNA Microarray Data , 2002 .

[24]  Pierre R. Bushel,et al.  Assessing Gene Significance from cDNA Microarray Expression Data via Mixed Models , 2001, J. Comput. Biol..

[25]  K. Ariizumi,et al.  Genomic scale analysis of the human keratinocyte response to broad‐band ultraviolet‐B irradiation , 2002, Photodermatology, photoimmunology & photomedicine.

[26]  Arnold J. Stromberg,et al.  Statistical implications of pooling RNA samples for microarray experiments , 2003, BMC Bioinform..

[27]  L. Wodicka,et al.  Regional and strain-specific gene expression mapping in the adult mouse brain. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[28]  C. Ballaré,et al.  Convergent Responses to Stress. Solar Ultraviolet-B Radiation and Manduca sexta Herbivory Elicit Overlapping Transcriptional Responses in Field-Grown Plants of Nicotiana longiflora1[w] , 2003, Plant Physiology.

[29]  S. Muse,et al.  Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. , 2003, Genetics.

[30]  L. Kruglyak,et al.  Genetic Dissection of Transcriptional Regulation in Budding Yeast , 2002, Science.

[31]  Vivian G. Cheung,et al.  The genetics of variation in gene expression , 2002, Nature Genetics.

[32]  J. Josse,et al.  Quantitative trait loci underlying gene product variation: a novel perspective for analyzing regulation of genome expression. , 1994, Genetics.

[33]  P. Herrlich,et al.  Nuclear and non-nuclear targets of genotoxic agents in the induction of gene expression. Shared principles in yeast, rodents, man and plants. , 1997, Biological chemistry.

[34]  J. Nap,et al.  Genetical genomics: the added value from segregation. , 2001, Trends in genetics : TIG.

[35]  D. Grant,et al.  Expanding the genetic map of maize with the intermated B73 × Mo17 (IBM) population , 2002, Plant Molecular Biology.

[36]  A. Stapleton,et al.  Intraspecific comparisons reveal differences in the pattern of ultraviolet radiation responses in four maize (Zea mays L.) varieties. , 2001, Journal of photochemistry and photobiology. B, Biology.

[37]  Russell D. Wolfinger,et al.  The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster , 2001, Nature Genetics.

[38]  C. Ballaré.  Stress Under the Sun: Spotlight on Ultraviolet-B Responses , 2003, Plant Physiology.