Abstract
An alternative to complete genome sequencing is development and analysis of ESTs—fragments of transcribed coding DNA sequences. The EST collections also enhanced the development of cDNA microarray technologies, which make possible assessing the transcription levels of several thousand genes in a studied tissue of an organism in the same experiment. This paper provides an overview of the results of experiments with a barley microarray, Affymetrix Barley1 GeneChip. The variation in transcription levels of over 22000 genes in germinating barley grain of 150 barley double haploid lines produced by crossing cultivars Steptoe and Morex. Variation in gene expression of each gene is a quantitative trait, which can be mapped in population of double haploids as the genetic loci determining its variation (expressed QTL or eQTL). A regulatory locus (eQTL) can colocalize with the corresponding gene on genetic map (cis-eQTL) or be distant from it, frequently on another chromosome (trans-eQTL). Thus, it is possible to detect and analyze cis- and trans-regulatory loci for genes on a genome-wide scale. The design of the Affymetrix oligonucleotide arrays makes it possible not only to concurrently test the transcription level of several thousand genes, but also to simultaneously detect the polymorphic regions in cDNA sequences, thereby finding a considerable fraction of all nucleotide substitutions between the compared genotypes. Two types of data (the expression levels of several thousand genes and the presence of polymorphic sites in their sequences) can be obtained concurrently when processing the results of the same experiment. The details of both procedures are illustrated with explanatory examples.
Similar content being viewed by others
References
Michalek, W., Weschke, W., Pleissner, K.P., and Graner, A., EST Analysis in Barley Defines a Unigene Set Comprising 4.000 Genes, Theor. Appl. Genet., 2002, vol. 104, no. 1, pp. 97–103.
Zhang, H., Sreenivasulu, N., Weschke, W., et al., Large-Scale Analysis of the Barley Transcriptome Based on Expressed Sequence Tags, Plant J., 2004, vol. 40, pp. 276–290.
Mergaert, P., Gamas, P., and Becker, A., Transcriptome Analysis, EMBO Practical Course on the New Plant Model System Medicago truncatula: Manuals. Module, 2001.
Rensink, W.A. and Buell, C.R., Microarray Expression Profiling Resources for Plant Genomics, Trends Plant Sci., 2005, vol. 10, pp. 603–609.
Kane, M.D., Jatkoe, T.A., Stumpf, C.R., et al., Assessment of the Sensitivity and Specificity of Oligonucleotide (50mer) Microarrays, Nucleic Acids Res., 2000, vol. 28, pp. 4552–4557.
Richmond, T. and Somerville, S.C., Chasing the Dream: Plant EST Microarrays, Curr. Opin. Plant Biol., 2000, vol. 3, pp. 108–116.
Lockhart, D.J. and Winzeler, E.A., Genomics, Gene Expression and DNA Arrays, Nature, 2000, vol. 405, no. 6788, pp. 827–836.
Close, T.J., Wanamaker, S.I., Caldo, R.A., et al., A New Resource for Cereal Genomics: 22K Barley GeneChip Comes of Age, Plant Physiol., 2004, vol. 134, pp. 960–968.
Jansen, R.A. and Nap, J.P., Genetical Genomics: The Added Value from Segregation, Trends Genet., 2001, vol. 17, pp. 388–391.
Gupta, P.K. and Rustgi, S., Molecular Markers from the Transcribed Expressed Region of the Genome in Higher Plants, Funct. Integr. Genomics, 2004, vol. 4, no. 3, pp. 139–162.
Brem, R.B., Yvert, G., Clinton, R., and Kruglyak, L., Genetic Dissection of Transcriptional Regulation in Budding Yeast, Science, 2002, vol. 296, pp. 752–755.
Schadt, E.E., Monks, S.A., Drake, T.A., et al., Genetics of Gene Expression Surveyed in Maize, Mouse and Man, Nature, 2003, vol. 422, no. 6929, pp. 297–302.
Darvasi, A., Genomics: Gene Expression Meets Genetics, Nature, 2003, vol. 422, no. 6929, pp. 269–270.
DeCook, R., Lall, S., Nettleton, D., and Howell, S.H., Genetic Regulation of Gene Expression during Shoot Development in Arabidopsis, Genetics, 2006, vol. 172, no. 2, pp. 1155–1164.
West, M.A., Kim, K., Kliebenstein, A., et al., Global eQTL Mapping Reveals the Complex Genetic Architecture of Transcript Level Variation in Arabidopsis, Genetics, 2007, vol. 175, pp. 1441–1450.
Jordan, M., Somers, D.J., and Banks, T.W., Identifying Regions of the Wheat Genome Controlling Seed Development by Mapping Expression Quantitative Trait Loci, Plant Biotechnol. J., 2007, vol. 5, pp. 442–453.
Luo, Z.W., Potokina, E., Druka, A., et al., Robust, High Density Genotyping from Gene-Expression Data in Species with Un-Sequenced Genomes, Genetics, 2007, vol. 176, pp. 789–800.
Potokina, E., Druka, A., Luo, Z., et al., Gene Expression Quantitative Trait Locus Analysis of 16.000 Barley Genes Reveals a Complex Pattern of Genome Wide Transcriptional Regulation, Plant J., 2008, vol. 53, pp. 90–101.
Potokina, E., Druka, A., Luo, Z., et al., Tissue Dependent Limited Pleiotropy Affects Gene Expression in Barley. Plant J., 2008, vol. 56, pp. 287–296.
Kleinhofs, A., Kilian, A., Saghai, M., et al., A Molecular, Isozyme and Morphological Map of the Barley (Hordeum vulgare) Genome, Theor. Appl. Genet., 1993, vol. 86, pp. 705–712.
Rostoks, N., Borevitz, J.O., Hedley, P.E., et al., Single-Feature Polymorphism Discovery in the Barley Transcriptome, Genome Biol., 2005, vol. 6, p. R54.
Ronald, J., Akey, J.M., Whittle, J., et al., Simultaneous Genotyping Gene-Expression Measurement and Detection of Allele-Specific Expression with Oligonucleotide Arrays, Genome Res., 2005, vol. 15, pp. 284–291.
West, M.A., van Leeuwen, H., Kozik, A., et al., High-Density Haplotyping with Microarray Based Expression and Single Feature Polymorphism Markers in Arabidopsis, Genome Res., 2006, vol. 16, pp. 787–795.
Cui, X., Xu, J., Asghar, R., et al., Detecting Single-Feature Polymorphisms Using Oligonucleotide Arrays and Robustified Projection Pursuit, Bioinformatics, 2005, vol. 21, pp. 3852–3858.
Zeng, Z.B., Theoretical Basis for Separation of Multiple Linked Gene Effect in Mapping Quantitative Trait Loci, Proc. Natl. Acad. Sci. USA, 1993, vol. 90, pp. 10972–10976.
Rostoks, N. and Ramsay, L., MacKenzie K. Et Al. Recent History of Artificial Outcrossing Facilitates Whole-Genome Association Mapping in Elite Inbred Crop Varieties, Proc. Natl. Acad. Sci. USA, 2006, vol. 103, pp. 18656–18661.
Gvozdev, V.A., Mechanisms of Gene Activity Regulation during Transcription, Sorosovskii Obrazovatel’nyi Zh., 1996, no. 2, pp. 22–31.
Kota, R., Wolf, M., Michalek, W., and Graner, A., Application of Denaturing High-Performance Liquid Chromatography for Mapping of Single Nucleotide Polymorphisms in Barley (Hordeum vulgare L.), Genome, 2001, vol. 44, pp. 1–6.
Stern, D.L., Evolutionary Developmental Biology and the Problem of Variation, Evolution, 2000, vol. 54, pp. 1079–1091.
Wray, G.A., The Evolutionary Significance of cis-Regulatory Mutations, Nat. Rev. Genet., 2007, vol. 8, no. 3, pp. 206–216.
Carroll, S.B., Evolution at Two Levels: On Genes and Form, PLoS Biol., 2005, vol. 3, no. 7, p. e245.
Ruse, C.E., Parker, S.G., Molecular Genetics and Age-Related Disease, Age Ageing, 2001, vol. 30, pp. 449–454.
Author information
Authors and Affiliations
Corresponding author
Additional information
Original Russian Text © E.K. Potokina, A. Druka, Z. Luo, R. Waugh, M.J. Kearsey, 2009, published in Genetika, 2009, Vol. 45, No. 11, pp. 1493–1505.
Rights and permissions
About this article
Cite this article
Potokina, E.K., Druka, A., Luo, Z. et al. The transcriptome analysis of barley (Hordeum vulgare L.) using the Affymetrix Barley1 GeneChip. Russ J Genet 45, 1317–1328 (2009). https://doi.org/10.1134/S1022795409110064
Received:
Published:
Issue Date:
DOI: https://doi.org/10.1134/S1022795409110064