Maize Root Transcriptome by Serial Analysis of Gene Expression

• Published in: Plant physiology (Bethesda) Vol. 138; no. 3; pp. 1700 - 1710
• Main Authors: Poroyko, V, Hejlek, L.G, Spollen, W.G, Springer, G.K, Nguyen, H.T, Sharp, R.E, Bohnert, H.J
• Format: Journal Article
• Language: English
• Published: Rockville, MD American Society of Plant Biologists 01.07.2005; American Society of Plant Physiologists
• Subjects: Agronomy. Soil science and plant productions; Arabidopsis thaliana; Base Sequence; Biological and medical sciences; Classical and quantitative genetics. Population genetics. Molecular genetics; Corn; DNA, Plant; DNA, Plant - genetics; Enzymes; Enzymes - genetics; expressed sequence tags; Fundamental and applied biological sciences. Psychology; Gene expression; gene expression regulation; Gene Expression Regulation, Plant; Gene Library; Generalities. Genetics. Plant material; Genes; genetics; Genetics and breeding of economic plants; Genetics, Genomics, and Molecular Evolution; Genomes; messenger RNA; Molecular genetics; molecular sequence data; nucleotide sequences; plant genetics; Plant Proteins; Plant Proteins - genetics; Plant Roots; Plant Roots - genetics; Plants; Reverse Transcriptase Polymerase Chain Reaction; Ribosomal proteins; RNA; RNA, Plant; RNA, Plant - genetics; root tips; Sage; transcription (genetics); Transcription, Genetic; transcriptome; Transcriptomes; transcriptomics; Zea mays; Zea mays - genetics; Monocotyledones; Zea mays; Root; Transcription; Gene expression; Arabidopsis thaliana; Complementary DNA; Gene; Cruciferae; Gramineae; Dicotyledones; Angiospermae; Spermatophyta
• ISSN: 0032-0889; 1532-2548
• DOI: 10.1104/pp.104.057638

Serial Analysis of Gene Expression was used to define number and relative abundance of transcripts in the root tip of well-watered maize seedlings (Zea mays cv FR697). In total, 161,320 tags represented a minimum of 14,850 genes, based on at least two tags detected per transcript. The root transcriptome has been sampled to an estimated copy number of approximately five transcripts per cell. An extrapolation from the data and testing of single-tag identifiers by reverse transcription-PCR indicated that the maize root transcriptome should amount to at least 22,000 expressed genes. Frequency ranged from low copy number (2-5, 68.8%) to highly abundant transcripts (100[rightwards arrow]1,200; 1%). Quantitative reverse transcription-PCR for selected transcripts indicated high correlation with tag frequency. Computational analysis compared this set with known maize transcripts and other root transcriptome models. Among the 14,850 tags, 7,010 (47%) were found for which no maize cDNA or gene model existed. Comparing the maize root transcriptome with that in other plants indicated that highly expressed transcripts differed substantially; less than 5% of the most abundant transcripts were shared between maize and Arabidopsis (Arabidopsis thaliana). Transcript categories highlight functions of the maize root tip. Significant variation in abundance characterizes transcripts derived from isoforms of individual enzymes in biochemical pathways.