title: Genes and Small RNA Transcripts Exhibit Dosage-Dependent Expression Pattern in Maize Copy-Number Alterations.
abstract: Copy-number alterations are widespread in animal and plant genomes, but their immediate impact on gene expression is still unclear. In animals, copy-number alterations usually exhibit dosage effects, except for sex chromosomes which tend to be dosage compensated. In plants, genes within small duplications (<100 kb) often exhibit dosage-dependent expression, whereas large duplications (>50 Mb) are more often dosage compensated. However, little or nothing is known about expression in moderately-sized (1-50 Mb) segmental duplications, and about the response of small RNAs to dosage change. Here, we compared maize (Zea mays) plants with two, three, and four doses of a 14.6-Mb segment of chromosome 1 that contains ∼300 genes. Plants containing the duplicated segment exhibit dosage-dependent effects on ear length and flowering time. Transcriptome analyses using GeneChip and RNA-sequencing methods indicate that most expressed genes and unique small RNAs within the duplicated segments exhibit dosage-dependent transcript levels. We conclude that dosage effect is the predominant regulatory response for both genes and unique small RNA transcripts in the segmental dosage series we tested. To our knowledge this is the first analysis of small RNA expression in plant gene dosage variants. Because segmental duplications comprise a significant proportion of eukaryotic genomes, these findings provide important new insight into the regulation of genes and small RNAs in response to dosage changes.
authors.affiliation: Department of Genetics, Development and Cell Biology, Department of Agronomy, Iowa State University, Ames, Iowa 50011.
authors.forename: Tao
authors.initials: T
authors.lastname: Zuo
authors.affiliation: Department of Genetics, Development and Cell Biology, Department of Agronomy, Iowa State University, Ames, Iowa 50011.
authors.forename: Jianbo
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Department of Statistics, Iowa State University, Ames, Iowa 50011.
authors.forename: Andrew
authors.initials: A
authors.lastname: Lithio
authors.affiliation: Virtual Reality Application Center, Iowa State University, Ames, Iowa 50011.
authors.forename: Sudhansu
authors.initials: S
authors.lastname: Dash
authors.affiliation: School of Biological Sciences, Illinois State University, Normal, Illinois 61790.
authors.forename: David F
authors.initials: DF
authors.lastname: Weber
authors.affiliation: Corn Insects and Crop Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Iowa State University, Ames, Iowa 50011 Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011.
authors.forename: Roger
authors.initials: R
authors.lastname: Wise
authors.affiliation: Department of Statistics, Iowa State University, Ames, Iowa 50011.
authors.forename: Dan
authors.initials: D
authors.lastname: Nettleton
authors.affiliation: Department of Genetics, Development and Cell Biology, Department of Agronomy, Iowa State University, Ames, Iowa 50011 thomasp@iastate.edu.
authors.forename: Thomas
authors.identifier: 0000-0002-9933-7556
authors.initials: T
authors.lastname: Peterson
mesh_terms: D032461:Chromosomes, Plant / Q000235:genetics; D018628:Gene Dosage / Q000235:genetics*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D018745:Genome, Plant; D018749:RNA, Plant / Q000096:biosynthesis / Q000235:genetics; D056916:Segmental Duplications, Genomic / Q000235:genetics*; D017423:Sequence Analysis, RNA; D003313:Zea mays / Q000235:genetics*
chemical_list: D018749:RNA, Plant
keywords: copy-number alterations; dosage effect; maize; phenotypic variations; small RNAs