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Title:   Author  item
                                            ZUO, TAO - Iowa State Universityitem
                                            ZHANG, JIANBO - Iowa State Universityitem
                                            LITHIO, ANDREW - Iowa State Universityitem
                                            DASH, SUDHANSU - Iowa State Universityitem
                                            WEBER, DAVID - Illinois State Universityitem
                                            Wise, Rogeritem
                                            NETTLETON, DAN - Iowa State Universityitem
                                            PETERSON, THOMAS - Iowa State University
  Submitted to: Genetics
                                    Publication Type: Peer Reviewed Journal
                                    Publication Acceptance Date: 4/4/2016
                                    Publication  Date: 4/29/2016
                                    Citation: Zuo, T., Zhang, J., Lithio, A., Dash, S., Weber, D., Wise, R.P., Nettleton, D., Peterson, T. 2016. Genes and small RNA transcripts exhibit dosage-dependent expression pattern in maize copy-number alterations. Genetics. 203(1):1177-1190. doi: 10.1534/genetics.116.188235.Interpretive Summary: DNA copy-number alterations, whether involving chromosome segments or entire chromosomes, can have dramatic effects on the overall health of the organism. For example, aneuploidy, one kind of DNA copy-number alteration, is usually detrimental and may cause severe genetic disorders. Trisomy 21, one of the best-known examples in humans, causes Down Syndrome and most other aneuploidies result in severe developmental disorders and do not survive to term. To further delve into the question of DNA copy-number alterations and their effect on crop plants, we compared sibling maize plants that contain two, three and four doses of a segment of chromosome 1 that contains ~300 genes. Segmental tetrasomic plants are significantly shorter, have smaller ears, flower later than normal siblings, and also exhibit gene dosage-dependent transcript levels. These results indicate that the number of copies of a chromosomal segment affects the output of both protein-coding and non-coding transcripts in maize. This results in negative effects on stature and yield. Our study provides valuable insights into the effects of copy-number-variation in maize and understanding how gene expression responds to copy number change. These results are valuable to modern plant breeders who rely on genetic and genomic data to advance yield, nutrition and disease resistance in crops.
                                Technical 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 that 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.


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