Mendelian and Non-Mendelian Regulation of Gene Expression in Maize

Li, L., Petsch, K., Shimizu, R., Liu, S., Xu, W. W., Ying, K., Yu, J., Scanlon, M. J., Schnable, P. S., Timmermans, M. C. P., Springer, N. M., Muehlbauer, G. J. (January 2013) Mendelian and Non-Mendelian Regulation of Gene Expression in Maize. PLoS Genetics, 9 (1). Article number e1003202. ISSN 15537390 (ISSN)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/23341782
DOI: 10.1371/journal.pgen.1003202

Abstract

Transcriptome variation plays an important role in affecting the phenotype of an organism. However, an understanding of the underlying mechanisms regulating transcriptome variation in segregating populations is still largely unknown. We sought to assess and map variation in transcript abundance in maize shoot apices in the intermated B73×Mo17 recombinant inbred line population. RNA-based sequencing (RNA-seq) allowed for the detection and quantification of the transcript abundance derived from 28,603 genes. For a majority of these genes, the population mean, coefficient of variation, and segregation patterns could be predicted by the parental expression levels. Expression quantitative trait loci (eQTL) mapping identified 30,774 eQTL including 96 trans-eQTL "hotspots," each of which regulates the expression of a large number of genes. Interestingly, genes regulated by a trans-eQTL hotspot tend to be enriched for a specific function or act in the same genetic pathway. Also, genomic structural variation appeared to contribute to cis-regulation of gene expression. Besides genes showing Mendelian inheritance in the RIL population, we also found genes whose expression level and variation in the progeny could not be predicted based on parental difference, indicating that non-Mendelian factors also contribute to expression variation. Specifically, we found 145 genes that show patterns of expression reminiscent of paramutation such that all the progeny had expression levels similar to one of the two parents. Furthermore, we identified another 210 genes that exhibited unexpected patterns of transcript presence/absence. Many of these genes are likely to be gene fragments resulting from transposition, and the presence/absence of their transcripts could influence expression levels of their ancestral syntenic genes. Overall, our results contribute to the identification of novel expression patterns and broaden the understanding of transcriptional variation in plants. © 2013 Lin et al.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
organism description > plant > maize
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene expression
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function
organism description > plant
CSHL Authors:
Communities: CSHL Post Doctoral Fellows
CSHL labs > Timmermans lab
Depositing User: Matt Covey
Date: January 2013
Date Deposited: 01 Apr 2013 14:27
Last Modified: 22 Dec 2014 21:26
Related URLs:
URI: http://repository.cshl.edu/id/eprint/28054

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