Comprehensive analysis of imprinted genes in maize reveals limited conservation with other species and allelic variation for imprinting
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2013
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Abstract
In plants, a subset of genes exhibit imprinting in endosperm tissue such that
expression is primarily from the maternal or paternal allele. Imprinting may
arise as a consequence of mechanisms for silencing of transposons during
reproduction, and in some cases imprinted expression of particular genes may
provide a selective advantage such that it is conserved across species.
Separate mechanisms for the origin of imprinted expression patterns and
maintenance of these patterns may result in substantial variation in the
targets of imprinting in different species. Here we present deep sequencing of
RNAs isolated from reciprocal crosses of four diverse maize genotypes,
providing a comprehensive analysis of imprinting in maize that allows
evaluation of imprinting at more than 95% of endosperm-expressed genes. We find
that over 500 genes exhibit statistically significant parent-of-origin effects
in maize endosperm tissue, but focused our analyses on a subset of these genes
that had >90% expression from the maternal allele (69 genes) or from the
paternal allele (108 genes) in at least one reciprocal cross. Over 10% of
imprinted genes show evidence of allelic variation for imprinting. A comparison
of imprinting in maize and rice reveals that only 13% of genes with syntenic
orthologs in both species exhibit conserved imprinting. Genes that exhibit
conserved imprinting in maize relative to rice have elevated dN/dS ratios
compared to other imprinted genes, suggesting a history of more rapid
evolution. Together, these data suggest that imprinting only has functional
relevance at a subset of loci that currently exhibit imprinting in maize.
| Reference Key |
springer2013comprehensive
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| Authors | Amanda J. Waters; Paul Bilinski; Steve R. Eichten; Matthew W. Vaughn; Jeffrey Ross-Ibarra; Mary Gehring; Nathan M. Springer |
| Journal | arXiv |
| Year | 2013 |
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