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Type: Journal article
Title: A Genome-Wide survey of imprinted genes in rice seeds reveals imprinting primarily occurs in the endosperm
Author: Luo, M.
Taylor, J.
Spriggs, A.
Zhang, H.
Wu, X.
Russell, S.
Singh, M.
Koltunow, A.
Citation: PLoS Genetics, 2011; 7(6):e1002125-1-e1002125-14
Publisher: Public Library Science
Issue Date: 2011
ISSN: 1553-7390
Statement of
Ming Luo, Jennifer M. Taylor, Andrew Spriggs, Hongyu Zhang, Wianjun Wu, Scott Russell, Mohan Singh, Anna Koltunow
Abstract: Genomic imprinting causes the expression of an allele depending on its parental origin. In plants, most imprinted genes have been identified in Arabidopsis endosperm, a transient structure consumed by the embryo during seed formation. We identified imprinted genes in rice seed where both the endosperm and embryo are present at seed maturity. RNA was extracted from embryos and endosperm of seeds obtained from reciprocal crosses between two subspecies Nipponbare (Japonica rice) and 93-11 (Indica rice). Sequenced reads from cDNA libraries were aligned to their respective parental genomes using single-nucleotide polymorphisms (SNPs). Reads across SNPs enabled derivation of parental expression bias ratios. A continuum of parental expression bias states was observed. Statistical analyses indicated 262 candidate imprinted loci in the endosperm and three in the embryo (168 genic and 97 non-genic). Fifty-six of the 67 loci investigated were confirmed to be imprinted in the seed. Imprinted loci are not clustered in the rice genome as found in mammals. All of these imprinted loci were expressed in the endosperm, and one of these was also imprinted in the embryo, confirming that in both rice and Arabidopsis imprinted expression is primarily confined to the endosperm. Some rice imprinted genes were also expressed in vegetative tissues, indicating that they have additional roles in plant growth. Comparison of candidate imprinted genes found in rice with imprinted candidate loci obtained from genome-wide surveys of imprinted genes in Arabidopsis to date shows a low degree of conservation, suggesting that imprinting has evolved independently in eudicots and monocots.
Keywords: Endosperm; genomic imprinting; embryos; rice; genetic loci; gene expression; Arabidopsis thaliana; seeds
Rights: © 2011 Luo et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
RMID: 0030056973
DOI: 10.1371/journal.pgen.1002125
Appears in Collections:Genetics publications

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