Ming LuoJennifer M. TaylorAndrew SpriggsHongyu ZhangXianjun WuScott RussellMohan SinghAnna Koltunow2016-01-082016-03-302016-01-082016-03-302011-06-23Luo M, Taylor JM, Spriggs A, Zhang H, Wu X, Russell S, et al. (2011) A Genome-Wide Survey of Imprinted Genes in Rice Seeds Reveals Imprinting Primarily Occurs in the Endosperm. PLoS Genet 7(6): e1002125. doi:10.1371/journal.pgen.1002125http://hdl.handle.net/11244/23529We thank Claudia Kohler, Philip Wolff, and Isabelle Weinhofer for discussions concerning this paper and sharing their Arabidopsis seed imprinted gene data with us prior to publication. The technical support of Susan Johnson and assistance with figures is acknowledged. We thank Soussanith Nokham for processing of images; Narayana Upadhyaya for providing rice lines; and Jean Finnegan, Matt Tucker, Steve Swain, Tony Ashton, and Ben Trevaskis for critical reading of the manuscript.Author Summary The expression of maternal or paternal alleles in either a preferentially or exclusively uniparental manner, termed imprinting, is prevalent in the transient endosperm of seeds in the model plant Arabidopsis . Cereals form seeds where both the embryo and endosperm are present at seed maturity. They are an important world food source. To date, very few imprinted genes have been identified in cereal seeds. How parental gene expression biases contribute to rice seed development has not yet been studied in detail. The deep resolution of transcript sequencing platforms was used to identify loci expressed in a parentally biased manner in the embryo and endosperm of Indica and Japonica rice at a genome-wide level. We identified 262 candidate imprinted loci expressed in the endosperm, experimentally verified 56 of these, and found novel features pertaining to their expression. Only one gene was found to be imprinted in the rice embryo. Imprinting in Arabidopsis and rice seeds is confined primarily to the endosperm, but the identified loci do not share extensive sequence conservation. Imprinting thus appears to have evolved independently in these plant species.en-USAttribution 3.0 United StatesEndosperm,Genomic imprinting,Embryos,Rice,Genetic loci,Gene expression,Seeds,Plant genomicsResearch Article10.1371/journal.pgen.1002125false