A Genome-Wide Survey of Imprinted Genes in Rice Seeds Reveals Imprinting Primarily Occurs in the Endosperm

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.

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.