a genome-wide survey of imprinted genes in rice seeds reveals imprinting primarily occurs in the endosperm一个全基因组印迹基因在水稻种子的调查揭示了印记主要发生在胚乳中.pdfVIP

A Genome-Wide Survey of Imprinted Genes in Rice Seeds Reveals Imprinting Primarily Occurs in the Endosperm 1 1 1 1,2 2 3 Ming Luo , Jennifer M. Taylor , Andrew Spriggs , Hongyu Zhang , Xianjun Wu , Scott Russell , Mohan 4 5 Singh , Anna Koltunow * 1 CSIRO Plant Industry, Canberra, Australia, 2 Rice Research Institute of Sichuan Agricultural University, Chengdu, Sichuan, China, 3 Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma, United States of America, 4 Plant Molecular Biology and Biotechnology Laboratory, The University of Melbourne, Melbourne, Australia, 5 CSIRO Plant Industry, Waite Campus, Adelaide, Australia 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 t