title: Characterization of the genome expression trends in the heading-stage panicle of six rice lineages.
abstract: To study how changes in gene regulation shape phenotypic variations in rice, we performed a comparative analysis of genome expression in the heading-stage panicle from six lineages of cultivated and wild rice, including Oryza sativa subsp. indica, japonica and javanica, O. nivara , O. rufipogon and O. glaberrima. While nearly three-quarters of the genes are expressed at a constant level in all six lineages, a large portion of the genome, ranging from 1767 to 4489 genes, exhibited differential expression between Asian domesticated and wild rice with repression or down-regulation of genome expression in Asian cultivated rice as the dominant trend. Importantly, we found this repression was achieved to a large extent by the differential expression of a single member of paralogous gene families. Functional analysis of the differentially expressed genes revealed that genes related to catabolism are repressed while genes related to anabolism up-regulated. Finally, we observed that distinct evolutionary forces may have acted on gene expression and the coding sequences in the examined rice lineages.
authors.affiliation: Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China.
authors.forename: Zhi-Yu
authors.initials: ZY
authors.lastname: Peng
authors.forename: Huiyong
authors.initials: H
authors.lastname: Zhang
authors.forename: Tingting
authors.initials: T
authors.lastname: Liu
authors.forename: Katherine M
authors.initials: KM
authors.lastname: Dzikiewicz
authors.forename: Songgang
authors.initials: S
authors.lastname: Li
authors.forename: Xiangfeng
authors.initials: X
authors.lastname: Wang
authors.forename: Guocheng
authors.initials: G
authors.lastname: Hu
authors.forename: Zhengge
authors.initials: Z
authors.lastname: Zhu
authors.forename: Xinghua
authors.initials: X
authors.lastname: Wei
authors.forename: Qi-Hui
authors.initials: QH
authors.lastname: Zhu
authors.forename: Zongxiu
authors.initials: Z
authors.lastname: Sun
authors.forename: Song
authors.initials: S
authors.lastname: Ge
authors.forename: Ligeng
authors.initials: L
authors.lastname: Ma
authors.forename: Lei
authors.initials: L
authors.lastname: Li
authors.forename: Xing-Wang
authors.initials: XW
authors.lastname: Deng
mesh_terms: D019070:Cell Lineage; D016000:Cluster Analysis; D018556:Crops, Agricultural / Q000145:classification* / Q000235:genetics*; D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D046228:Microarray Analysis; D008957:Models, Genetic; D012275:Oryza / Q000145:classification* / Q000235:genetics*; D012984:Software