Characterization of the genome expression trends in the heading-stage panicle of six rice lineages.
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.
Peng
Zhi-Yu
ZY
Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China.
Zhang
Huiyong
H
Liu
Tingting
T
Dzikiewicz
Katherine M
KM
Li
Songgang
S
Wang
Xiangfeng
X
Hu
Guocheng
G
Zhu
Zhengge
Z
Wei
Xinghua
X
Zhu
Qi-Hui
QH
Sun
Zongxiu
Z
Ge
Song
S
Ma
Ligeng
L
Li
Lei
L
Deng
Xing-Wang
XW
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