A transcriptomic analysis of superhybrid rice LYP9 and its parents.
By using a whole-genome oligonucleotide microarray, designed based on known and predicted indica rice genes, we investigated transcriptome profiles in developing leaves and panicles of superhybrid rice LYP9 and its parental cultivars 93-11 and PA64s. We detected 22,266 expressed genes out of 36,926 total genes set collectively from 7 tissues, including leaves at seedling and tillering stages, flag leaves at booting, heading, flowering, and filling stages, and panicles at filling stage. Clustering results showed that the F1 hybrid's expression profiles resembled those of its parental lines more than that which lies between the 2 parental lines. Out of the total gene set, 7,078 genes are shared by all sampled tissues and 3,926 genes (10.6% of the total gene set) are differentially expressed genes (DG). As we divided DG into those between the parents (DG(PP)) and between the hybrid and its parents (DG(HP)), the comparative results showed that genes in the categories of energy metabolism and transport are enriched in DG(HP) rather than in DG(PP). In addition, we correlated the concurrence of DG and yield-related quantitative trait loci, providing a potential group of heterosis-related genes.
Wei
Gang
G
State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
Tao
Yong
Y
Liu
Guozhen
G
Chen
Chen
C
Luo
Renyuan
R
Xia
Hongai
H
Gan
Qiang
Q
Zeng
Haipan
H
Lu
Zhike
Z
Han
Yuning
Y
Li
Xiaobing
X
Song
Guisheng
G
Zhai
Hongli
H
Peng
Yonggang
Y
Li
Dayong
D
Xu
Honglin
H
Wei
Xiaoli
X
Cao
Mengliang
M
Deng
Huafeng
H
Xin
Yeyun
Y
Fu
Xiqin
X
Yuan
Longping
L
Yu
Jun
J
Zhu
Zhen
Z
Zhu
Lihuang
L
D002874:Chromosome Mapping; D016000:Cluster Analysis; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D006823:Hybrid Vigor; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics* / Q000378:metabolism*; D010641:Phenotype; D040641:Quantitative Trait Loci