A transcriptomic analysis of superhybrid rice LYP9 and its parents

Abstract

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 (DGHP), the comparative results showed that genes in the categories of energy metabolism and transport are enriched in DGHP rather than in DGPP. In addition, we correlated the concurrence of DG and yield-related quantitative trait loci, providing a potential group of heterosisrelated genes.heterosis ͉ hybrid rice ͉ transcriptome ͉ quantitative trait loci ͉ differentially expressed genes

Heterosis

“…A null hypothesis is that gene expression will be additive in the hybrid compared with the expression in the parents. For many genes, this is the result found, but depending on the particular study, there are varying numbers of genes that exhibit a nonadditive behavior (Sun et al, 2004;Swanson-Wagner et al, 2006Wang et al, 2006;Meyer et al, 2007;Uzarowska et al, 2007;Zhuang and Adams, 2007;Chen et al, 2008;Guo et al, 2008;Hoecker et al, 2008;Pea et al, 2008;Stupar et al, 2008;Zhang et al, 2008;Tirosh et al, 2009;Wei et al, 2009;Andorf et al, 2010;He et al, 2010;Jahnke et al, 2010;Paschold et al, 2010;Riddle et al, 2010). The various studies have utilized diverse species, different inbred lines within species, distinct tissues, and a variety of microarray platforms, which might account for the differences found to some degree.…”

Integrated analysis of phenome, genome, and transcriptome of hybrid rice uncovered multiple heterosis-related loci for yield increase

“…We first sequenced the genome of the paternal variety 93-11 (31) and then profiled and compared the transcriptomes of LYP9 and its two parents at various life stages (32). Subsequently, we released the whole-genome sequence of the other parental line, PA64S (33), and developed a recombinant inbred line (RIL) population consisting of 219 RILs derived from LYP9 and a backcross population (RILBC1) derived from crossing each RIL with the female parent PA64S (34).…”

Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids

“…The availability of the complete genomic sequence for the japonica (cv Nipponbare) and indica (cv 93-11) subspecies of rice (Goff et al, 2002;Yu et al, 2002) has already enabled the investigation of transcriptome activity in a range of tissues and developmental stages (Li et al, 2006;Nobuta et al, 2007), the high-resolution mapping of epigenetic modifications for chromosomes (Li et al, 2008b), and the genome-wide identification of genetic variation in gene expression between rice subspecies and their hybrids (Zhang et al, 2008a;Wei et al, 2009). The high growth vigor of hybrids between Nipponbare and 93-11 also provides a good opportunity for the investigation of the molecular basis of heterosis in rice (Zhang et al, 2008a).…”