Transcriptional control of nutrient partitioning during rice grain filling

Abstract

SummaryCereal grains accumulate carbohydrates, storage proteins and fatty acids via different pathways during their development. Many genes that participate in nutrient partitioning during grain filling and that affect starch quality have been identified. To understand how the expression of these genes is coordinated during grain development, a genomic approach to surveying the participation and interactions of all the pathways is necessary.Using recently published rice genome information, we designed a rice GeneChip microarray that covers half the rice genome. By monitoring the expression of 21 000 genes in parallel, we identified genes involved in the grain filling process and found that the expression of genes involved in different pathways is coordinately controlled in a synchronized fashion during grain filling. Interestingly, a known promoter element in genes encoding seed storage proteins, AACA, is statistically over-represented among the 269 genes in different pathways with diverse functions that are significantly up-regulated during grain filling. By expression pattern matching, a group of transcription factors that have the potential to interact with this element was identified. We also found that most genes in the starch biosynthetic pathway show multiple distinct spatial and temporal expression patterns, suggesting that different isoforms of a given enzyme are expressed in different tissues and at different developmental stages. Our results reveal key regulatory machinery and provide an opportunity for modifying multiple pathways by manipulating key regulatory elements for improving grain quality and quantity.

Global Patterns of Gene Expression in the Aleurone of Wild-Type and dwarf1 Mutant Rice

“…Previous work by others and our own analyses (Supplemental Fig. 1) indicate that the false positive rate for the rice array is 0.5% (Zhu et al, 2003) or less (0.37%; Supplemental Fig. 1), with a 2-fold cutoff and approximately 1.9% with a 1.5-fold cutoff (Supplemental Fig.…”

“…All microarray experiments were done using the custom-built Genechip described by Zhu et al (2003). Preparation of cDNA and cRNA, fluorescent labeling, hybridization to the chip, and quality control steps were done exactly as described previously (Zhu et al, 2003).…”

“…We have used an oligonucleotide microarray containing 23,780 probe sets representing approximately 21,000 rice genes (Zhu et al, 2003) to examine transcript profiles in rice aleurone. Approximately one-half of the genes in the rice genome are represented on this array (Goff et al, 2002).…”

Ubiquitination-mediated protein degradation and modification: an emerging theme in plant-microbe interactions

“…The enhanced resistance of the spl11 mutant to the two pathogens correlates with the constitutive expression of several defense-related genes and lesion development on Ubiquitination-mediated protein degradation in plant-microbe interactions 420 npg the leaves [80]. The constitutive activation of defense responses in the spl11 mutant was further confirmed when an array-based expression profiling was performed using the Sygenta rice gene chips that harbor nearly half of all rice genes [81] to analyze the impact of the spl11 mutation on the rice transcriptome. Comparison of the global transcripts between the wild-type plants and the spl11 mutant plants in three types of leaf tissues with different lesion development phenotypes revealed that the spl11 mutation causes significant changes in the rice transcriptome (data not shown).…”

Identification and Functional Characterization an Ortholog of OsENOD93-1 Gene in Wheat Using in-silico Approach

“…OsENOD93-1 gene consists of three exons and two introns, encodes a 116 amino acids long protein. Zhu et al, 2003 revealed that OsENOD93-1 showed a high level of expression in root, especially at the panicle emergence stage. Bi et al, 2009 suggested that OsENOD93-1 gene significantly responded to both N induction and N reduction.…”