Genome-wide analysis of spatio-temporal gene expression patterns during early embryogenesis in rice

Abstract

Embryogenesis in rice is different from that of most dicotolydonous plants in that it shows a non-stereotypic cell division pattern, formation of dorsal-ventral polarity, and endogenous initiation of the radicle. To reveal the transcriptional features associated with developmental events during rice early embryogenesis, we used microarray analysis coupled with laser microdissection to obtain both spatial and temporal transcription profiles. Our results allowed us to determine spatial expression foci for each expressed gene in the globular embryo, which revealed the importance of phytohormone-related genes and a suite of transcription factors to early embryogenesis. Our analysis showed the polarized expression of a small number of genes along the apical-basal and dorsal-ventral axes in the globular embryo, which tended to fluctuate in later developmental stages. We also analyzed gene expression patterns in the early globular embryo and how this relates to expression in embryonic organs at later stages. We confirmed the accuracy of the expression patterns found by microarray analysis of embryo subdomains using in situ hybridization. Our study identified homologous genes from Arabidopsis thaliana with known functions in embryogenesis in addition to unique and uncharacterized genes that show polarized expression patterns during embryogenesis. The results of this study are presented in a database to provide a framework for spatiotemporal gene expression during rice embryogenesis, to serve as a resource for future functional analysis of genes, and as a basis for comparative studies of plant embryogenesis.

Cloning and evaluation of reference genes for quantitative real-time PCR analysis inAmorphophallus

“…Gene expression analysis plays a significant role in identifying the expression profile and function of these genes (Huggett et al, 2005; Itoh et al, 2016). RT-qPCR is a preferred method to study gene expression because of its unique advantages (Bustin et al, 2009).…”

“…Selecting a suitable reference gene and using a set of standardized experimental conditions are among the most important factors for quantifying gene expression by RT-qPCR (Bustin et al, 2009; Hellemans & Vandesompele, 2014). Suitable reference genes have been identified for many crops and especially for model plants (Dekkers et al, 2012; Czechowski et al, 2005; Itoh et al, 2016). Reference genes that are used as appropriate normalization genes usually have high copy numbers and relatively stable expression (Thellin et al, 1999).…”

Rice Functional Genomics Research: Past Decade and Future

“…Gene expression microarrays were used to analyze and compare the transcriptomes of super hybrid rice LYP9 and its parental cultivars 93-11 and PA64s (Wei et al, 2009). Gene expression profiles of reproductive meristems in early inflorescences and the spatial and temporal transcription profiles during early embryogenesis were dissected by using a laser microdissection and RNA-seq approach (Harrop et al, 2016;Itoh et al, 2016). Wang et al (2014c) used an Affymetrix GeneChip Rice Genome Array to analyze the expression quantitative trait loci (eQTLs) in rice seedlings and flag leaves during heading period from recombinant inbred lines (RILs) derived from a cross between Zhenshan 97 and Minghui 63.…”

Autonomous and non‐autonomous functions of the maize Shohai1 gene, encoding a RWP‐RK putative transcription factor, in regulation of embryo and endosperm development

“…For instance, shai1 mutations could alter cell division patterns very early, including the first zygote division, and the mutant embryos might restore relatively normal growth and differentiation up to late transition stages. Gene expression analyses with developing embryos of maize and rice by laser-capture microdissection show that Shai1 and the rice ortholog are expressed in very early stage embryos (Zhan et al, 2015;Itoh et al, 2016). Interestingly, the rice Shai1 ortholog is expressed both in the apical and basal regions of globular embryos at comparable levels (Itoh et al, 2016).…”