Digital Gene Expression Signatures for Maize Development    

Abstract

Genome-wide expression signatures detect specific perturbations in developmental programs and contribute to functional resolution of key regulatory networks. In maize (Zea mays) inflorescences, mutations in the RAMOSA (RA) genes affect the determinacy of axillary meristems and thus alter branching patterns, an important agronomic trait. In this work, we developed and tested a framework for analysis of tag-based, digital gene expression profiles using Illumina's high-throughput sequencing technology and the newly assembled B73 maize reference genome. We also used a mutation in the RA3 gene to identify putative expression signatures specific to stem cell fate in axillary meristem determinacy. The RA3 gene encodes a trehalose-6-phosphate phosphatase and may act at the interface between developmental and metabolic processes. Deep sequencing of digital gene expression libraries, representing three biological replicate ear samples from wild-type and ra3 plants, generated 27 million 20-to 21-nucleotide reads with frequencies spanning 4 orders of magnitude. Unique sequence tags were anchored to 3#-ends of individual transcripts by DpnII and NlaIII digests, which were multiplexed during sequencing. We mapped 86% of nonredundant signature tags to the maize genome, which associated with 37,117 gene models and unannotated regions of expression. In total, 66% of genes were detected by at least nine reads in immature maize ears. We used comparative genomics to leverage existing information from Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) in functional analyses of differentially expressed maize genes. Results from this study provide a basis for the analysis of short-read expression data in maize and resolved specific expression signatures that will help define mechanisms of action for the RA3 gene.

A Genome-Wide Regulatory Framework Identifies Maize Pericarp Color1 Controlled Genes

“…The overall distribution of gene expression between pericarp and silk tissues is very similar and also very similar to genomewide expression patterns established for maize root, shoot, and leaf tissues (Eveland et al, 2010) (see Supplemental Figure 3 online). As anticipated, given that silks and pericarps have the same developmental origin, the ovary wall (Kiesselbach, 1980;Huang and Sheridan, 1994), the patterns of gene expression are more similar between pericarps and silks than with other plant organs (root, shoot, or leaf), with the difference in P1 genotype influencing gene expression patterns to a lesser extent than the origin of the tissue (see Supplemental Figure 3B online).…”

Six-rowed spike4 ( Vrs4 ) controls spikelet determinacy and row-type in barley

“…Although RA2 and RA3 act independently in maize, we found that HvRA2 may regulate transcripts of HvSRA and T6P synthase, which in turn may regulate specific growth responses through synthesis of T6P (Fig. 4C) (27). Moreover, HvRA2 coopted a genus-specific function for the row-type pathway through regulation of Vrs1 (control over lateral spikelet fertility), thereby clearly indicating different gene sets and networks for inflorescence development compared with maize (Fig.…”

Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

“…Our data suggest a model in which deletions in both maize genomes occur at the same overall rate, but purifying selection is (24). All P values were calculated using cumulative binomial distributions assuming an equal chance of gene copies on maize1 or maize2 dominating total expression for the gene pair.…”