Transcriptome analysis of embryo maturation in maize

Abstract

BackgroundMaize is one of the most important crops in the world. With the exponentially increasing population and the need for ever increased food and feed production, an increased yield of maize grain (as well as rice, wheat and other grains) will be critical. Maize grain development is understood from the perspective of morphology, hormone responses, and storage reserve accumulation. This includes various studies on gene expression during embryo development and maturation but a global study of gene expression of the embryo has not been possible until recently. Transcriptome analysis is a powerful new tool that can be used to understand the genetic basis of embryo maturation.ResultsWe undertook a transcriptomic analysis of normal maturing embryos at 15, 21 and 27 days after pollination (DAP), of one elite maize germplasm line that was utilized in crosses to transgenic plants. More than 19,000 genes were analyzed by this method and the challenge was to select subsets of genes that are vitally important to embryo development and maturation for the initial analysis. We describe the changes in expression for genes relating to primary metabolic pathways, DNA synthesis, late embryogenesis proteins and embryo storage proteins, shown through transcriptome analysis and confirmed levels of transcription for some genes in the transcriptome using qRT-PCR.ConclusionsNumerous genes involved in embryo maturation have been identified, many of which show changes in expression level during the progression from 15 to 27 DAP. An expected array of genes involved in primary metabolism was identified. Moreover, more than 30% of transcripts represented un-annotated genes, leaving many functions to be discovered. Of particular interest are the storage protein genes, globulin-1, globulin-2 and an unidentified cupin family gene. When expressing foreign proteins in maize, the globulin-1 promoter is most often used, but this cupin family gene has much higher expression and may be a better candidate for foreign gene expression in maize embryos. Results such as these allow identification of candidate genes and promoters that may not otherwise be available for use. mRNA seq data archived in NCBI SRA; Accession number: ACC=SRA060791 subid=108584.

Proteomic analysis of maize grain development using iTRAQ reveals temporal programs of diverse metabolic processes

“…Large-scale genome-wide expression analyses using microarrays, cDNA libraries, and RNA sequencing (RNA-seq) have described large numbers of genes that are preferentially expressed in embryogenesis or accumulation of storage compounds during maize grain development [1, 9–13]. For example, a dynamic transcriptomics analysis using an RNA-seq strategy in maize embryo, endosperm, and whole grain from fertilization to maturity identified 26,105 genes involved in programming grain development; moreover, 1258 of these genes were determined to be grain-specific [10].…”

Dynamic Transcriptome Landscape of Maize Embryo and Endosperm Development

“…To date, only two studies have focused on identifying important regulators and processes required for embryo, endosperm, and/or whole seed development in maize based on a genome-wide transcriptional profile produced by RNA-seq (Liu et al, 2008;Teoh et al, 2013). However, these studies were limited by the low number of samples used and they did not provide an extensive, global view of transcriptome dynamics over the majority of seed development stages.…”

Somatic Embryogenesis and Plant Regeneration From an Elite Tropical Maize Inbred Line

“…During this phase changes in gene expression happens in the cells leading to the accumulation of storage material (Teoh et al, 2013) and acquisition of desiccation tolerance. Maturation of somatic embryos have been reported in the absence of 2,4-D as well as in the presence of others growth regulators such as cytokines (Ombori et al, 2008;Akoyi et al, 2013), or abscisic acid (ABA).…”