Utility of RNA Sequencing for Analysis of Maize Reproductive Transcriptomes

Abstract

Transcriptome sequencing is a powerful method for studying global expression patterns in large, complex genomes. Evaluation of sequence-based expression profi les during reproductive development would provide functional annotation to genes underlying agronomic traits. We generated transcriptome profi les for 12 diverse maize (Zea mays L.) reproductive tissues representing male, female, developing seed, and leaf tissues using high throughput transcriptome sequencing. Overall, ~80% of annotated genes were expressed. Comparative analysis between sequence and hybridization-based methods demonstrated the utility of ribonucleic acid sequencing (RNA-seq) for expression determination and differentiation of paralagous genes (~85% of maize genes). Analysis of 4975 gene families across reproductive tissues revealed expression divergence is proportional to family size. In all pairwise comparisons between tissues, 7 (pre-vs. postemergence cobs) to 48% (pollen vs. ovule) of genes were differentially expressed. Genes with expression restricted to a single tissue within this study were identifi ed with the highest numbers observed in leaves, endosperm, and pollen. Coexpression network analysis identifi ed 17 gene modules with complex and shared expression patterns containing many previously described maize genes. The data and analyses in this study provide valuable tools through improved gene annotation, gene family characterization, and a core set of candidate genes to further characterize maize reproductive development and improve grain yield potential.

Dynamic Transcriptome Landscape of Maize Embryo and Endosperm Development

“…To generate a comprehensive catalog of seed-specific genes, results from this study were compared with 25 published nonseed RNA-seq data sets (Jia et al, 2009;Wang et al, 2009a;Li et al, 2010;Davidson et al, 2011;Bolduc et al, 2012), including root, shoot, shoot apical meristem, leaf, cob, tassel, and immature ear (Supplemental Table S2). In total, we identified 1,258 seed-specific genes, including 91 TFs from a variety of families (Supplemental Data Set S4).…”

RNA-Seq of Arabidopsis Pollen Uncovers Novel Transcription and Alternative Splicing

“…8, C and D). Another pollen RNA-Seq data set from maize (Zea mays; Davidson et al, 2011) is publicly available from the Short Read Archive (SRR189771) and contains around 25 million 35-base reads. We obtained the sequences, aligned them onto the genome, and made the data publicly available for visualization in IGB.…”

Functions of Multiple Genes Encoding ADP-Glucose Pyrophosphorylase Subunits in Maize Endosperm, Embryo, and Leaf

“…Publicly available whole-transcriptome RNA sequencing data (RNA-Seq; Li et al, 2010;Davidson et al, 2011;Waters et al, 2011) provided a quantitative measure of the steady-state levels of specific mRNAs in endosperm as well as embryo and leaf (www.qTeller.com; Fig. 1A).…”

“…Transcript levels measured by RNA-Seq were extracted from the qTeller analysis (J. Schnable, personal communication; www.qTeller.com) of publicly available data sets containing raw whole-transcriptome sequence data Davidson et al, 2011;Waters et al, 2011). qTeller uses the GSNAP algorithm (Wu and Nacu, 2010) to map sequence reads to gene models in the inbred B73 reference genome and the CUFFLINKS algorithm (Trapnell et al, 2010) to quantify transcript abundance based on counts of aligned reads.…”