Transcriptome Profiling of Wheat Inflorescence Development from Spikelet Initiation to Floral Patterning Identified Stage-Specific Regulatory Genes

Abstract

Early reproductive development in cereals is crucial for final grain number per spike and hence the yield potential of the crop. To date, however, no systematic analyses of gene expression profiles during this important process have been conducted for common wheat (Triticum aestivum). Here, we studied the transcriptome profiles at four stages of early wheat reproductive development, from spikelet initiation to floral organ differentiation. K-means clustering and stage-specific transcript identification detected dynamically expressed homeologs of important transcription regulators in spikelet and floral meristems that may be involved in spikelet initiation, floret meristem specification, and floral organ patterning, as inferred from their homologs in model plants. Small RNA transcriptome sequencing discovered key microRNAs that were differentially expressed during wheat inflorescence development alongside their target genes, suggesting that miRNA-mediated regulatory mechanisms for floral development may be conserved in cereals and Arabidopsis. Our analysis was further substantiated by the functional characterization of the ARGONAUTE1d (AGO1d) gene, which was initially expressed in stamen primordia and later in the tapetum during anther maturation. In agreement with its stage-specific expression pattern, the loss of function of the predominantly expressed B homeolog of AGO1d in a tetraploid durum wheat mutant resulted in smaller anthers with more infertile pollens than the wild type and a reduced grain number per spike. Together, our work provides a first glimpse of the gene regulatory networks in wheat inflorescence development that may be pivotal for floral and grain development, highlighting potential targets for genetic manipulation to improve future wheat yields.

Transcriptome Association Identifies Regulators of Wheat Spike Architecture

“…However, the allohexaploid wheat genome makes genetic dissection highly challenging. Recent breakthroughs in genome sequencing have enabled transcriptome analysis possible for this important food crop (Feng et al, 2017;Li et al, 2014). In this study, we analyzed the transcriptomes of young spikes in 90 winter wheat lines and correlated expression with variations in spike complexity traits (spikelet number per spike, floret number per spike, and seed number per spike).…”

“…In wheat, increased transcription levels of Q, an AP2-like gene, was markedly associated with spike compactness, suggesting that the Q gene may be implicated in spike development (Simons et al, 2006), although its role in spike complexity remains unclear. Feng et al (2017) reported that a durum wheat ARGONAUTE1d gene mutant produced shorter spikes and fewer grains per spike than wild-type controls. In addition, recent studies have shown the mechanisms underlying the genetic regulation of rare supernumerary spikelet variations.…”

“…In wheat, increased transcription levels of Q, an AP2-like gene, was markedly associated with spike compactness, suggesting that the Q gene may be implicated in spike development (Simons et al, 2006), although its role in spike complexity remains unclear. Feng et al (2017) underlying the genetic regulation of rare supernumerary spikelet variations. For example, wheat Photoperiod1 (Ppd1) was identified as a regulator of paired spikelet formation (Boden et al, 2015).…”

Evolutionary and ecological functional genomics, from lab to the wild

“…Three RNA‐seq papers (Lister et al ., ; Mortazavi et al ., ; Nagalakshmi et al ., ) on Arabidopsis, yeast and mice, respectively, mark the start of this tool's use for functional genomic studies. Contemporarily, RNA‐seq is used at ever‐larger scales for functional characterization of developmental, environmental response and economically important phenotypes (Becker et al ., ; Feng et al ., ; Giacomello et al ., ; Leydon et al ., ; Liu et al ., ), and is often used to validate epigenomic measurements (Wang et al ., ). There are numerous studies that employ whole‐genome gene expression analysis not just for model plant species and crops, but also for lesser‐known plant species including Japanese lawn grass (Xie et al ., ), Cunninghamia lanceolata (Cao et al ., ), mangrove fern (Zhang et al ., ), wild oil‐tea camelia (Chen et al ., ), curry tree (Meena et al ., ) and Banksia (He et al ., ).…”

Comparative study of chemical treatments in combination with extrusion for the partial conversion of wheat and sorghum insoluble fiber into soluble

“…This treatment hydrolyzes the long polysaccharide chain to smaller fractions to increase their solubility. Moreover, in a study, soluble dietary fiber content in black soybean hull was increased by using hydrogen peroxide (Feng et al, ). Furthermore, the dietary fiber ratio of whole grain barley was modified by carboxymethylation (Park, Lee, & Lee, ).…”