A Genome-wide View of Transcriptome Dynamics During Early Spike Development in Bread Wheat

Abstract

Wheat spike development is a coordinated process of cell proliferation and differentiation with distinctive phases and architecture changes. However, the dynamic alteration of gene expression in this process remains enigmatic. Here, we characterized and dissected bread wheat spike into six developmental stages, and used genome-wide gene expression profiling, to investigate the underlying regulatory mechanisms. High gene expression correlations between any two given stages indicated that wheat early spike development is controlled by a small subset of genes. Throughout, auxin signaling increased, while cytokinin signaling decreased. Besides, many genes associated with stress responses highly expressed during the double ridge stage. Among the differentially expressed genes (DEGs), were identified 375 transcription factor (TF) genes, of which some homologs in rice or Arabidopsis are proposed to function in meristem maintenance, flowering time, meristem initiation or transition, floral organ development or response to stress. Gene expression profiling demonstrated that these genes had either similar or distinct expression pattern in wheat. Several genes regulating spike development were expressed in the early spike, of which Earliness per se 3 (Eps-3) was found might function in the initiation of spikelet meristem. Our study helps uncover important genes associated with apical meristem morphology and development in wheat.

Cytokinin dehydrogenase: a genetic target for yield improvement in wheat

“…As there was no increase in spikelet number, this implies more filled florets. In the light of the results for rice where OsCKX2 was associated with grain number (Ashikari et al , ), and wheat where TaCKX2.2.1‐3D was associated with grain weight (Zhang et al , ), the results by Li et al () suggest a difference in function between the TaCKX2.2.1 genes on chromosomes 3A and 3D. This leads to the potential of stacking mutations in TaCKX2.2.1‐3D and TaCKX2.2.1‐3A to address both seed number and seed size in bread wheat, even though the RNA‐seq data show similar profiles for both gene family members (Fig S2C).…”

“…Grain number per spike in wheat was enhanced when a conserved fragment of TaCKX2.2.1‐3A (originally TaCKX2.4 ) was targeted by RNA interference (Li et al , ). Li et al () showed a strong correlation between grain number and reduced expression of TaCKX2.2.1‐3A in T 3 plants. Moreover, increased grain number was due to an increased grain number per spike.…”

Heritable temporal gene expression patterns correlate with metabolomic seed content in developing hexaploid oat seed

“…As we had both temporal and genetic breadth in our design, we estimated the heritability of our transcriptome, a novelty compared to previous studies (Li et al , , ; Wan et al , ; Yi et al , ; Zhang et al , ). Within a TCoE set, we asked two questions: (i) which transcripts are strongly correlated with each other across genotypes such that they are similarly affected by genetic background?…”

“…Investigation of the transcriptome through time is useful for understanding physiological processes occurring during seed maturation and for conducting genetic improvement. Much effort has been made to understand biological processes underlying observed temporal gene expression patterns, including transcriptome studies in maize (Li et al , ; Yi et al , ), wheat (Li et al , ; Wan et al , ) and barley (Zhang et al , ). However, in each case, only one cultivar was examined, which may reflect genotype‐dependent or genotype‐specific results and thus may have limitations for plant improvement.…”

Comparative analysis based on transcriptomics and metabolomics data reveal differences between emmer and durum wheat in response to nitrogen starvation

“…(2014) demonstrated the relevant role of the chloroplast DEAD-box RH3 on the growth and stress response in Arabidopsis thaliana . Interestingly, it is reported that in bread wheat the MIKC-type MADS-box TFs have key roles in plant growth (Ma et al ., 2017; Li et al ., 2018); however, even if one of these transcription factors (Traes_5AL_13E2DEC48) was a central node in the durum wheat-specific network, it was down-regulated under N starvation in comparison to the optimal N condition.…”