Transcriptional signatures of wheat inflorescence development

Abstract

In order to maintain global food security, it will be necessary to increase yields of the cereal crops that provide most of the calories and protein for the world’s population, which includes common wheat (Triticum aestivum L.). An important wheat yield component is the number of grain-holding spikelets which form on the spike during inflorescence development. Characterizing the gene regulatory networks controlling the timing and rate of inflorescence development will facilitate the selection of natural and induced gene variants that contribute to increased spikelet number and yield. In the current study, co-expression and gene regulatory networks were assembled from a temporal wheat spike transcriptome dataset, revealing the dynamic expression profiles associated with the progression from vegetative meristem to terminal spikelet formation. Consensus co-expression networks revealed enrichment of several transcription factor families at specific developmental stages including the sequential activation of different classes of MIKC-MADS box genes. This gene regulatory network highlighted interactions among a small number of regulatory hub genes active during terminal spikelet formation. Finally, the CLAVATA and WUSCHEL gene families were investigated, revealing potential roles for TtCLE13, TtWOX2, and TtWOX7 in wheat meristem development. The hypotheses generated from these datasets and networks further our understanding of wheat inflorescence development.

Systematic mining and functional analysis of factors regulating wheat spike development for breeding selection

“…However, wheat is an allohexaploid of large genome plant with generally triple genes number, large proportion of intergenic regions, more complex sub-genome interaction, and long LD intervals (Hao et al, 2020; Li et al, 2022a; Pang et al, 2020), which greatly reduced the accuracy of association study (Huang and Han, 2014). Other types of information, such as genes expression network provides different filter for identification of key regulators, as proved by previous studies (Li et al, 2018; VanGessel et al, 2022; Wang et al, 2017).…”

“…In this study, we conducted a comprehensive profiling of the epigenomic landscape over time, including various histone modifications, chromatin accessibility, and transcriptomes of developing wheat spikes, spanning from vegetative development (SAM) to terminal spikelet stage where spike architecture is determined. This enabled us to analyze the transcriptional regulation governing the critical processes of flowering transition, spikelet formation, and floret development, all of which significantly impact wheat inflorescence architecture (Sakuma and Schnurbusch, 2020; VanGessel et al, 2022; Luo et al, 2023).…”

“…Cell identity transition, driven by hormone signaling and transcriptional regulatory networks, plays a crucial role in the initiation, distribution, and termination of spikelets (Youssef and Hansson, 2019; VanGessel et al, 2022; Qi et al, 2019). Understanding these regulatory networks can offer potential candidates for shaping inflorescence structure.…”

“…However, GWAS alone provides limited insights into causal variants and genes due to linkage disequilibrium. To address this, gene co-expression networks have been utilized, leveraging stage-specific transcriptome data and population-wide RNA-seq to identify key regulators (Wang et al, 2017; Li et al, 2018; VanGessel et al, 2022). Moreover, investigations into chromatin features have revealed associations with tissue-specific or stress-induced gene expression and subgenome-biased expression patterns in wheat (Li et al, 2019b; Concia et al, 2020; Yuan et al, 2022; Zhao et al, 2023).…”

Wheat plant height locusRHT25encodes a PLATZ transcription factor that interacts with DELLA (RHT1)

“…We also observed a relative higher abundance of PLATZ-A1 compared to PLATZ-B1 transcripts at different stages of spike development in RNA-seq data for tetraploid wheat Kronos (Fig. S6B) (31). We also explored PLATZ-A1 transcript levels in different sections of the elongating peduncle in Kronos plants at ear emergence (Zadok 55) using qRT-PCR.…”