Transcriptome profiling of developing leaf and shoot apices to reveal the molecular mechanism and co-expression genes responsible for the wheat heading date

Abstract

Background Wheat is one of the most widely planted crops worldwide. The heading date is important for wheat environmental adaptability, as it not only controls flowering time but also determines the yield component in terms of grain number per spike. Results In this research, homozygous genotypes with early and late heading dates derived from backcrossed progeny were selected to conduct RNA-Seq analysis at the double ridge stage (W2.0) and androgynous primordium differentiation stage (W3.5) of the leaf and apical meristem, respectively. In total, 18,352 differentially expressed genes (DEGs) were identified, many of which are strongly associated with wheat heading date genes. Gene Ontology (GO) enrichment analysis revealed that carbohydrate metabolism, trehalose metabolic process, photosynthesis, and light reaction are closely related to the flowering time regulation pathway. Based on MapMan metabolic analysis, the DEGs are mainly involved in the light reaction, hormone signaling, lipid metabolism, secondary metabolism, and nucleotide synthesis. In addition, 1,225 DEGs were annotated to 45 transcription factor gene families, including LFY, SBP, and MADS-box transcription factors closely related to flowering time. Weighted gene co-expression network analysis (WGCNA) showed that 16, 336, 446, and 124 DEGs have biological connections with Vrn1-5 A, Vrn3-7B, Ppd-1D, and WSOC1, respectively. Furthermore, TraesCS2D02G181400 encodes a MADS-MIKC transcription factor and is co-expressed with Vrn1-5 A, which indicates that this gene may be related to flowering time. Conclusions RNA-Seq analysis provided transcriptome data for the wheat heading date at key flower development stages of double ridge (W2.0) and androgynous primordium differentiation (W3.5). Based on the DEGs identified, co-expression networks of key flowering time genes in Vrn1-5 A, Vrn3-7B, WSOC1, and Ppd-1D were established. Moreover, we discovered a potential candidate flowering time gene, TraesCS2D02G181400. Taken together, these results serve as a foundation for further study on the regulatory mechanism of the wheat heading date.

Genome sequencing of Sitopsis species provides insights into their contribution to the B subgenome of bread wheat

“…Six seedlings were separately sampled at 0 h, 5 min, 0.5 h, 1 h, 6 h, and 12 h after application of heat stress. We selected three genes from OG0272, OG0283, and OG2039 for RT-qPCR, which was performed as described previously ( Yang et al., 2021 ). The primer sequences used in this research are listed in Supplemental Table 10 .…”

A Glu209Lys substitution in DRG1/TaACT7, which disturbs F‐actin organization, reduces plant height and grain length in bread wheat

“…Data processing and analysis were performed according to the methods described in Yang et al . (2021).…”

GSK3 regulates VRN1 to control flowering time in wheat

“…In this study, we observed that the gsk3 mutant shows late heading and flowering (Figure 1A–C), as mentioned in a previous report (Cheng et al, 2020). Our earlier transcriptome analysis (Yang et al, 2021) showed that GSK3 is highly expressed in the shoot apex and leaves of wheat variety YZ4110 at the W2.0 and W3.5 stages (Figure S1). This result raises the interesting question of how GSK3 regulates the heading and flowering dates of wheat.…”