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; it not only controls flowering time but also determines the yield component in terms of the 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 the 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. MapMan metabolic analysis showed that the DEGs mainly functioned in 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 that closely related to the flowering time. Weighted gene co-expression network analysis (WGCNA) showed that 16, 336, 446, and 124 DEGs had biological connections with Vrn1-5A, Vrn3-7B, Ppd-1D, and WSOC1, respectively. Furthermore, TraesCS2D02G181400 is a MADS-MIKC transcriptional factor that is co-expressed with Vrn1-5A, which indicates this gene is a potential gene related to the flowering timeConclusions: The RNA-seq analysis enriched the transcriptome data of wheat heading date at the key flower development stages of double ridge (W2.0) and androgynous primordium differentiation (W3.5). Based on the DEGs, the co-expression networks of key flowering time genes in Vrn1-5A, 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 wheat heading date.