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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.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07797-7.

bmc genomics

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