Arabidopsis REM16 acts as a B3 domain transcription factor to promote flowering time via directly binding to the promoters of <i>SOC1</i> and <i>FT</i>

et al. 2021

BMC Genomics

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.

Section: Discussionmentioning

confidence: 99%

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

et al. 2021

BMC Genomics

“…S13a), we identi ed two CONSTANS-like proteins (TraesCS5A02G166100, TraesCS5D02G170700). The homolog of both TraesCS5A02G166100 and TraesCS5D02G170700 in Arabidopsis is AT5G15840, which is a zinc nger transcription factor-like protein that acts upstream of FT and SOC1 and is mainly involved in owering regulation under long-day conditions [25]. Through Ppd-1D coexpression network construction (Fig.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome Profiling of Developing Leaf and Shoot Apices to Reveal the Molecular Mechanism and Coexpression Genes Responsible for the Wheat Heading Date

et al. 2020

Preprint

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 and androgynous primordium differentiation stage of the leaf and apical meristem, respectively. In total, 18,352 differentially expressed genes (DEGs) were identified. Five common GO terms and 214 common metabolic pathways were obtained by MapMan software. In addition, 1,225 DEGs were annotated to 52 transcription factor gene families, and we discovered that most of the LFY, SBP, and MADS-box genes were highly expressed during the apical development of wheat with the early heading date. Additionally, weighted gene coexpression network analysis (WGCNA) found that the DEGs clustered into 17 coexpression modules, and 16, 336, 446, and 124 DEGs had biological connections with Vrn1-5A, Vrn3-7B, Ppd-1D, and WSOC1, respectively. The 16 genes connected with Vrn1-5A were divided into three types of expression patterns. We further identified one important flowering time gene, TraesCS2D02G181400, which is a MADS-MIKC transcriptional factor and has a biological connection with Vrn1-5A. Gene function showed that this gene was differentially expressed at the A2.0 and L3.5 stages between the genotypes with early and late heading.Conclusions: The RNA-seq analysis results in our present research are a valuable bioinformatics resource for further study of the molecular mechanism of the wheat heading date. Overall, our results shed light on the genetic architecture of wheat flowering time.

“…Two CONSTANS-like proteins (TraesCS5A02G166100, TraesCS5D02G170700) were also discovered. The homolog of both TraesCS5A02G166100 and TraesCS5D02G170700 in Arabidopsis is AT5G15840, which is a zinc nger transcription factor-like protein that acts upstream of FT and SOC1 and is mainly involved in owering regulation under long-day conditions [30]. In the Ppd-1D co-expression network (Fig.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2020

Preprint

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.