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

Yuxin Yang,Xueying Zhang,Xu Liu,Lifen Wu,Chuan Xia,Xiuying Kong,Guoxiang Liu,Lichao Zhang

doi:10.1186/s12864-021-07797-7

Abstract

BackgroundWheat 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.ResultsIn 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.ConclusionsRNA-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.

Highlights

Wheat is one of the most widely planted crops worldwide
Principal component analysis (PCA) of the eight raw sequencing datasets clustered the samples into four groups according to genotype, which showed good repeatability between the samples for subsequent analysis (Fig. S1)
We found known key heading date genes to be differentially expressed, such as Vrn1-5 A, Vrn3-7B, Ppd-1D, and Wheat SOC1 (WSOC1) [3, 9, 14], but we identified new Differentially expressed gene (DEG) involved in the process

Summary

Introduction

Wheat is one of the most widely planted crops worldwide. The heading date is important for wheat environmental adaptability, as it controls flowering time and determines the yield component in terms of grain number per spike. The heading date or flowering time is an important adaptive trait for crop genetic breeding. Vrn-2 is the main flowering suppressor gene, and it is downregulated by vernalization and short-day treatment [1, 4, 7]. Ppd-1 accelerates flowering by upregulating Vrn expression under long-day conditions [12, 13]. Wheat SOC1 (WSOC1) is a key regulatory gene in the gibberellin regulatory pathway and affects the heading date in polyploid wheat [14]; upregulation of WSOC1 can accelerate spike development [15]

Objectives

Methods

Results

Discussion

Conclusion