RNA-Seq analysis of gene expression for floral development in crested wheatgrass (Agropyron cristatum L.)

Abstract

Crested wheatgrass [Agropyron cristatum L. (Gaertn.)] is widely used for early spring grazing in western Canada and the development of late maturing cultivars which maintain forage quality for a longer period is desired. However, it is difficult to manipulate the timing of floral transition, as little is known about molecular mechanism of plant maturity in this species. In this study, RNA-Seq and differential gene expression analysis were performed to investigate gene expression for floral initiation and development in crested wheatgrass. Three cDNA libraries were generated and sequenced to represent three successive growth stages by sampling leaves at the stem elongation stage, spikes at boot and anthesis stages. The sequencing generated 25,568,846; 25,144,688 and 25,714,194 qualified Illumina reads for the three successive stages, respectively. De novo assembly of all the reads generated 311,671 transcripts with a mean length of 487 bp, and 152,849 genes with an average sequence length of 669 bp. A total of 48,574 (31.8%) and 105,222 (68.8%) genes were annotated in the Swiss-Prot and NCBI non-redundant (nr) protein databases, respectively. Based on the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway database, 9,723 annotated sequences were mapped onto 298 pathways, including plant circadian clock pathway. Specifically, 113 flowering time-associated genes, 123 MADS-box genes and 22 CONSTANS-LIKE (COL) genes were identified. A COL homolog DN52048-c0-g4 which was clustered with the flowering time genes AtCO and OsHd1 in Arabidopsis (Arabidopsis thaliana L.) and rice (Oryza sativa L.), respectively, showed specific expression in leaves and could be a CONSTANS (CO) candidate gene. Taken together, this study has generated a new set of genomic resources for identifying and characterizing genes and pathways involved in floral transition and development in crested wheatgrass. These findings are significant for further understanding of the molecular basis for late maturity in this grass species.

RNA-Seq Analysis of Plant Maturity in Crested Wheatgrass (Agropyron cristatum L.)

“…The CO homologous gene DN69810-c0-g1 and FT homologous genes DN67303-c0-g12 and DN74350-c1-g11 showed specific expression at the VS stage. This is consistent with our previous report that CO and FT homologs showed specific expression in the leaves of crested wheatgrass for promoting flowering [ 28 ]. CO is expressed in the vasculature of A. thaliana leaves which can activate FT expression in flowering [ 40 ].…”

“…The research outputs presented here helped to confirm the effectiveness of RNA-Seq and differential gene expression analysis in investigation of genes related to specific traits in species without a reference genome [ 28 ]. These technologies have made the informative genomic investigation of a complex trait such as plant maturity in a non-model, polyploidy plant practically possible.…”

“…We initiated a research project in 2014 using the RNA-Seq technique to profile the transcriptome of flowering, analyze gene expressions for floral initiation and development with the aim to identify differentially expressed genes (DEGs) associated with late maturity in crested wheatgrass. Our research so far has generated a set of genomic resources for studying genes and pathways involved in floral transition and development, and has revealed the conserved photoperiod-circadian clock-CO-FT regulatory circuit for flowering initiation in crested wheatgrass [ 28 ]. In this communication, we will specifically report the research findings on differentially expressed genes associated with late maturity from an RNA-Seq analysis of plant maturity in early and late maturing lines.…”

Molecular Characterization and Expression Profile of PaCOL1, a CONSTANS-like Gene in Phalaenopsis Orchid

“…For annotated genes (n = 234) involved in the developmental process, we found 48 (3% in upregulated dataset) corresponding to the flower-development-associated process ( Figure 4D). In addition, we found 78 upregulated genes including MYBs, MADS-box proteins, bZIPs, ATPases, helicases, ubiquitination enzymes (UEs), and zinc-finger proteins as putative flowering-regulation candidate genes [47][48][49][50]. Thus, PaCOL1 may affect transcript levels of flowering-related Arabidopsis genes under SD conditions.…”

Genotyping-by-Sequencing Enhances Genetic Diversity Analysis of Crested Wheatgrass [Agropyron cristatum (L.) Gaertn.]

“…Development of high forage-quality, late-maturing CWG cultivars is limited by the relatively long varietal development process, few studies to assess genetic variability of the germplasm, and lack of an effective marker system for marker-assisted and/or genomic selection/breeding. Recent RNA-seq studies in CWG have identified flowering time related genes and flowering related differentially expressed genes [ 28 , 29 ]. This emphasizes the need for genetic diversity studies of CWG for the management and utilization of proper genetic resources in a breeding program as exogamous perennial forage species are often morphologically comparable, though they are genetically highly heterogeneous and heterozygous [ 30 , 31 ].…”