Morpho-physiological integrators, transcriptome and coexpression network analyses signify the novel molecular signatures associated with axillary bud in chrysanthemum

Abstract

Background: Axillary bud is an important agronomic and economic trait in cut chrysanthemum. Bud outgrowth is an intricate process controlled by complex molecular regulatory networks, physio-chemical integrators and environmental stimuli. Temperature is one of the key regulators of bud's fate. However, little is known about the temperature-mediated control of axillary bud at molecular levels in chrysanthemum. A comprehensive study was designed to study the bud outgrowth at normal and elevated temperature in cut chrysanthemum. Leaf morphology, histology, physiological parameters were studied to correlate the leaf activity with bud morphology, sucrose and hormonal regulation and the molecular controllers. Results: Temperature caused differential bud outgrowth along bud positions. Photosynthetic leaf area, physiological indicators and sucrose utilization were changed considerable due to high temperature. Comparative transcriptome analysis identified a significant proportion of bud position-specific genes.Weighted Gene Coexpression Network Analysis (WGCNA) showed that axillary bud control can be delineated by modules of coexpressed genes; especially, MEtan3, MEgreen2 and MEantiquewhite presented group of genes specific to bud length. A comparative analysis between different bud positions in two temperatures revealed the morphophysiological traits associated with specific modules. Moreover, the transcriptional regulatory networks were configured to identify key determinants of bud outgrowth. Cell division, organogenesis, accumulation of storage compounds and metabolic changes were prominent during the bud emergence.

Analyses of the photosynthetic characteristics, chloroplast ultrastructure, and transcriptome of apple (Malus domestica) grown under red and blue lights

“…The prepared sections were placed in xylene for 20 min, absolute ethanol for 20 min, and 75 % alcohol for 5 min, after which they were rinsed with water (i.e., dewaxing). The sections were then placed in Safranin-O staining solution for 2 h [ 53 ]. After washing off the excess dye, the sections were treated with 50 %, 70 %, and 80 % alcohol solutions for 5 s each.…”

Transcriptional Cascade in the Regulation of Flowering in the Bamboo Orchid Arundina graminifolia

“…Preferentially expressed/stage specific genes were mined using a stage specificity (SS) scoring algorithm. This algorithm compares the gene expression in a specific stage with its maximum expression in other stages [ 30 ]. The higher SS score of a gene in a particular stage signifies its expression at that stage.…”

Stage Specificity, the Dynamic Regulators and the Unique Orchid Arundina graminifolia

“…The stage specific DEGs were blasted into the Arabidopsis genome using Blast-2.10.0+ system and Arabidopsis locus IDs were selected at an Evalue of 1 × e −5 . The IDs were run in BINGO app using Cytoscape [53] to ascertain the clustering of co-expressed gene sets. Pathway enrichment of stage-specific gene sets was made using MapMan(v3.6.0RC1) (https://mapman.gabipd.org/mapman-version-3.6.0; accessed on 1 September 2021) with TAIR10 (best Arabidopsis homolog) as reference.…”

“…Stage-specific/preferentially expressed gene sets were identified using stage specificity (SS) scoring algorithm. This scoring algorithm identifies genes specific to each developmental stage or position by comparing the expressions of genes in a particular stage with their maximum values in other stages [53]. Higher SS score of genes in a specific stage provides the significant expression of those genes at that stage.…”

“…Higher SS score of genes in a specific stage provides the significant expression of those genes at that stage. The stage-specific genes sets were used to make heatmap through ggplot2 utility in R. Moreover, the gene sets were blasted to get Arabidopsis locus IDs to perform clustering analysis using "Bingo" application in Cytoscape [53].…”