Phytohormones and Transcriptome Analyses Revealed the Dynamics Involved in Spikelet Abortion and Inflorescence Development in Rice

Abstract

Panicle degeneration, sometimes known as abortion, causes heavy losses in grain yield. However, the mechanism of naturally occurring panicle abortion is still elusive. In a previous study, we characterized a mutant, apical panicle abortion1331 (apa1331), exhibiting abortion in apical spikelets starting from the 6 cm stage of panicle development. In this study, we have quantified the five phytohormones, gibberellins (GA), auxins (IAA), abscisic acid (ABA), cytokinins (CTK), and brassinosteroids (BR), in the lower, middle, and upper parts of apa1331 and compared these with those exhibited in its wild type (WT). In apa331, the lower and middle parts of the panicle showed contrasting concentrations of all studied phytohormones, but highly significant changes in IAA and ABA, compared to the upper part of the panicle. A comparative transcriptome of apa1331 and WT apical spikelets was performed to explore genes causing the physiological basis of spikelet abortion. The differential expression analysis revealed a significant downregulation and upregulation of 1587 and 978 genes, respectively. Hierarchical clustering of differentially expressed genes (DEGs) revealed the correlation of gene ontology (GO) terms associated with antioxidant activity, peroxidase activity, and oxidoreductase activity. KEGG pathway analysis using parametric gene set enrichment analysis (PGSEA) revealed the downregulation of the biological processes, including cell wall polysaccharides and fatty acids derivatives, in apa1331 compared to its WT. Based on fold change (FC) value and high variation in expression during late inflorescence, early inflorescence, and antherdevelopment, we predicted a list of novel genes, which presumably can be the potential targets of inflorescence development. Our study not only provides novel insights into the role of the physiological dynamics involved in panicle abortion, but also highlights the potential targets involved in reproductive development.

Full-length transcriptome and RNA-Seq analyses reveal the resistance mechanism of sesame in response to Corynespora cassiicola

“…The aims of this study were to gain insights into the differences in the molecular mechanisms between resistant and susceptible varieties to cope with C. cassiicola infection and to identify potentially excellent disease-resistance genes in the resistant variety. It has been reported that starch and soluble sugars [ 55 ], phytohormones [ 56 ], and photosynthetic efficiency [ 57 , 58 ] can be used as important reference indicators of plant phenotypic change. In this study, the changes of leaf spot expansion at different time points were recorded as phenotypic observation.…”

Comprehensive transcriptome analysis reveals heat-responsive genes in flowering Chinese cabbage (Brassica campestris L. ssp. chinensis) using RNA sequencing

“…Another study found that genes involved in protein protection, biotic stress responses, oxidative stress, programmed cell death, and metabolism were differentially expressed during heat stress (Kotak et al, 2007). Only limited transcriptome data are available for flowering Chinese cabbage under heat stress relative to Chinese cabbage, maize, rice, and Arabidopsis (Song et al, 2014a;Chen et al, 2017;Fan et al, 2017;Huang et al, 2017;Ali et al, 2022).…”

“…Using RNA-seq, researchers can identify the expressed genes, particularly those with low abundance. To date, microarrays and RNA-Seq projects have been undertaken in many species, including rice, Chinese cabbage, maize, cotton, Arabidopsis, and vegetables, to detect genes responsive to heat and cold stress (Grover et al, 2013;Nakashima et al, 2014;Ikram et al, 2020;Song et al, 2021;Ali et al, 2022). For example, in Arabidopsis, nearly 30% of DEGs associated with abiotic stresses were identified, and 2,409 genes were involved in salt, cold, and drought stresses (Kreps et al, 2002).…”