Gene Mapping, Genome-Wide Transcriptome Analysis, and WGCNA Reveals the Molecular Mechanism for Triggering Programmed Cell Death in Rice Mutant pir1

Abstract

Programmed cell death (PCD) is involved in plant growth and development and in resistance to biotic and abiotic stress. To understand the molecular mechanism that triggers PCD, phenotypic and physiological analysis was conducted using the first three leaves of mutant rice PCD-induced-resistance 1(pir1) and its wild-type ZJ22. The 2nd and 3rd leaves of pir1 had a lesion mimic phenotype, which was shown to be an expression of PCD induced by H2O2-accumulation. The PIR1 gene was mapped in a 498 kb-interval between the molecular markers RM3321 and RM3616 on chromosome 5, and further analysis suggested that the PCD phenotype of pir1 is controlled by a novel gene for rice PCD. By comparing the mutant with wild type rice, 1679, 6019, and 4500 differentially expressed genes (DEGs) were identified in the three leaf positions, respectively. KEGG analysis revealed that DEGs were most highly enriched in phenylpropanoid biosynthesis, alpha-linolenic acid metabolism, and brassinosteroid biosynthesis. In addition, conjoint analysis of transcriptome data by weighted gene co-expression network analysis (WGCNA) showed that the turquoise module of the 18 identified modules may be related to PCD. There are close interactions or indirect cross-regulations between the differential genes that are significantly enriched in the phenylpropanoid biosynthesis pathway and the hormone biosynthesis pathway in this module, which indicates that these genes may respond to and trigger PCD.

Programmed Cell Death May Be Involved in the Seedless Phenotype Formation of Oil Palm

“…This suggests that PCD mechanism plays a vital role in inducing seedless fruits. In rice, up-regulation of lignin biosynthesis genes, including 4CL, resulted in an increased content of lignin and led to activate PCD ( Chen et al, 2020 ). It was also reported that overexpression of OsAAE3 , which encodes a 4CL like protein, can lead to PCD, which contributed to the repressing of floral development and decreased fertility rate of the anther ( Liu et al, 2017a ).…”

Altered Expression of OsAAP3 Influences Rice Lesion Mimic and Leaf Senescence by Regulating Arginine Transport and Nitric Oxide Pathway

“…Besides, bursts of production of NO and ROS usually occur very early in the defense response and are often important for the initiation of hypersensitive response, together with lipid peroxidation, transcriptional reprogramming, ion fluxes and cell wall fortification [ 31 ]. We suggest that our findings about OsAAP3 in cell death and lesion mimic in rice leaves are linked to the hypersensitive response, like some mutants display hypersensitive response-like lesion in the absence of pathogens attacks [ 11 , 32 ].…”

“…It has been reported that overexpression of lignin synthesis enzyme gene OsAAE3 leads to an increase in H 2 O 2 content, which triggers PCD induced by ROS [ 36 ]. Recently, a mutant pir1 showed that the spontaneous lesions mimic phenotype is caused by PCD in the mutant leaves [ 32 ]. And KEGG analysis revealed that DEGs were most highly enriched in phenylpropanoid biosynthesis [ 32 ].…”

“…Recently, a mutant pir1 showed that the spontaneous lesions mimic phenotype is caused by PCD in the mutant leaves [ 32 ]. And KEGG analysis revealed that DEGs were most highly enriched in phenylpropanoid biosynthesis [ 32 ]. In this study, the expression levels in the flavonoids and phenolics pathway, which closely related to lignin metabolism, were changed in OsAAP3 OE and Ri lines compared with WT ( Figure S4 ).…”

Identification of Potential Shade Response Regulators in Endangered Species Magnolia Sinostellata

“…Weighted gene co-expression network analysis (WGCNA) is an effective tool to identify co-expressed modules and hub genes 27 , which has been applied in various plants including Camellia sinensis 28 , hot peppers 29 , rice 30 and wheat 27 to explore various abiotic stresses response molecular mechanisms. It is a signi cant way to understand gene function and association from the trancriptome-wide [31][32][33] . However, there is no previous report of using WGCNA to identify shade response hub genes in M. sinostellata.…”