Transcriptome sequencing analysis and WGCNA reveal the internal molecular mechanism that triggers programmed cell death in rice mutant zj-lm

A spontaneous lesion mimic mutant named ZheJing-lesion mimic ( zj-lm ) was characterized from the mutant library of Japonica rice ( Oryza sativa ) cultivar Zhejing22 (ZJ22), while ZheJing-lesion mimic-recover ( zj-lm-r ) was a revertant of zj-lm reinduced by ethyl methane sulfonate. Programmed cell death (PCD) is a ubiquitous process in the development of organisms which can resist biotic and abiotic stresses by taking the way of active death controlled by its own genes. To further understand the trigger mechanism of PCD, the three materials under study were comprehensively analyzed. Phenotypic and physiological analysis revealed that zj-lm and zj-lm-r showed significant differences from ZJ22 in plant height, dry weight, fresh weight, 1000-grain weight and other important agronomic traits. It was worth noting that the lesion mimic phenotype appeared in the third leaf from top of zj-lm . Histochemical staining experiment verified that the occurrence of zj-lm lesion was accompanied by a large number of cell death and excessive accumulation of reactive oxygen species. Transcriptome analysis indicated that there were significant differences in gene expression between the leaves with and without lesion mimic phenotype. In addition, based on the Weighted Gene Co-Expression Network Analysis of transcriptome data, the lightsteelblue1 module among fifteen identified modules was found to be closely related to the triggering of PCD. The differentially expressed genes (DEGs) in this module are mainly involved in “endocytosis”, “biosynthesis of phenylalanine, tyrosine and tryptophan” and “glutathione metabolism”. There were also close interactions and cross regulation between these DEGs. Our study confirmed that these genes might play an important role in the triggering of PCD in rice, and a hypothetical working model was also proposed for rice PCD.