Transcriptome analyses reveal multiple differences associated with chloroplast development in the EMS-induced maize mutant

we have obtained a novel EMS-induced chlorophyll-deficient mutant from the progeny of Mt128 (MT), generating from the wild type (WT) maize inbred line DP128 (WT). Three types of leaf color were segregated from the self-fertilized progenies of MT, including green, narrow-white striped and albino and named by wtg, wts and wta respectively. We found that assay of Chl and carotenoid content was also significantly different between wts and WT, especially for wta and WT. In addition, leaf transcriptome sequencing of wtg, wts and wta and WT were also carried out. The DEGs were identified related to chloroplast components and development, Chl biosynthesis, and photosynthesis. By performing pair-wise comparisons of each group, the total number of 3,685 (1,181 up-regulated, 2,504 up-regulated), 2,624 (1,028 up-regulated, 1,596 up-regulated) and 6,693 (3,018 up-regulated, 3,675 up-regulated) genes were found as differentially regulated in wtg, wts and wta respectively, compared with WT. Of those, 75 co-modulated DEGs with great alteration were identified among comparison groups. More interestingly, most of the DEGs were found significantly involved in photosynthesis including PSI, PSII, cytochrome b6f complex and F-type ATPase. GO enrichment of DEGs revealed that most were involved in chloroplast development, chlorophyll biosynthesis, or photosynthesis. KEGG enrichment analysis indicated that the five significantly enriched pathways for co-modulated DEGs were as follows: Benzoxazinoid biosynthesis, Photosynthesis, Starch and sucrose metabolism, Phenylpropanoid biosynthesis and Photosynthesis-antenna proteins in all EMS-induced mutant genotypes. In addition, qPCR analysis validated that the expression level of genes encoding photosynthetic proteins was significantly decreased in all EMS-induced mutant genotypes. The results showed that EMS-induced would provide an approach to generating mutants that can be used in crop breeding research.