A large deletion conferring pale green leaves of maize

BACKGROUND: The structural basis of chloroplast and the regulation of chloroplast biogenesis remain largely unknown in maize. Gene mutations in these pathways have been linked to the abnormal leaf color phenotype observed in some mutants. Large scale structure variants (SVs) are crucial for genome evolution, but few validated SVs have been reported in maize and little is known about their functions though they are abundant in maize genomes. RESULTS: In this research, a spontaneous maize mutant, pale green leaf-shandong (pgl-sd), was studied. Genetic analysis showed that the phenotype of pale green leaf was controlled by a recessive Mendel factor mapped to a 156.8-kb interval on the chromosome 1 delineated by molecular markers gy546 and gy548. There were 7 annotated genes in this interval. Reverse transcription quantitative PCR analysis, SV prediction, and de novo assembly of pgl-sd genome revealed that a 137.8-kb deletion, which was verified by Sanger sequencing, might cause the pgl-sd phenotype. This deletion contained 5 annotated genes, three of which, including Zm00001eb031870, Zm00001eb031890 and Zm00001eb031900, were possibly related to the chloroplast development. Zm00001eb031870, encoding a Degradation of Periplasmic Proteins (Deg) homolog, and Zm00001eb031900, putatively encoding a plastid pyruvate dehydrogenase complex E1 component subunit beta (ptPDC-E1-β), might be the major causative genes for the pgl-sd mutant phenotype. Plastid Degs play roles in protecting the vital photosynthetic machinery and ptPDCs provide acetyl-CoA and NADH for fatty acid biosynthesis in plastids, which were different from functions of other isolated maize leaf color associated genes. The other two genes in the deletion were possibly associated with DNA repair and disease resistance, respectively. The pgl-sd mutation decreased contents of chlorophyll a, chlorophyll b, carotenoids by 37.2%, 22.1%, and 59.8%, respectively, and led to abnormal chloroplast. RNA-seq revealed that the transcription of several other genes involved in the structure and function of chloroplast was affected in the mutant. CONCLUSIONS: It was identified that a 137.8-kb deletion causes the pgl-sd phenotype. Three genes in this deletion were possibly related to the chloroplast development, which may play roles different from that of other isolated maize leaf color associated genes. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-023-04360-2.