Deletion of the gene encoding the magnesium chelatase I subunit resulted in a novel wheat leaf colour mutant

Leaf colour mutants are ideal germplasm resources for investigating the mechanisms of chlorophyll (Chl) synthesis, chloroplast development and photosynthesis. In this study, we obtained a yellow-leaf mutant, designated SN288-2. The variant presented a yellow-leaf phenotype and halted the development of chloroplasts at the seedling stage, with reduced accumulation of Chl. The yellow-leaf phenotype reverted to the normal phenotype in the wheat revival stage. In addition, the ratio of the crucial Chl precursors protoporphyrin IX (Proto IX) and Mg-protoporphyrin IX (Mg-Proto IX) was relatively high in yellow leaves. Bulked segregant analysis sequencing (BSA-Seq) revealed that the aberrant phenotype was controlled by two recessive genes located on chromosomes 7A and 7D, designated Y1-7A and Y2-7D, respectively. Subsequent research focused on Y1-7A. We identified TraesCS7A03G1163900 as a viable candidate for Y1-7A, encoding a major subunit of Mg-chelatase that is essential for Chl synthesis. Whole-genome resequencing and Sanger sequencing revealed a 5.3 kb deletion on the long arm of chromosome 7A in SN388-2 that encompasses the entire Y1-7A sequence. Quantitative real-time PCR (qRT-PCR) revealed that the Y1-7A gene was predominantly expressed in green tissues and that the encoded protein was localized within the chloroplast. Moreover, weighted gene coexpression network analysis (WGCNA) revealed a gene module associated with leaf development and Chl content restoration. Consequently, these results provide a new theory regarding the regulation of Chl synthesis and chloroplast development. Overall, the loss of Y1-7A impaired the function of Mg-chelatase and blocked the conversion of Proto IX to Mg-Proto IX.