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

SummaryLeaf 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.