A single nucleotide mutation of the OsPORA gene revealed by MutMap analysis of a rice yellow leaf mutant line

Chlorophylls are the most important pigments that harvest light energy in photosynthesis and elucidation of genes involved in chlorophyll metabolism is essential for developing rice varieties with increased photosynthesis efficiency and yield. A yellow mutant rice line was selected from an Ac/Ds insertion mutant population and named ylm. The phenotype of F₁ and F₂ plants derived from a cross between ylm and Dongjin and between ylm and Nipponbare indicated that a single recessive gene is responsible for the mutant phenotype. The resequencing of the ylm mutant line and Dongjin (wild type) revealed 118,424 homozygous single nucleotide polymorphisms (SNPs) between ylm line and Dongjin. MutMap analysis was performed by sequencing a DNA pool made from 44 mutant type plants in ylm/Dongjin F₂ population, and it was found that the causative gene, which was named yl, was located in 32–36 Mbp region on chromosome 4. In this region, we found a non-synonymous SNP in the Os04g0678700 which was reported as OsPORA encoding a NADPH:protochlorophyllide oxidoreductase involved in the chlorophyll biosynthesis. This SNP was regarded as the causative SNP for the ylm phenotype. We produced complementation transgenic lines by introducing wild type OsPORA from Dongjin to ylm. The two independent OsPORA gene complementation transgenic lines recovered wild type phenotype which proved that the SNP in this gene is responsible for the mutant phenotype. These results will be helpful in expanding our knowledge about genes involved in rice chlorophyll metabolism and developing rice varieties with increased photosynthesis efficiency and yield.