Genetic Analysis and Fine Mapping of Gene ygl98 for Yellow-Green Leaf of Rice

A yellow-green leaf mutant ygl98 was isolated by ethyl methane sulfonate (EMS) mutagenesis. The whole plant exhibited yellow-green character throughout the growing period. The contents of chlorophyll and carotenoid decreased by 45.3% and 45.6%, respectively, compared with its wild-type parent 10079. At maturity stage, the number of productive panicles per plant, seed-setting rate, and plant height of the mutant were reduced by 14.4%, 10.7%, and 7.4%, respectively. Under electron microscope, the chloroplasts in the ygl98 mutant were out-of-shape. A lot of cystic structures and poor thylakoids were observed in the chloroplasts of the ygl98 mutant, and grana stacks appeared to be less dense compared to those of the wild type. Genetic analysis showed that the yellow-green leaf character of the ygl98 mutant was controlled by one pair of recessive nuclear genes. Genetic mapping of the mutant gene was conducted using 771 yellow-green leaf individuals from the F₂ mapping population of ygl98/Zhefu 802. Finally, the mutant gene was mapped between insert/deletion (InDel) markers I3 and I4 on the long arm of chromosome 3 with the genetic distances of 0.07 cM and 0.19 cM, respectively. The physical distance between the 2 markers was 44.2 kb harboring 8 predicted genes annotated. Sequencing analysis of these candidate genes between the mutant and its wild type revealed that the single base change (G1 522A) of the gene for magnesium-chelatase ChlD subunit resulted in a missense mutation (A508T) in the encoded product. The same gene mutation caused by OsChlD (Chlorina-1) was documented previously. The Chlorina-1 mutant displays a severe yellowish-green leaf phenotype only at seedling stage, and the abnormal leaf color is first observed on the leaves of 2- to 3-week-old seedlings, while the ygl98 mutant exhibits yellow-green character throughout the growing period. The different phenotypes of the 2 mutants may be caused by the different mutational sites of OsChlD genomic sequence.