Identification and Fine Mapping of qCD2, a Major QTL Governing Leaf Premature Senescence in Rice (Oryza sativa L.)

Chlorophyll content is a key determinant of photosynthetic efficiency and grain yield in rice (Oryza sativa L.), while premature chlorophyll degradation during the reproductive stage can markedly reduce crop productivity. However, the genetic basis underlying chlorophyll degradation and its environmental responsiveness remains incompletely understood. In this study, an F2 population derived from a cross between the japonica cultivar Shennong0530-9 and the indica cultivar Habataki was used to identify quantitative trait loci (QTLs) associated with chlorophyll content at different developmental stages. A total of 22 QTLs were detected; among these, qCD2 consistently showed a major and stable effect on chlorophyll degradation after heading. Fine mapping using residual heterozygous lines delimited qCD2 to a 54.0 kb genomic interval on the short arm of chromosome 2 containing nine predicted genes. Near-isogenic lines (NIL-qCD2) carrying the qCD2 allele exhibited accelerated chlorophyll loss after heading, accompanied by disrupted chloroplast ultrastructure, reduced photosynthetic capacity, and significant decreases in grain yield and grain quality compared with the recurrent parent. Furthermore, the chlorophyll-deficient phenotype became progressively more severe under elevated temperature conditions, indicating that the phenotypic effect associated with qCD2 is temperature sensitive. Consistent with these physiological changes, the expression patterns of genes involved in chloroplast development, photosynthesis, and leaf senescence were significantly altered in NIL-qCD2. Collectively, these results identify qCD2 as a stable QTL associated with chlorophyll degradation during the reproductive stage and provide a foundation for future identification of the causal gene, providing valuable genetic resources for the molecular breeding of rice with improved photosynthetic efficiency, grain yield, and grain quality.