Fine mapping and candidate gene analysis of leaf tip premature senescence and Dwarf Mutant dls-1 in Rice

Abstract

Premature leaf senescence negatively affects rice yield and quality. Identifying premature senescence mutants and examining their gene functions are important for the genetic improvement of crops. In this study, a leaf senescence mutant dls-1 was obtained from japonica Yundao by ethyl methane sulfonate mutagenesis, which showed the phenotypes of premature leaf senescence, reduced plant height and decreased yield-associated traits including panicle length, seed setting rate, and 1000-grain weight. Biochemical analysis revealed the accumulation of reactive oxygen species in dls-1 leading to increased apoptosis rates, stomata length extension, higher water loss, and a decline in leaf silicification. Transcriptomic data showed that pathogen resistance-related genes were down-regulated in dls-1, causing increased sensitivity to bacterial-induced blight. Genetic analysis indicated that the mutant trait of dls-1 was controlled by a single recessive nuclear gene, and the gene was fine-mapped to a 159 kb region on rice chromosome 1 using map-based cloning strategy. A total of 23 open reading frames were found in the interval, and no similar phenotypic genes have been reported. However, all candidate coding genes and promoter regions were sequenced, and no mutation sites were found. RNA-seq analysis and qRT-PCR showed that the candidate gene LOC_Os01g71670, encodes a rice endo-1,3-β-glucanase, showed significantly different expression levels in dls-1 compared to the wild-type. LOC_Os01g71670 is highly homologous with GII in barley, and Gns4 and glu1 in rice, which participates in the hormone response pathway affecting plant growth and development, and also involve in the regulation of PR2 expression. Taken together with the phenotypes of dls-1, we conclude that LOC_Os01g71670 may be the candidate gene, causing the premature senescence of the leaf tip and loss of pathogen resistance.