Fine mapping and candidate gene analysis of a lesion mimic mutant spl-3t in rice

The lesion mimic mutant spl-3t was obtained by chemical mutagen EMS from Yun Rice. After three successive generations of planting, the phenotype was obvious, the characters were stable and consistent, and no isolation was found. The mutant had no obvious phenotype in seedlings, and grow slight rust brown necrotic lesions after 4–5 weeks. After the heading, the lesions gradually spread to the surrounding area and eventually formed irregular patches with the center withered and reddish brown. Necrotic plaques in mature stage are linked to sheets and cover entire leaves. Spl-3t accumulated significantly callose content in the leaves compared with the wild type of Cloud Rice. It was also found that spl-3t was sensitive to Xanthomonas oryzae pv.oyzae. At the same time, spl-3t also had reduced in plant height, seeded setting rate and rised in spike length.Genetic analysis showed that the spl-3t mutation was controlled by a single recessive nuclear gene. The spl-3t gene was located in the 109-kb region of chromosome 3 of rice by map-based cloning. There were 15 candidate genes in this region. No similar phenotype was reported at present.We sequenced the coding region and promoter region of all the candidate genes and found no mutation sites that were different from the wild type. By RNA-seq analysis and qRT-PCR verification, we found that the heat shock transcription factor ( LOC_Os03g06630 ) of the candidate gene was significantly different from the wild type in spl-3t , which was a defense response to heat stress. The central regulator, which plays an important role in high temperature response, can up-regulate the protective gene during heat treatment to obtain higher basic heat tolerance. Therefore, it is speculated that the epigenetic modification of the gene results in the generation of lesion mimic traits. This study provides new evidence and basis for the molecular mechanism of lesion formation.