Fine mapping of LOW TILLER 1, a gene controlling tillering and panicle branching in rice

Tillering and panicle branching are important agronomic traits that affect rice grain yield. In this study, we characterized the low tiller 1 (lt1) mutant, which was isolated from an ethyl methanesulfonate-treated population of the indica cultivar Shuhui 527. The lt1 mutant had fewer tillers, thicker culms, fewer panicle branches, abnormal spikelets and larger grains. The transcript levels of cell proliferation and expansion-associated genes were altered in the lt1 plant, implying that LT1 affected grain size by regulating cell proliferation and expansion. Genetic analysis showed that the lt1 mutant phenotype was a single, recessive mutation. Using SSR and SNP markers, the LT1 gene was narrowed to a 63 kb distance between the markers ID6 and S12 on the chromosome 6. DNA sequencing revealed no mutations in this region. Despite this, two candidate genes, LOC_Os06g40780/MOC1 and LOC_Os06g40840, exhibited lower expression levels in both tiller buds and young panicles in lt1 compared to wild type. Thus, LOC_Os06g40780/MOC1 or LOC_Os06g40840 may be responsible for the lt1 mutant phenotypes, but more work will be needed for the cloning and functional analysis of LT1. This work lays the foundation for elucidation of the molecular mechanism for tillering and panicle branching, and provides new opportunities for improving rice grain yield.