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Identification of grain shape genes can facilitate breeding of rice cultivars with optimal grain shape and appearance quality. In this study, we selected two rice germplasms, namely Longliheinuo-dwarf (LH) and N643, with different grain shape, to construct a genetic population for quantitative trait locus (QTL) analysis. A major QTL (<i>qGS7</i>), controlling the ratio of grain length to grain width, was mapped on the chromosome 7 in a BC₁F₄ line. By high-resolution linkage analysis, <i>qGS7</i> was delimited to a 52.8 kb region including eight predicted genes. Through sequence alignment and real-time PCR expression analysis of these ORFs, ORF3 (LOC_Os07g42410) was selected as the candidate gene for further analysis. Single nucleotide polymorphisms (SNP) diversity analysis of ORF3 revealed that a single nucleotide deletion in the 7th exon resulted in a frameshift in parent LH and the parent in which a premature stop codon was identified. It was a rare mutation that caused grain shape difference. Real-time PCR analyses showed that the expression characteristics of ORF3 was in accordance with the development of spikelets. Of the 18 agronomic traits investigation in <i>qGS7</i> near isogenic lines (NILs) showed that <i>qGS7</i> not only changed grain shape but also affected plant height, panicle curvature, panicle length, the length of second leaf from the top, and chalkiness.