By constructing nearly isogenic lines (NILs) that differ only at a single quantitative trait locus (QTL), we fine mapped the yield-improving QTL qGY2-1 to a 102.9-kb region on rice chromosome 2. Comparison analysis of the genomic sequences in the mapped QTL region between the donor (Dongxiang wild rice, Oryza rufipogon Griff.) and recurrent (Guichao2, Oryza sativa ssp. indica) parents used for the development of NILs identified the haplotypes of a leucine-rich-repeat receptor kinase (LRK) gene cluster, which showed extensive allelic variation. We found that the LRK gene cluster consists of 7 or 8 LRK gene copies arranged in a tandem fashion throughout orthologous genomic region in Guichao2 and Dongxiang wild rice, respectively, thus formed two haplotypes. The sequences between genes in the cluster had a very high rate of divergence. More important, the genes themselves also differed between two haplotypes: only 92% identity was observed for one allele, and another allele was found to have completely lost its allelic counterpart in Guichao2. The other 6 shared genes all showed >98% identity, and 4 of these exhibited obvious regulatory variation. The same haplotype segments also differed in length (43.9-kb in Guichao2 vs. 52.6-kb in Dongxiang wild rice). Such extensive sequence variation was also observed between orthologous regions of indica (cv. 93-11) and japonica (cv. Nipponbare) subspecies of Oryza sativa. Different rates of sequence divergence within the cluster have resulted in haplotype variability in 13 rice accessions, thus providing an unprecedented opportunity for analyzing genomic evolution and for investigating the origin of cultivated rice. Furthermore, we also performed transgenic research with the candidate genes for QTL.We also detected allelic expression variation in this gene cluster, in which some genes gave unequal expression of alleles in hybrids, ranged from unequal expression of the two alleles simultaneously to expression of a single allele regardless of the parent-of-origin, and both dominance complementation and some overdominance of allelic expression within the cluster occurred. The fact that allele-specific transcript accumulation of LRK6 in hybrids suggested that the differences in gene expression may be result from ds-regulatory variation. These allelic variations in structure and expression suggest that the LRK gene cluster identified in our study should be a particularly good candidate for the source of the yield QTL, thus help us understand the molecular basis of QTL and heterosis. We also identified 278 OsLRK genes in rice subspecies japonica (cv. Nipponbare) using a genome-wide search strategy, and then investigated their distribution on chromosomes. Comparison between indica and japonica revealed sequences variation in regulatory regions and coding regions of 102 and 64 OsLRKs genes,respectively. Allelic variation of these OsLRK genes provided a clue to understand the differentiation of two rice subspecies.