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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.