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Background  Most agronomic traits in rice are complex and polygenic. The identification of quantitative trait loci (QTL) for grain length is an important objective of rice genetic research and breeding programs.    Results  Herein, we identified 99 QTL for grain length by GWAS based on approximately 10 million single nucleotide polymorphisms from 504 cultivated rice accessions ( Oryza sativa  L.), 13 of which were validated by four linkage populations and 92 were new loci for grain length. We scanned the Ho (observed heterozygosity per locus) index of coupled-parents of crosses mapping the same QTL, based on linkage and association mapping, and identified two new genes for grain length. We named this approach as Ho-LAMap. A simulation study of six known genes showed that Ho-LAMap could mine genes rapidly across a wide range of experimental variables using deep-sequencing data. We used Ho-LAMap to clone a new gene,  OsLG3 , as a positive regulator of grain length, which could improve rice yield without influencing grain quality. Sequencing of the promoter region in 283 rice accessions from a wide geographic range identified four haplotypes that seem to be associated with grain length. Further analysis showed that  OsLG3  alleles in the  indica  and  japonica  evolved independently from distinct ancestors and low nucleotide diversity of  OsLG3  in  indica  indicated artificial selection. Phylogenetic analysis showed that  OsLG3  might have much potential value for improvement of grain length in  japonica  breeding.    Conclusions  The results demonstrated that Ho-LAMap is a potential approach for gene discovery and  OsLG3  is a promising gene to be utilized in genomic assisted breeding for rice cultivar improvement.    Electronic supplementary material  The online version of this article (doi:10.1186/s12915-017-0365-7) contains supplementary material, which is available to authorized users.

OsLG3 contributing to rice grain length and yield was mined by Ho-LAMap