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Background  Kernel weight and size are important components of grain yield in cereals. Although some information is available concerning the map positions of quantitative trait loci (QTL) for kernel weight and size in maize, little is known about the molecular mechanisms of these QTLs.  qGW4.05  is a major QTL that is associated with kernel weight and size in maize. We combined linkage analysis and association mapping to fine-map and identify candidate gene(s) at  qGW4.05.Results  QTL  qGW4.05  was fine-mapped to a 279.6-kb interval in a segregating population derived from a cross of Huangzaosi with LV28. By combining the results of regional association mapping and linkage analysis, we identified GRMZM2G039934 as a candidate gene responsible for  qGW4.05 . Candidate gene-based association mapping was conducted using a panel of 184 inbred lines with variable kernel weights and kernel sizes. Six polymorphic sites in the gene GRMZM2G039934 were significantly associated with kernel weight and kernel size.    Conclusion  The results of linkage analysis and association mapping revealed that GRMZM2G039934 is the most likely candidate gene for  qGW4.05.  These results will improve our understanding of the genetic architecture and molecular mechanisms underlying kernel development in maize.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-016-0768-6) contains supplementary material, which is available to authorized users.

Fine-mapping of qGW4.05, a major QTL for kernel weight and size in maize