Objective To analyze the phenotypic characteristic of maize shrunk endosperm mutant and fine mapping of related genes, and lay a foundation for further understanding molecular mechanism of maize kernel development.

Method The spontaneous shrunk endosperm mutant shank2021(sh2021) was isolated from maize inbred line B73. Morphological and cytological characteristics were observed. A segregating population was developed, and the bulked segregant analysis (BSA) was used for preliminary gene mapping. The recombinant plants were screened for further narrowing the mapping interval. Finally the candidate genes controlling grain defect traits were speculated by transcriptome sequencing combined with gene function annotation analysis.

Result Compared with wild type, sh2021 displayed sunken and shrunken kernels, darker color, irregular grain arrangement, and lower 100-grain weight. The scanning electron microscope observation revealed that sh2021 had smaller endosperm cells and starch granules, and the starch granules were varied in size. The genetic analysis results indicated that sh2021 was caused by a single recessive gene mutation. The BSA indicated that the target gene was located on a 13.25 Mb fragment at the end of chromosome 3. By further expanding the segregating population and screening recombinant plants, the target gene was narrowed down to an interval of 529.60 kb between markers ID5 and ID9. Transcriptome sequencing and gene annotation of sh2021 and wild type indicated that Zm00001d044119, Zm00001d044120, Zm00001d044122, Zm00001d044129, and Zm00001d044142 mighted be candidate genes controlling maize kernel development.

Conclusion The identification of sh2021 provides abundant experimental materials for the study of kernel development, and lays a foundation for further map-based cloning and functional analysis of sh2021.