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In maize, starch mutants have facilitated characterization of key genes involved in endosperm starch biosynthesis such as  large subunit of AGPase Shrunken2  ( Sh2 ) and  isoamylase type DBE Sugary1  ( Su1 ). While many starch biosynthesis enzymes have been characterized, the mechanisms of certain genes (including  Sugary enhancer1 ) are yet undefined, and very little is understood about the regulation of starch biosynthesis. As a model, we utilize commercially important sweet corn mutations,  sh2  and  su1 , to genetically perturb starch production in the endosperm. To characterize the transcriptomic response to starch mutations and identify potential regulators of this pathway, differential expression and coexpression network analysis was performed on near-isogenic lines (NILs) (wildtype,  sh2 , and  su1 ) in six genetic backgrounds. Lines were grown in field conditions and kernels were sampled in consecutive developmental stages (blister stage at 14 days after pollination (DAP), milk stage at 21 DAP, and dent stage at 28 DAP). Kernels were dissected to separate embryo and pericarp from the endosperm tissue and 3′ RNA-seq libraries were prepared. Mutation of the  Su1  gene led to minimal changes in the endosperm transcriptome. Responses to loss of  sh2  function include increased expression of sugar (SWEET) transporters and of genes for ABA signaling. Key regulators of starch biosynthesis and grain filling were identified. Notably, this includes Class II trehalose 6-phosphate synthases,  Hexokinase1 , and  Apetala2  transcription factor-like (AP2/ERF) transcription factors. Additionally, our results provide insight into the mechanism of  Sugary enhancer1 , suggesting a potential role in regulating GA signaling via GRAS transcription factor  Scarecrow-like1 .

Genetic Perturbation of the Starch Biosynthesis in Maize Endosperm Reveals Sugar-Responsive Gene Networks