| Summary: | Starch, the main form of stored energy in plants, plays an important role in maize (<i>Zea mays</i> L.) kernel development. The <i>Shrunken-2</i> (<i>Sh2</i>) gene encodes the large subunit of the rate-limiting starch biosynthetic enzyme ADP-glucose pyrophosphorylase (AGPase). The <i>sh2</i> mutant exhibits impaired AGPase activity, resulting in the partial or complete loss of starch synthesis. Here, we investigated the transcriptional regulatory framework of <i>sh2</i> through transcriptome and co-expression network analysis using an F<sub>2</sub> population derived from the maize reference line B73 and sweet corn inbred line HZ508. We identified 5175 differentially expressed genes (DEGs), including 2878 upregulated and 2297 downregulated genes in <i>sh2</i> mutant lines. DEGs are associated with various biological processes including nutrient reservoir activity, transferase activity, catalytic activity, water deprivation and glycogen metabolism. At the genetic level, 2465 DEGs, including 357 transcription factors, were involved in transcription. In addition, the maize floury and opaque mutant genes <i>fl1</i>, <i>ndk2,</i> <i>o7</i> and <i>o2</i>, which regulate the biosynthesis of 22KD zein, were co-expressed with the differential expressed transcription factor genes, thus suggesting that zein content might be a key regulator coordinating the expression of genes determining starch accumulation in maize endosperm.
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