SiFEA4 encoding the bZIP transcription factor regulates panicle architecture in foxtail millet (Setaria italica)

<title>Abstract</title> <p>Panicle architecture was a key factor determining the crop yield. Panicle developed from the inflorescence meristem (IM), whose size and activity influenced the final morphological structure of the panicle. In this study, a foxtail millet landrace WY159 showing the phenotype of panicle apex branching was identified, which might be caused by abnormal differentiation of IM. Through map-based cloning, the candidate gene Seita.4G118000 (designated SiFEA4) encoding a bZIP transcription factor was isolated. Compared with the variety Yugu1 with normal panicle development, there was a 2649 bp deletion in the promoter region of SiFEA4 in WY159, which leaded to a significant downregulation of its expression. Furthermore, using the CRISPR/Cas9 gene editing technology, two homozygous SiFEA4 knockout mutants were obtained. Compared with the wild-type Ci846, the SiFEA4 knockout mutant showed an enlarged, flattened and then centrally depressed IM, ultimately resulting in the panicle apex branching phenotype. Meanwhile, the SiFEA4 gene knockout mutant also exhibited the decreased plant height, increased number of panicle primary branches, and slender panicle primary branches. In addition, RNA-seq analysis revealed that SiFEA4 regulated panicle development likely through the plant hormone signaling pathway. By integrating DAP-seq and RNA-seq analyses, 89 potential direct downstream target genes of SiFEA4 were identified, including SiERF109, SiCDF1, SiPL3, and SiAGL61, which are related to inflorescence development. In summary, this study revealed the important role of SiFEA4 in regulating panicle architecture, providing a new insight into the genetic regulatory mechanism of inflorescence development in foxtail millet.</p>