A Natural Promoter-Variant Transcription Factor OsFC1 Integrates Phytohormone Signaling with Nitrate Transport via Affecting OsNPF6.3 Transcription to Regulate Rice Tillering

Abstract Tillering is a key determinant of rice yield and is regulated by both phytohormone signaling and nitrogen availability. However, how strigolactone-related pathways interface with nitrate-associated processes during tillering remains unclear. Here, we show that the TCP transcription factor OsFC1, a component of strigolactone- and brassinosteroid-associated pathways, exhibits natural promoter haplotypes that are associated with tillering-related variation. OsFC1 overexpression ( OsFC1 -OE) reduced the transcript abundance of the nitrate transporter gene OsNPF6.3 , whereas OsFC1 knockdown ( OsFC1 -Ri) increased OsNPF6.3 expression. OsFC1 bound to the promoter region of OsNPF6.3 that harbours a TCP-binding motif (GTGGGCCC), and this binding correlated with reduced OsNPF6.3 transcript abundance. Overexpression of OsNPF6.3 in OsFC1 -OE plants restored axillary bud elongation and increased tiller number, while knockout of OsNPF6.3 in OsFC1 -Ri plants suppressed bud outgrowth and reduced tillering. Together, our findings reveal that OsFC1 acts as a critical molecular link integrating phytohormone signaling and nitrate transport to coordinate rice tillering via affecting OsNPF6.3 transcription.