Identification and Characterization of a Panicle Weight-Associated SCoT Marker in Foxtail Millet

Foxtail millet (Setaria italica L.) is a climate-resilient cereal crop increasingly recognized for its role in food security and sustainable agriculture. This study aimed to identify SCoT loci associated with main panicle weight (MPW), characterize their functional relevance, and validate their potential for selecting high-productivity genotypes. Seven Indonesian foxtail millet local genotypes were analyzed using 12 SCoT primers, yielding 109 loci. Association analysis identified seven loci associated with MPW. Among them, the SCoT-32 (700 bp) showed a significant association (R² = 0.6841, p = 0.0217), with the band occurring only in high-MPW genotypes and absent in low-MPW genotypes. Sequence characterization of the SCoT32_700 locus positioned it near an NB ARC domain gene on chromosome 7, suggesting a regulatory role in panicle development. Bioinformatics analyses classified the locus as a putative long non-coding RNA (lncRNA), supported by stable secondary structure predictions and RNAcentral homology to known Setaria italica lncRNAs. Validation in 20 F5 lines partially confirmed the association, with the 700 bp fragment explaining 17.2% of MPW variation. These findings highlight the potential of SCoT markers, particularly SCoT32_700, as functional markers for yield-related traits.