A Systematic Review of Thousand-Grain Weight Genes in Rice and Foxtail Millet: Toward Functional Markers for Yield Improvement

Foxtail millet (Setaria italica (L.) P. Beauv.) is a climate-resilient crop with high potential for cultivation in low-input agricultural systems. However, its genetic improvement lags behind major crops such as rice. The objectives of this study were to identify agronomic traits associated with grain yield and to determine candidate genes for thousand-grain weight (TGW) in foxtail millet using a systematic literature review (SLR) combined with sequence based analysis. Rice was included in the SLR due to its close synteny with foxtail millet and its extensive genetic studies. In accordance with PRISMA 2020 guidelines, 116 articles were selected from the Scopus and PubMed databases. The results showed that TGW has a strong positive correlation with rice grain yield. Eight candidate genes (GS3, GW5, TGW6, GW2, GS5, GW8, GS2, and GW5L) controlling grain size and grain weight were identified based on their recurrence across studies and subsequently used to identify homologs in foxtail millet. The sequence of a foxtail millet homolog of TGW6, SiTGW6 (Seita.1G350400), was further analyzed to find potential variants and co-inherited genes. Sequence analysis identified SNPs in the SiTGW6 region, including a variant at 40,392,218 bp (MAF 0.17; moderate effect) that warrants further investigation for SNP based marker development. Analysis within the linkage disequilibrium (LD)-decay region identified Seita.1G350500.1, which contains BRCT, HAD-like, and FCP1 domains involved in transcriptional regulation. This study identifies SiTGW6 as a potential genetic target, with both SNP-based and linkage-marker development serving as a foundation for gene-based functional markers and prospective precision breeding in foxtail millet.