Genetic Diversity of Agronomic Traits and Identification of Genes Regulating Thousand‐Grain Weight in Foxtail Millet ( Setaria italica ) Germplasm Resources

Abstract

Thousand‐grain weight (TGW) is a critical determinant of grain yield in foxtail millet. To elucidate the molecular regulatory network governing this trait, we systematically evaluated the main agronomic traits and genetic diversity of 40 core germplasm accessions, aiming to identify elite genetic resources. Subsequently, transcriptomic differential expression analysis, weighted gene co‐expression network analysis (WGCNA), pathway enrichment analysis, and inter‐pathway interaction network analysis were performed on materials with contrasting TGW (high vs. low), with the goal of pinpointing key candidate genes involved in TGW regulation. The phenotypic analysis results indicated that the Shannon‐Wiener diversity index (H′) of eight agronomic traits ranged from 1.82 to 2.04, and the coefficients of variation (CV) ranged from 21.83% to 68.14%. Genetic parameter analysis indicated that TGW exhibited the highest broad‐sense heritability (87.10%). The GE variance components were significant for all traits ( p  < 0.05). Meanwhile, for TGW, plant height (PH), and panicle length (PL), these components were significantly smaller than the genotypic variances, except for SW and PD. Cluster analysis classified the 40 germplasm accessions into four groups. Group III exhibited superior overall performance, particularly for TGW, highlighting its application potential in high‐yield breeding. Principal component analysis (PCA) extracted four principal components, explaining 84.97% of the total variation. Correlation analysis revealed a highly significant positive association between TGW and both GWMP and panicle weight per main stem (PWMS). Transcriptomic data revealed that pathways related to carbohydrate metabolism, sugar transport, starch biosynthesis, and cell wall formation were significantly enhanced in high‐TGW materials, collectively constituting the core regulatory network for TGW formation. Through integrative analysis of multiple datasets, the cell wall invertase gene CIN1 was identified as a key candidate gene, whose expression level showed a significant positive correlation with TGW. Furthermore, the transcription factor WRKY50 was predicted to regulate CIN1 , potentially contributing to TGW determination in foxtail millet. These findings provide candidate genes and a theoretical basis for molecular breeding and the discovery of yield‐related genes in foxtail millet.