Phenotypic Diversity Analysis and Comprehensive Evaluation of Foxtail Millet Germplasm Resources Evaluated in Northern Xinjiang

Foxtail millet (Setaria italica L.) is an important functional food crop with high photosynthetic efficiency and drought tolerance, and it plays a significant role in arid and semi-arid agricultural systems. However, germplasm resources from Xinjiang remain inadequately characterized, limiting their use in breeding programs. This study systematically evaluated 203 foxtail millet germplasm accessions using 8 qualitative traits and 13 quantitative traits across two growing seasons (2023–2024) in northern Xinjiang. Phenotypic variation and diversity, trait correlations, and phenotypic grouping were analyzed using the Shannon–Weaver diversity index (H′ = −Σ pi ln pi), coefficient of variation (CV), Pearson correlation, principal component analysis (PCA), and hierarchical cluster analysis. Among qualitative traits, leaf posture during flowering exhibited the highest phenotypic diversity index (H′ = 1.072), whereas leaf sheath color showed the lowest (H′ = 0.359). Predominant phenotypes included green seedling leaf color (77.83%), semi-erect seedling leaf posture (57.14%), drooping leaf posture during flowering (50.74%), curved panicle neck (74.88%), spindle-shaped panicle (83.25%), and yellow grain color (84.73%). Among quantitative traits, grain weight per panicle (GWE; CV = 38.91%), single panicle weight (SEW; CV = 37.65%), and yield (CV = 37.31%) showed the highest variability. Yield was strongly and positively correlated with SEW (r = 0.925, p < 0.001) and GWE (r = 0.925, p < 0.001), and SEW and GWE were almost collinear (r = 0.996). PCA of 12 standardized traits (SEW excluded to avoid redundancy with GWE) extracted five components explaining 65.55% of total phenotypic variation. Hierarchical clustering of the unstandardized trait means (yield in kg·mu−1), in which yield contributed most strongly to group separation, divided the accessions into four groups: Group I (129 accessions, 63.55%) was intermediate (mean yield 3532 kg·ha−1); Group II (37 accessions, 18.23%) had the lowest yield (1650 kg·ha−1) and panicle weights; Group III (32 accessions, 15.76%) had high yield (5282 kg·ha−1); and Group IV (5 accessions, 2.46%), all breeding lines, had the highest yield (6814 kg·ha−1), the heaviest panicles, and the thickest stems. The evaluated foxtail millet germplasm showed substantial phenotypic diversity under irrigated conditions at a single site, providing candidate materials for yield improvement and for further evaluation of stress resistance and adaptation. Group III and Group IV accessions are candidate parents for high-yield breeding; however, this requires validation in multi-location trials because only one irrigated site was evaluated and lodging and drought responses were not measured. Entry-mean repeatability of accession means across the two seasons ranged from 72.1% to 99.99%, and these values are likely upper bounds because genotype × year interaction could not be separated from residual error. These findings provide a phenotypic baseline for germplasm utilization in Xinjiang foxtail millet improvement programs.