The tomato seed microbiome is mainly shaped by host genotype and production site.

The seed microbiome plays a crucial role in plant health and productivity, yet the extent to which the plant genotype influences its composition remains unclear. We conducted a large-scale study using 100 tomato (Solanum lycopersicum L.) genotypes from 12 geographical locations in China, subjecting all seeds to the same processing to assess seed microbiome plasticity. The plant genotype was identified as the primary factor shaping microbiome structure (R² = 0.56, P = 0.001), followed by geographic location (R² = 0.11, P = 0.001), and insect resistance of the cultivar (R² = 0.07, P = 0.001). A rather small core microbiome of 21 amplicon sequence variants (ASVs) was shared across all tomato genotypes. Ubiquitous seed microbiome members found in 90% of the samples included Pseudomonas, Lactobacillus, Leuconostoc, and Ralstonia. A Random Forest modeling approach showed that tomato traits and their production environment can be predicted via seed microbiome features; core microbiome members, including Lactobacillus and Pseudomonas, were connected to specific tomato traits. This study unveils key factors influencing seed microbiome assembly and emphasizes the crucial role of host traits that can enable new venues for seed microbiomes in plant breeding and sustainable crop production. IMPORTANCE: Seeds not only carry the plant's genetic material but also host distinct microbial communities that can influence early plant growth and performance. In a large-scale study involving 100 tomato genotypes collected from 12 geographical locations in China, we examine how plant genotype shapes the seed microbiome. The research findings reveal that plant genotype, more than location or parents' geography, primarily influences microbial community structure (R² = 0.56 vs 0.11). These findings highlight the strong association between host genetics and seed microbiome assembly. Understanding these interactions provides valuable opportunities for integrating microbiome-based strategies into plant breeding and crop improvement programs, ultimately supporting more resilient and sustainable agricultural systems.