Background: Ethyl methyl sulfonate (EMS) mutagenesis is widely used because of its advantages of inducing point mutations and no need for genetic transformation. To identify germplasm resources of processed tomatoes with superior comprehensive traits suitable for cultivation in Xinjiang. Methods: In this study, tomato seeds were treated with 2% EMS reagent for 12 h, 21 quality traits and 20 quantitative traits of 33 processed tomatoes derived from EMS-mutagenized“M82”were evaluated. Results: The results indicated that for traits such as hypocotyl color, growth habit, plant type, leaf type, and leaf shape, the range of quantitative trait variation was 8.45–37.25%, with a genetic diversity index ranging from 1.25 to 2.07. Conclusions: Cluster analysis of quantitative traits categorized the 33 EMS-mutagenized “M82” processed tomato resources into five groups: Group I contained 22 robust germplasm samples; Group II consisted of a single potential high-quality germplasm; Group III comprised five germplasm with a small and extreme plant type; Group IV included four high-yield germplasm; and Group V represented one moderate, conventional germplasm. Raw data from 15 quantitative traits across the 33 accessions were standardized using the “extreme method” to extract six comprehensive factors. The top 10 germplasm resources based on the comprehensive score were 76, 137, 97, 102, 19, 104, 21, 108, 17, and 147. It provides some theoretical basis for realizing the high-yield and high-quality cultivation and variety breeding of processed tomatoes in Xinjiang.

Water management is a key factor affecting crop physiology and rhizosphere microbial ecology in protected agriculture. However, the responses of root development and bacterial community structure to different lower irrigation limits and drip irrigation flow rates in coir substrates remain poorly understood. This study investigated greenhouse-grown tomatoes in the Gobi region under three lower irrigation limits (30%, 50%, and 70% of substrate water-holding capacity) and two drip irrigation flow rates (1 and 2 L·h⁻¹). Substrate moisture, root traits, bacterial community structure, co-occurrence networks, and functional potential were evaluated. Increasing the lower irrigation limit maintained higher and more stable substrate moisture and generally enhanced root length, root surface area, root tip number, and root activity. W3Q1 promoted greater spatial expansion of the root system, whereas W2Q2 produced the largest root volume and maintained relatively high root activity. Irrigation combination significantly altered bacterial community structure but had limited effects on bacterial richness. W2Q1 enriched Bacillota-related taxa, whereas W2Q2 enriched Pseudomonadota and exhibited greater bacterial network connectivity and modularity. FAPROTAX-based functional prediction indicated that the bacterial communities were mainly associated with chemoheterotrophy, organic matter decomposition, and nitrogen transformation. Overall, the lower irrigation limit primarily regulated substrate moisture and root traits, whereas the effects of drip irrigation flow rate were trait- and irrigation-limit-dependent, with significant main and interaction effects on root volume. These findings provide a basis for optimizing precision irrigation in coir-substrate tomato cultivation in arid greenhouse systems.