Roots impact plants capacity to absorb water and nutrients and thus play a vital role in tolerance to drought, salinity, and nutrient stress. In tomato (
Solanum lycopersicum) breeding programs, wild tomato species have been commonly used to increase disease resistance and fruit quality and yield. However, tomato has seldom been bred for water/nutrient use efficiency or resilience to abiotic stress. Meanwhile, little knowledge of the genetic control of root traits in tomato is available. In this study, a mapping population consisting of 181 F2 progenies derived from a cross between an advanced breeding line RvT1 ( S. lycopersicum) and a wild species Lche4 ( Solanum cheesmaniae) was evaluated for root and shoot traits in the greenhouse. Root phenotypes were studied for the early seedling stage. Heritability estimates show that root traits are moderately or highly heritable. Root mass was highly correlated with root size (length, surface area, and volume). Shoot mass and chlorophyll content (SPAD) were moderately correlated with root mass and size. Genotyping-by-sequencing was applied to discover single nucleotide polymorphism (SNP) markers. Seven hundred and forty-two SNPs were successfully mapped, and a medium-dense linkage map was created that covered 1319.47 centimorgans (cM) with an average distance of 1.78 cM between adjacent markers. Using composite interval mapping, multiple quantitative trait loci (QTL) mapping and nonparametric mapping, 29 QTLs were identified for 12 root and shoot traits on eight chromosomes. Those QTLs of major and minor effect were involved in the differences among the F2 population. Two QTL hotspot regions associated with root mass, size, shoot mass and SPAD were identified on chromosomes 1 and 4, which was consistent with the correlation among traits. Five QTLs for shoot length and eight QTLs for SPAD were accounting for 40.01% and 55.53% of the phenotypic variation. Two QTLs were associated with 18.26% of the total variation for specific root length. The wild parent Lche4 has been characterized as a potential genetic donor of higher specific root length and might be a good parent to modify the root system of cultivated tomato.