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Background  Root system architecture is important for water acquisition and nutrient acquisition for all crops. In soybean breeding programs, wild soybean alleles have been used successfully to enhance yield and seed composition traits, but have never been investigated to improve root system architecture. Therefore, in this study, high-density single-feature polymorphic markers and simple sequence repeats were used to map quantitative trait loci (QTLs) governing root system architecture in an inter-specific soybean mapping population developed from a cross between  Glycine max  and  Glycine soja.Results  Wild and cultivated soybean both contributed alleles towards significant additive large effect QTLs on chromosome 6 and 7 for a longer total root length and root distribution, respectively. Epistatic effect QTLs were also identified for taproot length, average diameter, and root distribution. These root traits will influence the water and nutrient uptake in soybean. Two cell division-related genes ( D type cyclin  and  auxin efflux carrier protein)  with insertion/deletion variations might contribute to the shorter root phenotypes observed in  G. soja  compared with cultivated soybean. Based on the location of the QTLs and sequence information from a second  G. soja  accession, three genes ( slow anion channel associated 1 like ,  Auxin responsive NEDD8-activating complex  and  peroxidase ), each with a non-synonymous single nucleotide polymorphism mutation were identified, which may also contribute to changes in root architecture in the cultivated soybean. In addition,  Apoptosis inhibitor 5-like  on chromosome 7 and  slow anion channel associated 1-like  on chromosome 15 had epistatic interactions for taproot length QTLs in soybean.    Conclusion  Rare alleles from a  G. soja  accession are expected to enhance our understanding of the genetic components involved in root architecture traits, and could be combined to improve root system and drought adaptation in soybean.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1334-6) contains supplementary material, which is available to authorized users.

Genetic variants in root architecture-related genes in a Glycine soja accession, a potential resource to improve cultivated soybean