Topsoil-foraging root system architecture and N-use efficiency governed by small-effect QTL coevolved during jute (Corchorus olitorius L.) domestication

Background and Aims The genetic basis of topsoil-foraging root system architecture (RSA) contrary to a steep-cheap-deep root ideotype typical of most annual crops and how it has evolved in jute ( Corchorus olitorius ) during its domestication as a bast-fibre crop are unknown. Methods For jute is cross-incompatible with wild Corchorus species, we used a population (F ₂ -F _2:3 ) founded by a bast fibre-shy mutant with impaired fibre development, nitrate reductase activity (NRA) and RSA and its corresponding wild-type (WT). To detect QTL for leaf and root NRA, 11 RSA-related traits and shoot biomass, we generated whole-plant transcriptomes and constructed a genome-integrated genetic map comprising both genic and genomic SNPs. Results We identified a total of 154 QTL anchoring 107 unique SNP loci, with 140 exerting small effects. However, 75 % of these QTL were identified as multi-trait QTL associated with 42 SNP loci suggesting a well-coordinated pleiotropic genetic control of NRA and RSA. By analyzing and relating the mutant to WT ratios of the QTL number, additive effects and explained phenotypic variance over the 14 traits, we showed that additive effects contributed to tweaking the RSA. We identified many QTL with regulatory roles and reconstructed a multidimensional QTL gene network of the complex interactions governing the RSA in jute characterized by much lower root to shoot ratio (RSR). Conclusion A gradual domestication of topsoil-foraging RSA in jute was driven by the coordinated actions of many small-effect QTL, with an interplay of above- and below-ground NRA modulated by key regulatory genes stabilizing its RSR.