Dissection of quantitative trait loci governing root system architecture under aluminium toxicity stress conditions in Brassica carinata-derived Brassica juncea introgression lines

Abstract Background Aluminium (Al) toxicity in acidic soils is a major constraint limiting rapeseed–mustard productivity, particularly affecting Brassica juncea cultivation in acid-prone regions. The narrow genetic base of B. juncea restricts genetic improvement for Al toxicity stress tolerance. To enhance genetic variability and introgress beneficial genomic regions, Brassica carinata -derived B. juncea introgression lines (ILs) were developed and evaluated to dissect the genetic basis of root system architecture and stress tolerance under Al toxicity conditions. Results Significant genetic variability was observed among the ILs for fourteen morpho-physiological traits evaluated under Al toxicity stress. Genotyping-by-sequencing generated 7,434 high-quality SNP markers, which were used to construct a high-density linkage map spanning 3,234.9 cM with an average marker interval of 2.3 cM. QTL analysis identified 24 significant QTLs, including 17 associated with root and shoot morphological traits and 7 linked to stress tolerance indices. Notable QTLs included qRV.1B.1 for root volume and qNF.3B.3 for number of forks, explaining 26.3% and 26.0% of phenotypic variation, respectively. Three QTL hotspots were detected, including a prominent region on chromosome 2B harboring QTLs for multiple stress tolerance indices. Several putative candidate genes with known roles in stress response pathways were identified within these QTL regions, including COBRA-like involved in cell wall expansion, peroxidase and cytochrome P450 associated with oxidative detoxification, and GATA , SAUR-like , zinc-knuckle, and DNA damage-inducible proteins involved in stress signalling and regulation. Conclusions This study elucidates the genetic architecture of Aluminium toxicity tolerance and identifies key QTLs and putative candidate genes governing root system architecture and stress adaptation in Brassica juncea introgression lines. The results demonstrate that interspecific introgression from B. carinata generated useful variation for root traits, enabling the identification of genomic regions associated with aluminium toxicity tolerance through GBS-based QTL mapping. These findings provide valuable genomic resources and promising targets for marker-assisted breeding to develop Aluminium toxicity-tolerant cultivars suitable for acidic soil environments.