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Interspecific hybridization resulted in the creation of <i>B. juncea</i> introgression lines (ILs) generated from <i>B. carinata</i> with increased productivity and adaptability. Forty ILs were crossed with their respective <i>B. juncea</i> recipient parents to generate introgression line hybrids (ILHs) and the common tester (SEJ 8) was used to generate test hybrids (THs). Mid-parent heterosis in ILHs and standard heterosis in THs were calculated for eight yield and yield-related traits. Heterotic genomic regions were dissected using ten ILs with significant mid-parent heterosis in ILHs and standard heterosis in THs for seed yield. A high level of heterosis for seed yield was contributed by 1000 seed weight (13.48%) in D31_ILHs and by total siliquae/plant (14.01%) and siliqua length (10.56%) in PM30_ILHs. The heterotic ILs of DRMRIJ 31 and Pusa Mustard 30 were examined using polymorphic SNPs between the parents, and a total of 254 and 335 introgressed heterotic segments were identified, respectively. This investigation discovered potential genes, viz., <i>PUB10</i>, <i>glutathione S transferase</i>, <i>TT4</i>, <i>SGT</i>, <i>FLA3</i>, <i>AP2/ERF</i>, <i>SANT4</i>, <i>MYB</i>, and <i>UDP-glucosyl transferase 73B3</i> that were previously reported to regulate yield-related traits. The heterozygosity of the <i>FLA3</i> gene significantly improved siliqua length and seeds per siliqua in ILHs of Pusa Mustard 30. This research proved that interspecific hybridization is an effective means of increasing the diversity of cultivated species by introducing new genetic variants and improving the level of heterosis.