Genetic Analysis of Synthetic <scp> <i>Brassica juncea</i> </scp> Lines Developed by Hybridizing <scp> <i>B. rapa</i> </scp> and <scp> <i>B. nigra</i> </scp> for Broadening the Genetic Base of Indian Mustard

ABSTRACT The narrow genetic base of cultivated Brassica juncea (Indian mustard) limits the genetic improvement and adaptability of this vital oilseed crop. To address this, a novel set of resynthesized B. juncea (RBJ) lines was developed through interspecific hybridization between diverse accessions of B. rapa and B. nigra , aiming to restore and broaden the allelic diversity. Ninety resynthesized lines, along with cultivated checks, were evaluated for agro‐morphological traits under field conditions. Genetic diversity was further assessed using genome‐wide SNP markers derived from genotyping by sequencing (GBS). Multivariate analyses, including PCA, correlation and cluster analysis, were performed to study morphological variability, whereas STRUCTURE and phylogenetic analyses were used to infer the population structure and relationships. The resynthesized lines exhibited extensive phenotypic variation across yield‐contributing traits such as plant height, number of secondary branches, siliquae per plant and seed yield. Traits with high heritability and genetic advance indicated the predominance of additive gene effects, suggesting the potential for direct selection. SNP‐based diversity analysis revealed clear genetic differentiation among RBJ lines, with STRUCTURE and iTOL clustering supporting the morphological grouping. The integration of phenotypic and molecular analyses demonstrated significant untapped genetic variability among the resynthesized B. juncea lines. These RBJ genotypes constitute valuable prebreeding resources for broadening the genetic base of Indian mustard and hold strong potential for developing high‐yielding, climate‐resilient cultivars. The identified high‐yielding and diverse RBJ lines also hold promise for developing superior cultivars suited to the edible oil and bio‐based industrial sectors, thereby supporting sustainable oilseed production.