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Low erucic acid is a major breeding target to improve the edible oil quality in Brassica juncea. The single nucleotide polymorphism (SNP) in fatty acid elongase 1 (FAE1.1 and FAE1.2) gene was exploited to expedite the breeding program. The paralogs of FAE1 gene were sequenced from low erucic acid genotype Pusa Mustard 30 and SNPs were identified through homologous alignment with sequence downloaded from NCBI GenBank. Two SNPs in FAE1.1 at position 591 and 1265 and one in FAE1.2 at 237 were found polymorphic among low and high erucic acid genotypes. These SNPs either create or change the recognition site of restriction enzymes. Transition of a single nucleotide at position 591 and 1265 in FAE1.1, and at position 237 in FAE1.2, leads to a change in the recognition site of Hpy99I, BglII and MnlI restriction enzymes, respectively. Two CAPS markers for FAE1.1 and one for FAE1.2 were developed to differentiate low and high erucic acid genotypes. The efficiency of these CAPS markers was found 100 per cent when validated in Brassica juncea, and B. nigra genotypes and used in back-cross breeding. These CAPS markers will facilitate in marker-assisted selection for improvement of oil quality in Brassica juncea.

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The response to selection in any crop improvement program depends on the degree of variance and heritability. The objective of the current study was to explain variance and heritability components in Indian mustard Brassica juncea (L). Czern & Coss to recognize promising genotypes for effective breeding. Two hundred and eighty-nine diverse accessions of Indian mustard belonging to four continents were analyzed for yield and yield-related traits (20 traits) over two seasons (2017–2018 and 2018–2019) using an alpha lattice design. The genetic variance was found to be significant (P ≤ 0.01) for the individual and under pooled analysis for all of the evaluated traits, demonstrating the presence of significant genetic variability in the diversity panel, which bids greater opportunities for utilizing these traits in future breeding programs. High heritability combined with high genetic advance as percent of mean and genotypic coefficient of variation was observed for flowering traits, plant height traits, seed size, and seed yield/plant; hence, a better genetic gain is expected upon the selection of these traits over subsequent generations. Both correlation and stepwise regression analysis indicated that the main shoot length, biological yield, total seed yield, plant height up to the first primary branch, seed size, total siliqua count, days to flowering initiation, plant height at maturity, siliquae on the main shoot, main shoot length, and siliqua length were the most significant contributory traits for seed yield/plant. Also, promising genotypes were identified among the diversity panel, which can be utilized as a donor to improve Indian mustard further. These results indicated a greater scope for improving seed yield per plant directly through a selection of genotypes having the parsimonious combination of these nine traits.