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Search for genic SSRs from transcriptome sequence data of Brassica juncea and B. nigra and from unigene databank of B. rapa resulted in identification of 20,529 SSRs from 330,827 gene sequences. Identified SSRs (named as unigene microsatellite; UGM) were characterized based on their number of repeats, type of motif and base composition. Primers were designed for 2118 UGMs after in silico polymorphism survey and were tested across 11 different genotypes of B. juncea and B. rapa for PCR amplification and polymorphism. It resulted in clear-cut amplification from 1993 UGMs of which 1319 UGMs showed polymorphism. It was observed that a priori in silico polymorphism survey helped in increasing the polymorphism percentage (6.1–13.2) by PCR amplification. We also report here the development of first SSR-based linkage map of Brassica juncea using a DH mapping population derived from F1 of the cross between the lines EH-2 and Pusajaikisan. The map consisted of 860 markers comprising 462 UGMs, 157 BAC-derived SSRs and 241 intron polymorphic markers and covered a total genetic length of 2073.6 cM. The study also reports an interesting observation of appearance of novel non-parental bands in the mapping population from 18 SSRs and 13 IP markers. Search of Arabidopsis genes orthologous to their primer sequences showed that 11 of such Arabidopsis genes code for proteins involved in various abiotic stresses. The highly transferable genic SSRs developed in the study would serve as valuable resources for comparative genome mapping, mapping of qualitative and quantitative traits, gene cloning and marker-assisted breeding in Brassica species.

Alloplasmic Brassica juncea was synthesized by repeatedly backcrossing amphidiploid of Erucastrum gallicum × B. juncea with pollen of B. juncea. The E. gallicum cytoplasm was also transferred to B. napus and B. carinata through alloplasmic (E. gallicum) B. juncea. RFLP analyses of organelle DNA confirmed the presence of E. gallicum cytoplasm in all the alloplasmics. The cytoplasm of E. gallicum, though alien, did not induce stable cytoplasmic male sterility in any of the oilseed brassicas. Many useful variants such as early flowering and dwarf phenotypes were isolated in the alloplasmics of B. napus and B. carinata. These morphotypes provide useful genetic variability for the improvement of crop brassicas.

Divergence of 25 accessions of Brassica juncea of Indian, CIS (Commonwealth of Independent States, former USSR) and synthetic origin was studied by D2 analysis. On the basis of divergence, ten accessions were selected and crossed in a diallel fashion without reciprocals to study the combining ability and heterosis. None of the accessions was found to be a good general combiner for all the nine quantitative characters that were studied. Significant heterosis over better parent for single plant yield was recorded in CIS x Indian and synthetic x CIS crosses (5 each) followed by Indian x synthetic types (3). The analysis of component characters showed that the mean performance of the majority of hybrids was intermediate for five out of six yield attributing traits, thus exhibiting dominance or partial dominance effect. To estimate the contribution of such yield attributing traits towards heterosis for yield, a comparison was made among three parameters viz. heterosis over mid parent (MP), better parent (BP) and better yielding parent (BYP) of the concerned hybrid. It was observed that estimation of heterosis from BYP was a more accurate method to determine the contribution of component characters towards yield heterosis than the analysis based on MP and BP. From the component character analysis, it was concluded that characters like number of primary and secondary branches, number of siliqua per plant and siliqua density contributed significantly towards heterosis in yield. Plot level yield trials of two selected hybrids (Skorospieka II x RH30 and Donskaja IV x Varuna) over two growing seasons revealed 29.4 to 91.8% heterosis over BYP.