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Intron Polymorphism (IP) markers were used to unravel the genetic variation and relationship among 26 genotypes representing six cultivated Brassica species described in the classical U triangle. One hundred and twenty-five Arabidopsis thaliana-derived IP markers were assayed and 90 to 100% cross-transferability was observed in the six Brassica species suggesting that IP markers were highly conserved during the evolution of different Brassica species. The number of alleles observed in species at each locus ranged from one to ten with an average of 2.89 alleles per primer pair and there was no consensus between the number of alleles amplified in diploid and tetraploid species. The size range of amplified alleles was 120-1250bp, which reflects enormous deletions/insertions in different alleles. In B. juncea, 100% cross-transferability had been obtained and 121 IP markers resulted in polymorphic amplicons with PIC value of 0.04 to 0.48. The dendrogram divided all the 26 genotypes into two groups composed of B. napus/B. rapa/B. oleracea and B. carinata/B. nigra/B. juncea. A-genome present in B. juncea and B. napus/B. rapa seems distinct from each other and hence provides a great opportunity for generating diversity through resynthesizing amphidiploids from different available sources of Agenome. The A and B genomes are more similar in comparison to C genome in tetra-diploid species.The evolutionary relationship established between various Brassica species would support in formulating suitable breeding approaches for widening the genetic base of Brassica amphidiploids by exploiting the genetic diversity found in diploid progenitor gene pools.

Six earlier reported markers closely linked to low glucosinolate QTLs of Brassica juncea, spread across ‘A’ genome (A2, A3 and A9) were validated in a recombinant inbred line (RIL) population of a cross between Pusa Mustard-21 (low erucic acid) and EC-597325 (double low) genotypes, to utilize them in marker-assisted selection (MAS). Of them, four markers viz., GER 1 amplified alleles of 650 bp and of 950 bp, GER 5 amplified 310 bp and 350 bp, At5gAJ67 amplified 500 bp and 450 bp and Myb28 amplified alleles of size 900 bp and 920 bp in EC597325 and Pusa Mustard-21, respectively and therefore differentiated low and high glucosinolate parents. These four polymorphic markers were then used to genotype the phenotyped RIL population consisting 608 plants. Marker-trait association was tested for goodness of fit using 2 test. Of the four markers, GER1 and GER5 showed higher phenotypic variance (R2 value) compared to the others, indicating their significance in determination of glucosinolates and prospects for use in MAS for development of Indian mustard genotypes with low glucosinolates content.