A high-density linkage map in Brassica juncea (Indian mustard) using AFLP and RFLP markers

A high-density genetic linkage map of Brassica juncea (2n = 36) was constructed with 996 AFLP (amplified fragment length polymorphism) and 33 RFLP (restriction fragment length polymorphism) markers using a F1-derived doubled-haploid (DH) population of 123 individuals. This mapping population was developed by crossing a well-adapted, extensively grown Indian variety Varuna and a canola quality line Heera. The two lines are highly divergent and contain a number of contrasting qualitative and quantitative traits of high agronomic value. AFLPs were generated by the use of restriction enzymes EcoRI or PstI in combination with either MseI or TaqI. Using 91 primer pairs, a total of 1,576 parental polymorphic bands were detected of which 996 were used for mapping. In addition, 33 RFLP markers, developed from genomic clones of B. napus, were added to the map. The segregation of each marker and linkage analysis was performed using the program JoinMap version 2.0. The 1,029 mapped-markers were aligned in 18 linkage groups, which is the haploid chromosome number of the species, at LOD values ranging from 5 to 8. The total map length was 1,629 cM with an average marker interval of 3.5 cM. AFLP markers generated by EcoRI were more clustered, whereas PstI markers showed more extensive distribution. A set of 26 primer pairs (9 EcoRI/MseI, 6 EcoRI/TaqI, 6 PstI/MseI and 5 PstI/TaqI) generating 385 markers were identified for AFLP-based whole-genome selection as these markers covered 96% of the genome mapped with the 91 primer pairs. The map developed in the present study could be used for dissection and the transfer of agronomically important traits and favourable QTLs from ill-adapted exotic germplasm to cultivated Indian varieties.