Jute is an important natural fibre crop, which is only second to cotton in its importance at the global level. It is mostly grown in Indian subcontinent and has been recently used for the development of genomics resources.We recently initiated a programme to develop simple sequence repeat markers and reported a set of 2469 SSR that were developed using four SSR-enriched libraries (Mir et al. 2009). In this communication, we report an additional set of 607 novel SSR in 393 SSR containing sequences. However, primers could be designed for only 417 potentially useful SSR. Polymorphism survey was carried out for 374 primer pairs using two parental genotypes (JRO 524 and PPO4) of a mapping population developed for fibre fineness; only 66 SSR were polymorphic. Owing to a low level of polymorphism between the parental genotypes and a high degree of segregation distortion in recombinant inbred lines, genotypic data of only 53 polymorphic SSR on the mapping population consisting of 120 RIL could be used for the construction of a linkage map; 36 SSR loci were mapped on six linkage groups that covered a total genetic distance of 784.3 cM. Hopefully, this map will be enriched with more SSR loci in future and will prove useful for identification of quantitative trait loci/genes for molecular breeding involving improvement of fibre fineness and other related traits in jute.

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A simple Miniprep based on early elimination of highly acidic and proteinaceous mucilages through ethanol washing of the tissue homogenates has been developed for the extraction of genomic DNA from mature leaves and seeds of Corchorus spp. As compared to high cetyltrimethylammonium bromide (CTAB)-NaCl DNA extraction followed by ethanol-based removal of remnant mucilages from the DNA pellet, this simple miniprep consistently and reproducibly recovers high amounts of DNA with good spectral qualities at A260/A280 and A260/A230. The purified DNA is efficiently digested by restriction endonucleases, and is suitable for PCR amplification of nuclear microsatellites with expected allele sizes.

Amplified fragment length polymorphism (AFLP) analysis was conducted to investigate the level of polymorphism in four jute genotypes including two genotypes (JRC 321 and CMU 010) of Corchorus capsularis (the white jute) and two genotypes (JRO 524 and PPO4) of Corchorus olitorius (the tossa jute). Out of 1024 primer combinations that were tried, as many as 281 combinations of selective primers (13 EcoRI and 64 MseI) were selected, which produced a total of 9092 amplicons, including 752 (8.3%) polymorphic bands in C. capsularis and a total of 8856 amplicons including 1477 (16.7%) polymorphic bands in C. olitorius. The average number of bands/primer combination was 32.3 for C. capsularis and 31.5 for C. olitorius. For C. capsularis, highest polymorphism of 56.6% was shown by primer combination E35M50, while for C. olitorius highest polymorphism of 50% was shown by E41M91. In C. olitorius, 30-50% polymorphism was observed with 27 primer combinations, but in C. capsularis only 3 primer combinations gave this level of polymorphism. Similarly, in C. capsularis <10% polymorphism was detected by 115 primer combinations while in C. olitorius, <10% polymorphism was shown by only 56 primer combinations. These results indicate a higher level of polymorphism in C. olitorius relative to that in C. capsularis. The occurrence of such a large number of polymorphic AFLP markers will facilitate preparation of molecular maps and QTL analysis in jute.