Development of SSR markers and construction of a linkage map in jute

Abstract

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.

Isolation and characterization of genomic microsatellite markers for small cardamom (Elettaria cardamomum Maton) for utility in genetic diversity analysis

“…Apart from that more variation was observed in the microsatellite motif (AG/CT)n. The locus ECM47a with the compound microsatellite motif (CT) 17 TCAA(TC) 9 showed an allelic variation of more than 25 bp. Similar reports are there in jute (Das et al 2012) and rice (Blair et al 1999) where more polymorphism was detected in dinucleotide repeats especially (AG/CT)n Among the amplified primers 86.4 % was monomorphic and 13.6 % was polymorphic. The total number of alleles observed for polymorphic markers was 22 with an average of 3.6 alleles per locus.…”

Discovery of large-scale SNP markers and construction of linkage map in a RIL population of jute (Corchorus capsularis)

“…Several jute linkage maps have been previously developed with successive adoption of new molecular marker technologies (Das et al 2012;Topdar et al 2013). The linkage map constructed in the present study exhibits a regular marker distribution, but a significantly longer cumulative genetic map (2016 cM).…”

“…However, in jute, molecular markers were used rather late in the beginning of twenty-first century (Islam et al 2005). Jute SSRs were developed and polymorphism was studied using parental genotypes of a mapping population developed for fibre fineness (Mir et al , 2009Das et al 2012). Although molecular markers have been developed for fibre yield and quality in jute, so far no molecular marker has been developed for screening resistance against stem rot pathogen M. phaseolina.…”

Comparative genomics of two jute species and insight into fibre biogenesis

“…Whole-genome optical mapping was used to improve the assemblies, resulting increase in N50 of the scaffolds to 4.0 Mb for C. olitorius and 8.5 Mb for C. capsularis (Supplementary Information and Supplementary Tables 3-6). We anchored ∼60% of each assembly to seven genetic linkage groups using a set of 1,389 molecular markers from a consensus genetic linkage map [8][9][10][11][12] ( Supplementary Fig. 3 and Supplementary Table 7).…”