Development and Characterization of Large‐Scale Simple Sequence Repeats in Jute

Abstract

Jute is an important crop of the Indian subcontinent and comprises tossa jute (Corchorus olitorius) and white jute (C. capsularis). The yield and fiber quality of this crop remained stagnant for many years and could not be improved through conventional plant breeding. Also, no effort has been made to develop molecular markers on a scale required for marker‐assisted selection (MAS) to supplement conventional plant breeding. As a first step toward deploying MAS for jute improvement, 2469 simple sequence repeats (SSRs) were developed in tossa jute (JRO 524) using four SSR‐enriched genomic libraries. A random subset of 100 SSRs (25 SSRs from each library) was used to detect polymorphism between the parental genotypes of each of the two recombinant inbred line (RIL) mapping populations. The RILs are being developed from JRO 524 × PPO4 (for fiber fineness) and JRC 321 × CMU 010 (for lignin content) crosses to prepare molecular maps and conduct quantitative trait loci (QTL) analyses. Both SSR length polymorphism and ± polymorphism (null alleles, i.e., presence and absence of specific SSR) were detected; 50 SSRs detected polymorphism between the two genotypes of tossa jute, whereas 45 SSRs detected polymorphism between the two genotypes of white jute. This SSR allelic polymorphism in jute is higher than that reported in other crops and is adequate for construction of genetic maps for QTL analysis. The large‐scale SSRs will also prove useful in studying genetic diversity, population structure, and association mapping.

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

“…Genomic DNAs of RIL lines including mapping parents were screened by using a larger set of genome-wide 2496 pairs of SSR markers (Mir et al 2009) for polymorphism detection. Primer synthesis, selection of polymorphic markers and PCR amplifications were performed.…”

“…A total of 86 of 376 genomic DNA-derived SSRs and EST-SSRs (40 %) designed by Mir et al 2009 revealed polymorphism between the parental genotypes, of which 66 were selected for screening of the mapping population on the basis of consistency of amplification. A subset of 48 SSR markers generated data of sufficient quality to generate a framework genetic map, and 40 loci (85 %) were assigned to nine…”

“…Varietal development in jute would be facilitated by newer genomic tools through identification and selection of preferred genes. It has been recognized that molecular marker-based approaches, particularly marker-assisted breeding, have the potential to accelerate the pace of achieving the targeted goals in any crop breeding programme (Mir et al 2009). …”

“…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.…”

The genetic diversity of leaf vegetable jute mallow (Corchorus spp.): A review

“…They are unlimited in number and are not affected by environmental factors, growth stage and agronomic practices (Mir et al 2009). In many studies conducted, the diversity of the genotypes at species level is very low for many accessions of Jute mallow and hence it is important to focus on the variation that exists between different species and establish how this variation can be used to improve the crop.…”