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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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.

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the study was undertaken to identify the quantitative trait loci (QtLs) governing yield and its related traits using a recombinant inbred line (RIL) population derived from the popular rice hybrid, KRH-2 (IR58025A/KMR3R). A genetic map spanning 294.2 cM was constructed with 126 simple sequence repeats (SSR) loci uniformly distributed across the rice genome. QTL analysis using phenotyping and genotyping information identified a total of 22 QTLs. Of these, five major effect QTLs were identified for the following traits: total grain yield/plant (qYLD3-1), panicle weight (qPW3-1), plant height (qPH12-1), flag leaf width (qFLW4-1) and panicle length (qPL3-1), explaining 20.23-22.76% of the phenotypic variance with LOD scores range of 6.5-10.59. Few genomic regions controlling several traits (QTL hotspot) were identified on chromosome 3 for total grain yield/plant (qYLD3-1) and panicle length (qPL3-1). Significant epistatic interactions were also observed for total grain yield per plant (YLD) and panicle length (PL). While most of these QTLs were observed to be co-localized with the previously reported QTL regions, a novel, major QTL associated with panicle length (qPL3-1) was also identified. SNP genotyping of selected high and low yielding RILs and their QTL mapping with 1,082 SNPs validated most of the QTLs identified through SSR genotyping. This facilitated the identification of novel major effect QTLs with much better resolution and precision. In-silico analysis of novel QTLs revealed the biological functions of the putative candidate gene (s) associated with selected traits. Most of the high-yielding RILs possessing the major yield related QTLs were identified to be complete restorers, indicating their possible utilization in development of superior rice hybrids.