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

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Abstract

Jute is the most important bast fibre crop of the world. Stem rot disease caused by Macrophomina phaseolina is a major constraint of jute cultivation. Recent advances in genomics and bioinformatics have enabled the development of high-throughput genotyping, allowing the construction of saturated linkage maps for identification of resistant lines. In the present study, single nucleotide polymorphism (SNP) markers associated with expressed sequence tags (ESTs) were developed and were used to generate comprehensive linkage maps for Corchorus capsularis. From a set of 43,335 variant nucleotide positions detected through in silico analysis, 768 SNPs were selected for genotyping of a recombinant inbred line population. A total of 705 SNPs (91.7 %) successfully detected segregating polymorphisms. In addition to EST–SNPs, genomic simple sequence repeats were assigned to the genetic map in order to obtain an evenly distributed genome-wide coverage. Nine linkage groups were constructed from genetic maps with estimated cumulative total map length of 2016 cM and average inter-locus interval of 4.2 cM. SNP assay and linkage mapping are important set of tools for marker-assisted selection, and it could be used for identifying resistance to M. phaseolina in jute cultivars. This is the first report of developing SNP markers and SNP-based linkage map in jute.

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Acknowledgments

We acknowledge the Xcelris Labs Ltd., Ahmedabad, for assistance in SNP detection and analysis work. The research was funded by Indian Council of Agricultural Research (ICAR), New Delhi. Comments and suggestions on the manuscript from three anonymous reviewers are gratefully acknowledged.

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Authors and Affiliations

  1. Central Research Institute for Jute and Allied Fibres (CRIJAF), Barrackpore, Kolkata, 700120, West Bengal, India

    Chinmay Biswas, Piyali Dey, P. G. Karmakar & Subrata Satpathy

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  1. Chinmay Biswas
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  2. Piyali Dey
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  3. P. G. Karmakar
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  4. Subrata Satpathy
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Correspondence to Chinmay Biswas.

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Biswas, C., Dey, P., Karmakar, P.G. et al. Discovery of large-scale SNP markers and construction of linkage map in a RIL population of jute (Corchorus capsularis). Mol Breeding 35, 119 (2015). https://doi.org/10.1007/s11032-015-0311-8

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  • DOI: https://doi.org/10.1007/s11032-015-0311-8

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