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

Jute is an important crop of the Indian subcontinent and comprises tossa jute (Corchorus olitorius) and white jute (C. capsularis). The yield and fi ber 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 fi rst 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 fi ber fi neness) 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 specifi c 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. R.R. Mir, S. Banerjee, M. Das, H.S. Balyan, and P.K. Gupta, Molecular Biology Lab., Dep. of Genetics and Plant Breeding, Ch. Charan Singh Univ., Meerut 250004 (U.P.), India. V. Gupta and A.K. Tyagi, Dep. of Plant Molecular Biology, Univ. of Delhi South Campus, New Delhi 110 021, India. M.K. Sinha, Division of Crop Improvement, Central Research Institute for Jute and Allied Fibres, Barrackpore 743 101, West Bengal, India. R.R. Mir and S. Banerjee contributed equally to this work. Received 15 Oct. 2008. *Corresponding author ([email protected]). Abbreviations: AFLP, amplifi ed fragment length polymorphism; MAS, marker-assisted selection; PCR, polymerase chain reaction; QTL, quantitative trait loci; RAPD, random amplifi ed polymorphic DNA; RIL, recombinant inbred line; SSR, simple sequence repeat; STMS, sequence-tagged microsatellite site. Published in Crop Sci. 49:1687–1694 (2009). doi: 10.2135/cropsci2008.10.0599 © Crop Science Society of America 677 S. Segoe Rd., Madison, WI 53711 USA All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher.