CROP SCIENCE, VOL. 54, JULY– AUGUST 2014 WWW.CROPS.ORG 1609 RESEARCH P eroxidases (POXs) and phenylalanine ammonia-lyase (PAL) are key enzymes linking primary and secondary cellular metabolic pathways. Peroxidases are glycoprotein enzymes con- taining heme cofactor catalyzing H 2 O 2 –dependent (sometimes independent) oxidoreduction. These enzymes are members of a large superfamily (class I, II, and III) performing diverse roles in cells, including scavenging of reactive oxygen species produced during biotic and abiotic stresses (Mittler et al., 2004; Gill and Tuteja, 2010; Zhang et al., 2013), initiating constitutive defense response against pathogens (Schopfer, 2001; Passardi et al., 2005), thickening of xylem parenchyma (Hilaire et al., 2001), cell wall lignifcation and suberization by polymerization of complex Genetic Analysis of Population Structure Using Peroxidase Gene and Phenylalanine Ammonia-Lyase Gene-Based DNA Markers: A Case Study in Jute ( Corchorus spp.) Pratik Satya,* Ruby Banerjee, Chinmay Biswas, Maya Karan, Swagata Ghosh, and Nasim Ali ABSTRACT Information on genetic structure of population and crop genetic diversity provides crucial input for genetic improvement of crop species. Plant peroxi- dase gene (POG) and phenylalanine ammonia-lyase gene (PALG) sequences are multigene families that can be used to design DNA marker systems for genetic diversity and population structure analysis. In the present study, genetic diversity and popula- tion structure of 110 Corchorus genotypes were investigated with 17 POG and six PALG markers and compared with results based on 15 simple sequence repeat (SSR) markers. A protocol for using PALG sequences as DNA markers was established, and an earlier protocol for POG marker system was improved. A total of 269 POG and PALG loci were identifed revealing 89.2% and 98.5% polymorphism for POG and PALG markers, respectively. The SSR markers amplifed 61 alleles in the population. The PALG markers generated comparatively more num- ber of observed and effective alleles, with higher Shannon’s information index and expected hetero- zygosity. Pairwise comparison of population using Nei’s genetic distance and genetic identity revealed close association between geographically isolated populations of C. olitorius. Wild Corchorus species exhibited more genetic association with C. olitorius than C. capsularis. Analysis of molecular variance identifed 67, 88, and 56% within population varia- tions for POG, PALG, and SSR, respectively. Bayes- ian structure and hierarchical clustering analyses based on POG polymorphism identifed fve distinct groups and allelic variations between geographi- cally isolated Indian and African C. olitorius popula- tions with low genetic admixture. PALG-based pop- ulation structure analysis revealed three groups with high genetic admixture among populations, while SSR-based structure identifed three genetic groups with low admixture. A combination of all the marker systems improved population structure-based clas- sifcation, ftting well to phylogenetic classifcation. The results establish POG and PALG markers as effcient functional DNA marker systems and pro- vide valuable information for genetic enhancement of cultivated Corchorus species. P. Satya, R. Banerjee, C. Biswas, M. Karan, and S. Ghosh, Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata 700120, West Bengal, India; and N. Ali, Ramakrishna Mission Vive- kananda Univ., Narendrapur, West Bengal, India. Received 5 Aug. 2013. *Corresponding author (pscrijaf@gmail.com, satyapratik123@ redifmail.com). Abbreviations: AFLP, amplifed fragment length polymorphism; AMOVA, analysis of molecular variance; D, genetic distance; H e , expected heterozygosity; I, Nei’s genetic identity; K, number of subpopulations; MCMC, Markov chain Monte Carlo; N a , number of observed alleles; N e , number of efective alleles; PAGE, polyacrylamide gel electrophore- sis; PAL, phenylalanine ammonia-lyase; PALG, phenylalanine ammonia- lyase gene; PALGP, phenylalanine ammonia-lyase gene polymorphism; PCR, polymerase chain reaction; PIC, polymorphism information con- tent; POG, peroxidase gene; POGP, peroxidase gene polymorphism; POX, peroxidase; FPT, population diferentiation; RP, resolving power; SI, Shannon’s information index; SSR, simple sequence repeat. Published in Crop Sci. 54:1609–1620 (2014). doi: 10.2135/cropsci2013.08.0518 © Crop Science Society of America | 5585 Guilford 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.