Genomic Simple Sequence Repeat Markers Reveal Patterns of Genetic Relatedness and Diversity in Sesame

Sesame (Sesamum indicum L. syn. Sesamum orientale L.) is an orphan crop species with most molecular genetic research work done in the last decade. In this study, we used a pyrosequencing approach for the development of genomic simple-sequence repeat (SSR) markers in sesame. Our approach proved successful in identifying 19,816 nonredundant SSRs, 5727 of which were identified in a contig assembly that covers 19.29% of the sesame genome. Mononucleotide repeats were the most abundant SSR type identified in the sesame genome (48.5% of all SSRs), followed by dinucleotide SSRs (45.0%). Adenine–thymine-rich motifs were predominant, representing 81.7, 51.7, 66.5, and 22.1% of the mononucleotide, dinucleotide, trinucleotide, and tetranucleotide SSRs, respectively. As a result of this work, we introduce 933 experimentally validated sesame specific markers, 849 of which are also applicable in Sesamum mulayanum (syn. Sesamum orientale var. malabaricum Nar.), the wild progenitor of cultivated sesame. Using a subset of the newly identified SSR markers, we analyzed molecular genetic diversity and population structure of a collection of world accessions. Results of the two analyses almost overlapped and suggested correlation between genetic similarity and geographical proximity. Indeed, a pattern of gene flow among sesame diversity centers was apparent, with levels of variability in some regions similar to that seen in the domestication origin of the crop. Taken together with the high rate of genomic marker transferability detected between S. indicum and S. mulayanum, our results represent additional molecular genetic evidence for designating the two taxa as cultivated and wild forms of the same species. Sesame is a member of the Pedaliaceae family and is one of the most ancient oil seed crops (Ashri, 1998; Bedigian, 2003). Sesame is cultivated in tropical, subtropical, and southern temperate regions of the world, but mainly in Asia, Africa, and South America (Anilakumar et al., 2010). Myanmar leads in sesame production with 890,000 tons, followed by India (636,000 tons), China (588,000 tons), Sudan (562,000 tons), and Tanzania (420,000 tons) (FAOSTAT, 2014). While its leaves are edible (Bedigian, 2003), sesame is mainly cultivated for its seeds. Sesame seeds are very nutritious with almost 50% oil and up to 25% protein content (Anilakumar et al., 2010). The species deserves its reputation as “queen of the oil seeds” (Bedigian and Harlan, 1986) because of its oil’s resistance to oxidative deterioration and a high, unsaturated fatty acid content of nearly 85%. In addition, polyunsaturated fatty acids constitute more than half of the unsaturated fatty acid fraction in seeds (Anilakumar et al., 2010). The excellent stability of sesame oil is attributed to the presence of antioxidant lignans such as sesamin, sesamolin, and sesaminol (Abou-Gharbia et al., 2000). The health benefits of these compounds, including antioxidant, antiaging, antihypertensive, anticancer, cholesterol lowering, and antimutagenic properties are reported by several authors (Anilakumar et al., 2010). Because sesame can set seed without significant yield loss under high temperature and drought, its cultivation is feasible and relatively easy in regions with such climatic conditions. However, sesame is the least productive oil seed crop and is mainly grown by small holders (Bhat et al., 1999; Bisht et al., 2004). Sesame productivity is Published in The Plant Genome 8 doi: 10.3835/plantgenome2014.11.0087 © Crop Science Society of America 5585 Guilford Rd., Madison, WI 53711 USA An open-access publication 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. Izmir Inst. of Technology, Dep. of Molecular Biology & Genetics, Urla, Izmir 35430 Turkey. Received 25 Nov. 2014. Accepted 8 Jan. 2015. *Corresponding author (samidoganlar@iyte.edu.tr). Abbreviations: AARI, Aegean Agricultural Research Institute; EST, expressed sequence tag; Mb, megabase; PCR, polymerase chain reaction; SSR, simple-sequence repeat. Published March 20, 2015