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Molecules 2014, 19(4), 5150-5162; doi:10.3390/molecules19045150
Article

Development of Simple Sequence Repeat (SSR) Markers of Sesame (Sesamum indicum) from a Genome Survey

, , , , , ,  and *
Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops of the Ministry of Agriculture, Wuhan 430062, China These authors contributed equally to this work.
* Author to whom correspondence should be addressed.
Received: 17 February 2014 / Revised: 31 March 2014 / Accepted: 14 April 2014 / Published: 22 April 2014
(This article belongs to the Section Organic Synthesis)
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Abstract

Sesame (Sesamum indicum), an important oil crop, is widely grown in tropical and subtropical regions. It provides part of the daily edible oil allowance for almost half of the world’s population. A limited number of co-dominant markers has been developed and applied in sesame genetic diversity and germplasm identity studies. Here we report for the first time a whole genome survey used to develop simple sequence repeat (SSR) markers and to detect the genetic diversity of sesame germplasm. From the initial assembled sesame genome, 23,438 SSRs (≥5 repeats) were identified. The most common repeat motif was dinucleotide with a frequency of 84.24%, followed by 13.53% trinucleotide, 1.65% tetranucleotide, 0.3% pentanucleotide and 0.28% hexanucleotide motifs. From 1500 designed and synthesised primer pairs, 218 polymorphic SSRs were developed and used to screen 31 sesame accessions that from 12 countries. STRUCTURE and phylogenetic analyses indicated that all sesame accessions could be divided into two groups: one mainly from China and another from other countries. Cluster analysis classified Chinese major sesame varieties into three groups. These novel SSR markers are a useful tool for genetic linkage map construction, genetic diversity detection, and marker-assisted selective sesame breeding.
Keywords: SSR; genetic diversity; genome survey; sesame SSR; genetic diversity; genome survey; sesame
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Wei, X.; Wang, L.; Zhang, Y.; Qi, X.; Wang, X.; Ding, X.; Zhang, J.; Zhang, X. Development of Simple Sequence Repeat (SSR) Markers of Sesame (Sesamum indicum) from a Genome Survey. Molecules 2014, 19, 5150-5162.

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