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

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.

Illumina-Based <i>De Novo</i> Transcriptome Analysis and Identifications of Genes Involved in the Monolignol Biosynthesis Pathway in <i>Acacia koa</i>

“…In A. koa, dinucleotide repeats were the predominant motif as in many other plants, such as A. thaliana, Arachis hypogaea, Brassica napus, Beta vulgaris, Brassica oleracea, G. max, Vitis vinifera, and Sesamum indicum (Kumpatla and Mukhopadhyay, 2005;Wei et al, 2014). The frequency of SSR repeat motifs in A. koa obtained in this study was consistent with that of other plant species.…”

Genome survey of pistachio (Pistacia vera L.) by next generation sequencing: Development of novel SSR markers and genetic diversity in Pistacia species

“…So far, NGS has been applied to genomics-based strategies to discover sequences for new SSR markers in plants, in a time and cost-effective manner [24]. SSR development studies from a genome survey were performed in different plant species [25–27]. Genome survey studies also provide information about genome structure of a plant species, including estimates of genome size, levels of heterozygosity, and repeat contents.…”

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

“…Reports on SSR marker development in sesame are limited and most work involved the development of genic SSRs, either from expressed sequence tag (EST) sequences in public databases (Wei et al, 2008;Yepuri et al, 2013) or transcriptome sequencing (Wei et al, 2011;Zhang et al, 2012;Wu et al, 2014). Fewer authors described genomic SSRs in sesame (Dixit et al, 2005;Spandana et al, 2012;Wei et al, 2014;Surapaneni et al, 2014). While genic markers have their own advantages such as lower development costs and a high degree of interspecific conservation, an abundance of genomic markers is a prerequisite for the equal representation of both gene-rich and noncoding regions in linkage groups.…”