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

Abstract

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.

Comparative assessment of genetic diversity in Sesamum indicum L. using RAPD and SSR markers

“…The extent of polymorphism and diversity reported herein is comparable to genetic diversity reported for certain varieties of sesame grown in India as well as for germplasm from other countries, such as Turkey (Ercan et al 2004; Frary et al 2015; Uncu et al 2015) and Cambodia and Vietnam (Pham et al 2009). Up to 73% polymorphism was reported for core collection of sesame from China (Zhang et al 2010) and for Indian genotypes (Kumar and Sharma 2011).…”

“…The molecular techniques of RAPD (Bhat et al 1999; Ercan et al 2004; Kumar and Sharma 2009; Pham et al 2011; Akbar et al 2011; Mahdizadeh et al 2012), AFLP (amplified fragment length polymorphism) (Laurentin and Karlovsky 2006, 2007), ISSR (inter-simple sequence repeats) (Kim et al 2002; Parsaeian et al 2011; Kumar and Sharma 2011; Nyongesa et al 2013; Woldesenbet et al 2015), SSR (Spandana et al 2012; Dixit et al 2005; Cho et al 2011; Wang et al 2012; Yepuri et al 2013; Wei et al 2014; Surapaneni et al 2014; Uncu et al 2015; Dossa et al 2016; Sehr et al 2016), and SRAP (sequence-related amplified polymorphism) (Li and Quiros 2001; Li et al 2007; Zhang et al 2010) have been used to evaluate the genetic diversity in sesame of different origins. Morphologically, Indian collection of sesame is characterized by variable forms being cultivated in different agroclimatic zones.…”

High-throughput single nucleotide polymorphism (SNP) identification and mapping in the sesame (Sesamum indicum L.) genome with genotyping by sequencing (GBS) analysis

“…In addition to SNP loci, a total of 2,465 genomic SSR markers introduced in our previous work (Uncu et al 2015) were incorporated in the HapMap files. In order to locate the SSR markers to their positions in the genome assembly, the FASTA file containing the assembly scaffolds (http://ocri-genomics.…”

“…Moreover, the reference assembly allowed saturation of the pseudomolecules with SSRs, in addition to the SNP markers. In a previous study, we identified 5,727 genomic SSR loci in a contig assembly generated through pyrosequencing of the sesame genome (Uncu et al 2015). Out of the 5,727 loci, 2,465 allowed successful primer design with sufficient length of flanking sequences.…”

“…Following NGSbased transcriptome sequencing approaches, Wei et al (2011) and Zhang et al (2012) identified 7,702 and 2,164 potential SSR (simple sequence repeat) loci, respectively. In another recent study, we identified 19,816 non-redundant SSRs in the sesame genome using a pyrosequencing approach and made a total of 933 experimentally validated markers publicly available (Uncu et al 2015). Sequencing of the genome also served for SSR marker development in sesame.…”