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

Abstract

Sesame (Sesamum indicum L. syn. Sesamum orientale L.) is considered to be the first oil seed crop known to man. Despite its versatile use as an oil seed and a leafy vegetable, sesame is a neglected crop and has not been a subject of molecular genetic research until the last decade. There is thus limited knowledge regarding genome-specific molecular markers that are indispensible for germplasm enhancement, gene identification, and marker-assisted breeding in sesame. In this study, we employed a genotyping by sequencing (GBS) approach to a sesame recombinant inbred line (RIL) population for high-throughput single nucleotide polymorphism (SNP) identification and genotyping. A total of 15,521 SNPs were identified with 14,786 SNPs (95.26 %) located along sesame genome assembly pseudomolecules. By incorporating sesame-specific simple sequence repeat (SSR) markers developed in our previous work, 230.73 megabases (99 %) of sequence from the genome assembly were saturated with markers. This large number of markers will be available for sesame geneticists as a resource for candidate polymorphisms located along the physical chromosomes of sesame. Defining SNP loci in genome assembly sequences provides the flexibility to utilize any genotyping strategy to survey any sesame population. SNPs selected through a high stringency filtering protocol (770 SNPs) for improved map accuracy were used in conjunction with SSR markers (50 SSRs) in linkage analysis, resulting in 13 linkage groups that encompass a total genetic distance of 914 cM with 432 markers (420 SNPs, 12 SSRs). The genetic linkage map constitutes the basis for future work that will involve quantitative trait locus (QTL) analyses of metabolic and agronomic traits in the segregating RIL population.

Genetic dissection and fine mapping of a novel dt gene associated with determinate growth habit in sesame

“…Zhang et al [ 49 ] reported a SNP map comprised of 3041 bins including 30,193 SNPs in 13 LGs. Uncu et al [ 50 ] published an improved map of 13 LGs encompassed 432 markers (420 SNPs, 12 SSRs). In the present study, a genotyping by sequencing (GBS) approach was employed for high-throughput SNP identification and genotyping, then a high density bin map was constructed, which consisted of 1184 bins (13,679 SNPs), with an average of 0.918 cM between adjacent bins, while the bin marker density was similar to the map density of one bin per 0.98 cM described by Zhang et al [ 49 ].…”

Association Study Reveals Novel Genes Related to Yield and Quality of Fruit in Cape Gooseberry (Physalis peruviana L.)

“…Genotyping By Sequencing (GBS) has allowed high-throughput identification of molecular markers in the rose (Heo et al, 2017 ), apple (Norelli et al, 2017 ), pepper (Taranto et al, 2016 ), and pigeonpea (Saxena et al, 2017 ) at low costs (Voss-fels and Snowdon, 2016 ). The success of GBS in maize (Elshire et al, 2011 ), potato (Uitdewilligen et al, 2013 ), sesame (Uncu et al, 2016 ), and wheat (Poland et al, 2012 ; Kobayashi et al, 2016 ) suggest a role for the technique in non-model specialty crops. This technique is based on the reduction of genome complexity through methylation-sensitive restriction enzymes (Elshire et al, 2011 ), making it possible to search for polymorphisms in species with large genomes, high diversity, or without a reference genome (Poland and Rife, 2012 ).…”

A Combinatorial Approach of Biparental QTL Mapping and Genome-Wide Association Analysis Identifies Candidate Genes for Phytophthora Blight Resistance in Sesame

“…As an orphan or neglected crop, a high-density genetic map in sesame is still limited. Six dense SNP genetic maps have been so far constructed for sesame (Mei et al, 2017; Uncu et al, 2016; Wu et al, 2014; Wang et al, 2016; Zhang et al, 2013a; 2016). Most of these six genetic maps have been applied for QTL mapping using reduced representation genome sequencing (RRGS), while only the genotyping-by-sequencing (GBS) generated 770 SNPs and 50 SSRs were used to construct the first sesame linkage map (Uncu et al, 2016).…”

“…Six dense SNP genetic maps have been so far constructed for sesame (Mei et al, 2017; Uncu et al, 2016; Wu et al, 2014; Wang et al, 2016; Zhang et al, 2013a; 2016). Most of these six genetic maps have been applied for QTL mapping using reduced representation genome sequencing (RRGS), while only the genotyping-by-sequencing (GBS) generated 770 SNPs and 50 SSRs were used to construct the first sesame linkage map (Uncu et al, 2016). Moreover, SSR markers widely used for genetic diversity and association mapping of germplasm lines to analyze quantitative traits or tagging to the various disease-related genes (Li et al, 2014; Liu et al, 2015; Wu et al, 2014; Wang et al, 2017).…”