Construction of a high-density genetic map for sesame based on large scale marker development by specific length amplified fragment (SLAF) sequencing

Abstract

BackgroundThe genetics and molecular biology of sesame has only recently begun to be studied even though sesame is an important oil seed crop. A high-density genetic map for sesame has not been published yet due to a lack of sufficient molecular markers. Specific length amplified fragment sequencing (SLAF-seq) is a recently developed high-resolution strategy for large-scale de novo SNP discovery and genotyping. SLAF-seq was employed in this study to obtain sufficient markers to construct a high-density genetic map for sesame.ResultsIn total, 28.21 Gb of data containing 201,488,285 pair-end reads was obtained after sequencing. The average coverage for each SLAF marker was 23.48-fold in the male parent, 23.38-fold in the female parent, and 14.46-fold average in each F2 individual. In total, 71,793 high-quality SLAFs were detected of which 3,673 SLAFs were polymorphic and 1,272 of the polymorphic markers met the requirements for use in the construction of a genetic map. The final map included 1,233 markers on the 15 linkage groups (LGs) and was 1,474.87 cM in length with an average distance of 1.20 cM between adjacent markers. To our knowledge, this map is the densest genetic linkage map to date for sesame. 'SNP_only’ markers accounted for 87.51% of the markers on the map. A total of 205 markers on the map showed significant (P < 0.05) segregation distortion.ConclusionsWe report here the first high-density genetic map for sesame. The map was constructed using an F2 population and the SLAF-seq approach, which allowed the efficient development of a large number of polymorphic markers in a short time. Results of this study will not only provide a platform for gene/QTL fine mapping, map-based gene isolation, and molecular breeding for sesame, but will also serve as a reference for positioning sequence scaffolds on a physical map, to assist in the process of assembling the sesame genome sequence.

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

“…These two multiplex reduced representation sequencing approaches yielded a total of 3,673 and 3,769 polymorphic loci, respectively. In this work, the percentage of SNP markers used for linkage analysis in the RIL population was 4.96 % (770 markers), lower than those reported by Zhang et al (2013b) and Wu et al (2014), who incorporated 34.63 % (1,272 markers) and 35.21 % (1,327 markers) of the markers they identified into their linkage analyses, respectively. Presumably, this was the result of the high stringency SNP filtering protocol applied in this work, which included a high LD filter for recombinant inbred populations that eliminates SNPs with a high rate of falsely genotyped individuals.…”

“…In addition to the default properties of the GBS data analysis protocol, successful polymorphism discovery is also dependent on the underlying SNP density that reflects the level of existing diversity in the population (Glaubitz et al 2014). While the average number of reads obtained from each genotype was roughly comparable in the present study (1,758,127 reads) and other work that utilized SLAF-seq (1,416,287 reads) (Zhang et al 2013b) and RAD tag sequencing (1,644,718 reads) (Wu et al 2014) approaches, GBS yielded over four times as many SNPs than the other two approaches. This result can be attributed to population choice, since the studies by Zhang et al (2013b) and Wu et al (2014) both employed mapping populations derived from parental accessions with similar geographical origins (China).…”

“…A low rate of marker polymorphism has been consistently reported for sesame by several authors (Dixit et al 2005;Wei et al 2009;Wang et al 2012;Zhang et al 2013b). In addition, as sesame is a neglected crop species, the number of available sesame-specific markers is limited.…”

“…Because GBS analysis yielded an excess of SNPs, a sufficient number of SNPs (770 SNPs) were still retained as a result of filtering and used in linkage analysis for the construction of a genetic linkage map of the sesame genome. The first report of high-throughput SNP identification and genotyping in sesame describes the application of the SLAF-seq approach (Zhang et al 2013b). More recently, RAD tag sequencing was applied on a sesame RIL population (Wu et al 2014).…”

Correlation and cluster analysis of white seeded sesame (Sesamum indicum L.) genotypes oil yield in northern Ethiopia

“…It is a diploid species with 2× = 2n = 26 chromosomes. It is a self-pollinated crop, containing 60 species organized into 16 genera (Zhang et al, 2013). Ethiopian sesame is among the highest quality in the world, as seeds are naturally produced at nearorganic levels.…”