Development of an SSR-based genetic map in sesame and identification of quantitative trait loci associated with charcoal rot resistance

Abstract

Sesame is prized for its oil. Genetic improvement of sesame can be enhanced through marker-assisted breeding. However, few simple sequence repeat (SSR) markers and SSR-based genetic maps were available in sesame. In this study, 7,357 SSR markers were developed from the sesame genome and transcriptomes, and a genetic map was constructed by generating 424 novel polymorphic markers and using a cross population with 548 recombinant inbred lines (RIL). The genetic map had 13 linkage groups, equalling the number of sesame chromosomes. The linkage groups ranged in size from 113.6 to 179.9 centimorgans (cM), with a mean value of 143.8 cM over a total length of 1869.8 cM. Fourteen quantitative trait loci (QTL) for sesame charcoal rot disease resistance were detected, with contribution rates of 3–14.16% in four field environments; ~60% of the QTL were located within 5 cM at 95% confidence interval. The QTL with the highest phenotype contribution rate (qCRR12.2) and those detected in different environments (qCRR8.2 and qCRR8.3) were used to predict candidate disease response genes. The new SSR-based genetic map and 14 novel QTLs for charcoal rot disease resistance will facilitate the mapping of agronomic traits and marker-assisted selection breeding in sesame.

QTL Mapping of Charcoal Rot Resistance in PI 567562A Soybean Accession

“…Although there was no reported QTL conditioning charcoal rot resistance in soybean, several reports describe mapping in common bean (Hernandez-Delgado et al, 2009), sesame (Sesamum indicum L.; Wang et al, 2017), cowpea [Vigna unguiculata (L.) Walp. Each of these intervals contained >100 candidate genes that included transcriptional activation, signal transduction, and defense-related genes.…”

“…Further work will be needed to closely analyze these genomic regions and determine the physiological and molecular mechanisms determining the resistance response. Although there was no reported QTL conditioning charcoal rot resistance in soybean, several reports describe mapping in common bean (Hernandez-Delgado et al, 2009), sesame (Sesamum indicum L.; Wang et al, 2017), cowpea [Vigna unguiculata (L.) Walp. ; Muchero et al, 2011], and sorghum [Sorghum bicolor (L.) Moench.…”

SSRMMD: A Rapid and Accurate Algorithm for Mining SSR Feature Loci and Candidate Polymorphic SSRs Based on Assembled Sequences

“…Owing to their abundance, codominant inheritance, multi-allelic nature, transferability, and ease of analysis via PCR (Varshney et al, 2005;Ramu et al, 2009;Kaur et al, 2015), simple sequence repeat (SSR) markers have been successfully adopted in various genetic studies such as quantitative trait loci mapping (Qin et al, 2015;Wang et al, 2017), genotyping (Gramazio et al, 2018), genetic diversity (Nachimuthu et al, 2015;Zhou R. et al, 2015), and DNA fingerprinting (Zhang et al, 2015). Indeed, numerous genome-wide SSR markers have been identified in plants and animals in recent years, such as those in rice (Zhang et al, 2007), maize (Xu et al, 2013), cucumber (Liu et al, 2015), bee (Liu et al, 2016), tobacco (Wang et al, 2018), and snake (Liu et al, 2019).…”

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

“…The first intraspecific linkage map (Wei et al, 2009) was constituted of 8 EST-SSR (Expressed Sequence Tags), 25 AFLP (Amplified Fragment Length Polymorphism) and 187 RSAMPL (Random Selective Amplification of Microsatellite Polymorphic Loci) markers were grouped into 30 linkage groups (LGs) spanning 936.72 cM. Subsequently, two intraspecific genetic maps were constructed using backcross (BC 1 ) by (Specific Length Amplified Fragment Sequencing (SLAF) and recombinant inbred line (RIL) population using 424 SSR markers grouped into 13 actual sesame linkage groups (SLG) (Mei et al, 2017; Wang et al, 2017). Nevertheless, the level of marker saturation is still low in the context of both fine mapping and genomic synteny.…”

“…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). Four main complexity reduction methods have been described to date: deep resequencing according to the principal of paired-end sequencing and de novo sequencing (RNA-Seq) using Illumina HiSeq 2000 platform can detect SNPs, small InDels and structural variants, restriction site-associated DNA (RAD) sequencing, reduced representation libraries (RRL), specific-locus amplified fragment (SLAF) sequencing, and GBS.…”