A High-Density SNP Genetic Map Construction Using ddRAD-Seq and Mapping of Capsule Shattering Trait in Sesame

Abstract

The seed-bearing capsule of sesame shatters at harvest. This wildish trait makes the crop unsuitable for mechanized harvesting and also restricts its commercial potential by limiting the cultivation for countries that have no access to low-cost labor. Therefore, the underlying genetic basis of the capsule shattering trait is highly important in order to develop mechanization-ready varieties for sustainable sesame farming. In the present study, we generated a sesame F2 population derived from a cross between a capsule shattering cultivar (Muganli-57) and a non-shattering mutant (PI 599446), which was used to construct a genetic map based on double-digest restriction-site-associated DNA sequencing. The resulting high-density genetic map contained 782 single-nucleotide polymorphisms (SNPs) and spanned a length of 697.3 cM, with an average marker interval of 0.89 cM. Based on the reference genome, the capsule shattering trait was mapped onto SNP marker S8_5062843 (78.9 cM) near the distal end of LG8 (chromosome 8). In order to reveal genes potentially controlling the shattering trait, the marker region (S8_5062843) was examined, and a candidate gene including six CDSs was identified. Annotation showed that the gene encodes a protein with 440 amino acids, sharing ∼99% homology with transcription repressor KAN1. Compared with the capsule shattering allele, the SNP change and altered splicing in the flanking region of S8_5062843 caused a frameshift mutation in the mRNA, resulting in the loss of function of this gene in the mutant parent and thus in non-shattering capsules and leaf curling. With the use of genomic data, InDel and CAPS markers were developed to differentiate shattering and non-shattering capsule genotypes in marker-assisted selection studies. The obtained results in the study can be beneficial in breeding programs to improve the shattering trait and enhance sesame productivity.

Discovering favorable genes, QTLs, and genotypes as a genetic resource for sesame (Sesamum indicum L.) improvement

“…Additionally, Wang et al (2017) developed a genetic map with 13 linkage groups (chromosome numbers) and discovered 14 QTLs responsible for sesame resistance to charcoal rot disease. More recent results from Liang et al (2021) , Asekova et al (2021) , XU et al (2021) , and Yol et al (2021) have reported high-density genetic linkage maps of sesame using 1,354 bins, 1,662 SNPs, 424 SNPs, and 782 SNPs, respectively ( Figure 4 ). Furthermore, Li et al (2021) developed a super-dense genetic linkage map of 17 QTLs of seed coat color using 22,375 marker bins in 13 LGs ( Figure 4 ).…”

“…In Bulgaria, four sesame varieties (victoria, aida, valya, and nevena) have been developed that are suitable for mechanized farming (Myint et al, 2020). Although the shattering trait is considered to be qualitative and controlled by a single major gene (Yol et al, 2021), this topic has received less attention, and research to identify indehiscent/shattering resistant candidate genes for sesame is required. Wongyal et al (1997) aimed to develop shattering-resistant genotypes using gamma rays and ethyl methanesulfonate (EMS)induced mutations in the Kasetsart University Sesame Breeding Project in Thailand.…”

“…In Bulgaria, four sesame varieties (victoria, aida, valya, and nevena) have been developed that are suitable for mechanized farming ( Myint et al, 2020 ). Although the shattering trait is considered to be qualitative and controlled by a single major gene ( Yol et al, 2021 ), this topic has received less attention, and research to identify indehiscent/shattering resistant candidate genes for sesame is required.…”

“…Hence, identifying the gene and localization plays a role in the improvement of sesame capsule indehiscence, which complicates mechanized farming. However, Yol et al (2021) suggested improving this trait using gene editing tools instead of agronomic improvement approaches because of the reduced suitability of lower-yielding genotypes for mechanized harvesting. The genes, gene locations, and genetic materials associated with indehiscence traits in sesame can be used as resources for the future improvement of this trait in sesame research programs.…”

Current Progress, Applications and Challenges of Multi-Omics Approaches in Sesame Genetic Improvement

“…Subsequently, the restriction-site associated DNA sequencing (RAD-seq) method was utilized to construct a high-density genetic map with 1230 markers, and several grain yield-related QTLs were identified [ 21 ]. Up to now, eight more genetic linkage maps have been constructed in sesame with SLAF-seq, RAD-seq, ddRAD-seq or GBS [ 30 , 31 , 32 , 33 ]. These genetic maps have been used to identify QTLs related to yield and yield components, seed quality, disease resistance, stress tolerance, and other traits in sesame.…”