Genome-Wide Discovery of InDel Markers in Sesame (Sesamum indicum L.) Using ddRADSeq

Abstract

The development and validation of different types of molecular markers is crucial to conducting marker-assisted sesame breeding. Insertion-deletion (InDel) markers are highly polymorphic and suitable for low-cost gel-based genotyping. From this perspective, this study aimed to discover and develop InDel markers through bioinformatic analysis of double digest restriction site-associated DNA sequencing (ddRADSeq) data from 95 accessions belonging to the Mediterranean sesame core collection. Bioinformatic analysis indicated the presence of 7477 InDel positions genome wide. Deletions accounted for 61% of the InDels and short deletions (1–2 bp) were the most abundant type (94.9%). On average, InDels of at least 2 bp in length had a frequency of 2.99 InDels/Mb. The 86 InDel sites having length ≥8 bp were detected in genome-wide analysis. These regions can be used for the development of InDel markers considering low-cost genotyping with agarose gels. In order to validate these InDels, a total of 38 InDel regions were selected and primers were successfully amplified. About 13% of these InDels were in the coding sequences (CDSs) and in the 3′- and 5′- untranslated regions (UTRs). Furthermore, the efficiencies of these 16 InDel markers were assessed on 32 sesame accessions. The polymorphic information content (PIC) of these 16 markers ranged from 0.06 to 0.62 (average: 0.33). These results demonstrated the success of InDel identification and marker development for sesame with the use of ddRADSeq data. These agarose-resolvable InDel markers are expected to be useful for sesame breeders.

Development and Application of Novel InDel Markers in Flax (Linum usitatissimum L.) Through Whole-Genome Re-Sequencing

“…Based on the re-sequencing data, 17,110 InDels were detected with a density of 54.12 InDel/Mb in the whole genome. (1,651,856) [28], the number of InDels detected in this study was low but was higher than that of cucumber (Cucumis sativus) (10,470) [34] and sesame (Sesamum indicum L.) (7,477) [37]. Compared with other markers in ax, the number of InDels was less than that of SNPs [16,19] and more than most SSR markers [8,10,13,43].…”

“…Owing to the low cost and high e ciency of sequencing, InDel can be developed easily using high-throughput sequencing [27,28]. InDel markers have been used in rice [29][30][31], jute [32], quinoa [33], cabbage [25], cucumber [34], tomato [35] and other crops [26,28,[36][37][38], and are mainly used for germplasm resource identi cation, genetic diversity analysis, and genetic map construction. However, there are no reports available on the development and application of InDel markers in ax.…”

Development and application of novel InDel markers in flax (Linum usitatissimum L.) through whole-genome re-sequencing

“…(25,924) [38], tea plant (Camellia sinensis (L.) O. Kuntze) (255,218) [36], and pepper (Capsicum spp. L.) (1,651,856) [28], the number of InDels detected in this study was low but was higher than that of cucumber (Cucumis sativus) (10,470) [34] and sesame (Sesamum indicum L.) (7,477) [37]. Compared with other markers in ax, the number of InDels was less than that of SNPs [16,19] and more than most SSR markers [8, 10,13,43].…”

“…Owing to the low cost and high e ciency of sequencing, InDel can be developed easily using high-throughput sequencing [27,28]. InDel markers have been used in rice [29][30][31], jute [32], quinoa [33], cabbage [25], cucumber [34], tomato [35] and other crops [26,28,[36][37][38], and are mainly used for germplasm resource identi cation, genetic diversity analysis, and genetic map construction. However, there are no reports available on the development and application of InDel markers in ax.…”

Development and Application of Novel Indel Markers in Flax (Linum Usitatissimum L.) Through Whole-genome Re-sequencing

“…Owing to the low cost and high e ciency of sequencing, InDel can be developed easily using highthroughput sequencing (Liu et al 2016;Guo et al 2019). InDel markers have been used in rice (Hayashi et al 2006;Wu et al 2013;Sahu et al 2017), jute (Yang et al 2018), quinoa , cabbage (Lv et al 2013), cucumber (Adedze et al 2021), tomato, (Ngan et al 2016) and other crops (Liu et al 2013;Liu et al 2019;Guo et al 2019;Kizil et al 2020;Wang et al 2020), and are mainly used for germplasm resource identi cation, genetic diversity analysis, and genetic map construction. However, there are no reports available on the development and application of InDel markers in ax.…”