Comprehensive Characterization of Simple Sequence Repeats in Eggplant (Solanum melongena L.) Genome and Construction of a Web Resource

Abstract

We have characterized the simple sequence repeat (SSR) markers of the eggplant (Solanum melongena) using a recent high quality sequence of its whole genome. We found nearly 133,000 perfect SSRs, a density of 125.5 SSRs/Mbp, and also about 178,400 imperfect SSRs. Of the perfect SSRs, 15.6% were complex, with two stretches of repeats separated by an intervening block of <100 nt. Di- and trinucleotide SSRs accounted, respectively, for 43 and 37% of the total. The SSRs were classified according to their number of repeats and overall length, and were assigned to their linkage group. We found 2,449 of the perfect SSRs in 2,086 genes, with an overall density of 18.5 SSRs/Mbp across the gene space; 3,524 imperfect SSRs were present in 2,924 genes at a density of 26.7 SSRs/Mbp. Putative functions were assigned via ontology to genes containing at least one SSR. Using this data we developed an “Eggplant Microsatellite DataBase” (EgMiDB) which permits identification of SSR markers in terms of their location on the genome, type of repeat (perfect vs. imperfect), motif type, sequence, repeat number and genomic/gene context. It also suggests forward and reverse primers. We employed an in silico PCR analysis to validate these SSR markers, using as templates two CDS sets and three assembled transcriptomes obtained from diverse eggplant accessions.

Genome Wide Characterization and Comparative Analysis of Simple Sequence Repeats in Cucurbita Genomes

“…This pattern was also found in other genomes [18,43,44]. On the contrary, the frequency of the GC or CCG type was very low in the genomic level [45,46]. GC, TC or GA types have relatively stable structures.…”

Construction of a SNP-Based Genetic Map Using SLAF-Seq and QTL Analysis of Morphological Traits in Eggplant

“…Eggplant linkage maps were constructed with both intra-and inter-specific populations (Nunome et al, 2001(Nunome et al, , 2003Doganlar et al, 2002a;Wu et al, 2009;Barchi et al, 2010Barchi et al, , 2012Barchi et al, , 2018Miyatake et al, 2012Miyatake et al, , 2016Lebeau et al, 2013;Portis et al, 2014). The intraspecific genetic map generated using an F 2 population derived from 305E40 × 67/3 has wide application.…”

“…The first genetic map in eggplant contained 181 markers, all of which were dominant markers (RAPDs and AFLPs) that were sorted into 21 linkage groups (Nunome et al, 2001). After that, several linkage maps were constructed using mostly dominant markers (Doganlar et al, 2002a,b;Barchi et al, 2010), although the co-dominant SSR markers were introduced into map construction (Nunome et al, 2003). Nunome et al (2009) developed an enriched SSR-based genetic map containing 236 SSR markers, which were assigned into 14 linkage groups spanning 959.1 cM, with a mean marker interval of 4.3 cM.…”

“…In the past decades, a number of eggplant linkage maps have been constructed with both dominant and co-dominant DNA markers, which have been used to map disease resistance and plant morphology traits (Nunome et al, 2001(Nunome et al, , 2003(Nunome et al, , 2009Wu et al, 2009;Barchi et al, 2010Barchi et al, , 2012Barchi et al, , 2018Lebeau et al, 2013;Frary et al, 2014;Miyatake et al, 2016). The first eggplant genetic map was constructed by Nunome et al (2001) using dominant markers [randomly amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) markers] and an intra-specific EWF 2 population; several markers were associated with fruit shape and color.…”

“…However, the map contained only 181 markers and covered 21 linkage groups. Subsequently, Nunome et al (2003Nunome et al ( , 2009) developed ∼1000 simple sequence repeat (SSR) markers with which two genetic maps were constructed using the same F 2 population. Although these linkage maps are saturated, they have been useful as important co-dominant marker resources for markerassisted selection in eggplant breeding.…”