Solanum melongena L., also known as eggplant, belongs to the family Solanaceae and is ranked as one of the beneficial vegetables worldwide. The crop ranks among high-valued vegetables with the highest antioxidant activity and nutritional value (Liu et al., 2018). The Indo-Burma region is considered the primary origin and center of eggplant’s domestication, where the highest diversity of this crop is found (Augustinos et al., 2016). The crop enjoys extensive cultivation throughout the tropics and warm temperate regions, especially in Southern USA and Mediterranean regions (Liu et al., 2018). Despite its profitability and nutritional value, the breeding attempts for this vegetable are limited compared to other members of the Solanaceae family, such as potato and tomato (Hurtado et al., 2012). The study of genetic diversity is vital in breeding programs because it provides useful utilization of germplasm in the advancement of closely related species (Jasim et al., 2018). It is essential to assess polymorphisms among existing cultivars and select parents for hybridization. Generally, morphological characterization is considered the first step towards exploring genetic variation in eggplant (Sulaiman et al., 2020). However, morphological characters have particular limitations in distinguishing homozygous from heterozygous. Aside from this, morphological characters cannot define the exact level of diversity among existing germplasm due to additive gene action of disclosure of economically important traits (Jasim et al., 2018). Molecular markers are not environmentally controlled and can reveal the genotypic difference at the DNA level.

Hence, molecular markers play a crucial role in analyzing plant genealogy, gene mapping, construction of genetic maps, evolution, germplasm characterization, selection for characters, diversity study, and the determination of genome organization (Zuki et al., 2020; Sarif et al., 2020).Microsatellites, also known as simple sequence repeats (SSR), have become one of the most prevalent genetic markers due to their co-dominance inheritance, multi-allelic nature, reproducibility, high genome coverage, abundance and are polymerase chain reaction (PCR)-based (Demir et al., 2010; Chukwu et al., 2020). The first set SSR marker for eggplant was developed from the screening of small insert of di- and trinucleotide repeats of genomic libraries (Nunome et al., 2003). Subsequently, a set of small SSR markers from genic DNA sequence developed by Stàgel et al. (2008) developed was lodged in public databases. Similarly, over 1,000 SSR markers were identified by Nunome et al. (2009) while screening enriched cDNA and gDNA libraries. Barchi et al. (2011) isolated a wide-range of approximately 2,000 putative eggplant SSRs markers from restriction-site associated DNA tags out of which a subset exhibited polymorphism among the mapping population parents. A wide range of SSR markers is publicly obtainable for eggplant, either from genomic SSRs (genomic libraries of SSR enriched) or EST-SSR (genic libraries). Genomic SSRs are usually related to non-coding parts, but EST-SSRs are derived from expressed regions of the genome (Muñoz-Falcón et al., 2011). Meanwhile, EST-SSRs are less polymorphic compared to genomic SSRs (Muñoz-Falcón et al., 2011). The main objective of this study was to evaluate genetic diversity among collected materials using both genomic SSR and EST-SSR polymorphic markers and examine suitable parents for heterotic hybridization in future breeding programs. This study will be useful in the germplasm conservation and characterization for future breeding programs of eggplant resources.

This research revealed the level of genetic diversity among the available germplasm of eggplant collected from three different countries using the SSR marker (Fig. 2). The determination of genetic variation among germplasm is vital in the breeding and conservation of genetic resources. It is also important in genetic improvement and exploitation of genes for tolerance against abiotic stress. The detection of polymorphism within germplasm is important in breeding. There are reports (Nunome et al., 2003; Stàgel et al., 2008; Demir et al., 2010) of low polymorphism frequency within intraspecific lines and cultivars among crops of Solanaceae family, and this is possibly due to their autogamous nature. Eggplant is an autogamous crop, and most of the materials are commercial varieties, so low heterozygosity is not unexpected (Cericola et al., 2013). The more or less similar value of H_o (0.038) was also reported by Augustinos et al. (2016). The low value of H_o was also observed by Liu et al. (2018) and Vilanova et al. (2012), who reported 0.03 and 0.06 in their respective study. The high value of homozygosity indicates that pure lines can be found from the selection of individuals among this germplasm (Vilanova et al., 2014; Gramazio et al., 2019). Although molecular diversity depends on the number of markers, types of markers, and the tested accessions (Augustinos et al., 2016; Tümbilen et al., 2011; Gramazio et al., 2019). The high average value of PIC, the high mean number of alleles per locus, and high levels of observed heterozygosity in this research are comparable with other studies, thus indicating that great diversity exists among the collected germplasm. The study reported by Nunome et al. (2003) showed an average value of the observed number of alleles per locus was 3.1, and the expected heterozygosity value was 0.38 when an evaluation was conducted within 11 germplasm of S. melongena using 16 polymorphic dinucleotide genomic microsatellites. Thirty-eight S. melongena accessions were evaluated using 11 EST-SSR polymorphic markers, the mean value of alleles per locus was 3.1 and the average PIC value was 0.38, according to a report by Stàgel et al. (2008). From their study, it was observed that genomic SSR markers are more polymorphic compared to EST-SSRs. This was in tandem with reports by Kalia et al. (2011), Vilanova et al. (2012), and Nunome et al. (2009). Five eggplants SSRs, developed by Nunome et al. (2009), chosen for the high value of PIC, showed an average of 5alleles/locus. Considering the five SSRs with the highest value of PIC, the average number of alleles per locus in this study was 5, which is greater than the value reported by Demir et al. (2010). This indicates a wide diversity exists with different origins and types.

SSR marker is useful for the analysis of genetic diversity in eggplant. For this study, the PIC value range from 0.660 to 0.966, with an average value of 0.830. This value was higher than the mean PIC value of 0.401, 0.47, and 0.507, reported by Vilanova et al. (2012), Muñoz-Falcón et al. (2011), and Liu et al. (2018), respectively. A PIC value greater than 0.5 indicates a highly polymorphic locus. A PIC value of 0.25–0.50 shows an intermediate polymorphic locus, while a PIC of lower than 0.25 indicates a low polymorphic locus (Gramazio et al., 2019; Kalia et al., 2011; Nunome et al., 2009; Ge et al., 2013). In this research, the average value of PIC was 0.830, indicating a high level of polymorphism in the loci. Genetic diversity level measured in eggplants varies in different literature studies. Hurtado et al. (2012) recorded a high genetic diversity study for some Chinese accessions, i.e., He = 0.494, and some Sri Lankan accessions, i.e., He = 0.540, which is similar to that observed in this study (He = 0.493). This research showed Nei’s index and Shanon’s information index values of 0.488 and 0.849, respectively, which were higher than the result recorded by Ge et al. (2013), where Nei’s index value & Shannon’s index value 0.323 and 0.570, respectively. This may be due to different materials, sample sizes, and different types of markers used.

The dendrogram coefficient range varied from 3.51 to 12.89, indicating a high amount of variation present among existing materials. Higher diversity was observed among genotypes of Groups I to VI due to their different morphological characters. The accessions were admixtured from different countries, indicating that these accessions had a common origin or more or less the same morphological characters. On the other hand, the accessions which were distant from one another, meaning that these accessions had different agronomical traits or distinct origin. The accessions from different clusters but different origins suggest an exchange of genetic materials by plant breeders from different geographical locations. Dissimilarities among accessions could be due to environmental influence occurring over a long period of time.

The AMOVA showed highly significant genetic differences within populations. This result indicates that high genetic dissimilarities existed among the accessions within the population (77%), while there are low significant differences among the populations (23%), showing the presence of low genetic dissimilarities among the population. This research results were similar to previous research by Mazid et al. (2013), in which 67% variation was present within groups of 41 rice genotypes while there was 33% variation among the 41 rice genotypes.

The microsatellite markers are valuable tools in determining the genetic relationship among eggplant accessions such as those from three different countries (Bangladesh, Malaysia, and Thailand) used in this study. These markers also helped to reveal a high level of polymorphism within the population and a low polymorphism level among populations. Through the improvement of eggplant accessions and widening of their genetic base, the population which has the least genetic similarities could be selected as parental materials. Therefore, hybridization should be conducted using two distant populations like any accessions of Cluster I with Cluster V. Hence, accessions EB12, ET11, ET13, ET15, ET16, and ET17 could be crossed with accessions EM3, EB34, and EB3 for improvement in the future breeding program. The molecular variance analysis showed that 77% of total genetic variations were due to differences within populations, whereas 23% genetic variation was exhibited among populations.