The advancement of next-generation sequencing has generated scores of datasets for many plant species that provide useful genomic materials for developing efficient molecular markers for genetic analyses [27]. Recently, technological advancement in high throughput DNA sequencing offers new information to accelerate the development of molecular markers. SSR markers are more efficient in constructing linkage maps and for genetic analyses in crops owing to their high polymorphism and specificity [27]. Many SSR markers have previously been designed and used for variety identification, genetic diversity analysis and construction of linkage maps in sweet potato [28–30] compared to other molecular markers as a result of its co-dominant nature, consistency, high polymorphism, and reproducibility [31]. Although several studies have reported the use of SSR markers in sweet potato, their number and availability are limited with only a few being polymorphic compared to other crops.
To identify valuable SSR markers for sweet potato genetic improvement, the sweet potato genome was searched and a total of 2,431 SSR markers were successfully developed. The distribution density was 159.77 Mb per SSR or 6.26 kb per one SSR on average which was lower than the average density recorded for pigeon pea (8.4 kb), cotton (20.0 kb), and soybean (23.80 kb) but almost the same as that of sesame (6.55 kb), and relatively higher compared to that of rice (3.4 kb) and radish (4.93 kb) [32]. However, the differences in frequency and abundance could be attributed to the size of the database, tools for SSR data-mining, the length of repeat motifs and the application of different repeat unit thresholds [33]. In our current study, mono-, di- and trinucleotides were the most common SSRs with dinucleotides showing the highest frequency (38.50%) followed by trinucleotides (31.46%) and mononucleotide (12.77%; Additional file 2: Figure A1). This finding contrasts with previous reports showing trinucleotides as the most dominant repeat motifs in sweet potato followed by dinucleotides [10, 13]. Other studies also suggested trinucleotides as the second predominant repeat motifs in sweet potato which is in agreement with our current findings [12].
The main repeat types among the identified SSRs were A/T (12.61%), AT/AT (61.51%), AAT/ATT (27.42%), and AAAT/ATTT (13.32%, Additional 2: Figure A1). In agreement with our current study, Wang et al. [10] identified AAT/ATT as the dominant SSR motif in the sweet potato. Similarly, Yang et al. [27] identified AAAT/ATTT as the most frequent repeat motif among tetranucleotides in Welsh onion. However, previous studies identified AG/CT, AAG/CTT, and AT/TA motifs as the most dominant motif types in sweet potato [34], conflicting with our findings.
Out of the 100 randomly selected primer pairs screened, 50 primer pairs (50%) produced clear stable bands and amplified 251 alleles in the 24 sweet potato materials (Table 4). The number of alleles recorded was 5.02 per locus on average for values ranging between 1 and 13. Consistent with our results, previous studies reported a higher number of alleles per locus using SSR markers to analyze the genetic diversity of sweet potato germplasm. This indicates a high polymorphism among the sweet potato accessions studied. Yada et al. [35] had 2 to 6 alleles per primer while Buteler et al. [36] recorded 3 to 10 alleles per SSR and high polymorphism in sweet potato. Roullier et al. [14] reported 4 to 23 alleles per locus among 329 accessions from South America, Central America, and the Caribbean using 13 SSR primers; Veasey et al. [37] also reported 3 to 10 alleles per locus in Brazilian sweet potato accessions while Tumwegamire et al. [15] reported 2 to 11 per locus in East African sweet potato varieties. Conversely, Hwang et al. [38] had low polymorphism and recorded 1 to 4 alleles per SSR using varied annealing temperatures and SSR primers. The result of our current study confirms the exceptional discriminatory ability of SSR markers [39].
As a hexaploid plant distinguishing between homozygous and heterozygous sites becomes difficult hence dominant markers are preferred over collinear markers [8, 9]. Previous studies reported the high polymorphism of sweet potato which is attributed to the large genome size and high heterozygosity [38] influenced by its mating systems (self-incompatibility and outcrossing). Again, the polyploidy (autohexaploid) of sweet potato combined with the large chromosome number (2n = 6x = 90) makes sweet potato SSR primers highly polymorphic [30, 40]. Hence, it is likely for sweet potato genotypes to have huge genetic distances among them even in smaller populations [41]. Overall, vegetative propagation could be very effective in conserving the genetic diversity and heterozygosity of sweet potato.
The average SSR-based genetic distance among the 24 sweet potato varieties was 0.740 on average for values ranging between 0.605 and 1.00 (Additional file 1: Table A1 ). The genetic similarity coefficient range of 0.66 to 0.87 with a mean value of 0.765 recorded in this study is high, indicating a low diversity in the sweet potato materials studied (Fig. 2). The result is consistent with Hwang et al. [38] who recorded a high similarity coefficient of 0.64 on average and thus, concluded a low diversity among the accessions studied. On the contrary, Yada et al. [35] reported an average similarity coefficient of 0.57 by evaluating the genetic diversity of cultivars from Uganda. Zhang et al. [42] observed a low similarity coefficient (0.588) amid sweet potato varieties from South America. Tumwegamire et al. [15] also recorded a similarity coefficient of 0.54 on average when the genetic diversity of farmer varieties of both white- and orange-fleshed sweet potato from East Africa were assessed. Similarly, David et al. [43] reported a low genetic similarity coefficient of 0.54 on average and concluded a high diversity among the studied accessions. Thus, the differences could be attributed to the number and type of markers used and the genotypic variances. The clustering results revealed no direct relationship between the national and regional sources of germplasm, indicating a more frequent exchange of germplasm in sweet potato cultivation and breeding. The above results show the effectiveness and feasibility of the developed SSR markers for assessing genetic diversity in sweet potato.