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For Lb-1, we selected and sequenced 144 positive clones, which yielded 109 contigs containing 33 simple sequence repeat (SSR) sequences. From these sequences, 24 primer pairs were designed and tested. Six were eliminated from the analysis because they did not amplify fragments under the various conditions tested, two had amplification artifacts that made genotyping impossible and five were monomorphic. Thus, 11 polymorphic loci were obtained from Lb-1. In addition to this library, more two genomic libraries were constructed, Lb-2 and Lb-3, with the aim of increasing the number of loci and providing greater robustness in the analysis. A total of 192 positive clones were selected and sequenced, but due to the time required for amplification tests of primer pairs and genotyping, added to the costs involved, we selected only the best sequences of each library to design primer pairs according to the desired parameters. Thirty-two additional primer pairs were designed: 23 from Lb-2 and 9 from Lb-3. From these, four primer pairs were eliminated because they did not amplify fragments, nine had amplification artifacts and five were monomorphic. Thus, more 14 polymorphic loci were obtained (ten from Lb-2 and four from Lb-3).

Twenty-five markers were polymorphic and successfully transferred to the other Paspalum species tested. The description of the number of bands per locus and the PIC and DP values for both P. plicatulum accessions and other Paspalum species are shown in Table 2. Two loci were excluded from statistical analyses because they presented high indices of missing data (Pp-UNICAMP05 and Pp-UNICAMP20). Of the 23 loci analyzed, the number of bands per locus for P. plicatulum ranged from 3 to 15, with an average of 7.74. Among the species of the Plicatula group, the number of bands ranged from 2 to 17, with an average of 8.65 bands per locus.

Private bands were observed for all species, with the exception of P. rojasii (Table 3). We use the term “private band” to describe bands that are observed in only one species (Fig. 1). Paspalum plicatulum had the highest number of these bands, with more than half of the analyzed loci (52%) showing at least one band unique to this species. Paspalum atratum showed the second highest value of private bands, which were observed in 32% of loci. The number of private bands observed, can decrease as more individuals of other species are analyzed. However, this result was interesting since only three individuals of P. atratum were analyzed. Private bands in a population are a simple measure of genetic distinctiveness. For the purposes of conservation and management, private bands are crucial for early detection and intervention in populations at early stages of introgression and for prioritizing conservation and recovery programs [31]. Furthermore, a large, reliable, well-chosen set of species-diagnostic markers can be used to help identify species, which is extremely valuable in the management of germplasm banks.

PIC values obtained for the 23 loci analyzed ranged from 0.33 to 0.88, with an average of 0.69 for P. plicatulum, and from 0.35 to 0.90, with an average of 0.71 across the species from the Plicatula group. According to the classification proposed by Botstein [32], twenty of our loci were classified as highly informative (PIC ? 0.5). DP values ranged from 0.33 to 1.00, with a mean of 0.82 observed for P. plicatulum. When the PIC and DP of each locus were analyzed together, five loci presented the highest values in both indexes: Pp-UNICAMP21, Pp-UNICAMP17, Pp-UNICAMP18, Pp-UNICAMP19 and Pp-UNICAMP24, in order of higher informativeness.

Microsatellite markers were satisfactorily cross-amplified for Paspalum species within the Plicatula group. Paspalum atratum presented the highest detected transferability (89.86%); this species is closely related to P. plicatulum. Paspalum atratum is highly polymorphic and is related to the “common” biotype of P. plicatulum [16]. Killeen [33] relates P. plicatulum var. robustum Hack. in synonymy to P. atratum. The transferability rates of the loci were also high for P. compressifolium (85.87%), P. lenticulare (82.61%) and P. guenoarum (78.26%). The success of transferability between species, as observed for other Paspalum species [34, 35] and between correlated grass species [36, 37], allows the reduction of time and costs in the development of new markers. Only the Pp-UNICAMP23 locus could not be amplified in P. rojasii. Pp-UNICAMP01 did not amplify in P. rhodopedum, P. rojasii or P. lepton. A total of eight loci did not amplify in P. lepton, which may have occurred due to the use of only one accession of this species in the study. The results of the cross-amplification tests are shown in Table 4.

The Bayesian analyses of population structure were input into STRUCTURE HARVESTER for computation of mean LnP(K) and ?K, which peaked at K? = 3, suggesting that three genetic clusters were sufficient to interpret the Paspalum germplasm data (Fig. 2); the results are also presented for K = 6, which was the second best K (Additional file 1). From the eight species from Plicatula group analyzed, 16 accessions were assigned to cluster 1 (red), 20 were assigned to cluster 2 (blue) and ten were assigned to cluster 3 (green) (Fig. 3) (Additional file 2). Two accessions of P. plicatulum did not sort to defined clusters. There was a tendency of P. plicatulum individuals to cluster with each other, but mainly in clusters 1 and 3. The remaining species were mostly classified into a mixed subgroup (cluster 2). However, no clear pattern for the assignment of individuals based on species was observed. The results of this analysis can be extremely useful in breeding programs to guide the choice of accessions to cross. Because the gene pool is shared between accessions of the same cluster, the success rates of crossing them may be higher.

Additionally, two DAPC analyses were performed, and the results are presented as multidimensional scaling plots in Figs. 4 and 5. For both, we retained the first 16 principal components of the PCA, which explained 65% of the variation. In the first approach, we used DAPC to investigate the genetic structure of the sampled individuals, using species information pre-established by taxonomic classification (Fig. 4). The data were divided into two clear clusters: the first cluster consisted only of P. atratum individuals, and the second cluster consisted of all individuals from the remaining seven Paspalum species. The genetic closeness of these species favors sharing alleles, which complicates delineation between the different taxa of the Plicatula group. This difficulty was also reported by Cidade et al. [17]. However, the separation of P. atratum genotypes into a distinct cluster could be related to the efficiency of amplification of the developed loci and the detection of a high number of unique bands. DAPC has been proposed as an alternative to Bayesian clustering [30] as the method does not assume a population genetic model and yields better visualization of the relative distances between groups. In the second approach, we assumed no prior information about groupings of the accessions evaluated. Therefore, we searched for the best-supported number of clusters using the K-means algorithm. Inspection of BIC values (Additional file 3) revealed that two clusters were the most probable to explain the variance in these groups of accessions as the number of clusters should be ?2, as stated by the software. However, we selected three clusters to illustrate the true genetic clusters and consequently compared the results to the three clusters obtained with STRUCTURE (Fig. 5). The allocation of individuals to clusters from DAPC was similar to those achieved by STRUCTURE, and both analyses showed the same pattern of clustering. Essentially, clusters 1 (red), 2 (blue) and 3 (green) of DAPC reflect the division of gene pools 1 (red), 2 (blue) and 3 (green) detected by STRUCTURE, respectively (Additional file 2).

In both analyses, there was no clear delimitation of taxa within our dataset, compared to that expected according to the number of species studied here. In general, Paspalum species of the Plicatula group do not present a clear boundary forming an intricate agamic complex [16]. During species identification, it is common to distinguish among related species using only a few morphological descriptors. In Fig. 3, the unique accession of P. lepton was located in cluster 1, where there is a higher concentration of P. plicatulum accessions. Paspalum lepton is associated with P. plicatulum based on general morphological aspects of both plant and spikelet, although the latter species does not possess leptomorph rhizomes. Paspalum lepton is also associated with P. rhodopedum by the presence of long leptomorph rhizomes, however, the most typical accessions of P. lepton are characterized by the presence of small and gray plants [38]. In Fig. 3, the accessions of P. rhodopedum appeared to be divided into two clusters. Distinguishing the studied species through taxonomic identification using only morphological characters has proven to be a difficult task. P. rhodopedum is strongly related to P. rojasii, and it is practically impossible to distinguish the two species without the presence of the base of the plant [16]. Zuloaga et al. [39] proposed the synonymization of these species, but P. rhodopedum has leptomorph rhizomes, and P. rojasii has pachymorph rhizomes. Zuloaga et al. [39] synonymized P. guenoarum and P. rojasii. These authors also synonymized P. rhodopedum to P. guenoarum var. rojasii, even though the first has long and characteristic leptomorph rhizomes [16], as an Israeli chandelier, and P. guenoarum does not have rhizomes. Figure 3 shows that accessions of P. rojasii grouped with P. guenoarum and P. rhodopedum. Paspalum atratum is morphologically similar to P. plicatulum and P. lenticulare [38]. One of the morphological characteristics that distinguish P. atratum from P. lenticulare is that the first has an unbranched stem and the other has a branched colm [16]. The presence of fungi from the genus Bipolaris is another morphological characteristic that can be observed in the field for both P. atratum and P. lenticulare. P. compressifolium is a species of glaucous leaves and extremely flat fan-shaped sheaths and is also taxonomically associated with P. plicatulum. The accessions of P. compressifolium analyzed here showed a different grouping pattern compared to the other species considered in this study. Although the accessions were scattered among themselves and in different clusters, they were grouped with P. plicatulum (Fig. 3). However, P. plicatulum has wide morphological variability, is poorly understood and there is no consensus in the interpretation of the type specimen. The difficulty in defining this taxon and even the entire Plicatula group was highlighted by Killeen [33].

This result was expected because in a previous study [17], microsatellite markers (SSRs) developed for P. notatum and P. atratum were used in different Paspalum species, which allowed the authors to distinguish many different taxa, except for species belonging to the Plicatula group. Although high genetic variability within its species was observed, there was no clear distinction between different species in this botanical group. Furthermore, it is commonly known that the Plicatula group presents natural variation in morphological types [40], coupled with hybridization throughout its evolution and high genetic variability within its species [17], making it a highly complex group with difficult taxonomic interpretation [17, 33]. However, a more detailed and accurate analysis of the P. notatum accessions was undertaken, species from which molecular markers were developed and where species varieties could be separated (var. saurae and var. otatum) with the aid of private bands. Therefore, we believe that the absence of delimitation between the taxa observed in our study may be related to the low number of genotypes of different species used in the analysis as the initial objective was only to test the transferability of loci.

The private bands identified in our study for seven different species from the Plicatula group present potential applications for species identification of samples and/or new collections, what is mandatory for conservation, cytogenetics, breeding and other uses for Paspalum. However, these bands need further validation with larger numbers of genotypes from each species to be brought into practical use.

The microsatellites developed here are the first SSR markers developed for P. plicatulum and are highly transferrable to other species of the Plicatula group. These markers showed high polymorphism and were efficient in detecting genetic variations in the different species. These markers can be employed in future investigations of breeding programs, mating systems and kinship studies.