Genetic diversity and population structure analyses of Plectranthus edulis (Vatke) Agnew collections from diverse agro-ecologies in Ethiopia using newly developed EST-SSRs marker system

Abstract

Background: Plectranthus edulis (Vatke) Agnew (locally known as Ethiopian dinich or Ethiopian potato) is one of the most economically important edible tuber crops indigenous to Ethiopia. Evaluating the extent of genetic diversity within and among populations is one of the first and most important steps in breeding and conservation measures. Hence, this study was aimed at evaluating the genetic diversity and population structure of this crop using collections from diverse agro-ecologies in Ethiopia.

Results: Twenty polymorphic expressed sequence tag based simple sequence repeat (EST-SSRs) markers were developed for P. edulis based on EST sequences of P. barbatus deposited in the GenBank. These markers were used for genetic diversity analyses of 287 individual plants representing 12 populations, and a total of 128 alleles were identified across the entire loci and populations. Different parameters were used to estimate the genetic diversity within populations; and gene diversity index (GD) ranged from 0.31 to 0.39 with overall mean of 0.35. Hierarchical analysis of molecular variance (AMOVA) showed significant but low population differentiation with only 3% of the total variation accounted for variation among populations. Likewise, cluster and STRUCTURE analyses did not group the populations into sharply distinct clusters, which could be attributed to historical and contemporary gene flow and the reproductive biology of the crop.

Conclusions: These newly developed EST-SSR markers are highly polymorphic within P. edulis and hence are valuable genetic tools that can be used to evaluate the extent of genetic diversity and population structure of not only P. edulis but also various other species within the Lamiaceae family. Among the 12 populations studied, populations collected from Wenbera, Awi and Wolaita showed a higher genetic diversity as compared to other populations, and hence these areas can be considered as hot spots for in-situ conservation as well as for identification of genotypes that can be used in breeding programs.

Keywords: Ethiopian dinich; Expressed sequence tags; Genetic diversity; Plectranthus edulis; Population structure; Simple sequence repeats.

Fig. 1

Map of Ethiopia showing its Federal Regions (left bottom) and tuber sample collection sites, representing the 12 studied populations, within four of the Federal Regions (left upper) (see Table 1 for full description of the populations). The map was original and constructed using geographic coordinates and elevation data gathered from each collection sites using global positioning system (GPS)

Fig. 2

Neighbor-joining tree generated based on simple matching dissimilarity coefficients over 1000 replicates for 60 individual samples randomly selected from the 12 populations studied. Numbers at the roots of the branches are bootstrap values, and bootstrap values of less than 59% were not shown

Fig. 3

Unweighted pair-group method with arithmetic mean (UPGMA) dendrogram showing genetic relationships among the 12 populations considered based on Nei’s unbiased genetic distance over 1000 replicates. Numbers at the roots of the branches are bootstrap values, and bootstrap values of less than 59% were not shown

Fig. 4

Principal coordinates analysis (PCoA) bi-plot showing the clustering pattern of 60 samples randomly selected from the 12 populations. Samples coded with the same symbol and color belong to the same population. Note: The percentages of variation explained by the first 3 axes (1, 2 and 3) are 14.1, 9.6, and 8.9%, respectively

Fig. 5

Delta K value estimated using Evano et al [44] method (a) and Bayesian model-based estimation of population structure (K = 3) (b) for the 287 P. edulis individual plants in twelve pre-determined populations