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

BackgroundPlectranthus 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.ResultsTwenty 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.ConclusionsThese 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.Electronic supplementary materialThe online version of this article (10.1186/s12863-018-0682-z) contains supplementary material, which is available to authorized users.

Genetic Diversity of the Endangered Dalbergia odorifera Revealed by SSR Markers

“…However, the frequent migration indicated by the relatively high gene flow was opposite to the fragmented distributions of the investigated populations, for which, the putative explanation may be that of frequent human actions, primarily due to overexploitation and illegal logging [12]. Similar observations were also found for Acer miaotaiense (P. C. Tsoong) [34] and Plectranthus edulis (Vatke) Agnew [47]. Additionally, a genetic drift could not be ignored, since the population sizes are so small that any reduction in size could result in genetic drift.…”

“…Genetic diversity in wild plant species is often related to the geographic range, population size, longevity, mating system, migration, and balancing selection [34,45,46]. Higher genetic diversity is expected to reflect a better adaption to the environments of a species [47]. However, the medium genetic diversity level of D. odorifera was indicated by the observed and expected heterozygosity of 0.28 and 0.37, respectively.…”

Transcriptome-wide analysis of expressed resistance gene analogs (RGAs) in mango

“…Similar in silico approaches in EST-SSR marker development were performed by other studies focusing on other plants, such as bamboo (Cai et al, 2019), mint (Kumar et al, 2015), castor (Thatikunta et al, 2016), Ethiopian potato (Gadissa et al, 2018) and Elymus species (Zhang et al, 2019). The EST-derived SSR markers generated in this study can be used for functional analysis of R genes, once verified by wet lab experiments.…”

Development of EST-SSR Markers and Association Mapping with Floral Traits in Syringa Oblata

“…Over the past years, SSRs were successfully developed in different ornamental plants via data mining, such as Magnolia ashei [19], Lagerstroemia indica [20], Paeonia suffruticosa [21], and Rosa hybrida [22]. In addition, SSRs have also been widely used in plant genetics and breeding for genetic diversity analysis [23], cultivar identi cation [24], DNA ngerprinting [25], linkage mapping [26], and association mapping [27]. So far, only 14 pairs of polymorphic SSR markers have been developed for S. vulgaris [28] and S. josikaea [29], through conventional methods, however, it is greatly limited due to a prevalent lack of genomic and transcriptomic information.…”