Genetic diversity assessment of yams (Dioscorea spp.) from Ethiopia using inter simple sequence repeat (ISSR) markers

Abstract

The genetic diversity and relationships of 70 accessions of yam belonging to Dioscorea cayenensis/Dioscorea rotundata complex (55), Dioscorea bulbifera (13) and Dioscorea alata (2, as a reference) were assessed using six inter simple sequence repeat (ISSR) primers. DNA was extracted from a bulk of two plants per accession using a modified cetyl trimethyl ammonium bromide (CTAB) method. Six ISSR primers amplified 77 fragments with 75 (97.40%) polymorphism at genus level. The genetic diversity, estimated by gene diversity and Shannon's index were 0.36 and 0.53, respectively, revealing a high level of genetic variation at genus level. At species level, 75 bands were amplified for D. cayenensis/D. rotundata complex, out of which 71 were polymorphic accounting for 92.2% polymorphism. Gene diversity and Shannon's index for D. cayenensis/D. rotundata complex were 0.33 and 0.49, respectively. In the case of D. bulbifera, a total of 64 bands were scored, out of which 55 were found to be polymorphic which resulted in 71.4% polymorphism. Gene diversity and Shannon's index for this species were 0.24 and 0.47, respectively. Genetic diversity analysis of D. cayenensis/D. rotundata complex accessions showed that Gedeo was the most diverse among populations and South among groups. Analysis of molecular variance (AMOVA) indicated the presence of higher proportion of variation within species (63.9%) than among species (36.1%). AMOVA for D. cayenensis/D. rotundata complex also showed higher within population variation (53.6) than among populations (46.4). In addition, cluster analysis for relationship between D. cayenensis/D. rotundata complex accessions showed grouping of some of the accessions according to their population but it failed to produce clear species boundary between D. cayenensis/D. rotundata complex. The results suggest that there is a high level of genetic diversity in Ethiopia yams to be exploited for future improvement (breeding) of the crop.

Assessing the genetic diversity of Dioscorea alata and related species from Colombia through inter-simple sequence repeat (ISSR) markers

“…Our results agree with Ousmael et al (2019), who assessed the genetic diversity of 77 accessions of Dioscorea spp. using six ISSR primers, finding high genetic diversity at the genus level with Shannon index of 0.36 and 0.53, respectively.…”

“…Moreover, Loko et al (2016) found 96% variation within populations and only 4% among populations using 41 microsatellite markers to study the genetic diversity and relationships between 64 local varieties of yam. The high variation within populations could be due mainly to evolutionary dynamics and/or admixture in the field possibly facilitated by pollen flow (Ousmael et al, 2019). Our results demonstrate that the genetic diversity of a yam germplasm bank can be efficiently enriched when wild type genotypes are collected in one region and a low number of rare or diverse genotypes from other regions are later incorporated.…”

“…The analysis of molecular variance (AMOVA) showed that 86% of the variation was due to differences within groups, while 14% was attributed to differences among groups (Table 4). Similarly, Ousmael et al (2019) found a higher proportion of variation within species (63.9%) than among species (36.1%) using ISSR markers to study the genetic diversity of yam (Dioscorea spp.) Moreover, Loko et al (2016) found 96% variation within populations and only 4% among populations using 41 microsatellite markers to study the genetic diversity and relationships between 64 local varieties of yam.…”

“…Assessing the genetic diversity of a plant species using molecular DNA markers is an important tool for cultivar identification, taxonomic and phylogenetic studies, genetic mapping, and germplasm management and conservation (Onda and Mochida, 2016). The genetic diversity of yam has been characterized using several markers, including RFLP (Mukherjee and Bhat, 2013), SSR (Arnau et al, 2017;Mulualem et al, 2018), AFLP (Rivera-Jiménez et al, 2011;Wendawek et al, 2013), ISSR (Kung et al, 2016;Ousmael et al, 2019), and SNP (Agre et al, 2019). Bhattacharjee et al (2018) constructed a genetic linkage map for D. alata based on 380 EST-SSR markers.…”

Genetic diversity and population structure of Uganda’s yam (Dioscorea spp.) genetic resource based on DArTseq

“…The genetic variation in this study was also explained using AMOVA analysis that partitioned total variation within the population rather than among population indicating close evolutional relationships and admixture among yam genotypes, especially those that were sourced from Ghana and Nigeria. Similar results were reported by Kedra et al [ 58 ] in yams from Ethiopia, Loko et al [ 59 ] in guinea yams from Benin, Muluneh et al [ 60 ] in yams from Ethiopia, and Wendawek et al [ 61 ] in cultivated and wild yams in Ethiopia wherein within-population variation were higher than among population.…”