Nuclear DNA content and genetic structure of yams (Dioscorea species, Dioscoreaceae) cultivated in Southwestern Ethiopia
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Yams (Dioscorea species, Dioscoreaceae) are grown either for their starchy tubers or medicinal properties and are important crops in the tropics and sub-tropics. Ethiopia is regarded as an isolated centre of yam production in Africa. Many wild and domesticated varieties have been lost over time due to various constraints of production. A clear understanding of their diversity (especially that of D. cayenensis complex domesticated from native wild yam) is needed for conservation and improvement. The study was conducted on three species of Dioscorea that were collected from Bench and Sheko districts in SW Ethiopia, namely, D. alata, D. bulbifera and the D. cayenensis complex. The main objective of this study was to investigate the genetic structure of cultivated and managed yams from SW Ethiopia. Chloroplast single nucleotide polymorphisms (SNPs), nuclear DNA content and morphological observations were used to assess the diversity present. DNA content was measured by including Lycopersicum esculentum as an internal standard, staining the samples with propidium iodide (PI) using a Becton Dickinson LSR II flow cytometer. Inter and intraspecific DNA content variation was tested using GenStat statistical software (v14). Alignment and UPGMA tree construction were constructed using CLC Genomics Workbench (v4.8). Morphological characterization was carried out using plants grown in glasshouses using IPGRI/IITA descriptors. Explants were also grown on Murashige and Skoog medium (MS) and Woody Plant medium (WP) to test for suitable growth medium. Overall, the mean 2C DNA contents of D. alata, and D. bulbifera were 1.153 ± 0.02 and 2.374 ± 0.02, respectively. These values are comparable to reported 2C values of D. alata and D. bulbifera from other parts of Africa. 2C value of the D. cayenensis complex was 1.275 ± 0.02 and comparable to D. praehensilis, D. abyssinica and D. cayenensis-rotundata complex reported earlier. Successful amplification in D. alata using primers ndhH-Exon,, ycf1-rrn5 and rrn4,5-trnN is reported. Five chlorotypes were defined based on SNPs from the sequence of products from the three primers, with addition of West African D. praehensilis and D. abyssinica sequences. The occurrence of an individual from D. praehensilis with the same chlorotype as the D. cayenensis complex, and comparable DNA amounts might indicate that they could be same the taxonomic entity with different gene expression in different environments. Intraspecific morphological variation was observed in all three species studied. In addition to MS, WP was found to be suitable to grow yams in culture. This study shows the potential for genetic diversity in aiding the global yam breeding efforts from Ethiopian landraces.