Genetic diversity and population structure of Vernonia amygdalina Del. in Uganda based on genome wide markers

Abstract

Determining the extent and distribution of genetic diversity is an essential component of plant breeding. In the present study, we explored the genetic diversity and population structure ofVernonia amygdalina, a fodder, vegetable and medicinal species of Africa and some parts of Yemen. Most empirical studies demonstrate that populations that are separated by geographic or ecological factors may experience genetic differentiation resulting from restricted gene flow between populations. A total of 238 individuals were sampled from two populations: i) Lake Victoria crescent (LVC) and ii) Southern and Eastern Lake Kyoga basin (SEK) agroecological zones of Uganda and genotyped using DArT platform. Of the two populations, the overall mean observed heterozygosity (Ho) was low to medium (Ho = 0.07[silicoDArTs] and 0.2[SNPs]). Inbreeding levels were also very low (-0.04 to -0.08) suggesting the presence of random mating. Partitioning of genetic structure in the two populations indicated that SEK exhibited a higher genetic diversity than LVC. The principal coordinates analysis (PCA) showed no geographical structuring, consistent with the low genetic differentiation (Fst= 0.00) and the low Euclidean genetic distance (1.38–1.39) between the LVC and SEK populations. However, STRUCTURE analysis with admixture models revealed weak possible genetic clusters with very small genetic distance among them. Overall, the results suggest low genetic diversity and weak genetic differentiation between the two populations. One possible explanation of the results could be the presence of human assisted gene flow over long distances.