Analysis of Genetic Diversity and Population Structure of Wild Loquat (Uapaca Kirkiana (Müell) Arg.)) Using Dartseq-Generated Single Nucleotide Polymorphisms
Gati, Jane Maurine
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Uapaca kirkiana (Müell) Arg, is a popular fruit tree that grows in the wild and is majorly found in the Miombo Woodland. It is popularly known as sugar plum or the wild loquat by the English name. It is a species of plant in the Euphorbiaceae family. U. kirkiana has been found to grow naturally south of the equator in Mozambique, Tanzania, Burundi, Zambia, Malawi, Zimbabwe, Burundi, Angola and Democratic Republic of Congo. There are 60 known species of the genus Uapaca. Increased consumption and utilization of U. kirkiana has led to high demand for the fruit and tree. Increased population and human activities have led to high pressure on land. As a result, forest reserves and national parks have been cleared to create space for the growing demand leading to loss of biodiversity. The domestication of U. kirkiana is a more significant step towards the management and conservation of biodiversity. Information on the amount as well as the distribution of genetic diversity is essential in effective management of germplasm resources. However, minimal molecular genetic evaluation on U. kirkiana has been carried out. The objectives of the research were to assess the genetic diversity and population genetic parameters, genetic relationships and population structure in U. kirkiana sampled from International Centre for Research in Agroforestry gene bank locations. Leaf material from 500 samples of U. kirkiana were collected, air-dried and well-preserved using silica gel then kept at –20 C till the extraction of DNA. The extraction of genomic DNA was done using the Cetyl Trimethyl Ammonium Bromide method with variations. Samples were then loaded onto 96 well plates and were sequenced at the Diversity Arrays Technology Pty. Ltd Australia. Data analysis was conducted through R, PHYLIP, and iTOL applications. The populations were divided into four groups by discriminant analysis of principal components and in the Neighbor joining analysis where cluster 1 had a total of 3 individuals, cluster 2 with 47, cluster 3 with 2 and cluster 4 with 289 individuals. However, the grouping pattern did not correspond to the geographical distribution of the plant. The overall genetic diversity was low with a value of Ht=0.1040. Analysis of molecular variance results indicated a high genetic density of 93.4% within samples and a lower genetic density of 1.3% between populations. Since the population was divided into four clusters, it would be economical to select a representative sample of each cluster to be preserved for germplasm conservation. The genetic diversity was low across the populations which may have been a result of the tree conservation strategy. The Germplasm conservation unit at International Centre for Research in Agroforestry may want to use populations that are genetically distant to increase diversity and enhance the long-term existence of the fruit tree. Genetic information obtained from this study will be beneficial in the domestication program and the genetic resources unit at the International Centre for Research in Agroforestry. Further analysis of U. kirkiana accessions for sex markers will lead to identification of the sex-specific markers at the molecular level and this information will be helpful in selection of the most desirable.