Assessment of the Genetic Diversity of the Traditional Tree Species Kigelia africana (Sausage Tree) Using Molecular Markers for Conservation Genomics in Kenya

Abstract

This study is the first to explore the genetic composition of ancient Kigelia africana across a distribution range in Kenya. Kigelia africana is a native forest species of Kenya as far as we know it; it is widely planted in the central regions of the country by the Kikuyu tribe who inhabit this region for making their traditional brew Muratina. Unlike other tree species like Acacia, Kigelia africana has seldom been studied, although there is ample evidence of its great ecological and economic value. Because of cultural reasons, natural populations are rare in the wild. Hence the study seeks to explore the genetic diversity and composition of ancient the tree distributed across various regions in Kenya. In this study, four ancient tree populations were investigated to explore the genetic diversity and composition of Kigelia africana through DArTseq technology. Thirty-two (32) Plant seed samples were obtained from various locations, their DNA extracted, libraries prepared, and sequenced using the Illumina 2500 high throughput sequencer. A total of 8,556 SilicoDArT and 3,703 SNP markers were selected and used. The average PIC was 0.45 and 0.41 for the SilicoDArT and SNPs respectively. The population structure and average linkage hierarchical clustering based on the SNPs revealed two distinct subpopulations and a few smaller admixture groups. Both marker types identified all 32 landraces as potential duplicates with very low genetic diversity between individuals. The heterozygosity defining the genetic variation within each subpopulation was around 0.25. A mantel test showed good harmony between DArTseq and SNP marker data sets. It also showed no significant correlation between genetic diversity and the geographical coordinates of the tree samples. The results of this study provide important information and insights for decision-makers, farmers, and breeders to make the necessary actions to conserve this culturally important tree.