Genetic Diversity and Population Structure of Doum Palm (Hyphaene compressa) Using Genotyping by Sequencing

Abstract

Doum palm (Hyphaene compressa) is a perennial economic plant primarily growing in Kenya’s Arid and Semi-Arid Lands (ASALs). It is heavily relied upon for food, animal feed, construction materials and medicine, making it an ideal plant for resource sustainability. However, the limited information on its genetic resources has hindered its breeding and conservation studies. This study used the genotyping by sequencing approach to identify Single Nucleotide Polymorphisms. These SNPs were further used to assess the genetic diversity and population structure of 96 H. compressa accessions from Coastal, Northern and Eastern ASAL regions of Kenya using two approaches; reference-based and de novo-based assemblies. STRUCTURE analysis grouped the sampled accessions into two genetic clusters (Cluster 1 and Cluster 2). Cluster 1 included accessions from the Northern region, whereas Cluster 2 included all accessions from Eastern and Coastal regions. Accessions from Kwale (Coastal) had mixed ancestry from both Cluster 1 and Cluster 2. These STRUCTURE findings were further supported by principal components analysis, discriminant analysis of principal components and phylogenetic analysis. Analysis of molecular variance indicated greater genetic variation within populations (92.7%) than among populations (7.3%). An overall FST of 0.074 was observed, signifying moderate genetic differentiation among populations. The results of this study will provide information useful in breeding, marker-assisted selection and conservation management of H. compressa.

Unlocking the economic potential of Hyphaene species known as mikoche in Tanzania

“…For example, Hyphaene coriacea is abundantly available on sand dunes and along creeks behind mangroves from Somalia to Mozambique, South Africa and Madagascar (Martins & Shackleton, 2021) and Turkana, Samburu and Marsabit of Kenya (Lokuruka, 2008). In addition, Hyphaene thebaica is widely available in Djibouti, whereas Hyphaene compressa is commonly found in the coastal region of Tanzania and Kenya, and H. petersiana is found on the shores of Lake Eyasi of Tanzania (Omire et al, 2022;Stauffer et al, 2018).…”

“…Moreover, there is still limited awareness, knowledge and technology available for cultivating and utilising Hyphaene trees. Unfortunately, no policy or law currently regulates the cultivation, utilisation and conservation of Hyphaene trees as a natural resource (Martins & Shackleton, 2017;Omire et al, 2022). This can make it difficult for farmers and other stakeholders to realise the potential benefits of the Hyphaene trees.…”

“…For example, in recent years, severe drought has resulted in food shortage and insecurity, water scarcity, and loss of livestock due to crop failure, loss of pasture, and drying of water sources (Mdemu, 2021). Various strategies can be employed to address these challenges, including research on genetic diversity and population structure, resource conservation, diversification, and improving resource efficiency (Omire et al, 2022). Unfortunately, there is limited literature about the economic importance of Hyphaene trees in Tanzania.…”