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.

Highlights

  • IntroductionWendl., known as the East African doum palm, is a member of the Arecaceae family

  • The present study aimed to identify genome-wide SNPs, assess the level of genetic diversity, determine the population structure and estimate gene flow between H. compressa accessions collected from four ASAL regions of Kenya using Genotyping by Sequencing (GBS) approach

  • Paired-end sequencing of 96 H. compressa accessions yielded an average of 2.4 million reads per sample

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Summary

Introduction

Wendl., known as the East African doum palm, is a member of the Arecaceae family. It is integral in the agroforestry system of coastal and riverine parts of Africa (Amwatta, 2004; Uhl and Moore, 2019). The doum palm grows in the arid and semi-arid lands (ASALs) of Kenya (Maundu and Tengnas, 2005). It is a valuable source of food, animal feed, medicine for headaches and worms, as well as non-wood products for construction and weaving.

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