SilicoDArT and SNP markers for genetic diversity and population structure analysis of Trema orientalis; a fodder species
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Date
2022
Journal Title
Journal ISSN
Volume Title
Publisher
Plos one
Abstract
Establishing the genetic diversity and population structure of a species can guide the selection
of appropriate conservation and sustainable utilization strategies. Next-generation
sequencing (NGS) approaches are increasingly being used to generate multi-locus data for
genetic structure determination. This study presents the genetic structure of a fodder species
-Trema orientalis based on two genome-wide high-throughput diversity array technology
(DArT) markers; silicoDArT and single nucleotide polymorphisms (SNPs). Genotyping
of 119 individuals generated 40,650 silicoDArT and 4767 SNP markers. Both marker types
had a high average scoring reproducibility (>99%). Genetic relationships explored by principal
coordinates analysis (PCoA) showed that the first principal coordinate axis explained
most of the variation in both the SilicoDArT (34.2%) and SNP (89.6%) marker data. The
average polymorphic information content did not highly differ between silicoDArT (0.22) and
SNPs (0.17) suggesting minimal differences in informativeness in the two groups of markers.
The, mean observed (Ho) and expected (He) heterozygosity were low and differed
between the silicoDArT and SNPs respectively, estimated at Ho = 0.08 and He = 0.05 for silicoDArT
and Ho = 0.23 and He = 0.19 for SNPs. The population of T. orientalis was moderately
differentiated (FST = 0.20–0.53) and formed 2 distinct clusters based on maximum
likelihood and principal coordinates analysis. Analysis of molecular variance revealed that
clusters contributed more to the variation (46.3–60.8%) than individuals (32.9–31.2%).
Overall, the results suggest a high relatedness of the individuals sampled and a threatened
genetic potential of T. orientalis in the wild. Therefore, genetic management activities such
as ex-situ germplasm management are required for the sustainability of the species. Ex-situ
conservation efforts should involve core collection of individuals from different populations
to capture efficient diversity. This study demonstrates the importance of silicoDArT and
SNP makers in population structure and genetic diversity analysis of Trema orientalis, useful
for future genome wide studies in the species.
Description
Keywords
SilicoDArT, SNP markers, Genetic diversity, Population structure analysis, Trema orientalis, Fodder species
Citation
Nantongo JS, Odoi JB, Agaba H, Gwali S (2022) SilicoDArT and SNP markers for genetic diversity and population structure analysis of Trema orientalis; a fodder species. PLoS ONE 17(8): e0267464. https://doi.org/10.1371/journal. pone.0267464