SilicoDArT and SNP markers for genetic diversity and population structure analysis of Trema orientalis; a fodder species

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dc.contributor.authorSsali Nantongo, Judith
dc.contributor.authorOdoi, Juventine Boaz
dc.contributor.authorAgaba, Hillary
dc.contributor.authorGwali, Samson
dc.date.accessioned2022-12-28T11:56:20Z
dc.date.available2022-12-28T11:56:20Z
dc.date.issued2022
dc.description.abstractEstablishing 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.en_US
dc.identifier.citationNantongo 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.0267464en_US
dc.identifier.urihttps://doi.org/10.1371/journal. pone.0267464
dc.identifier.urihttps://nru.uncst.go.ug/handle/123456789/6694
dc.language.isoenen_US
dc.publisherPlos oneen_US
dc.subjectSilicoDArTen_US
dc.subjectSNP markersen_US
dc.subjectGenetic diversityen_US
dc.subjectPopulation structure analysisen_US
dc.subjectTrema orientalisen_US
dc.subjectFodder speciesen_US
dc.titleSilicoDArT and SNP markers for genetic diversity and population structure analysis of Trema orientalis; a fodder speciesen_US
dc.typeArticleen_US
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