Patterns of Genome-Wide Variation in Glossina fuscipes fuscipes Tsetse Flies from Uganda

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dc.contributor.authorGloria-Soria, Andrea
dc.contributor.authorDunn, W. Augustine
dc.contributor.authorTelleria, Erich L.
dc.contributor.authorEvans, Benjamin R.
dc.contributor.authorOkedi, Loyce
dc.contributor.authorEchodu, Richard
dc.contributor.authorWarren, Wesley C.
dc.contributor.authorMontague, Michael J.
dc.contributor.authorAksoy, Serap
dc.contributor.authorCaccone, Adalgisa
dc.date.accessioned2022-11-20T09:54:06Z
dc.date.available2022-11-20T09:54:06Z
dc.date.issued2016
dc.description.abstractThe tsetse fly Glossina fuscipes fuscipes (Gff) is the insect vector of the two forms of Human African Trypanosomiasis (HAT) that exist in Uganda. Understanding Gff population dynamics, and the underlying genetics of epidemiologically relevant phenotypes is key to reducing disease transmission. Using ddRAD sequence technology, complemented with whole-genome sequencing, we developed a panel of 73,000 single-nucleotide polymorphisms (SNPs) distributed across the Gff genome that can be used for population genomics and to perform genome-wide-association studies. We used these markers to estimate genomic patterns of linkage disequilibrium (LD) in Gff, and used the information, in combination with outlier-locus detection tests, to identify candidate regions of the genome under selection. LD in individual populations decays to half of its maximum value (r2 max/2) between 1359 and 2429 bp. The overall LD estimated for the species reaches r2 max/2 at 708 bp, an order of magnitude slower than in Drosophila. Using 53 infected (Trypanosoma spp.) and uninfected flies from four genetically distinct Ugandan populations adapted to different environmental conditions, we were able to identify SNPs associated with the infection status of the fly and local environmental adaptation. The extent of LD in Gff likely facilitated the detection of loci under selection, despite the small sample size. Furthermore, it is probable that LD in the regions identified is much higher than the average genomic LD due to strong selection. Our results show that even modest sample sizes can reveal significant genetic associations in this species, which has implications for future studies given the difficulties of collecting field specimens with contrasting phenotypes for association analysis.en_US
dc.identifier.citationGloria-Soria, A., Dunn, WA, Telleria, EL, Evans, BR, Okedi, L., Echodu, R., ... & Caccone, A. (2016). Patterns of genome-wide variation in Glossina fuscipes fuscipes tsetse flies from Uganda. G3: Genes, Genomes, Genetics , 6 (6), 1573-1584. doi:10.1534/g3.116.027235/-/DC1en_US
dc.identifier.other10.1534/g3.116.027235/-/DC1
dc.identifier.urihttps://nru.uncst.go.ug/handle/123456789/5353
dc.language.isoenen_US
dc.publisherGenes, Genomes, Geneticsen_US
dc.subjectTsetse fliesen_US
dc.subjectLinkageen_US
dc.subjectDisequilibriumen_US
dc.subjectAssociationen_US
dc.titlePatterns of Genome-Wide Variation in Glossina fuscipes fuscipes Tsetse Flies from Ugandaen_US
dc.typeArticleen_US
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