Patterns of Genome-Wide Variation in Glossina fuscipes fuscipes Tsetse Flies from Uganda
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Date
2016
Journal Title
Journal ISSN
Volume Title
Publisher
Genes, Genomes, Genetics
Abstract
The 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.
Description
Keywords
Tsetse flies, Linkage, Disequilibrium, Association
Citation
Gloria-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/-/DC1