Biology subjects

Vrieling, K.

Publications and source records attributed to Vrieling, K..

3 recordsLinked to original sources

bioRxiv2024

Uncovering large effect loci and epistasis for lifespan in standing genetic variation in the fruit fly Drosophila melanogaster

Lifespan is a heritable trait with a polygenic architecture. Experimental evolution in combination with re-sequencing has often been used to identify candidate loci for lifespan in Drosophila melanogaster. Previous experiments showed that Drosophila populations experimentally evolved to increase late-life reproduction showed a correlated responses in development time, body size, but also lifespan. Subsequent whole genome sequencing allowed for the identification of candidate loci that correlated to lifespan differentiation. However, it remains difficult to assess whether candidate loci affect lifespan and to what extent such loci pleiotropically underpin multiple traits. Furthermore, recent studies indicate that lifespan effects of loci are often context dependent, but genotype-by-genotype interactions remain understudied. Therefore, here, we report on a study where we genotyped 3210 individuals for 32 candidate loci that emerged from our evolve and re-sequence experiment and tested, (1) whether these loci significantly affected lifespan, (2) the effect size of each locus, and, (3) how these loci mutually interact, i.e. determine the level of epistasis in moulding lifespan. Of the 32 loci, six showed significant main effect associations, of which three loci showed effects of 6.6 days difference in lifespan or larger, while the overall average lifespan was 41.7 days. Eight additional significant pairwise interactions between loci were found, of which four (single) main effects and one three-way interaction was significant. Lastly, we found that alleles that increased lifespan did not necessarily have higher frequencies in populations that showed increased lifespan, indicating that lifespan itself had not been the major target of selection. Our study indicates that individual genotyping following an evolve and re-sequencing study is essential to understand the mechanistic basis of polygenetic adaptation.

evolutionary biology↗

bioRxiv2021

Refining Bulk Segregant Analyses: Ontology-Mediated Discovery of Flowering Time Genes in Brassica oleracea

AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSBackgroundC_ST_ABSBulk segregant analysis (BSA) can help identify quantitative trait loci (QTLs), but this may result in substantial bycatch of functionally irrelevant genes. Here we develop a Gene Ontology-mediated approach to zoom in on specific markers implicated in flowering time from among QTLs identified by BSA of the giant woody Jersey kale phenotyped in four bulks of flowering onset. ResultsOur BSA yielded tens of thousands of candidate genes. We reduced this by two orders of magnitude by focusing on genes annotated with terms contained within relevant subgraphs of the Gene Ontology. A further enrichment test led to the pathway for circadian rhythm in plants. The genes that enriched this pathway are attested from previous research as regulating flowering time. Some of these genes were also identified as having functionally significant variation compared to Arabidopsis ConclusionsWe validated and confirmed our ontology-mediated results through a more targeted, homology-based approach. However, our ontology-mediated approach produced additional genes of putative importance, showing that the approach aids in exploration and discovery. We view our method as potentially applicable to the study of other complex traits and therefore make our workflows available as open-source code and a reusable Docker container.

bioinformatics↗

bioRxiv2019

Whole genome sequencing and the application of a SNP panel reveal primary evolutionary lineages and genomic diversity in the lion (Panthera leo)

BackgroundPrevious phylogeographic studies of the lion (Panthera leo) have improved our insight into the distribution of genetic variation, as well as a revised taxonomy which now recognizes a northern (Panthera leo leo) and a southern (Panthera leo melanochaita) subspecies. However, existing whole range phylogeographic studies on lions either consist of very limited numbers of samples, or are focused on mitochondrial DNA and/or a limited set of microsatellites. The geographic extent of genetic lineages and their phylogenetic relationships remain uncertain, clouded by massive sampling gaps, sex-biased dispersal and incomplete lineage sorting. ResultsIn this study we present results of low depth whole genome sequencing and subsequent variant calling in ten lions sampled throughout the geographic range, resulting in the discovery of >150,000 Single Nucleotide Polymorphisms (SNPs). Phylogenetic analyses revealed the same basal split between northern and southern populations as well as four population clusters on a more local scale. Further, we designed a SNP panel, including 125 autosomal and 14 mitochondrial SNPs, which was tested on >200 lions from across their range. Results allow us to assign individuals to one of these four major clades (West & Central Africa, India, East Africa, or Southern Africa) and delineate these clades in more detail. ConclusionsThe results presented here, particularly the validated SNP panel, have important applications, not only for studying populations on a local geographic scale, but also for tracing samples of unknown origin for forensic purposes, and for guiding conservation management of ex situ populations. Thus, these genomic resources not only contribute to our understanding of the evolutionary history of the lion, but may also play a crucial role in conservation efforts aimed at protecting the species in its full diversity.

evolutionary biology↗