SNP‐skimming: A fast approach to map loci generating quantitative variation in natural populations

Abstract

Genome-wide association mapping (GWAS) is a method to estimate the contribution of segregating genetic loci to trait variation. A major challenge for applying GWAS to non-model species has been generating dense genome-wide markers that satisfy the key requirement that marker data is error-free. Here we present an approach to map loci within natural populations using inexpensive shallow genome sequencing. This ‘SNP skimming’ approach involves two steps: an initial genome-wide scan to identify putative targets followed by deep sequencing for confirmation of targeted loci. We apply our method to a test dataset of floral dimension variation in the plant Penstemon virgatus, a member of a genus that has experienced dynamic floral adaptation that reflects repeated transitions in primary pollinator. The ability to detect SNPs that generate phenotypic variation depends on population genetic factors such as population allele frequency, effect size, and epistasis as well as sampling effects contingent on missing data and genotype uncertainty. However, both simulations and the Penstemon data suggest that the most significant tests from the initial SNP skim are likely to be true positives – loci with subtle but significant quantitative effects on phenotype. We discuss the promise and limitations of this method and consider optimal experimental design for a given sequencing effort. Simulations demonstrate that sampling a larger number of individual at the expense of average read depth per individual maximizes the power to detect loci.

GOOGA: A platform to synthesize mapping experiments and identify genomic structural diversity

“…Even after numerous filtering steps (see S1 Appendix), SNP-level calls remain problematic (see S1 Fig for an illustration with data from three Mimulus recombinants). Under-calling of heterozygotes is often problematic with MSG data; both alleles appear less frequently than the binomial distribution predicts [55, 56]. Aggregating signal from closely linked SNPs addresses both low coverage and allele dropout in heterozygotes.…”

The role of dispersal limitation and reforestation in shaping the distributional shift of a forest herb under climate change

“…Only large, connected habitats were sampled to exclude populations in non-equilibrium states. We used single nucleotide polymorphism (SNP) skimming (Wessinger et al, 2018) to construct SNP matrices containing 406 pairwise Nei's genetic distances (Nei, 1978). The SNP matrix was constructed with the R packages "adegenet v.2.1.2", "vcfR v.1.8.0", "tidyverse v.1.2.1" and the genetic distances were calculated with "stAMPP v.1.6.1".…”

Conservation implications of genetic structure in the narrowest endemic quillwort from the Eastern Amazon

“…The genetic diversity analysis of I. cangae individuals was performed using the genome skimming approach (Figure 2a) (Malé et al, 2014;Weitemier et al, 2014;Wessinger et al, 2018). Shotgun paired-end libraries were constructed from 50 ng of isolated DNA.…”