Estimating genomic diversity and population differentiation – an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri

BMC Genomics

Research Article

Marianne Leuzinger¹  Alex Widmer¹  Marie Roumet¹  Martin C. Fischer¹  Rolf Holderegger²  Kentaro K. Shimizu³  Christian Rellstab⁴  Felix Gugerli⁴ 

[1] ETH Zürich, Institute of Integrative Biology, Universitätstrasse 16, 8092, Zürich, Switzerland;ETH Zürich, Institute of Integrative Biology, Universitätstrasse 16, 8092, Zürich, Switzerland;WSL Swiss Federal Research Institute, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland;Institute of Evolutionary Biology and Environmental Studies and Institute of Plant Biology, University of Zurich, Winterthurerstrasse 190, 8057, Zürich, Switzerland;WSL Swiss Federal Research Institute, Zürcherstrasse 111, 8903, Birmensdorf, Switzerland;

关键词: Microsatellites;    SSR;    Arabidopsis halleri;    Genetic diversity;    Expected heterozygosity;    SNPs;    Population genomics;    Whole-genome re-sequencing;    Pool-Seq;    Conservation units;   

DOI  :  10.1186/s12864-016-3459-7

 received in 2016-04-01, accepted in 2016-12-22,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundMicrosatellite markers are widely used for estimating genetic diversity within and differentiation among populations. However, it has rarely been tested whether such estimates are useful proxies for genome-wide patterns of variation and differentiation. Here, we compared microsatellite variation with genome-wide single nucleotide polymorphisms (SNPs) to assess and quantify potential marker-specific biases and derive recommendations for future studies. Overall, we genotyped 180 Arabidopsis halleri individuals from nine populations using 20 microsatellite markers. Twelve of these markers were originally developed for Arabidopsis thaliana (cross-species markers) and eight for A. halleri (species-specific markers). We further characterized 2 million SNPs across the genome with a pooled whole-genome re-sequencing approach (Pool-Seq).ResultsOur analyses revealed that estimates of genetic diversity and differentiation derived from cross-species and species-specific microsatellites differed substantially and that expected microsatellite heterozygosity (SSR-He) was not significantly correlated with genome-wide SNP diversity estimates (SNP-He and θWatterson) in A. halleri. Instead, microsatellite allelic richness (Ar) was a better proxy for genome-wide SNP diversity. Estimates of genetic differentiation among populations (FST) based on both marker types were correlated, but microsatellite-based estimates were significantly larger than those from SNPs. Possible causes include the limited number of microsatellite markers used, marker ascertainment bias, as well as the high variance in microsatellite-derived estimates. In contrast, genome-wide SNP data provided unbiased estimates of genetic diversity independent of whether genome- or only exome-wide SNPs were used. Further, we inferred that a few thousand random SNPs are sufficient to reliably estimate genome-wide diversity and to distinguish among populations differing in genetic variation.ConclusionsWe recommend that future analyses of genetic diversity within and differentiation among populations use randomly selected high-throughput sequencing-based SNP data to draw conclusions on genome-wide diversity patterns. In species comparable to A. halleri, a few thousand SNPs are sufficient to achieve this goal.

【 授权许可】

CC BY   
© The Author(s). 2017