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Single nucleotide polymorphism discovery via genotyping by sequencing to assess population genetic structure and recurrent polyploidization in Andropogon gerardii
Author(s) -
McAllister Christine A.,
Miller Allison J.
Publication year - 2016
Publication title -
american journal of botany
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.218
H-Index - 151
eISSN - 1537-2197
pISSN - 0002-9122
DOI - 10.3732/ajb.1600146
Subject(s) - biology , andropogon , population , evolutionary biology , genetics , lineage (genetic) , single nucleotide polymorphism , ecology , genotype , gene , demography , sociology
PREMISE OF THE STUDY: Autopolyploidy, genome duplication within a single lineage, can result in multiple cytotypes within a species. Geographic distributions of cytotypes may reflect the evolutionary history of autopolyploid formation and subsequent population dynamics including stochastic (drift) and deterministic (differential selection among cytotypes) processes. Here, we used a population genomic approach to investigate whether autopolyploidy occurred once or multiple times in Andropogon gerardii , a widespread, North American grass with two predominant cytotypes. METHODS: Genotyping by sequencing was used to identify single nucleotide polymorphisms (SNPs) in individuals collected from across the geographic range of A. gerardii . Two independent approaches to SNP calling were used: the reference‐free UNEAK pipeline and a reference‐guided approach based on the sequenced Sorghum bicolor genome. SNPs generated using these pipelines were analyzed independently with genetic distance and clustering. KEY RESULTS: Analyses of the two SNP data sets showed very similar patterns of population‐level clustering of A. gerardii individuals: a cluster of A. gerardii individuals from the southern Plains, a northern Plains cluster, and a western cluster. Groupings of individuals corresponded to geographic localities regardless of cytotype: 6 x and 9 x individuals from the same geographic area clustered together. CONCLUSIONS: SNPs generated using reference‐guided and reference‐free pipelines in A. gerardii yielded unique subsets of genomic data. Both data sets suggest that the 9 x cytotype in A. gerardii likely evolved multiple times from 6 x progenitors across the range of the species. Genomic approaches like GBS and diverse bioinformatics pipelines used here facilitate evolutionary analyses of complex systems with multiple ploidy levels.