Thumbnail Image
Publication

Genotyping by Sequencing and Plastome Analysis Finds High Genetic Variability and Geographical Structure in Dactylis glomerata L. in Northwest Europe Despite Lack of Ploidy Variation

Hodkinson, Trevor R.
; 
Perdereau, Aude
; 
Klaas, Manfred
; 
Cormican, Paul
; 
Barth, Susanne
Citations
Altmetric:
Keywords
diversity, Dactylis glomerata, forage, GBS, marginal land, genetic resources, phylogeography, plastome, SNPs
Date
2019-06-28
Collections
Crop Science
Show all metadata
Files
Thumbnail Image
main article
Adobe PDF, 1.93 MB
Research Projects
Organizational Units
Journal Issue
URI
http://hdl.handle.net/11019/2289
Citation
Hodkinson, T.R.; Perdereau, A.; Klaas, M.; Cormican, P.; Barth, S. Genotyping by Sequencing and Plastome Analysis Finds High Genetic Variability and Geographical Structure in Dactylis glomerata L. in Northwest Europe Despite Lack of Ploidy Variation. Agronomy 2019, 9, 342. https://doi.org/10.3390/agronomy9070342
Abstract
Large collections of the forage and bioenergy grass Dactylis glomerata were made in northwest (NW) Europe along east to west and north to south clines for genetic resource conservation and to inform breeding programmes of genetic diversity, genepools, and ploidy. Leaves were sampled for genetic analysis and seed and rhizome for ex-situ conservation. Genotyping by sequencing (GBS) was used to assay nuclear DNA diversity and plastome single nucleotide polymorphism (SNP) discovery was undertaken using a long-read PCR and MiSeq approach. Nuclear and plastid SNPs were analysed by principal component analysis (PCA) to compare genotypes. Flow cytometry revealed that all samples were tetraploid, but some genome size variation was recorded. GBS detected an average of approximately 10,000 to 15,000 SNPs per country sampled. The highest average number of private SNPs was recorded in Poland (median ca. 2000). Plastid DNA variation was also high (1466 SNPs, 17 SNPs/kbp). GBS data, and to a lesser extent plastome data, also show that genetic variation is structured geographically in NW Europe with loose clustering matching the country of plant origin. The results reveal extensive genetic diversity and genetic structuring in this versatile allogamous species despite lack of ploidy variation and high levels of human mediated geneflow via planting.
Funder
EU
Grant Number
289461
Embedded videos