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

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.

A multispecies amplicon sequencing approach for genetic diversity assessments in grassland plant species

“…They were also lower than an estimate based on genic regions in L. perenne (35.6 SNPs/kbp; Ruttink et al, 2015 ). The SNP densities we found in our sequence capture data are closer to the 17 SNPs/kbp reported for a set of plastomes from a comprehensive sampling of D. glomerata from western Europe (Hodkinson et al, 2019 ).…”

MORPHOLOGICAL CHARACTERIZATION OF ORCHARDGRASS (Dactylis glomerata L.) NATURALLY SPREAD IN EASTERN ANATOLIA, TÜRKIYE

“…Our findings are in complete agreement with the finding Uysal et al, (2015) and Hodkinson et al, (2019) where the principal components represented 72.66% of total variation observed in orchardgrass ecotypes, collected from natural pastures part of the Eastern Anatolia Region and some of them province have not same ecological feature.…”

“…To determine the genetic diversity of orchardgrass in this study, the genotype were collected from various locations of the Eastern Anatolia, Türkiye, and then planted in the same site, in order to neutralize the effect of environmental factors. The method used in the current study is consistent with that used in previous researcers (Ayan et al 2006;Mut and Ayan 2008;Uysal et al 2015;Hodkinson et al, 2019). Many studies determined the genetic variability of orchardgrass genotypes in collected from different locations.…”

A multispecies amplicon sequencing approach for genetic diversity assessment in grassland plant species

“…SNP density per species (Table 3) were lower than a genome-wide estimate in L. multiflorum (31 SNPs/kbp; Knorst et al, 2019) and than an estimate based on genic regions in L. perenne (35.6 SNPs/kbp; Ruttink et al, 2015). The SNP densities we found in our sequence capture data (Table 3) are closer to the 17 SNPs/kbp reported for a set of plastomes from a comprehensive sampling of D. glomerata from western Europe (Hodkinson et al, 2019).…”