Genetic Diversity of Northern Wheatgrass (Elymus lanceolatus ssp. lanceolatus) as Revealed by Genotyping-by-Sequencing

Abstract

Recent advances in next generation sequencing technologies make genotyping-by-sequencing (GBS) more feasible for the molecular characterization of plant germplasm with complex and unsequenced genomes. This study represents the first preliminary effort using GBS to discover genome-wide genetic variants of northern wheatgrass (Elymus lanceolatus ssp. lanceolatus (Scribn. and J. G. Sm.) Gould) plants and to assess the genetic diversity present in four cultivated and six wild accessions. The effort generated the first novel set of genomic resources and 5659 single nucleotide polymorphism (SNP) markers for this tetraploid grass. The diversity analysis revealed 8.8% of SNP variation residing among the 10 accessions and 1.9% SNP variation present between cultivated and wild accessions. The Bayesian analysis identified three major clusters of the assayed samples, and the principal coordinates analysis revealed the genetic distinctness of the two accessions collected from Nevada and Wyoming. The flow cytometry analysis confirmed the tetraploid nature of some of the assayed samples and estimated the average genome size to be 9.3-9.4 Gb for this species. These findings are useful for the genetic improvement of this native grass species for forage production and rangeland reclamation. The findings are also encouraging for the broad application of genotyping-by-sequencing in the characterization of genome-wide genetic variability in non-model polyploid plants.

Genotyping-by-Sequencing Enhances Genetic Diversity Analysis of Crested Wheatgrass [Agropyron cristatum (L.) Gaertn.]

“…Also, the experimental cost for sampling genome-wide variants in this study was roughly $12,000, suggesting the feasibility of a wider application of GBS to characterize other perennial polyploid grass species. The results of the present study, along with those published in northern wheatgrass and wild oat [ 12 , 13 ], demonstrate the utility of GBS in molecular characterization of non-model plants with complex ploidy and genetic structures.…”

“…This approach has been successfully applied in the study of diploid and polyploid genomes in oat ( Avena sativa ) [ 10 , 11 , 12 ] and genetic diversity analysis of northern wheatgrass ( Elymus lanceolatus ssp. Lanceolatus ) [ 13 ].…”

“…The molecular characterization is now more feasible than before with the advanced sequencing technology and reduced cost to acquire informative markers such as SNPs in non-model polyploid CWG plants. Recent GBS studies in polyploid plants [ 10 , 13 ] demonstrate the likelihood that GBS will unveil genetic variability on a genome-wide scale in CWG plants, and characterize CWG germplasm for breeding and genetic research.…”

Population structure and phylogeography of Elymus mutabilis and its genetic relationships with E. transbaicalensis (Poaceae)

“…The main drawbacks are relatively high proportion of missing data, uneven genome coverage and potential issues related to polyploidy. Diversity studies using GBS in Elymus have previously been done by Li et al (2018), analyzing E. lanceolatus ssp. lanceolatus .…”