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.
Highlights
Genotyping-by-sequencing (GBS) has emerged as a powerful genomic approach for characterizing the genetic diversity of non-model plants on a genome-wide scale [1,2,3,4]
The accession TMP24008 was identified as an octoploid, but not a tetraploid, northern wheatgrass. These identifications were done after genotyping-by-sequencing of the 144 samples for the 12 accessions as described below, but only the samples of the 10 accessions listed in Table 1 were used for the bioinformatics and genetic diversity analysis
Assessing the distribution of minor allele frequency for the data set of the 5659 single nucleotide polymorphism (SNP) markers revealed a wide range of minor allele frequencies from 0.05 to 0.50 with the average of 0.184 and displayed a gradual reduction of minor alleles with increased occurrence frequencies from 0.125 to 0.5 (Figure 1A)
Summary
Genotyping-by-sequencing (GBS) has emerged as a powerful genomic approach for characterizing the genetic diversity of non-model plants on a genome-wide scale [1,2,3,4]. To address some of these challenges, Tinker et al [11] developed a GBS-based pipeline called Haplotag that can generate tag-level haplotype and single nucleotide polymorphism (SNP) data for polyploid organisms. Successful applications of this approach have been reported in a comparative analysis of diploid, tetraploid, and hexaploid genomes of 27 oat species [12] and in an adaptation study of cultivated oat [13]
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