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

Abstract

Molecular characterization of unsequenced plant species with complex genomes is now possible by genotyping-by-sequencing (GBS) using recent next generation sequencing technologies. This study represents the first use of GBS application to sample genome-wide variants of crested wheatgrass [Agropyron cristatum (L.) Gaertn.] and assess the genetic diversity present in 192 genotypes from 12 tetraploid lines. Bioinformatic analysis identified 45,507 single nucleotide polymorphism (SNP) markers in this outcrossing grass species. The model-based Bayesian analysis revealed four major clusters of the samples assayed. The diversity analysis revealed 15.8% of SNP variation residing among the 12 lines, and 12.1% SNP variation present among four genetic clusters identified by the Bayesian analysis. The principal coordinates analysis and dendrogram were able to distinguish four lines of Asian origin from Canadian cultivars and breeding lines. These results serve as a valuable resource for understanding genetic variability, and will aid in the genetic improvement of this outcrossing polyploid grass species for forage production. These findings illustrate the potential of GBS application in the characterization of non-model polyploid plants with complex genomes.

Genome-wide genetic diversity and population structure of Garcinia kola (Heckel) in Benin using DArT-Seq technology

“…SNP markers are the most widely used genotyping markers due to their abundance in the genome [13]. Diversity array technology (DArT) along with other high throughput sequencing techniques have been increasingly adopted as a rapid and low-cost molecular techniques for SNP discovery, genotyping, and genetic variability analysis for various plant species as they allow for the study of the genetic diversity of a large number of entities and complex genomes [14][15][16][17]. The present study investigates the current level of genetic diversity and population structure of G. kola populations in Benin using a DArT genotyping by sequencing (GBS) approach.…”

Advancing Bromegrass Breeding Through Imaging Phenotyping and Genomic Selection: A Review

“…With the advances in high-throughput phenotyping technologies and flexible, low-cost single nucleotide polymorphism marker platforms, such as genotyping-bysequencing (GBS) (Elshire et al, 2011), GS has recently emerged as a prospect for improving yield of forage species. GBS can provide the high-density markers typically needed for GS based complex traits selection in forage species (Hayes et al, 2013;Baral et al, 2018). Thus, GS can enhance the rate of genetic gain by reducing the length of a breeding cycle and increasing selection accuracy (Fu et al, 2017).…”

“…These studies, together, suggest that GS is successful in alfalfa and perennial ryegrass breeding (Table 6). However, bromegrass (allo-auto-octoploid) is much more genetically complex compared to ryegrass (diploid) and alfalfa (auto-tetraploid) (Baral et al, 2018). High density genetic markers along with appropriate plant breeding schemes may be considered to address genetic complexity and to increase prediction accuracy of target traits in bromegrass.…”

Advancing crested wheatgrass [Agropyron cristatum (L.) Gaertn.] breeding through genotyping-by-sequencing and genomic selection

“…The rate of genetic gain in forage species is < 1% per year [16,19], which is lower than that of major cereal crop species. Several factors such as a highly outcrossing nature due to self-incompatibility, prevalence of high levels of genetic heterozygosity and heterogeneity within crested wheatgrass species [15], genotypic and environmental effects and their interactions are bottlenecks towards accelerated breeding of crested wheatgrass. Thus, it is difficult to perform trait evaluation through current methods of phenotypic evaluation alone.…”