Genotyping-by-Sequencing Derived Single Nucleotide Polymorphisms Provide the First Well-Resolved Phylogeny for the Genus Triticum (Poaceae)

Abstract

Wheat (Triticum spp.) has been an important staple food crop for mankind since the beginning of agriculture. The genus Triticum L. is composed of diploid, tetraploid, and hexaploid species, majority of which have not yet been discriminated clearly, and hence their phylogeny and classification remain unresolved. Genotyping-by-sequencing (GBS) is an easy and affordable method that allows us to generate genome-wide single nucleotide polymorphism (SNP) markers. In this study, we used GBS to obtain SNPs covering all seven chromosomes from 283 accessions of Triticum-related genera. After filtering low-quality and redundant SNPs based on haplotype information, the GBS assay provided 14,188 high-quality SNPs that were distributed across the A (71%), B (26%), and D (2.4%) genomes. Cluster analysis and discriminant analysis of principal components (DAPC) allowed us to distinguish six distinct groups that matched well with Triticum species complexity. We constructed a Bayesian phylogenetic tree using 14,188 SNPs, in which 17 Triticum species and subspecies were discriminated. Dendrogram analysis revealed that the polyploid wheat species could be divided into groups according to the presence of A, B, D, and G genomes with strong nodal support and provided new insight into the evolution of spelt wheat. A total of 2,692 speciesspecific SNPs were identified to discriminate the common (T. aestivum) and durum (T. turgidum) wheat cultivar and landraces. In principal component analysis grouping, the two wheat species formed individual clusters and the SNPs were able to distinguish up to nine groups of 10 subspecies. This study demonstrated that GBS-derived SNPs could be used efficiently in genebank management to classify Triticum species and subspecies that are very difficult to distinguish by their morphological characters.

Genome-Wide SNP Markers for Genotypic and Phenotypic Differentiation of Melon (Cucumis melo L.) Varieties Using Genotyping-by-Sequencing

“…Various SNP-based molecular markers have been developed and successfully used in plant species identification [5,26,53,60]. Among these, CAPS markers have been found to be promising for detecting the intra-and interspecies variation of different species [61].…”

“…Recently, genotyping-by-sequencing (GBS) approaches have been used as an efficient and affordable method for identifying a large number of genomic markers to differentiate species and subspecies [24,25]. In our earlier study, GBS-derived SNPs were efficiently used to classify Triticum species and subspecies that are very difficult to distinguish based on their morphological characteristics [26]. Genotyping-by-sequencing has also been used in the melon population, and highly informative genome-wide SNPs have been generated successfully [27,28].…”

Detecting Major Introgressions in Wheat and their Putative Origins Using Coverage Analysis

“…Using this method and a wide range of wheat relatives 8,26,27 (Table S2), we detected nine large introgressions in the 10 wheat RQAs, located on chromosomes 2A, 2B, 2D, 3D, and 4A (Figure 1, Table S3, Supplementary Data 1). For all nine introgressions, we identified a putative donor.…”

“…Interestingly, we also detected regions with decreased coverage on chromosomes 2A and 4AL in Triticum boeoticum (2n=2x=14, A b ) and Triticum monococcum (2n=2x=14, A b ), while no decrease in coverage in these regions was detected in polyploid relatives including Triticum dicoccoides (2n=4x=28, BA), Triticum dicoccon (2n=4x=28, BA), Triticum spelta (2n=6x=42, BAD), and Triticum sphaerococcum (2n=6x=42, BAD) (Figure 2), suggesting that these introgressions may be common to all these polyploid taxa. One exception was accession K240104 of T. dicoccoides originating from Syria 27 , in which a low-coverage region was detected on chromosome 2A. This low-coverage region on chromosome 2A is located at about 395-407 Mb in Chinese Spring and harbours 17 annotated protein-coding genes (TraesCS2A01G257500 -TraesCS2A01G259100).…”

The History of Lentil (Lens culinaris subsp. culinaris) Domestication and Spread as Revealed by Genotyping-by-Sequencing of Wild and Landrace Accessions

“…GBS was able to detect SNPs for the particular set of individuals used, thus avoiding the ascertainment bias that occurs when panels of SNPs developed in a small number of commercial varieties are used to screen landraces or wild plants ( Heslot et al, 2013 ; Chu et al, 2020 ). Other than in lentil ( Wong et al, 2015 ), GBS has been used to investigate phylogenetic relationships within carrot ( Arbizu et al, 2016 ), amaranth ( Stetter and Schmid, 2017 ), coffee ( Hamon et al, 2017 ), and wheat ( Hyun et al, 2020 ).…”