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 species-specific 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.
Highlights
Wheat (Triticum spp.) is the most widely cultivated food crop worldwide
The combined Haplotag analysis generated a total of 1,542,332 single nucleotide polymorphism (SNP) from the raw variants, and a total of 52,186 SNPs were called after filtering out duplicated reads (Supplementary Figure S1)
A total 14,395 SNPs at 80% missing level was selected for Triticum species discrimination, which includes 114 accessions
Summary
Wheat (Triticum spp.) is the most widely cultivated food crop worldwide. The large amount of wheat accessions in the world’s genebanks has reflects the importance of wheat as a world crop (FAO, 2010). Available data clarify the economic importance of wheat as the total world wheat production has increased substantially from 521 million tons (mt) in 1987 to 751 mt in 2016. Among food crops worldwide, wheat reveals the greatest range in its area of cultivation, from 67◦N in Scandinavia and Russia to 45◦S in Argentina, including regions in the tropics and subtropics, with different varieties sown according to the climate (Feldman, 1995). There is an increasing global demand for wheat products based on the consumption in new markets beyond its region of climatic adaptation. Modern plant breeders are challenged to make novel varieties suitable to various climatic conditions in order to increase crop yield
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
