Abstract
Structural variations (SVs) such as copy number and presence–absence variations are polymorphisms that are known to impact genome composition at the species level and are associated with phenotypic variations. In the absence of a reference genome sequence, their study has long been hampered in wheat. The recent production of new wheat genomic resources has led to a paradigm shift, making possible to investigate the extent of SVs among cultivated and wild accessions. We assessed SVs affecting genes and transposable elements (TEs) in a Triticeae diversity panel of 45 accessions from seven tetraploid and hexaploid species using high-coverage shotgun sequencing of sorted chromosome 3B DNA and dedicated bioinformatics approaches. We showed that 23% of the genes are variable within this panel, and we also identified 330 genes absent from the reference accession Chinese Spring. In addition, 60% of the TE-derived reference markers were absent in at least one accession, revealing a high level of intraspecific and interspecific variability affecting the TE space. Chromosome extremities are the regions where we observed most of the variability, confirming previous hypotheses made when comparing wheat with the other grasses. This study provides deeper insights into the genomic variability affecting the complex Triticeae genomes at the intraspecific and interspecific levels and suggests a phylogeny with independent hybridization events leading to different hexaploid species.
Highlights
Bread wheat is one of the most consumed crops in the world (Hawkesford et al, 2013), and a better knowledge of the extent of genomic diversity among wheat and its wild relatives is needed to meet the challenge of ensuring food security in the context of climate change and sustainability of agriculture
To study the extent of SVs in the wheat genome, chromosome 3B was flow-sorted from 45 accessions belonging to seven wheat species: hexaploid T. aestivum (Tae), T. spelta (Tsp), T. macha (Tma), and tetraploid T. durum (Tdu), T. dicoccoides (Tde), T. dicoccum (Tdi), and T. carthlicum (Tca) (Table 1)
The 45 resequencing datasets were mapped on the complete Chinese Spring (CS) genome sequence (IWGSC RefSeq_v1.0)
Summary
Bread wheat is one of the most consumed crops in the world (Hawkesford et al, 2013), and a better knowledge of the extent of genomic diversity among wheat and its wild relatives is needed to meet the challenge of ensuring food security in the context of climate change and sustainability of agriculture. Chromosome 3B is the largest of the 21 wheat chromosomes and, the only chromosome that can be isolated individually from any wheat cultivar using flow cytometric sorting (Doležel et al, 2007) This is why chromosome 3B was established as the model to study the wheat genome. Chromosomal extremities are the regions where most of recombination events occur, are enriched in genes, and are depleted in TEs (Choulet et al, 2014; Daron et al, 2014). They are enriched in non-syntenic and recently duplicated genes whose functions are related to adaptation (Glover et al, 2015; Pingault et al, 2015). These conclusions were drawn through comparisons with rice, maize, Brachypodium, and sorghum, but little is known about the extent of structural variability among Triticeae and at the intraspecific level
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