Abstract
SummaryWild emmer wheat (Triticum turgidum ssp. dicoccoides) is the progenitor of wheat. We performed chromosome‐based survey sequencing of the 14 chromosomes, examining repetitive sequences, protein‐coding genes, miRNA/target pairs and tRNA genes, as well as syntenic relationships with related grasses. We found considerable differences in the content and distribution of repetitive sequences between the A and B subgenomes. The gene contents of individual chromosomes varied widely, not necessarily correlating with chromosome size. We catalogued candidate agronomically important loci, along with new alleles and flanking sequences that can be used to design exome sequencing. Syntenic relationships and virtual gene orders revealed several small‐scale evolutionary rearrangements, in addition to providing evidence for the 4AL‐5AL‐7BS translocation in wild emmer wheat. Chromosome‐based sequence assemblies contained five novel miRNA families, among 59 families putatively encoded in the entire genome which provide insight into the domestication of wheat and an overview of the genome content and organization.
Highlights
Wheat, a major cereal food crop, is rich in carbohydrates, proteins and minerals and is grown on over 220 million hectares of land worldwide (Henry et al, 2016; Mayer et al, 2014)
The formation of T. aestivum occurred through at least two spontaneous hybridizations accompanied by whole-genome duplications
To circumvent genome complexity of tetraploid T. dicoccoides, all 14 chromosomes were individually isolated by flow cytometry from two genotypes, based on bi-parametric analysis of GAA microsatellite content and DAPI fluorescence intensity, as described earlier (Akpinar et al, 2015b)
Summary
A major cereal food crop, is rich in carbohydrates, proteins and minerals and is grown on over 220 million hectares of land worldwide (Henry et al, 2016; Mayer et al, 2014). While the allotetraploid wheat was domesticated and is being cultivated as durum wheat, wild populations that diverged into subspecies continue to exist. T. dicoccoides genotype TR39477 exhibits outstanding tolerance to drought, whereas another genotype, TTD-22, is highly susceptible to this stress (Ergen and Budak, 2009; Ergen et al, 2009). Such genetic diversity should allow researchers to explore the molecular basis of these traits and discover favourable alleles for breeding. This resource remains largely untapped (Akpinar et al, 2015a; Budak et al, 2013a; Ergen and Budak, 2009; Nevo and Chen, 2010)
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