simon.krattinger@kaust.edu.sa

Since the dawn of agriculture, bread wheat cultivation has been tightly interwoven with human history, culture, and migration in the Fertile Crescent and beyond. The suggested birthplace of bread wheat comprises an area along the southern shores of the Caspian Sea. This is where a hybridization between a tetraploid wheat and Tausch’s goatgrass (Aegilops tauschii) created bread wheat, the most widely cultivated crop species today. Previous reports indicated that an Ae. tauschii accession belonging to lineage 2 (L2) was the main contributor of the bread wheat D genome.

Here, we analyzed comprehensive Ae. tauschii genomic resources generated by the Open Wild Wheat Consortium to shed light on the composition, origin, and evolution of the bread wheat D genome. We used a k-mer based approach (IBSpy) to resolve the haplotype composition of the bread wheat D genome at a fine, 50-kb resolution.

We found that the bread wheat D genome represents a tapestry of haplotypes from different Ae. tauschii lineages and subpopulations, with only ~75% of the bread wheat D genome originating from Ae. tauschii L2 accessions from the southern Caspian Sea region. In particular, we reveal the dynamics of introgressions from the genetically distinct and geographically restricted Ae. tauschii lineage 3 (L3) into the bread wheat D genome. Ae. tauschii L3 is geographically restricted to modern-day Georgia and contemporary elite bread wheat cultivars contain around 1% of L3 introgressions. These L3 genomic segments are comparable to the Neanderthals’ genetic footprints in the human genome. Our analyses revealed a wide range of L3 introgression patterns across bread wheat landraces, with a cumulative size of L3 segments spanning a total of 660 Mb (16%) of the bread wheat D genome.

Our study revealed a complex evolutionary history of the bread wheat D genome. Following its emergence in the southern Caspian Sea region, bread wheat dispersal was accompanied by extensive gene flow from different Ae. tauschii populations. Although the proportions of alternative haplotype blocks in individual wheat cultivars are often low, the different segments can accumulate to considerable lengths across various wheat genotypes. These findings raise important questions about the adaptive potential of alternative haplotype blocks for wheat improvement.