Einkorn (Triticum monococcum) was the first wheat species domesticated by humans, around 10,000 years ago, playing an important role in the establishment of agriculture in the Middle East. Now, researchers have completed the first complete genome map of the ancient grain including annotated, chromosome-scale, reference assemblies of one wild and one domesticated einkorn accession—as well as whole-genome sequencing of an einkorn diversity panel.

The 5.2-billion-letter-long sequence provides a window into the evolutionary origins of different wheat species. In addition, it could help farmers and crop breeders with genomics-assisted improvement of einkorn and bread wheat—developing varieties with enhanced disease resistance, higher yields, and improved hardiness.

This work is published in Nature in the article, “Einkorn genomics sheds light on history of the oldest domesticated wheat.

“By understanding the genetic diversity and evolutionary history of einkorn, researchers can now leverage its potential for future breeding efforts and the development of more resilient and nutritious wheat varieties,” said Hanin Ahmed, PhD, a former graduate student at King Abdullah University of Science & Technology (KAUST) in Saudi Arabia, where the research was performed.

wheat genome
Painting of Triticum monococcum showing the domesticated (left) and wild (right) einkorn wheat spikes. [Robyn Palescandolo for KAUST’s Center for Desert Agriculture.]

Einkorn is still consumed today, cherished for its unique flavor profile and numerous nutritional benefits. However, its significance in global food production over the millennia has gradually declined as the popularity of bread wheat soared.

Bread wheat varieties generally produce higher yields, making them more economically viable for large-scale commercial agriculture. Yet, compared to its wild cousins, modern bread wheat has a reduced genetic diversity—and many breeders are now concerned about how existing crops will fare in the face of climate change and new disease threats. Because einkorn has maintained a larger gene pool, it could hold the genetic secrets needed to develop bread wheat that can continue to feed the world’s growing population.

Now, a team of researchers from KAUST, deployed a combination of DNA sequencing technologies to create high-quality genome assemblies for wild and domesticated einkorn varieties. More specifically, they used a combination of PacBio circular consensus sequencing, optical mapping, and chromosome conformation capture.

Researchers had previously assumed that the evolution of wheat was a steady process with limited mixing of different wheat species. But, according to Simon Krattinger, PhD, associate professor of plant science at KAUST, “Our genomic analyses now show that the history of wheat is much more complex and involved a lot of mixing and gene flow between different wheat species,” including einkorn, which likely grew in close proximity to other wheat varieties, leading to DNA mixing between the two closely related species that remains evident to this day.

Indeed, the introduction of einkorn genes into the modern bread wheat genome in the past may have played a role in assisting bread wheat to adapt to changing climatic conditions, Krattinger noted. And if history is any indication, the same could hold true for the future, especially with the aid of modern molecularly guided breeding techniques.

“Our lab’s resources will help to precisely transfer beneficial genes from einkorn into bread wheat,” Krattinger added.

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