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Ancient Barley Sequencing Study Finds Similarity to Modern Levantine Plants

Barley field in Lancaster County, Penn.

NEW YORK (GenomeWeb) – Barley landraces found in the present-day Levant have not changed much in the past 6,000 years, according to a new genomic analysis.

Barley was domesticated some 10,000 years ago in the Fertile Crescent, a region that includes portions of modern-day Iraq, Jordan, Lebanon, and Israel, and much of what's known about its domestication is derived from morphological studies of ancient remains and population genetics study of modern-day samples.

However, an archaeological excavation in Israel recently uncovered barley seeds dating back some 6,000 years, so an international team of researchers led by the Leibniz Institute of Plant Genetics and Crop Plant Research's Nils Stein sought to sequence these ancient grains, as they reported this week in Nature Genetics.

Stein and his colleagues also compared their ancient samples to a new dataset of 267 modern landraces and wild accessions — which was also reported in Nature Genetics this week — to find that their ancient samples were similar to present-day ones from the Southern Levant.

"For us, ancient DNA works like a time capsule that allows us to travel back in history and look into the domestication of crop plants at distinct time points in the past," said Johannes Krause from the Max Planck Institute for the Science of Human History in a statement.

Stein, Krause, and their colleagues extracted DNA from 10 ancient barley grains and sequenced them to generate 7.3 million to 21.5 million paired-end reads, which they then aligned to the barley reference genome. From this, they estimated the endogenous DNA content to be between 0.4 percent and 96.4 percent, and they noted that eight of the 10 samples exhibited DNA size and damage patterns consistent with that seen in other ancient DNA samples, suggesting that these samples were authentic.

They then treated the five DNA extracts with the largest portions of endogenous DNA with uracil-DNA glycosylase to limit the nucleotide misincorporation that can occur with damaged ancient DNA. These samples were then deeply sequenced to yield 82.5 million to 5.1 billion reads.

Meanwhile, researchers led by the James Hutton Institute's Robbie Waugh collected 267 georeferenced barley landraces and wild accessions to examine their geographic diversity. Exome sequencing of these samples yielded 30.7 paired-end reads, which they also mapped against the reference. In total, they identified more than 1.6 million SNPs and 143,000 short indels. In their analyses, Waugh and his colleagues uncovered allelic variations in barley that corresponded with their location of origin and environment.

Stein, Krause, and their colleagues then used this set of exomes in their own study as a comparison set.

Based on identity by state, the researchers calculated the relatedness of the ancient samples to the wild barley accessions from Waugh and his colleagues. From this, they found that their closest present-day genetic relative hailed from a site in the Upper Jordan Valley. An analysis relying on wild barley and landraces from the Fertile Crescent similarly pointed to that region for the greatest similarity with domesticated accessions. This Israel-Jordan region, the researchers noted, has previously been suggested as the center of barley domestication.

A principal components and admixture analysis suggested that there are otherwise strong genetic differences between wild and domesticated barley accessions. The ancient samples were assigned to the domesticated group, however both the ancient samples and the modern landraces from the Levant exhibited an increased level of wild ancestry. These and D statistic-based analyses suggested to the researchers that there was gene flow between wild and domesticated barley where they coexisted.

This, they added, indicates that modern-day landraces in the Levant are "remarkably similar" to their ancient selves.

"This similarity is an amazing finding considering to what extent the climate, but also the local flora and fauna, as well as the agricultural methods, have changed over this long period of time," first author Martin Mascher from the Leibniz Institute added in a statement.

This similarity also led the researchers to speculate that immigrants and conquerors that came to the region didn't bring their own seeds with them, but rather used local varieties.