Israelis part of gene sequencers of 6,000-year-old barley grains

The cave, which was very difficult to reach and was used by humans about 6,000 years ago, was probably used only as a very temporary refuge, they suggested.

Einstien statue Hebrew University (photo credit: HEBREW UNIVERSITY)
Einstien statue Hebrew University
(photo credit: HEBREW UNIVERSITY)
An international team of researchers has succeeded for the first time in sequencing the genome of Chalcolithic barley grains, making the 6,000-yearold seeds the oldest plant genome ever to be reconstructed.
The results – which underscore the importance of Israel as a center for domestication from which agriculture spread to the rest of the world – have just been published in the online version of the journal Nature Genetics.
They had been found in the Yoram Cave on the southern cliff of the Masada fortress in the Judean Desert, close to the Dead Sea. Genetically, the prehistoric barley is very similar to present-day barley grown in the Southern Levant, said the scientists, thus supporting the existing hypothesis of barley domestication having occurred in the Upper Jordan Valley.
Members of the research team are from the Leibniz Institute of Plant Genetics and Crop Plant Research in Gatersleben, Germany; Bar-Ilan University; the Hebrew University of Jerusalem; the Max Planck Institute for the Science of Human History in Jena, Germany; the University of Haifa; the James Hutton Institute of the UK; the University of California at Santa Cruz; the University of Minnesota- St. Paul; and the University of Tübingen, Germany.
The analyzed grains, together with tens of thousands of other plant remains, were retrieved during a systematic archeological excavation headed by Dr. Uri Davidovich of HU’s archeology institute and Dr. Nimrod Marom of the Zinman archeology institute at the University of Haifa. The archeobotanical analysis was led by BIU Prof. Ehud Weiss.
The cave, which was very difficult to reach and was used by humans about 6,000 years ago, was probably used only as a very temporary refuge, they suggested.
Most studies of archeobotanical findings have been limited to the comparison of ancient and present-day specimens based on their structure. Up to now, only prehistoric corn has been genetically reconstructed. In this research, the team succeeded in sequencing the complete genome of the 6,000-year-old barley grains.
“These archeological remains provided a unique opportunity for us to finally sequence a Chalcolithic plant genome. The genetic material has been well-preserved for several millennia due to the extreme dryness of the region,” said Weiss.
To determine the age of the ancient seeds, the researchers split the grains and subjected half of them to radiocarbon dating while the other half was used to extract the ancient DNA.
“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,” explained Dr. Johannes Krause, director of the archeogenetics at the Max Planck Institute.
Wheat and barley were grown 10,000 years ago in the Fertile Crescent, a sickle-shaped region stretching from present-day Iraq and Iran through Turkey and Syria into Lebanon, Israel and Jordan. Even now, the wild forms of these two crops persist in the region and are among the major model species studied at the University of Haifa’s evolution institute. “It was from there that grain farming originated and later spread to Europe, Asia and North Africa,” explained Prof. Tzion Fahima of that university.
“Our analyses show that the seeds cultivated 6,000 years ago greatly differ genetically from the wild forms we find today in the region. However, they show considerable genetic overlap with present- day domesticated lines from the region,” said Dr. Nils Stein, who directed the comparison of the ancient genome with modern genomes at the Leibniz Institute with the support of Prof. Robbie Waugh and colleagues at the James Hutton Institute and Prof. Gary Muehlbauer of the University of Minnesota. “This demonstrates that the domestication of barley in the Fertile Crescent was already well advanced very early.”
The comparison of the ancient seeds with wild forms from the region and with so-called “landraces” (local barley lines grown by farmers in the Near East) enabled to geographically suggest, according to Fahima and colleagues, “the origin of the domestication of barley within the Upper Jordan Valley – a hypothesis that is also supported by two archeological sites in the surrounding area where the hitherto earliest remains of barley cultivation have been found.
The genetic overlap with present-day domesticated lines from the region is also important, they said. “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,” says Dr. Martin Mascher from the Leibniz Institute who was the lead author of the study. The researchers therefore assume that conquerors and immigrants coming to the region did not bring their own crop seeds from their former homelands, but continued cultivating the locally adapted extant landraces.
Combining archeology, archeobotany, genetics and computational genomics in an interdisciplinary study has produced novel insights into the origins of our crop plants. “This is just the beginning of a new and exciting line of research,” predicted Dr. Verena Schuenemann, from Tuebingen University, the study’s second lead author. “DNA-analysis of archeological remains of prehistoric plants will provide us with novel insights into the origin, domestication and spread of crop plants.”