Archaeogenomics of European wheat: a proof of concept study

从考古遗址中发现的植物遗骸是有关史前农业的主要信息来源。有时这些植物遗骸含有保存的DNA。通过研究这种“古老”的DNA，人们可以研究小麦、大麦和玉米等作物自被驯化以来是如何进化的，包括这些植物适应人类新环境的方式。古代DNA分析相对容易与植物已保存干燥，因为在这些条件下的DNA不会分解太多。不幸的是，干燥的物质并不常见，只有在沙漠或洞穴等干燥环境中才能找到。烧焦的遗骸更常见，这些是谷物和植物的其他部分，它们在烹饪时被烧毁，或者存在于着火的商店中。在欧洲的考古遗址中经常发现烧焦的小麦和大麦颗粒，这些颗粒有时含有古老的DNA。问题是DNA保存得很差，因为分子暴露在高温下，导致它们分解成很短的片段。为了获得DNA序列，首先需要使用称为聚合酶链式反应（PCR）的技术复制从考古标本中提取的DNA分子。聚合酶链反应对短的DNA片段并不起作用，试图用它来研究烧焦的遗骸中的古代DNA也不是很成功。这是令人沮丧的，因为对烧焦遗骸的古代DNA分析可以告诉我们很多关于史前农业的信息，特别是在欧洲。例如，我们知道大麦现在适应了北方欧洲的寒冷气候，但我们不知道导致这种适应的基因变化是在第一批农民将作物转移到这些地区时发生的，还是这些变化只是在后来发生的。我们可以发现我们是否可以在保存下来的北方欧洲种植的最早的大麦品种中研究古代DNA。然而，在烧焦的植物遗骸中研究古代DNA的努力中，一直困扰着人们的问题可能会有一个解决方案。在过去的五年中，已经开发了用于DNA测序的新方法。这些“下一代”方法非常适合短DNA分子的研究，并已成功用于尼安德特人骨骼和灭绝的长毛猛犸象的古代DNA。在这个项目中，我们将测试这些新方法是否也适用于烧焦的植物遗骸。我们将用希腊阿西罗斯一个粮仓里的小麦粒来尝试它们，这个粮仓大约在3000年前被烧毁，留下了大量烧焦的种子，考古学家在20世纪80年代挖掘这个遗址时发现了这些种子。我们希望通过使用下一代方法，我们将能够从Assiros谷物中获得小麦基因序列。

Plant remains recovered from archaeological sites are a major source of information concerning prehistoric agriculture. Sometimes these plant remains contain preserved DNA. By studying this 'ancient' DNA it has been possible to examine how crops such as wheat, barley and maize have evolved since they were domesticated, including the way in which these plants have adapted to the new environments to which they have been taken by humans. Ancient DNA analysis is relatively easy with plants that have been preserved by desiccation, as under these conditions the DNA does not break down too much. Unfortunately, desiccated material is uncommon, being found only in dry environments such as deserts or inside caves. Charred remains are much commoner, these being grains and other parts of plants that became burnt while they were being cooked, or were present in stores that caught fire. Charred grains of wheat and barley are often found at European archaeological sites, and these sometimes contain ancient DNA. The problem is that the DNA is only poorly preserved, because the high temperatures to which the molecules have been exposed have resulted in them becoming broken down into very short fragments. To obtain DNA sequences it is first necessary to make copies of the DNA molecules extracted from an archaeological specimen, using the technique called the polymerase chain reaction (PCR). PCR does not work particularly well with short DNA fragments, and attempts to use it to study the ancient DNA in charred remains have not been very successful. This is frustrating because ancient DNA analysis of charred remains could tell us a great deal about prehistoric agriculture, especially in Europe. For example, we know that barley is nowadays adapted to the cold climates of northern Europe, but we do not know if the genetic changes that resulted in this adaptation occurred as the crops were being moved to these regions by the first farmers, or if these changes only occurred later. We could find out if we could study ancient DNA in preserved remains of some of the earliest barley varieties that were grown in northern Europe. There might, however, be a solution to the problems that have plagued attempts to study ancient DNA in charred plant remains. During the last five years new methods for DNA sequencing have been developed. These 'next generation' methods are ideally suited to the study of short DNA molecules, and have been used successfully with ancient DNA from Neanderthal bones and extinct woolly mammoths. In this project we will test whether these new methods will also work with charred plant remains. We will try them out with wheat grains from a granary at Assiros in Greece, which burnt down approximately 3000 years ago, leaving large amounts of charred seeds which were recovered when archaeologists excavated the site in the 1980s. We hope that by using next generation methods we will be able to obtain sequences of wheat genes from the Assiros grains.