Archaeogenomics of European wheat: a proof of concept study

从考古遗址中发现的植物残骸是史前农业信息的主要来源。有时这些植物残骸含有保存完好的DNA。通过研究这种“古老的”DNA，有可能研究小麦、大麦和玉米等作物自被驯化以来是如何进化的，包括这些植物是如何适应人类带它们去的新环境的。古代植物的DNA分析相对容易，因为在这种条件下，DNA不会分解太多。不幸的是，干燥的材料并不常见，只能在沙漠或洞穴等干燥环境中找到。烧焦的遗骸更常见，这些是谷物和植物的其他部分，它们在烹饪时被烧焦，或者存在于着火的仓库中。烧焦的小麦和大麦谷物经常在欧洲的考古遗址中发现，这些谷物有时含有古代的DNA。问题是DNA只是保存得很差，因为分子暴露在高温下导致它们被分解成非常短的片段。为了获得DNA序列，首先需要使用聚合酶链反应（PCR）技术对从考古标本中提取的DNA分子进行复制。聚合酶链反应对短的DNA片段并不是特别有效，而且用它来研究烧焦遗骸中的古代DNA的尝试也不是很成功。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，尤其是在欧洲。例如，我们知道大麦现在已经适应了北欧的寒冷气候，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，还是这些变化只是后来才发生的。如果我们能研究保存下来的一些最早的大麦品种的DNA，我们就能找到答案，这些大麦品种生长在北欧。然而，对于那些一直困扰着研究烧焦植物遗骸中古代DNA的问题，或许有一个解决方案。在过去的五年中，新的DNA测序方法得到了发展。这些“新一代”方法非常适合研究短DNA分子，并已成功地用于研究尼安德特人骨骼和已灭绝的猛犸象的古代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（Assiros）的一个粮仓里的小麦谷物进行试验，该粮仓大约在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年代挖掘该遗址时发现了这些种子。我们希望通过使用下一代方法，我们将能够从阿西罗斯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.