Archaeogenomics of Sorghum domestication and adaptation

在过去的十年里，我们对进化和基因组水平的理解在后基因组时代有了很大的进步。令许多人惊讶的是，人们通常会发现，很少有强烈的选择性扫描，而且越来越明显的是，进化通常是许多座位上微小变化的交响乐。植物的驯化进化，以及随后在驯化下的进化，也显示出与作物基因组测序相同的模式。这也让许多人感到惊讶，因为直到最近，人们还认为与驯化相关的性状选择--驯化综合症--非常强大，野生和驯化形式之间的转换和快速。在基因组证据的佐证中，驯化综合症特征的选择强度也直接从考古记录中估计出来，并发现比之前假设的要弱得多，完全在自然选择下通常发现的范围内。基于模型的证据进一步证实了驯化综合症的弱选择。弱选择的一个后果是基因组中的选择签名也很弱。事实上，它们是如此脆弱，以至于我们可能无法全部检测到它们，因为它们自驯化以来已经腐烂了太多。此外，驯化后野生和驯化种群之间的基因导入流也可能使驯化作物的遗传多样性模式复杂化。理想情况下，我们希望在这些微弱的选择信号腐烂之前，以及在导入事件发生之前的一段时间里，我们能够获得遗传信息。技术的进步使我们现在可以从考古样本中产生基因组，这将对实现这些理想目标大有裨益。在这项研究中，我们将使用第三代单分子测序技术重建高粱的考古基因组，这些时间点几乎可以追溯到驯化时间的一半。我们将把这些与现代基因组进行对比，我们也将在这个项目中重建现代基因组。高粱是这项研究的首选作物，原因有很多。它是最新驯化的作物之一，因此相对容易获得生物分子保存良好的考古样品，这些样品与驯化时间非常接近。它是近亲繁殖者，基因组很小，这使得基因组重建不是太雄心勃勃。高粱在干旱地区也是一种重要的作物，具有适应干旱的进化史。有趣的是，高粱栽培小种对干旱和病虫害的耐受性逐渐增强，有人认为这是反复导入不同野生品种的结果。通过将考古基因组与高粱所有五个栽培小种和四个野生品种的现代基因组进行比较，我们将更好地了解高粱驯化的进化是如何发生的，以及它是如何适应干旱条件的。这项研究将建立驯化进化的重要原理，这可能被证明对一般进化研究具有重要意义。它还将提供对当今世界面临的最重要的粮食安全问题之一的洞察，即一种作物如何进化出耐旱性，以及这是否可以转化为其他作物。

Our understanding of evolution and the genomic level has progressed substantially over the last decade in the post genomic era. To the surprise of many, it has typically been found that strong selective sweeps have been few, and it is becoming apparent that evolution generally progresses as a symphony of small changes over many loci. The evolution of domestication of plants, and subsequent evolution under domestication, is also showing the same pattern as crop genomes are sequenced. This also has been a surprise for many because until recently it had been assumed the selection of traits associated with domestication, the domestication syndrome, had been very strong and the transition between wild and domesticated forms and rapid. In corroboration of genomic evidence, the strength of selection of domestication syndrome traits has also been estimated directly from the archaeological record and found to be much weaker than previously supposed, well within the range normally found under natural selection. Further corroboration is found with model-based evidence for weak selection of the domestication syndrome.A consequence of weak selection is that the signatures of selection in the genome are also weak. So weak, in fact, that we may not be able to detect them all because they have decayed too much since the time of domestication. Furthermore, the patterns of genetic diversity seen in domesticated crops can also be complicated by introgressive gene flow between the wild and domesticated populations after domestication. Ideally, we would like to have genetic information from a time before these weak signatures of selection had decayed, and before introgression events had occurred. Technological advance is such that we can now generate genomes from archaeological samples, which would go a long way to achieving these ideal goals. In this study we will reconstruct archaeological genomes of the crop Sorghum from time points that stretch almost half way back to the time of domestication using third generation single molecule sequencing technology. We will contrast these to modern genomes, which we will also reconstruct in this project.Sorghum is the crop of choice for this study for many reasons. It is one of the most recent crops to be domesticated, and so relatively easy to obtain archaeological samples of good biomolecular preservation that are significantly close to the time of domestication. It is an inbreeder and has a small genome, which makes genome reconstruction not too ambitious. Sorghum is also a crop of major importance in arid areas that has an evolutionary history of adaptation to drought tolerance. Interestingly, the cultivated races of Sorghum sowed a progressively increased tolerance to drought and pests, and it has been suggested that this was a consequence of repeated introgressions with the different wild varieties. By comparing archaeological genomes with modern genomes of all five cultivated races and four wild varieties of Sorghum we will understand better how the evolution of domestication of Sorghum occurred and how it became adapted to drought conditions.This study will establish important principles in the evolution of domestication, which will likely prove important for studies in evolution in general. It will also provide insight into one of the most important issues of food security facing the world today, how a crop evolved drought tolerance, and whether that is something that could be translated to other crops.