Archaeogenomics of Sorghum domestication and adaptation

在后基因组时代，我们对进化和基因组水平的理解在过去十年中取得了实质性进展。令许多人惊讶的是，人们通常发现，强烈的选择性扫描很少，而且越来越明显的是，进化通常是在许多位点上进行的小变化的交响乐。植物驯化的进化，以及驯化下的后续进化，也显示出与作物基因组测序相同的模式。这对许多人来说也是一个惊喜，因为直到最近，人们一直认为与驯化相关的性状选择，驯化综合征，已经非常强大，野生和驯化形式之间的过渡非常迅速。在基因组证据的佐证中，驯化综合征性状的选择强度也直接从考古记录中估计出来，发现比以前假设的要弱得多，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征的弱选择，弱选择的一个后果是基因组中的选择标记也很弱。事实上，它们太弱了，以至于我们可能无法全部发现它们，因为它们自驯化以来已经腐烂得太厉害了。此外，在驯化作物中看到的遗传多样性模式也可以通过驯化后野生和驯化群体之间的渐渗基因流动而变得复杂。理想的情况是，我们希望获得的遗传信息来自于这些微弱的选择信号衰减之前，也就是基因渗入事件发生之前。技术的进步使得我们现在可以从考古样本中产生基因组，这将大大有助于实现这些理想目标。在这项研究中，我们将使用第三代单分子测序技术，从几乎可以追溯到驯化时间的一半的时间点重建农作物高粱的考古基因组。我们将把它们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。它是最近被驯化的作物之一，因此相对容易获得生物分子保存良好的考古样本，这些样本与驯化时间非常接近。它是一种近亲繁殖动物，基因组较小，这使得基因组重建并不太雄心勃勃。高粱也是干旱地区的一种重要作物，具有适应耐旱性的进化历史。有趣的是，高粱的栽培品种对干旱和害虫的耐受性逐渐增加，有人认为这是不同野生品种重复基因渗入的结果。通过对高粱的5个栽培品种和4个野生品种的考古基因组与现代基因组的比较，我们将更好地了解高粱驯化的进化过程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则，这可能对一般的进化研究具有重要意义。它还将深入了解当今世界面临的最重要的粮食安全问题之一，作物如何进化耐旱性，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.