The genomic landscape and the effect of linked selection during the repeated domestication of grain amaranth

植物种群不断适应它们的环境。适应的来源是突变和重组。虽然点突变的适应性效应已经得到了广泛的研究，但重组的作用和基因组景观却很少受到关注。然而，最近的例子显示了重组和染色质可及性对适应性表型的重要性。染色质可及性和重组率在适应过程中可以改变。因此，这些因素不仅影响适应，而且本身也可能受到选择的影响。在种群基因组水平上，适应性塑造了整个基因组的多样性模式。由于连锁不平衡，不仅直接受选择影响的位点多样性降低，连系的中性位点多样性也降低。连锁选择的范围很大程度上是未知的，并影响观察到的遗传多样性的解释。染色质可接近性可以作为基因组功能部分的代理，以评估连锁选择的强度作为与开放染色质距离的函数。作物驯化是植物适应的一种非常合适的模式，因为所选择的性状是已知的，而且适应种群的祖先通常是已知的，而且仍然可以找到。苋菜已经从单一祖先独立驯化了三次，为研究作物驯化过程中重组和染色质可及性的重要性及其对连锁选择的影响提供了一个理想的研究系统。在本项目中，我们将构建3种苋菜及其野生祖先的独立遗传图谱，以评估驯化过程中重组率的变化，并确定大规模的重排。这将为所有四个物种产生高质量的遗传图谱，并使我们能够绘制适应相关的表型。此外，我们将构建跨物种和组织的独立染色质可及性图，以深入了解开放染色质的稳定性。预计在驯化过程中，重组和染色质景观会发生改变，并可能在作物物种之间发生分化。结合新生成的开放染色质作为基因组功能空间的代理数据和物种特异性重组图谱以及群体尺度遗传多样性估计，我们将研究4种苋菜物种的连锁选择模式及其在驯化过程中的变化。我们将研究这些模式是否进化趋同，或者籽粒苋菜物种之间的信号是否不同，尽管它们有共同的祖先。我们的结果将为基因组景观和作物进化之间的相互作用提供新的见解。

Plant populations constantly adapt to their environment. The sources for adaptation are mutations and recombination. While the adaptive effect of point mutations has been extensively studied, the role of recombination and the genomic landscape have received less attention. Yet, recent examples have shown the importance of recombination and chromatin accessibility for adaptive phenotypes. Chromatin accessibility and recombination rates can be altered during adaptation. Hence these factors not only influence adaptation but might themselves be shaped by selection.On the population genomic level, adaptation shapes the diversity pattern across the genome. As a result of linkage disequilibrium, not only sites directly affected by selection show reduced diversity, but also linked neutral sites. The extend of linked selection is vastly unknown and affects the interpretation of observed genetic diversity.Chromatin accessibility can be employed as proxy for the functional part of the genome, to evaluate the strength of linked selection as a function of the distance from open chromatin. Crop domestication is a well-suited model for plant adaptation, because selected traits are known, and the ancestors of the adapted populations are often known and still available. Grain amaranth has been domesticated three times independently from a single ancestor and provides an ideal study system to study the importance of recombination and chromatin accessibility during crop domestication, and the consequences on linked selection.In this project, we will construct independent genetic maps for each of the three grain amaranth species and their wild ancestor to evaluate the change in recombination rates during domestication and to identify large scale rearrangements. This will yield high quality genetic maps for all four species and allow us to map adaptation related phenotypes. Furthermore, we will construct independent chromatin accessibility maps across species and tissues to gain insights into the stability of open chromatin. It is expected that recombination and chromatin landscapes are altered during domestication and potentially diverged between crop species. Combining the newly generated data of open chromatin as proxy for functional space in the genome and species-specific recombination maps with population scale genetic diversity estimates, we will study the patterns of linked selection in the four amaranth species and their change during domestication. We will study if these patterns evolve convergently or if the signals differ between grain amaranth species, despite their common ancestry. Our results will give new insights into the interplay between the genomic landscape and crop evolution.