Oat domestication - understanding the origin of a European cereal

燕麦可以说是唯一的“欧洲”谷类食品。之前的研究表明，它最接近的野生近亲在土耳其各地小麦和大麦首次驯化的地点附近被发现，但考古证据表明，最初作为作物使用是在农业发展的后期，然后是在中欧，而不是在它的原始环境中。对这种转移的一个看似合理的解释是，定居在破土动工中的野生近亲(Avena Sterilis)种群已经适应了作为农业杂草的生活。这种新的杂草在野外传播的能力较弱，但在大麦等耕种的谷类作物上非常成功。法图阿可以通过这些作物传播到整个欧洲，然后在其他作物失败的艰难时期成为一种作物。事实上，燕麦传统上是在贫瘠的土地上种植的，在土壤肥力低的轮作结束时种植，这可能是这种二次驯化的遗留问题。在某些阶段，完全不粉碎的燕麦会被选择来更容易地收获和储存谷物，而完全驯化则会施加更大的压力(失去芒，更大的颗粒尺寸等等)。这种模式的一个复杂之处在于，燕麦似乎已经驯化了两次。大多数品种现在类似于春季播种的‘白色’燕麦，与土耳其中部的野生种群关系最密切。然而，在地中海周围，传统的地方品种通常是秋季播种的红色燕麦(A.byzantina)，与土耳其西南部的野生种群关系最密切。现代育种计划在很大程度上是基于这两种类型之间的杂交，英国独特的冬季燕麦品种可能特别依赖于A.byzantina的特征。我们对了解红燕麦和白燕麦的起源以及法图亚燕麦的作用有着浓厚的兴趣。这不仅是出于对农业发展的好奇心，也是因为需要为现代作物增加新的变异。每一个驯化步骤都造成了遗传瓶颈，潜在有价值的种质已经丢失。更好地了解这些瓶颈以及野生种群中的自然变异，将有助于找到有用的变异纳入育种计划。按序列进行基因分型(GBS)是最近一种高通量的方法，可以揭示整个基因组的遗传变异。它对特定限制酶位点附近的短序列进行采样，并且不需要事先知道存在哪些变体。可以处理数百个样本，这使其成为多样性筛选的理想选择。我们有500多个杂草、野生和地方品种的小组已经由GBS筛选。不幸的是，燕麦基因组几乎和小麦一样大和复杂，目前还没有参考文献将GBS标签与邻近基因联系起来。即使当第一批参考文献可用时(预计在2018年)，它们也将来自现代品种，这些品种可能不同于我们正在研究的祖先种群。在这个项目中，我们将弥合GBS和基因组参考之间的差距，以直接或通过改进现有参考来评估基因变异。在第一步中，我们将使用新开发的测序方法来削减构建红色燕麦参考的成本。在第二个项目中，我们将与一位德国大麦专家合作，他开发了外显子组捕获，这是一种仅针对基因区域进行采样和测序的方法，我们将与加拿大合作伙伴合作，后者部分基于我们的基因组数据创建了燕麦外显子组捕获。我们将使用一种改进的设计，从220个关键的GBS小组材料中恢复全面的基因序列集合。最后，我们将从祖先那里获得序列，这将允许与现代栽培品种进行基因含量和序列的比较，并将加强对外显子组和GBS数据的分析。与创造了杂交种群的波兰合作伙伴合作，我们将确定支撑驯化的关键基因。

Oats can claim to be the only 'European' cereal. Previous work indicated that its closest wild relatives are found around Turkey near sites where wheat and barley were first domesticated, but archaeological evidence points to first use as a crop only late in the development of agriculture and then in Central Europe, rather than in its original environment. A plausible explanation for this transfer is that a population of the wild relative (Avena sterilis), which colonises broken ground, had become adapted to life as an agricultural weed. The new weed (A. fatua) is less able to spread in the wild but is very successful at colonising tilled fields of cereals such as barley. A. fatua could have spread across Europe with those crops and then become a crop in its own right in hard times where others failed. Indeed, oats have traditionally been grown on poor ground and at the end of rotations when soil fertility is low, a possible legacy of this secondary domestication. At some stage completely non-shattering oats would have been selected for easier grain harvest and storage, and greater pressure would have been applied for full domestication (loss of awns, larger grain size and so on). A complication for this model is that oats appear to have been domesticated twice. Most cultivars now resemble 'white' oats (A. sativa), sown in the spring and most closely related to wild populations in central Turkey. However, around the Mediterranean, traditional landraces are often 'red' oats (A. byzantina), sown in autumn and most closely related to wild populations in south western Turkey. Modern breeding programmes are largely based on crosses between these two types, and the UK's unique winter oat cultivars may be particularly dependent on A. byzantina traits. We have a strong interest in understanding the origin of both red and white oats, and the role of A. fatua. This is not only driven by curiosity about the development of agriculture but also by the need to add new variation to the modern crop. Each domestication step has created genetic bottlenecks where potentially valuable germplasm has been lost. Better understanding of these bottlenecks, and of natural variation in wild populations, will help find useful variation to incorporate into breeding programmes.Genotyping-by-sequence (GbS) is a recent high throughput method to reveal genetic variation across entire genomes. It samples short sequences adjacent to specific restriction enzyme sites, and does not require prior knowledge of which variants are present. Hundreds of samples may be processed, making it ideal for diversity screens. We have panels of over 500 weedy, wild and landrace accessions already screened by GbS. Unfortunately, the oat genome is almost as large and complex as that of wheat, and no reference is yet available to associate GbS tags with neighbouring genes. Even when the first references become available (expected in 2018), they will have been derived from modern cultivars which may differ from the ancestral stocks we are studying. In this project we will bridge the gap between GbS and genome references to assess gene variation either directly or by improving the references available. In the first step we will use a newly developed sequencing approach to cut the cost of building a red oat reference. In the second we will work with a German barley expert who developed exome capture, a method that samples and sequences only targeted gene regions, and with a Canadian partner who has created an exome capture for oats, based in part on our genome data. We will use an improved design to recover comprehensive collections of gene sequences from 220 key GbS panel accessions. Finally we will obtain sequence from progenitors that will allow comparisons of gene content and order with modern cultivars, and will enhance analysis of exome and GbS data. Working with a Polish partner who has created hybrid populations, we will identify key genes underpinning domestication.