Comparative population genomics of red clover domestication and improvement

我们建议使用在很大程度上未驯化的红三叶饲料作物作为解开一个关键驯化特性的模型。豆科牧草对反刍动物具有较高的饲用价值，其固氮能力使其在改善土壤肥力方面提供了有用的生态系统服务。尽管有这些特性，但它们在畜牧业中的使用量下降，特别是在70年代的S和80年代的S，这主要是由于廉价的化学生产的氮肥的可获得性。转向更可持续农业的努力，特别是减少使用化石燃料制造的化肥，阻止了这种下降，人们对这些豆类作物的兴趣越来越大，特别是在与牧草混合的作物中。因此，迫切需要加快他们的基因改良，由于缺乏投资，这项工作在后来几年陷入停滞。这项建议旨在利用最近开发的红三叶基因组学资源，评估欧洲范围内种质资源的遗传多样性和表型多样性。红三叶在温带农业中的重要性仅次于紫花苜蓿。遗传改良计划最基本的要求之一是能够获得你种质中的遗传变异。有迹象表明，大多数最近的欧洲繁殖种群的基数相对较小。由于最近的育种历史，基本上未驯化的红三叶作物是一个理想的候选者，可以全面评估驯化在作物改良计划期间改变基因组格局方面的作用。换句话说，我们的目标是通过以红三叶为模型，在作物改良计划中描述驯化对基因组的影响。我们将使用来自欧洲各地不同栖息地的种群集合和精英育种材料。我们将使用这个多样性小组来评估全基因组的核苷酸多样性，并使用这些信息来告诉我们基因组的哪些区域由于繁殖或环境适应而受到选择压力。重点将放在一个关键的驯化特性上，即俯卧与直立的生长习惯，这对牧草作物的耐牧性和持久性有深远的影响。生长习性较平卧的植物对放牧的耐受性更强，也更持久。另一方面，还有一个与屈膝相关的收益惩罚。因此，揭示遗传结构对于遗传改良具有重要意义，也将使我们对植物的这一基本特征有新的认识。为此，我们将使用两种类型的植物材料：由生态型和具有不同程度俯卧生长习性的自然种群组成的多样性小组，并与全部直立的精英育种群体进行比较。其次，我们将通过从优良材料中杂交一个直立的母本和从平卧的自然种群中提取的五个花粉供体来产生分离这一特征的种群。对这些群体的农艺性状和生长性状的表型分析将伴随着对各种饲草品质性状的化学分析，并通过获得全基因组SNP多态数据。这将通过在绘图种群中进行限制相关DNA(RAD)标记分析以及多样性小组来实现。结合改进的基因组序列组合，这将使我们能够识别和绘制正在选择的基因组区域，并能够识别控制这一特征的一些基因。这将为驯化特征的架构提供新的见解。与Germinal Holdings Ltd的合作为我们提供了一条进入育种计划的管道，这将确保我们获得的基因组数据和知识将有助于红三叶的遗传改良。

We propose to use the largely undomesticated red clover forage crop as a model for unravelling a key domestication trait. Forage legumes have superior feeding value for ruminant animals, and their nitrogen fixing capability enables them to provide useful ecosystem services in terms of improvement of soil fertility. Despite these properties their use in livestock agriculture declined particularly in Europe in the 70's and 80's, chiefly due to the availability of cheap chemically produced nitrogen fertilizer. The drive towards more sustainable agriculture, particularly less use of fertilizer manufactured from fossil fuels has halted the decline, and there is increasing interest in these legume crops, particularly in mixtures with forage grasses. There is thus an urgent need to accelerate their genetic improvement, which has stalled in later years due to lack of investment. This proposal aims to use recently developed genomics resources for red clover, second only to alfalfa in importance in temperate agriculture, to assess the genetic and phenotypic diversity of a European-wide collection of germplasm. One of the most fundamental requirements for genetic improvement programmes is to have access to genetic variation within your germplasm. There are suggestions that most recent European breeding populations have a relatively narrow base. With a very recent history of breeding, the largely undomesticated red clover crop is an ideal candidate to provide a comprehensive assessment of the role of domestication in changing the genome landscape during a crop improvement programme. In other words we will aim to characterise the genomic impact of domestication in a crop improvement programme by using red clover as a model.We will use a collection of populations from a range of habitats from throughout Europe together with elite breeding material. We will use this diversity panel to assess the genome-wide nucleotide diversity and use this information to tell us which regions of the genome have been subject to selective pressures either as a result of breeding or environmental adaptation. The focus will be on a key domestication trait, namely prostrate versus erect growth habit, which has a profound effect on grazing tolerance and persistency in forage crops. Plants with more prostrate growth habits are likely to be more tolerant to grazing and be more persistent. On the other hand, there is a yield penalty associated with prostrateness. Unravelling the genetic architecture is thus of major importance for genetic improvement, and will also give us novel insight into this fundamental trait in plants.We will use two types of plant material for this: A diversity panel consisting of ecotypes and natural populations with varying degrees of prostrate growth habit, and compare with elite breeding populations, all of which are erect. Secondly, we will generate populations segregating for this trait by crossing an erect female parent from elite material with five pollen donors taken from the prostrate natural populations. Phenotypic analysis of agronomic and growth traits in these populations will be accompanied by chemical analysis of various forage quality traits, and by obtaining genome-wide SNP polymorphism data. This will be achieved by restriction associated DNA (RAD) marker analysis in the mapping populations, as well as the diversity panel. In combination with the improved genome sequence assembly, this will enable us to identify and map genomic regions under selection, and allow identification of some of the genes governing this trait. This will provide novel insight into the architecture of domestication traits. The partnership with Germinal Holdings Ltd gives us a pipeline into the breeding programme, which will ensure that the genomic data and knowledge we obtain will benefit genetic improvement of red clover.