Comparative population genomics of red clover domestication and improvement

红三叶草驯化和改良的比较群体基因组学

• 批准号: BB/L023563/1
• 负责人: Leif Skot
• 金额: $ 36.05万
• 依托单位: Aberystwyth University
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2014
• 资助国家: 英国
• 起止时间: 2014 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FL023563%2F1
• 关键词: Comparative; population; genomics; red; clover

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.

我们建议使用大部分未驯化的红三叶草饲料作物作为解开一个关键的驯化性状的模型。豆科牧草对反刍动物具有上级饲用价值，其固氮能力使其能够在改善土壤肥力方面提供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在70年代和80年代在欧洲特别下降，主要是由于廉价的化学生产的氮肥的可用性。推动更可持续的农业，特别是减少使用化石燃料制造的肥料，已经阻止了这种下降，人们对这些豆类作物，特别是与牧草的混合物越来越感兴趣。因此，迫切需要加快他们的遗传改良，由于缺乏投资，遗传改良在后来几年停滞不前。该提案旨在利用最近开发的红三叶草基因组学资源，在温带农业中的重要性仅次于苜蓿，以评估欧洲范围内收集的种质的遗传和表型多样性。遗传改良计划最基本的要求之一是获得种质中的遗传变异。有迹象表明，大多数最近的欧洲繁殖种群有一个相对狭窄的基础。随着最近的育种历史，很大程度上未驯化的红三叶草作物是一个理想的候选人，以提供一个全面的评估驯化的作用，改变基因组景观在作物改良计划。换句话说，我们的目标是通过使用红三叶草作为模型，在作物改良计划中验证驯化的基因组影响。我们将使用来自整个欧洲的一系列栖息地的种群集合以及精英育种材料。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育种或环境适应而受到选择压力。重点将放在一个关键的驯化性状，即匍匐与直立生长习性，这对牧草作物的耐牧性和持久性有着深远的影响。具有更多匍匐生长习性的植物可能更耐放牧，更持久。另一方面，有一个产量惩罚与prostrateness。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性状有新的认识。为此，我们将使用两种类型的植物材料：一个由生态型和具有不同程度的匍匐生长习性的自然种群组成的多样性小组，并与所有直立生长的优良育种种群进行比较。其次，我们将产生群体分离的这一特点，杂交直立母本从精英材料与五个花粉供体从匍匐自然种群。这些群体的农艺性状和生长性状的表型分析将伴随着各种牧草质量性状的化学分析，并获得全基因组SNP多态性数据。这将通过作图群体中的限制性相关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装，这将使我们能够识别和映射选择下的基因组区域，并允许识别一些控制这种性状的基因。这将为驯化特征的结构提供新的见解。与Germinal Holdings Ltd的合作为我们进入育种计划提供了一条管道，这将确保我们获得的基因组数据和知识将有利于红三叶草的遗传改良。

项目成果

Large scale SNP analysis reveals genomic diversity within European and Asian red clover (Trifolium pratense L.) germplasm

大规模 SNP 分析揭示了欧洲和亚洲红三叶草 (Trifolium pratense L.) 种质内的基因组多样性

• 发表时间: 2017
• 作者: Jones C

Population structure of red clover ecotypes collected from Europe and Asia

欧洲和亚洲红三叶草生态型的种群结构

• 发表时间: 2018
• 作者: Jones, C.

Identification of loci controlling timing of stem elongation in red clover using genotyping by sequencing of pooled phenotypic extremes.

• DOI: 10.1007/s00438-022-01942-x
• 发表时间: 2022-11
• 期刊: Molecular genetics and genomics : MGG

Allele Frequency Changes Provide Evidence for Selection and Identification of Candidate Loci for Survival in Red Clover (Trifolium pratense L.)

• DOI: 10.3389/fpls.2019.00718
• 发表时间: 2019-06-11
• 期刊: FRONTIERS IN PLANT SCIENCE
• 影响因子: 5.6
• 作者: Ergon, Ashild;Skot, Leif;Rognli, Odd Arne
• 通讯作者: Rognli, Odd Arne

Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement.

• DOI: 10.1038/srep17394
• 发表时间: 2015-11-30
• 期刊: Scientific reports
• 影响因子: 4.6
• 作者: De Vega JJ;Ayling S;Hegarty M;Kudrna D;Goicoechea JL;Ergon Å;Rognli OA;Jones C;Swain M;Geurts R;Lang C;Mayer KF;Rössner S;Yates S;Webb KJ;Donnison IS;Oldroyd GE;Wing RA;Caccamo M;Powell W;Abberton MT;Skøt L
• 通讯作者: Skøt L