Population genomics and evolution of adaptive traits in Pines

松树种群基因组学和适应性特征的进化

• 批准号: NE/K012177/1
• 负责人: Stephen Cavers
• 金额: $ 53.73万
• 依托单位: NERC CEH (Up to 30.11.2019)
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2013
• 资助国家: 英国
• 起止时间: 2013 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FK012177%2F1
• 关键词: Population; genomics; evolution; adaptive; traits

During their evolution, forest trees have migrated (by seed dispersal) and adapted to new environments. This 'local adaptation' caused changes in the parts of the genome that control a tree's ability to survive and reproduce in different climates. As a result, forest trees often show strong differences between populations in observable characters (phenotype), for example in height or shape, in timing of growth, or in ability to withstand cold temperatures or water deficit. Although a lot of research has been done on differences in tree phenotype and how this is shaped by the environment, very little is known about the mutations, genes and biochemical pathways involved. However, information about the genes that control adaptive traits and how they evolve would be useful for conservation, restoration and forest management, particularly in the face of future climate change. For example, if we know how a particular set of genes (genotype) evolved to fit a certain type of environment, we can make better predictions about how changes in that environment will affect the trees. Similarly, foresters want to plant the best tree for their land, which will grow tall and straight, and stay free from disease. But at the moment it takes many years to grow trees to find out which types are the best. By knowing which genes control these important traits, good seedlings can be chosen very early on to provide the best crop from the forest. As forest tree species make up the majority of biodiversity on land and are very important for the economies of many countries, this work can make a big difference. The project will study how genes control phenotypes in different environments, in four closely-related pine tree species. These are: Scots pine, which is the most widespread pine tree species of all; Dwarf mountain pine, which comes from the mountains of Central and Eastern Europe; Mountain pine, from the mountains of Spain, France and the Western Alps; and Peat-bog pine from the Central European lowlands. Right now, as a result of several years of work by the scientists in the team, we can look at more genes in these species than ever before. By integrating this knowledge with the very latest genetic techniques and a living collection of plants from each of the species we will look for genomic regions and networks involved in the species divergence and adaptations. We hope this will let us understand the link between genotypes and phenotypes, how the environment drives evolution in these tree species and what this means for how forest will change in the future. Worldwide, it will be one of the largest surveys of the genome ever in natural populations of forest trees and will be the first to use molecular data at the whole genome scale of several closely related species to study how tree species evolve. To make sure the project makes a difference, we will publish our results in international science journals and make our data freely available. We will spread awareness of what we are doing by taking part in Edinburgh's Science Festival and National Science and Engineering Week, by press releases and other special publications and by visits to local schools. We are also talking to forest tree breeders, who work on growing better trees for forestry, about the best ways to use genetic information available in natural populations. Working with them, we will translate what we find out into new ways to grow better trees, but also into better ways to conserve the genetic diversity in natural forests. If both of these messages get across, to foresters and the public, then our project can have a real impact.

在它们的进化过程中，森林树木（通过种子传播）迁移并适应新的环境。这种“局部适应”导致了基因组中控制树木在不同气候下生存和繁殖能力的部分发生了变化。因此，森林树木在种群之间往往在可观察的性状（表型）上表现出很大的差异，例如在高度或形状、生长时间或抵御低温或缺水的能力方面。尽管人们对树木表型的差异以及环境对其的影响进行了大量研究，但对其中涉及的突变、基因和生化途径所知甚少。然而，关于控制适应性性状的基因及其如何进化的信息将对保护、恢复和森林管理有用，特别是在面临未来气候变化的情况下。例如，如果我们知道一组特定的基因（基因型）如何进化以适应某种类型的环境，我们就可以更好地预测环境的变化将如何影响树木。同样，护林员想要为他们的土地种植最好的树，这些树会长得又高又直，不会生病。但目前需要很多年的时间来种植树木，以找出哪种类型的树是最好的。通过了解控制这些重要性状的基因，可以很早就选择好的幼苗，从森林中获得最好的作物。由于森林树种构成了陆地生物多样性的大部分，对许多国家的经济非常重要，这项工作可以产生很大的影响。该项目将研究基因如何在不同环境下控制四种亲缘关系密切的松树的表型。它们是：苏格兰松，这是所有松树中分布最广的一种；矮山松，产自中欧和东欧的山区；山松，产自西班牙、法国和西阿尔卑斯山脉；以及中欧低地的泥炭沼泽松。现在，作为团队中科学家几年工作的结果，我们可以在这些物种中看到比以往更多的基因。通过将这些知识与最新的遗传技术和每个物种的活植物集合相结合，我们将寻找与物种分化和适应有关的基因组区域和网络。我们希望这将让我们了解基因型和表型之间的联系，环境如何推动这些树种的进化，以及这对森林未来的变化意味着什么。在世界范围内，这将是有史以来对森林树木自然种群进行的最大规模的基因组调查之一，并将是第一次在几个密切相关物种的全基因组尺度上使用分子数据来研究树种是如何进化的。为了确保该项目发挥作用，我们将在国际科学期刊上发表我们的研究结果，并免费提供我们的数据。我们将通过参加爱丁堡科学节和国家科学与工程周，通过新闻稿和其他特别出版物以及访问当地学校来宣传我们所做的事情。我们还与林木育种家讨论了利用自然种群中现有遗传信息的最佳方法，他们致力于为林业种植更好的树木。与他们合作，我们将把我们的发现转化为种植更好树木的新方法，同时也转化为更好地保护天然林遗传多样性的方法。如果这两个信息都能传达给林务人员和公众，那么我们的项目就能产生真正的影响。

项目成果

Development of a single nucleotide polymorphism array for population genomic studies in four European pine species.

开发用于四种欧洲松树种群基因组研究的单核苷酸多态性阵列。

• DOI: 10.1111/1755-0998.13223
• 发表时间: 2020
• 期刊: Molecular ecology resources
• 影响因子: 7.7
• 作者: Perry A

Early phenology and growth trait variation in closely related European pine species.

• DOI: 10.1002/ece3.3690
• 发表时间: 2018-01
• 期刊: Ecology and evolution
• 影响因子: 2.6
• 作者: Wachowiak W;Perry A;Donnelly K;Cavers S
• 通讯作者: Cavers S

Taming the massive genome of Scots pine with PiSy50k, a new genotyping array for conifer research.

• DOI: 10.1111/tpj.15628
• 发表时间: 2022-03
• 期刊: PLANT JOURNAL
• 影响因子: 7.2
• 作者: Kastally, Chedly;Niskanen, Alina K.;Perry, Annika;Kujala, Sonja T.;Avia, Komlan;Cervantes, Sandra;Haapanen, Matti;Kesalahti, Robert;Kumpula, Timo A.;Mattila, Tiina M.;Ojeda, Dario, I;Tyrmi, Jaakko S.;Wachowiak, Witold;Cavers, Stephen;Karkkainen, Katri;Savolainen, Outi;Pyhajarvi, Tanja
• 通讯作者: Pyhajarvi, Tanja

High genetic similarity between Polish and North European Scots pine (Pinus sylvestris L.) populations at nuclear gene loci

波兰和北欧樟子松 (Pinus sylvestris L.) 种群在核基因位点上具有高度遗传相似性

• DOI: 10.1007/s11295-014-0739-8
• 发表时间: 2014
• 期刊: Tree Genetics & Genomes
• 影响因子: 2.4
• 作者: Wachowiak W

Identifying and testing marker-trait associations for growth and phenology in three pine species: implications for genomic prediction

识别和测试三种松树生长和物候的标记性状关联：对基因组预测的影响

• DOI: 10.1101/2020.12.22.423987
• 发表时间: 2020
• 作者: Perry A