Genomics of Adaptation in European Pines (GAP)

欧洲松树适应基因组学 (GAP)

• 批准号: NE/H003959/1
• 负责人: Stephen Cavers
• 金额: $ 43.78万
• 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: 2010
• 资助国家: 英国
• 起止时间: 2010 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FH003959%2F1
• 关键词: Genomics; Adaptation; European; Pines; GAP

Natural selection is a geographically variable force, determined in part by local environmental conditions. As phenotype is a product of a genotype and its environment, and phenotype determines fitness, then spatial environmental variability should produce differently adapted populations, with phenotypes optimised to local conditions. This process of divergent selection is an important mechanism for maintaining genetic diversity within species, and is particularly critical for long-lived sedentary organisms like trees, where adaptation to local conditions is crucial, as they will be in one place for life and that lifetime may be centuries long. If we are to form reasonable predictions of the likely impacts of environmental change on tree species, then we must begin to understand the process of local adaptation at a genomic level and identify the genes, and the mutations in those genes, that are involved in control of tree phenotype. However, several evolutionary forces act to counter divergent selection, of which gene flow is the most significant, and demographic processes such as extinction and recolonisation may confound local adaptation. Therefore, successful detection of the molecular signature of local adaptation requires parallel evaluation of evolutionary and demographic processes, as both shape genetic variation in natural populations. This project will integrate data from the gene to phenotype to population scale and apply this to a specially selected group of European tree species, in which clear adaptive divergence is present and where post-glacial colonisation dynamics have played a strong role. The project will take advantage of a large new genomic resource to study links between phenotypic variation and nucleotide polymorphism in nuclear genes related to environmental stress, phenology and wood formation, and in the mitochondrial genome in natural populations of four pine species. The species include a generalist, Pinus sylvestris (Scots pine), and three habitat specialist species from the P. mugo complex i.e. P. mugo (dwarf mountain pine), P. uncinata (mountain pine) and P. uliginosa (peat-bog pine). The species form an excellent system for study of neutral and adaptive variation due to close phylogenetic relationships but strong contrasts in geographic distribution, biology and ecology. Fundamentally, the project will integrate genomic and phenotypic data and statistics to make a unique and ground-breaking contribution to a developing field of biodiversity research. The application of genomic approaches to the study of local adaptation is in its infancy and this project will make two major new contributions to the science: the largest analysis of genomic data in natural pine populations, and deployment of a unique experimental design, placing intraspecific adaptive divergence in the context of recent evolutionary history. In addition, the information generated by the project, on adaptive loci, will be of direct application in gene conservation and breeding programs. This will enhance management of forest genetic resources and tree production quality, particularly under the climate change scenarios currently affecting adaptive optima of most forest tree species. Project outputs will also be of direct application in science-based conservation, for example, in conserving genetic resources in the remnant Scots Pine forest fragments in Scotland. CEH's strong links with statutory bodies responsible for management of the UK forest resource and experience in communicating scientific outputs to end users will facilitate effective delivery of results. In summary, the project is an excellent opportunity to take immediate advantage of new genomic data, a ready-made collection and the skills of highly qualified and experienced researchers. All of these key project components are in place and available now, so the project promises high impact for low risk and with significant potential for downstream research.

自然选择是一种地理上可变的力量，部分取决于当地的环境条件。由于表型是基因型及其环境的产物，表型决定适应性，因此空间环境变异性应产生不同适应的种群，并根据当地条件优化表型。这种不同选择的过程是维持物种内遗传多样性的重要机制，对于树木等长期定居的生物体尤其重要，因为它们将在一个地方生活，寿命可能长达数百年，因此适应当地条件至关重要。如果我们要对环境变化对树种的可能影响做出合理的预测，那么我们必须开始在基因组水平上理解局部适应的过程，并确定与控制树木表型有关的基因以及这些基因中的突变。然而，一些进化力量的作用，以对抗不同的选择，其中基因流是最重要的，和人口的过程，如灭绝和分化可能混淆当地的适应。因此，要成功地检测到局部适应的分子特征，就需要同时评估进化和人口统计过程，因为两者都会塑造自然种群中的遗传变异。该项目将整合从基因到表型到人口规模的数据，并将其应用于一组特别选择的欧洲树种，其中存在明显的适应性分歧，并且冰后期殖民动态发挥了重要作用。该项目将利用大量新的基因组资源，研究与环境胁迫、物候和木材形成有关的核基因中的表型变异和核苷酸多态性之间的联系，以及四种松树自然种群中线粒体基因组中的这种联系。这些物种包括一个多面手，欧洲赤松（苏格兰松），和三个来自P. mugo复合体的栖息地专业物种，即P. mugo（矮山松），P. uncinata（山松）和P. uliginosa（泥炭沼泽松）。该物种形成了一个很好的系统，中性和适应性变化的研究，由于密切的系统发育关系，但在地理分布，生物学和生态学的强烈对比。从根本上说，该项目将整合基因组和表型数据和统计数据，为生物多样性研究的发展领域做出独特和开创性的贡献。基因组学方法的应用，以研究当地的适应性是在其起步阶段，该项目将作出两个重大的新贡献的科学：最大的分析基因组数据在天然松树种群，并部署一个独特的实验设计，把种内适应性分歧的背景下，最近的进化史。此外，该项目产生的关于适应性基因座的信息将直接应用于基因保护和育种计划。这将加强对森林遗传资源和树木生产质量的管理，特别是在目前影响大多数森林树种最佳适应能力的气候变化情景下。项目产出也将直接应用于以科学为基础的保护，例如，保护苏格兰残存的苏格兰松林片段的遗传资源。CEH与负责管理英国森林资源的法定机构的密切联系以及向最终用户传达科学成果的经验将促进成果的有效交付。总之，该项目是一个极好的机会，可以立即利用新的基因组数据，现成的收集和高素质和经验丰富的研究人员的技能。所有这些关键项目组成部分现在都已到位，因此该项目有望以低风险产生高影响，并具有下游研究的巨大潜力。

项目成果

Genetic variation for needle traits in Scots pine (Pinus sylvestris L.)

• DOI: 10.1007/s11295-016-1000-4
• 发表时间: 2016-06-01
• 期刊: TREE GENETICS & GENOMES
• 影响因子: 2.4
• 作者: Donnelly, Kevin;Cavers, Stephen;Ennos, Richard A.
• 通讯作者: Ennos, Richard A.

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

• DOI: 10.1111/eva.13345
• 发表时间: 2022-03
• 期刊: Evolutionary applications
• 影响因子: 4.1
• 作者: Perry A;Wachowiak W;Beaton J;Iason G;Cottrell J;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

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

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

• DOI: 10.1101/2021.06.29.450162
• 发表时间: 2021-06
• 期刊: The Plant Journal
• 作者: Chedly Kastally;Alina K. Niskanen;A. Perry;S. Kujala;K. Avia;Sandra Cervantes;M. Haapanen;Robert Kesälahti;T. Kumpula;Tiina M. Mattila;D. I. Ojeda;J. Tyrmi;W. Wachowiak;S. Cavers;K. Kärkkäinen;O. Savolainen;T. Pyhäjärvi