Genomic isolation and transcriptomic differentiation between two ecologically divergent hybridising European forest trees, Populus alba and P. tremula

两种生态上不同的杂交欧洲林木白杨和欧洲山杨之间的基因组分离和转录组分化

• 批准号: NE/E016731/1
• 负责人: Michael Fay
• 金额: $ 35.62万
• 依托单位: Royal Botanic Gardens
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2008
• 资助国家: 英国
• 起止时间: 2008 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FE016731%2F1
• 关键词: Genomic; isolation; transcriptomic; differentiation; between

Barriers to gene flow between divergent populations or species result from selection on divergent phenotypes and from negative genomic interactions in hybrids. Most of our knowledge of the genomic make-up of such barriers to gene exchange stems from a small number of model organisms. The recent sequencing of the Populus genome creates the opportunity to address the genetics of barriers to gene flow in a tree genus with extensive natural hybridization and pronounced interspecific character differences. The applicants have studied the genetics of reproductive isolation and interspecific differences in morphological, yield-related, and ecophysiological traits in several Populus species, including interspecific controlled crosses between the North-American taxa P. trichocarpa and P. deltoides and natural hybrid zones between the European species P. alba and P. tremula. Studies of controlled crosses indicate a heritable basis and complex genetic architecture of interspecific trait differences associated with yield and biomass accumulation. Work on natural hybrid zones indicates that the genetic basis of reproductive isolation in European Populus can be dissected using approaches related to the conceptual frameworks of 'population genomics' as utilized in evolutionary genetics and 'admixture mapping' as utilized in human genetics. The present project is focused on P. alba and P. tremula, two hybridizing, ecologically divergent (flood-plain vs. upland pioneer) species with wide overlapping geographic ranges across Europe. Hybrid zones between these species have formed in multiple locations and are known to contain a high proportion of recombinant backcrosses to P. alba. Thus, hybrid zones or 'admixed populations' offer a powerful tool for the analysis of genetic loci involved in reproductive isolation, a subset of which is expected to be related to ecological divergence. We propose to study intraspecific variation for genomic isolation and its breakdown in three replicate hybrid zones of P. alba and P. tremula in Europe. We plan to use two complementary approaches: (i) a genomic scan using a genome-wide set of codominant mapped molecular genetic markers identified within a previous project, (ii) a candidate gene approach based on the extensive expressed sequence tag (EST) database available for Populus, and on additional candidate genes for ecological divergence identified via microarray-based transcriptomics in a 'tied studentship' associated with this proposal. The genomic scan (i) will allow us to ask what proportion of genetic markers points to linked loci contributing to reproductive isolation in all three of the studied hybrid zones, and what proportion of markers points to intraspecific variation for genomic isolation, either due to variation in linked isolation genes or due to exogeneous selection associated with local differences in the environment. The candidate gene work (ii) will allow us to ask which genomic regions carrying candidate genes for ecological divergence (or genes with great interspecific expression divergence and relation to flooding tolerance; tied studentship) introgress more or less frequently across hybrid zones than expected under neutrality. We will also use our molecular genetic dataset to conduct a replicated 'admixture mapping' genomic scan for loci controlling leaf morphological differences by testing for excess ancestry of mapped markers in plants with extreme leaf traits. The proposed work represents a significant step forward in our long-term goal to understand the genetic basis and origin of inter- and intraspecific barriers to gene flow and trait differences in Populus. This topic is of great relevance not only for ecological & evolutionary genetics, but also for breeding activities in the important 'biomass' crop Populus, and for our ability to predict the conditions under which tree populations are likely to respond successfully in situ to the expected rate of climate change.

不同种群或物种之间基因流动的障碍来自于对不同表型的选择和杂交中负的基因组相互作用。我们对这种基因交换障碍的基因组构成的大部分知识来自少数模式生物。最近对杨树基因组的测序创造了一个机会来解决基因流动在一个具有广泛的自然杂交和明显的种间特征差异的树种中的障碍。申请人研究了几种杨树种的生殖隔离遗传学和形态、产量相关和生理生态性状的种间差异，包括北美分类群P. trichocarpa和P. deltoides的种间控制杂交，以及欧洲种P. alba和P. tremula的自然杂交区。对照杂交研究表明，与产量和生物量积累相关的种间性状差异具有遗传基础和复杂的遗传结构。对自然杂交带的研究表明，可以使用与进化遗传学中使用的“种群基因组学”和人类遗传学中使用的“混合图谱”概念框架相关的方法来剖析欧洲杨生殖隔离的遗传基础。目前的项目主要集中在P. alba和P. tremula，两个杂交的，生态上不同的物种（洪泛平原vs.高地先锋），在欧洲有广泛的重叠地理范围。这些物种之间的杂交带已经在多个地点形成，并且已知含有高比例的重组回交到白僵菌。因此，杂交区或“混合种群”为分析与生殖隔离有关的遗传位点提供了一个强大的工具，其中一个子集预计与生态分化有关。我们拟在欧洲的三个重复杂交区研究白藻和甲藻的基因组分离及其分解的种内变异。我们计划使用两种互补的方法：(i)使用在先前项目中鉴定的全基因组共显性分子遗传标记进行基因组扫描，（ii）基于杨树可用的广泛表达序列标签（EST）数据库的候选基因方法，以及通过基于微阵列的转录组学在与本提案相关的“捆绑学生”中鉴定的其他生态差异候选基因。基因组扫描(i)将使我们能够询问在所有三个所研究的杂交区域中，有多少比例的遗传标记指向导致生殖隔离的连锁位点，以及有多少比例的标记指向基因组隔离的种内变异，这种变异要么是由于连锁隔离基因的变异，要么是由于与当地环境差异相关的外源选择。候选基因工作（ii）将使我们能够询问哪些基因组区域携带生态差异候选基因（或具有巨大种间表达差异并与洪水耐受性相关的基因；绑定学生）在杂交区中比中性下预期的更频繁或更少地渗入。我们还将使用我们的分子遗传数据集进行复制的“混合定位”基因组扫描，通过测试具有极端叶片性状的植物中映射标记的过量祖先来控制叶片形态差异。我们的长期目标是了解杨树基因流动和性状差异的种间和种内障碍的遗传基础和起源，这项工作是向前迈出的重要一步。这个主题不仅与生态和进化遗传学有关，而且与重要的“生物质”作物杨树的育种活动有关，也与我们预测树木种群可能在原地成功应对预期气候变化速率的能力有关。

项目成果

Genetics and genomics of Populus

• DOI: 10.1007/978-1-4419-1541-2
• 发表时间: 2010
• 作者: S. Jansson;R. Bhalerao;A. Groover