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

不同种群或物种之间的基因流动障碍是由于对不同表型的选择和杂交后代的负基因组相互作用造成的。我们关于这种基因交换障碍的基因组构成的大部分知识都来自于少数模式生物。最近对杨树基因组的测序为解决树属基因流动障碍的遗传学创造了机会，该树属具有广泛的自然杂交和明显的种间性状差异。申请人研究了几种杨树的生殖隔离遗传学以及形态、产量相关和生态生理性状的种间差异，包括北美三果杨和三角杨的种间控制杂交，以及欧洲三果杨和三果杨的自然杂交区。对控制杂交的研究表明，与产量和生物量积累相关的种间性状差异具有可遗传的基础和复杂的遗传结构。对天然杂交区的研究表明，欧洲杨树生殖隔离的遗传基础可以使用与进化遗传学中使用的“种群基因组学”概念框架和人类遗传学中使用的“混合图谱”相关的方法来剖析。本项目的重点是白杨和白杨，这是两个在欧洲各地地理范围广泛重叠的杂交的、生态上不同的物种(洪泛区和高地拓荒者)。这些种之间的杂交区已经在多个位置形成，并且已知包含高比例的重组回交。因此，杂交区或“混合种群”为分析与生殖隔离有关的遗传基因座提供了一个强大的工具，其中的一个子集预计与生态分化有关。我们建议研究白杨和白杨在欧洲的三个重复杂交区的基因组分离及其破坏的种内变异。我们计划使用两种互补的方法：(I)使用先前项目中确定的一组共显性作图分子遗传标记的全基因组扫描，(Ii)基于可用于杨树的广泛的表达序列标签(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确定的其他生态差异的候选基因，与本提议相关。基因组扫描(I)将允许我们询问在所有三个研究的杂交区中，有多大比例的遗传标记指向有助于生殖隔离的连锁基因，以及多大比例的标记指向基因组隔离的种内变异，要么是由于连锁隔离基因的变异，要么是由于与环境局部差异相关的外源选择。候选基因工作(II)将允许我们询问哪些基因组区域携带生态分歧的候选基因(或具有较大种间表达差异并与耐涝有关的基因；学生关系)在中性条件下跨越杂交区的频率比预期的更高或更低。我们还将使用我们的分子遗传数据集，通过测试具有极端叶片性状的植物中所映射标记的额外祖先，来进行复制的“混合作图”基因组扫描，以寻找控制叶片形态差异的基因座。这项拟议的工作代表着我们在了解杨树种间和种内基因流动障碍和性状差异的遗传基础和起源的长期目标方面向前迈出了重要的一步。这一主题不仅与生态和进化遗传学密切相关，而且与重要的‘生物量’作物杨树的育种活动以及我们预测树木种群可能在当地成功地对预期的气候变化速度做出反应的能力有关。

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.