Genomic analysis of adaptive divergence and hybrid speciation in Senecio

摘要：塞内西奥地区适应性分化和杂交物种形成的基因组分析这项研究的提出源于最近在不列颠群岛发现的一种新的二重性杂交物种的起源，这种物种的材料是300年前从西西里岛埃特纳火山的一个杂交区传入英国牛津的。这一发现代表了空间隔离在杂交物种形成中至关重要的第一个实证证明，并为研究新物种及其衍生的杂交材料之间适应性差异的遗传基础提供了一个系统。因此，提供了一个独特的机会来详细分析这种形式的物种形成的遗传基础，在起源的时候，而不是很久以后。这种新的杂交物种具有很强的入侵性，在其最近在英国大部分地区的快速传播过程中，它与一种本地物种杂交，形成了两个新的多倍体物种和一种新的本地分类单元变体。在过去的20年里，私家侦探一直在详细调查影响这个迅速发展的团体成员的起源和建立的因素。这项新的研究将建立在“Senecio杂交物种形成过程中基因组和转录组的变化”项目（NER/T/S/2001/00995）中出现的新颖和令人兴奋的数据的基础上，该项目由NERC环境基因组学计划资助。这导致了二倍体杂交新物种Senecio squalidus（牛津ragwort）及其亲本物种S. aethensis和S.菊花的基因组图谱的生成，基于对三个物种之间的成对杂交产生的F2定位群体中大量分子标记位点的分离数据。同时完成了数量性状位点（QTL）分析，在相同的定位群体中分别鉴定出若干个QTL，以区分3个物种。此外，微阵列分析检测到三个物种之间花组织中基因表达的全基因组改变，并确定了一组控制部分这种变异的候选基因。因此，适当的基因组资源现在是适当的研究遗传基础的适应分化和二倍体杂交种形成在这组二倍体Senecio。我们计划使用一种涉及基因组扫描的方法，该方法使用一组扩增片段长度多态性位点（aflp）与QTL和候选基因定位相结合。将对大量AFLP位点的DNA多态性进行全基因组调查，以分离基因组中受正向选择或平衡选择影响的部分。由于“遗传搭便车”，被选择固定的适应性基因两侧的中性标记将表现出变异水平的降低和等位基因频率的倾斜分布，而受平衡选择影响的位点则相反。在确定了基因组中受选择影响的部分之后，我们将以两种方式研究这些部分的功能和作用。首先，我们将确定区分三种二倍体Senecio物种的控制性状的qtl是否被带有选择特征的aflp所包围。其次，我们将确定候选基因是否具有已知的功能，并可能控制与分化和物种形成有关的性状，这些基因的两侧是否也带有选择的特征。当这些特征被发现时，我们将得出结论，相关的qtl和候选基因可能在该二倍体Senecio群体的生态分离和物种形成中发挥了重要作用。这项研究将涉及大量的分子工作和计算机模拟。该结果将为我们目前对适应分化在二倍体杂交物种形成中的作用的理解以及植物入侵的遗传基础提供重要的进展。

Summary: Genomic analysis of adaptive divergence and hybrid speciation in Senecio The research proposed stems from the recent discovery of the origin of a new diploid hybrid species in the British Isles from material introduced 300 years ago to Oxford, England, from a hybrid zone on Mount Etna, Sicily. This discovery represents the first empirical demonstration of spatial isolation being of critical importance in hybrid speciation, and provides a system for investigating the genetic basis of adaptive divergence between the new species and the hybrid material from which it is derived. Thus a unique opportunity is presented to analyse in detail the genetic basis of this form of speciation at the time of origin rather than long afterwards. The new hybrid species is highly invasive and during its recent, rapid spread through large parts of the United Kingdom, it has hybridized with a native species resulting in the formation of two new polyploid species and a new variant form of the native taxon. The factors affecting the origins and establishment of members of this rapidly evolving group have been the subject of detailed investigation by the PI over the past 20 years. The new research will build on novel and exciting data that emerged from the project 'Changes to genome and transcriptome during hybrid speciation in Senecio' (NER/T/S/2001/00995) funded under the NERC Environmental Genomics Initiative. This led to the generation of genomic maps of the diploid hybrid neospecies, Senecio squalidus (Oxford ragwort), and its parent species, S. aethnensis and S. chrysanthemifolius, based on segregation data for numerous molecular marker loci in F2 mapping populations created from pair-wise crosses between the three species. Also completed was a quantitative trait locus (QTL) analysis on the same mapping populations, which identified several QTLs for each of a number of morphological traits that distinguish the 3 species. In addition, microarray analyses detected genome-wide alterations to gene expression in floral tissues between the three species and identified a set of candidate genes controlling part of this variation. Thus appropriate genomic resources are now in place to investigate the genetic basis of adaptive divergence and diploid hybrid speciation in this group of diploid Senecio. This we plan to do using an approach involving genome scans that employ a battery of amplified fragment length polymorphism loci (AFLPs) integrated with QTL and candidate gene mapping. Genome-wide surveys of DNA polymorphism over a large number of AFLP loci will be undertaken to isolate parts of the genome subject to positive directional or balancing selection. Due to 'genetic hitch-hiking', neutral markers flanking adaptive genes fixed by selection will exhibit reduced levels of variation and a skewed distribution of allele frequencies, while the opposite will be the case for loci subject to balancing selection. After identifying parts of the genome subjected to selection, we shall investigate the function and role of such segments in two ways. First we shall determine if QTLs controlling traits that distinguish the three diploid Senecio species are flanked by AFLPs bearing the signature of selection. Second, we shall determine if candidate genes of known function and likely to control traits implicated in divergence and speciation are flanked by AFLP loci also bearing the signature of selection. When such signatures are found we shall conclude that the QTLs and candidate genes concerned are likely to have had an important role in ecological isolation and speciation in this group of diploid Senecio. The research will involve considerable molecular work and computer simulation. The results will provide significant advances to our current understanding of the role of adaptive divergence in diploid hybrid speciation, and to the genetic basis of invasiveness in plants.