橐吾属是一个高度多样化的类群，自然杂交和基因渗入较为普遍。本项目拟在已有研究基础之上，以舟叶橐吾和东俄洛橐吾4个杂交区为研究对象，研究其基因渗入和遗传结构。1. 采用分子系统学方法和SSR分子标记来确定基因渗入的物种，判断杂交发生的程度；2. 采用基于第二代高通量测序的RAD-Seq技术，用STACKS软件分析所获得的序列数据，分析并比较4个杂种区内各个位点的渗入率，估计在中性条件下期望的渗入频率，鉴定outlier位点，推断其受到的选择压力；3. 采用cstacks建立一致性序列的目录，以这些一致性序列为参考序列，将杂交群体的reads与这些序列比对，统计杂交群体在所有RAD标签上的亲本特异性SNP的频率。从基因组水平揭示所研究杂交区的遗传结构和适应性渗入的发生规律，以及基因渗入在杂交物种形成中的作用，阐明在物种间存在基因流的情况下基因组很多位点可以自由交换而遗传整合性却得以保持的机制。

Ligularia (Asteraceae) is a highly diverse taxon in Hengduan mountains region. The natural hybridization and gene introgression occur frequently in sympatric Ligularia species. We have carried out some researches on natural hybrids of Ligularia, such as, natural hybrid of L. paradoxa and L. duciformis, natural hybrid of L. subspicata and nelumbifolia, of L.subspicata and vellarea, and so on. Now, the objectives of this project are to examine the gene introgression of four hybrid zones of L. cymbulifera and L. tongolensis. 1. Internal transcribed spacer and three chloroplast DNA fragment sequences are used to determine the hybrids and the relationship between putative parents and hybrids.Combined with the data of SSR molecular markers, the filial generations (F1, later-generation hybrids or backcross hybrids) and the species which gene introgession have taken will be ascertained. 2. RAD-seq technology which based on the next-generation sequencing by Illumina Genome Analyzeris used to obtain rough reads. After assembling, STACKS is used to analyze the reads. The reference sequences are designated from catalogue of the uniformity sequences constructed by cstacks for identifying outlier loci and comparing the introgression rate of each locus in the 4 hybrid zones. 3. The frequency of the parental species specific SNP of hybrid populations are acquired though comparison all RAD markers reads with reference sequences for estimating the desired infiltration frequency under neutral conditions, and to conclude the selection impression. On genome level, the discipline of adaptive gene introgression in hybrid zones mainly between L. cymbulifera and L. tongolensis is studied in our project, which will proclaim the vital importance of introgression in hybrid speciation and clarify the mechanism how the genetic integration is maintained while numerous genome alleles exchange freely when gene flow among species.