白豆杉为我国特有濒危裸子植物。本项目拟采用RAD-PE技术，基于统计遗传分析，开展白豆杉的适应性种群基因组学研究，着重分析种群基因组分化中的气候和土壤效应。研究内容有：（1）对取自白豆杉天然种群的个体，利用RAD-PE进行全基因组测序，从头组装重叠群，鉴定SNP和基因型；（2）利用获得的SNP数据，在全基因组范围检测白豆杉种群的核苷酸多样性及其在种群内和种群间的分配，研究种群基因组变异式样的成因；（3）对种群基因组学参数在白豆杉全基因组的分布进行高斯核平滑分析，分辨在种群间变异水平或分化程度显著改变的基因组区域，筛选受选择作用的基因或基因网络；(4) 鉴别与气候和土壤因子关联的SNP，研究白豆杉借助哪些基因的核苷酸变异对气候和土壤改变做出响应；（5）逐个解析气候和土壤因子对白豆杉种群适应性基因组分化的相对贡献，探究基因组区域是否发生平行进化。研究结果可为白豆杉迁地保育策略的制定提供依据。

Pseudotaxus chienii (Cheng) Cheng (Taxaceae) is an endangered conifer endemic to China. In this project, we propose to study the adaptive population genomics of P. chienii by using RAD-PE (Restriction-site Associated DNA Paired-End) sequencing and statistical genetic approaches. We place emphasis on disentangling the effects of climate and soil factors on the population genomic differentiation. The main research contents are as follows: (1) Whole-genome sequence data will be generated by using RAD-PE to sequence the individuals of P. chienii sampled from its natural populations. Then the paired reads will be de novo assembled into contigs for SNP (Single Nucleotide Polymorphism) and genotype identification. (2) By using the SNP data, we will conduct a genome-wide scan to estimate the nucleotide diversity and its partition within and among populations, and explore the reasons that contribute to the formation of population genomic pattern. (3) A Gaussian kernel-smoothing analysis of the SNP data will be applied to to assess the distribution of population genomic parameters across the whole genome. We will attempt to reveal the genomic regions that exhibit significant changes of levels of diversity or differentiation and identify the gene or gene networks that have responded to natural selection. (4) This project will identify the SNPs that are closely associated with climate and soil factors and find the genes whose nucleotide variations are involed in the response of P. chienii to climate and soil changes. And (5) we will disentangle the relative contribution of climate and soil factors to the population genomic differentiation of P. chienii and to explore whether its genomic regions have experienced parallel evoluton. These studies can provide fresh insights for the development of an efficient ex-situ conservation strategy for P. chienii. .