白豆杉的适应性种群基因组学研究：解析气候和土壤因子效应

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. .

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。

本项目对我国特有的濒危裸子白豆杉开展了种群基因组学研究，着重解析了驱动白豆杉天然种群发生适应性遗传分化的关键气候和环境因子。已完成以下研究内容并获得重要结果：第一，借助Illumina平台通过限制位点相关DNA双末端测序（RAD-PE），实现了单核苷酸多态性（SNP）的鉴定。第二，对栖息于不同气候和土壤条件的种群，从WorldClim获得了气候变量数据，自己测定了各种群的20个土壤成分指标；发现白豆杉和其他松杉类植物相比，其天然种群具有中等水平的遗传变异和分化；白豆杉的适应性进化主要源自核而非叶绿体基因组；相较于土壤条件，气候因子在种群水平驱动基因组的分化过程中所起的作用更大；预测在气候变化条件下，白豆杉的南部适宜生境将会收缩；此外，还鉴别出仅同土壤因子相关以及既同土壤因子又同降雨量相关的适应性座位；建议对白豆杉分布于浙江之外的种群予以优先保护。第三，在全基因组范围检测了种群的遗传变异水平、遗传变异在种群内和种群间的分配，种群遗传分化程度和地理距离之间的相关性，重建了种群间的进化关系；结合白豆杉的生物、生态学特性，明确了影响种群基因组分化式样的成因；给出了种群遗传参数在基因组水平的分布式样。第四，利用核和叶绿体基因组序列数据完成了白豆杉的谱系地理分析，重点解析了遗传结构，种群历史动态，以及地理距离、气候因子、植被变量和土壤因子等变量之间的差异与遗传距离的关联。项目的研究结果发表在Molecular Phylogenetics and Evolution、Frontiers in Genetics、Frontiers in Plant Science、Ecology and Evolution、Applications in Plant Sciences、Mitochondrial DNA及Scientific Reports等重要SCI国际学术刊物，被国内外其他研究组多次引用。