基于基因组、气候因子、物候期的互作高通量发掘桃适应性相关基因

Plant species are divided into different ecotypes results from the variation of geographic distributions. Approach based on the interactions between genome, climate factors, and phenotypes is the major mathod for adaptation associated genes high-throughput mining. Seven distinct ecotypes of peach collections will be used as materials in this project. Firstly, we will detect the loci associated with each climate factors through the correlation analysis between climate factors and SNPs. Secondly，Through genomic regions undergone selection detecting, we can obtain the genomic regions underlying the adaptive genetic basis of each ecotype. Meanwhile，Given the adaptive traits, flowering time and chilling requirement, the association loci will be detected through a genome-wide association study based on the phenotypes and SNPs. Subsequently, the association loci which are associated with climate adaptation will be detected by searching for loci with elevated differentiation among seven ecotypes. Based on these analysis, we can obtained the loci involved in the interactions between blooming date, chilling requirement and climate. Finally，We will test the robust association loci and alternative association loci by the genome-wide association studies of flowering time and chilling requirement which will be conducted at Dalian (North) and Kunming (South), respectively. Based on that, we will verify the stable SNPs using natural population and genetic population. Our study will conduct high-throughput adaptation associated genes mining through the interaction between genome, climate factors, and phenological phase in peach which will provide theoretical evidences for peach genetic adaptation research at genome-wide level.

地理分布的差异导致植物形成了不同的生态型，通过研究不同生态型基因组、环境因子、表现型的互作是高通量发掘与适应性相关基因的重要手段。本项目拟采用我国特征鲜明的7个生态型的桃种质资源为材料，首先重点开展气候因子与基因组SNP的相关性分析，获得与各气候因子适应性相关的基因组区段；其次，对基因组受选择区段分析确定各生态型适应自身生存环境的基因组区段；同时，选择适应性性状需冷量和开花期，通过全基因组关联分析获得其关联位点，分析关联位点在不同生态型间的分化，阐明需冷量和开花期与环境的互作位点，以及生态型间变异机制；最后，利用大连（北方）和昆明（南方）种植的相同品种的需冷量和开花期全基因组关联分析，获得稳定关联位点和可变关联位点，稳定位点在自然群体和遗传群体中验证。本研究基于基因组、气候因子、物候期三者的互作发掘与适应性相关的基因，为全基因组水平揭示桃生态适应性的遗传基础提供理论依据。

适应性是决定物种生存能力和物种多样性的重要基础，地理分布的差异导致植物形成了不同的生态型，长期的自然选择导致不同生态型产生了适应不同环境类型的遗传变异，通过研究不同生态型基因组、环境因子、表现型的互作能够高通量发掘适应性相关基因。本项目收集了来自全国不同地区的桃种质资源480份，通过全基因组测序技术鉴定了基因组近500万SNP和20万SV变异信息，并收集了样本生存地的51个环境因子，其中包括温度、降水、日照、辐射等与物种生存息息相关的环境因子；通过比较基因组研究，鉴定了142个驯化区间、104个改良区间，通过受选择区间注释发现果实大小主要在驯化过程中受选择，而果实风味在驯化和改良过程中均受到选择，并鉴定了多个果实大小和可溶性固形物含量的候选基因，阐明了肉质进化路线；亲缘关系和群体结构分析表明，桃地方品种和野生资源可分为7个生态型，7个生态型环境条件各具特色，包含了极端和温和的气候类型；通过受选择分析，鉴定到2092个受选择区段，揭示了7个生态型适应不同环境的遗传基础，通过基因富集分析发现，受选择基因多与胁迫响应相关，同时包含多个已知参与特定胁迫响应相关基因，并解析了适应干旱和高海拔的进化机制；利用基因组-环境关联分析，鉴定到与51个环境因子关联的基因组位点9393个，包括5个温度相关关联热点和6个降水相关关联位点，并获得了桃抗寒性候选基因PpAHP5；利用关联分析鉴定到多个开花期和需冷量关联的新位点，并发现了位于8号染色体上与开花期和需冷量适应不同纬度密切相关的位点SVP,鉴定了控制需冷量和开花期的候选基因。本项目的完成为桃分子育种和全基因组选择提供了材料，为桃基因组学研究奠定了基础。