多组学结合挖掘光核桃高原适应性相关基因

High altitude adaptation plays essential roles for the survival of plant species at high-altitude regions. The Prunus mira was the ancestor of cultivated peach which originated from Tibet Plateau and an abundance of natural population of Prunus mira was existed on Tibet Plateau. Understanding the genetic basis underlying the high altitude adaptation of Prunus mira contribute to fruit breeding in high-altitude regions and mechanism of adaptive evolution. Here we performed a project to comprehensively reveal the genetic basis of high altitude adaptation by combining genomics, transcriptomics, and metabonomics. Based on the assemblied high-quality reference genome for Prunus mira using both Illumina and Pacbio sequencing that we have finished previously. We will analyze the gene family expansion and contraction and the specific genomic regions in Prunus mira genome by compared genomes of other species. A total of 200 Prunus mira accessions will be sequenced with a depth of 20 ×. Using this resequencing data, we will identify the genome-wide SNPs, SVs, and CNVs. The genes undergone positive selection will be identified by screening for genomic regions with sharp reduction of nucleotide diversity and high genetic differentiation. To detect the metabolites in peach fruit, the metabolomic analysis of 200 accessions will be performed using GC-MS or LC-MS. The genomic loci or genes association with metabolites will be identified through genome-wide metabolic association studies (mGWAS). The overlapped genes between positive selection genes and metabolites associated genes were termed as candidate genes. To determine the key genes and metabolites in high-altitude adaptation, the RNA-seq analyses and metabolomics was performed in the same cultivars grown in Zhengzhou (low-altitude) and Lhasa (high-altitude) as well as the peach cultivars before and after UV-B treatment. The full sequence and promoter sequence of candidate genes will be cloned and sequenced to mine the key variations underlying adaptation evolution. The key candidate genes will be transformed into the model plant Arabidposis to further verify their biological functions. Our research will performed the combine analyses included genome, tramscriptome, metabolome will be carried out to reveal the complicated mechanism of high-altitude adaptation in Prunus mira.

高原适应性是植物在高海拔地区生存的前提，光核桃原产于青藏高原，在青藏高原拥有大量自然群体分布，研究其高原适应性对高原果树育种，了解物种适应性进化机制具有重要意义。本研究拟通过基因组、转录组及代谢组多组学结合的方式全方位解析光核桃高原适应性。首先对200份青藏高原不同海拔光核桃种质进行全基因组变异检测，检测正选择基因；对200份光核桃种质进行代谢组分析，检测代谢物，进行代谢物关联分析，获得代谢物关联的基因；正选择基因与代谢物关联分析共有基因定义为候选基因，并通过转录组测序验证，确定关键候选基因；克隆关键候选基因基因全长及启动子，分析变异机制，并转入拟南芥进行验证。本研究基于基因组、转录组、代谢组联合分析探究光核桃高原适应性以及次生代谢物在高原适应性中的作用。

光核桃是青藏高原特有的古老果树资源，其遗传多样性丰富、生态类型多样、水平和海拔分布范围广，生存环境面临高紫外辐射、低氧、低气压等恶劣条件，但其寿命比栽培桃长。收集、评价和保护这些独特的资源对研究高原适应性、发掘基因资源具有重要价值。在前期十余年野外考察和研究基础上，我们采集了光核桃部分不同育性花的样本进行了花粉的电镜扫描和花蕾的代谢组学分析，研究发现光核桃花粉的育性可能主要与黄酮生物合成相关。收集评价了拉萨试验园桃和野外光核桃种质资源395份。完成了339份桃和光核桃资源的重测序和代谢组分析、开展了转录组分析。构建了SNP的系统发育树，基于⽐对结果，进⾏了可变剪接预测分析、基因结构优化分析以及新基因的发掘，发掘新基因1,054个，其中864个得到功能注释,4,037个基因的结构得到优化。进⾏了基因表达量分析和部分基因的验证。开展了与海拔相关的表型数据、基因组、代谢组和转录组的联合分析定位。2021年度研究团队在国际期刊《当代生物学》发表了核心研究结果西藏李属植物高原适应性的遗传基础。对关联样本的脂溶性代谢组进行了分析、撰写类胡萝卜素代谢论文，开展了野外光核桃不同垂直梯度的生理研究。在国际期刊《食品化学》在线发表研究论文海拔对西藏光核桃果实类胡萝卜素含量的影响研究，揭示了海拔梯度对光核桃果实类胡萝卜素含量的影响，挖掘到4个直接相关的基因。