RESEARCH-PGR: Impact of Transposable Element Bursts on the Rice Genome and Epigenome

在序列和表观遗传水平上使基因组多样化的机制是表型变异的基础。随着气候变化的加速，理解和应用使作物基因组多样化的机制来养活后代是至关重要的。大多数动植物基因组来自转座元件(TES)，即DNA的可移动片段，当它们从一个基因组位置转置到另一个基因组位置时，拷贝数往往会增加。TES插入邻近基因并改变其调控的能力以及促进基因组重排和表观遗传学变化的能力最近被认为是适应性进化的重要贡献。简单地说，TES可以撼动其他方面(结构上)保守的基因组。该项目利用长读DNA测序技术和单细胞表观遗传学分析来揭示快速扩增的被称为mPING的TE如何实时改变水稻基因组，同时避免宿主(表观遗传)沉默和突变插入。在更广泛的影响方面，该项目还解决了农业劳动力的危机，农业劳动力是科学中最古老和最不多样化的，该项目通过每年多达2000名新生的真实研究经验，向拉美裔服务机构的本科生介绍植物基因组学的兴奋。这个项目的研究目标有两个。首先，通过对水稻TE家族Ping/mPING的大规模扩增，了解三个重组自交系群体产生的结构基因组变异的总体情况。根据先前的结果，预计将确定至少50,000个额外的mPING插入位点[~15%在可访问的染色质区域(ACR)]和许多结构变体(SVS)，包括拷贝数和存在的变体和反转。第二个目标是通过构建水稻单细胞顺式调控图谱并评估mPING插入到目标RI系中的影响，来确定这些损伤的子集对表观遗传调控和生殖隔离的影响。虽然~50,000个新的mPING插入片段中的绝大多数可能是中性的或通过进化时间的选择而被淘汰，但在短期内，它们将提供一个宝贵的工具来更快地评估ACRS的功能，并且比目前可用的任何其他方法的成本低得多。该项目的结果将揭示快速TE扩增重塑表观基因组、导致生殖隔离的潜力，并对SVS来说，快速产生盘根体下的基因组变异。该项目产生的所有数据将通过存放在NCBI短读档案库(SRA)和基因表达总览(GEO)等已建立的长期序列存储库中获得。该奖项反映了NSF的法定使命，并已通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

Mechanisms that diversify genomes, at both the sequence and epigenetic levels, underlie phenotypic variation. With accelerated climate change, it is essential that mechanisms diversifying crop genomes be understood and applied to feed future generations. Most plant and animal genomes are derived from transposable elements (TEs), mobile fragments of DNA that often increase in copy number as they transpose from one genomic locus to another. The ability of TEs to insert near genes and alter their regulation and to promote genomic rearrangements and epigenetic changes has recently been recognized as a significant contributor to adaptive evolution. Stated simply, TEs can shake up otherwise (structurally) conservative genomes. This project exploits long read DNA sequencing technology and single cell epigenetic analyses to reveal how the rapidly amplifying TE called mPing alters, in real time, the rice genome, while avoiding host (epigenetic) silencing and mutagenic insertions. With respect to broader impacts, this project also addresses a crisis in the agricultural workforce, which is the oldest and least diverse among the sciences, by introducing undergraduates at a Hispanic Serving Institution to the excitement of plant genomics through authentic research experiences for up to 2000 incoming students/year. The research goals of this project are two-fold. The first is to understand the totality of structural genomic variation generated in three recombinant inbred (RI) populations by the massive amplification of the rice TE family Ping/mPing. Based on prior results, it is anticipated that at least 50,000 additional mPing insertion sites [with ~15% in accessible chromatin regions (ACRs)] and numerous structural variants (SVs) including copy number and presence absence variants and inversions will be identified. The second goal is to determine the consequences of a subset of these lesions on epigenetic regulation and reproductive isolation by generating a rice single cell cis-regulatory atlas and assessing the impact of mPing inserts in targeted RI lines. While the vast majority of the ~50,000 de novo mPing insertions may be neutral or eliminated by selection over evolutionary time, in the short term they will provide an invaluable tool to evaluate the function of ACRs more quickly and for far less cost than any other method currently available. Results of this project will reveal the potential of rapid TE amplification to reshape the epigenome, lead to reproductive isolation, and, for SVs, to rapidly generate the genomic variation that underlies pangenomes. All data generated by this project will be made available through deposition at established long-term sequence repositories such as the NCBI Short Read Archive (SRA) and Gene Expression Omnibus (GEO).This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.