RESEARCH-PGR: Uncovering the role of transposons in maize variation

至关重要的是继续开发高产作物品种，同时尽量减少对环境的影响。为了实现这一目标，植物育种依靠物种内部的遗传变异来寻找新的优先性状。大多数努力都集中在描述变异的特征上，这些变异发生在基因组的单个核苷酸的变化上。然而，有证据表明，转座因子是同一物种的不同品种之间的基因组变异性的主要来源。转座因子，最初被称为“跳跃基因”，是可以复制额外拷贝并移动到新的基因组位置的小片段DNA。转座因子最早是由芭芭拉·麦克林托克在玉米中发现的，约占玉米基因组的85%。众所周知，转座因子可以通过改变基因表达的时间和方式影响附近的DNA并引起表型。一个有趣的问题是，由转座因子组成的绝大多数基因组实际上是如何起作用并对性状做出贡献的。本项目通过记录不同玉米品种中转座因子的变异来解决这个问题，然后研究转座因子如何在玉米中产生表型变异。从这个项目中获得的知识可以揭示所有新的玉米育种潜力，并可以帮助塑造基于转座因子的未来作物改良。在此过程中，本科生和研究生将通过实践研讨会和培训，接受基因组计算和定量分析方面的培训。所有资源将通过公共网站提供。转座因子（te）占玉米和其他作物基因组序列的大部分。位点特异性和细胞遗传学研究表明，te在植物物种中可能是高度可变的，并且可以解释农学上重要的QTL。然而，关于TEs在作物基因组、表观基因组、转录组和表型多样性中的作用的知识还很缺乏，部分原因是这些序列的高度重复性，迄今为止，在现有技术的支持下，这些序列难以实现。这些活动将为玉米TEs的研究提供注释和多样性资源。在本项目中，将利用这些资源通过使用数量遗传学和群体遗传学方法来研究te在促进表型变异方面的作用。这些努力将阐明利用TE变异知识通过环境相互作用了解基因型的潜力，并改善作物物种的基因型-表型预测。该项目将监测外源基因对动态玉米基因组的贡献，并识别在现代玉米品种中迁移的外源基因。本研究将通过分析TE对染色质和基因表达的影响来监测TE变异影响表型的机制。这些实验将揭示TE多态性在玉米表观基因组、转录组和表型变异中的作用。该项目将提供有关TEs作用的基础知识，可用于加强玉米改良和对非生物胁迫的反应。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

It is critical to continue developing varieties of crops that are highly productive while minimizing environmental impact. To accomplish this, plant breeding relies upon the genetic variation within a species to find new priorty traits. Most efforts are focused on characterizing the variations that occur as changes to a single nucleotide of the genome. However, there is evidence that transposable elements are a major source of variability among the genomes of different varieties of the same species. Transposable elements, originally called "jumping genes," are small pieces of DNA that can make additional copies and move to new genomic locations. Transposable elements, first discovered in corn (maize) by Barbara McClintock, account for approximately 85% of the corn genome. It is known that transposable elements can influence nearby DNA and cause phenotypes by changing when and how genes are expressed. An intriguing ongoing question is how this vast majority of the genome composed of transposable elements actually functions and contributes to traits. This project addresses this question by documenting the variation of transposable elements in different varieties of corn, and then examines how transposable elements create phenotypic variation in corn. The knowledge from this project can reveal all new breeding potential for corn and can help shape future crop improvement based on transposable elements. In the process, undergraduate and graduate students will be trained in computational and quantitative analysis of genomes through hands-on workshops and training. All resources will be available through public websites.Transposable elements (TEs) account for the majority of genome sequence in maize and other crops. Locus-specific and cytogenetic studies suggest that TEs can be highly variable within plant species and account for agronomically important QTL. However, knowledge of the role of TEs in contributing to genomic, epigenomic, transcriptomic and phenotypic diversity in crop plants is lacking, in part due to the highly repetitive nature of these sequences, which has, to date, made them recalcitrant given available technologies. The activities will develop annotation and diversity resources to enable the study of TEs in maize. Within this project these resources will be utilized to study the role of TEs in contributing to phenotypic variation through the use of quantitative genetics and population genetics approaches. These efforts will elucidate the potential to utilize knowledge of TE variation to understand genotype by environment interactions and to improve genotype-phenotype predictions in crop species. The project will monitor how TEs contribute to a dynamic maize genome and identify TEs that are moving in modern maize varieties. The research will monitor the mechanisms through which TE variation can influence phenotype through the analysis of TE influences on chromatin and gene expression. These experiments will shed light upon the role of TE polymorphisms in contributing to variation in the maize epigenome, transcriptome and phenome. This project will provide foundational knowledge of the role of TEs that can be used to enhance maize improvement and responses to abiotic stress.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.