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

RESEARCH-PGR：揭示转座子在玉米变异中的作用

基本信息

批准号：
1934384
负责人：
Candice Hirsch
金额：
$ 410.94万
依托单位：
University of Minnesota-Twin Cities
依托单位国家：
美国
项目类别：
Standard Grant
财政年份：
2019
资助国家：
美国
起止时间：
2019-09-01 至 2024-08-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1934384&HistoricalAwards=false
关键词：
RESEARCH PGR Uncovering role transposons

项目摘要

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.

继续开发高产作物品种并尽量减少对环境的影响至关重要。为了实现这一目标，植物育种依赖于物种内的遗传变异来寻找新的优先性状。大多数努力都集中在表征基因组单个核苷酸变化时发生的变异。然而，有证据表明转座元件是同一物种不同品种基因组变异的主要来源。转座元件最初被称为“跳跃基因”，是 DNA 的小片段，可以产生额外的拷贝并移动到新的基因组位置。转座元件由芭芭拉·麦克林托克 (Barbara McClintock) 在玉米中首次发现，约占玉米基因组的 85%。众所周知，转座元件可以影响附近的 DNA，并通过改变基因表达的时间和方式来引起表型。一个有趣的持续问题是，绝大多数由转座元件组成的基因组实际上是如何发挥作用并影响性状的。该项目通过记录不同玉米品种中转座元件的变异来解决这个问题，然后研究转座元件如何在玉米中产生表型变异。该项目的知识可以揭示玉米的所有新育种潜力，并有助于塑造基于转座元件的未来作物改良。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。所有资源都可以通过公共网站获得。转座元件（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 在植物物种内具有高度可变性，并解释了农艺上重要的 QTL。然而，人们对 TE 在促进作物基因组、表观基因组、转录组和表型多样性方面的作用缺乏了解，部分原因是这些序列的高度重复性，迄今为止，这使得它们在现有技术下难以实现。这些活动将开发注释和多样性资源，以促进玉米 TE 的研究。在该项目中，这些资源将用于通过使用定量遗传学和群体遗传学方法来研究 TE 在表型变异中的作用。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并改进作物物种基因型-表型预测的潜力。该项目将监测 TE 如何对动态玉米基因组做出贡献，并识别在现代玉米品种中移动的 TE。该研究将通过分析 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、转录组和表型组变异中的作用。该项目将提供关于 TE 作用的基础知识，可用于增强玉米改良和对非生物胁迫的反应。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。

项目成果

期刊论文数量（16）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Critical role of insertion preference for invasion trajectory of transposons

DOI：
10.1093/evolut/qpad128
发表时间：
2023-08-05
期刊：
EVOLUTION
影响因子：
3.3
作者：
Munasinghe，Manisha;Springer，Nathan;Brandvain，Yaniv
通讯作者：
Brandvain，Yaniv

Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes

DOI：
10.1073/pnas.2010250117
发表时间：
2020-09-22
期刊：
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
影响因子：
11.1
作者：
Crisp, Peter A.;Marand, Alexandre P.;Springer, Nathan M.
通讯作者：
Springer, Nathan M.

Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposons

DOI：
10.1093/genetics/iyaa003
发表时间：
2021-01-01
期刊：
GENETICS
影响因子：
3.3
作者：
Noshay, Jaclyn M.;Marand, Alexandre P.;Springer, Nathan M.
通讯作者：
Springer, Nathan M.

Genetic and epigenetic variation in transposable element expression responses to abiotic stress in maize

DOI：
10.1093/plphys/kiab073
发表时间：
2021-02-16
期刊：
PLANT PHYSIOLOGY
影响因子：
7.4
作者：
Liang, Zhikai;Anderson, Sarah N.;Springer, Nathan M.
通讯作者：
Springer, Nathan M.

Modeling chromatin state from sequence across angiosperms using recurrent convolutional neural networks

DOI：
10.1002/tpg2.20249
发表时间：
2021-11
期刊：
bioRxiv
影响因子：
0
作者：
Travis Wrightsman;Alexandre P. Marand;Peter A. Crisp;Nathan M. Springer;E. Buckler
通讯作者：
Travis Wrightsman;Alexandre P. Marand;Peter A. Crisp;Nathan M. Springer;E. Buckler