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.

至关重要的是要继续开发多种作物，这些农作物富有生产力，同时最大程度地降低了环境影响。为此，植物育种依赖于物种内的遗传变异来找到新的priorty特征。大多数努力集中在表征由于基因组的单个核苷酸变化而发生的变化。但是，有证据表明，可转座元素是同一物种不同种类的基因组之间的主要变化来源。可替代的元素（最初称为“跳跃基因”）是一小部分DNA，可以制作其他副本并转移到新的基因组位置。芭芭拉·麦克林托克（Barbara McClintock）最初在玉米（玉米）发现的转座元素约占玉米基因组的85％。众所周知，转座元件可以通过改变何时以及如何表达基因来影响附近的DNA并引起表型。一个有趣的持续问题是，由可转座元素组成的绝大多数基因组如何实际发挥作用并有助于性状。该项目通过记录不同品种玉米中可转座元素的变化来解决这个问题，然后检查可旋转元素如何在玉米中产生表型变化。该项目的知识可以揭示玉米的所有新育种潜力，并可以帮助基于转座元素来塑造未来的作物改善。在此过程中，本科生和研究生将通过动手研讨会和培训对基因组进行计算和定量分析培训。所有资源都将通过公共网站获得。转移元素（TES）说明了玉米和其他农作物中大多数基因组序列。基因座特异性和细胞遗传学研究表明，TES在植物物种中可能是高度变化的，并说明了农艺上重要的QTL。然而，缺乏对作物植物中TE的作用在产生基因组，表观基因组，转录组和表型多样性的知识，部分原因是这些序列的高度重复性性质，迄今为止，这些序列具有可用的技术，这使它们使它们顽固。这些活动将开发注释和多样性资源，以使TES在玉米中进行研究。在该项目中，这些资源将用于研究TE通过使用定量遗传学和种群遗传学方法来促进表型变异的作用。这些努力将阐明利用TE变异知识以通过环境相互作用来理解基因型的潜力，并改善作物物种中的基因型 - 表型预测。该项目将监视TE如何为动态玉米基因组做出贡献，并确定在现代玉米品种中移动的TE。该研究将通过分析对染色质和基因表达的影响来监测TE变异可以影响表型的机制。这些实验将阐明多态性在玉米表观基因组，转录组和现象体变异方面的作用。该项目将提供有关TE的作用的基本知识，该知识可用于增强玉米的改善和对非生物压力的反应。该奖项反映了NSF的法定任务，并被认为是值得通过基金会的知识分子和更广泛影响的评估审查标准来通过评估来支持的。

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