Is Abiotic Stress Tolerance Achieved by Network Restructuring or Invention of New Genetic Modules?

非生物胁迫耐受性是通过网络重组还是新基因模块的发明来实现的吗？

• 批准号: 1616827
• 负责人: Maheshi Dassanayake
• 金额: $ 90万
• 依托单位: Louisiana State University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-08-15 至 2021-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1616827&HistoricalAwards=false
• 关键词: Abiotic; Stress; Tolerance; Achieved; Network

The project involves exploration of how plants adapt naturally to harsh environments, in order to understand stress tolerance mechanisms and inform development of food and energy crops that can better tolerate changing environments. The outcomes have broad societal relevance, as crop production is frequently constrained by environmental stresses, such as salinity. This project will provide a learning platform for diverse teams to design new computational and molecular tools for studying naturally existing genetic variation. These teams will consist of biological and computer science graduate students, undergraduates, including underrepresented minorities, high school students and instructors, and international collaborators. The project also supports career development for two beginning investigators. Data generated from this project will be used to design an interactive visual data analysis interface with contributions from high school student programmers. Other activities include plant nutrient awareness events for the public and K-12 students, a summer workshop to train high school teachers and students in PCR and DNA fingerprinting, and discussions with local high school students on ethical issues related to genetic engineering. DNA sequence datasets and bioinformatics programs resulting from this project will be shared publicly, which will enable scientific activities ranging from basic research exploring mechanisms in genetics and evolution to generating markers and resources for crop improvement. This project will investigate how a species achieves stress adaptation compared to a closely related stress sensitive species by analyzing genomic signatures that lead to transcriptomic responses to stress, followed by targeted transgenics and molecular phenotyping. The overall analysis will be tested in a conceptual framework that highlights stress adaptation achieved by modifications in existing core stress response systems, and/or recruitment of new genetic components. Extremophile plants represent emerging models for understanding genetic mechanisms governing plant survival under extreme abiotic stresses. Schrenkiella parvula and Eutrema salsugineum, the two most salt-tolerant species among known wild relatives of Brassica crops, will be used as model genomes, and multiple salt stresses will be applied to study adaptation compared to the stress sensitive model A. thaliana. Genomes of both S. parvula and E. salsugineum show extensive overall synteny with the A. thaliana genome, which enables comparative studies benefiting from the wealth of genetic information available on A. thaliana. Inter-species comparative RNAseq methods are planned to uncover the dynamics of abiotic stress responsive gene regulation caused by excessive Na+, K+, or Li+ salts. Transgenic plants in all test species will be created targeting representative genes in major stress responsive units identified. Molecular level phenotyping will be achieved via ionomic and metabolomic profiling of wild-type and transgenic lines collected from control and stress-treated samples. Finally, descriptive genetic modules will be developed with a core data set linking genomic restructuring that enables improved stress adaptation in known and novel stress responsive pathways, in both stress-adapted and stress-sensitive species. The work will provide a strategic case study that can be expanded to other organisms, to evaluate genomic organization via targeted genetic studies assisted by transgenic plants, transcriptomic regulation, and metabolomes used for molecular phenotyping.This project is co-funded by the Genetic Mechanisms Cluster in the Division of Molecular and Cellular Biosciences in the Biological Sciences Directorate and by the NSF EPSCoR Program.

该项目涉及探索植物如何自然适应恶劣环境，以了解胁迫耐受机制，并为能够更好地适应不断变化的环境的粮食和能源作物的开发提供信息。这些成果具有广泛的社会意义，因为作物生产经常受到环境压力的限制，如盐度。该项目将为不同的团队提供一个学习平台，以设计新的计算和分子工具来研究自然存在的遗传变异。这些团队将由生物和计算机科学研究生、本科生（包括代表性不足的少数民族）、高中生和教师以及国际合作者组成。该项目还支持两名初出茅庐的调查员的职业发展。从这个项目中产生的数据将被用来设计一个交互式的可视化数据分析界面与高中生程序员的贡献。其他活动包括为公众和K-12学生举办植物营养素宣传活动，举办暑期讲习班，培训高中教师和学生进行聚合酶链反应和DNA指纹鉴定，并与当地高中学生讨论与遗传工程有关的伦理问题。该项目产生的DNA序列数据集和生物信息学程序将公开共享，这将使科学活动从探索遗传和进化机制的基础研究到产生作物改良的标记和资源。该项目将研究一个物种如何实现压力适应相比，一个密切相关的压力敏感的物种，通过分析基因组签名，导致转录组反应的压力，其次是有针对性的转基因和分子表型。整体分析将在一个概念框架中进行测试，该框架强调通过修改现有核心应激反应系统和/或招募新的遗传成分来实现应激适应。极端植物代表了理解极端非生物胁迫下植物生存遗传机制的新兴模型。小Schrenkiella parvula和盐生Eutrema salsugineum是芸苔属作物已知野生近缘种中最耐盐的两个物种，将被用作模式基因组，与胁迫敏感模式A相比，将应用多重盐胁迫来研究适应性。thaliana.两个S. parvula和E. Salsugineum与A.拟南芥基因组，这使得比较研究受益于丰富的遗传信息，可在A。thaliana.物种间比较RNAseq方法计划揭示由过量Na+，K+或Li+盐引起的非生物胁迫响应基因调控的动态。所有测试物种中的转基因植物将针对所鉴定的主要胁迫响应单位中的代表性基因而产生。将通过从对照和应激处理样品中收集的野生型和转基因品系的离子组学和代谢组学分析来实现分子水平表型分析。最后，描述性的遗传模块将开发一个核心数据集连接基因组重组，使改善压力适应已知的和新的压力响应途径，在压力适应和压力敏感的物种。这项工作将提供一个战略性的案例研究，可以扩展到其他生物体，通过有针对性的遗传研究辅助转基因植物，转录调控和代谢组用于分子phenotyping.This项目是共同资助的遗传机制集群的分子和细胞生物科学部在生物科学理事会和NSF EPSCoR计划的基因组组织进行评估。

项目成果

Cross species multi‐omics reveals cell wall sequestration and elevated global transcript abundance as mechanisms of boron tolerance in plants

跨物种多组学揭示细胞壁隔离和整体转录丰度升高是植物耐硼的机制

• DOI: 10.1111/nph.17295
• 发表时间: 2021
• 期刊: New Phytologist
• 影响因子: 9.4
• 作者: Wang, Guannan;DiTusa, Sandra Feuer;Oh, Dong‐Ha;Herrmann, Achim D.;Mendoza‐Cozatl, David G.;O'Neill, Malcolm A.;Smith, Aaron P.;Dassanayake, Maheshi
• 通讯作者: Dassanayake, Maheshi

Genome-wide analysis of brassinosteroid responsive small RNAs in Arabidopsis thaliana

• DOI: 10.1007/s13258-020-00964-2
• 发表时间: 2020-07
• 期刊: Genes & Genomics
• 影响因子: 2.1
• 作者: S. Park;Jae H. Choi;Dong-ha Oh;John C. Johnson;M. Dassanayake;D. Jeong;M. Oh

Positive Selection and Heat-Response Transcriptomes Reveal Adaptive Features of the Arabidopsis Desert Relative, Anastatica hierochuntica

正选择和热响应转录组揭示了拟南芥沙漠近缘植物Anastatica hierochuntica的适应性特征

• 发表时间: 2021
• 期刊: bioRxiv
• 作者: Eshela, Gil;Duppena, Nick;Wang, Guannan;Oh, Dong-Ha;Kazachkova, Yana;Herzyk, Pawel;Amtmann, Anna;Gordon, Michal;Chalifa-Caspi, Vered;Oscar, Michelle Arland
• 通讯作者: Oscar, Michelle Arland

Balancing growth amidst salinity stress – lifestyle perspectives from the extremophyte model Schrenkiella parvula

• DOI: 10.1101/2021.08.27.457575
• 发表时间: 2021-08
• 期刊: bioRxiv
• 作者: Kieu-Nga Tran;P. Pantha;Guannan Wang;Narender Kumar;Chathura Wijesinghege;Hyewon Hong;John C. Johnson;Ross Kelt;Megan G. Matherne;Ashley Clement;David Tran;Colt Crain;Dong-ha Oh;Prava Adhikari;Maryam Foroozani;P. Finnegan;D. Longstreth;J. Larkin;Aaron P. Smith;M. Dassanayake

GOMCL: a toolkit to cluster, evaluate, and extract non-redundant associations of Gene Ontology-based functions

• DOI: 10.1186/s12859-020-3447-4
• 发表时间: 2020-04
• 期刊: BMC Bioinformatics
• 影响因子: 3
• 作者: Guannan Wang;Dong-ha Oh;M. Dassanayake