RII Track-2 FEC: Comparative Genomics and Phenomics Approach to Discover Genes Underlying Heat Stress Resilience in Cereals

RII Track-2 FEC：通过比较基因组学和表型组学方法来发现谷物中热应激恢复能力的基因

• 批准号: 1736192
• 负责人: Harkamal Walia
• 金额: $ 578.37万
• 依托单位: University of Nebraska-Lincoln
• 依托单位国家: 美国
• 项目类别: Cooperative Agreement
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-08-01 至 2023-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1736192&HistoricalAwards=false
• 关键词: RII; Track; FEC; Comparative; Genomics

Non-technical DescriptionThis Research Infrastructure Improvement (RII) Track-2 Focused EPSCoR Collaborations (RII Track-2 FEC) award is a joint project among the University of Nebraska-Lincoln, Arkansas State University, and Kansas State University. The project will create the foundational knowledge needed to improve wheat and rice yields under stressful environments. Trends at the global-, regional-, and farm-level point to an increase in minimum night temperatures that is significantly higher than the rate of increase in maximum day temperatures. Increases in night temperatures significantly decrease the grain yield and quality of major crops such as rice and wheat, which together provide over 50% of the caloric intake for humans worldwide. To ensure global food security, there is an urgent need to improve crop resilience to high night temperature stress-induced yield and quality losses. This project will build upon complementary expertise and infrastructure in Nebraska, Kansas, and Arkansas to develop novel research infrastructure and make discoveries that ultimately lead to development of higher yielding and resilient cultivars for the U.S. farmers. This program will create opportunities to collaborate with key industry partners to ensure that promising discoveries are translated into applications with economic benefit for farmers. Planned workforce development activities will focus on mentoring six early career faculty members, training of postdocs and graduate and undergraduate students, and broadening the participation of underrepresented minorities and underserved rural population in STEM fields.Technical DescriptionThis project aims to elucidate the physiological and genetic basis of high night temperature resiliency of rice and wheat, translate these discoveries into genetic and phenotypic markers for public and private breeding programs, and develop a broad continuum for STEM education. To this end, the investigators are taking a multidisciplinary approach involving plant physiologists, quantitative geneticists, computational biologists, biochemists, engineers, informaticians, and precision agronomists. This program is building genome to phenome linkages using automated image-based phenomics approaches in combination with transcriptomics and metabolomics applied to wheat and rice diversity panels. Gene and pathways discovered from this approach will be functionally tested for their role in improving the temperature resilience in rice and wheat. The planned approach integrates across greenhouse and field scales; captures complex interactions between the environment and genome during grain development at high spatiotemporal resolution; and couples genomics and phenomics outcomes within a quantitative, model-based framework. This research will make the integrated dataset more accessible to biologists through a visualization platform. Six early career faculty will be mentored for professional progress and interactions with international phenomic communities. An Interdisciplinary graduate course will be developed for students in plant sciences, agricultural engineering, computational biology, biochemistry, statistics, and computer sciences. On-line offerings of this course will ensure student participation from all three participating universities.

该研究基础设施改进（RII） Track-2重点EPSCoR合作（RII Track-2 FEC）奖是内布拉斯加大学林肯分校、阿肯色州立大学和堪萨斯州立大学之间的联合项目。该项目将创造在压力环境下提高小麦和水稻产量所需的基础知识。全球、区域和农场层面的趋势表明，夜间最低温度的上升幅度明显高于白天最高温度的上升幅度。夜间气温的升高显著降低了稻米和小麦等主要作物的粮食产量和质量，而这两种作物加起来为全世界人类提供了50%以上的热量摄入。为了确保全球粮食安全，迫切需要提高作物对高温夜间应激引起的产量和质量损失的抵御能力。该项目将以内布拉斯加州、堪萨斯州和阿肯色州的互补专业知识和基础设施为基础，开发新的研究基础设施，并做出发现，最终为美国农民开发出更高产量和适应力强的品种。该项目将创造与主要行业合作伙伴合作的机会，以确保有希望的发现转化为为农民带来经济效益的应用。计划中的劳动力发展活动将侧重于指导六名早期职业教师，培训博士后、研究生和本科生，扩大代表性不足的少数民族和服务不足的农村人口在STEM领域的参与。本项目旨在阐明水稻和小麦耐高温性的生理和遗传基础，将这些发现转化为公共和私人育种计划的遗传和表型标记，并为STEM教育开发一个广泛的连续体。为此，研究人员正在采取多学科方法，包括植物生理学家、数量遗传学家、计算生物学家、生物化学家、工程师、信息学家和精确农学家。该项目利用基于图像的自动表型组学方法，结合应用于小麦和水稻多样性面板的转录组学和代谢组学，建立基因组与表型组的联系。从这种方法中发现的基因和途径将在功能上测试它们在提高水稻和小麦的温度抗逆性方面的作用。规划的方法整合了温室和田间规模；以高时空分辨率捕捉谷物发育过程中环境与基因组之间复杂的相互作用；并将基因组学和表型学的结果结合在定量的、基于模型的框架内。这项研究将使生物学家更容易通过可视化平台访问整合的数据集。六名早期职业教师将获得专业进步和与国际现象社区互动的指导。将为植物科学、农业工程、计算生物学、生物化学、统计学和计算机科学的学生开设跨学科研究生课程。本课程的在线课程将确保所有三所参与大学的学生参与。

项目成果

Genomic Bayesian Confirmatory Factor Analysis and Bayesian Network To Characterize a Wide Spectrum of Rice Phenotypes

• DOI: 10.1534/g3.119.400154
• 发表时间: 2018-10
• 期刊: G3: Genes|Genomes|Genetics
• 作者: Haipeng Yu;Malachy T. Campbell;Qi Zhang;H. Walia;G. Morota

3D Reconstruction of Plant Leaves for High-Throughput Phenotyping

• DOI: 10.1109/bigdata.2018.8622428
• 发表时间: 2018-12
• 期刊: 2018 IEEE International Conference on Big Data (Big Data)
• 作者: Feiyu Zhu;S. Thapa;T. Gao;Y. Ge;H. Walia;Hongfeng Yu

Endoplasmic reticulum stress pathway mediates the early heat stress response of developing rice seeds

内质网应激途径介导发育中水稻种子的早期热应激反应

• DOI: 10.1111/pce.14103
• 发表时间: 2021
• 期刊: Cell & Environment
• 作者: Sandhu, Jaspreet;Irvin, Larissa;Liu, Kan;Staswick, Paul;Zhang, Chi;Walia, Harkamal
• 通讯作者: Walia, Harkamal

Utilizing random regression models for genomic prediction of a longitudinal trait derived from high-throughput phenotyping

• DOI: 10.1002/pld3.80
• 发表时间: 2018-09-01
• 期刊: PLANT DIRECT
• 影响因子: 3
• 作者: Campbell, Malachy;Walia, Harkamal;Morota, Gota
• 通讯作者: Morota, Gota

ShinyAIM: Shiny-based application of interactive Manhattan plots for longitudinal genome-wide association studies

• DOI: 10.1002/pld3.91
• 发表时间: 2018-10-01
• 期刊: PLANT DIRECT
• 影响因子: 3
• 作者: Hussain, Waseem;Campbell, Malachy;Morota, Gota
• 通讯作者: Morota, Gota