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RESEARCH-PGR: PanAnd - Harnessing convergence and constraint to predict adaptations to abiotic stress for maize and sorghum

RESEARCH-PGR：PanAnd - 利用收敛和约束来预测玉米和高粱对非生物胁迫的适应

基本信息

批准号：
1822330
负责人：
Edward Buckler
金额：
$ 499.84万
依托单位：
Cornell University
依托单位国家：
美国
项目类别：
Continuing Grant
财政年份：
2018
资助国家：
美国
起止时间：
2018-09-01 至 2023-08-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1822330&HistoricalAwards=false
关键词：
RESEARCH PGR PanAnd Harnessing convergence

项目摘要

Maize, sorghum, sugarcane, and Miscanthus are the most productive and water efficient crops and biofuels in the world. This productivity is due to a shared physiology and genetic ancestry over the last 15 million years. While these four crops will be extensively used, they are closely related to another 800 species that dominate grasslands across the world and are adapted to numerous environmental stresses including flooding, drought, heat, and frost. The project team will use modern genomics and machine learning to survey and analyze these related species, determining the most important genetic features they share that allow them to adapt to heat and drought. The results of this work will be used by commercial and public sector plant breeders to make maize and sorghum more productive and resilient to extreme weather. Key to this long-term impact is training the next generation of scientists in computational biology to address fundamental questions. These skills will be developed through hackathons and bioinformatics training workshops. The project will communicate this science to the general public through venues such as a traveling museum exhibit.The Andropogoneae tribe of grasses contains a thousand species that collectively represent over a billion years of evolutionary history. It has used NADP-C4 photosynthesis and a wide range of adaptations to become a dominant clade on earth. This project will use the diversity and evolution across this tribe to understand the rules of adaptive convergence and constraint in plant genomes. The project team will sample and analyze the worldwide spectrum of genetic diversity in Andropogoneae to develop detailed models testing whether (1) quantitative estimates of evolutionary constraint improve predictions of fitness-related traits, and (2) convergent environmental adaptations shared across the Andropogoneae explain a substantial proportion of total adaptive variance. These hypotheses will be tested by assembling the gene and regulatory content of 57 species as well as whole genome sequencing of another 700 species. For eight species, diversity across their natural range of adaptation will be surveyed at the sequence level. Evolutionary and machine learning models will be used to quantify the disruptive impact of a mutation in every ancestral genomic element. The inter and intra-specific surveys will also permit an estimation of the prevalence of convergent evolution. This project addresses two key elements of the genotype to phenotype problem - how to quantify the disruptive impact of mutations and how to determine whether adaptive solutions to environmental stresses are convergently shared across species.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.

玉米、高粱、甘蔗和芒属是世界上最高产、最节水的作物和生物燃料。这种生产力归功于过去1500万年来共同的生理和基因祖先。虽然这四种作物将被广泛使用，但它们与另外800种物种密切相关，这些物种主导着世界各地的草原，并适应包括洪水、干旱、高温和霜冻在内的众多环境压力。该项目团队将使用现代基因组学和机器学习来调查和分析这些相关物种，确定它们共同拥有的最重要的基因特征，使它们能够适应炎热和干旱。这项工作的结果将被商业和公共部门的植物育种者用来提高玉米和高粱的产量和对极端天气的适应能力。这一长期影响的关键是培训下一代计算生物学科学家，以解决根本问题。这些技能将通过黑客马拉松和生物信息学培训讲习班来发展。该项目将通过巡回博物馆展览等场所向公众传播这项科学。仙人掌部落的草包含1000个物种，这些物种共同代表了10亿多年的进化史。它利用NADP-C4光合作用和广泛的适应成为地球上的一个优势支系。这个项目将利用这个部落的多样性和进化来理解植物基因组中适应性收敛和约束的规则。该项目团队将采样和分析世界范围内的雄配子体遗传多样性，以开发详细的模型，以测试(1)对进化约束的定量估计是否改善了对与健康相关的特征的预测，以及(2)整个雄配子体共有的收敛的环境适应是否解释了总适应方差的很大比例。这些假说将通过汇集57个物种的基因和调控内容以及另外700个物种的全基因组测序来检验。对于8个物种，将在序列水平上调查其自然适应范围的多样性。进化和机器学习模型将被用来量化每个祖先基因组元素突变的破坏性影响。种间和种内调查还将使人们能够估计趋同进化的普遍程度。该项目解决了从基因到表型问题的两个关键因素--如何量化突变的破坏性影响，以及如何确定环境压力的适应性解决方案是否在物种之间一致共享。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势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（25）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

rTASSEL: An R interface to TASSEL for analyzing genomicdiversity

rTASSEL：TASSEL 的 R 接口，用于分析基因组多样性

DOI：
10.21105/joss.04530
发表时间：
2022
期刊：
Journal of Open Source Software
影响因子：
0
作者：
Monier, Brandon;Casstevens, Terry M.;Bradbury, Peter J.;Buckler, Edward S.
通讯作者：
Buckler, Edward S.

A multiple genome alignment workflow shows the impact of repeat masking and parameter tuning on alignment of functional regions in plants

DOI：
10.1101/2021.06.01.446647
发表时间：
2021-06
期刊：
bioRxiv
影响因子：
0
作者：
Yaoyao Wu;Lynn C. Johnson;Baoxing Song;C. Romay;Michelle C. Stitzer;A. Siepel;E. Buckler;Armin Scheben
通讯作者：
Yaoyao Wu;Lynn C. Johnson;Baoxing Song;C. Romay;Michelle C. Stitzer;A. Siepel;E. Buckler;Armin Scheben

A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants

DOI：
10.1002/tpg2.20204
发表时间：
2022-04
期刊：
The Plant Genome
影响因子：
0
作者：
Yaoyao Wu;Lynn C. Johnson;Baoxing Song;C. Romay;Michelle C. Stitzer;A. Siepel;E. Buckler;Armin Scheben
通讯作者：
Yaoyao Wu;Lynn C. Johnson;Baoxing Song;C. Romay;Michelle C. Stitzer;A. Siepel;E. Buckler;Armin Scheben

Two teosintes made modern maize