Research-PGR Orphan Genes: An Untapped Genetic Reservoir of Novel Traits Driving Evolutionary Adaptation and Crop Improvement

研究-PGR孤儿基因：驱动进化适应和作物改良的新性状的未开发遗传库

• 批准号: 1546858
• 负责人: Eve Wurtele
• 金额: $ 217.53万
• 依托单位: Iowa 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: 2016-08-01 至 2022-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1546858&HistoricalAwards=false
• 关键词: Research; PGR; Orphan; Genes; Untapped

Genes confer the primary traits that are passed on from generation to generation in plants and animals. Where, when and how new genes arise are far-reaching biological questions with practical implications. If scientists could identify emergent genes that confer new traits, the breeding potential for crops could be greatly expanded. During the quest for understanding where new genes come from, it is now known that genes can arise anew from regions of the genome where there were none previously. These so-called "orphan genes" may be key ways that species can evolve and adapt to challenging environments through the expression of new traits. To uncover orphan genes, this project taps into the sequenced genomes of maize, a major crop of worldwide importance, and Brassica, another model crop. Both species have major genomic resources available for orphan gene discovery. The research will identify orphan genes and evaluate traits possibly conferred by the genes in maize lines adapted to particular conditions. Candidate orphan genes that influence agronomically important traits will be selected and functionally analyzed. Computational tools will be developed to mine the sequence datasets and the resulting data will be integrated into community databases. At all stages, students will be trained in computational and genomic science. To reach high school students and early undergraduate students, new computer games modules are being developed and tested with the intention of increasing an understanding of the function and potential of orphan genes. A long-term outcome is that researchers and society will be able to design new solutions to improving crops through harnessing orphan genes. The premise that new genes can arise from non-genic DNA sequences is borne out from massive DNA and RNA sequencing data. This concept sharply contrasts with the long-accepted view that novel gene functions primarily arise from a slow process of accumulated mutations and rearrangements of already-established genes. A hypothesis is that a major role of orphan genes is to regulate the defense and metabolic responses that enable evolutionary adaptation to new environments. This research will identify orphan genes of major agronomic species, focusing first on maize and Brassica. These results will inform a systematic analysis of orphan genes at the level of subspecies, thus categorizing orphan genes in the context of the adaptation and selection that has occurred as the result of human intervention for improved agronomic traits. Based on the resultant data, specific orphan genes will be selected for experimental functional analysis. Data will be integrated into community databases, and code will be available to the public. New computer game modules will be targeted to high school and early undergraduate students. The goal is to develop data and computational tools that facilitate predictive understanding of the function of orphan genes in driving evolutionary adaptation, to harness these resources for improving crops, and to disseminate the information to researchers and students. These capabilities will empower researchers to explore the significance of recently-emerged orphan genes, and transform fundamental knowledge into innovative solutions that improve crop traits.

基因赋予在动植物中一代世代相传的主要特征。新基因的何时何地，何时何地出现是深远的生物学问题，具有实际的影响。如果科学家能够鉴定出赋予新特征的新兴基因，则可能会大大扩展农作物的繁殖潜力。在了解新基因来自何处的过程中，现在众所周知，基因可以从以前没有的基因组地区重新产生。这些所谓的“孤儿基因”可能是物种可以通过表达新特征来发展和适应充满挑战环境的关键方式。为了揭示孤儿基因，该项目挖掘了玉米的测序基因组，这是全球重要性的主要农作物，而另一种模型作物Brassica。这两种物种都有可用于孤儿基因发现的主要基因组资源。该研究将识别孤儿基因，并评估玉米线中可能赋予的特征，该基因适合特定条件。将选择并在功能上分析影响农艺上重要特征的候选孤儿基因。将开发计算工具来开采序列数据集，并将结果数据集成到社区数据库中。在各个阶段，学生将接受计算和基因组科学的培训。为了吸引高中生和早期的本科生，正在开发和测试新的计算机游戏模块，以增加对孤儿基因功能和潜力的了解。一个长期的结果是，研究人员和社会将能够通过利用孤儿基因来设计新的解决方案来改善农作物。非基因DNA序列可能产生的新基因的前提是由大量的DNA和RNA测序数据所证实的。 这个概念与长期被接受的观点形成鲜明对比：新型基因的功能主要是由于已经建立的基因的积累突变和重排的缓慢过程引起的。一个假设是，孤儿基因的主要作用是调节能够进化适应新环境的防御和代谢反应。 这项研究将确定主要农艺物种的孤儿基因，首先关注玉米和甘蓝。这些结果将为亚种水平的孤儿基因进行系统分析，从而在适应和选择的背景下对孤儿基因进行分类，这是由于人类干预改善农艺性状而发生的。根据所得数据，将选择特定的孤儿基因进行实验功能分析。数据将集成到社区数据库中，代码将向公众提供。新的电脑游戏模块将针对高中和早期的本科生。 目的是开发数据和计算工具，以促进对孤儿基因推动进化适应的功能的预测理解，利用这些资源来改善农作物，并向研究人员和学生传播信息。 这些能力将使研究人员有能力探索最近出现的孤儿基因的重要性，并将基本知识转化为改善作物特征的创新解决方案。