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

基因赋予植物和动物代代相传的主要特征。新基因在何处、何时以及如何产生，是具有实际意义的深远生物学问题。如果科学家能够识别出赋予新性状的新基因，农作物的育种潜力将大大扩大。在寻求了解新基因来自何处的过程中，现在人们知道基因可以从基因组中以前没有的区域重新出现。这些所谓的“孤儿基因”可能是物种通过表达新特征来进化和适应挑战性环境的关键途径。为了发现孤儿基因，该项目利用玉米（一种全球重要的主要作物）和芸苔属（另一种模式作物）的测序基因组。这两个物种都有主要的基因组资源可用于孤儿基因的发现。这项研究将确定孤儿基因，并评估适应特定条件的玉米品系中基因可能赋予的性状。将选择影响农艺学重要性状的候选孤儿基因并进行功能分析。将开发计算工具来挖掘序列数据集，并将所得数据纳入社区数据库。在所有阶段，学生将接受计算和基因组科学的培训。为了让高中生和大学生接受教育，正在开发和测试新的电脑游戏模块，目的是增加对孤儿基因的功能和潜力的了解。一个长期的结果是，研究人员和社会将能够设计新的解决方案，通过利用孤儿基因来改善作物。新基因可以从非基因DNA序列中产生的前提已经从大量的DNA和RNA测序数据中得到了证实。 这一概念与长期接受的观点形成鲜明对比，即新的基因功能主要来自已建立基因的累积突变和重排的缓慢过程。一种假说认为，孤儿基因的主要作用是调节防御和代谢反应，使进化适应新的环境。 这项研究将确定主要农艺物种的孤儿基因，首先集中在玉米和芸苔属。这些结果将为在亚种水平上对孤儿基因进行系统分析提供信息，从而在人为干预改善农艺性状的适应和选择的背景下对孤儿基因进行分类。根据所得数据，将选择特定孤儿基因进行实验功能分析。数据将被纳入社区数据库，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。 目标是开发数据和计算工具，促进对孤儿基因在驱动进化适应中的功能的预测性理解，利用这些资源来改善作物，并将信息传播给研究人员和学生。 这些能力将使研究人员能够探索最近出现的孤儿基因的重要性，并将基础知识转化为改善作物性状的创新解决方案。

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.