Collaborative: RUI: Engaging undergraduates in genomic questions and environmental context: building a database of complex phenotypes for plant knockout mutants

“敲除”生物体基因组中的单个基因的突变会产生什么影响？令人不满的是，今天的植物遗传学家只能说：“这要视情况而定。”只有一小部分突变是致命的或有重大影响。对于绝大多数人来说，至多只检测到了微妙的影响。植物遗传学准备利用模式物种拟南芥的一系列“敲除”突变株，在纠正这种情况方面取得快速进展。在该植物基因组的27,000多个独特基因中，约67%的基因已经具有敲除作用，即在一个目标基因中携带一小段标记的破坏性DNA。受酵母遗传学进步的启发，该项目将在良性和具有挑战性的环境中培育这些基因敲除的大亚集，量化生态性能属性(例如，种群增长率、水果产量)。我们预测，就像在酵母中一样，这种方法将揭示突变株和对照株之间重要的表型差异，并可能揭示尚未发现的全基因组模式。该项目主要是本科生机构的合作，将培训年轻科学家如何通过研究人员网络解决主要的基因组问题。该项目将包括筛选7000个可用的T-DNA品系，以识别那些只在一个基因上发生突变的品系，并将这些结果提供给生物界。与植物表现相关的性状将在3000多个单一突变系中进行测量，跨越多种环境。将发展网络基础设施，以传播共同协议，并对数据进行存档和索引。超过50名本科生研究人员将参与收集和分析数据并交流结果。该项目还包括一项关于参与分布式研究网络如何影响本科生在科学界获得社会资本的研究。这方面的工作结果将为更大范围的、对本科生通过参与研究网络实现的结果的实证研究奠定基础。

What is the effect of a mutation that "knocks out" a single gene in an organism's genome? Unsatisfyingly, today's plant geneticists can only say: "It depends." Only a small minority of mutations are lethal or have a significant impact. For the vast majority, at most only subtle effects have been detected. Plant genetics is poised to progress rapidly in remedying this situation, using a collection of "knockout" mutant strains of the model species Arabidopsis thaliana. Knockouts, carrying a tiny tagged segment of disruptive DNA in one targeted gene, are already available for ~67% of the 27,000+ unique genes in this plant's genome. Inspired by progress in yeast genetics, the project will grow large subsets of these knockouts in benign and challenging environments, quantifying ecological performance attributes (e.g., population growth rate, fruit yield). We predict that, as in yeast, such an approach will reveal important phenotypic differences between mutant and control lines and possibly reveal undiscovered genome-wide patterns. The project is a collaboration of primarily undergraduate institutions and will train young scientists in how major genomic questions are addressed by networks of researchers. The project will involve screening 7000 available T-DNA lines to identify those that have mutations at only one gene, providing these results to the biological community. Traits relevant to plant performance will be measured in over 3000 single-mutant lines, across multiple environments. Cyberinfrastructure will be developed to disseminate common protocols and to archive and index data. Over 50 undergraduate researchers will be involved in collecting and analyzing data and communicating results. The project also includes a study of how participating in a distributed research network influences undergraduates' access to social capital within the scientific community. Results from this aspect of the work will lay the foundation for a larger scale, empirical study of the outcomes undergraduates realize by participating in research networks.