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

“敲除”生物体基因组中单个基因的突变会产生什么影响？令人不满意的是，今天的植物遗传学家只能说：“看情况。”只有一小部分突变是致命的或有重大影响。对绝大多数人来说，最多只能检测到细微的影响。利用模式物种拟南芥（Arabidopsis thaliana）的一系列“敲除”突变株，植物遗传学有望在补救这种情况方面取得迅速进展。敲除，在一个目标基因中携带一个微小的标记片段的破坏性DNA，已经可以用于该植物基因组中27,000多个独特基因中的约67%。受酵母遗传学进展的启发，该项目将在良性和具有挑战性的环境中培养这些基因敲除的大量亚群，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控制系之间重要的表型差异，并可能揭示未被发现的全基因组模式。该项目主要是本科院校的合作，并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系，以确定那些只有一个基因突变的T-DNA系，并将这些结果提供给生物界。与植物性能相关的性状将在3000多个单突变品系中，在多种环境中进行测量。将发展网络基础设施，以传播共同协议并存档和索引数据。50多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大学生在科学界获得社会资本的研究。这方面的研究结果将为更大规模的大学生参与研究网络成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.