Slovak Radka, Göschl Christian, Su Xiaoxue, Shimotani Koji, Shiina Takashi, Busch Wolfgang
Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, 1030 Vienna, Austria.
Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto 606-8522, Japan.
Plant Cell. 2014 Jun;26(6):2390-2403. doi: 10.1105/tpc.114.124032. Epub 2014 Jun 10.
Large-scale phenotyping of multicellular organisms is one of the current challenges in biology. We present a comprehensive and scalable pipeline that allows for the efficient phenotyping of root growth traits on a large scale. This includes a high-resolution, low-cost acquisition setup as well as the automated image processing software BRAT. We assess the performance of this pipeline in Arabidopsis thaliana under multiple growth conditions and show its utility by performing genome-wide association studies on 16 root growth traits quantified by BRAT each day during a 5-d time-course experiment. The most significantly associated genome region for root growth rate is a locus encoding a calcium sensing receptor. We find that loss of function and overexpression of this gene can significantly alter root growth in a growth condition dependent manner and that the minor natural allele of the Calcium Sensor Receptor locus is highly significantly enriched in populations in coastal areas, demonstrating the power of our approach to identify regulators of root growth that might have adaptive relevance.
多细胞生物的大规模表型分析是当前生物学面临的挑战之一。我们提出了一个全面且可扩展的流程，能够大规模高效地对根系生长性状进行表型分析。这包括一个高分辨率、低成本的采集装置以及自动化图像处理软件BRAT。我们在多种生长条件下评估了该流程在拟南芥中的性能，并通过在一个为期5天的时间进程实验中，对BRAT每天定量的16个根系生长性状进行全基因组关联研究，展示了其效用。根系生长速率最显著相关的基因组区域是一个编码钙传感受体的基因座。我们发现该基因的功能缺失和过表达能够以生长条件依赖的方式显著改变根系生长，并且钙传感受体基因座的次要自然等位基因在沿海地区的种群中高度显著富集，这证明了我们的方法在识别可能具有适应性相关性的根系生长调节因子方面的强大能力。
