GERMINATOR: a software package for high-throughput scoring and curve fitting of Arabidopsis seed germination
GERMINATOR: a software package for high-throughput scoring and curve fitting of Arabidopsis seed germination
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DOI：
10.1111/j.1365-313x.2009.04116.x
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发表时间：
2010-04-01
期刊：
影响因子：
7.2
通讯作者：
Hilhorst, Henk W. M.
中科院分区：
文献类型：
--
作者：
Joosen, Ronny V. L.;Kodde, Jan;Hilhorst, Henk W. M.
在过去的几十年里，种子生理学研究为许多重要的科学发现做出了贡献，并为生产高质量的种子提供了宝贵的工具。这类研究的一个重要工具是准确量化发芽;然而，收集累积发芽数据是一项非常艰巨的任务，通常禁止执行大型实验。在本文中，我们提出了发芽器包：一个简单的，高成本效益和灵活的程序，高通量的自动评分和评价发芽，可以实现，而不使用复杂的机器人。发芽器包包含三个模块：（i）设计实验设置，具有复制和随机化样品的各种选项;（ii）基于单个图像上突出胚根和种皮之间的颜色对比度自动评分发芽;以及（iii）累积发芽数据的曲线拟合以及各种发芽参数的提取，概括和可视化。曲线拟合模块可以分析一般累积发芽数据，并可用于所有植物物种。我们表明，自动评分系统的工程拟南芥和芸苔属。种子，但也可能适用于其他物种。在本文中，我们展示了准确性，再现性和灵活性的发芽包。我们已经成功地应用它来评估自然变异的耐盐性在一个大的人口重组自交系，并能够确定几个耐盐性的数量性状基因座。发芽仪是一种低成本的成套设备，可由一个人一天几次监测数千次发芽试验。
P>Over the past few decades seed physiology research has contributed to many important scientific discoveries and has provided valuable tools for the production of high quality seeds. An important instrument for this type of research is the accurate quantification of germination; however gathering cumulative germination data is a very laborious task that is often prohibitive to the execution of large experiments. In this paper we present the germinator package: a simple, highly cost-efficient and flexible procedure for high-throughput automatic scoring and evaluation of germination that can be implemented without the use of complex robotics. The germinator package contains three modules: (i) design of experimental setup with various options to replicate and randomize samples; (ii) automatic scoring of germination based on the color contrast between the protruding radicle and seed coat on a single image; and (iii) curve fitting of cumulative germination data and the extraction, recap and visualization of the various germination parameters. The curve-fitting module enables analysis of general cumulative germination data and can be used for all plant species. We show that the automatic scoring system works for Arabidopsis thaliana and Brassica spp. seeds, but is likely to be applicable to other species, as well. In this paper we show the accuracy, reproducibility and flexibility of the germinator package. We have successfully applied it to evaluate natural variation for salt tolerance in a large population of recombinant inbred lines and were able to identify several quantitative trait loci for salt tolerance. germinator is a low-cost package that allows the monitoring of several thousands of germination tests, several times a day by a single person.