germinator: a software package for high-throughput scoring and curve fitting of Arabidopsis seed germination

Abstract

SUMMARYOver 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.

Single-seed oxygen consumption measurements and population-based threshold models link respiration and germination rates under diverse conditions

“…The germination rates (inverse of the times to germination) of seeds are among the most sensitive indicators of seed vigour, but as obtaining such data generally requires repeated and closely spaced observations, they are seldom applied except for research purposes (Matthews and Powell, 2011). Image analysis methods that semi-automate the data collection process have improved this situation (Joosen et al, 2010) but an analyst is still required to conduct the image capture for each sample at frequent times.…”

phenoSeeder - A Robot System for Automated Handling and Phenotyping of Individual Seeds

“…It might even be considered for seed germination studies using blotting paper, allowing one to correlate germination not only with seed traits obtained from projections (Joosen et al, 2010;Demilly et al, 2014) but also with seed volume, mass, or density. Regarding the large diversity of seeds and the high complexity of seed traits, we conclude that the phenoSeeder approach enabling automated identification and monitoring of relevant traits of individual seeds provides a wide range of valuable options for applications in seed biology.…”

GerminaQuant: a new tool for germination measurements

“…They are indispensable for human society as food sources and as starting materials for new crops (Joosen et al 2010). Seed physiology and technology have provided valuable tools for the production of high-quality seeds, seed treatments and optimal storage conditions.…”

“…There are, however, some freely spreadsheets which in stricto sensu are not really a software but a set of spreadsheets developed on Microsoft ® Excel package. On this category are included the spreadsheets developed by Ranal et al (2009), Joosen et al (2010 and Miranda et al (2014). The major limitation of the spreadsheets proposed by Miranda et al (2014) and Ranal et al (2009) is the impossibility of working with different treatments in the same file at the same time; each treatment or situation must be interpreted in different spreadsheets which are time consuming in addition to being tedious.…”

“…The major limitation of the spreadsheets proposed by Miranda et al (2014) and Ranal et al (2009) is the impossibility of working with different treatments in the same file at the same time; each treatment or situation must be interpreted in different spreadsheets which are time consuming in addition to being tedious. The spreadsheets proposed by Joosen et al (2010) would be the only, therefore allowing the calculation of two or more treatments at the same time. However, this "software" is not a tool of universal domain, it requires the user to deeply understand the functioning of these spreadsheets to better explore the tool and its features.…”