SeedGerm: a cost-effective phenotyping platform for automated seed imaging and machine-learning based phenotypic analysis of crop seed germination.

The New Phytologist
Joshua ColmerJi Zhou

Abstract

Efficient seed germination and establishment are important traits for field and glasshouse crops. Large-scale germination experiments are laborious and prone to observer errors, leading to the necessity for automated methods. We experimented with five crop species, including tomato, pepper, Brassica, barley, and maize, and concluded an approach for large-scale germination scoring. Here, we present the SeedGerm system, which combines cost-effective hardware and open-source software for seed germination experiments, automated seed imaging, and machine-learning based phenotypic analysis. The software can process multiple image series simultaneously and produce reliable analysis of germination- and establishment-related traits, in both comma-separated values (CSV) and processed images (PNG) formats. In this article, we describe the hardware and software design in detail. We also demonstrate that SeedGerm could match specialists' scoring of radicle emergence. Germination curves were produced based on seed-level germination timing and rates rather than a fitted curve. In particular, by scoring germination across a diverse panel of Brassica napus varieties, SeedGerm implicates a gene important in abscisic acid (ABA) signalling in seed...Continue Reading

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Citations

Nov 17, 2020·Frontiers in Plant Science·Chen ShenLimin Shao
Dec 9, 2020·Plant Biotechnology Journal·Philipp E Bayer, David Edwards
Jan 16, 2021·Scientific Reports·Nicolas MerieuxEdwin Grappin
Dec 15, 2020·Plant Phenomics : a Science Partner Journal·Pengliang WeiJingfeng Huang
Jun 2, 2021·Horticulture Research·Biyun Yang, Yong Xu

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