Multi-dimensional machine learning approaches for fruit shape phenotyping in strawberry
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Abstract
Background
Shape is a critical element of the visual appeal of strawberry fruit and is influenced by both genetic and non-genetic determinants. Current fruit phenotyping approaches for external characteristics in strawberry often rely on the human eye to make categorical assessments. However, fruit shape is an inherently multi-dimensional, continuously variable trait and not adequately described by a single categorical or quantitative feature. Morphometric approaches enable the study of complex, multi-dimensional forms but are often abstract and difficult to interpret. In this study, we developed a mathematical approach for transforming fruit shape classifications from digital images onto an ordinal scale called the Principal Progression of k Clusters (PPKC). We use these human-recognizable shape categories to select quantitative features extracted from multiple morphometric analyses that are best fit for genetic dissection and analysis.
Results
We transformed images of strawberry fruit into human-recognizable categories using unsupervised machine learning, discovered 4 principal shape categories, and inferred progression using PPKC. We extracted 68 quantitative features from digital images of strawberries using a suite of morphometric analyses and multivariate statistical approaches. These analyses defined informative feature sets that effectively captured quantitative differences between shape classes. Classification accuracy ranged from 68% to 99% for the newly created phenotypic variables for describing a shape.
Conclusions
Our results demonstrated that strawberry fruit shapes could be robustly quantified, accurately classified, and empirically ordered using image analyses, machine learning, and PPKC. We generated a dictionary of quantitative traits for studying and predicting shape classes and identifying genetic factors underlying phenotypic variability for fruit shape in strawberry. The methods and approaches that we applied in strawberry should apply to other fruits, vegetables, and specialty crops.
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Now published in GigaScience doi: 10.1093/gigascience/giaa030
Mitchell J. Feldmann 1Department of Plant Sciences, University of California, Davis. One Shields Ave, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Mitchell J. FeldmannFor correspondence: mjfeldmann@ucdavis.eduMichael A. Hardigan 1Department of Plant Sciences, University of California, Davis. One Shields Ave, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRandi A. Famula 1Department of Plant Sciences, University of California, Davis. One Shields Ave, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Randi A. FamulaCindy M. López 1Department …
Now published in GigaScience doi: 10.1093/gigascience/giaa030
Mitchell J. Feldmann 1Department of Plant Sciences, University of California, Davis. One Shields Ave, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Mitchell J. FeldmannFor correspondence: mjfeldmann@ucdavis.eduMichael A. Hardigan 1Department of Plant Sciences, University of California, Davis. One Shields Ave, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRandi A. Famula 1Department of Plant Sciences, University of California, Davis. One Shields Ave, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Randi A. FamulaCindy M. López 1Department of Plant Sciences, University of California, Davis. One Shields Ave, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteAmy Tabb 2USDA-ARS-AFRS, 2217 Wiltshire Rd, Kearneysville, WV 25430, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Amy TabbGlenn S. Cole 1Department of Plant Sciences, University of California, Davis. One Shields Ave, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteSteven J. Knapp 1Department of Plant Sciences, University of California, Davis. One Shields Ave, Davis, CA 95616, USAFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Steven J. Knapp
A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa030 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.
These peer reviews were as follows:
Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102204 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102205 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102208
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