Abstract
BackgroundLeaf hairiness (pubescence) is an important plant phenotype which regulates leaf transpiration, affects sunlight penetration, and provides increased resistance or susceptibility against certain insects. Cotton accounts for 80% of global natural fibre production, and in this crop leaf hairiness also affects fibre yield and value. Currently, this key phenotype is measured visually which is slow, laborious and operator-biased. Here, we propose a simple, high-throughput and low-cost imaging method combined with a deep-learning model, HairNet, to classify leaf images with great accuracy.ResultsA dataset of sim 13,600 leaf images from 27 genotypes of Cotton was generated. Images were collected from leaves at two different positions in the canopy (leaf 3 & leaf 4), from genotypes grown in two consecutive years and in two growth environments (glasshouse & field). This dataset was used to build a 4-part deep learning model called HairNet. On the whole dataset, HairNet achieved accuracies of 89% per image and 95% per leaf. The impact of leaf selection, year and environment on HairNet accuracy was then investigated using subsets of the whole dataset. It was found that as long as examples of the year and environment tested were present in the training population, HairNet achieved very high accuracy per image (86–96%) and per leaf (90–99%). Leaf selection had no effect on HairNet accuracy, making it a robust model.ConclusionsHairNet classifies images of cotton leaves according to their hairiness with very high accuracy. The simple imaging methodology presented in this study and the high accuracy on a single image per leaf achieved by HairNet demonstrates that it is implementable at scale. We propose that HairNet replaces the current visual scoring of this trait. The HairNet code and dataset can be used as a baseline to measure this trait in other species or to score other microscopic but important phenotypes.
Highlights
Leaf hairiness is an important plant phenotype which regulates leaf transpiration, affects sunlight penetration, and provides increased resistance or susceptibility against certain insects
We propose that our deep learning model replaces the current visual inspection
Genotype selection A total of 27 genetically diverse Gossypium hirsutum Cotton genotypes were selected based on their known leaf hairiness to represent the full gamut of observable leaf hairiness variations
Summary
Leaf hairiness (pubescence) is an important plant phenotype which regulates leaf transpiration, affects sunlight penetration, and provides increased resistance or susceptibility against certain insects. Cotton accounts for 80% of global natural fibre production, and in this crop leaf hairiness affects fibre yield and value This key phenotype is measured visually which is slow, laborious and operator-biased. The most widely commercially cultivated species of Cotton is Gossypium hirsutum L., which is bred across the globe for traits such as improved yield, insect resistance, fibre length and strength, water use efficiency and adaptation to a changing climate. In these breeding efforts, leaf hairiness, referred to as leaf pubescence, is a key phenotype which is still measured manually [5]. An intermediate level of leaf hairiness (hirsute trait) is a highly desirable selection trait for elite cotton varieties (Fig. 1A)
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