RESUMO
BACKGROUND: Cotton accounts for 80% of the global natural fibre production. Its leaf hairiness affects insect resistance, fibre yield, and economic value. However, this phenotype is still qualitatively assessed by visually attributing a Genotype Hairiness Score (GHS) to a leaf/plant, or by using the HairNet deep-learning model which also outputs a GHS. Here, we introduce HairNet2, a quantitative deep-learning model which detects leaf hairs (trichomes) from images and outputs a segmentation mask and a Leaf Trichome Score (LTS). RESULTS: Trichomes of 1250 images were annotated (AnnCoT) and a combination of six Feature Extractor modules and five Segmentation modules were tested alongside a range of loss functions and data augmentation techniques. HairNet2 was further validated on the dataset used to build HairNet (CotLeaf-1), a similar dataset collected in two subsequent seasons (CotLeaf-2), and a dataset collected on two genetically diverse populations (CotLeaf-X). The main findings of this study are that (1) leaf number, environment and image position did not significantly affect results, (2) although GHS and LTS mostly correlated for individual GHS classes, results at the genotype level revealed a strong LTS heterogeneity within a given GHS class, (3) LTS correlated strongly with expert scoring of individual images. CONCLUSIONS: HairNet2 is the first quantitative and scalable deep-learning model able to measure leaf hairiness. Results obtained with HairNet2 concur with the qualitative values used by breeders at both extremes of the scale (GHS 1-2, and 5-5+), but interestingly suggest a reordering of genotypes with intermediate values (GHS 3-4+). Finely ranking mild phenotypes is a difficult task for humans. In addition to providing assistance with this task, HairNet2 opens the door to selecting plants with specific leaf hairiness characteristics which may be associated with other beneficial traits to deliver better varieties.
RESUMO
BACKGROUND: 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 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. RESULTS: A dataset of [Formula: see text] 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. CONCLUSIONS: HairNet 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.