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HairNet2: deep learning to quantify cotton leaf hairiness, a complex genetic and environmental trait

Authors :
Moshiur Farazi
Warren C. Conaty
Lucy Egan
Susan P. J. Thompson
Iain W. Wilson
Shiming Liu
Warwick N. Stiller
Lars Petersson
Vivien Rolland
Source :
Plant Methods, Vol 20, Iss 1, Pp 1-19 (2024)
Publication Year :
2024
Publisher :
BMC, 2024.

Abstract

Abstract 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.

Details

Language :
English
ISSN :
17464811
Volume :
20
Issue :
1
Database :
Directory of Open Access Journals
Journal :
Plant Methods
Publication Type :
Academic Journal
Accession number :
edsdoj.307372dac3e741bca13f82732c72ebb2
Document Type :
article
Full Text :
https://doi.org/10.1186/s13007-024-01149-8