Leaf to panicle ratio (LPR): a new physiological trait indicative of source and sink relation in japonica rice based on deep learning

doi:10.1186/s13007-020-00660-y

	Leaf to panicle ratio (LPR): a new physiological trait indicative of source and sink relation in japonica rice based on deep learning
	Yang, Zongfeng ; Gao, Shang 1; Xiao, Feng ; Li, Ganghua ; Ding, Yangfeng ; Guo, Qinghua1 ; Paul, Matthew J.; Liu, Zhenghui 3
	2020
发表期刊	PLANT METHODS
卷号	16 期号:1
摘要	Background Identification and characterization of new traits with sound physiological foundation is essential for crop breeding and production management. Deep learning has been widely used in image data analysis to explore spatial and temporal information on crop growth and development, thus strengthening the power of identification of physiological traits. Taking the advantage of deep learning, this study aims to develop a novel trait of canopy structure that integrate source and sink in japonica rice. Results We applied a deep learning approach to accurately segment leaf and panicle, and subsequently developed the procedure of GvCrop to calculate the leaf to panicle ratio (LPR) of rice canopy during grain filling stage. Images of training dataset were captured in the field experiments, with large variations in camera shooting angle, the elevation and the azimuth angles of the sun, rice genotype, and plant phenological stages. Accurately labeled by manually annotating the panicle and leaf regions, the resulting dataset were used to train FPN-Mask (Feature Pyramid Network Mask) models, consisting of a backbone network and a task-specific sub-network. The model with the highest accuracy was then selected to check the variations in LPR among 192 rice germplasms and among agronomical practices. Despite the challenging field conditions, FPN-Mask models achieved a high detection accuracy, with Pixel Accuracy being 0.99 for panicles and 0.98 for leaves. The calculated LPR displayed large spatial and temporal variations as well as genotypic differences. In addition, it was responsive to agronomical practices such as nitrogen fertilization and spraying of plant growth regulators. Conclusion Deep learning technique can achieve high accuracy in simultaneous detection of panicle and leaf data from complex rice field images. The proposed FPN-Mask model is applicable to detect and quantify crop performance under field conditions. The newly identified trait of LPR should provide a high throughput protocol for breeders to select superior rice cultivars as well as for agronomists to precisely manage field crops that have a good balance of source and sink.
关键词	Plant phenotyping Leaf and panicle detection Deep learning Physiological trait Leaf to panicle ratio (LPR) Japonica rice
学科领域	Biochemical Research Methods ; Plant Sciences
DOI	10.1186/s13007-020-00660-y
收录类别	SCI
语种	英语
WOS关键词	HIGH-THROUGHPUT ; SEGMENTATION ; PHENOMICS ; YIELD ; WHEAT ; AREA ; EAR
WOS研究方向	Biochemistry & Molecular Biology ; Plant Sciences
WOS记录号	WOS:000566943100003
出版者	BMC
文献子类	Article
出版地	LONDON
EISSN	1746-4811
资助机构	National Key R&D Program, Ministry of Science and Technology, China [2017YFD0300103] ; National Natural Science Foundation of ChinaNational Natural Science Foundation of China (NSFC) [31771719] ; National High Technology Research and Development Program of ChinaNational High Technology Research and Development Program of China [2014AA10A605] ; Biological and Biotechnological Sciences Research Council of the United Kingdom ; Designing Future Wheat Strategic Programme [BB/P016855/1]
作者邮箱	qguo@ibcas.ac.cn ; liuzh@njau.edu.cn
作品OA属性	Green Published, gold, Green Submitted
引用统计	被引频次：21[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.ibcas.ac.cn/handle/2S10CLM1/21593
专题	植被与环境变化国家重点实验室
作者单位	1.Nanjing Agr Univ, Coll Agr, Nanjing 210095, Peoples R China 2.Chinese Acad Sci, Inst Bot, State Key Lab Vegetat & Environm Change, Beijing 100093, Peoples R China 3.Paul, Matthew J.] Rothamsted Res, Plant Sci, Harpenden AL5 2JQ, Herts, England 4.Nanjing Agr Univ, Collaborat Innovat Ctr Modern Crop Prod, Nanjing 210095, Peoples R China
推荐引用方式 GB/T 7714	Yang, Zongfeng,Gao, Shang,Xiao, Feng,et al. Leaf to panicle ratio (LPR): a new physiological trait indicative of source and sink relation in japonica rice based on deep learning[J]. PLANT METHODS,2020,16(1).
APA	Yang, Zongfeng.,Gao, Shang.,Xiao, Feng.,Li, Ganghua.,Ding, Yangfeng.,...&Liu, Zhenghui.(2020).Leaf to panicle ratio (LPR): a new physiological trait indicative of source and sink relation in japonica rice based on deep learning.PLANT METHODS,16(1).
MLA	Yang, Zongfeng,et al."Leaf to panicle ratio (LPR): a new physiological trait indicative of source and sink relation in japonica rice based on deep learning".PLANT METHODS 16.1(2020).

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