About Plant Phenomics

Plant Phenomics

Plant Phenomics is an open-access scientific journal devoted to plant phenotyping — the measurement of plant traits — at every scale from the single cell to the whole plant population. It is published in affiliation with the State Key Laboratory of Crop Genetics and Germplasm Enhancement at Nanjing Agricultural University (NAU) in Nanjing, Jiangsu, China (ISSN 2643-6515). Launched in 2018 as the second journal in the American Association for the Advancement of Science (AAAS) Science Partner Journal programme, it began publishing in 2019, distributed by AAAS; as of January 2025 it is no longer published with AAAS and its current home is on Elsevier's ScienceDirect platform. Its founding editors-in-chief were Seishi Ninomiya of the University of Tokyo, Frédéric Baret of the French National Institute for Agricultural Research, and Zong-Ming (Max) Cheng, jointly of the University of Tennessee and Nanjing Agricultural University, and the journal's mission — advancing phenotyping through sensor systems and data analytics, and connecting phenomics to genomics, genetics and breeding — has made it one of the defining journals of a young discipline.

A journal for a new discipline

Phenomics is the systematic study of the phenome: the full set of observable traits of an organism, produced by its genotype interacting with its environment. For most of the history of plant breeding, those traits — height, leaf area, flowering time, drought response, yield — were recorded by eye and by hand, plant by plant. Genomics, by contrast, became fast and cheap: a genome can now be sequenced far more quickly than a field of plants can be carefully measured. That imbalance, often called the phenotyping bottleneck, is the problem Plant Phenomics was created to address. The journal publishes work that closes the gap with cameras, sensors, imaging platforms, drones, robotics, machine learning and models, so that trait measurement can keep pace with DNA sequencing and the genetic gains that modern breeding promises can actually be identified in the field and the greenhouse.

Launch as a Science Partner Journal

AAAS announced Plant Phenomics as the second title in its Science Partner Journal (SPJ) programme, a scheme in which AAAS distributed English-language journals owned by partner institutions while the partners retained editorial independence from the Science family of journals. The journal is the official journal of Nanjing Agricultural University and is published in affiliation with the university's State Key Laboratory of Crop Genetics and Germplasm Enhancement. Its editorial office opened for submissions in September 2018, and the journal officially launched in January 2019, publishing under a Creative Commons Attribution (CC BY) licence so that all content was freely available on publication. Huan Yin of Nanjing Agricultural University served as managing editor at the launch. The SPJ framing mattered: it paired a Chinese agricultural university's specialist laboratory with the distribution and visibility of the publisher of Science, an arrangement designed to give a new, narrowly focused field an international audience from its first issue.

From AAAS to Elsevier

The journal's publishing arrangements have since changed. The AAAS Science Partner Journal site records that, as of January 2025, Plant Phenomics is no longer published with AAAS, and the journal's current articles, author guidance and special issues appear on Elsevier's ScienceDirect under the same ISSN, 2643-6515. On ScienceDirect the journal lists an article publishing charge of US$3,000 and editors-in-chief including Frédéric Baret, Zong-Ming Cheng and Seishi Ninomiya — all present from the founding team — alongside Yanfeng Ding of Nanjing Agricultural University. The continuity of editors and of the Nanjing affiliation through the change of platform underlines that what moved was distribution and production, not the journal's identity: it remains Nanjing Agricultural University's phenomics journal, rooted in the State Key Laboratory of Crop Genetics and Germplasm Enhancement, now reaching readers through one of the largest commercial science platforms instead of the AAAS partner programme.

Aims and scope

The journal states its mission as publishing novel research that will advance all aspects of plant phenotyping from the cellular level to the plant population level, through innovative combinations of interdisciplinary domains including genomics, genetics, physiology, molecular biology, bioinformatics, statistics, mathematics and computer science. Its scope covers the latest technologies in plant phenotyping for data acquisition, data management, data interpretation and modelling, and their practical applications across all plant sciences. That breadth is deliberate. A phenomics paper may be primarily about hardware — a sensor, a gantry, a drone payload — or primarily about software — an algorithm that extracts leaf area from images — or primarily about biology, where high-throughput trait data reveal how a gene or a stress treatment changes a plant. Plant Phenomics is organised to hold all three kinds of contribution in one place, judged by whether they advance phenotyping itself.

Data acquisition: sensors, imaging and platforms

Acquisition is the foundation of the field, and a large share of the journal's content concerns how trait data are captured. Papers since launch have covered high-throughput phenotyping platforms, unmanned aerial vehicle (UAV) imagery for assessing environmental stress, and imaging systems deployed in greenhouses, growth chambers and open fields. The underlying technologies include RGB and multispectral cameras, thermal imaging, fluorescence imaging and three-dimensional reconstruction, each suited to different traits: canopy cover and growth from visible images, water status and stress from thermal data, photosynthetic performance from fluorescence. By publishing platform descriptions alongside the biological studies that use them, the journal documents not just results but the instruments that make a new kind of result possible — an important function in a field where the measurement method is often the innovation.

Data interpretation, machine learning and modelling

Raw images do not phenotype a plant; analysis does. A second major strand of the journal therefore concerns data management, interpretation and modelling: mathematical and computational methods that turn sensor output into traits. Convolutional neural networks for phenotyping and for plant disease diagnosis were among the topics the journal highlighted in its early years, and its current calls for papers — including a special issue on plant modelling, big data analytics and high-throughput phenotyping for smart agriculture — emphasise advanced algorithms for efficient phenotyping, three-dimensional trait-focused phenotyping, model-assisted phenotyping that integrates functional-structural plant models and process-based models, and artificial intelligence for plant phenomics. The journal's author guidance reflects this range, accepting research articles, methods articles, dataset articles and software and hardware articles alongside reviews, perspectives, correspondence and editorials — formats that let a dataset, a piece of code or an instrument be a publication in its own right.

Connecting phenomics to genomics and breeding

The journal's stated ambition goes beyond measurement for its own sake: it aims to connect phenomics to other research domains — genomics, genetics and physiology named at launch — to address key challenges in plant science and agriculture. The logic is straightforward. Genome-wide association and genomic selection depend on accurate trait data across large populations; the better and faster the phenotyping, the more powerful the genetics. Phenomics-genomics linkage is explicitly among the themes of its recent special issues, alongside phenotyping for abiotic and biotic stress tolerance and phenotyping for smart crop management. For breeders, the practical promise is selection based on traits measured early, often and non-destructively, rather than on end-of-season harvest alone. For basic plant science, high-resolution trait time series make it possible to watch development and stress responses unfold rather than inferring them from a single endpoint.

Indexing, metrics and standing

Plant Phenomics is indexed in the Science Citation Index Expanded (SCIE) of the Web of Science and in Scopus, as the commissioning record for this profile notes, and listings also record coverage in the Directory of Open Access Journals and PubMed. It received its inaugural Journal Impact Factor of 6.961 in the 2022 Journal Citation Reports, ranking third among 90 journals in Agronomy, eighteenth among 238 in Plant Sciences and sixth among 34 in Remote Sensing — an unusual triple presence that captures the journal's position between agriculture, plant biology and sensing technology. Scopus-based listings put its CiteScore at 10.6 in recent releases, with Q1 standing in agronomy and crop science and plant science. For a journal that began publishing only in 2019, those rankings mark a rapid establishment: within its first citation cycle it was already competing with long-established titles in three separate categories.

Open access and readership in Nanjing and beyond

The journal was open access from its first issue, publishing under CC BY during its AAAS period and continuing as an open-access title on ScienceDirect, where the article publishing charge is listed at US$3,000. Open access suits its subject: phenotyping methods are meant to be adopted, adapted and built upon by breeding programmes, agricultural institutes and technology developers, many of them outside wealthy university systems, and free availability removes the paywall between a method and the people positioned to use it. Its base remains Nanjing — a major centre of Chinese agricultural research, home to Nanjing Agricultural University and its crop genetics state key laboratory — but its authorship, editorship and readership are international, spanning the University of Tokyo, French agricultural research and American land-grant universities as well as Chinese institutes. In a directory of Chinese magazines and journals, Plant Phenomics stands out as a case of a specialist Chinese university laboratory creating, with international partners, the journal of record for an emerging global discipline — and sustaining that role through a change of publisher without losing its name, its ISSN or its mission.