CEPAMS will nurture excellent research and will focus on the improvement of food crops and the production of high-value, beneficial products from plants and microbes.

Collaborative research is funded by the Chinese Academy of Sciences, the UK Biotechnology and Biological Sciences Research Council and the Newton Fund.

Initial projects are structured around three key themes.

icon 3

Growth and Development

  • JIC partner: Enrico Coen
    IGDB partner: Yongbiao Xue

    Genomes bear the scars of their history.  These scars can give important clues to how adaptation and diversity can arise during evolution.   Of particular interest are genomic islands – regions of the genome that exhibit exceptionally low or high degrees of divergence. One hypothesis is that these islands derive from a limited repertoire of alleles that have been repeatedly deployed during evolution.  Alternatively, they may derive from novel functional variants that have arisen independently. We aim to test these hypotheses by studying genomic islands in Antirrhinum, where they have been previously identified at the self- incompatibility and flower colour loci. By studying allelic variations at these loci in both a phylogenetic and genomic context, we aim to establish how alleles and traits have evolved in different lineages. This should allow us to determine how islands arise, persist and decay, identifying the processes and genes that shape natural diversity and provide the raw material for plant breeding.

  • JIC partner: Robert Sablowski
    IGDB partner: Yuling Jiao

    The shape of plants not only contributes to nature’s beauty, but also affects plant adaption to the environment and crop yield. Two key determinants of plant shape are stem height and the way the shoot branches.

    Independent work at IGDB on shoot branching and at JIC on stem elongation converged on the same key regulatory gene, called ATH1. This gene functions very close to the apical meristem, a group of constantly dividing cells that is located at the shoot tip and supplies new cells to make leaves, flowers and the stem.

    In this project, we will combine our resources and complementary technical expertise to test the hypothesis that both roles of ATH1 reflect a single function in controlling growth at the boundaries between the meristem and stem tissues. The project will uncover basic mechanisms that determine plant shape and that may be used to for crop improvement.

  • JIC partner: Xiaoqi Feng
    IGDB partner: Weicai Yang

    Large-scale chromatin reprogramming occurs during reproductive development in plants, however, the mechanism and function of such reprogramming are unclear. Using a combination of proteomics and genomics, we will investigate factors responsible for the chromatin reconfiguration in the male sexual lineage, and through this elucidate its biological significance.

    As germline fitness is directly related to reproductive success, answering these questions has implications for plant breeding. Moreover, germlines represent an excellent model to reveal basic principles of chromatin configuration, and shed light on how these principles can be employed to modify genome function. The model we use, Arabidopsisthaliana, has advantages in the accessibility of large germ cell populations and the mild phenotypes of chromatin mutants, in comparison to mammals. Our work therefore has the potential to generate pioneering knowledge about germline chromatin reconfiguration, which has common features in plants and mammals.

  • JIC partner: Mike Bevan
    IGDB partner: Yunhai Li

    Mike Bevan at JIC and Yunhai Li at IGDB in Beijing have a collaborative research programme  that is identifying genes in Arabidopsis and rice that influence seed and organ size, and yield. They have identified a novel mechanism that controls the duration of cell proliferation during organ formation. Mutations of components of this system develop organ with more cells and are therefore larger. Our future work aims to understand more about the mechanisms involved as they provide new insights into a poorly understood part of biology, and because this knowledge is increasingly important for making new crops that have higher yields of seeds.

icon 2

Crop Productivity

  • JIC/TSL partner: Cyril Zipfel
    IGDB partner: Jian-Min Zhou

    Plants perceive pathogen-associated molecular patterns (PAMPs) via pattern recognition receptors (PRRs), leading to PAMP-triggered immunity (PTI). The Arabidopsis thaliana leucine-rich repeat receptor kinases FLS2 and EFR are amongst the best-characterized plant PRRs. Ligand-binding triggers the instantaneous association between FLS2/EFR and the LRR-RK BAK1 that acts as a co-receptor, leading to trans-phosphorylation between these proteins. Direct substrates for the FLS2/EFR-BAK1 complexes are cytoplasmic kinases, such as BIK1. Notably, BIK1 is a central signaling integrator that acts downstream of several PRRs and appears to be the merging node of a common PTI pathway. Yet, hardly anything is know about substrates for BIK1 and related PBL proteins, and thus on how these key regulators ultimately drive PTI signaling. The main objective of this joint project is to fill this gap by identifying and characterizing BIK1 (and PBLs) substrates capitalizing on the most recent findings and know-how from both laboratories in a collaborative and integrated approach.

  • JIC partner: Christine Faulkner
    PSC Shanghai partner: Rosa Lozano-Duran

    The Tomato yellow leaf curl virus (TYLCV) is a tomato pathogen that can cause catastrophic yield loss. A central element of plant defence against viruses, including TYLCV, is RNA silencing. Small RNAs (sRNA) triggered by virus infection act as a mobile signal to spread RNA silencing; both the virus itself and the silencing signal move throughout the plant, from cell-to-cell, via plasmodesmata. The C4 protein of TYLCV binds to both RNA and a host plasmodesmal receptor, and has been suggested to facilitate both virus cell-to-cell spread and silencing suppression. This project will combine expertise in plant-virus interactions (Rosa Lozano-Duran, PSC, Shanghai) and plasmodesmata (Christine Faulkner, JIC) to investigate the role of the C4 protein in virus and sRNA movement, with the aim of elucidating mechanisms of virus infection and host defence.

  • JIC partner: Anne Osbourn
    SIPPE partner: Bin Han

    Oat is a cereal crop that is used for food, feed and forage. It has a variety of distinct agronomic strengths including low input requirements, high biotic/abiotic stress tolerance (including take-all resistance), distinctive starch granule properties and healthy grain quality. A better understanding of the genes underpinning important traits in oat is expected to have wide potential for crop improvement.  Common cultivated oat (Avena sativa) has a hexaploid genome of ~11,300 Mb that has not yet been sequenced.  We recently sequenced the genome of diploid oat (Avena strigosa; genome size 3.92 Gb).  Here we will build on this exciting and very significant foundation by: 1) annotating the oat genome sequence; 2) carrying out comparative genomics to investigate why oat is so different from other cereals; 3) mining the oat genome for pathways for the synthesis of specialized metabolites; 4) establishing and validating a prototype reverse genetics platform to enable functional analysis in oat.

  • JIC partner: Dale Sanders & Tony Miller
    SIPPE partner: Jiming Gong

    Large parts of the world are subject to drought and salt-stress and these factors limit secure food production in many of the poorest countries. Professor Gong’s lab has shown that during stress treatments plants allocate more nitrate to their roots. This process has been named SINAR, plant stress initiated nitrate allocation to roots. Both tissue storage and long distance transport of nitrate is mediated by specific membrane proteins that have been characterized in the Sanders/Miller lab at JIC. SINAR results in sub-optimal growth as nitrate assimilation in leaves is more efficient, making use of the greater energy and carbon availability in photosynthetic tissues. This research will determine the role of the SINAR response in plant nitrogen use efficiency. A range of different approaches will be used to generate plants with altered SINAR response and the results will inform on how the plant senses and signals nitrogen status.

icon 1

Natural Products

  • JIC partner: Sarah O’Connor
    SIPPE partner: Youli Xiao

    Medicinal plants produce many secondary metabolites, particularly alkaloids, which have potent biological activities. Plant derived alkaloids are a potent source of medicinal compounds. For example, more than 4000 alkaloids were identified in traditional Chinese medicine, and 50 of these compounds are used as pharmaceuticals clinically. However, the capacity to harness plant alkaloids is hindered by the fact that these compounds are often produced in low levels, or by plants that are challenging to cultivate. Understanding the biosynthesis of these compounds will pave the way to better production strategies for these compounds, as well as analogues of these compounds that may have improved or modified biological activity. In this proposal, we will uncover the biosynthetic pathways of several medicinally active alkaloids.

  • JIC partner: Janneke Balk
    IGDB partner: Hong-Qing Ling

     The laboratories of Dr Janneke Balk (JIC) and Professor Hong-Qing Ling (CAS Bejing) will start a collaboration to discover how plants sense iron. Plants are very efficient in taking up iron from the soil, which they need to grow big and strong. It also ends up in fruits and vegetables, from which we obtain our dietary iron.

    Plants will only take up as much iron as they need, because an excess of iron in toxic. For this they need to know how much iron there is in the cell, so they can adjust the uptake and usage as required. Currently we do not know how the level of iron is sensed, and how this information is conveyed to regulatory mechanisms. Both labs have several mutant lines in the model species Arabidopsis that appear to have a defect in regulating the amount of iron, which may be due to an inability to sense iron. We will test this using a number of molecular tools that each lab has available.

  • JIC partner: Tony Miller
    IGDB partner: Yiping Tong

     Nitrate is the main nitrogen (N) source for cereal crops such as wheat, thus understanding nitrate signaling in cereal crops is important and valuable for engineering crops with improved N use efficiency. Although several regulators have been identified in nitrate sensing and signaling in Arabidopsis, the equivalent information in cereals is missing. Specific nitrate transporters were found to regulate seed nitrate content and lateral root formation in Arabidopsis. A nitrate-inducible NAC transcription factor in wheat that is involved in regulating grain nitrate content and lateral root formation has recently been identified. This research will identify if wheat also has these nitrate-sensitive processes regulated by specific transporters.

  • JIC partner: Cathie Martin
    SIPPE partner: Hong Wei Xue

     There is a growing consensus that strengthening the local production of essential medicines is a priority in developing countries. At least five thousand plant species are used medicinally in China. The traditional Chinese medicine Shan Dou Gen, used to treat jaundice, hepatitis, bladder tumours and melanoma, is derived from the root of the legume Sophora tonkinensis Gapne.

    The project will focus on the isolation of the genes underpinning the biosynthetic pathway of active compounds (prenylated flavonoids such as sophoranone and soporadin) in this plant. Increasing the production of these compounds in root cultures will allow for scale up of production for therapeutic uses.

Research Conduct

Responsible research conduct is the practice of performing scientific investigations with integrity. It involves the awareness and application of established professional norms and ethical principles in the performance of all activities related to scientific research.

As an international centre of excellence, it is expected that CEPAMS will conduct its research according to appropriate ethical, legal and professional frameworks, obligations and standards.

This document sets out the overarching policy for responsible research conduct in CEPAMS, recognising that implementation of such a policy will be the responsibility of the participating institutes.

Guiding principles

Those involved in CEPAMS research are expected to adhere to the following seven guiding principles for responsible research conduct:

(i) honesty – in reporting research outputs (including methodology, interpretation and implications of results);

(ii) fairness – in acknowledging the work and contribution of others;

(iii) rigour – in conducting, reporting and publishing research data and in drawing conclusions from that data (including record keeping of the primary data);

(iv) transparency – in accounting for research outputs and in disclosing potentially conflicting activities and interests;

(v) independence – in keeping with norms of academic freedom and the impartial conduct of research irrespective of funding body;

(vi) respect – for colleagues and for the ethical policies/regulations applicable to research;

(vii) accountability – to funders and to society.


This policy applies to all those working in CEPAMS laboratories and those involved in CEPAMS collaborative projects. The policy is implemented through and underpinned by the processes in place at each of the institutes. Individual scientists will be covered by the processes and expectations of their home institute. CEPAMS Group Leaders, being faculty members of more than one institute, will be covered by the processes and expectations of their home institute and those of the John Innes Centre.


This policy will be communicated to all those working in CEPAMS laboratories and those involved in CEPAMS collaborative projects. It will be placed in the public domain via the CEPAMS website.