The John Innes Centre Publications Repository contains details of all publications resulting from our researchers.

The repository also includes Open Access publications, which can be identified by the icons found on search results.

 Green open access publications are marked by the PDF icon. Click on the publication title, or the PDF icon, and read a pre-print PDF version of the publication.  Gold open access publications have the gold open padlock icon. You can read the full version of these papers on the publishing journal’s website without a subscription. 

The creation of this publications repository was funded by BBSRC.

Recent Publications

Lee K. J., Coen E. S., Calder G., Hindle C., Newman J., Robinson S., Avondo J. (2017)

Macro optical projection tomography for large scale 3D imaging of plant structures and gene activity

Journal of Experimental Botany (68 (3)) 527-538

Publisher's version: 10.1093/jxb/erw452

ID: 55629

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Optical projection tomography (OPT) is a well-established method for visualising gene activity in plants and animals. However, a limitation of conventional OPT is that the specimen upper size limit precludes its application to larger structures. To address this problem we constructed a macro version called Macro OPT (M-OPT). We apply M-OPT to 3D live imaging of gene activity in growing whole plants and to visualise structural morphology in large optically cleared plant and insect specimens up to 60 mm tall and 45 mm deep. We also show how M-OPT can be used to image gene expression domains in 3D within fixed tissue and to visualise gene activity in 3D in clones of growing young whole Arabidopsis plants. A further application of M-OPT is to visualise plant-insect interactions. Thus M-OPT provides an effective 3D imaging platform that allows the study of gene activity, internal plant structures and plant-insect interactions at a macroscopic scale.

Kenzhebayeva S. S., Doktyrbay G., Capstaff N., Sarsu F., Omirbekova N. Z. H., Eilam T., Tashenev D. K., Miller A. J. (2017)

Searching a spring wheat mutation resource for correlations between yield, grain size, and quality parameters

Journal of Crop Improvement (31 (tbc)) 1-20

Publisher's version: 10.1080/15427528.2016.1276990

ID: 55621

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To broaden genetic variation, an irradiated wheat (Triticum aestivum L.) M5 population was generated in the background of spring wheat cv. Almaken. This resource was used to measure components of productivity, including grain number and grain weight (GW) per main spike, GW per plant (GWP), 1000-grain weight (TGW), grain size and grain shape, and some quality parameters. Some mutant lines, mostly in the 200-Gy-dosed germplasm, had 2–4 times higher grain iron and zinc concentrations and 7–11% higher protein content relative to the parent line. Some irradiated lines had significantly larger TGW, and grain area (GA), length, and width than the parent, cv. Almaken. The largest GA and grain length (GL) were 30–40% greater than those of the parent. Correlations for Zn concentration versus GA = 0.191, p ˂ 0.01, grain protein content (GPC) versus GA = 0.128, p ˂ 0.05, GPC versus GL = 0.113, p ˂ 0.05, and GPC versus grain width = 0.191, p˂0.001 were observed in 200 Gy-dosed mutants. In 100 Gy-dosed mutants, correlations for Fe concentration versus GWP = 0.302, p ˂ 0.001 and Fe concentration versus TGW = 0.153, p ˂ 0.01 were found. The mutant lines showed the capacity to biofortify wheat grain without negatively impacting on crop productivity and this population offers promising donors for improving grain parameters such as GA, length, and width and quality. The data presented showed how the genetic variation generated through radiation could be used to test the linkage between various important grain parameters.

Reimegård J., Kundu S., Pendle A., Irish V. F., Shaw P., Nakayama N., Sundström J. F., Emanuelsson O. (2017)

Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana.

Nucleic acids research (10) 1-10

Publisher's version: 10.1093/nar/gkx087

ID: 55608

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Co-expression of physically linked genes occurs surprisingly frequently in eukaryotes. Such chromosomal clustering may confer a selective advantage as it enables coordinated gene regulation at the chromatin level. We studied the chromosomal organization of genes involved in male reproductive development in Arabidopsis thaliana. We developed an in-silico tool to identify physical clusters of co-regulated genes from gene expression data. We identified 17 clusters (96 genes) involved in stamen development and acting downstream of the transcriptional activator MS1 (MALE STERILITY 1), which contains a PHD domain associated with chromatin re-organization. The clusters exhibited little gene homology or promoter element similarity, and largely overlapped with reported repressive histone marks. Experiments on a subset of the clusters suggested a link between expression activation and chromatin conformation: qRT-PCR and mRNA in situ hybridization showed that the clustered genes were up-regulated within 48 h after MS1 induction; out of 14 chromatin-remodeling mutants studied, expression of clustered genes was consistently down-regulated only in hta9/hta11, previously associated with metabolic cluster activation; DNA fluorescence in situ hybridization confirmed that transcriptional activation of the clustered genes was correlated with open chromatin conformation. Stamen development thus appears to involve transcriptional activation of physically clustered genes through chromatin de-condensation

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