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

Gangappa S. N., Berriri S., Kumar S. V. (2017)

PIF4 Coordinates Thermosensory Growth and Immunity in Arabidopsis.

Current Biology (27) 243-249

Publisher's version: 10.1016/j.cub.2016.11.012

ID: 55511

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Temperature is a key seasonal signal that shapes plant growth. Elevated ambient temperature accelerates growth and developmental transitions, while compromising plant defenses leading to increased susceptibility. Suppression of immunity at elevated temperature is at the interface of trade-off between growth and defense. Climate change and the increase in average growth season temperatures threaten biodiversity and food security. Despite its significance, the molecular mechanisms that link thermosensory growth and defense responses are not known. Here we show that PHYTOCHROME INTERACTING FACTOR4 (PIF4)-mediated thermosensory growth and architecture adaptations are directly linked to suppression of immunity at elevated temperature. PIF4 positively regulates growth and development and negatively regulates immunity. We also show that natural variation of PIF4-mediated temperature response underlies variation in the balance between growth and defense among Arabidopsis natural strains. Importantly we find that modulation of PIF4 function alters temperature sensitivity of defense. Perturbation of PIF4-mediated growth has resulted in temperature resilient disease resistance. This study reveals a molecular link between thermosensory growth and immunity in plants. Elucidation of the molecular mechanisms that define environmental signal integration is key to develop novel strategies for breeding temperature-resilient disease resistance in crops.

Krasileva K. V., Vazquez-Gross H. A., Howell T., Bailey P., Paraiso F., Clissold L., Simmonds J., Ramirez Gonzalez R. H., Wang X., Borrill P., Fosker C., Ayling S., Phillips A., Uauy C., Dubcovsky J. (2017)

Uncovering hidden variation in polyploid wheat

Proceedings of the National Academy of Sciences of the United States of America (early edition) early edition

Publisher's version: 10.1073/pnas.1619268114

ID: 55546

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Comprehensive reverse genetic resources, which have been key to understanding gene function in diploid model organisms, are missing in many polyploid crops. Young polyploid species such as wheat, which was domesticated less than 10,000 y ago, have high levels of sequence identity among subgenomes that mask the effects of recessive alleles. Such redundancy reduces the probability of selection of favorable mutations during natural or human selection, but also allows wheat to tolerate high densities of induced mutations. Here we exploited this property to sequence and catalog more than 10 million mutations in the protein-coding regions of 2,735 mutant lines of tetraploid and hexaploid wheat. We detected, on average, 2,705 and 5,351 mutations per tetraploid and hexaploid line, respectively, which resulted in 35-40 mutations per kb in each population. With these mutation densities, we identified an average of 23-24 missense and truncation alleles per gene, with at least one truncation or deleterious missense mutation in more than 90% of the captured wheat genes per population. This public collection of mutant seed stocks and sequence data enables rapid identification of mutations in the different copies of the wheat genes, which can be combined to uncover previously hidden variation. Polyploidy is a central phenomenon in plant evolution, and many crop species have undergone recent genome duplication events. Therefore, the general strategy and methods developed herein can benefit other polyploid crops.


Plant growth and development are defined by environmental cues. The transcription factor PHYTOCHROME INTERACTING FACTOR 4 (PIF4) is the central signaling hub that integrates environmental cues, including light and temperature, to regulate growth and development. The thermosensory mechanisms controlling the PIF4-mediated temperature response, and its integration with other environmental responses, remain poorly understood. DE-ETIOLATED 1 (DET1) and CONSTITUTIVE PHOTOMORPHOGENESIS 1 (COP1), key regulators of light signaling, have been proposed to control thermosensory growth by transcriptional regulation of PIF4, through ELONGATED HYPOCOTYL 5 (HY5). Here, we show that DET1/COP1 and HY5 regulate thermosensory elongation through distinct mechanisms. DET1 and COP1 are essential for promoting PIF4 expression and stabilizing PIF4 protein. Furthermore, HY5 inhibits elongation growth through competitive chromatin binding to PIF4 targets, not through transcriptional regulation of PIF4. Our findings reveal a mechanistic framework in which DET1/COP1 and HY5 regulatory modules act independently to regulate growth through the environmental signal integrator PIF4.

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