Professor Andrew Charles Allan

BSc(Hons), PhD

Research | Current

The CHIPs lab (Colour and Health in Plants)

red_fruitIn the "CHIPs" Lab, we have 5 post-docs and 2 research associates, all working on aspects of fruit biology.

We have genomes (apple, peach, strawberry), expressed genes (kiwifruit, berries), greenhouses full of plants, and great people - physiologists, molecular biologists, and biochemists….all enthusiasts for plant biology!

We are funded in the FRST program, HortGenomics, with the objective of producing "Elite plants with new colour & health attributes", and in the FRST program "Pipfruit; A juicy future" which focuses on fruit quality and texture. In my lab we have the target of understanding the production of fruit health and colour compounds, such as the red anthocyanin, yellow and orange carotenoids and the green chlorophylls, as well as the colourless flavonoids. With this understanding it will be possible to develop (via breeding - usually) fruit with novel appearance, colour changes that indicate harvest and eating ripeness and healthy fruit with enhanced levels of antioxidants.

Through this research we will enhance our understanding of the biosynthesis, regulation and development of plant pigments and health compounds. We exploit whole genome sequences that are available for an increasing number of plants. Also allelic diversity found in the germplasm and breeding resources, at both the genetic and epigenetic level.

Our lab uses transformation of model plants (Arabidopsis, tobacco, strawberry) for gene function testing as well as transformation of kiwifruit, apple, and other species.

Some of our projects

  1. The red fleshed apple
    We have used extremes in the germplasm to find the mutations that give apples red foliage and red flesh. This mutation results from an autoregulatory loop set up by a major gene (MYB10) gaining the ability to up-regulate itself. We have extended our knowledge of these genes into many other fruits (peaches, cherries, strawberries, bayberries, mangosteen etc).

  2. New Kiwifruit colours (Transcriptional regulation of Carotenoid biosynthesis in plants)
    Our research group is investigating carotenoid pigment accumulation in plant flowers and fruit and how the carotenoid biosynthetic pathway is regulated by transcriptional and post-transcriptional events. We have identified two transcription factors that appear to function in regulating gene expression of carotenoid biosynthetic genes in kiwifruit.
    The aim of this project is to understand how these transcription factors control carotenogenesis using model plants. Project objectives:
    1. Elucidate the effect of transcription factor gene expression on carotenoid accumulation in transient/stable transgenic plants (Arabidopsis & N. benthamiana) using high performance liquid chromatography systems.
    2. Analyse changes in endogenous gene expression profiles in model plants expressing the transcription factor genes using Gene array and Quantitative PCR methods.
    3. Investigate the changes in plastid structure during carotenogenesis using transgenic model plants expressing the transcription factor genes.
    4. Understand promoter function by characterising potential cis-elements in transcription factor gene promoters using bioinformatics tools and in-planta assays.
  3. Genomes that we eat
    Apple, strawberry and kiwifruit comparative genomics.


Postgraduate supervision

Graduate research projects can be carried out in my lab at Plant&Food Research or based in the SBS labs. Projects are funded by MBIE.

You are very welcome to make contact by email or come and discuss graduate opportunities with me.


Associate Professor at SBS and Science Group Leader, Discovery for Impact, at Plant & Food Research

Areas of expertise

Plant Molecular Science

Selected publications and creative works (Research Outputs)

  • Li, Y., Lin-Wang, K., Liu, Z., Allan, A. C., Qin, S., Zhang, J., & Liu, Y. (2020). Genome-wide analysis and expression profiles of the StR2R3-MYB transcription factor superfamily in potato (Solanum tuberosum L.). International journal of biological macromolecules, 148, 817-832. 10.1016/j.ijbiomac.2020.01.167
  • Peng, Y., Cordiner, S. B., Sawyer, G. M., McGhie, T. K., Espley, R. V., Allan, A. C., & Hurst, R. D. (2020). Kiwifruit with high anthocyanin content modulates NF-kappa B activation and reduces CCL11 secretion in human alveolar epithelial cells. JOURNAL OF FUNCTIONAL FOODS, 6510.1016/j.jff.2019.103734
  • Wang, W.-Q., Wang, J., Wu, Y.-Y., Li, D.-W., Allan, A. C., & Yin, X.-R. (2020). Genome-wide analysis of coding and non-coding RNA reveals a conserved miR164-NAC regulatory pathway for fruit ripening. The New phytologist, 225 (4), 1618-1634. 10.1111/nph.16233
  • Zhu, Y.-C., Zhang, B., Allan, A. C., Kui, L.-W., Yun, Z., Ke, W., ... Xu, C.-J. (2020). DNA demethylation is involved in the regulation of temperature-dependent anthocyanin accumulation in peach. PLANT JOURNAL10.1111/tpj.14680
  • Nardozza, S., Cooney, J., Boldingh, H. L., Hewitt, K. G., Trower, T., Jones, D., ... Richardson, A. C. (2020). Phytohormone and Transcriptomic Analysis Reveals Endogenous Cytokinins Affect Kiwifruit Growth under Restricted Carbon Supply. METABOLITES, 10 (1)10.3390/metabo10010023
  • Nardozza, S., Boldingh, H. L., Kashuba, M. P., Feil, R., Jones, D., Thrimawithana, A. H., ... McGhie, T. K. (2019). Carbon starvation reduces carbohydrate and anthocyanin accumulation in red-fleshed fruit via trehalose 6-phosphate and MYB27. Plant, cell & environment10.1111/pce.13699
  • Karim, S. K. A., Allan, A., Schaffer, R., & David, K. (2019). Differential expression of specific genes regulating ‘royal gala’ (Malus x domestica) fruit development. Malaysian Applied Biology, 48 (5), 19-27.
    Other University of Auckland co-authors: Karine David
  • Plunkett, B. J., Henry-Kirk, R., Friend, A., Diack, R., Helbig, S., Mouhu, K., ... Putterill, J. (2019). Apple B-box factors regulate light-responsive anthocyanin biosynthesis genes. Scientific reports, 9 (1)10.1038/s41598-019-54166-2
    Other University of Auckland co-authors: Joanna Putterill

Contact details

Alternative contact

Team Leader, Colour in Plants
Plant&Food Research
120 Mt Albert Rd,
Private Bag 92169
Mt Albert, Auckland
New Zealand


Primary office location

COMMERCE A - Bldg 114
Level 1, Room 108
New Zealand

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