Dr Robert James Schaffer

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Senior Lecturer

Research | Current

My lab is based at the Crown Research Institute, Plant & Food Research (PFR) and our current research focus is fruit texture. Fruit texture is a complex trait that requires an understanding of development, cellular arrangement, and cell wall chemistry. The biggest change in fruit texture occurs during ripening, which is both developmentally and hormonally controlled, and due to this much of our research is investigating this.

At present our main focus is on three fruit with diverse textures, namely kiwifruit (Actinidia sp.), apple (Malus X domestica) and pears (Pyrus communis). There is the full genome available for each of these species allowing rapid identification of gene environments. We use transcriptomics combined with gene mining and mapping to identify candidate genes controlling fruit ripening and texture. Functional analysis of these genes is tested through the generation of transgenics and use of transient assays developed at PFR.

PFR has integrated research, with programs spanning basic biology through to industry related applied research. Students have the potential to work with scientists with across a range of disciplines both within PFR and with our close collaborations with the University of Auckland and research groups in Europe and the US.

Research themes for potential projects cover three main areas.

Fruit ripening

In kiwifruit, apples, and pears the plant hormone ethylene controls many aspects of ripening. We have created transgenic lines that are suppressed for ethylene biosynthesis (ACC OXIDASE) in both apple and kiwifruit (Schaffer et al. 2007, Atkinson et al. 2011). These lines allow us to study the ethylene regulated ripening by controlled application of ethylene. Using these resources we have developed a sensitivity - dependency model that shows different ripening characters are controlled with different sensitivities to ethylene (Johnston et al. 2009), and can describe the progression of ripening in regular apple varieties.

Ripening is not solely controlled by ethylene, there is now considerable evidence that other plant hormones are involved (McAtee et al 2013). One in particular is the requirement of a low auxin concentration for ripening to progress. Suppression a MADS box gene related to the tomato ripening inhibitor gene (RIN), MADS8, as well as causing loss of flesh tissue (Ireland et al. 2013) also causes a high auxin at maturation and has reduced developmentally controlled ripening and lower ethylene (Schaffer et al. 2013, Ireland et al. 2013).

Research in this area can utilise our world leading postharvest facilities which offers extensive storage and fruit characterisation tools, and can draw upon expertise of experienced postharvest scientists.


Figure 1. A Control ‘Royal Gala’ Apples (A) and transgenic lines with the
ethylene biosynthesis gene (ACO1) suppressed (B) at fruit maturation.

Fruit cell walls

Plant cell walls are made up of complex sugar polymers that protect the cell and determines many of the fruit texture characters. During fruit ripening there is a strong up-regulation of cell wall related genes such as expansins and hydrolases (cell wall enzymes that cleave the sugar polymers). The genome sequence has revealed hundreds of cell wall related genes in plants making this a particularly complex area. However, suppression of a single cell wall hydrolase in apple (POLYGALACTURONASE 1 - PG1), results in apples that are firmer after storage (Atkinson et al. 2012). The transcriptional control of this gene occurs through transcription factors associated with the ethylene pathway and surprisingly, through the cold response pathway (Tacken et al. 2010). Using this information, we further showed that cold can independently contribute to apple fruit softening.

Research in this area can utilise our close links to cell wall biochemists, and microscopy unit that has a close collaboration with the Knox lab and utilises their unique monoclonal antibodies for cell wall epitopes (Figure 2).


Figure 2. Immunolocalisation of low esterified pectin using the JIM5 antibody (red)
combined with a blue cellulose stain. A) Control ‘Royal Gala’ Apples following storage
and B) PG1-suppressed apples following storage.

Flesh Development and fruit size

For consumers in particular, the edible flesh is an important component of fruit. One of the first selections of cultivated crops is fruit size. Fruit size is determined early in fruit development, with a strong relationship between number of cell divisions and final fruit size. The control of cell division is in part controlled by hormones. In collaboration with Dr. K David’s lab we have investigated the control of auxin controlling apple fruit size (Devoghalaere et al. 2012), and suppression of a MADS box gene associated with the SEPALLATA class (MADS8), appears to be associated with a loss of flesh tissue in apple (Ireland et al. 2013, Schaffer et al. 2013).

Research in this area will can utilise our close links to the David Lab at the University of Auckland, and recently we have developed protocols for testing hormone concentrations in house.




Figure 3. Royal Gala control apples (A,B) and MADS8-suppressed
apples (C,D) at maturity. Compared to the control, the MADS8
suppressed apples have greatly reduced flesh tissue.
The cellular makeup of these apples show lack of cell expansion,
and the fruit do not ripen.



Current Students

  • Mareike Knabel (PhD student based in Plant and Food Research, Palmerston North): Genetic control of dwarfing in pears
  • Patrick Collins (PhD student based at Plant and Food Research, Auckland) Effect of skin on fruit quality in apples
  • Ling Hoong (Masters Student based at Plant and Food Research, Auckland) Flesh development in apple

Co supervision

  • Niels Niewenhuisen (PhD Student): Transcriptional control of flavour volatiles
  • Chirstina Fullerton (PhD Student): The control of fruit softening in kiwifruit

Former students in my lab

  • Emma Tacken MSc (Completed 2008) and PhD (completed 2012): Transcriptional control of POLYGALACTURONASE1 in apple (currently undertaking postdoctoral research in CSIRO Canberra Australia)
  • Hilary Ireland Honours (Completed 2011): Flesh development and control of ripening in apples (currently research associate in my lab)
  • Peter McAtee MSc and Phd (Completed 2014): Control of fruit maturation in kiwifruit
  • Isaac Harvey MSc (Complete 2014): Comparison of texture in apples and pears

Areas of expertise

Plant Molecular Science

Selected publications and creative works (Research Outputs)

  • Boase, M., Tiffin, H., Zhang, H., Hunter, D., Erridge, Z., Wang, L., ... Brummell, D. (2019). Genome Editing of Tomato with CRISPR/Cas 9 Targeting Fruit Softening Genes. IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-ANIMAL. (pp. 1).
  • Peace, C. P., Bianco, L., Troggio, M., van de Weg, E., Howard, N. P., Cornille, A., ... Schaffer, R. J. (2019). Apple whole genome sequences: recent advances and new prospects. HORTICULTURE RESEARCH, 610.1038/s41438-019-0141-7
  • Gunaseelan, K., McAtee, P. A., Nardozza, S., Pidakala, P., Wang, R., David, K., ... Schaffer, R. J. (2019). Copy number variants in kiwifruit ETHYLENE RESPONSE FACTOR/APETALA2 (ERF/AP2)-like genes show divergence in fruit ripening associated cold and ethylene responses in C-REPEAT/DRE BINDING FACTOR-like genes. PloS one, 14 (5)10.1371/journal.pone.0216120
    Other University of Auckland co-authors: Karine David
  • Chen, Y., Grimplet, J., David, K., Castellarin, S. D., Terol, J., Wong, D. C. J., ... Talon, M. (2018). Ethylene receptors and related proteins in climacteric and non-climacteric fruits. Plant science : an international journal of experimental plant biology, 276, 63-72. 10.1016/j.plantsci.2018.07.012
    Other University of Auckland co-authors: Karine David
  • Fullerton, C. G., Hallett, I. C., Schaffer, R. J., Perera, C., & Schröder R (2018). Cell-wall and structural changes during softening in two Actinidia chinensis var. Chinensis genotypes with contrasting softening rates. Acta Horticulturae. 10.17660/ActaHortic.2018.1218.24
    Other University of Auckland co-authors: Conrad Perera
  • Thongkum, M., McAtee, P. M., Schaffer, R. J., Allan, A. C., & Ketsa, S. (2018). Characterization and differential expression of ethylene receptor genes during fruit development and dehiscence of durian ( Durio zibethinus ). Scientia Horticulturae, 240, 623-630. 10.1016/j.scienta.2018.06.052
    Other University of Auckland co-authors: Andrew Allan
  • Boase, M. R., Tiffin, H., Zhang, H., Hunter, D., Erridge, Z., Wang, L., ... Schaffer, R. (2018). Gene editing of tomato via Agrobacterium-mediated transformation with CRISPR/Cas 9 constructs targeting cell wall genes. Paper presented at 14th Quadrennial Congress of the International-Association-of-Plant-Biotechnology (IAPB), Dublin, IRELAND. 19 August - 24 August 2018. IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-PLANT. (pp. 2).
  • Gambi, F., Pilkington, S. M., McAtee, P. A., Donati, I., Schaffer, R. J., Montefiori, M., ... Burdon, J. (2018). Fruit of three kiwifruit ( Actinidia chinensis ) cultivars differ in their degreening response to temperature after harvest. Postharvest Biology and Technology, 141, 16-23. 10.1016/j.postharvbio.2018.03.009

Contact details

Alternative contact


Plant & Food Research LTD
120 Mount Albert Road
Private Bag 92169
New Zealand

Primary office location

Level 3, Room 301
New Zealand