Apple Black Spot Control

Te Kunenga ki Pūrehuroa Massey University is collaborating with New Zealand’s Bioeconomy Science Institute and France’s National Institute for Agriculture, Food and Environment (INRAE) to find novel control methods for Apple Black Spot. Also known as Scab disease, it is caused by a fungus and is the most economically important disease of apples worldwide.

Dr Jo Bowen of the New Zealand Science Institute for Bioeconomy (BSI) says apples are worth $2.5 billion to the New Zealand with exports earning over $1.2 billion annually. The disease can result in significant economic losses for commercial apple growers, and requires treatment with fungicide sprays, which are expensive to apply and can create consumer resistance for those concerned about their health and the environment.

Apple black spot disease is caused by the fungus Venturia inaequalis. If not adequately controlled, it can result in economic losses of 70 to 100% for our commercial apple orchardists.  Blemished fruit can’t be sold, and leaf infections decrease the growth and yield of apple trees through premature leaf drop and reduced photosynthesis.

Dr Bowen is working with Te Kunenga ki Pūrehuroa Massey University’s Dr Carl Mesarich, to better understand how the black spot fungus, apples and other naturally occurring microorganisms interact at the molecular level. 

How the fungus causes black spot

In late autumn, infected leaves fall to the ground where the black spot fungus survives the winter. In spring, when temperatures start to rise, it releases spores that are carried by wind to young, freshly unfurled apple leaves. Once on the leaf, the fungus gets under the waxy surface layer and grows by delivering small protein virulence factors (termed effectors) into and around the underlying plant cells.

Those initial infections produce more spores that are spread by wind and rain-splash to nearby leaves and fruit, causing multiple rounds of infection through spring and early summer. Crucially, every time the fungus produces new spores, these rupture through the cuticle of apple leaves and fruit, to give the characteristic scabby lesions people recognize. 

Current control methods

• Fungicidal sprays that kill the fungus or inhibit spore germination (typically 10-16 per season) 
• Biological controls including applying beneficial microbes and compounds that induce a plant’s defences 
• Cultural controls, including removal of diseased debris, pruning for better airflow, and drip (rather than overhead) irrigation 
• Integrated pest management (IPM) – a strategic combination of some of the above options, which relies on close monitoring of orchard conditions and pathogen abundance, and taking timely actions 
• Use of AI to help detect the disease early and allow targeted IPM interventions 

Some of these, especially fungicides, can add significantly to the costs of production, and some may be ruled out for specific export markets. However, because fungicides are very effective, they are the main control method currently, with 10 to 16 applications typically used per season to keep the disease in check. 

Other complications are that the fungus can develop resistance to fungicides over time, and their use is limited to specific times of year to avoid residues on produce – a phytosanitary requirement for many of our markets. Consumers are also requiring that fewer pesticides are used given their potential impacts on human health and the environment. 

The collaborative studies are aimed at finding out how the fungus infects susceptible plant cells, without triggering the plant’s defences, and how resistant plants recognise and combat that infection. 

Dr Mesarich explains that unlike animals, plants don’t have mobile immune cells or long-term memory of past infections. Instead, each cell defends itself using built-in immune receptors either at the cell surface or inside the cell. The presence of immune receptors depends on their particular resistance genes. Some apple cultivars like ‘Royal Gala’ or ‘Granny Smith’, are completely susceptible to black spot because they lack any resistance genes that are active against the fungus. 

However, there are other cultivars that possess one, or sometimes two, resistance genes that provide some protection. One is the cultivar ‘Goodness Me’, which features two black spot resistance genes and was recently launched by Prevar* in conjunction with the breeding programme of the Bioeconomy Science Institute. 

How infection occurs

The black spot fungus infects susceptible apple cultivars by delivering small proteins known as “effectors” into the plant tissue. Resistant cultivars have immune receptors that recognize and neutralize these effectors.

As well, the fungus may mutate and consequently evade detection over time. These are a problem when resistant apple cultivars carry only one resistance gene. It means that one season an orchard can be disease free - and the next it may be riddled with black spot because the fungus has adapted. This is a worldwide problem and leads to further reliance on fungicides. 

The research

So, the research is asking, how can durable resistance be developed? Most potential black spot effectors have now been identified, but not all are recognised by apple immune receptors, so the research team is monitoring fungal variants to predict which effectors are likely to enable the fungus to invade undetected. They then use that information to guide spraying or other control measures. 

The team is also working to determine which fungus effectors are recognised by immune receptors of apple, as well as the molecular mechanisms that enable the pathogen to overcome the corresponding resistance genes. Identifying the most important effectors that apple immune receptors do recognise provides an opportunity to breed resistant varieties or develop resistance genetically.

They are also assessing the use of microorganisms, such as bacteria and yeasts normally found on the surface of apples, to see whether any would be an effective biological control of the fungus. So far, they have found a number that are antagonistic to the fungus and could bealong with the resistance gene approac, to reduce the use of pesticides.

Other approaches taken are the use of peptide sprays, or RNA interference (RNAi) mechanisms such as applications (through spraying or selective breeding) of double-stranded RNA, that will disrupt the production of effectors without affecting the naturally occurring microorganisms found in the orchard. 

In addition to the work being done to understand infection pathways and biological control agents, another significant step is the study of the natural disease resistance of some apple accessions (cultivars) and certain wild species, to see if that resistance can be enhanced and/or transferred to new varieties.

As Dr Mesarich explains, ‘We are seeking to identify resistance genes that can be introduced into apple cultivars to provide long lasting protection. For example, it we stack several resistance genes in apple, especially those that correspond to effectors that are important for the pathogen’s ability to cause disease, then the pathogen will find it more difficult to break these resistances and cause disease.’

Dr Mesarich adds the research is a team effort, involving collaboration between Te Kunenga ki Pūrehuroa Massey University and the  Bioeconomy Science Institute, but also international partners like INRAE. Currently (in 2026) there are three Massey PhD students, all co-supervised through the BSI, with one student undertaking a three-month placement at INRAE, funded through the Agricultural Life Sciences PhD Travel Grant (administered by Te Kunenga ki Pūrehuroa Massey University). The research by the three PhD students is primarily made possible by funding from BioProtection Aotearoa, a Centre of Research Excellence in New Zealand, while the team at the BSI comprises three scientists, supported through internal funding. 

The ultimate goal of this research programme is to use all of this knowledge to inform long-lasting, durable disease control strategies that will ultimately support the development of spray-free orchards. 

* Prevar is a private joint venture company owned by the industry.  It was established in 2004 to develop and commercialise new apple and pear varieties for licensing in NZ and worldwide.