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Rot risk assessment – General


Research has shown that Cox orchards vary considerably in the actual losses due to rots in store and the main fungi responsible for the losses. Therefore, actual rotting in store is very much related to orchard site.

The purpose of rot risk assessment is to:

(1) identify those orchards with fruit likely to have significant rotting in store, so that appropriate measures can be taken to minimise losses and

(2) avoid unnecessary treatment on orchards where the risk of rotting in store is minimal.

Rot risk assessment is based on assessment of various factors pre-harvest from which a decision can be made on the likely rotting in store and therefore the need for treatment.

The system has been developed for Cox because, in general, losses due to rots in store for other varieties such as Bramley, Gala and Jonagold are usually minimal. The system, however, is probably applicable to all varieties.

The factors assessed pre-harvest are as follows:

  • daily rainfall
  • orchard factors
  • fungal inoculum (brown rot and canker)
  • crop load
  • % bareground
  • % crop <½ metre from ground
  • orchard rot history
  • fruit storage potential (mineral composition and firmness)

Rainfall measurement

The most significant factor influencing rotting in stored fruit is rainfall. Rainfall varies considerably from place to place and is most influenced by height. Summer rainfall is particularly localised. Therefore, to get an accurate assessment of rot risk in store, growers need to obtain daily rainfall from a representative orchard on the holding.

This can be obtained from either an automatic weather station if one is in use, or achieved using a simple rain gauge as follows:

  • Where possible, the gauge used should be a standard copper gauge with a five-inch collecting funnel. Readings should be taken using a tapered glass measure calibrated in mm.
  • The site chosen for the gauge should be level, clear of overhanging objects, which might drip into the funnel, and there should be no objects close to the gauge which could cause eddy effects and thus inaccurate catches when rainfall events occur in windy conditions.
  • The gauge should be installed so that the rim of the collecting funnel is one foot above ground and should be level and firm. A ring of gravel around the gauge will prevent large raindrops from splashing back into the funnel from the ground when rainfall is heavy.
  • While it is not essential that the gauge is read daily or at the same time each day, it is standard practice for met. stations to take daily readings at 0900 hr GMT in order that readings are comparable. It is probably a good idea if growers follow the same practice.

Average rainfall

Total monthly rainfall (mm) for 1998, 2005 and 50 year average for East Malling




50 year average

























The rainfall criteria are based on rainfall for south east England. The table above shows 50 year monthly average rainfall for East Malling to illustrate average rainfall figures on which to judge the rot risk based on rainfall. On this basis, 1998 would be considered May and August below average and 2005, below average for June but average for the other months. Obviously regions which normally have higher average rainfall than south east England will inherently have a higher rot risk.

Collected rainfall information is used as follows:

Rainfall criteria

Fungal rot Rainfall criteria 
Botrytis Rainfall June – harvestscore as average


Neonectria Rainfall blossom – harvestscore as average


Gloeosporium Rainfall in month prior to harvestscore as average


Phytophthora Rainfall in 15 days prior to harvestlow or no rain = low risk

20 mm or >= high risk


Orchard factors

Since some fungicide treatments for rot control may need to be applied early in the season assessment of orchard factors needs to be done initially pre-bloom and repeated nearer harvest. Near harvest assessments of inoculum are particularly important for rots such as brown rot, the incidence of which can change very rapidly as the fruit matures.

  • Do a general walk through the orchard examining trees for canker, low hanging fruit, rot incidence etc.
  • Make more formal assessments on at least 20 trees selected at random following a W pattern across the orchard.
  • Follow procedures for assessment of orchard factors affecting rotting in store in the table below.

Orchard rot history

Keeping records for individual orchards, of losses due to rots, and the fungi responsible, when the fruit is being graded from store can provide valuable information on the current problems in the orchard and the ones likely to occur in future. The following procedure is recommended for determining orchard rot history:

  • Gloves should be worn when handling rotted fruit as a precaution.
  • Where fruit from a single orchard is being graded, save the rots separately in a suitable container. When grading is complete, weigh the total amount of rots and express as a percentage of the total graded fruit to obtain an estimate of losses due to rots. If the number of bins is excessive, then select a random sample of bins as they go over the grader and estimate losses from these.
  • Remove at least one hundred of the rots selected at random and identify the cause of the rotting.
  • Record the number of each type of rot present and express as a percentage of the total rots. Records of orchard rot history should be kept for each orchard (see below).

In this way a database can be built up for each orchard providing information to assist in decisions on treatment and storage potential.

Fruit storage potential

The mineral composition of fruits is closely correlated to the level of rots found after medium or long-term Controlled Atmosphere (CA) storage.

Increased levels of nitrogen and potassium are associated with higher levels of rots while increased calcium levels in the fruit tend to reduce rot incidence. The importance of adequate concentrations of calcium and phosphorous in apple fruit has been well established through research during the past 30 years and fruit mineral thresholds have been defined for ensuring a high probability of freedom from both fungal wastage and physiological disorders.

Samples of fruit for mineral analysis should be taken from orchards which may be stored, two to three weeks prior to harvest. The suitability of fruit for storage is based on the results of the mineral analysis. Details of sampling and fruit internal standards can be found in Section 3 – Storage, packing and marketing.

The suitability of the fruit from an orchard for storage is the most important aspect of rot risk assessment. If the fruit is not suitable for storage then it will be scheduled for early marketing and storage rot risk is in most cases irrelevant.

Using rot risk assessment to make decisions

Once a rot risk has been identified for fruit from an orchard that is intended for medium – long-term storage, then decisions on treatment or time of marketing can be made.

  • This information for Neonectria rot, Phytophthora rot and brown rot is summarised in below.
  • For Gloeosporium and Botrytis (latent) rot, research did not identify any clear factors on which risk assessment could be based. Decisions on risk are therefore mainly based on rot history and rainfall.
  • For Penicillium rot, Mucor rot and Botrytis (wound) rot, risk assessment is purely dependent on crop damage. Attention to crop handling and hygiene at harvest should avoid these problems.

Where decisions based on rot risk are made at harvest, options for control or minimising losses due to rots are based on reducing the storage time (earlier marketing).

Where orchard fungicide sprays are considered, decisions will need to be made much earlier, even at the start of the season. In these cases, decisions can be made based on rot history from packhouse records, or from orchard types identified as at risk, e.g. for Phytophthora – potential low hanging fruit, a high percentage bare ground or for Neonectria rot – a high incidence of cankered trees.


Procedures for assessment of orchard factors affecting rotting in store

Fungal rot  Timing Factor Assessment procedure Criteria for risk 
Brown rot  July / August Incidence of brown rot in orchard Select 20 trees at random and assess incidence of brown rot on tree and on floor to obtain % fruit with brown rot Brown rot incidence >1% = high risk
Neonectria rot April Incidence of canker Select 20 trees at random and assess incidence of cankered trees >25% trees with canker = high risk5-25% = moderate risk

<5% = low risk

0 = no risk


Gloeosporium rot  July Crop load Select 20 trees at random and assess crop load as light, moderate or heavy. light crop = risk
Phytophthora rot July and August / September (1) % bareground 







(2) % crop <½ metre from ground

Inspect whole orchardEstimate bareground under trees taking into account mulch and weed cover





Select 20 trees at random and assess % crop <½ metre from ground

(1) 100% bareground (overall herbicide) = high risk(2) Overall grass or mulch or weed cover (0% bareground) = low risk

(3) herbicide strip (20% or >bareground) = risk


15% or >= risk

Orchard rot history – example of packhouse records

Orchard name

 Year % rot incidence  % loss due to rots
Brown rot Phytophthora rot Neonectria rot Gloeosporium rot Botrytis rot Penicillium rot Mucor rot Other rot


Fungicide sprays for control of storage rots efficacy

Active ingredient  Trade names Fungicide group Safety to Typhs Storage rots controlled
captan Captan 80 WDGPP Captan 80 WG


phthalimide safe NeonectriaGloeosporium



cyprodinil + fludioxonil Switch anilinopyri-midine + cyanopyrrole safe Brown rotNeonectria





metalaxyl-M + mancozeb  Fubol Gold (EAMU 2282/2013 )  phenylamide + dithiocarbamate safe (applied to orchard floor) Phytophthora
pyraclostrobin + boscalid Bellis strobylurine (QoI)+ anilide safe GloeosporiumBotrytis




Fungicide sprays for control of storage rots – safety factors


Active ingredient

Hazards  Harvest interval (days)


 Max. no sprays Buffer zone
human fish + aquatic life bees width(m)
captan  h, ir, c t u 14 12 sm
cyprodinil + fludioxonil a, c d u 3 3 5 m
metalaxyl-M + mancozeb  h, ir d u 28 2 sm
pyraclostrobin + boscalid h d u 7 4 40 m

d = dangerous; h = harmful; ir = irritating, a = may cause allergic reaction, t = toxic

PH = post harvest; Pre bb = pre-bud burst, sm=statutory minimum of 5 m for broadcast air assisted sprayers

u=uncategorised/unclassified/unspecified, c=closed cab required for air assisted sprayers


Apple store diseases – wound pathogens – Rot management options

Fungal rot

Inoculum sources

Control options

Penicillium rot

Dirty fruit bins

Damaged fruit

  • Bin hygiene
  • Selective picking – only sound fruit in the bin
  • Good harvest supervision

Mucor rot

Dirty fruit bins

Damaged fruit

Soil contamination

Botrytis rot

Dirty fruit bins

Damaged fruit

Plant debris

Apple orchard diseases – Rot management options

Fungal rot

Assessment timing

Orchard Risk

Rot history



Brown rot

July / August

orchard incidence  high (>1%)



  • Selective picking at harvest and / or
  • Market fruit early

Orchard incidence low



  • Selective picking at harvest

Botrytis (eye rot)



Moderate-high incidence

Rain June to Harvest average or > average

  • Market fruit by January
Rain June to Harvest < average
  • No specific action needed


Low incidence Rain June-Harvest =average or < average
  • No specific action needed

Neonectria rot


Moderate-high incidence cankered trees

Moderate – high incidence


Apply fungicide spray in blossom and petal fall

Low incidence cankered trees

Low incidence


No fungicide treatment in blossom/petal fall needed

August / September

Low-high incidence cankered trees


>average rain blossom-harvest

Market fruit before January if no sprays applied in blossom/petal fall

Moderate-high incidence cankered trees


average rain blossom-harvest

High incidence cankered trees



Apple orchard diseases – Rot management options continued

Fungal rot

Assessment timing

Orchard Risk

Rain in 15 days pre-harvest


% bare ground

% crop <0.5 m above ground

Phytophthora rot

Mid July

0% = overall grass, weed cover or mulch



No sprays needed

20% or > bareground



Apply fungicide 28 and 14 days pre-harvest or delay action until harvest

August / September / Harvest

0% = overall grass, weed cover or mulch



No specific action as risk very low

20% or > bareground

> 15%

low or no rain = low risk

  • No specific action as risk very low

20 mm or > = high risk

  • Selective pick at harvest or
  • Market fruit early to minimise losses if no fungicide treatment applied

< 15%


No specific action as risk very low