Seed storage and germination

Updated November 2023 to include results from 2022 season

Seed storage and stratification

The practicalities of handling apple seeds haven’t changed that much over the last hundred years. Their storage and germination has been reviewed by Ellis (1985). Apple seeds require ‘stratification’ (cold treatment) before they will germinate. This is achieved by keeping the seeds in moist conditions and subjecting them to a period of cold to allow after-ripening, during which embryo changes occur (Janick et al. 1996). The practical guidelines quoted below come from a number of sources, listed chronologically.


Source 1: Bagenal NB, 1939 Fruit Growing: Modern Cultural Methods.

‘The apple pips should be sown in shallow wooden boxes or earthenware pans containing one-third leaf mould, two-thirds good loam and a little sharp sand. The boxes or pans must be well drained with plenty of broken crocks at the bottom. They are placed in cold frames and need not be pampered in any way until after the seeds have germinated the following spring, when they will need protection from frost.  The seedlings are potted up when a few inches high and gradually hardened off ready for planting out when the late frosts are over.  The seedlings can either be left to grow on their own roots or, after two or three seasons’ growth their shoots may be cut off and grafted in the spring.’


Source 2: MAFF. 1963. Fruit Tree Raising: Rootstocks and Propagation. 

‘Provided the seed remains in the fruit, or as wet pomace, until sown or stratified, a good germination is obtained. Thus the safest place for the seed is in the fruit which should be kept outdoors, netted against birds, until midwinter when all may be mashed and left to rot and germination begins, or until the soil is fit for sowing the pomace in drills, whichever takes place first.


If, however, the seed has been separated from the fruit and allowed to dry then it is necessary to break dormancy by special treatment. Essentially, the process consists of thoroughly soaking the seed in water for two or three days, and then keeping it moist and cold for 6-8 weeks either outdoors or in a cold store. Freezing is not required but the temperatures should remain in the region of 1 - 6.7°C for most of the time. The seed begins to grow towards the end of this period and it should then be sown without delay. Thus, for sowing at the end of February, dry seed should be wetted and chilled from early January. Germinating seed should never be allowed to become dry.'


Source 3: Garner RJ, 1967. The Grafter’s Handbook. 

From Chapter 3: Rootstocks and their Propagation:

'The majority of seeds, once dried, keep well in sealed containers at temperatures ranging from just above freezing to around 4.5°C. The quickest way to germinate apple seeds is to sow them immediately they are taken from the fruit, so they have no time to dry.'


Stratification: 'On a small scale the seed may be placed in plant pots between layers of moist sand or sand-peat mixtures. The pots are usually buried completely in open ground. One method is to stratify the seed immediately after extraction, whilst still wet, and to sow it in the open in early spring. An alternative treatment suitable for small batches, is to extract the seed when the fruit is ripe in the autumn, drop it into a vessel of water and swill occasionally over a period of two days, and then sow directly in pots or boxes, which are placed under glass. Given warmth, germination takes place in two or three weeks, but otherwise is delayed till spring.'


Source 4: Crassweller RM. Growing new fruit tree plants from seed.

'Apple seeds require a period of cold exposure known as ‘stratification’ before they germinate. Temperatures between 4.4 -10°C are effective, with an optimum of 4.4 - 5°C over 70-80 days. Seeds should be stored dry in a sealed container at the appropriate temperature, either outside or in a refrigerator. Alternatively, they can be sown immediately after extracting from fruit and overwinter naturally in a seedbed.'


'If seeds have not previously received a cold treatment then in mid-January mix the seeds with either moist (not wet) peat moss, sand or shredded paper towels. Return the mixture to the container and replace lid. Place container and seeds in the refrigerator until after the last severe spring frosts. The seeds should remain in the refrigerator for at least 60 days.'


Source 5: Janick et al. 1996. Apples

'In most breeding programs seeds are extracted slightly before fruit maturity, rather than left inside the fruit. It is advisable to surface sterilize the seeds in Calcium Hypochlorite solution (10 g in 140 ml water and filtered) for 5 min, and then wash them before stratification.'


The ‘after-ripening’ process occurs at temperatures between 0 - 10°C, the optimum being 3 - 5°C. The period required varies from 6 to 14 weeks, depending in part on the temperature. The process is reversed if seeds are stored at temperatures above 17°C, such that a longer period of cold will be required to allow them to germinate. The easiest stratification technique is to leave seeds in the fruit and store them at a cold temperature above freezing. However, rots can cause problems with this method. Seeds can be stratified in polyethylene bags containing moist filter paper or moistened peat moss, which is slightly fungistatic. The stratification process is usually completed in 6 weeks, but should be checked periodically for radicle emergence. When 50% of seeds have germinated they are planted in seed trays with individual cells, and placed under optimum conditions for seedling growth.


Source 6: AHDB, 2010. Membership of the East Malling Rootstock Club.

‘When the fruits have ripened naturally, the seeds are extracted and then washed and soaked in water for 2-3 days with daily rinses to remove germination–inhibiting compounds. They are then air-dried and stored at 3°C until the following January.’


‘Seeds are stratified in the cold-store (>4°C ) in trays of moist compost and perlite mix for 16 weeks. After this period the trays are placed in a greenhouse (at 18°C ) for germination. Seedlings are potted individually when they become large enough to handle and are grown on for a couple of months. In their first summer, seedlings are planted out in the field and left to establish for a whole season. The following summer they are budded with suitable scion variety and left to grow.’ 

Germination rates at Ystwyth Valley Apple breeders

Graph of seedling emergence from crosses made in 2013, 2014 and 2015

Following stratification our seeds are sown into pots containing compost during early January. These are placed in cold frames outdoors. A small percentage of the seeds have already germinated when they are sown, with visible primary root or radicle. Germination and seedling emergence occur during late January and early February, at relatively low temperatures ranging from 5-10°C. 

The numbers of emerging seedlings increase in a sigmoidal pattern over time. The emergence patterns of seeds sown in each of the years 2014-2023 are shown above. The first seedlings emerge 0-20 days after sowing, and the vast majority during the subsequent 20 days. Our germination and emergence rates have generally improved since we began experimenting in 2011 (Table below).  We might be able to improve them further, if we removed all the seeds that fail to develop properly prior to sowing. A few seedlings die following emergence, due to fungal infection. These are removed from pots to minimize further infection and losses. The low number of seeds planted in 2020 reflects the failure of most of the crosses made in 2019 due to frost damage to the pollinated flowers.

Germination and emergence rates for seeds sown between 2011 and 2022.  Data are for seeds collected from crosses where both parents are known.
Germination and emergence rates for seeds sown between 2011 and 2022. Data are for seeds collected from crosses where both parents are known.


AHDB, 2010Membership of the East Malling Rootstock Club, Project TF182. Agriculture and Horticulture Development Board 2010. UK.

Bagenal NB. 1939 Fruit Growing: Modern Cultural Methods., Ward, Lock & Co. Ltd London 399p.

Crassweller RMGrowing new fruit tree plants from seed.

Ellis, RH. 1985. Seed storage and germination of apple and pear. In: Long term storage

of major temperate fruits. Int. Board Plant Genetic Resources, Rome.

Garner RJ. 1967The Grafter’s Handbook, Faber & Faber, London, 3rd ed. 263p.

Janick J, Cummins JN, Brown SK and Hemmat M. 1996. Apples. In: Janick J, Moore JN, eds, Fruit Breeding, Volume I: Tree and Tropical Fruits. John Wiley & Sons, Inc. 1-77.

MAFF. 1963. Fruit Tree Raising: Rootstocks and Propagation, Ministry of Agriculture, Fisheries and Food, Bulletin 135. HMSO London, 4th ed. 52p.