The university's scheme was chosen over four other bids to look after the 60ha collection, after its maintenance went to tender in September for the second time in a year.
DEFRA issued an open competition specification to manage the National Fruit Collection - which includes plant genetic resources of apples, pears, plums, cherries and other fruit - following difficulties between the Brogdale Horticultural Trust (BHT) and its landlord Hillreed Land.
The specification included the option of moving the collections to a new site, with the intention of ensuring DEFRA was getting the best value for money for this work.
The specification also included scientific curation and horticultural management of this important genetic resource.
The university will take over the maintenance and curation of the collections from April.
University of Reading head of horticulture and landscape Professor Paul Hadley said: "The university aims to research molecular characterisation, build a new database and use genotypes as a resource - but we won't be going down the GM road. There is the potential for the collection for selecting genotypes (the genetic constitution of the fruit) suitable for use in a future changed climate."
Hadley was also hoping to use funding from DEFRA as a "platform" for bringing in further research and funding from national, European and international sources.
Farm Advisory Services Team (FAST), which gives technical support to fruit growers, will be responsible for the day-to-day management of the maintenance of the collection. FAST member Tim Biddlecombe said: "We are very pleased that the collections are going to stay at Brogdale as the continuity of data is very important.
"We have got the expertise in how to make sure the spraying, pruning and mowing are done correctly, and we are relocating to Brogdale early in the New Year."
Minister for sustainable farming and food Lord Rooker said: "Local support stressing the importance of retaining the collections at Brogdale has been continuous since the start of the tendering process and we are delighted with the final outcome."
One of the rival bids, from Imperial College London, wanted to take the fruit collection to East Malling Research, Kent.